From 69a393db50474d33139c98b19b0ce062b33a0255 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Simon-Martin=20Schr=C3=B6der?= Date: Tue, 16 Jun 2020 21:30:47 +0200 Subject: [PATCH 01/17] Update MorphoCut installation instructions PlanktonScope-related things are now merged into master of the MorphoCut repository. --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c0dcd74..8c68f80 100644 --- a/README.md +++ b/README.md @@ -188,12 +188,14 @@ https://www.pyimagesearch.com/2019/09/16/install-opencv-4-on-raspberry-pi-4-and- Install MorphoCut ================= -`Installing MorphoCut `_ +[Installing MorphoCut](https://morphocut.readthedocs.io/en/stable/installation.html) MorphoCut is packaged on PyPI and can be installed with pip: -:: - sudo apt-get install python3-scipy - pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis + +```sh +sudo apt-get install python3-scipy +pip3 install -U git+https://github.com/morphocut/morphocut.git +``` Finishing the install ===================== From 4a158c8c7c90ce17fc3d70f43899db2cfb62b86a Mon Sep 17 00:00:00 2001 From: tpollina Date: Mon, 6 Jul 2020 17:10:32 +0200 Subject: [PATCH 02/17] Update README.md Divide Installation in Basic/Expert Installations to make it easier --- README.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8c68f80..62681a5 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,16 @@ -PlanktonScope Installation -========================== +PlanktonScope +============= + +This GitHub is part of a community that you can find on this website : https://www.planktonscope.org/ + +PlanktonScope Basic Installation +================================ + +Before going further, notice that you can download the image disk already setup without having to deal with all these command lines. +Jump here : http://planktonscope.su.domains/Images_raspberry/Raspbian_Buster_Morphocut_WiFi.img + +PlanktonScope Expert Installation +================================= ************************************* Install Raspbian on your Raspberry Pi From c8dffd590b818e4e5712e26adc28082f0011609d Mon Sep 17 00:00:00 2001 From: tpollina Date: Mon, 6 Jul 2020 17:11:00 +0200 Subject: [PATCH 03/17] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 62681a5..85b7983 100644 --- a/README.md +++ b/README.md @@ -3,14 +3,14 @@ PlanktonScope This GitHub is part of a community that you can find on this website : https://www.planktonscope.org/ -PlanktonScope Basic Installation -================================ +Basic Installation +================== Before going further, notice that you can download the image disk already setup without having to deal with all these command lines. Jump here : http://planktonscope.su.domains/Images_raspberry/Raspbian_Buster_Morphocut_WiFi.img -PlanktonScope Expert Installation -================================= +Expert Installation +=================== ************************************* Install Raspbian on your Raspberry Pi From ac6e3204e550ba7c957a653054dd6db2083e3df6 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 16:55:16 +0200 Subject: [PATCH 04/17] Rename config.txt to config.json --- config.txt => config.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename config.txt => config.json (100%) diff --git a/config.txt b/config.json similarity index 100% rename from config.txt rename to config.json From 2412e73b1bb87e9ea560b1729198a8b55687d1e6 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 16:55:43 +0200 Subject: [PATCH 05/17] Delete _config.yml --- _config.yml | 1 - 1 file changed, 1 deletion(-) delete mode 100644 _config.yml diff --git a/_config.yml b/_config.yml deleted file mode 100644 index 2f7efbe..0000000 --- a/_config.yml +++ /dev/null @@ -1 +0,0 @@ -theme: jekyll-theme-minimal \ No newline at end of file From 889d2eedae1cbae0ebc41ff41f412b238afa5e47 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 16:56:04 +0200 Subject: [PATCH 06/17] Delete StackFlow_v3.py --- scripts/StackFlow_v3.py | 116 ---------------------------------------- 1 file changed, 116 deletions(-) delete mode 100644 scripts/StackFlow_v3.py diff --git a/scripts/StackFlow_v3.py b/scripts/StackFlow_v3.py deleted file mode 100644 index 82f7110..0000000 --- a/scripts/StackFlow_v3.py +++ /dev/null @@ -1,116 +0,0 @@ -#!/usr/bin/env python -# coding: utf-8 - -################################################################################ -# A) Import the librairies needed to execute the script -################################################################################ -#Activate pinout to control the LEDs and the RELAY -from gpiozero import LED -#Allow to access the I2C BUS from the Raspberry Pi -import smbus -#Time librairy in order to sleep when need -from time import sleep -#Picamera library to take images -from picamera import PiCamera -#Enable calculation of remaining duration and datetime -from datetime import datetime, timedelta -#Enable creation of new folders -import os -from adafruit_motor import stepper -from adafruit_motorkit import MotorKit -from time import sleep - -kit = MotorKit() -pump_stepper = kit.stepper1 -pump_stepper.release() - - -################################################################################ -# C) Configuration file -################################################################################ - - -camera = PiCamera() -camera.resolution = (3280, 2464) -camera.iso = 60 -sleep(3) -camera.shutter_speed = 300 -camera.exposure_mode = 'off' -g = camera.awb_gains -camera.awb_mode = 'off' -camera.awb_gains = g -nb_frame=2000 - -pump_stepper.release() -################################################################################ -# E) Define simple functions making the whole sequence -### - -################################################################################ - - -print("###############") -print("IMAGING") -print("###############") - -#Inform on the statut of the operation -print("Imaging : engaged") -#start the preview only during the acquisition -camera.start_preview(fullscreen=False, window = (160, 0, 640, 480)) - - -#get the actual date -date_now = datetime.now().strftime("%m_%d_%Y") -day_now="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now) - -#create a directory if the directory doesn't exist yet -if not os.path.exists(day_now): - os.makedirs(day_now) - -#get the actual date -hour_now = datetime.now().strftime("%H") -hour="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now)+"/"+str(hour_now) - -#create a directory if the directory doesn't exist yet -if not os.path.exists(hour): - os.makedirs(hour) - - -#allow the camera to warm up - -for i in range(200): - pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SINGLE) - sleep(0.01) - -for frame in range(nb_frame): - - #get the time now - time = datetime.now().strftime("%M_%S_%f") - #create a filename from the date and the time - filename="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now)+"/"+str(hour_now)+"/"+str(time)+".jpg" - - #capture an image with the specified filename - camera.capture(filename) - - #wait to complete the imaging process and print info on the terminal - print("Imaging : "+str(frame)+"/"+str(nb_frame)) - - for i in range(10): - pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SINGLE) - sleep(0.01) - sleep(0.5) - - -#stop the preview during the rest of the sequence -camera.stop_preview() -pump_stepper.release() - -#Inform on the statut of the operation -print("Imaging : done") - - -################################################################################ - -################################################# -# F) Execute the sequence -################################################################################ From c474b3a7e69812ae9fdba0ad7145eb7f9e0f5cbf Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 16:56:17 +0200 Subject: [PATCH 07/17] Delete Morphocut_segmentation.py --- scripts/Morphocut_segmentation.py | 140 ------------------------------ 1 file changed, 140 deletions(-) delete mode 100644 scripts/Morphocut_segmentation.py diff --git a/scripts/Morphocut_segmentation.py b/scripts/Morphocut_segmentation.py deleted file mode 100644 index 94531a5..0000000 --- a/scripts/Morphocut_segmentation.py +++ /dev/null @@ -1,140 +0,0 @@ - -import datetime -import os - -from skimage.util import img_as_ubyte -from skimage.filters import threshold_otsu - - -from morphocut import Call -from morphocut.contrib.ecotaxa import EcotaxaWriter -from morphocut.contrib.zooprocess import CalculateZooProcessFeatures -from morphocut.core import Pipeline -from morphocut.file import Find -from morphocut.image import ( - ExtractROI, - FindRegions, - ImageReader, - ImageWriter, - RescaleIntensity, - RGB2Gray, -) -from morphocut.stat import RunningMedian -from morphocut.str import Format -from morphocut.stream import TQDM, Enumerate - -import_path = "/home/pi/Desktop/PlanktonScope_acquisition/01_17_2020/16_2" -export_path = "/home/pi/Desktop/PlanktonScope_acquisition/01_17_2020/16" -archive_fn = os.path.join(export_path, "17_morphocut_processed.zip") - -# Meta data that is added to every object -global_metadata = { - "process_datetime": datetime.datetime.now(), - "sample_project": "PlanktonScope Villefranche", - "sample_ship": "Kayak de Fabien", - "sample_operator": "Thibaut Pollina", - "sample_id": "Flowcam_PlanktonScope_comparison", - "sample_sampling_gear": "net", - "object_date": 20200117, - "object_time": 150000, - "object_lat": 43.696146, - "object_lon": 7.308359, - "object_depth_min": 0, - "object_depth_max": 1, - "acq_fnumber_objective": 16, - "acq_celltype": 400, - "acq_camera": "Pi Camera V2.1", - "acq_instrument": "PlanktonScope V2.1", - "acq_software": "Node-RED Dashboard and raw python", - "acq_instrument_ID": "copepode", - "acq_camera_resolution" : "(3280, 2464)", - "acq_camera_iso" : 60, - "acq_camera_shutter_speed" : 100, - "acq_camera_exposure_mode" : "off", - "acq_camera_awb_mode" : "off", - "process_pixel": 1.19 - -} - -if __name__ == "__main__": - print("Processing images under {}...".format(import_path)) - - # Create export_path in case it doesn't exist - - os.makedirs(export_path, exist_ok=True) - # Define processing pipeline - with Pipeline() as p: - # Recursively find .jpg files in import_path. - # Sort to get consective frames. - abs_path = Find(import_path, [".jpg"], sort=True, verbose=True) - - # Extract name from abs_path - name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path) - - # Show progress bar for frames - TQDM(Format("Frame {name}", name=name)) - - # Read image - img = ImageReader(abs_path) - - - # Convert image to uint8 gray - img_gray = RGB2Gray(img) - - #img_gray = Call(img_as_ubyte, img_gray) - - # Apply threshold find objects - - #threshold = 200 # - #threshold = Call(threshold_otsu, img_gray) - threshold = 180 # - - mask = img_gray < threshold - - - # Write corrected frames - - ImageWriter(frame_fn, mask) - - # Find objects - regionprops = FindRegions( - mask, img_gray, min_area=300, padding=10, warn_empty=name - ) - - # For an object, extract a vignette/ROI from the image - roi_orig = ExtractROI(img, regionprops, bg_color=255) - #roi_gray = ExtractROI(img_gray, regionprops, bg_color=255) - - # Generate an object identifier - i = Enumerate() - - object_id = Format("{name}_{i:d}", name=name, i=i) - - # Calculate features. The calculated features are added to the global_metadata. - # Returns a Variable representing a dict for every object in the stream. - #meta = CalculateZooProcessFeatures( - # regionprops, prefix="object_", meta=global_metadata - #) - # If CalculateZooProcessFeatures is not used, we need to copy global_metadata into the stream: - # meta = Call(lambda: global_metadata.copy()) - # https://github.com/morphocut/morphocut/issues/51 - - # Add object_id to the metadata dictionary - #meta["object_id"] = object_id - - # Generate object filenames - - orig_fn = Format(os.path.join(export_path, "{object_id}.jpg"), object_id=object_id) - #gray_fn = Format("{object_id}-gray.jpg", object_id=object_id) - - ImageWriter(orig_fn, roi_orig) - - # Write objects to an EcoTaxa archive: - # roi image in original color, roi image in grayscale, metadata associated with each object - #EcotaxaWriter(archive_fn, [(orig_fn, roi_orig)], meta) - - # Progress bar for objects - TQDM(Format("Object {object_id}", object_id=object_id)) - - # Execute pipeline - p.run() From 10bc0c2535c1406b17c05554a0983f91bf0f3194 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:21:16 +0200 Subject: [PATCH 08/17] Delete store_retrieve.json --- flows/store_retrieve.json | 1170 ------------------------------------- 1 file changed, 1170 deletions(-) delete mode 100644 flows/store_retrieve.json diff --git a/flows/store_retrieve.json b/flows/store_retrieve.json deleted file mode 100644 index 02147cb..0000000 --- a/flows/store_retrieve.json +++ /dev/null @@ -1,1170 +0,0 @@ -[ - { - "id": "103f6179.d5012f", - "type": "tab", - "label": "Sample", - "disabled": false, - "info": "" - }, - { - "id": "f6f450aa.8ed73", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "sample_ship", - "label": "Name of the ship", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_ship", - "x": 1170, - "y": 100, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "8f3a0dab.4d614", - "type": "ui_dropdown", - "z": "103f6179.d5012f", - "name": "sample_sampling_gear", - "label": "Sampling gear", - "tooltip": "", - "place": "Select", - "group": "aac2eaf7.0cdab8", - "order": 7, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "Plankton net", - "value": "net", - "type": "str" - }, - { - "label": "Niskin bottle 12L", - "value": "niskin_12L", - "type": "str" - }, - { - "label": "Niskin bottle 24L", - "value": "niskin_24L", - "type": "str" - }, - { - "label": "Pass Hull", - "value": "pass_hull", - "type": "str" - } - ], - "payload": "", - "topic": "sample_sampling_gear", - "x": 1130, - "y": 220, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "e046b933.316b28", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "sample_operator", - "label": "Name of the operator", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 6, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_operator", - "x": 1150, - "y": 180, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "2ff04681.e99aea", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "sample_project", - "label": "Name of the project*", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 1160, - "y": 60, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "75615576.3a38cc", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "sample_id", - "label": "ID of the station*", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "sample_id", - "x": 1170, - "y": 140, - "wires": [ - [ - "e17096e4.74caf8" - ] - ] - }, - { - "id": "b77eb8b0.a222a8", - "type": "ui_date_picker", - "z": "103f6179.d5012f", - "name": "acq_date", - "label": "Date :", - "group": "aac2eaf7.0cdab8", - "order": 10, - "width": 0, - "height": 0, - "passthru": true, - "topic": "", - "x": 1176, - "y": 640, - "wires": [ - [ - "4fa687df.1aa1d8" - ] - ] - }, - { - "id": "86d5ed81.6dc99", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_time", - "label": "Time :", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 11, - "width": 0, - "height": 0, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 1176, - "y": 680, - "wires": [ - [ - "26461e30.b461b2" - ] - ] - }, - { - "id": "26461e30.b461b2", - "type": "function", - "z": "103f6179.d5012f", - "name": "set time global", - "func": "var time = new Date(msg.payload);\nglobal.set('generic_acq_time',time);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute+\"00\";\nglobal.set('object_time',time_UTC);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1396, - "y": 680, - "wires": [ - [ - "da16d746.4b12e8" - ] - ] - }, - { - "id": "4fa687df.1aa1d8", - "type": "function", - "z": "103f6179.d5012f", - "name": "set date global", - "func": "var date = new Date(msg.payload);\nglobal.set('generic_acq_date',date);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1396, - "y": 640, - "wires": [ - [ - "da16d746.4b12e8" - ] - ] - }, - { - "id": "da16d746.4b12e8", - "type": "function", - "z": "103f6179.d5012f", - "name": "get global", - "func": "msg.payload={\n generic:{\n \"generic_sample_date\":global.get(\"generic_sample_date\"),\n \"generic_sample_time\":global.get(\"generic_sample_time\"),\n \"generic_acq_date\":global.get(\"generic_acq_date\"),\n \"generic_acq_time\":global.get(\"generic_acq_time\")\n },\n sample:{\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_date\":global.get(\"sample_date\"),\n \"sample_time\":global.get(\"sample_time\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\")\n },\n acquisition:{\n \"acq_id\":global.get(\"acq_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\")\n },\n object:{\n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\")\n \n },\n process:{\n //PROCESS\n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n }\n};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1693, - "y": 60, - "wires": [ - [ - "28df8fd6.06fb7" - ] - ] - }, - { - "id": "6dd1657e.c52e4c", - "type": "file", - "z": "103f6179.d5012f", - "name": "", - "filename": "/home/pi/PlanktonScope/log/config.txt", - "appendNewline": true, - "createDir": true, - "overwriteFile": "true", - "encoding": "none", - "x": 2043, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "3a43748d.52464c", - "type": "function", - "z": "103f6179.d5012f", - "name": "set optical config", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - 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"label": "Min fraction size (μm)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 16, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 1136, - "y": 520, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "220c7464.306a8c", - "type": "ui_numeric", - "z": "103f6179.d5012f", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 17, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 1136, - "y": 560, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c3b1ab59.484178", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 9, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_id", - "x": 1186, - "y": 400, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "3bb0adb4.de5412", - "type": "ui_dropdown", - "z": "103f6179.d5012f", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "aac2eaf7.0cdab8", - "order": 13, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 1166, - "y": 480, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c19a2c73.7512f", - "type": "ui_text_input", - "z": "103f6179.d5012f", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "aac2eaf7.0cdab8", - "order": 14, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 1166, - "y": 600, - "wires": [ - [ - "d911efe0.ea7f1" - ] - ] - }, - { - "id": "c9b2c48c.40d068", - "type": "comment", - "z": "103f6179.d5012f", - "name": "sample", - "info": "SAMPLE: a collection event\n\n sample_id [t] : unique identifier\n sample_*** [f] or [t] : other fields relative to the sample\n", - "x": 990, - "y": 20, - "wires": [] - }, - { - "id": "8abc2578.2ebcf8", - "type": "comment", - "z": "103f6179.d5012f", - "name": "acquisition", - "info": "ACQUISITION: metadata relative to the image acquisition\n\n acq_id [t] : unique identifier. If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n", - "x": 996, - "y": 360, - "wires": [] - }, - { - "id": "91ab2c80.0f453", - "type": "comment", - "z": "103f6179.d5012f", - "name": "object", - "info": "OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace \"Cnidaria Date: Tue, 14 Jul 2020 18:21:23 +0200 Subject: [PATCH 09/17] Delete mqtt_nodered.json --- flows/mqtt_nodered.json | 1 - 1 file changed, 1 deletion(-) delete mode 100644 flows/mqtt_nodered.json diff --git a/flows/mqtt_nodered.json b/flows/mqtt_nodered.json deleted file mode 100644 index abeb85e..0000000 --- a/flows/mqtt_nodered.json +++ /dev/null @@ -1 +0,0 @@ -[{"id":"259c8713.b50e28","type":"tab","label":"Main","disabled":false,"info":""},{"id":"6d0d6fc7.d30bb","type":"ui_text_input","z":"259c8713.b50e28","name":"sample_ship","label":"Name of the ship","tooltip":"","group":"3e1ba03d.f01d8","order":3,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"sample_ship","x":1370,"y":140,"wires":[["de9708c2.d00068"]]},{"id":"43b12fe4.c5aa3","type":"ui_dropdown","z":"259c8713.b50e28","name":"sample_sampling_gear","label":"Sampling gear","tooltip":"","place":"Select","group":"3e1ba03d.f01d8","order":5,"width":0,"height":0,"passthru":true,"options":[{"label":"Plankton net","value":"net","type":"str"},{"label":"Niskin bottle 12L","value":"niskin_12L","type":"str"},{"label":"Niskin bottle 24L","value":"niskin_24L","type":"str"},{"label":"Pass 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sample\n","x":810,"y":60,"wires":[]},{"id":"f93037f1.6a6238","type":"comment","z":"259c8713.b50e28","name":"acquisition","info":"ACQUISITION: metadata relative to the image acquisition\n\n acq_id [t] : unique identifier. If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n","x":800,"y":720,"wires":[]},{"id":"734ba3db.3f82fc","type":"comment","z":"259c8713.b50e28","name":"object","info":"OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace 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config.txt","info":"","x":1690,"y":20,"wires":[]},{"id":"72e1e23b.a8a67c","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1040,"wires":[]},{"id":"d473399b.081ae8","type":"link in","z":"259c8713.b50e28","name":"","links":["72e1e23b.a8a67c","c93577b9.a1e438","829cc940.327648"],"x":1635,"y":100,"wires":[["e001a28.555566"]]},{"id":"c93577b9.a1e438","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1140,"wires":[]},{"id":"829cc940.327648","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04","d473399b.081ae8"],"x":1675,"y":1180,"wires":[]},{"id":"98e2e9e0.fb7418","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"actuator/pump","vt":"str"},{"t":"eq","v":"Missing entry :","vt":"str"}],"checkall":"true","repair":false,"outputs":2,"x":1670,"y":600,"wires":[["61fb057d.3c251c"],["46a536f0.c83138"]]},{"id":"46a536f0.c83138","type":"ui_toast","z":"259c8713.b50e28","position":"dialog","displayTime":"3","highlight":"","sendall":true,"outputs":1,"ok":"OK","cancel":"","raw":false,"topic":"","name":"","x":1830,"y":620,"wires":[[]]},{"id":"24ffcf03.2a51b","type":"ui_button","z":"259c8713.b50e28","name":"stop pump","group":"707d9797.c8e798","order":5,"width":4,"height":1,"passthru":true,"label":"STOP PUMP","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"actuator/wait","x":1370,"y":660,"wires":[["e2a7220a.09d43"]]},{"id":"7eb16c3b.294e54","type":"comment","z":"259c8713.b50e28","name":"turn ON the LED","info":"","x":260,"y":121,"wires":[]},{"id":"4f74f017.00a58","type":"function","z":"259c8713.b50e28","name":"focus.js","func":"state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;","outputs":1,"noerr":0,"x":1520,"y":400,"wires":[["b7d9455c.026588"]],"info":"### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"},{"id":"52cc1de5.b78e84","type":"ui_button","z":"259c8713.b50e28","name":"stop focus","group":"fbd92986.1028c8","order":5,"width":4,"height":1,"passthru":true,"label":"STOP FOCUS","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"actuator/wait","x":1370,"y":460,"wires":[["e46763fe.7fc83"]]},{"id":"39cad6fb.1503ca","type":"ui_button","z":"259c8713.b50e28","name":"","group":"c6a276ac.3eb74","order":1,"width":12,"height":1,"passthru":false,"label":"Reboot","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"reboot","x":2620,"y":60,"wires":[["95b876d4.07c708","99d61fbe.b244b"]]},{"id":"1f53f29b.feee4d","type":"exec","z":"259c8713.b50e28","command":"sudo","addpay":true,"append":"","useSpawn":"false","timer":"2","oldrc":false,"name":"cmd","x":2930,"y":60,"wires":[[],[],[]]},{"id":"e325458b.95bff8","type":"ui_button","z":"259c8713.b50e28","name":"","group":"c6a276ac.3eb74","order":2,"width":12,"height":1,"passthru":false,"label":"Shutdown","tooltip":"","color":"","bgcolor":"#AD1625","icon":"","payload":"off","payloadType":"str","topic":"shutdown","x":2620,"y":120,"wires":[["95b876d4.07c708","99d61fbe.b244b"]]},{"id":"95b876d4.07c708","type":"python3-function","z":"259c8713.b50e28","name":"action","func":"#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg","outputs":1,"x":2790,"y":80,"wires":[["d348474b.d756a8","1f53f29b.feee4d"]]},{"id":"d348474b.d756a8","type":"exec","z":"259c8713.b50e28","command":"i2cdetect -y 1","addpay":false,"append":"","useSpawn":"false","timer":"1","oldrc":false,"name":"i2c update","x":2950,"y":120,"wires":[[],[],[]]},{"id":"99d61fbe.b244b","type":"link out","z":"259c8713.b50e28","name":"","links":["3517d063.27073"],"x":2735,"y":20,"wires":[]},{"id":"cdd1b550.da18e8","type":"mqtt in","z":"259c8713.b50e28","name":"","topic":"receiver/#","qos":"0","datatype":"auto","broker":"b77ffa1b.942258","x":720,"y":2000,"wires":[["6920281d.dc9b48"]]},{"id":"6920281d.dc9b48","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"receiver/pump","vt":"str"},{"t":"eq","v":"receiver/focus","vt":"str"},{"t":"eq","v":"receiver/image","vt":"str"},{"t":"cont","v":"receiver/segmentation","vt":"str"}],"checkall":"true","repair":false,"outputs":4,"x":870,"y":2000,"wires":[["2f66e917.fee586"],["363ee47e.ed522c"],["45a52868.fe37c8"],["469cc189.903d"]]},{"id":"2f66e917.fee586","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"},{"t":"eq","v":"Interrompted","vt":"str"}],"checkall":"true","repair":false,"outputs":3,"x":1050,"y":1800,"wires":[["5c0d0c35.3bcf14"],["cd01157d.0892d8"],["68e02bf4.7013e4"]]},{"id":"5c0d0c35.3bcf14","type":"change","z":"259c8713.b50e28","name":"The pump has started","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has started","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1440,"y":1760,"wires":[[]]},{"id":"cd01157d.0892d8","type":"change","z":"259c8713.b50e28","name":"The pump has finished.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has finished.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1430,"y":1800,"wires":[[]]},{"id":"68e02bf4.7013e4","type":"change","z":"259c8713.b50e28","name":"The pump has been stopped.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The pump has been stopped.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1420,"y":1840,"wires":[[]]},{"id":"363ee47e.ed522c","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"},{"t":"eq","v":"Interrompted","vt":"str"}],"checkall":"true","repair":false,"outputs":3,"x":1050,"y":1920,"wires":[["c088b72f.326d98"],["36934381.14442c"],["89329cfe.c8f4"]]},{"id":"c088b72f.326d98","type":"change","z":"259c8713.b50e28","name":"The focus has started","rules":[{"t":"set","p":"payload","pt":"msg","to":"The focus has started","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1440,"y":1880,"wires":[[]]},{"id":"36934381.14442c","type":"change","z":"259c8713.b50e28","name":"The focus has finished.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The focus has finished.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1430,"y":1920,"wires":[[]]},{"id":"89329cfe.c8f4","type":"change","z":"259c8713.b50e28","name":"The focus has been stopped.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The focus has been stopped.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1420,"y":1960,"wires":[[]]},{"id":"fdb3b132.8b341","type":"mqtt out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1810,"y":380,"wires":[]},{"id":"e46763fe.7fc83","type":"mqtt out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1510,"y":460,"wires":[]},{"id":"61fb057d.3c251c","type":"mqtt out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1810,"y":580,"wires":[]},{"id":"e2a7220a.09d43","type":"mqtt out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1510,"y":660,"wires":[]},{"id":"577f7f72.6b68b","type":"ui_button","z":"259c8713.b50e28","name":"","group":"8cfadfab.327d7","order":7,"width":19,"height":1,"passthru":false,"label":"Start Acquisition","tooltip":"","color":"","bgcolor":"","icon":"","payload":"","payloadType":"str","topic":"actuator/image","x":1360,"y":1660,"wires":[["5218ba30.bbe844"]]},{"id":"d5111b87.2a64a8","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_sleep_before","label":"Sleep duration before acquisition (s)","tooltip":"","group":"8cfadfab.327d7","order":1,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_sleep_before","x":1340,"y":1360,"wires":[["3d141631.d548ba"]]},{"id":"3d141631.d548ba","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1360,"wires":[]},{"id":"74c89905.79d968","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_sleep_during","label":"Sleep duration between acquisition (s)","tooltip":"","group":"8cfadfab.327d7","order":2,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_sleep_during","x":1340,"y":1520,"wires":[["644e95b9.04b7ac"]]},{"id":"644e95b9.04b7ac","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1520,"wires":[]},{"id":"b50cf2f4.bfb84","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":501,"wires":[]},{"id":"1e75fd6c.234753","type":"ui_slider","z":"259c8713.b50e28","name":"flowrate","label":"Flowrate (ml/min)*","tooltip":"","group":"707d9797.c8e798","order":1,"width":0,"height":0,"passthru":true,"outs":"end","topic":"flowrate","min":0,"max":"20","step":"0.1","x":1380,"y":501,"wires":[["b50cf2f4.bfb84"]]},{"id":"3345fc41.8341b4","type":"function","z":"259c8713.b50e28","name":"get generic.flowrate","func":"msg.payload = msg.payload.generic_flowrate;\nreturn msg;","outputs":1,"noerr":0,"x":1030,"y":501,"wires":[["1e75fd6c.234753"]]},{"id":"32510458.f42f9c","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":501,"wires":[["3345fc41.8341b4"]]},{"id":"3cd0a17b.0cc42e","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1440,"wires":[]},{"id":"62fea790.2840a8","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_path","label":"DIrectory to store the images","tooltip":"","group":"8cfadfab.327d7","order":3,"width":12,"height":1,"passthru":true,"mode":"text","delay":300,"topic":"generic_path","x":1370,"y":1440,"wires":[["3cd0a17b.0cc42e"]]},{"id":"73e051a8.5875e","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_volume_before","label":"Volume to pass before to begin","tooltip":"","group":"8cfadfab.327d7","order":5,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_volume_before","x":1330,"y":1400,"wires":[["5ea01613.8cc9d8"]]},{"id":"5ea01613.8cc9d8","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1400,"wires":[]},{"id":"26549e4b.5dbf72","type":"ui_text_input","z":"259c8713.b50e28","name":"generic_nb_frame","label":"Number of frame per acquisition","tooltip":"","group":"8cfadfab.327d7","order":4,"width":12,"height":1,"passthru":true,"mode":"number","delay":300,"topic":"generic_nb_frame","x":1350,"y":1480,"wires":[["61382d0b.60c534"]]},{"id":"61382d0b.60c534","type":"link out","z":"259c8713.b50e28","name":"","links":["7532db82.1dcf04"],"x":1475,"y":1480,"wires":[]},{"id":"d5df5489.6523e8","type":"function","z":"259c8713.b50e28","name":"get generic_sleep_before","func":"msg.payload = msg.payload.generic_sleep_before;\nreturn msg;","outputs":1,"noerr":0,"x":1050,"y":1360,"wires":[["d5111b87.2a64a8"]]},{"id":"835c262e.00b468","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1360,"wires":[["d5df5489.6523e8"]]},{"id":"9b2fe59b.be48c8","type":"function","z":"259c8713.b50e28","name":"get generic_volume_before","func":"msg.payload = msg.payload.generic_volume_before;\nreturn msg;","outputs":1,"noerr":0,"x":1060,"y":1400,"wires":[["73e051a8.5875e"]]},{"id":"a07dad70.7c48","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1400,"wires":[["9b2fe59b.be48c8"]]},{"id":"54dfe4df.c6837c","type":"function","z":"259c8713.b50e28","name":"get generic_path","func":"msg.payload = msg.payload.generic_path;\nreturn msg;","outputs":1,"noerr":0,"x":1030,"y":1440,"wires":[["62fea790.2840a8"]]},{"id":"9fb166d6.86f908","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1440,"wires":[["54dfe4df.c6837c"]]},{"id":"1aa409a4.7b3866","type":"function","z":"259c8713.b50e28","name":"get generic_nb_frame","func":"msg.payload = msg.payload.generic_nb_frame;\nreturn msg;","outputs":1,"noerr":0,"x":1040,"y":1480,"wires":[["26549e4b.5dbf72"]]},{"id":"51e769aa.92a138","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1480,"wires":[["1aa409a4.7b3866"]]},{"id":"ce6ded0a.8ee37","type":"function","z":"259c8713.b50e28","name":"get generic_sleep_during","func":"msg.payload = msg.payload.generic_sleep_during;\nreturn msg;","outputs":1,"noerr":0,"x":1050,"y":1520,"wires":[["74c89905.79d968"]]},{"id":"3fa20f41.11e61","type":"link in","z":"259c8713.b50e28","name":"","links":["b368cae7.dd66b8"],"x":895,"y":1520,"wires":[["ce6ded0a.8ee37"]]},{"id":"5218ba30.bbe844","type":"function","z":"259c8713.b50e28","name":"image.js","func":"state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar generic_sleep_before= global.get(\"generic_sleep_before\");\nvar generic_volume_before= global.get(\"generic_volume_before\");\nvar generic_path= global.get(\"generic_path\");\nvar generic_nb_frame= global.get(\"generic_nb_frame\");\nvar generic_sleep_during= global.get(\"generic_sleep_during\");\n\nif (generic_sleep_before === undefined || generic_sleep_before === \"\" || generic_sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before start the acquisition\";\n \n}else if (generic_volume_before === undefined || generic_volume_before === \"\" || generic_volume_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume before acquisition\";\n \n}else if (generic_path === undefined || generic_path === \"\" || generic_path === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Directory to store the images\";\n \n}else if (generic_nb_frame === undefined || generic_nb_frame === \"\" || generic_nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of frames per acquisition\";\n \n}else if (generic_sleep_during === undefined || generic_sleep_during === \"\" || generic_sleep_during === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration in between each acquisition\";\n \n}else {\n generic_nb_step = 507*generic_volume_before\n generic_nb_frame=generic_nb_frame-1\n msg.payload=generic_sleep_before+' '+generic_nb_step+' '+generic_path+' '+generic_nb_frame+' '+generic_sleep_during;\n}\nreturn msg;","outputs":1,"noerr":0,"x":1520,"y":1660,"wires":[["8142bee4.882c2"]],"info":"### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"},{"id":"8142bee4.882c2","type":"switch","z":"259c8713.b50e28","name":"","property":"topic","propertyType":"msg","rules":[{"t":"eq","v":"actuator/image","vt":"str"},{"t":"eq","v":"Missing entry :","vt":"str"}],"checkall":"true","repair":false,"outputs":2,"x":1670,"y":1660,"wires":[["a4b8aae3.cc3ad8"],["54420752.4a4ab8"]]},{"id":"54420752.4a4ab8","type":"ui_toast","z":"259c8713.b50e28","position":"dialog","displayTime":"3","highlight":"","sendall":true,"outputs":1,"ok":"OK","cancel":"","raw":false,"topic":"","name":"","x":1830,"y":1680,"wires":[[]]},{"id":"a4b8aae3.cc3ad8","type":"mqtt out","z":"259c8713.b50e28","name":"","topic":"","qos":"","retain":"","broker":"cb2f36fe.1c7038","x":1810,"y":1640,"wires":[]},{"id":"ca843dd8.d1c62","type":"exec","z":"259c8713.b50e28","command":"python3.7 /home/pi/PlanktonScope/script/mqtt_pump_focus_image.py","addpay":true,"append":"","useSpawn":"false","timer":"","oldrc":false,"name":"","x":430,"y":420,"wires":[[],[],[]]},{"id":"45a52868.fe37c8","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"},{"t":"eq","v":"Interrompted","vt":"str"},{"t":"cont","v":"jpg","vt":"str"}],"checkall":"true","repair":false,"outputs":4,"x":1050,"y":2080,"wires":[["113c9b93.455814"],["29a7c6de.6ac2ea"],["f1b07b24.b85718"],["446a811b.25e4b"]]},{"id":"177a91d4.f1016e","type":"switch","z":"259c8713.b50e28","name":"","property":"payload","propertyType":"msg","rules":[{"t":"eq","v":"Start","vt":"str"},{"t":"eq","v":"Done","vt":"str"}],"checkall":"true","repair":false,"outputs":2,"x":1190,"y":2200,"wires":[["5d717a25.3437e4"],["7d713b16.235164"]]},{"id":"29a7c6de.6ac2ea","type":"change","z":"259c8713.b50e28","name":"The acquisition has finished.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The acquisition has finished.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1420,"y":2080,"wires":[[]]},{"id":"f1b07b24.b85718","type":"change","z":"259c8713.b50e28","name":"The acquisition has been stopped.","rules":[{"t":"set","p":"payload","pt":"msg","to":"The acquisition has been stopped.","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1400,"y":2120,"wires":[[]]},{"id":"113c9b93.455814","type":"change","z":"259c8713.b50e28","name":"The acquisition has started","rules":[{"t":"set","p":"payload","pt":"msg","to":"The acquisition has started","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":1420,"y":2040,"wires":[[]]},{"id":"446a811b.25e4b","type":"function","z":"259c8713.b50e28","name":"img_counter.js","func":"img_counter=global.get('img_counter')\nimg_counter=img_counter+1\nglobal.set('img_counter',img_counter)\nmsg.payload = img_counter\nreturn msg;","outputs":1,"noerr":0,"x":1300,"y":2160,"wires":[["57014db.1bbe0b4","95f4a476.261718"]]},{"id":"803b507f.9e38c","type":"function","z":"259c8713.b50e28","name":"obj_counter.js","func":"obj_counter=global.get('obj_counter')\nobj_counter=obj_counter+1\nglobal.set('obj_counter',obj_counter)\nmsg.payload = obj_counter\nreturn 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"label": "Min fraction size (μm)", - "tooltip": "", - "group": "a72a9ec6.bb144", - "order": 2, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 140, - "y": 320, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "918b69e2.7e6e88", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "a72a9ec6.bb144", - "order": 3, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 140, - "y": 360, - "wires": [ - [ - "8861710f.55b92" - ] - ] - }, - { - "id": "86d762dc.47911", - "type": "ui_switch", - "z": "7f885510.6173fc", - "name": "light_state", - "label": "Light", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 1, - "width": 2, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "true", - "onvalueType": "bool", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "bool", - "officon": "", - "offcolor": "", - "x": 510, - "y": 160, - "wires": [ - [ - "b5a366b4.cb6918" - ] - ] - }, - { - "id": "b5a366b4.cb6918", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/light.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "light.py", - "x": 820, - "y": 160, - "wires": [ - [], - [], - [] - ], - "icon": "node-red/light.svg" - }, - { - "id": "5ea28a70.42ae14", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "up", - "group": "c62ffbd3.787ef8", - "order": 3, - "width": 1, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "up", - "payloadType": "str", - "topic": "up", - "x": 530, - "y": 280, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "27f16831.dde938", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "down", - "group": "c62ffbd3.787ef8", - "order": 5, - "width": 1, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "down", - "payloadType": "str", - "topic": "down", - "x": 530, - "y": 360, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "b110542b.5de4f8", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "kill_focus", - "group": "c62ffbd3.787ef8", - "order": 6, - "width": 2, - "height": 1, - "passthru": false, - "label": "Cancel focus", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 520, - "y": 400, - "wires": [ - [ - "d9dea2bc.47097" - ] - ] - }, - { - "id": "523fdeaa.50c6c", - "type": "function", - "z": "7f885510.6173fc", - "name": "focus", - "func": "if(msg.topic === \"nb_step\"){\n nb_step = msg.payload;\n global.set(\"nb_step\",nb_step);\n}\nif(msg.topic === \"up\"){\n\n nb_step = global.get(\"nb_step\");\n\n orientation = \"up\";\n\n msg.payload = String(nb_step).concat(' ', orientation);\n return msg;\n}\nif(msg.topic === \"down\"){\n \n nb_step = global.get(\"nb_step\");\n\n orientation = \"down\";\n msg.payload = String(nb_step).concat(' ', orientation);\n\n return msg;\n}\n\n", - "outputs": 1, - "noerr": 0, - "x": 670, - "y": 320, - "wires": [ - [ - "ada728bd.8e7818" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "ada728bd.8e7818", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/focus.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "focus.py", - "x": 820, - "y": 320, - "wires": [ - [], - [], - [] - ], - "icon": "node-red/sort.svg" - }, - { - "id": "d9dea2bc.47097", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash $HOME/PlanktonScope/scripts/killer.sh focus.py && bash $HOME/PlanktonScope/scripts/killer.sh focus.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Kill Focus", - "x": 820, - "y": 400, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-stop" - }, - { - "id": "2d0f6720.0f92f8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "Pi Camera settings", - "order": 7, - "width": 0, - "height": 0, - "format": "\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1010, - "y": 100, - "wires": [ - [] - ] - }, - { - "id": "9599b953.529c28", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "process_pixel", - "order": 3, - "width": 0, - "height": 0, - "format": "
\n Pixel resolution :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1600, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "612e2b9b.ed1684", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "min_size", - "order": 4, - "width": 0, - "height": 0, - "format": "
\n Smallest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "f84ab57a.556df8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "max_size", - "order": 5, - "width": 0, - "height": 0, - "format": "
\n Biggest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "45f53656.d631e8", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "832434ce.ebe498", - "name": "flowrate", - "order": 6, - "width": 0, - "height": 0, - "format": "
\n Suggested flowrate :\n \n ml/min\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1580, - "y": 200, - "wires": [ - [] - ] - }, - { - "id": "53ec5f97.7567c", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "3d740a07.4674e6", - "name": "Stream Pi Camera", - "order": 1, - "width": 0, - "height": 0, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 570, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "c84f1718.4af6b8", - "type": "ui_switch", - "z": "7f885510.6173fc", - "name": "fan_state", - "label": "Fan", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 2, - "width": 2, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "true", - "onvalueType": "bool", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "bool", - "officon": "", - "offcolor": "", - "x": 520, - "y": 220, - "wires": [ - [ - "dec2b84a.6faa18" - ] - ] - }, - { - "id": "dec2b84a.6faa18", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/fan.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "fan.py", - "x": 810, - "y": 220, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-spinner" - }, - { - "id": "477dc1bd.c3de8", - "type": "ui_text_input", - "z": "7f885510.6173fc", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "a61f7be8.af6418", - "order": 1, - "width": 4, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_id", - "x": 530, - "y": 680, - "wires": [ - [ - "263878b3.e0a478" - ] - ] - }, - { - "id": "3dd9a121.e386de", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload.split(' ').join('_');\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 340, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "c83fc403.8ba2d8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get magnification", - "func": "var magnification = global.get(\"magnification\");\nmsg.payload = magnification;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1410, - "y": 40, - "wires": [ - [ - "72d57e31.59234" - ] - ] - }, - { - "id": "48d9cc9c.852214", - "type": "function", - "z": "7f885510.6173fc", - "name": "get process_pixel", - "func": "var process_pixel = global.get(\"process_pixel\");\nmsg.payload = process_pixel;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1410, - "y": 80, - "wires": [ - [ - "9599b953.529c28" - ] - ] - }, - { - "id": "44969aec.4e87e4", - "type": "function", - "z": "7f885510.6173fc", - "name": "get sug_min", - "func": "var sug_min = global.get(\"sug_min\");\nmsg.payload = sug_min;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 120, - "wires": [ - [ - "612e2b9b.ed1684" - ] - ] - }, - { - "id": "a1201a.dc3f8fe8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get sug_max", - "func": "var sug_max = global.get(\"sug_max\");\nmsg.payload = sug_max;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 160, - "wires": [ - [ - "f84ab57a.556df8" - ] - ] - }, - { - "id": "89b9399b.9389a8", - "type": "function", - "z": "7f885510.6173fc", - "name": "get flowrate", - "func": "var sug_flowrate = global.get(\"sug_flowrate\");\nmsg.payload = sug_flowrate\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1390, - "y": 200, - "wires": [ - [ - "45f53656.d631e8" - ] - ] - }, - { - "id": "c650b922.6adef8", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 1180, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "e4c54d5a.19ff3", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_year", - "label": "/", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 3, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_year", - "format": "{{value}}", - "min": "19", - "max": "50", - "step": 1, - "x": 1010, - "y": 480, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "b45db708.cedec8", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_month", - "label": "/", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 2, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_month", - "format": "{{value}}", - "min": "1", - "max": "12", - "step": 1, - "x": 1000, - "y": 440, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "6351d257.6d7f1c", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_day", - "label": "Date*", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 1, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_day", - "format": "{{value}}", - "min": "1", - "max": "31", - "step": 1, - "x": 1010, - "y": 400, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "9ee03294.39987", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_hour", - "label": "Time*", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 4, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_hour", - "format": "{{value}}", - "min": "0", - "max": "24", - "step": 1, - "x": 1010, - "y": 520, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "5bd11314.ae6e4c", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "sample_minute", - "label": ":", - "tooltip": "", - "group": "106f0e1b.6478a2", - "order": 5, - "width": 2, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "sample_minute", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 1000, - "y": 560, - "wires": [ - [ - "c650b922.6adef8" - ] - ] - }, - { - "id": "8861710f.55b92", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 340, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "a8cb0c6e.7220d", - "type": "function", - "z": "7f885510.6173fc", - "name": "store generic", - "func": "global.set(\"acq_instrument\",\"PlanktonScope V2.1\");\nglobal.set(\"acq_software\",\"Node-RED Dashboard\");\nglobal.set(\"acq_camera\",\"Pi Camera V2.1\");\nglobal.set(\"acq_instrument_ID\",\"Odezenne\");", - "outputs": 1, - "noerr": 0, - "x": 350, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "263878b3.e0a478", - "type": "function", - "z": "7f885510.6173fc", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 680, - "y": 660, - "wires": [ - [] - ] - }, - { - "id": "4b3ea5bd.03248c", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "backward", - "group": "c62ffbd3.787ef8", - "order": 7, - "width": 3, - "height": 1, - "passthru": false, - "label": "Backward", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_back", - "payload": "backward", - "payloadType": "str", - "topic": "backward", - "x": 520, - "y": 460, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "cfe9783a.286438", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "foward", - "group": "c62ffbd3.787ef8", - "order": 9, - "width": 3, - "height": 1, - "passthru": true, - "label": "Forward", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "foward", - "payloadType": "str", - "topic": "foward", - "x": 530, - "y": 540, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "83d75b6b.6afa28", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "kill_pump", - "group": "c62ffbd3.787ef8", - "order": 10, - "width": 2, - "height": 1, - "passthru": false, - "label": "Cancel pump", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 520, - "y": 580, - "wires": [ - [ - "8fc930df.c7ae6" - ] - ] - }, - { - "id": "84fd85fd.426878", - "type": "function", - "z": "7f885510.6173fc", - "name": "pump", - "func": "if(msg.topic === \"volume\"){\n volume = msg.payload;\n global.set(\"volume\",volume);\n}\nif(msg.topic === \"foward\"){\n\n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" foward\";\n\n msg.payload = String(volume).concat(' ',flowrate, action);\n return msg;\n}\nif(msg.topic === \"backward\"){\n \n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" backward\";\n msg.payload = String(volume).concat(' ',flowrate, action);\n\n return msg;\n}\n\n", - "outputs": 1, - "noerr": 0, - "x": 670, - "y": 500, - "wires": [ - [ - "649f7ec8.06a84" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "649f7ec8.06a84", - "type": "exec", - "z": "7f885510.6173fc", - "command": "python3.7 $HOME/PlanktonScope/scripts/pump.py", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "pump.py", - "x": 820, - "y": 500, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-rotate-left" - }, - { - "id": "8fc930df.c7ae6", - "type": "exec", - "z": "7f885510.6173fc", - "command": "bash $HOME/PlanktonScope/scripts/killer.sh pump.py && bash $HOME/PlanktonScope/scripts/killer.sh pump.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Kill Pump", - "x": 820, - "y": 580, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-stop" - }, - { - "id": "6bf10b4c.c83c84", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "start", - "group": "a61f7be8.af6418", - "order": 2, - "width": 4, - "height": 1, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "play_circle_fill", - "payload": "", - "payloadType": "str", - "topic": "start", - "x": 530, - "y": 760, - "wires": [ - [ - "3fe055c2.6ab7da", - "82c90711.145108", - "e1dbc623.8df898", - "5a95f150.76ab3" - ] - ] - }, - { - "id": "2c9498e7.bf0c38", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "cancel", - "group": "a61f7be8.af6418", - "order": 3, - "width": 4, - "height": 1, - "passthru": false, - "label": "Cancel Acquisition", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "#333333", - "icon": "pause_circle_filled", - "payload": "", - "payloadType": "str", - "topic": "cancel", - "x": 530, - "y": 980, - "wires": [ - [ - "f2acb5e0.c2c898", - "2bfa509a.9fc06", - "a2a07a68.274a78", - "4cd6d848.672778" - ] - ] - }, - { - "id": "b0fda998.f0ad48", - "type": "file", - "z": "7f885510.6173fc", - "name": "logs.json", - "filename": "/var/www/logs.json", - "appendNewline": true, - "createDir": false, - "overwriteFile": "false", - "encoding": "none", - "x": 820, - "y": 760, - "wires": [ - [] - ] - }, - { - "id": "3fe055c2.6ab7da", - "type": "function", - "z": "7f885510.6173fc", - "name": "get global", - "func": "msg.payload = {\n \"sample\":{\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\")\n },\n \"object\":{\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\")\n },\n \"acquisition\":{\n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\")\n },\n \"process\":{\n \"process_pixel\":global.get(\"process_pixel\")\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 680, - "y": 760, - "wires": [ - [ - "b0fda998.f0ad48" - ] - ] - }, - { - "id": "f2acb5e0.c2c898", - "type": "exec", - "z": "7f885510.6173fc", - "command": "sed -ie '$d' /home/pi/PlanktonScope/logs.json", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "Remove last log", - "x": 700, - "y": 1000, - "wires": [ - [], - [], - [] - ], - "icon": "font-awesome/fa-close" - }, - { - "id": "2bfa509a.9fc06", - "type": "link out", - "z": "7f885510.6173fc", - "name": "cancel_pump", - "links": [ - "eadbf812.3ea798" - ], - "x": 635, - "y": 940, - "wires": [] - }, - { - "id": "eadbf812.3ea798", - "type": "link in", - "z": "7f885510.6173fc", - "name": "", - "links": [ - "2bfa509a.9fc06" - ], - "x": 715, - "y": 600, - "wires": [ - [ - "8fc930df.c7ae6" - ] - ] - }, - { - "id": "217d8bc.8fb7374", - "type": "ui_template", - "z": "7f885510.6173fc", - "group": "79767bcc.30bb94", - "name": "Instructions", - "order": 1, - "width": 0, - "height": 0, - "format": "

In case you forget dude but it's important to read this whenever you are not sure before clicking on any buttons.

\n
\n

Focusing :

\n

To focus, you need to specify a value for the number of steps. Then, you can click once but wait while the stage is moving.

\n

To cancel a focusing, click once on CANCEL FOCUS.

\n
\n

Pumping manually :

\n

To focus, you need to specify a value for the volume. Then, you can click once in order to pump manually a defined volume in a certain direction.

\n

To cancel a pumping event, click once on CANCEL PUMP.

\n

Do not run an acquisition if you are using the pump manually.

\n
\n

Start Acquisition :

\n

Taking images will requires few inputs :

\n
    \n
  1. Name of the project
    2. \n
  2. Name of the station
    3. \n
  3. Acquisition ID
    4. \n
  4. Volume
    5. \n
  5. M12 Lens
    6. \n
\n

If any of the previous settings are missing, it's going to be a real mess and delete previous acquisition. So check twice here !!

\n

The other inputs are always welcome ;)

\n
\n

Cancel Acquisition :

\n

I made this button CANCEL ACQUISITION to cancel an acquisition which maybe be fucked.

\n

Image you click it, it's going to delete the folder in which you save this acquisition, meaning execute :

\n

 

\nrm -r  /var/www/Name_of_the_project/Name_of_the_station/Acquisition_ID\n

 

\n

So if you made a great acquisition, then run a new one with the same input for Acquisition ID and finally click on this button, you are going to delete them both.

\n

Don't use it if you don't need it and please never click twice because the pi might burn.

\n
\n

ssh :

\n

To access the inside of the pi, you can use ssh from from terminal once your are connected to the WiFi by typing this command : ssh -Y planktonscope@192.168.4.1

\n

 

\n

The Password is : raspberry

\n
\n

Data :

\n

In order to access your acquisitions, you can either click on this link or get to the directory via ssh : /var/www/

\n
\n

In order to access the script via ssh, you can get to the directory : /home/pi/PlanktonScope/

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] - ] - }, - { - "id": "42d9d2cb.9d3f84", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "nb_step", - "label": "nb step (30μm/step)", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 4, - "width": 4, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "nb_step", - "format": "{{value}}", - "min": "1", - "max": "5000", - "step": 1, - "x": 520, - "y": 320, - "wires": [ - [ - "523fdeaa.50c6c" - ] - ] - }, - { - "id": "4287fe47.26a63", - "type": "ui_numeric", - "z": "7f885510.6173fc", - "name": "volume", - "label": "Volume (ml)*", - "tooltip": "", - "group": "c62ffbd3.787ef8", - "order": 8, - "width": 4, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "volume", - "format": "{{value}}", - "min": "1", - "max": "5000", - "step": 1, - "x": 520, - "y": 500, - "wires": [ - [ - "84fd85fd.426878" - ] - ] - }, - { - "id": "c627ea8d.f886e8", - "type": "ui_group", - "z": "", - "name": "Sample", - "tab": "6b01f851.598028", - "order": 1, - "disp": true, - 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"type": "ui_group", - "z": "", - "name": "Preview", - "tab": "6b01f851.598028", - "order": 2, - "disp": true, - "width": 12, - "collapse": false - }, - { - "id": "a61f7be8.af6418", - "type": "ui_group", - "z": "", - "name": "Acquisition", - "tab": "6b01f851.598028", - "order": 8, - "disp": true, - "width": 12, - "collapse": false - }, - { - "id": "79767bcc.30bb94", - "type": "ui_group", - "z": "", - "name": "Reminder", - "tab": "6b01f851.598028", - "order": 9, - "disp": true, - "width": 27, - "collapse": false - }, - { - "id": "6b01f851.598028", - "type": "ui_tab", - "z": "", - "name": "PlanktonScope GUI v2.1", - "icon": "date_range", - "order": 1, - "disabled": false, - "hidden": false - } -] From c32dd07d38be21f2a41c951410118e66fe72fcfe Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:21:40 +0200 Subject: [PATCH 11/17] Delete flow_chaetoceros.json --- flows/flow_chaetoceros.json | 4436 ----------------------------------- 1 file changed, 4436 deletions(-) delete mode 100644 flows/flow_chaetoceros.json diff --git a/flows/flow_chaetoceros.json b/flows/flow_chaetoceros.json deleted file mode 100644 index 17282c3..0000000 --- a/flows/flow_chaetoceros.json +++ /dev/null @@ -1,4436 +0,0 @@ -[ - 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"x": 586, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "259fd49a.160a3c", - "type": "ui_dropdown", - "z": "bdd6e33e.5db3b8", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 7, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 566, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "66a3425c.79aabc", - "type": "ui_text_input", - "z": "bdd6e33e.5db3b8", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "52159161.72187", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 566, - "y": 240, - "wires": [ - [] - ] - }, - { - "id": "5866c9a4.e1ca88", - "type": "ui_text_input", - "z": "bdd6e33e.5db3b8", - "name": "acq_instrument", - "label": "Acquisition instrument", - "tooltip": "PlanktonScope V2.1", - "group": "52159161.72187", - "order": 6, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_instrument", - "x": 556, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "76a6e6bb.a08b98", - "type": "json", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "action": "str", - "pretty": true, - "x": 1310, - "y": 100, - "wires": [ - [ - "f25890f5.f2549" - ] - ] - }, - { - "id": "594ec843.9d4458", - "type": "file in", - "z": "259c8713.b50e28", - "name": "", - "filename": "/home/pi/PlanktonScope/config.txt", - "format": "utf8", - "chunk": false, - "sendError": false, - "encoding": "none", - "x": 340, - "y": 60, - "wires": [ - [ - "3bc1a977.4e9c76" - ] - ] - }, - { - "id": "d9ca0e54.f8b58", - "type": "inject", - "z": "259c8713.b50e28", - "name": "on_load", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "", - "crontab": "", - "once": true, - "onceDelay": 0.1, - "x": 100, - "y": 60, - "wires": [ - [ - "594ec843.9d4458", - "ca38a11d.0ee54", - "807d5cce.2bb1e", - "fda01242.9576a8" - ] - ] - }, - { - "id": "3bc1a977.4e9c76", - "type": "json", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "action": "", - "pretty": false, - "x": 550, - "y": 60, - "wires": [ - [ - "7f101b25.0da4a4", - "99b5a67.080f258", - "a71ba4a6.c44c4", - "fe5585e.a1ab078", - "da9f1367.3a17a8", - "d8dbecd.f7b3b9", - "c986ae96.860ec8" - ] - ] - }, - { - "id": "2582798f.eddcc6", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_projet", - "func": "msg.payload = msg.payload.sample_project;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 40, - "wires": [ - [ - "a163194f.0b17c8" - ] - ] - }, - { - "id": "1590a418.9166dc", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_ship", - "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 120, - "wires": [ - [ - "6d0d6fc7.d30bb" - ] - ] - }, - { - "id": "1d28205b.58a37", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_id", - "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 80, - "wires": [ - [ - "914752eb.af1b" - ] - ] - }, - { - "id": "d96f9fa3.d4cfc", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_operator", - "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 160, - "wires": [ - [ - "458408d7.2b3b68" - ] - ] - }, - { - "id": "784e2f78.9b96f", - "type": "function", - "z": "173a6e6b.e5ca6a", - "name": "get sample_sampling_gear", - "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 280, - "y": 200, - "wires": [ - [ - "43b12fe4.c5aa3" - ] - ] - }, - { - "id": "47459dcd.81b594", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_id", - "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 210, - "y": 40, - "wires": [ - [ - "6ecc9468.0271dc" - ] - ] - }, - { - "id": "eec199a3.a5a768", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_instrument", - "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 80, - "wires": [ - [ - "5866c9a4.e1ca88" - ] - ] - }, - { - "id": "2d278f0a.1a97a", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_celltype", - "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 120, - "wires": [ - [ - "259fd49a.160a3c" - ] - ] - }, - { - "id": "4074b907.e527e8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_minimum_mesh", - "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 160, - "wires": [ - [ - "5aba848a.7a861c" - ] - ] - }, - { - "id": "bc37aba3.0d1e78", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_maximum_mesh", - "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 200, - "wires": [ - [ - "7cea16e.c42ace8" - ] - ] - }, - { - "id": "d973d64a.8801e8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_volume", - "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 240, - "wires": [ - [ - "66a3425c.79aabc" - ] - ] - }, - { - "id": "bc39179c.bb3c08", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_fnumber_objective", - "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 360, - "wires": [ - [ - "eb9181d8.25e01" - ] - ] - }, - { - "id": "47c7db4d.5eb014", - "type": "ui_numeric", - "z": "ad5a5663.ce893", - "name": "object_depth_min", - "label": "Minimum depth (m)", - "tooltip": "", - "group": "cef1e703.bcf3c8", - "order": 3, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "object_depth_min", - "format": "{{value}}", - "min": "0", - "max": "2000", - "step": "1", - "x": 610, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "20c46fd4.6b984", - "type": "ui_numeric", - "z": "ad5a5663.ce893", - "name": "object_depth_max", - "label": "Maximum depth (m)", - "tooltip": "", - "group": "cef1e703.bcf3c8", - "order": 2, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "object_depth_max", - "format": "{{value}}", - "min": "0", - "max": "2000", - "step": "1", - "x": 610, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "1a5edafb.a05cf5", - "type": "function", - "z": "259c8713.b50e28", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1020, - "y": 60, - "wires": [ - [ - "e001a28.555566" - ] - ] - }, - { - "id": "21f41837.bb6c88", - "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_depth_min", - "func": "msg.payload = msg.payload.object_depth_min;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 304, - "y": 120, - "wires": [ - [ - "47c7db4d.5eb014" - ] - ] - }, - { - "id": "c2f235f2.eee388", - "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_depth_max", - "func": "msg.payload = msg.payload.object_depth_max;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 304, - "y": 160, - "wires": [ - [ - "20c46fd4.6b984" - ] - ] - }, - { - "id": "23e45d82.a01f82", - "type": "ui_text_input", - "z": "4475ba6c.45604c", - "name": "process_id", - "label": "Id of the process", - "tooltip": "", - "group": "b1321ea9.cfcf28", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "process_id", - "x": 550, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "d899c841.e6c178", - "type": "function", - "z": "4475ba6c.45604c", - "name": "get process_id", - "func": "msg.payload = msg.payload.process_id+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 200, - "y": 80, - "wires": [ - [ - "23e45d82.a01f82" - ] - ] - }, - { - "id": "4fa9647b.8a2ebc", - "type": "gpsd", - "z": "ad5a5663.ce893", - "name": "", - "hostname": "localhost", - "port": "2947", - "tpv": true, - "sky": false, - "info": false, - "device": false, - "gst": false, - "att": false, - "x": 90, - "y": 220, - "wires": [ - [ - "2327c165.8397ae", - "bbb7cb31.15121" - ] - ] - }, - { - "id": "767b43a1.de21dc", - "type": "ui_worldmap", - "z": "ad5a5663.ce893", - "d": true, - "group": "cef1e703.bcf3c8", - "order": 1, - "width": 0, - "height": 0, - "name": "", - "lat": "1.5", - "lon": "1.5", - "zoom": "4", - "layer": "OSM grey", - "cluster": "1", - "maxage": "", - "usermenu": "hide", - "layers": "hide", - "panit": "false", - "panlock": "false", - "zoomlock": "false", - "hiderightclick": "true", - "coords": "deg", - "showgrid": "false", - "path": "/worldmap", - "x": 640, - "y": 200, - "wires": [] - }, - { - "id": "2327c165.8397ae", - "type": "function", - "z": "ad5a5663.ce893", - "name": "get object_lat & object_lon", - "func": "\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 320, - "y": 200, - "wires": [ - [ - "767b43a1.de21dc" - ] - ] - }, - { - "id": "fa47061e.34a218", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_min_esd", - "label": "Minimum size to segment (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 9, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_min_esd", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "5", - "x": 566, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "6f36bd6d.154d14", - "type": "ui_numeric", - "z": "bdd6e33e.5db3b8", - "name": "acq_max_esd", - "label": "Maximum size to segment (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 5, - "width": 0, - "height": 0, - "wrap": false, - "passthru": true, - "topic": "acq_max_esd", - "format": "{{value}}", - "min": "100", - "max": "2000", - "step": "5", - "x": 556, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "277b6764.edb1f8", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_min_esd", - "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 280, - "wires": [ - [ - "fa47061e.34a218" - ] - ] - }, - { - "id": "75b10c7c.8433a4", - "type": "function", - "z": "bdd6e33e.5db3b8", - "name": "get acq_max_esd", - "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 230, - "y": 320, - "wires": [ - [ - "6f36bd6d.154d14" - ] - ] - }, - { - "id": "5f4a72d1.9f6adc", - "type": "ui_text_input", - "z": "ae90e3e.7d9fba", - "name": "nb_step", - "label": "Number of step(s)", - "tooltip": "", - "group": "fbd92986.1028c8", - "order": 2, - "width": 8, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_step", - "x": 520, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "81a7627c.bac92", - "type": "function", - "z": "ae90e3e.7d9fba", - "name": "get generic_nb_step", - "func": "msg.payload = msg.payload.generic_nb_step;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 40, - "wires": [ - [ - "5f4a72d1.9f6adc" - ] - ] - }, - { - "id": "705dddc5.567bc4", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "DOWN", - "group": "fbd92986.1028c8", - "order": 3, - "width": 6, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "DOWN", - "payloadType": "str", - "topic": "actuator/focus", - "x": 520, - "y": 120, - "wires": [ - [ - "4f74f017.00a58" - ] - ] - }, - { - "id": "b0aacff7.56651", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "UP", - "group": "fbd92986.1028c8", - "order": 1, - "width": 6, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "UP", - "payloadType": "str", - "topic": "actuator/focus", - "x": 530, - "y": 81, - "wires": [ - [ - "4f74f017.00a58" - ] - ] - }, - { - "id": "3e9c4e74.aee022", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"manual_volume\");\nvar flowrate= global.get(\"flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"manual_volume\");\n nb_step=volume*507\n msg.volume = volume;\n flowrate = global.get(\"flowrate\");\n duration=(volume*60)/flowrate\n delay=(duration/nb_step)-0.005\n msg.topic = \"actuator/pump\";\n \n if(msg.payload === \"FORWARD\" & state===\"free\"){\n msg.payload='FORWARD '+delay+' '+nb_step;\n }\n if(msg.payload === \"BACKWARD\" & state===\"free\"){\n msg.payload='BACKWARD '+delay+' '+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 620, - "y": 140, - "wires": [ - [ - "98e2e9e0.fb7418" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "3f0df968.b0d286", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "BACKWARD", - "group": "707d9797.c8e798", - "order": 2, - "width": 6, - "height": 1, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_back", - "payload": "BACKWARD", - "payloadType": "str", - "topic": "actuator/pump", - "x": 470, - "y": 120, - "wires": [ - [ - "3e9c4e74.aee022" - ] - ] - }, - { - "id": "214fb242.9abb6e", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "FORWARD", - "group": "707d9797.c8e798", - "order": 4, - "width": 6, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "FORWARD", - "payloadType": "str", - "topic": "actuator/pump", - "x": 470, - "y": 160, - "wires": [ - [ - "3e9c4e74.aee022" - ] - ] - }, - { - "id": "1d58e86f.a3a9e8", - "type": "rpi-gpio out", - "z": "259c8713.b50e28", - "name": "", - "pin": "40", - "set": "", - "level": "0", - "freq": "", - "out": "out", - "x": 400, - "y": 100, - "wires": [] - }, - { - "id": "3e58f066.366b5", - "type": "ui_template", - "z": "259c8713.b50e28", - "group": "f5194cae.c84688", - "name": "Stream Pi Camera", - "order": 1, - "width": 24, - "height": 11, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 750, - "y": 340, - "wires": [ - [] - ] - }, - { - "id": "b7d9455c.026588", - "type": "switch", - "z": "ae90e3e.7d9fba", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 810, - "y": 100, - "wires": [ - [ - "fdb3b132.8b341" - ], - [ - "b9d996d6.37c2f8" - ] - ] - }, - { - "id": "b9d996d6.37c2f8", - "type": "ui_toast", - "z": "ae90e3e.7d9fba", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 970, - "y": 140, - "wires": [ - [] - ] - }, - { - "id": "ca38a11d.0ee54", - "type": "function", - "z": "259c8713.b50e28", - "name": "init LED", - "func": "msg.payload=1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 260, - "y": 100, - "wires": [ - [ - "1d58e86f.a3a9e8" - ] - ] - }, - { - "id": "98e2e9e0.fb7418", - "type": "switch", - "z": "407d8cdb.3cb7cc", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 770, - "y": 140, - "wires": [ - [ - "61fb057d.3c251c" - ], - [ - "46a536f0.c83138" - ] - ] - }, - { - "id": "46a536f0.c83138", - "type": "ui_toast", - "z": "407d8cdb.3cb7cc", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 930, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "24ffcf03.2a51b", - "type": "ui_button", - "z": "407d8cdb.3cb7cc", - "name": "stop pump", - "group": "707d9797.c8e798", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP PUMP", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 470, - "y": 200, - "wires": [ - [ - "e2a7220a.09d43" - ] - ] - }, - { - "id": "4f74f017.00a58", - "type": "function", - "z": "ae90e3e.7d9fba", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 660, - "y": 100, - "wires": [ - [ - "b7d9455c.026588" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "52cc1de5.b78e84", - "type": "ui_button", - "z": "ae90e3e.7d9fba", - "name": "stop focus", - "group": "fbd92986.1028c8", - "order": 4, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP FOCUS", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 510, - "y": 160, - "wires": [ - [ - "e46763fe.7fc83" - ] - ] - }, - { - "id": "39cad6fb.1503ca", - "type": "ui_button", - "z": "35488f4f.00498", - "name": "", - "group": "c6a276ac.3eb74", - "order": 1, - "width": 0, - "height": 0, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 220, - "y": 80, - "wires": [ - [ - "95b876d4.07c708" - ] - ] - }, - { - "id": "1f53f29b.feee4d", - "type": "exec", - "z": "35488f4f.00498", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 530, - "y": 80, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e325458b.95bff8", - "type": "ui_button", - "z": "35488f4f.00498", - "name": "", - "group": "c6a276ac.3eb74", - "order": 2, - "width": 0, - "height": 0, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 220, - "y": 140, - "wires": [ - [ - "95b876d4.07c708" - ] - ] - }, - { - "id": "95b876d4.07c708", - "type": "python3-function", - "z": "35488f4f.00498", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 390, - "y": 100, - "wires": [ - [ - "d348474b.d756a8", - "1f53f29b.feee4d" - ] - ] - }, - { - "id": "d348474b.d756a8", - "type": "exec", - "z": "35488f4f.00498", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 550, - "y": 140, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "cdd1b550.da18e8", - "type": "mqtt in", - "z": "91e5fd54.56f58", - "name": "", - "topic": "receiver/#", - "qos": "0", - "datatype": "auto", - "broker": "b77ffa1b.942258", - "x": 80, - "y": 40, - "wires": [ - [ - "6920281d.dc9b48" - ] - ] - }, - { - "id": "6920281d.dc9b48", - "type": "switch", - "z": "91e5fd54.56f58", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "receiver/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "receiver/focus", - "vt": "str" - }, - { - "t": "eq", - "v": "receiver/image", - "vt": "str" - }, - { - "t": "cont", - "v": "receiver/segmentation", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 4, - "x": 230, - "y": 40, - "wires": [ - [ - "2f66e917.fee586" - ], - [ - "363ee47e.ed522c" - ], - [ - "45a52868.fe37c8" - ], - [ - "469cc189.903d" - ] - ] - }, - { - "id": "2f66e917.fee586", - "type": "switch", - "z": "91e5fd54.56f58", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 470, - "y": 40, - "wires": [ - [ - "5c0d0c35.3bcf14" - ], - [ - "cd01157d.0892d8" - ], - [ - "68e02bf4.7013e4" - ] - ] - }, - { - "id": "5c0d0c35.3bcf14", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The pump has started", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 920, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "cd01157d.0892d8", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The pump has finished.", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 910, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "68e02bf4.7013e4", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The pump has been stopped.", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 900, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "363ee47e.ed522c", - "type": "switch", - "z": "91e5fd54.56f58", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 470, - "y": 200, - "wires": [ - [ - "c088b72f.326d98" - ], - [ - "36934381.14442c" - ], - [ - "89329cfe.c8f4" - ] - ] - }, - { - "id": "c088b72f.326d98", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The focus has started", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 920, - "y": 200, - "wires": [ - [] - ] - }, - { - "id": "36934381.14442c", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The focus has finished.", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - 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"broker": "cb2f36fe.1c7038", - "x": 910, - "y": 120, - "wires": [] - }, - { - "id": "e2a7220a.09d43", - "type": "mqtt out", - "z": "407d8cdb.3cb7cc", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 610, - "y": 200, - "wires": [] - }, - { - "id": "45a52868.fe37c8", - "type": "switch", - "z": "91e5fd54.56f58", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - }, - { - "t": "cont", - "v": "jpg", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 4, - "x": 470, - "y": 360, - "wires": [ - [ - "113c9b93.455814" - ], - [ - "29a7c6de.6ac2ea" - ], - [ - "f1b07b24.b85718" - ], - [ - "446a811b.25e4b", - "a57fea5b.59eb5" - ] - ] - }, - { - "id": "177a91d4.f1016e", - "type": "switch", - "z": "91e5fd54.56f58", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 650, - "y": 560, - "wires": [ - [ - "5d717a25.3437e4" - ], - [ - "7d713b16.235164" - ] - ] - }, - { - "id": "29a7c6de.6ac2ea", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The acquisition has finished.", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The acquisition has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 900, - "y": 400, - "wires": [ - [ - "a57fea5b.59eb5" - ] - ] - }, - { - "id": "f1b07b24.b85718", - "type": "change", - "z": "91e5fd54.56f58", - "name": "The acquisition has been stopped.", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The acquisition has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - 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"name": "", - "group": "8cfadfab.327d7", - "order": 1, - "width": 0, - "height": 0, - "label": "Memory load", - "chartType": "line", - "legend": "false", - "xformat": "auto", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": 1, - "removeOlderPoints": "", - "removeOlderUnit": "3600", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": false, - "outputs": 1, - "x": 950, - "y": 760, - "wires": [ - [] - ] - }, - { - "id": "1624f1bf.604bfe", - "type": "ui_chart", - "z": "91e5fd54.56f58", - "name": "", - "group": "8cfadfab.327d7", - "order": 8, - "width": 0, - "height": 0, - "label": "chart", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": true, - "ymin": "", - "ymax": "", - "removeOlder": 1, - "removeOlderPoints": "1000", - "removeOlderUnit": "3600", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": false, - "outputs": 1, - "x": 970, - "y": 700, - "wires": [ - [] - ] - }, - { - "id": "7f101b25.0da4a4", - "type": "subflow:173a6e6b.e5ca6a", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 750, - "y": 60, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "d8dbecd.f7b3b9", - "type": "subflow:ae90e3e.7d9fba", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 260, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "309468bc.ac83f8", - "type": "ui_text_input", - "z": "407d8cdb.3cb7cc", - "name": "manual_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 3, - "width": 8, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "manual_volume", - "x": 460, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "f859eeef.c59ed", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "get generic_manual_volume", - "func": "msg.payload = msg.payload.generic_manual_volume;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 80, - "wires": [ - [ - "309468bc.ac83f8" - ] - ] - }, - { - "id": "59b05f7f.9e83f8", - "type": "ui_slider", - "z": "407d8cdb.3cb7cc", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 480, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "d9a85435.ced5e", - "type": "function", - "z": "407d8cdb.3cb7cc", - "name": "get generic.flowrate", - "func": "msg.payload = msg.payload.generic_flowrate;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 190, - "y": 40, - "wires": [ - [ - "59b05f7f.9e83f8" - ] - ] - }, - { - "id": "c986ae96.860ec8", - "type": "subflow:407d8cdb.3cb7cc", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 300, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "99b5a67.080f258", - "type": "subflow:bdd6e33e.5db3b8", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 760, - "y": 100, - "wires": [ - [ - "1a5edafb.a05cf5" - ], - [ - "e001a28.555566" - ] - ] - }, - { - "id": "a71ba4a6.c44c4", - "type": "subflow:ad5a5663.ce893", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 740, - "y": 140, - "wires": [ - [ - "1a5edafb.a05cf5" - ], - [ - "e001a28.555566" - ] - ] - }, - { - "id": "9c301fc6.9a9318", - "type": "subflow:35488f4f.00498", - "z": "259c8713.b50e28", - "name": "System commands", - "env": [], - "x": 750, - "y": 460, - "wires": [] - }, - { - "id": "4d5b9f01.270e88", - "type": "exec", - "z": "344146df.e4d5ba", - "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "", - "timer": "", - "name": "RPi Temp.", - "x": 350, - "y": 80, - "wires": [ - [ - "4f3fb60b.912848" - ], - [], - [] - ] - }, - { - "id": "1c4bc7ff.94aa8", - "type": "inject", - "z": "344146df.e4d5ba", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "10", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 190, - "y": 80, - "wires": [ - [ - "4d5b9f01.270e88" - ] - ] - }, - { - "id": "4f3fb60b.912848", - "type": "python3-function", - "z": "344146df.e4d5ba", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 530, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "ee70d541.87713", - "type": "subflow:344146df.e4d5ba", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 300, - "y": 140, - "wires": [] - }, - { - "id": "c14cf94.1413e88", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_flush", - "label": "Duration of the flushing (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_flush", - "x": 520, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "d7b55d02.e41f1", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_seq", - "label": "Duration before sequence (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 4, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_seq", - "x": 510, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "8729ec5c.cf4ab8", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "nb_img", - "label": "Number of images per acquisition", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_img", - "x": 540, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "3808d004.94ea28", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_flush", - "func": "msg.payload = msg.payload.duration_flush;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 210, - "y": 80, - "wires": [ - [ - "c14cf94.1413e88" - ] - ] - }, - { - "id": "f7cc1192.5a51e8", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get nb_img", - "func": "msg.payload = msg.payload.nb_img;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 190, - "y": 120, - "wires": [ - [ - "8729ec5c.cf4ab8" - ] - ] - }, - { - "id": "10ce45f6.3036ca", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_seq", - "func": "msg.payload = msg.payload.duration_bef_seq;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 160, - "wires": [ - [ - "d7b55d02.e41f1" - ] - ] - }, - { - "id": "27bbe0f0.05b2c", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_img", - "label": "Duration before image (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_img", - "x": 510, - "y": 200, - "wires": [ - [] - ] - }, - { - "id": "70dfb6bb.9319", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_img", - "func": "msg.payload = msg.payload.duration_bef_img;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 200, - "wires": [ - [ - "27bbe0f0.05b2c" - ] - ] - }, - { - "id": "b31fd152.a5489", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_between", - "label": "Duration between acquisition (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 6, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_between", - "x": 510, - "y": 240, - "wires": [ - [] - ] - }, - { - "id": "a0b53585.93216", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_between", - "func": "msg.payload = msg.payload.duration_between;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 240, - "wires": [ - [ - "b31fd152.a5489" - ] - ] - }, - { - "id": "fee8c0fa.108778", - "type": "subflow:91e5fd54.56f58", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 760, - "y": 380, - "wires": [] - }, - { - "id": "fe5585e.a1ab078", - "type": "subflow:4475ba6c.45604c", - "z": "259c8713.b50e28", - "name": "process metadata", - "env": [], - "x": 750, - "y": 180, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ] - }, - { - "id": "da9f1367.3a17a8", - "type": "subflow:b73d5eb8.60ef3", - "z": "259c8713.b50e28", - "d": true, - "name": "Valve actuation", - "env": [], - "x": 740, - "y": 220, - "wires": [ - [ - "1a5edafb.a05cf5" - ] - ], - "icon": "node-red-dashboard/ui_switch.png" - }, - { - "id": "69799a39.13803c", - "type": "function", - "z": "b73d5eb8.60ef3", - "name": "get duration_bef_cycle", - "func": "msg.payload = msg.payload.duration_bef_cycle;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 220, - "y": 40, - "wires": [ - [ - "7a0b6294.e887c4" - ] - ] - }, - { - "id": "7a0b6294.e887c4", - "type": "ui_text_input", - "z": "b73d5eb8.60ef3", - "name": "duration_bef_cycle", - "label": "Duration before the cycles (s)", - "tooltip": "", - "group": "f41d0ecb.8be06", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "duration_bef_cycle", - "x": 510, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "a57fea5b.59eb5", - "type": "ui_toast", - "z": "91e5fd54.56f58", - "position": "top right", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 0, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1220, - "y": 360, - "wires": [] - }, - { - "id": "f7d3d0c4.0203", - "type": "exec", - "z": "1b486ba8.f8c41c", - "command": "sudo date -s", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 1010, - "y": 240, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "c5fcaba5.184e88", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = new Date();\n//get weekday\nvar weekday = new Array(7);\nweekday[0] = \"Sun\";\nweekday[1] = \"Mon\";\nweekday[2] = \"Tue\";\nweekday[3] = \"Wed\";\nweekday[4] = \"Thu\";\nweekday[5] = \"Fri\";\nweekday[6] = \"Sat\";\nvar w = weekday[d.getUTCDay()];\n//get Month\nvar month = new Array(12);\nmonth[0] = \"Jan\";\nmonth[1] = \"Feb\";\nmonth[2] = \"Mar\";\nmonth[3] = \"Apr\";\nmonth[4] = \"May\";\nmonth[5] = \"Jun\";\nmonth[6] = \"Jul\";\nmonth[7] = \"Aug\";\nmonth[8] = \"Sep\";\nmonth[9] = \"Oct\";\nmonth[10] = \"Nov\";\nmonth[11] = \"Dec\";\nvar n = month[d.getUTCMonth()];\n \n//get day\nvar day = d.getUTCDay()\n\n//get Hours\nvar Hours = d.getUTCHours();\n//get Minutes\nvar Minutes = d.getUTCMinutes();\n//get Seconds\nvar Seconds = d.getUTCSeconds();\n//get FullYear\nvar FullYear = d.getUTCFullYear();\n\n//Thu Aug 09 2012 23:34:04 GMT+0200 (GMT+02:00)\n\n//Thu Aug 9 21:31:26 UTC 2012\n\n//msg.payload = \"Thu Aug 9 21:31:26 UTC 2012\"\n\nmsg.payload = '\"'+w+\" \"+n+\" \"+day+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+\" UTC \"+FullYear+'\"';\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 40, - "wires": [ - [ - "a1c2a5e3.4aea58" - ] - ] - }, - { - "id": "807d5cce.2bb1e", - "type": "subflow:1b486ba8.f8c41c", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 280, - "y": 180, - "wires": [] - }, - { - "id": "a1c2a5e3.4aea58", - "type": "ui_template", - "z": "1b486ba8.f8c41c", - "group": "9214d59d.e7b52", - "name": "", - "order": 1, - "width": 0, - "height": 0, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 640, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "9b1b260f.e4b338", - "type": "function", - "z": "ad5a5663.ce893", - "name": "set object_time", - "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute;\nglobal.set('object_time',time_UTC);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 804, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "86aa9817.45a2e8", - "type": "function", - "z": "ad5a5663.ce893", - "name": "set object_date", - "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 804, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "546376f8.9d25d8", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "year", - "label": "Year", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 2, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "year", - "format": "{{value}}", - "min": "2020", - "max": "2030", - "step": 1, - "x": 630, - "y": 80, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "8a701d46.962ed8", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "month", - "label": "Month", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 3, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "month", - "format": "{{value}}", - "min": "1", - "max": "12", - "step": 1, - "x": 630, - "y": 120, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "3e39bc34.b3042c", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "day", - "label": "Day", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 4, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "day", - "format": "{{value}}", - "min": "1", - "max": "31", - "step": 1, - "x": 630, - "y": 160, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "6edc1533.cd3ab4", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "hour", - "label": "Hour", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 5, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "hour", - "format": "{{value}}", - "min": "0", - "max": "23", - "step": 1, - "x": 630, - "y": 200, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "1ba0f9e6.1be54e", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "minute", - "label": "Minute", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 6, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "minute", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 630, - "y": 240, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "fd050fce.2ffe28", - "type": "ui_numeric", - "z": "1b486ba8.f8c41c", - "name": "second", - "label": "Second", - "tooltip": "", - "group": "9214d59d.e7b52", - "order": 7, - "width": 3, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "second", - "format": "{{value}}", - "min": "0", - "max": "59", - "step": 1, - "x": 640, - "y": 280, - "wires": [ - [ - "dc685555.af057" - ] - ] - }, - { - "id": "e1cc68bb.7b045", - "type": "interval", - "z": "1b486ba8.f8c41c", - "name": "interval", - "interval": "1", - "onstart": false, - "msg": "ping", - "showstatus": true, - "unit": "seconds", - "statusformat": "YYYY-MM-D HH:mm:ss", - "x": 310, - "y": 40, - "wires": [ - [ - "c5fcaba5.184e88" - ] - ] - }, - { - "id": "23f1828c.afae3e", - "type": "ui_button", - "z": "1b486ba8.f8c41c", - "name": "", - "group": "9214d59d.e7b52", - "order": 8, - "width": 4, - "height": 1, - "passthru": false, - "label": "Update", - "tooltip": "", - "color": "black", - "bgcolor": "white", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 640, - "y": 320, - "wires": [ - [ - "cb4c9210.01c958" - ] - ] - }, - { - "id": "cb4c9210.01c958", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "update datetime", - "func": "var FullYear= global.get(\"year\");\nvar Month= global.get(\"month\");\nvar day= global.get(\"day\");\nvar Hours= global.get(\"hour\");\nvar Minutes= global.get(\"minute\");\nvar Seconds= global.get(\"second\");\n\nmsg.payload = new Date();\n//get Month\nvar month = new Array(12);\nmonth[1] = \"Jan\";\nmonth[2] = \"Feb\";\nmonth[3] = \"Mar\";\nmonth[4] = \"Apr\";\nmonth[5] = \"May\";\nmonth[6] = \"Jun\";\nmonth[7] = \"Jul\";\nmonth[8] = \"Aug\";\nmonth[9] = \"Sep\";\nmonth[10] = \"Oct\";\nmonth[11] = \"Nov\";\nmonth[12] = \"Dec\";\nvar n = month[Month];\n \nmsg.payload = '\"'+day+\" \"+n+\" \"+FullYear+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+'\"';\n\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 800, - "y": 320, - "wires": [ - [ - "7c1c8abf.4b984c", - "f7d3d0c4.0203" - ] - ] - }, - { - "id": "dc685555.af057", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 840, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "7c1c8abf.4b984c", - "type": "debug", - "z": "1b486ba8.f8c41c", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1010, - "y": 300, - "wires": [] - }, - { - "id": "92842b63.e0d7b8", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCFullYear();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 80, - "wires": [ - [ - "546376f8.9d25d8" - ] - ] - }, - { - "id": "48033b32.2bca94", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = new Date();\nmsg.payload = d\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 310, - "y": 80, - "wires": [ - [ - "92842b63.e0d7b8", - "94057891.b1a658", - "aab6990b.1cf718", - "42b00a98.b36bb4", - "e2370ad.c8e7ff8", - "9c43dfe1.eb6178" - ] - ] - }, - { - "id": "94057891.b1a658", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCMonth();\n\nmsg.payload = val+1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 120, - "wires": [ - [ - "8a701d46.962ed8" - ] - ] - }, - { - "id": "aab6990b.1cf718", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCDay();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 160, - "wires": [ - [ - "3e39bc34.b3042c" - ] - ] - }, - { - "id": "42b00a98.b36bb4", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCHours();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 200, - "wires": [ - [ - "6edc1533.cd3ab4" - ] - ] - }, - { - "id": "e2370ad.c8e7ff8", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCMinutes();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 240, - "wires": [ - [ - "1ba0f9e6.1be54e" - ] - ] - }, - { - "id": "9c43dfe1.eb6178", - "type": "function", - "z": "1b486ba8.f8c41c", - "name": "", - "func": "d = msg.payload;\n\nvar val = d.getUTCSeconds();\n\nmsg.payload = val;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 490, - "y": 280, - "wires": [ - [ - "fd050fce.2ffe28" - ] - ] - }, - { - "id": "ca843dd8.d1c62", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "python3.7 /home/pi/PlanktonScope/script/mqtt_pump_focus_image_segment_strem.py", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 520, - "y": 100, - "wires": [ - [], - [ - "a49ed5a6.5b73b8" - ], - [] - ] - }, - { - "id": "1af32c3e.856864", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/mqtt_pump_focus_image_segment_strem.py\"| head -1 | awk -F \" \" '{print$1}' ", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 660, - "y": 160, - "wires": [ - [ - "ddabe48c.369c68" - ], - [], - [] - ] - }, - { - "id": "ddabe48c.369c68", - "type": "exec", - "z": "66c23d37.f72cdc", - "command": "kill", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 1210, - "y": 120, - "wires": [ - [ - "6382060e.460ab8" - ], - [ - "6382060e.460ab8" - ], - [ - "6382060e.460ab8" - ] - ] - }, - { - "id": "fcaca139.5ed04", - "type": "ui_button", - "z": "66c23d37.f72cdc", - "name": "", - "group": "9214d59d.e7b52", - "order": 9, - "width": 12, - "height": 1, - "passthru": false, - "label": "Kill MQTT", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 80, - "y": 160, - "wires": [ - [ - "1af32c3e.856864" - ] - ] - }, - { - "id": "9d663990.fd2908", - "type": "ui_button", - "z": "66c23d37.f72cdc", - "name": "", - "group": "9214d59d.e7b52", - "order": 10, - "width": 12, - "height": 1, - "passthru": false, - "label": "Restart MQTT", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 100, - "y": 100, - "wires": [ - [ - "ca843dd8.d1c62" - ] - ] - }, - { - "id": "a49ed5a6.5b73b8", - "type": "ui_toast", - "z": "66c23d37.f72cdc", - "position": "top right", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 0, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 920, - "y": 100, - "wires": [] - }, - { - "id": "fda01242.9576a8", - "type": "subflow:66c23d37.f72cdc", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 270, - "y": 220, - "wires": [] - }, - { - "id": "bbb7cb31.15121", - "type": "debug", - "z": "ad5a5663.ce893", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "true", - "targetType": "full", - "x": 280, - "y": 360, - "wires": [] - }, - { - "id": "6382060e.460ab8", - "type": "debug", - "z": "66c23d37.f72cdc", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1380, - "y": 120, - "wires": [] - }, - { - "id": "b23ae409.085ad8", - "type": "ui_button", - "z": "8d959937.18735", - "name": "", - "group": "d170ac9c.3b4828", - "order": 1, - "width": 0, - "height": 0, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "actuator/image", - "x": 200, - "y": 100, - "wires": [ - [ - "715c6be9.55822c" - ] - ] - }, - { - "id": "715c6be9.55822c", - "type": "function", - "z": "8d959937.18735", - "name": "image.js", - "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar duration_bef_cycle= global.get(\"duration_bef_cycle\");\nvar duration_flush= global.get(\"duration_flush\");\nvar nb_img= global.get(\"nb_img\");\nvar duration_bef_seq= global.get(\"duration_bef_seq\");\nvar duration_bef_img= global.get(\"duration_bef_img\");\nvar duration_between= global.get(\"duration_between\");\n\nif (duration_bef_cycle === undefined || duration_bef_cycle === \"\" || duration_bef_cycle === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the cycles\";\n \n}else if (duration_flush === undefined || duration_flush === \"\" || duration_flush === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration of the flushing\";\n \n}else if (nb_img === undefined || nb_img === \"\" || nb_img === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Directory to store the images\";\n \n}else if (duration_bef_seq === undefined || duration_bef_seq === \"\" || duration_bef_seq === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the sequence\";\n \n}else if (duration_bef_img === undefined || duration_bef_img === \"\" || duration_bef_img === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before an image\";\n \n}else if (duration_between === undefined || duration_between === \"\" || duration_between === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration between sequence\";\n \n}else {\n nb_img=nb_img-1\n msg.payload=duration_bef_cycle+' '+duration_flush+' '+nb_img+' '+duration_bef_seq+' '+duration_bef_img+' '+duration_between;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 360, - "y": 100, - "wires": [ - [ - "bda62ebe.dd2e4" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "bda62ebe.dd2e4", - "type": "switch", - "z": "8d959937.18735", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/image", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 510, - "y": 100, - "wires": [ - [ - "366697a.e8f6068" - ], - [ - "e2049db5.46682" - ] - ] - }, - { - "id": "e2049db5.46682", - "type": "ui_toast", - "z": "8d959937.18735", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 690, - "y": 120, - "wires": [ - [] - ] - }, - { - "id": "366697a.e8f6068", - "type": "mqtt out", - "z": "8d959937.18735", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 670, - "y": 80, - "wires": [] - }, - { - "id": "3a85a060.ad2aa", - "type": "ui_button", - "z": "8d959937.18735", - "name": "Stop Acquisition", - "group": "d170ac9c.3b4828", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "label": "STOP ACQUISITION", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 200, - "y": 140, - "wires": [ - [ - "f59d51da.c3b078" - ] - ] - }, - { - "id": "f59d51da.c3b078", - "type": "mqtt out", - "z": "8d959937.18735", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 350, - "y": 140, - "wires": [] - }, - { - "id": "8ade1ac1.5c3408", - "type": "ui_switch", - "z": "8d959937.18735", - "name": "Segmentation", - "label": "Segmentation", - "tooltip": "", - "group": "d170ac9c.3b4828", - "order": 3, - "width": 0, - "height": 0, - "passthru": false, - "decouple": "false", - "topic": "actuator/segmentation_state", - "style": "", - "onvalue": "true", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "false", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 200, - "y": 180, - "wires": [ - [ - "7751b219.9a3e1c" - ] - ] - }, - { - "id": "7751b219.9a3e1c", - "type": "mqtt out", - "z": "8d959937.18735", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 350, - "y": 180, - "wires": [] - }, - { - "id": "2a677ff0.62e0f", - "type": "subflow:8d959937.18735", - "z": "259c8713.b50e28", - "name": "", - "env": [], - "x": 750, - "y": 420, - "wires": [] - } -] From ced62d7884a8739a1d7967d86e88004c018befc2 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:21:48 +0200 Subject: [PATCH 12/17] Delete flow_mqtt.json --- flows/flow_mqtt.json | 3502 ------------------------------------------ 1 file changed, 3502 deletions(-) delete mode 100644 flows/flow_mqtt.json diff --git a/flows/flow_mqtt.json b/flows/flow_mqtt.json deleted file mode 100644 index 3619162..0000000 --- a/flows/flow_mqtt.json +++ /dev/null @@ -1,3502 +0,0 @@ -[ - { - "id": "259c8713.b50e28", - "type": "tab", - "label": "Main", - "disabled": false, - "info": "" - }, - { - "id": "6d0d6fc7.d30bb", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_ship", - "label": "Name of the ship", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_ship", - "x": 1370, - "y": 140, - "wires": [ - [ - "de9708c2.d00068" - ] - ] - }, - { - "id": "43b12fe4.c5aa3", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "sample_sampling_gear", - "label": "Sampling gear", - "tooltip": "", - "place": "Select", - "group": "3e1ba03d.f01d8", - "order": 5, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "Plankton net", - "value": "net", - "type": "str" - }, - { - "label": "Niskin bottle 12L", - "value": "niskin_12L", - "type": "str" - }, - { - "label": "Niskin bottle 24L", - "value": "niskin_24L", - "type": "str" - }, - { - "label": "Pass Hull", - "value": "pass_hull", - "type": "str" - } - ], - "payload": "", - "topic": "sample_sampling_gear", - "x": 1330, - "y": 220, - "wires": [ - [ - "3c6a723.145778e" - ] - ] - }, - { - "id": "458408d7.2b3b68", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_operator", - "label": "Name of the operator", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 4, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_operator", - "x": 1350, - "y": 180, - "wires": [ - [ - "a2ae6c99.188f2" - ] - ] - }, - { - "id": "a163194f.0b17c8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_project", - "label": "Name of the project*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 1, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "sample_project", - "x": 1360, - "y": 60, - "wires": [ - [ - "1c2c7439.47115c" - ] - ] - }, - { - "id": "914752eb.af1b", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "sample_id", - "label": "ID of the station*", - "tooltip": "", - "group": "3e1ba03d.f01d8", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "sample_id", - "x": 1370, - "y": 100, - "wires": [ - [ - "30648de6.8ebc52" - ] - ] - }, - { - "id": "8a735175.23927", - "type": "ui_date_picker", - "z": "259c8713.b50e28", - "name": "acq_date", - "label": "Date :", - "group": "52159161.72187", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "topic": "", - "x": 1380, - "y": 1141, - "wires": [ - [ - "86aa9817.45a2e8" - ] - ] - }, - { - "id": "16d7de1c.b0c892", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_time", - "label": "Time :", - "tooltip": "", - "group": "52159161.72187", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 1380, - "y": 1181, - "wires": [ - [ - "9b1b260f.e4b338" - ] - ] - }, - { - "id": "9b1b260f.e4b338", - "type": "function", - "z": "259c8713.b50e28", - "name": "set object_time", - "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute+\"00\";\nglobal.set('object_time',time_UTC);\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1544, - "y": 1181, - "wires": [ - [ - "829cc940.327648" - ] - ] - }, - { - "id": "86aa9817.45a2e8", - "type": "function", - "z": "259c8713.b50e28", - "name": "set object_date", - "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1544, - "y": 1141, - "wires": [ - [ - "c93577b9.a1e438" - ] - ] - }, - { - "id": "e001a28.555566", - "type": "function", - "z": "259c8713.b50e28", - "name": "get global", - "func": "msg.payload={\n \n \"generic_nb_step\":global.get(\"generic_nb_step\"),\n \"generic_flowrate\":global.get(\"generic_flowrate\"),\n \"generic_manual_volume\":global.get(\"generic_manual_volume\"),\n \"generic_sleep_before\":global.get(\"generic_sleep_before\"),\n \"generic_volume_before\":global.get(\"generic_volume_before\"),\n \"generic_path\":global.get(\"generic_path\"),\n \"generic_nb_frame\":global.get(\"generic_nb_frame\"),\n \"generic_sleep_during\":global.get(\"generic_sleep_during\"),\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1880, - "y": 60, - "wires": [ - [ - "76a6e6bb.a08b98" - ] - ] - }, - { - "id": "f25890f5.f2549", - "type": "file", - "z": "259c8713.b50e28", - "name": "", - "filename": "/home/pi/PlanktonScope/config.txt", - "appendNewline": true, - "createDir": true, - "overwriteFile": "true", - "encoding": "none", - "x": 2233, - "y": 60, - "wires": [ - [] - ] - }, - { - "id": "f5c1aa13.3cfbf8", - "type": "function", - "z": "259c8713.b50e28", - "name": "set optical config", - "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1550, - "y": 1041, - "wires": [ - [ - "72e1e23b.a8a67c" - ] - ] - }, - { - "id": "eb9181d8.25e01", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 7, - "width": 12, - "height": 1, - "passthru": true, - "options": [ - { - "label": "f 25mm 1/2\" 5MP IR", - "value": 25, - "type": "num" - }, - { - "label": "f 16mm 1/2.5\" 5MP IR", - "value": 16, - "type": "num" - }, - { - "label": "f 12mm 1/2.5\" 5MP IR", - "value": 12, - "type": "num" - }, - { - "label": "f 8mm 1/2.5\" 5MP IR", - "value": 8, - "type": "num" - }, - { - "label": "f 6mm 1/2.5\" 5MP IR", - "value": 6, - "type": "num" - } - ], - "payload": "", - "topic": "acq_fnumber_objective", - "x": 1326, - "y": 1041, - "wires": [ - [ - "f5c1aa13.3cfbf8" - ] - ] - }, - { - "id": "5aba848a.7a861c", - "type": "ui_numeric", - "z": "259c8713.b50e28", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 8, - "width": 12, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 1336, - "y": 841, - "wires": [ - [ - "510bd72a.b42ea8" - ] - ] - }, - { - "id": "7cea16e.c42ace8", - "type": "ui_numeric", - "z": "259c8713.b50e28", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "52159161.72187", - "order": 9, - "width": 12, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 1336, - "y": 881, - "wires": [ - [ - "a3f18257.8a55e" - ] - ] - }, - { - "id": "6ecc9468.0271dc", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "52159161.72187", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_id", - "x": 1386, - "y": 721, - "wires": [ - [ - "b26183bf.aa217" - ] - ] - }, - { - "id": "259fd49a.160a3c", - "type": "ui_dropdown", - "z": "259c8713.b50e28", - "name": "acq_celltype", - "label": "Thickness flowcell*", - "tooltip": "", - "place": "Select option", - "group": "52159161.72187", - "order": 6, - "width": 12, - "height": 1, - "passthru": true, - "options": [ - { - "label": "200 μm µ-Slide I Luer", - "value": 200, - "type": "num" - }, - { - "label": "400 μm µ-Slide I Luer", - "value": 400, - "type": "num" - }, - { - "label": "600 μm µ-Slide I Luer", - "value": 600, - "type": "num" - }, - { - "label": "800 μm µ-Slide I Luer", - "value": 800, - "type": "num" - } - ], - "payload": "", - "topic": "acq_celltype", - "x": 1366, - "y": 801, - "wires": [ - [ - "d96d32ec.f88b9" - ] - ] - }, - { - "id": "66a3425c.79aabc", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "52159161.72187", - "order": 5, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 1366, - "y": 921, - "wires": [ - [ - "a3ec68a2.889ca8" - ] - ] - }, - { - "id": "6722bc48.d4f354", - "type": "comment", - "z": "259c8713.b50e28", - "name": "sample", - "info": "SAMPLE: a collection event\n\n sample_id [t] : unique identifier\n sample_*** [f] or [t] : other fields relative to the sample\n", - "x": 810, - "y": 60, - "wires": [] - }, - { - "id": "f93037f1.6a6238", - "type": "comment", - "z": "259c8713.b50e28", - "name": "acquisition", - "info": "ACQUISITION: metadata relative to the image acquisition\n\n acq_id [t] : unique identifier. If your acquisition differ for each sample you must have different identifier.\n acq_instrument [t] : name of the instrument (UVP, ZOOSCAN, FLOWCAM, etc.)\n acq_*** [f] or [t] : other fields relative to the acquisition\n", - "x": 800, - "y": 720, - "wires": [] - }, - { - "id": "734ba3db.3f82fc", - "type": "comment", - "z": "259c8713.b50e28", - "name": "object", - "info": "OBJECT: one object to be classified, usually one organism. One object can be represented by several images. In this tsv file, there is one line per image which means the object data gets repeated on several lines.\n\n object_id [t] : unique object name (will be displayed in Ecotaxa object page)\n object_link [f] : URL of an associated website\n object_lat [f] : latitude, decimal degrees\n object_lon [f] : longitude, decimal degrees\n object_date [f] : ISO8601 YYYYMMJJ UTC\n object_time [f] : ISO8601 HHMMSS UTC\n object_depth_min [f] : minimum depth of object, meters\n object_depth_max [f] : maximum depth of object, meters\n\nAnd, for already classified objects\n\n object_annotation_date [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_time [t] : ISO8601 YYYYMMJJ UTC\n object_annotation_category [t] : class of the object with optionnaly its direct parent following separated by left angle bracket without whitespace \"Cnidaria", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1210, - "y": 300, - "wires": [ - [] - ] - }, - { - "id": "b7d9455c.026588", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 400, - "wires": [ - [ - "fdb3b132.8b341" - ], - [ - "b9d996d6.37c2f8" - ] - ] - }, - { - "id": "b9d996d6.37c2f8", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1830, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "ca38a11d.0ee54", - "type": "function", - "z": "259c8713.b50e28", - "name": "init LED", - "func": "msg.payload=1;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 240, - "y": 161, - "wires": [ - [ - "1d58e86f.a3a9e8" - ] - ] - }, - { - "id": "75701b99.c6e974", - "type": "exec", - "z": "259c8713.b50e28", - "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "", - "timer": "", - "name": "RPi Temp.", - "x": 2190, - "y": 1080, - "wires": [ - [ - "aac61390.c13c6" - ], - [], - [] - ] - }, - { - "id": "1780384d.718198", - "type": "inject", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "10", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 2030, - "y": 1080, - "wires": [ - [ - "75701b99.c6e974" - ] - ] - }, - { - "id": "aac61390.c13c6", - "type": "python3-function", - "z": "259c8713.b50e28", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 2370, - "y": 1060, - "wires": [ - [] - ] - }, - { - "id": "603d5fab.08f56", - "type": "comment", - "z": "259c8713.b50e28", - "name": "save config.txt", - "info": "", - "x": 1690, - "y": 20, - "wires": [] - }, - { - "id": "72e1e23b.a8a67c", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1040, - "wires": [] - }, - { - "id": "d473399b.081ae8", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "72e1e23b.a8a67c", - "c93577b9.a1e438", - "829cc940.327648" - ], - "x": 1635, - "y": 100, - "wires": [ - [ - "e001a28.555566" - ] - ] - }, - { - "id": "c93577b9.a1e438", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1140, - "wires": [] - }, - { - "id": "829cc940.327648", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04", - "d473399b.081ae8" - ], - "x": 1675, - "y": 1180, - "wires": [] - }, - { - "id": "98e2e9e0.fb7418", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 600, - "wires": [ - [ - "61fb057d.3c251c" - ], - [ - "46a536f0.c83138" - ] - ] - }, - { - "id": "46a536f0.c83138", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1830, - "y": 620, - "wires": [ - [] - ] - }, - { - "id": "24ffcf03.2a51b", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "stop pump", - "group": "707d9797.c8e798", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP PUMP", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 1370, - "y": 660, - "wires": [ - [ - "e2a7220a.09d43" - ] - ] - }, - { - "id": "7eb16c3b.294e54", - "type": "comment", - "z": "259c8713.b50e28", - "name": "turn ON the LED", - "info": "", - "x": 260, - "y": 121, - "wires": [] - }, - { - "id": "4f74f017.00a58", - "type": "function", - "z": "259c8713.b50e28", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1520, - "y": 400, - "wires": [ - [ - "b7d9455c.026588" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "52cc1de5.b78e84", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "stop focus", - "group": "fbd92986.1028c8", - "order": 5, - "width": 4, - "height": 1, - "passthru": true, - "label": "STOP FOCUS", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "actuator/wait", - "x": 1370, - "y": 460, - "wires": [ - [ - "e46763fe.7fc83" - ] - ] - }, - { - "id": "39cad6fb.1503ca", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 9, - "width": 11, - "height": 1, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 2060, - "y": 960, - "wires": [ - [ - "95b876d4.07c708", - "99d61fbe.b244b" - ] - ] - }, - { - "id": "1f53f29b.feee4d", - "type": "exec", - "z": "259c8713.b50e28", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 2370, - "y": 960, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e325458b.95bff8", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 10, - "width": 13, - "height": 1, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 2060, - "y": 1020, - "wires": [ - [ - "95b876d4.07c708", - "99d61fbe.b244b" - ] - ] - }, - { - "id": "95b876d4.07c708", - "type": "python3-function", - "z": "259c8713.b50e28", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 2230, - "y": 980, - "wires": [ - [ - "d348474b.d756a8", - "1f53f29b.feee4d" - ] - ] - }, - { - "id": "d348474b.d756a8", - "type": "exec", - "z": "259c8713.b50e28", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 2390, - "y": 1020, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "99d61fbe.b244b", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "3517d063.27073" - ], - "x": 2175, - "y": 920, - "wires": [] - }, - { - "id": "cdd1b550.da18e8", - "type": "mqtt in", - "z": "259c8713.b50e28", - "name": "", - "topic": "receiver/#", - "qos": "0", - "datatype": "auto", - "broker": "b77ffa1b.942258", - "x": 2340, - "y": 720, - "wires": [ - [ - "6920281d.dc9b48" - ] - ] - }, - { - "id": "6920281d.dc9b48", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "receiver/pump", - "vt": "str" - }, - { - "t": "eq", - "v": "receiver/focus", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 2490, - "y": 720, - "wires": [ - [ - "2f66e917.fee586" - ], - [ - "363ee47e.ed522c" - ] - ] - }, - { - "id": "2f66e917.fee586", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 2650, - "y": 640, - "wires": [ - [ - "5c0d0c35.3bcf14" - ], - [ - "cd01157d.0892d8" - ], - [ - "68e02bf4.7013e4" - ] - ] - }, - { - "id": "5c0d0c35.3bcf14", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 600, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "cd01157d.0892d8", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 640, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "68e02bf4.7013e4", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The pump has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 680, - "wires": [ - [ - "61cf0388.fb10cc" - ] - ] - }, - { - "id": "61cf0388.fb10cc", - "type": "debug", - "z": "259c8713.b50e28", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "payload", - "targetType": "msg", - "x": 3030, - "y": 640, - "wires": [] - }, - { - "id": "363ee47e.ed522c", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Done", - "vt": "str" - }, - { - "t": "eq", - "v": "Interrompted", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 3, - "x": 2650, - "y": 780, - "wires": [ - [ - "c088b72f.326d98" - ], - [ - "36934381.14442c" - ], - [ - "89329cfe.c8f4" - ] - ] - }, - { - "id": "c088b72f.326d98", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has started", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 740, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "36934381.14442c", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has finished.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 780, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "89329cfe.c8f4", - "type": "change", - "z": "259c8713.b50e28", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "The focus has been stopped.", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 2820, - "y": 820, - "wires": [ - [ - "d11ec8dd.ad71d8" - ] - ] - }, - { - "id": "d11ec8dd.ad71d8", - "type": "debug", - "z": "259c8713.b50e28", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "payload", - "targetType": "msg", - "x": 3030, - "y": 780, - "wires": [] - }, - { - "id": "fdb3b132.8b341", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1810, - "y": 380, - "wires": [] - }, - { - "id": "e46763fe.7fc83", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1510, - "y": 460, - "wires": [] - }, - { - "id": "61fb057d.3c251c", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1810, - "y": 580, - "wires": [] - }, - { - "id": "e2a7220a.09d43", - "type": "mqtt out", - "z": "259c8713.b50e28", - "name": "", - "topic": "", - "qos": "", - "retain": "", - "broker": "cb2f36fe.1c7038", - "x": 1510, - "y": 660, - "wires": [] - }, - { - "id": "577f7f72.6b68b", - "type": "ui_button", - "z": "259c8713.b50e28", - "name": "", - "group": "8cfadfab.327d7", - "order": 7, - "width": 0, - "height": 0, - "passthru": false, - "label": "Start Acquisition", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "actuator/image", - "x": 1360, - "y": 1560, - "wires": [ - [ - "5218ba30.bbe844" - ] - ] - }, - { - "id": "d5111b87.2a64a8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_sleep_before", - "label": "Sleep duration before acquisition (s)", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 1, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_sleep_before", - "x": 1340, - "y": 1360, - "wires": [ - [ - "3d141631.d548ba" - ] - ] - }, - { - "id": "3d141631.d548ba", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1360, - "wires": [] - }, - { - "id": "74c89905.79d968", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_sleep_during", - "label": "Sleep duration between acquisition (s)", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 2, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_sleep_during", - "x": 1340, - "y": 1520, - "wires": [ - [ - "644e95b9.04b7ac" - ] - ] - }, - { - "id": "644e95b9.04b7ac", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1520, - "wires": [] - }, - { - "id": "b50cf2f4.bfb84", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 501, - "wires": [] - }, - { - "id": "1e75fd6c.234753", - "type": "ui_slider", - "z": "259c8713.b50e28", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 1380, - "y": 501, - "wires": [ - [ - "b50cf2f4.bfb84" - ] - ] - }, - { - "id": "3345fc41.8341b4", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic.flowrate", - "func": "msg.payload = msg.payload.generic_flowrate;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 501, - "wires": [ - [ - "1e75fd6c.234753" - ] - ] - }, - { - "id": "32510458.f42f9c", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 501, - "wires": [ - [ - "3345fc41.8341b4" - ] - ] - }, - { - "id": "3cd0a17b.0cc42e", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1440, - "wires": [] - }, - { - "id": "62fea790.2840a8", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_path", - "label": "DIrectory to store the images", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 3, - "width": 12, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "generic_path", - "x": 1370, - "y": 1440, - "wires": [ - [ - "3cd0a17b.0cc42e" - ] - ] - }, - { - "id": "73e051a8.5875e", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_volume_before", - "label": "Volume to pass before to begin", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 5, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_volume_before", - "x": 1330, - "y": 1400, - "wires": [ - [ - "5ea01613.8cc9d8" - ] - ] - }, - { - "id": "5ea01613.8cc9d8", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1400, - "wires": [] - }, - { - "id": "26549e4b.5dbf72", - "type": "ui_text_input", - "z": "259c8713.b50e28", - "name": "generic_nb_frame", - "label": "Number of frame per acquisition", - "tooltip": "", - "group": "8cfadfab.327d7", - "order": 4, - "width": 12, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "generic_nb_frame", - "x": 1350, - "y": 1480, - "wires": [ - [ - "61382d0b.60c534" - ] - ] - }, - { - "id": "61382d0b.60c534", - "type": "link out", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "7532db82.1dcf04" - ], - "x": 1475, - "y": 1480, - "wires": [] - }, - { - "id": "d5df5489.6523e8", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_sleep_before", - "func": "msg.payload = msg.payload.generic_sleep_before;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1050, - "y": 1360, - "wires": [ - [ - "d5111b87.2a64a8" - ] - ] - }, - { - "id": "835c262e.00b468", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1360, - "wires": [ - [ - "d5df5489.6523e8" - ] - ] - }, - { - "id": "9b2fe59b.be48c8", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_volume_before", - "func": "msg.payload = msg.payload.generic_volume_before;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1060, - "y": 1400, - "wires": [ - [ - "73e051a8.5875e" - ] - ] - }, - { - "id": "a07dad70.7c48", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1400, - "wires": [ - [ - "9b2fe59b.be48c8" - ] - ] - }, - { - "id": "54dfe4df.c6837c", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_path", - "func": "msg.payload = msg.payload.generic_path;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 1440, - "wires": [ - [ - "62fea790.2840a8" - ] - ] - }, - { - "id": "9fb166d6.86f908", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1440, - "wires": [ - [ - "54dfe4df.c6837c" - ] - ] - }, - { - "id": "1aa409a4.7b3866", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_nb_frame", - "func": "msg.payload = msg.payload.generic_nb_frame;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1040, - "y": 1480, - "wires": [ - [ - "26549e4b.5dbf72" - ] - ] - }, - { - "id": "51e769aa.92a138", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1480, - "wires": [ - [ - "1aa409a4.7b3866" - ] - ] - }, - { - "id": "ce6ded0a.8ee37", - "type": "function", - "z": "259c8713.b50e28", - "name": "get generic_sleep_during", - "func": "msg.payload = msg.payload.generic_sleep_during;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1050, - "y": 1520, - "wires": [ - [ - "74c89905.79d968" - ] - ] - }, - { - "id": "3fa20f41.11e61", - "type": "link in", - "z": "259c8713.b50e28", - "name": "", - "links": [ - "b368cae7.dd66b8" - ], - "x": 895, - "y": 1520, - "wires": [ - [ - "ce6ded0a.8ee37" - ] - ] - }, - { - "id": "5218ba30.bbe844", - "type": "function", - "z": "259c8713.b50e28", - "name": "image.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar generic_sleep_before= global.get(\"generic_sleep_before\");\nvar generic_volume_before= global.get(\"generic_volume_before\");\nvar generic_path= global.get(\"generic_path\");\nvar generic_nb_frame= global.get(\"generic_nb_frame\");\nvar generic_sleep_during= global.get(\"generic_sleep_during\");\n\nif (generic_sleep_before === undefined || generic_sleep_before === \"\" || generic_sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before start the acquisition\";\n \n}else if (generic_volume_before === undefined || generic_volume_before === \"\" || generic_volume_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume before acquisition\";\n \n}else if (generic_path === undefined || generic_path === \"\" || generic_path === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Directory to store the images\";\n \n}else if (generic_nb_frame === undefined || generic_nb_frame === \"\" || generic_nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of frames per acquisition\";\n \n}else if (generic_sleep_during === undefined || generic_sleep_during === \"\" || generic_sleep_during === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration in between each acquisition\";\n \n}else {\n generic_nb_step = 507*generic_volume_before\n msg.payload=generic_sleep_before+' '+generic_nb_step+' '+generic_path+' '+generic_nb_frame+' '+generic_sleep_during;\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1520, - "y": 1560, - "wires": [ - [ - "8142bee4.882c2" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "8142bee4.882c2", - "type": "switch", - "z": "259c8713.b50e28", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "actuator/image", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1670, - "y": 1560, - "wires": [ - [ - "a4b8aae3.cc3ad8" - ], - [ - "54420752.4a4ab8" - ] - ] - }, - { - "id": "54420752.4a4ab8", - "type": "ui_toast", - "z": "259c8713.b50e28", - "position": "dialog", - "displayTime": "3", - "highlight": "", - 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"name": "Disk Usage", - "x": 270, - "y": 400, - "wires": [ - [ - "45e1912a.36a23", - "84ac8611.1a6ac8" - ], - [], - [] - ] - }, - { - "id": "45e1912a.36a23", - "type": "ui_gauge", - "z": "1371dec5.76e671", - "name": "", - "group": "405183bc.d8991c", - "order": 1, - "width": 0, - "height": 0, - "gtype": "gage", - "title": "Disk", - "label": "Go", - "format": "{{value}}", - "min": 0, - "max": "256", - "colors": [ - "#00b500", - "#e6e600", - "#ca3838" - ], - "seg1": "", - "seg2": "", - "x": 470, - "y": 380, - "wires": [] - }, - { - "id": "4b2b9a70.6a9af4", - "type": "ui_chart", - "z": "1371dec5.76e671", - "name": "", - "group": "3da7da8f.179606", - "order": 2, - "width": 0, - "height": 0, - "label": "", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": "20", - "removeOlderPoints": "", - "removeOlderUnit": "60", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 220, - "wires": [ - [] - ] - }, - { - "id": "c7c8d192.3df27", - "type": "ui_chart", - "z": "1371dec5.76e671", - "name": "", - "group": "806d69c8.67fc58", - "order": 2, - "width": 0, - "height": 0, - "label": "", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": "20", - "removeOlderPoints": "", - "removeOlderUnit": "60", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "84ac8611.1a6ac8", - "type": "ui_chart", - "z": "1371dec5.76e671", - "name": "", - "group": "405183bc.d8991c", - "order": 2, - "width": 0, - "height": 0, - "label": "", - "chartType": "line", - "legend": "false", - "xformat": "HH:mm:ss", - "interpolate": "linear", - "nodata": "", - "dot": false, - "ymin": "", - "ymax": "", - "removeOlder": "4", - "removeOlderPoints": "", - "removeOlderUnit": "3600", - "cutout": 0, - "useOneColor": false, - "colors": [ - "#1f77b4", - "#aec7e8", - "#ff7f0e", - "#2ca02c", - "#98df8a", - "#d62728", - "#ff9896", - "#9467bd", - "#c5b0d5" - ], - "useOldStyle": true, - "outputs": 1, - "x": 470, - "y": 420, - "wires": [ - [] - ] - }, - { - "id": "1cd5b4c0.46af9b", - "type": "inject", - "z": "1371dec5.76e671", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "60", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 90, - "y": 280, - "wires": [ - [ - "3910d662.fa1f7a" - ] - ] - }, - { - "id": "96bbe41d.ee7928", - "type": "ui_switch", - "z": "1371dec5.76e671", - "name": "light_state", - "label": "Light", - "tooltip": "", - "group": "3ca00bf9.e5cac4", - "order": 2, - "width": 3, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "on", - "onvalueType": "str", - "onicon": "wb_incandescent", - "oncolor": "red", - "offvalue": "off", - "offvalueType": "str", - "officon": "", - "offcolor": "blue", - "x": 1050, - "y": 140, - "wires": [ - [ - "51145654.0ce2d8" - ] - ] - }, - { - "id": "8485d05.444903", - "type": "ui_switch", - "z": "1371dec5.76e671", - "name": "fan_state", - "label": "Fan", - "tooltip": "", - "group": "3ca00bf9.e5cac4", - "order": 3, - "width": 3, - "height": 1, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "on", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "off", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 1040, - "y": 80, - "wires": [ - [ - "2549f778.4eb828" - ] - ] - }, - { - "id": "2549f778.4eb828", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\nstate = msg[\"payload\"]\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif state == \"off\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif state == \"on\":\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 1190, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "a113b518.830008", - "type": "ui_button", - "z": "1371dec5.76e671", - "name": "", - "group": "3ca00bf9.e5cac4", - "order": 4, - "width": 7, - "height": 1, - "passthru": false, - "label": "Reboot", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "reboot", - "x": 720, - "y": 320, - "wires": [ - [ - "ee57d11c.ed1dd", - "d9234d01.e630d" - ] - ] - }, - { - "id": "d9a924bc.0ca078", - "type": "exec", - "z": "1371dec5.76e671", - "command": "sudo", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "2", - "oldrc": false, - "name": "cmd", - "x": 1030, - "y": 320, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "51145654.0ce2d8", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "light.py", - "func": "import RPi.GPIO as GPIO\n\nGPIO.setmode(GPIO.BCM)\nGPIO.setwarnings(False)\nGPIO.setup(21,GPIO.OUT)\n\nstate = msg[\"payload\"]\n\n \nif state == \"on\":\n GPIO.output(21,GPIO.HIGH)\nif state == \"off\":\n GPIO.output(21,GPIO.LOW)", - "outputs": 1, - "x": 1200, - "y": 140, - "wires": [ - [] - ] - }, - { - "id": "552d8bbb.cc4ca4", - "type": "ui_button", - "z": "1371dec5.76e671", - "name": "", - "group": "3ca00bf9.e5cac4", - "order": 5, - "width": 7, - "height": 1, - "passthru": false, - "label": "Shutdown", - "tooltip": "", - "color": "", - "bgcolor": "#AD1625", - "icon": "", - "payload": "off", - "payloadType": "str", - "topic": "shutdown", - "x": 720, - "y": 380, - "wires": [ - [ - "ee57d11c.ed1dd", - "d9234d01.e630d" - ] - ] - }, - { - "id": "3517d063.27073", - "type": "link in", - "z": "1371dec5.76e671", - "name": "", - "links": [ - "ec8da7a8.0eb558", - "d9234d01.e630d" - ], - "x": 895, - "y": 140, - "wires": [ - [ - "96bbe41d.ee7928", - "8485d05.444903" - ] - ] - }, - { - "id": "ee57d11c.ed1dd", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "action", - "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", - "outputs": 1, - "x": 870, - "y": 340, - "wires": [ - [ - "b7ab1ada.1f4158", - "d9a924bc.0ca078" - ] - ] - }, - { - "id": "b7ab1ada.1f4158", - "type": "exec", - "z": "1371dec5.76e671", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1050, - "y": 380, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "d9234d01.e630d", - "type": "link out", - "z": "1371dec5.76e671", - "name": "", - "links": [ - "3517d063.27073" - ], - "x": 835, - "y": 280, - "wires": [] - }, - { - "id": "bc503fa5.f46dd", - "type": "switch", - "z": "1371dec5.76e671", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "gt", - "v": "45", - "vt": "num" - }, - { - "t": "lte", - "v": "38", - "vt": "num" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 670, - "y": 80, - "wires": [ - [ - "a25d6486.e1ce28" - ], - [ - "5d4f3e71.1bad4" - ] - ] - }, - { - "id": "5d4f3e71.1bad4", - "type": "change", - "z": "1371dec5.76e671", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "off", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 840, - "y": 100, - "wires": [ - [ - "8485d05.444903" - ] - ] - }, - { - "id": "a25d6486.e1ce28", - "type": "change", - "z": "1371dec5.76e671", - "name": "", - "rules": [ - { - "t": "set", - "p": "payload", - "pt": "msg", - "to": "on", - "tot": "str" - } - ], - "action": "", - "property": "", - "from": "", - "to": "", - "reg": false, - "x": 840, - "y": 60, - "wires": [ - [ - "8485d05.444903" - ] - ] - }, - { - "id": "37507791.4d5508", - "type": "http request", - "z": "1371dec5.76e671", - "name": "toggle timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd={{{payload}}}", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 240, - "y": 780, - "wires": [ - [] - ] - }, - { - "id": "b9ff73e.19bd49", - "type": "ui_switch", - "z": "1371dec5.76e671", - "d": true, - "name": "timelapse", - "label": "toggle acquisition", - "tooltip": "", - "group": "1be83144.4fe4bf", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "decouple": "false", - "topic": "toggle", - "style": "", - "onvalue": "tl 1", - "onvalueType": "str", - "onicon": "", - "oncolor": "", - "offvalue": "tl 0", - "offvalueType": "str", - "officon": "", - "offcolor": "", - "x": 80, - "y": 660, - "wires": [ - [ - "37507791.4d5508", - "df47f1bb.1b0bf" - ] - ] - }, - { - "id": "9a52e6b.cbbc118", - "type": "exec", - "z": "1371dec5.76e671", - "command": "ls -l /var/www/html/media | grep \"th\" | tail -1 | awk -F \" \" '{print $9}' | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "get thumbail name", - "x": 770, - "y": 720, - "wires": [ - [ - "ca6bfbdf.4a71e8" - ], - [], - [] - ] - }, - { - "id": "df47f1bb.1b0bf", - "type": "switch", - "z": "1371dec5.76e671", - "name": "", - "property": "payload", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "tl 0", - "vt": "str" - }, - { - "t": "eq", - "v": "tl 1", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 230, - "y": 660, - "wires": [ - [ - "1cf57a24.20b176" - ], - [ - "faa67658.8edf18", - "c4524676.63b608" - ] - ] - }, - { - "id": "faa67658.8edf18", - "type": "delay", - "z": "1371dec5.76e671", - "name": "", - "pauseType": "delay", - "timeout": "1", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 420, - "y": 720, - "wires": [ - [ - "9a52e6b.cbbc118" - ] - ] - }, - { - "id": "ca6bfbdf.4a71e8", - "type": "ui_template", - "z": "1371dec5.76e671", - "d": true, - "group": "1be83144.4fe4bf", - "name": "", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n\n\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 980, - "y": 700, - "wires": [ - [] - ] - }, - { - "id": "3e73267.51682da", - "type": "exec", - "z": "1371dec5.76e671", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 750, - "y": 620, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "e8c9d8e.f1d5428", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\n \nreturn msg;", - "outputs": 1, - "x": 560, - "y": 600, - "wires": [ - [ - "3e73267.51682da" - ] - ] - }, - { - "id": "1cf57a24.20b176", - "type": "function", - "z": "1371dec5.76e671", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 600, - "wires": [ - [ - "e8c9d8e.f1d5428" - ] - ] - }, - { - "id": "e3b347e3.b19f98", - "type": "python3-function", - "z": "1371dec5.76e671", - "name": "actuate RGB", - "func": "import smbus\nbus = smbus.SMBus(1)\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 255)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 255)\nreturn msg;", - "outputs": 1, - "x": 570, - "y": 660, - "wires": [ - [ - "3e73267.51682da" - ] - ] - }, - { - "id": "c4524676.63b608", - "type": "function", - "z": "1371dec5.76e671", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 660, - "wires": [ - [ - "e3b347e3.b19f98" - ] - ] - }, - { - "id": "6a84252a.d52a0c", - "type": "ui_template", - "z": "bccd1f23.87219", - "group": "833bc5bb.217ba8", - "name": "Stream Pi Camera", - "order": 1, - "width": 14, - "height": 9, - "format": "
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 110, - "y": 100, - "wires": [ - [] - ] - }, - { - "id": "dc48dc42.98d18", - "type": "function", - "z": "bccd1f23.87219", - "name": "set global", - "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 1480, - "y": 400, - "wires": [ - [] - ] - }, - { - "id": "5b043fe6.df031", - "type": "function", - "z": "bccd1f23.87219", - "name": "focus.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\n\nvar nb_step= global.get(\"nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of step\"\n}\n\nelse {\n\n if(msg.topic === \"up\" & state ===\"free\"){\n nb_step = global.get(\"nb_step\");\n msg.nb_step = nb_step;\n msg.orientation = \"up\";\n msg.rgb = {r:255, g:0, b:255}\n msg.topic = \"Focus\"\n return msg;\n }\n \n if(msg.topic === \"down\" & state ===\"free\"){\n nb_step = global.get(\"nb_step\");\n msg.nb_step = nb_step;\n msg.orientation = \"down\";\n msg.rgb = {r:255, g:0, b:255}\n msg.topic = \"Focus\"\n return msg;\n }\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 980, - "y": 280, - "wires": [ - [ - "e7f18662.70dcf8" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "8c19fb64.8a1828", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "focus.py", - "func": "\nimport sys\n\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nnb_step = int(msg[\"nb_step\"])\norientation = msg[\"orientation\"]\n\nkit = MotorKit()\n\nstage = kit.stepper2\n\nstage.release()\n\n#0.25mm/step\n#31um/microsteps\n\n \nif orientation == 'up':\n for i in range(nb_step):\n stage.onestep(direction=stepper.FORWARD, style=stepper.MICROSTEP)\n sleep(0.001)\n \nif orientation == 'down':\n for i in range(nb_step):\n stage.onestep(direction=stepper.BACKWARD, style=stepper.MICROSTEP)\n sleep(0.001)\n \nstage.release()\n\nmsg[\"topic\"] = \"focus\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1280, - "y": 260, - "wires": [ - [ - "7b23bbd5.4483d4" - ] - ] - }, - { - "id": "21816a62.827a56", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\nkit = MotorKit()\n\npump_stepper = kit.stepper1\n\npump_stepper.release()\n\n \nif orientation == \"forward\":\n orientation=stepper.BACKWARD\nif orientation == \"backward\":\n orientation=stepper.FORWARD\n \nnb_step=volume*507 #if sleep(0.05) in between 2 steps\n#35000steps for 69g\n \n#nb_step=vol*460 if sleep(0) in between 2 steps\nduration=(volume*60)/flowrate\n \ndelay=(duration/nb_step)-0.005\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=orientation, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 580, - "y": 220, - "wires": [ - [ - "90fc64b2.db5df8" - ] - ] - }, - { - "id": "7b68bdbe.e57094", - "type": "function", - "z": "bccd1f23.87219", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"manual_volume\");\nvar flowrate= global.get(\"flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n if(msg.topic === \"forward\" & state===\"free\"){\n volume = global.get(\"manual_volume\");\n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = global.get(\"flowrate\");\n msg.rgb = {r:0, g:255, b:255};\n msg.topic = \"Pump\"\n }\n if(msg.topic === \"backward\" & state===\"free\"){\n volume = global.get(\"manual_volume\");\n msg.volume = volume;\n msg.orientation = \"backward\";\n msg.flowrate = global.get(\"flowrate\");\n msg.rgb = {r:0, g:255, b:255};\n msg.topic = \"Pump\";\n }\n}\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 280, - "y": 240, - "wires": [ - [ - "7994feb9.fcfc9" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "c0199136.20bd7", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "a208caf.0d23338", - "d17415a3.fca5c8" - ], - "x": 1235, - "y": 220, - "wires": [] - }, - { - "id": "da53c4c2.6b17b8", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1490, - "y": 460, - "wires": [ - [ - "1276a75f.d8d1a9" - ] - ] - }, - { - "id": "8778c73a.ddc6e8", - "type": "exec", - "z": "bccd1f23.87219", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1830, - "y": 500, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "a208caf.0d23338", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "c0199136.20bd7", - "2dff3966.a5b2d6" - ], - "x": 1375, - "y": 460, - "wires": [ - [ - "da53c4c2.6b17b8" - ] - ] - }, - { - "id": "9b5cac2c.6de57", - "type": "python3-function", - "z": "bccd1f23.87219", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nreturn msg;", - "outputs": 1, - "x": 1480, - "y": 540, - "wires": [ - [ - "8479740e.6373c8" - ] - ] - }, - { - "id": "7b23bbd5.4483d4", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4351408.b0b288", - "2bc762dd.1115ce", - "a50134c.ed45ac8" - ], - "x": 1395, - "y": 260, - "wires": [] - }, - { - "id": "e4351408.b0b288", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "7b23bbd5.4483d4", - "90fc64b2.db5df8" - ], - "x": 1375, - "y": 540, - "wires": [ - [ - "9b5cac2c.6de57" - ] - ] - }, - { - "id": "2dff3966.a5b2d6", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "a208caf.0d23338", - "d17415a3.fca5c8" - ], - "x": 535, - "y": 180, - "wires": [] - }, - { - "id": "90fc64b2.db5df8", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4351408.b0b288", - "2bc762dd.1115ce", - "a50134c.ed45ac8" - ], - "x": 695, - "y": 220, - "wires": [] - }, - { - "id": "1276a75f.d8d1a9", - "type": "function", - "z": "bccd1f23.87219", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1640, - "y": 460, - "wires": [ - [ - "8778c73a.ddc6e8" - ] - ] - }, - { - "id": "8479740e.6373c8", - "type": "function", - "z": "bccd1f23.87219", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 1640, - "y": 540, - "wires": [ - [ - "8778c73a.ddc6e8" - ] - ] - }, - { - "id": "17a53f92.824d2", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Instrument", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n Instrument :\n \n PlanktonScope V2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 150, - "y": 400, - "wires": [ - [] - ] - }, - { - "id": "d2b74a01.166498", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Software", - "order": 3, - "width": 0, - "height": 0, - "format": "
\n Software :\n \n Node-RED Dashboard V2.0\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 440, - "wires": [ - [] - ] - }, - { - "id": "a5c019f.91d15e8", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "567a49a4.244cb8", - "name": "Camera", - "order": 1, - "width": 0, - "height": 0, - "format": "
\n Camera :\n \n Pi Camera v2.1\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 480, - "wires": [ - [] - ] - }, - { - "id": "f59a2f0d.5e9af", - "type": "ui_numeric", - "z": "baa1e3d9.cb29d", - "name": "acq_minimum_mesh", - "label": "Min fraction size (μm)", - "tooltip": "", - "group": "404c301a.19c4e", - "order": 2, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_minimum_mesh", - "format": "{{value}}", - "min": 0, - "max": "300", - "step": "10", - "x": 120, - "y": 100, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "6008a8bb.259f08", - "type": "ui_numeric", - "z": "baa1e3d9.cb29d", - "name": "acq_maximum_mesh", - "label": "Max fraction size (μm)", - "tooltip": "", - "group": "404c301a.19c4e", - "order": 3, - "width": 5, - "height": 1, - "wrap": false, - "passthru": true, - "topic": "acq_maximum_mesh", - "format": "{{value}}", - "min": "200", - "max": "2000", - "step": "100", - "x": 120, - "y": 160, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "6b34c456.83178c", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "acq_id", - "label": "Acquisition unique ID*", - "tooltip": "", - "group": "4322c187.e73e5", - "order": 2, - "width": 5, - "height": 1, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "acq_id", - "x": 170, - "y": 300, - "wires": [ - [ - "a39af546.4c30c8" - ] - ] - }, - { - "id": "314ebbc0.040b84", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "store generic", - "func": "global.set(\"acq_instrument\",\"PlanktonScope V2.1\");\nglobal.set(\"acq_software\",\"Node-RED Dashboard\");\nglobal.set(\"acq_camera\",\"Pi Camera V2.1\");\nglobal.set(\"acq_instrument_ID\",\"copepode\");", - "outputs": 1, - "noerr": 0, - "x": 370, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "109cf039.1ca8d", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "cancel", - "group": "b7919ae2.c01788", - "order": 3, - "width": 4, - "height": 1, - "passthru": false, - "label": "Cancel Acquisition", - "tooltip": "", - "color": "#AD1625", - "bgcolor": "white", - "icon": "pause_circle_filled", - "payload": "stop", - "payloadType": "str", - "topic": "cancel", - "x": 570, - "y": 120, - "wires": [ - [ - "c339e7a4.7e7608", - "995fa523.83cba8" - ] - ] - }, - { - "id": "dae10d44.76f08", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1140, - "y": 560, - "wires": [ - [ - "d3ab1a14.86b8b8", - "ff805ffc.f9134" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "7789839d.69b48c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "4e0cd5ea.17e59c", - "name": "Optic Configuration", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Optic Configuration
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 130, - "y": 100, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "6ea6c306.f9c12c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "ef590206.24f6", - "name": "Fluidic Acquisition", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Fluidic Acquisition
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 130, - "y": 140, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "bb9eb153.9e36c", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "ae8f6620.073358", - "name": "Segmentation", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Segmentation
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 140, - "y": 180, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "eaf8ee7f.96f44", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "196518b2.4d53b7", - "name": "Gallery", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Gallery
\n", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 160, - "y": 220, - "wires": [ - [ - "2a65c3ec.49a6bc" - ] - ] - }, - { - "id": "f37444ff.d17068", - "type": "ui_text_input", - "z": "bccd1f23.87219", - "name": "nb_step", - "label": "Number of step(s)", - "tooltip": "", - "group": "fbd92986.1028c8", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "nb_step", - "x": 820, - "y": 340, - "wires": [ - [ - "2f51f4e2.4dcaec" - ] - ] - }, - { - "id": "811cd88c.daf528", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "down", - "group": "fbd92986.1028c8", - "order": 3, - "width": 0, - "height": 0, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_downward", - "payload": "down", - "payloadType": "str", - "topic": "down", - "x": 830, - "y": 300, - "wires": [ - [ - "5b043fe6.df031" - ] - ] - }, - { - "id": "edda4df4.76de2", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "up", - "group": "fbd92986.1028c8", - "order": 1, - "width": 0, - "height": 0, - "passthru": false, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_upwards", - "payload": "up", - "payloadType": "str", - "topic": "up", - "x": 830, - "y": 260, - "wires": [ - [ - "5b043fe6.df031" - ] - ] - }, - { - "id": "bb667f4c.06e44", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 235, - "y": 300, - "wires": [] - }, - { - "id": "e4892a16.664bf8", - "type": "link in", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "bb667f4c.06e44", - "2f51f4e2.4dcaec", - "4a0baa98.618744" - ], - "x": 1375, - "y": 400, - "wires": [ - [ - "dc48dc42.98d18" - ] - ] - }, - { - "id": "2f51f4e2.4dcaec", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 975, - "y": 340, - "wires": [] - }, - { - "id": "68962547.34a67c", - "type": "ui_text_input", - "z": "bccd1f23.87219", - "name": "manual_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 3, - "width": 4, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "manual_volume", - "x": 100, - "y": 340, - "wires": [ - [ - "4a0baa98.618744" - ] - ] - }, - { - "id": "4a0baa98.618744", - "type": "link out", - "z": "bccd1f23.87219", - "name": "", - "links": [ - "e4892a16.664bf8" - ], - "x": 235, - "y": 340, - "wires": [] - }, - { - "id": "34c81624.df1cea", - "type": "ui_slider", - "z": "bccd1f23.87219", - "name": "flowrate", - "label": "Flowrate (ml/min)*", - "tooltip": "", - "group": "707d9797.c8e798", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "outs": "end", - "topic": "flowrate", - "min": 0, - "max": "20", - "step": "0.1", - "x": 120, - "y": 300, - "wires": [ - [ - "bb667f4c.06e44" - ] - ] - }, - { - "id": "c1b1469.9650eb8", - "type": "ui_template", - "z": "eaae323a.31b3", - "group": "777a7c33.fcd804", - "name": "Settings", - "order": 1, - "width": 4, - "height": 4, - "format": "\n \n
Settings
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Sample
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"wires": [ - [ - "3dba84a2.0de1bc" - ] - ] - }, - { - "id": "207fbdbb.2fe2a2", - "type": "ui_text_input", - "z": "b771c342.49603", - "name": "", - "label": "Time :", - "tooltip": "", - "group": "cef1e703.bcf3c8", - "order": 3, - "width": 7, - "height": 1, - "passthru": true, - "mode": "time", - "delay": 300, - "topic": "", - "x": 210, - "y": 380, - "wires": [ - [ - "61f9d7df.83ffe8" - ] - ] - }, - { - "id": "61f9d7df.83ffe8", - "type": "function", - "z": "b771c342.49603", - "name": "set time global", - "func": "var dt = new Date(msg.payload);\nglobal.set('sample_hour',dt.getHours()-1);\nglobal.set('sample_min',dt.getMinutes());", - "outputs": 1, - "noerr": 0, - "x": 420, - "y": 380, - "wires": [ - [] - ] - }, - { - "id": "3dba84a2.0de1bc", - "type": "function", - "z": "b771c342.49603", - "name": "set date global", - "func": "var dt = new Date(msg.payload);\n\nglobal.set('sample_month',dt.getMonth() + 1);\nglobal.set('sample_day',dt.getDate());\nglobal.set('sample_year',dt.getFullYear());\n", - 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"payloadType": "str", - "topic": "backward", - "x": 120, - "y": 220, - "wires": [ - [ - "7b68bdbe.e57094" - ] - ] - }, - { - "id": "2cab680b.baf888", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "foward", - "group": "707d9797.c8e798", - "order": 4, - "width": 5, - "height": 1, - "passthru": true, - "label": "", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "arrow_forward", - "payload": "forward", - "payloadType": "str", - "topic": "forward", - "x": 130, - "y": 260, - "wires": [ - [ - "7b68bdbe.e57094" - ] - ] - }, - { - "id": "961d27e7.da65c8", - "type": "ui_switch", - "z": "bccd1f23.87219", - "name": "light_state", - "label": "Light", - "tooltip": "", - "group": "4248342d.e55fac", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "decouple": "false", - "topic": "", - "style": "", - "onvalue": "1", - "onvalueType": "num", - "onicon": "", - "oncolor": "", - "offvalue": "0", - "offvalueType": "num", - "officon": "", - "offcolor": "", - "x": 90, - "y": 40, - "wires": [ - [ - "cbb8afed.0a026" - ] - ], - "icon": "font-awesome/fa-lightbulb-o" - }, - { - "id": "cc966678.da8d08", - "type": "ui_dropdown", - "z": "bccd1f23.87219", - "name": "acq_fnumber_objective", - "label": "M12 Lens*", - "tooltip": "", - "place": "Select option", - "group": "4248342d.e55fac", - "order": 2, - "width": 0, - "height": 0, - "passthru": true, - "options": [ - { - "label": "f 25mm 1/2\" 5MP IR", - "value": 25, - "type": "num" - }, - { - "label": "f 16mm 1/2.5\" 5MP IR", - "value": 16, - "type": "num" - }, - { - "label": "f 12mm 1/2.5\" 5MP IR", - "value": 12, - "type": "num" - }, - { - "label": "f 8mm 1/2.5\" 5MP IR", - "value": 8, - "type": "num" - }, - { - "label": "f 6mm 1/2.5\" 5MP IR", - "value": 6, - "type": "num" - } - ], - "payload": "", - "topic": "acq_fnumber_objective", - "x": 870, - "y": 40, - "wires": [ - [ - "8038414a.34461" - ] - ] - }, - { - "id": "9b515beb.4aea48", - "type": "ui_template", - "z": "bccd1f23.87219", - "group": "4248342d.e55fac", - 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\n Biggest cells to explore :\n \n μm\n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 1420, - "y": 160, - "wires": [ - [] - ] - }, - { - "id": "ad87820f.b1d1e", - "type": "function", - "z": "bccd1f23.87219", - "name": "get magnification", - "func": "var magnification = global.get(\"magnification\");\nmsg.payload = magnification;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1250, - "y": 40, - "wires": [ - [ - "9b515beb.4aea48" - ] - ] - }, - { - "id": "d68a52ee.82e8e", - "type": "function", - "z": "bccd1f23.87219", - "name": "get process_pixel", - "func": "var process_pixel = global.get(\"process_pixel\");\nmsg.payload = process_pixel;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1250, - "y": 80, - "wires": [ - [ - "3d2360ad.e41e7" - ] - ] - }, - { - "id": "238f26b1.e2089a", - "type": "function", - "z": "bccd1f23.87219", - "name": "get sug_min", - "func": "var sug_min = global.get(\"sug_min\");\nmsg.payload = sug_min;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1230, - "y": 120, - "wires": [ - [ - "8e66977b.9166a8" - ] - ] - }, - { - "id": "6e0f6d36.a6b854", - "type": "function", - "z": "bccd1f23.87219", - "name": "get sug_max", - "func": "var sug_max = global.get(\"sug_max\");\nmsg.payload = sug_max;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1230, - "y": 160, - "wires": [ - [ - "26b32f2c.c64fc" - ] - ] - }, - { - "id": "bb2bb7ce.1d1458", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "858a0e3c.987fe", - "name": "Stream Pi Camera", - "order": 1, - "width": 14, - "height": 11, - "format": "
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 590, - "y": 40, - "wires": [ - [] - ] - }, - { - "id": "d0c5b57d.590818", - "type": "ui_ui_control", - "z": "baa1e3d9.cb29d", - "name": "", - "events": "change", - "x": 700, - "y": 80, - "wires": [ - [] - ] - }, - { - "id": "2fb129de.024a06", - "type": "ui_toast", - "z": "baa1e3d9.cb29d", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 650, - "y": 540, - "wires": [ - [] - ] - }, - { - "id": "61b4993e.1f3fb8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Check form", - "func": "var acq_celltype= global.get(\"acq_celltype\");\nvar acq_minimum_mesh= global.get(\"acq_minimum_mesh\");\nvar acq_maximum_mesh= global.get(\"acq_maximum_mesh\");\nvar acq_volume= global.get(\"acq_volume\");\nvar acq_id= global.get(\"acq_id\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Type of the flowcell\"\n}\nelse if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Lower fraction size\"\n}\nelse if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Upper fraction size\"\n}\nelse if (acq_volume === undefined || acq_volume === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to image\"\n}\nelse if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Acquisition ID\"\n}\nelse {\n msg.topic = \"Start\";\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 730, - "y": 280, - "wires": [ - [ - "9e7bd689.f9c278" - ] - ] - }, - { - "id": "9e7bd689.f9c278", - "type": "switch", - "z": "baa1e3d9.cb29d", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Start", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 870, - "y": 280, - "wires": [ - [ - "f7fa6acf.f6ed28" - ], - [ - "2fb129de.024a06" - ] - ] - }, - { - "id": "16de754c.cc969b", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "5517c651.b2f668", - "order": 1, - "width": 12, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 220, - "y": 480, - "wires": [ - [ - "222c851d.5d0a3a" - ] - ] - }, - { - "id": "84f3d040.5f7ea", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "5517c651.b2f668", - "order": 2, - "width": 12, - "height": 1, - "passthru": false, - "label": "Continue", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 220, - "y": 540, - "wires": [ - [ - "986d960a.c75908" - ] - ] - }, - { - "id": "f61aaed5.1e64", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "", - "group": "7a0b4877.a5d268", - "order": 1, - "width": 5, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Sample\"}", - "payloadType": "json", - "topic": "", - "x": 360, - "y": 520, - "wires": [ - [ - "6c792043.b6ff9" - ] - ] - }, - { - "id": "9ba6ec0a.22c96", - "type": "ui_button", - "z": "bccd1f23.87219", - "name": "", - "group": "7a0b4877.a5d268", - "order": 2, - "width": 5, - "height": 1, - "passthru": false, - "label": "Continue", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 360, - "y": 580, - "wires": [ - [ - "fe840e05.b46f3" - ] - ] - }, - { - "id": "c72f8fae.23bd4", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 2, - "width": 5, - "height": 1, - "passthru": false, - "label": "Previous", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_return", - "payload": "{\"tab\":\"Optic Configuration\"}", - "payloadType": "json", - "topic": "", - "x": 560, - "y": 80, - "wires": [ - [ - "d0c5b57d.590818" - ] - ] - }, - { - "id": "cf48a0b9.7f208", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 5, - "width": 0, - "height": 0, - "passthru": false, - "label": "Start", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "{\"tab\":\"Home\"}", - "payloadType": "json", - "topic": "", - "x": 570, - "y": 280, - "wires": [ - [ - "61b4993e.1f3fb8" - ] - ] - }, - { - "id": "389bef3.d94c61", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "acq_volume", - "label": "Volume to pass (ml)", - "tooltip": "", - "group": "4322c187.e73e5", - "order": 1, - "width": 5, - "height": 1, - "passthru": true, - "mode": "number", - "delay": 300, - "topic": "acq_volume", - "x": 150, - "y": 220, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "a39af546.4c30c8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set global join", - "func": "var value = msg.payload.split(' ').join('_');\nvar key = msg.topic;\n\nglobal.set(key,value);", - "outputs": 1, - "noerr": 0, - "x": 380, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "75b738f0.cea208", - "type": "ui_toast", - "z": "bccd1f23.87219", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1290, - "y": 320, - "wires": [ - [] - ] - }, - { - "id": "e7f18662.70dcf8", - "type": "switch", - "z": "bccd1f23.87219", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Focus", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 1130, - "y": 280, - "wires": [ - [ - "c0199136.20bd7", - "8c19fb64.8a1828" - ], - [ - "75b738f0.cea208" - ] - ] - }, - { - "id": "c2aeba5f.a2ac98", - "type": "ui_toast", - "z": "bccd1f23.87219", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 590, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "7994feb9.fcfc9", - "type": "switch", - "z": "bccd1f23.87219", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Pump", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 430, - "y": 240, - "wires": [ - [ - "21816a62.827a56", - "2dff3966.a5b2d6" - ], - [ - "c2aeba5f.a2ac98" - ] - ] - }, - { - "id": "201ad81d.4a6d78", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Start timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%201", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 980, - "y": 800, - "wires": [ - [] - ] - }, - { - "id": "c339e7a4.7e7608", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Stop timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%200", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 720, - "y": 120, - "wires": [ - [ - "eaab9f19.c68ba" - ] - ] - }, - { - "id": "b4d324de.a2bd28", - "type": "ui_worldmap", - "z": "b771c342.49603", - "group": "cef1e703.bcf3c8", - "order": 6, - "width": 0, - "height": 0, - "name": "", - "lat": "1.5", - "lon": "1.5", - "zoom": "4", - "layer": "OSM grey", - "cluster": "1", - "maxage": "", - "usermenu": "hide", - "layers": "hide", - "panit": "false", - "panlock": "false", - "zoomlock": "false", - "hiderightclick": "true", - "coords": "deg", - "showgrid": "false", - "path": "/worldmap", - "x": 780, - "y": 400, - "wires": [] - }, - { - "id": "cf3e1477.25af68", - "type": "function", - "z": "b771c342.49603", - "name": "set point", - "func": "var sample_id= global.get(\"sample_id\");\nvar object_lat= global.get(\"object_lat\");\nvar object_lon= global.get(\"object_lon\");\n\nif (sample_id === undefined || sample_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample ID\"\n}\nelse if (object_lat === undefined || object_lat === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample latitude\"\n}\n\nelse if (object_lon === undefined || object_lon === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Sample longitude\"\n}\n\nelse {\n msg.topic = \"Place\"\n msg.payload={\"name\":sample_id, \"lat\":object_lat, \"lon\":object_lon}\n}\nreturn msg;\n", - "outputs": 1, - "noerr": 0, - "x": 360, - "y": 440, - "wires": [ - [ - "105e9b1b.725865" - ] - ] - }, - { - "id": "d7a44df2.0fb29", - "type": "ui_button", - "z": "b771c342.49603", - "name": "", - "group": "cef1e703.bcf3c8", - "order": 5, - "width": 5, - "height": 1, - "passthru": false, - "label": "Place", - "tooltip": "", - "color": "#333333", - "bgcolor": "white", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 210, - "y": 440, - "wires": [ - [ - "cf3e1477.25af68" - ] - ] - }, - { - "id": "105e9b1b.725865", - "type": "switch", - "z": "b771c342.49603", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Place", - "vt": "str" - }, - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 550, - "y": 440, - "wires": [ - [ - "b4d324de.a2bd28" - ], - [ - "10c9c12a.feae6f" - ] - ] - }, - { - "id": "10c9c12a.feae6f", - "type": "ui_toast", - "z": "b771c342.49603", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 790, - "y": 460, - "wires": [ - [] - ] - }, - { - "id": "32f57168.89cbae", - "type": "comment", - "z": "baa1e3d9.cb29d", - "name": "generic info", - "info": "", - "x": 150, - "y": 360, - "wires": [] - }, - { - "id": "44094d9d.62c6c4", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1170, - "y": 120, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "eaab9f19.c68ba", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "wait RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, 0)\nbus.write_byte_data(0x0d, 0x02, 255)\nbus.write_byte_data(0x0d, 0x03, 0)\nreturn msg;", - "outputs": 1, - "x": 880, - "y": 120, - "wires": [ - [ - "154d5ce1.81ed03" - ] - ] - }, - { - "id": "154d5ce1.81ed03", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set free", - "func": "global.set(\"state\",\"free\");\nreturn msg", - "outputs": 1, - "noerr": 0, - "x": 1020, - "y": 120, - "wires": [ - [ - "44094d9d.62c6c4" - ] - ] - }, - { - "id": "f07dec1d.147ce", - "type": "ui_text_input", - "z": "baa1e3d9.cb29d", - "name": "comment", - "label": "Comment", - "tooltip": "", - "group": "b7919ae2.c01788", - "order": 1, - "width": 0, - "height": 0, - "passthru": true, - "mode": "text", - "delay": 300, - "topic": "comment", - "x": 160, - "y": 260, - "wires": [ - [ - "fb887036.12429" - ] - ] - }, - { - "id": "8bd55b54.8e3938", - "type": "file", - "z": "baa1e3d9.cb29d", - "name": "logs.json", - "filename": "/var/www/logs.json", - "appendNewline": false, - "createDir": false, - "overwriteFile": "false", - "encoding": "none", - "x": 2000, - "y": 1340, - "wires": [ - [ - "20a2d27e.7ccafe" - ] - ] - }, - { - "id": "99fd2803.0843a8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get global", - "func": "msg.payload = {\n \"comment\":global.get(\"comment\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\")\n }\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1820, - "y": 1340, - "wires": [ - [ - "8bd55b54.8e3938" - ] - ] - }, - { - "id": "ae692178.d44d1", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1240, - "y": 1260, - "wires": [ - [ - "783209c7.51c5a8" - ] - ] - }, - { - "id": "a3fd6b29.2ef5f8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1040, - "y": 1360, - "wires": [ - [ - "ae692178.d44d1", - "e0f9efda.fa4ce" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "e0f9efda.fa4ce", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1250, - "y": 1200, - "wires": [ - [ - "3b498e72.6e6292" - ] - ] - }, - { - "id": "7baf5071.dc3b2", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "i2cdetect -y 1", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "1", - "oldrc": false, - "name": "i2c update", - "x": 1570, - "y": 1200, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "783209c7.51c5a8", - "type": "link out", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "e1354861.0bb648", - "2bc762dd.1115ce", - "a50134c.ed45ac8", - "f0ef065a.362028" - ], - "x": 1335, - "y": 1260, - "wires": [] - }, - { - "id": "3b498e72.6e6292", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1420, - "y": 1200, - "wires": [ - [ - "7baf5071.dc3b2" - ] - ] - }, - { - "id": "cd56bb1c.8ce378", - "type": "ui_toast", - "z": "baa1e3d9.cb29d", - "position": "dialog", - "displayTime": "3", - "highlight": "", - "sendall": true, - "outputs": 1, - "ok": "OK", - "cancel": "", - "raw": false, - "topic": "", - "name": "", - "x": 1010, - "y": 1200, - "wires": [ - [] - ] - }, - { - "id": "c82e467c.99e208", - "type": "switch", - "z": "baa1e3d9.cb29d", - "name": "", - "property": "topic", - "propertyType": "msg", - "rules": [ - { - "t": "eq", - "v": "Missing entry :", - "vt": "str" - }, - { - "t": "eq", - "v": "Start", - "vt": "str" - } - ], - "checkall": "true", - "repair": false, - "outputs": 2, - "x": 850, - "y": 1220, - "wires": [ - [ - "cd56bb1c.8ce378" - ], - [ - "a3fd6b29.2ef5f8", - "a642fc0b.b6dd7" - ] - ] - }, - { - "id": "c6bd5987.c48f78", - "type": "http request", - "z": "baa1e3d9.cb29d", - "name": "Start timelapse", - "method": "GET", - "ret": "txt", - "paytoqs": false, - "url": "http://127.0.0.1/html/cmd_pipe.php?cmd=tl%201", - "tls": "", - "persist": false, - "proxy": "", - "authType": "", - "x": 1100, - "y": 1600, - "wires": [ - [] - ] - }, - { - "id": "8c15fd05.81b5", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get duration acquisition", - "func": "msg.delay = global.get(\"duration\");\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1290, - "y": 1360, - "wires": [ - [ - "2ff9c0cb.7288b", - "34929df1.bfe602" - ] - ] - }, - { - "id": "2ff9c0cb.7288b", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "wait duration", - "pauseType": "delayv", - "timeout": "1", - "timeoutUnits": "seconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 1510, - "y": 1360, - "wires": [ - [ - "99fd2803.0843a8", - "3475ecd5.6655f4", - "8f991d2e.6e8f3", - "e6a12f33.c7768" - ] - ] - }, - { - "id": "a642fc0b.b6dd7", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "", - "pauseType": "delay", - "timeout": "500", - "timeoutUnits": "milliseconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 810, - "y": 1540, - "wires": [ - [ - "c6bd5987.c48f78", - "8c15fd05.81b5" - ] - ] - }, - { - "id": "6aaa3bc6.b7dda4", - "type": "ui_gauge", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b5d61bc7.54fe48", - "order": 1, - "width": 10, - "height": 2, - "gtype": "donut", - "title": "", - "label": "%", - "format": "{{value}}", - "min": 0, - "max": "100", - "colors": [ - "#ffffff", - "#ffffff", - "#097479" - ], - "seg1": "", - "seg2": "", - "x": 2250, - "y": 1500, - "wires": [] - }, - { - "id": "34929df1.bfe602", - "type": "trigger", - "z": "baa1e3d9.cb29d", - "op1": "1", - "op2": "0", - "op1type": "str", - "op2type": "str", - "duration": "-1", - "extend": false, - "units": "s", - "reset": "done", - "bytopic": "all", - "name": "", - "x": 1960, - "y": 1600, - "wires": [ - [ - "e98903d2.f35c1" - ] - ] - }, - { - "id": "3475ecd5.6655f4", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "stop", - "func": "global.set(\"time_to_wait\",0);\nmsg.payload=\"done\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1810, - "y": 1500, - "wires": [ - [ - "34929df1.bfe602", - "6aaa3bc6.b7dda4" - ] - ] - }, - { - "id": "e98903d2.f35c1", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pulse", - "func": "var time_to_wait= global.get(\"time_to_wait\");\n\nif (time_to_wait === undefined || time_to_wait === \"\"|| time_to_wait == NaN) {\n time_to_wait=0\n global.set(\"time_to_wait\",time_to_wait);\n}else {\n time_to_wait++;\n global.set(\"time_to_wait\",time_to_wait);\n duration=global.get(\"duration\")/1000;\n percent=(100* time_to_wait/duration).toFixed(0)\n msg.payload=percent;\n return msg;\n \n}", - "outputs": 1, - "noerr": 0, - "x": 2110, - "y": 1600, - "wires": [ - [ - "6aaa3bc6.b7dda4" - ] - ] - }, - { - "id": "f0ef065a.362028", - "type": "link in", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "a61d4164.135dd", - "783209c7.51c5a8", - "260e60f3.878ad", - "c5ee25c5.3c1848" - ], - "x": 1635, - "y": 1560, - "wires": [ - [ - "3475ecd5.6655f4" - ] - ] - }, - { - "id": "8f991d2e.6e8f3", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "ls -l /var/www/html/media | grep \"th\" | tail -1 | awk -F \" \" '{print $9}' | awk -F \"_\" '{print $1\"_\"$2}'| tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "get thumbail name", - "x": 1850, - "y": 1280, - "wires": [ - [ - "9dcdbf1f.4aa21" - ], - [], - [] - ] - }, - { - "id": "e6a12f33.c7768", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "mkdir", - "func": "acq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/\"+acq_id\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1770, - "y": 1140, - "wires": [ - [ - "43c69256.b9633c" - ] - ] - }, - { - "id": "43c69256.b9633c", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mkdir", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "mkdir acq_id", - "x": 1910, - "y": 1140, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "517f13e8.e0793c", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "move", - "func": "file_prefix=msg.payload;\nacq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/html/media/\"+file_prefix+\"* /var/www/\"+acq_id+\"/\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 2330, - "y": 1240, - "wires": [ - [ - "83a1d49e.a29a48" - ] - ] - }, - { - "id": "9dcdbf1f.4aa21", - "type": "delay", - "z": "baa1e3d9.cb29d", - "name": "", - "pauseType": "delay", - "timeout": "200", - "timeoutUnits": "milliseconds", - "rate": "1", - "nbRateUnits": "1", - "rateUnits": "second", - "randomFirst": "1", - "randomLast": "5", - "randomUnits": "seconds", - "drop": false, - "x": 2090, - "y": 1260, - "wires": [ - [ - "517f13e8.e0793c" - ] - ] - }, - { - "id": "83a1d49e.a29a48", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mv", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 2480, - "y": 1260, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "20a2d27e.7ccafe", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "move", - "func": "file_prefix=msg.payload;\nacq_id=global.get(\"acq_id\")\nmsg.payload=\"/var/www/logs.json /var/www/\"+acq_id+\"/\";\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 2330, - "y": 1320, - "wires": [ - [ - "87cff57.f6d3708" - ] - ] - }, - { - "id": "87cff57.f6d3708", - "type": "exec", - "z": "baa1e3d9.cb29d", - "command": "mv", - "addpay": true, - "append": "", - "useSpawn": "false", - "timer": "", - "oldrc": false, - "name": "", - "x": 2480, - "y": 1340, - "wires": [ - [], - [], - [] - ] - }, - { - "id": "d91229e3.bf0f18", - "type": "while-loop", - "z": "baa1e3d9.cb29d", - "name": "", - "condi": "global.get(\"job\")===\"run\"", - "x": 1330, - "y": 200, - "wires": [ - [ - "427871db.b4902", - "a61b71c3.afaf" - ], - [ - "427871db.b4902", - "a61b71c3.afaf" - ] - ] - }, - { - "id": "217ff214.a25c2e", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Run", - "func": "global.set(\"job\",\"run\")\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 220, - "wires": [ - [ - "d91229e3.bf0f18" - ] - ] - }, - { - "id": "995fa523.83cba8", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "Stop", - "func": "global.set(\"job\",\"stop\")\nmsg.payload=\"stop\"\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1030, - "y": 180, - "wires": [ - [ - "d91229e3.bf0f18" - ] - ] - }, - { - "id": "d3ab1a14.86b8b8", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\norientation = str(msg[\"orientation\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1380, - "y": 520, - "wires": [ - [ - "444587e4.dc23a8" - ] - ] - }, - { - "id": "ff805ffc.f9134", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "actuate RGB", - "func": "import smbus\nfrom time import sleep\n\nbus = smbus.SMBus(1)\n\nrgb=msg['rgb']\nbus.write_byte_data(0x0d, 0x00, 0)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 1)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nbus.write_byte_data(0x0d, 0x00, 2)\nbus.write_byte_data(0x0d, 0x01, rgb[\"r\"])\nbus.write_byte_data(0x0d, 0x02, rgb[\"g\"])\nbus.write_byte_data(0x0d, 0x03, rgb[\"b\"])\nreturn msg;", - "outputs": 1, - "x": 1390, - "y": 460, - "wires": [ - [ - "a27b3163.19c31" - ] - ] - }, - { - "id": "444587e4.dc23a8", - "type": "link out", - "z": "baa1e3d9.cb29d", - "name": "", - "links": [ - "e1354861.0bb648", - "2bc762dd.1115ce", - "a50134c.ed45ac8", - "17d09d70.b50223" - ], - "x": 1475, - "y": 520, - "wires": [] - }, - { - "id": "a27b3163.19c31", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "set busy", - "func": "global.set(\"state\",\"busy\");\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1560, - "y": 460, - "wires": [ - [] - ] - }, - { - "id": "7c974057.4d3f", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get duration acquisition", - "func": "msg.delay = global.get(\"duration\");\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 1430, - "y": 620, - "wires": [ - [] - ] - }, - { - "id": "482c8e09.a77df", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\n\npump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SIMPLE)\nsleep(0.1)", - "outputs": 1, - "x": 1820, - "y": 280, - "wires": [ - [] - ] - }, - { - "id": "427871db.b4902", - "type": "debug", - "z": "baa1e3d9.cb29d", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 1850, - "y": 220, - "wires": [] - }, - { - "id": "a61b71c3.afaf", - "type": "trigger", - "z": "baa1e3d9.cb29d", - "op1": "1", - "op2": "0", - "op1type": "str", - "op2type": "str", - "duration": "-250", - "extend": false, - "units": "ms", - "reset": "stop", - "bytopic": "all", - "name": "", - "x": 1620, - "y": 280, - "wires": [ - [ - "482c8e09.a77df" - ] - ] - }, - { - "id": "f7fa6acf.f6ed28", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "pump.js", - "func": "state = global.get(\"state\");\n\nif (state == null){\n state=\"free\"\n}\n\nif(state===\"free\"||state===\"canceled\"){\n volume = global.get(\"acq_volume\");\n flowrate = global.get(\"sug_flowrate\");\n duration=(((volume*60)/flowrate)-2)*1000\n global.set(\"duration\",duration);\n \n msg.volume = volume;\n msg.orientation = \"forward\";\n msg.flowrate = flowrate;\n msg.rgb = {r:0, g:255, b:255}\n msg.state = state\n \n return msg;\n \n \n}", - "outputs": 1, - "noerr": 0, - "x": 1100, - "y": 340, - "wires": [ - [ - "dd817ccf.04ec" - ] - ], - "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" - }, - { - "id": "dd817ccf.04ec", - "type": "python3-function", - "z": "baa1e3d9.cb29d", - "name": "pump.py", - "func": "from adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\nfrom time import sleep\n\nkit = MotorKit()\npump_stepper = kit.stepper1\npump_stepper.release()\n\nstate = str(msg[\"state\"])\nvolume = int(msg[\"volume\"])\nflowrate = float(msg[\"flowrate\"])\n\n\nif(state==\"free\"):\n #35000steps will pass 69ml if sleep(0.05) in between 2 steps\n #1ml is about 35000/69=507steps\n nb_step=volume*507 \n #nb_step=vol*460 if sleep(0) in between 2 steps\n \n duration=(volume*60)/flowrate\n \n delay=(duration/nb_step)-0.005\n \nif(state==\"canceled\"):\n nb_step=0\n \nfor i in range(nb_step):\n pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.DOUBLE)\n sleep(delay)\n \nsleep(1)\npump_stepper.release()\n\nmsg[\"topic\"] = \"pump\"\nmsg[\"payload\"] = \"done\"\n\nreturn msg", - "outputs": 1, - "x": 1280, - "y": 340, - "wires": [ - [] - ] - }, - { - "id": "7a5b8294.92ad3c", - "type": "ui_button", - "z": "baa1e3d9.cb29d", - "name": "", - "group": "b7919ae2.c01788", - "order": 4, - "width": 5, - "height": 1, - "passthru": false, - "label": "Show", - "tooltip": "", - "color": "#097479", - "bgcolor": "white", - "icon": "keyboard_tab", - "payload": "", - "payloadType": "str", - "topic": "", - "x": 470, - "y": 380, - "wires": [ - [ - "e2919164.70927" - ] - ] - }, - { - "id": "29be525e.0c87fe", - "type": "ui_template", - "z": "baa1e3d9.cb29d", - "group": "b5d61bc7.54fe48", - "name": "show global", - "order": 2, - "width": 0, - "height": 0, - "format": "
\n \n
", - "storeOutMessages": true, - "fwdInMessages": true, - "templateScope": "local", - "x": 750, - "y": 380, - "wires": [ - [] - ] - }, - { - "id": "e2919164.70927", - "type": "function", - "z": "baa1e3d9.cb29d", - "name": "get global", - "func": "msg.payload = {\n \"comment\":global.get(\"comment\"),\n \"sample_project\":global.get(\"sample_project\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"sample_hour\":global.get(\"sample_hour\"),\n \"sample_minute\":global.get(\"sample_minute\"),\n \"sample_day\":global.get(\"sample_day\"),\n \"sample_month\":global.get(\"sample_month\"),\n \"sample_year\":global.get(\"sample_year\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"process_pixel\":global.get(\"process_pixel\"),\n \n \"acq_camera\":global.get(\"acq_camera\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_software\":global.get(\"acq_software\"),\n \"acq_instrument_ID\":global.get(\"acq_instrument_ID\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\")\n }\n\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 600, - "y": 380, - "wires": [ - [ - "29be525e.0c87fe", - "295bd912.8d2556" - ] - ] - }, - { - "id": "295bd912.8d2556", - "type": "debug", - "z": "baa1e3d9.cb29d", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 760, - "y": 440, - "wires": [] - }, - { - "id": "7ca7754c.0f731c", - "type": "inject", - "z": "eaae323a.31b3", - "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "", - "crontab": "", - "once": false, - "onceDelay": 0.1, - "x": 120, - "y": 420, - "wires": [ - [ - "4c6d21e3.0173c" - ] - ] - }, - { - "id": "cbb8afed.0a026", - "type": "rpi-gpio out", - "z": "bccd1f23.87219", - "name": "", - "pin": "40", - "set": "", - "level": "0", - "freq": "", - "out": "out", - "x": 280, - "y": 80, - "wires": [] - }, - { - "id": "4c6d21e3.0173c", - "type": "function", - "z": "eaae323a.31b3", - "name": "", - "func": "var d = new Date();\nvar t = d.getTime();\npayload={\"time\":\"message\",\"timestamp\":msg.payload}\nmsg.payload=payload;\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 250, - "y": 420, - "wires": [ - [ - "c82b48ad.8b5478" - ] - ] - }, - { - "id": "a256071b.25a008", - "type": "file", - "z": "eaae323a.31b3", - "name": "", - "filename": "/home/pi/Desktop/log/test.log", - "appendNewline": true, - "createDir": true, - "overwriteFile": "false", - "encoding": "none", - "x": 600, - "y": 420, - "wires": [ - [ - "3cd4bf1e.11ae3" - ] - ] - }, - { - "id": "3cd4bf1e.11ae3", - "type": "debug", - "z": "eaae323a.31b3", - "name": "", - "active": true, - "tosidebar": true, - "console": false, - "tostatus": false, - "complete": "false", - "x": 950, - "y": 420, - "wires": [] - }, - { - "id": "c82b48ad.8b5478", - "type": "csv", - "z": "eaae323a.31b3", - "name": "", - "sep": ",", - "hdrin": true, - "hdrout": "", - "multi": "one", - "ret": "\\n", - "temp": "timestamp,time", - "skip": "0", - "strings": true, - "x": 390, - "y": 420, - "wires": [ - [ - "a256071b.25a008" - ] - ] - } -] From 74c29fee376efebc1ca532bf20706e8cef96a810 Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:22:31 +0200 Subject: [PATCH 14/17] Update flows.json --- flows/flows.json | 4957 ++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 4604 insertions(+), 353 deletions(-) diff --git a/flows/flows.json b/flows/flows.json index efc88fd..84e7f3f 100644 --- a/flows/flows.json +++ b/flows/flows.json @@ -1,54 +1,488 @@ [ { - "id": "7f885510.6173fc", + "id": "ff9251a5.9c5e18", "type": "tab", - "label": "Home", + "label": "Main", "disabled": false, "info": "" }, { - "id": "55a31f5b.d4ec5", - "type": "tab", - "label": "Static Observation", - "disabled": false, - "info": "" + "id": "bba19d97.b32b1", + "type": "subflow", + "name": "Acquisition actuation", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#A6BBCF" }, { - "id": "c04dcc2a.47862", - "type": "tab", - "label": "Fluidic Acquisition", - "disabled": false, - "info": "" + "id": "c1d3ff7c.4384f", + "type": "subflow", + "name": "MQQT Cmds", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "5079cccb.298d14" + }, + { + "id": "197215b2.165f22" + } + ] + } + ], + "out": [], + "env": [], + "color": "#DDAA99" }, { - "id": "300f077.33624f8", - "type": "tab", - "label": "Segmentation", - "disabled": false, - "info": "" + "id": "c10e968b.87e488", + "type": "subflow", + "name": "Datetime update", + "info": "", + "category": "", + "in": [ + { + "x": 140, + "y": 80, + "wires": [ + { + "id": "93b9f3cd.759688" + } + ] + } + ], + "out": [], + "env": [], + "color": "#DDAA99", + "icon": "font-awesome/fa-clock-o" }, { - "id": "121f01ae.4c4abe", - "type": "tab", - "label": "Dashboard Control", - "disabled": false, - "info": "" + "id": "863e8384.56889", + "type": "subflow", + "name": "Acquisition inputs", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "3eaf4c98.d94b54" + }, + { + "id": "e50aa637.59ac68" + }, + { + "id": "8eeb9e9e.a50d7" + }, + { + "id": "e4e16eb9.5296c" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "c4527705.33a84", + "port": 0 + }, + { + "id": "f648e44.94e3998", + "port": 0 + }, + { + "id": "582e21b2.ad67a8", + "port": 0 + }, + { + "id": "f9705bc.3d322a8", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red-contrib-camerapi/photo.png" }, { - "id": "56d9742b.9ed99c", + "id": "5a287804.a10e2", + "type": "subflow", + "name": "Process metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 80, + "wires": [ + { + "id": "dfb4b682.601e1" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 80, + "wires": [ + { + "id": "11b31baf.95996c", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "a8ad6dec.1a393", + "type": "subflow", + "name": "MQTT Receive & Plot", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#F3B567", + "icon": "node-red/bridge.svg" + }, + { + "id": "9882c53a.0ccc8", + "type": "subflow", + "name": "Temperature regulation", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#FFCC66", + "icon": "font-awesome/fa-bolt" + }, + { + "id": "fbe9590f.bd63b8", + "type": "subflow", + "name": "System Commands", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#FFCC66", + "icon": "node-red-dashboard/ui_button.png" + }, + { + "id": "b45c6fb6.f6dfa8", + "type": "subflow", + "name": "Object metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "8a61177.8eaa1e8" + }, + { + "id": "3893c81e.a9b9e" + }, + { + "id": "bd643763.2a7768" + } + ] + } + ], + "out": [ + { + "x": 1060, + "y": 159, + "wires": [ + { + "id": "cf0b247b.e3e7c", + "port": 0 + }, + { + "id": "1675637a.1d762d", + "port": 0 + } + ] + }, + { + "x": 1060, + "y": 59, + "wires": [ + { + "id": "d485fec3.802e", + "port": 0 + }, + { + "id": "5196107b.a5eae8", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "6ca1a253.126bb4", + "type": "subflow", + "name": "Acquisition metadata", + "info": "", + "category": "", + "in": [ + { + "x": 50, + "y": 30, + "wires": [ + { + "id": "93a3fd29.c55938" + }, + { + "id": "9e9e7f8a.b66d4" + }, + { + "id": "b1105180.b4b78" + }, + { + "id": "ec403304.e34c58" + }, + { + "id": "7aac5c46.0669ec" + }, + { + "id": "c491cf7.36957b" + }, + { + "id": "e0644195.305068" + }, + { + "id": "e3fe6242.bfaf18" + }, + { + "id": "31d58fcd.ede758" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "21b35429.fe43a4", + "port": 0 + }, + { + "id": "f0595ff1.c4d568", + "port": 0 + }, + { + "id": "c4e69883.a0f3d", + "port": 0 + }, + { + "id": "12e818fa.b7301f", + "port": 0 + }, + { + "id": "b577dcd2.8d2c88", + "port": 0 + }, + { + "id": "f7f5ccc1.29a41", + "port": 0 + }, + { + "id": "bd733bef.7efd08", + "port": 0 + }, + { + "id": "a6057924.bc14", + "port": 0 + } + ] + }, + { + "x": 900, + "y": 360, + "wires": [ + { + "id": "5a5fcc9a.9ede14", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "626459d2.f9c98", + "type": "subflow", + "name": "Pump actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "f7b6f5e7.7b7ca" + }, + { + "id": "50093f5.8e35ec" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 40, + "wires": [ + { + "id": "fa485315.928ae", + "port": 0 + }, + { + "id": "2f9ec1a6.d5fb66", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "font-awesome/fa-recycle" + }, + { + "id": "5c516299.73e054", + "type": "subflow", + "name": "Focus actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "60dc5851.6962b" + } + ] + } + ], + "out": [ + { + "x": 800, + "y": 200, + "wires": [ + { + "id": "7297e2f7.dce564", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red/sort.svg" + }, + { + "id": "efeebffd.34c7e", + "type": "subflow", + "name": "Sample metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "78f5791d.946bd8" + }, + { + "id": "346d141f.ebab3c" + }, + { + "id": "2a09d440.119154" + }, + { + "id": "2d438355.ed942c" + }, + { + "id": "ac4a71a.c35309" + } + ] + } + ], + "out": [ + { + "x": 840, + "y": 40, + "wires": [ + { + "id": "1cb896c7.6dfc11", + "port": 0 + }, + { + "id": "288ba4b3.a9a2cc", + "port": 0 + }, + { + "id": "10f1e5c1.3cb69a", + "port": 0 + }, + { + "id": "aa90b06d.ca78e", + "port": 0 + }, + { + "id": "da0c5a96.74c0e", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "68d72e45.e7d58", "type": "ui_base", "theme": { "name": "theme-dark", "lightTheme": { "default": "#0094CE", - "baseColor": "#0094CE", + "baseColor": "#5900ce", "baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif", - "edited": false, + "edited": true, "reset": false }, "darkTheme": { "default": "#097479", - "baseColor": "#097479", + "baseColor": "#059276", "baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif", "edited": true, "reset": false @@ -62,11 +496,11 @@ "themeState": { "base-color": { "default": "#097479", - "value": "#097479", - "edited": false + "value": "#059276", + "edited": true }, "page-titlebar-backgroundColor": { - "value": "#097479", + "value": "#059276", "edited": false }, "page-backgroundColor": { @@ -74,11 +508,11 @@ "edited": false }, "page-sidebar-backgroundColor": { - "value": "#000000", + "value": "#ffffff", "edited": false }, "group-textColor": { - "value": "#0eb8c0", + "value": "#08dcb2", "edited": false }, "group-borderColor": { @@ -94,7 +528,7 @@ "edited": false }, "widget-backgroundColor": { - "value": "#097479", + "value": "#059276", "edited": false }, "widget-borderColor": { @@ -116,497 +550,4314 @@ "name": "Node-RED Dashboard", "hideToolbar": "false", "allowSwipe": "false", - "lockMenu": "false", + "lockMenu": "true", "allowTempTheme": "true", "dateFormat": "DD/MM/YYYY", "sizes": { - "sx": 48, - "sy": 48, - "gx": 6, - "gy": 6, - "cx": 6, - "cy": 6, - "px": 0, - "py": 0 + "sx": 56, + "sy": 56, + "gx": 5, + "gy": 5, + "cx": 5, + "cy": 5, + "px": 5, + "py": 5 } } }, { - "id": "c18fae15.516ce", - "type": "ui_tab", + "id": "44986592.b84004", + "type": "mqtt-broker", "z": "", - "name": "Home", - "icon": "dashboard", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "8eac3de.7c8234", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "888cbaa1.5d9318", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "f98c50f4.4bed48", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "3ee94635.002c9a", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "b0b1b2bb.385fe", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "659e81f6.f85fb8", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "52b67b31.c63a04", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "494e9f19.80f8e8", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "5ad5df6e.1d1e6", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": 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"c18fae15.516ce", - "order": 3, - "disp": false, - "width": "12", + "name": "Process metadata", + "tab": "", + "order": 8, + "disp": true, + "width": 24, "collapse": false }, { - "id": "edb89598.853498", + "id": "b2ce0fd5.641a8", "type": "ui_group", "z": "", - "name": "Gallery", - "tab": "c18fae15.516ce", - "order": 4, - "disp": false, - "width": "12", + "name": "MQTT Plots", + "tab": "", + "order": 11, + "disp": true, + "width": "24", "collapse": false }, { - "id": "98e9fd1a.1bbe5", - "type": "ui_tab", + "id": "516113d5.b6b5d4", + "type": "ui_group", "z": "", - "name": "Static Observation", - "icon": "dashboard", - "order": 2, - "disabled": false, - "hidden": false + "name": "Commands", + "tab": "", + "order": 12, + "disp": true, + "width": 24, + "collapse": false }, { - "id": "2e62c9a8.c191f6", - "type": "ui_tab", + "id": "488da474.92ee5c", + "type": "ui_group", "z": "", - "name": "Fluidic Acquisition", - "icon": "", - "order": 3, - "disabled": false, - "hidden": false + "name": "Object metadata", + "tab": "", + "order": 6, + "disp": true, + "width": "24", + "collapse": false }, { - "id": "609b39b5.d91f28", - "type": "ui_tab", + "id": "a302c12b.834e8", + "type": "ui_group", "z": "", - "name": "Segmentation", - "icon": "dashboard", - "order": 4, - "disabled": false, - "hidden": false + "name": "Acquisition metadata", + "tab": "", + "order": 7, + "disp": true, + "width": "24", + "collapse": false }, { - "id": "b253b89c.1c4458", - "type": "ui_tab", + "id": "95792df3.55e6e", + "type": "ui_group", "z": "", - "name": "Dashboard Control", - "icon": "dashboard", + "name": "Pump actuation", + "tab": "", "order": 5, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "8a415d41.11df38", + "type": "ui_group", + "z": "", + "name": "Focus actuation", + "tab": "", + "order": 4, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "ead03bfe.db2268", + "type": "ui_group", + "z": "", + "name": "Sample metadata", + "tab": "", + "order": 2, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "d4c113ac.dade38", + "type": "ui_group", + "z": "", + "name": "Streaming camera", + "tab": "", + "order": 3, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "cdb72118.692578", + "type": "ui_group", + "z": "", + "name": "Acquisition actuation", + "tab": "2b97fe34.a699fa", + "order": 10, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "9c86b3b7.54841", + "type": "ui_group", + "z": "", + "name": "Datetime", + "tab": "2b97fe34.a699fa", + "order": 1, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "48649115.fcd01", + "type": "ui_group", + "z": "", + "name": "Acquisition inputs", + "tab": "2b97fe34.a699fa", + "order": 9, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "beeb994e.b67688", + "type": "ui_group", + "z": "", + "name": "Process metadata", + "tab": "2b97fe34.a699fa", + "order": 8, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "eb610eb9.84fae8", + "type": "ui_group", + "z": "", + "name": "MQTT Plots", + "tab": "2b97fe34.a699fa", + "order": 11, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "82b3caaa.0518", + "type": "ui_group", + "z": "", + "name": "Commands", + "tab": "2b97fe34.a699fa", + "order": 12, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "f377d75b.32d27", + "type": "ui_group", + "z": "", + "name": "Object metadata", + "tab": "2b97fe34.a699fa", + "order": 6, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "60b93a5.a032344", + "type": "ui_group", + "z": "", + "name": "Acquisition metadata", + "tab": "2b97fe34.a699fa", + "order": 7, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "4153382f.45437", + "type": "ui_group", + "z": "", + "name": "Pump actuation", + "tab": "2b97fe34.a699fa", + "order": 5, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "69433259.f306fc", + "type": "ui_group", + "z": "", + "name": "Focus actuation", + "tab": "2b97fe34.a699fa", + "order": 4, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "417f91c9.193ab", + "type": "ui_group", + "z": "", + "name": "Sample metadata", + "tab": "2b97fe34.a699fa", + "order": 2, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "2b97fe34.a699fa", + "type": "ui_tab", + "z": "", + "name": "GUI", + "icon": "fa-eyedropper", + "order": 2, "disabled": false, "hidden": false }, { - "id": "498d73e3.d1c94c", + "id": "dc721eb.9ef51e", "type": "ui_group", - "name": "Group 1", - "tab": "98e9fd1a.1bbe5", - "order": 1, + "z": "", + "name": "Streaming camera", + "tab": "2b97fe34.a699fa", + "order": 3, "disp": true, - "width": 6 + "width": 24, + "collapse": false }, { - "id": "72fe0cc7.df9fd4", - "type": "ui_group", - "name": "Group 1", - "tab": "2e62c9a8.c191f6", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "54c8e6e0.223fc8", - "type": "ui_group", - "name": "Group 1", - "tab": "609b39b5.d91f28", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "5841eafd.95e5e4", - "type": "ui_group", - "name": "Group 1", - "tab": "b253b89c.1c4458", - "order": 1, - "disp": true, - "width": 6 - }, - { - "id": "df3ac001.1d82a", + "id": "853e90d6.4afd1", "type": "ui_button", - "z": "7f885510.6173fc", + "z": "bba19d97.b32b1", "name": "", - "group": "29a78fc9.b034c", + "group": "cdb72118.692578", "order": 1, - "width": 12, - "height": 6, + "width": 0, + "height": 0, "passthru": false, - "label": "Static Observation", + "label": "Start Acquisition", "tooltip": "", "color": "", "bgcolor": "", "icon": "", "payload": "", "payloadType": "str", - "topic": "Static Observation", - "x": 210, - "y": 260, + "topic": "actuator/image", + "x": 200, + "y": 100, "wires": [ [ - "82696634.821678" + "6e46e66c.654ff8" ] ] }, { - "id": "113ae8d3.b52867", - "type": "ui_button", - "z": "7f885510.6173fc", + "id": "6e46e66c.654ff8", + "type": "function", + "z": "bba19d97.b32b1", + "name": "image.js", + "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar sleep_before= global.get(\"custom_sleep_before\");\nvar nb_step= global.get(\"custom_nb_step\");\nvar nb_frame= global.get(\"custom_nb_frame\");\nvar segmentation= global.get(\"custom_segmentation\");\n\nif (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the acquisition\";\n \n}else if (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of step in between two frames\";\n \n}else if (nb_frame === undefined || nb_frame === \"\" || nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of image to save\";\n \n}else if (segmentation === undefined || segmentation === \"\" || segmentation === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Realize or not the segmentation\";\n \n}else {\n nb_frame=nb_frame-1\n \n msg.payload=sleep_before+' '+nb_step+' '+nb_frame+' '+segmentation;\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 360, + "y": 100, + "wires": [ + [ + "5a37b9e6.6e3e58" + ] + ], + "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" + }, + { + "id": "5a37b9e6.6e3e58", + "type": "switch", + "z": "bba19d97.b32b1", "name": "", - "group": "8c1b4542.a177a8", - "order": 1, + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "actuator/image", + "vt": "str" + }, + { + "t": "eq", + "v": "Missing entry :", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 2, + "x": 510, + "y": 100, + "wires": [ + [ + "75233be8.98e6f4" + ], + [ + "bee35f80.112d" + ] + ] + }, + { + "id": "bee35f80.112d", + "type": "ui_toast", + "z": "bba19d97.b32b1", + "position": "dialog", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 1, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 690, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "75233be8.98e6f4", + "type": "mqtt out", + "z": "bba19d97.b32b1", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 670, + "y": 80, + "wires": [] + }, + { + "id": "75d00421.d31e1c", + "type": "ui_button", + "z": "bba19d97.b32b1", + "name": "Stop Acquisition", + "group": "cdb72118.692578", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "label": "STOP ACQUISITION", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "actuator/wait", + "x": 200, + "y": 140, + "wires": [ + [ + "f2ce7a07.d3eff8" + ] + ] + }, + { + "id": "f2ce7a07.d3eff8", + "type": "mqtt out", + "z": "bba19d97.b32b1", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 350, + "y": 140, + "wires": [] + }, + { + "id": "977270e2.b70738", + "type": "mqtt out", + "z": "bba19d97.b32b1", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 350, + "y": 180, + "wires": [] + }, + { + "id": "23f3e613.20ad82", + "type": "exec", + "z": "c1d3ff7c.4384f", + "command": "python3.7 /home/pi/PlanktonScope/script/main.py", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 910, + "y": 140, + "wires": [ + [ + "87b835dc.107c6", + "2de12b49.050f44" + ], + [ + "87b835dc.107c6", + "2de12b49.050f44" + ], + [ + "87b835dc.107c6", + "2de12b49.050f44" + ] + ] + }, + { + "id": "1ef92011.66439", + "type": "exec", + "z": "c1d3ff7c.4384f", + "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 610, + "y": 200, + "wires": [ + [ + "c1fd2bf6.fa7198" + ], + [], + [] + ] + }, + { + "id": "c1fd2bf6.fa7198", + "type": "exec", + "z": "c1d3ff7c.4384f", + "command": "kill", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 1050, + "y": 200, + "wires": [ + [ + "87b835dc.107c6", + "2de12b49.050f44" + ], + [ + "87b835dc.107c6", + "2de12b49.050f44" + ], + [ + "87b835dc.107c6", + "2de12b49.050f44" + ] + ] + }, + { + "id": "9a6e378b.5ea938", + "type": "ui_button", + "z": "c1d3ff7c.4384f", + "name": "", + "group": "9c86b3b7.54841", + "order": 9, "width": 12, - "height": 6, + "height": 1, "passthru": false, - "label": "Segmentation", + "label": "Kill MQTT", "tooltip": "", "color": "", "bgcolor": "", "icon": "", "payload": "", "payloadType": "str", - "topic": "Segmentation", - "x": 220, + "topic": "", + "x": 80, + "y": 200, + "wires": [ + [ + "1ef92011.66439" + ] + ] + }, + { + "id": "e74e7b3d.2ba678", + "type": "ui_button", + "z": "c1d3ff7c.4384f", + "name": "", + "group": "9c86b3b7.54841", + "order": 10, + "width": 12, + "height": 1, + "passthru": false, + "label": "Restart MQTT", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "", + "x": 100, + "y": 140, + "wires": [ + [ + "23f3e613.20ad82" + ] + ] + }, + { + "id": "87b835dc.107c6", + "type": "ui_toast", + "z": "c1d3ff7c.4384f", + "position": "top right", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 0, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 1260, + "y": 140, + "wires": [] + }, + { + "id": "b60669a0.b480d8", + "type": "exec", + "z": "c10e968b.87e488", + "command": "sudo date -s", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 1010, + "y": 240, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "68aace8d.6bf5", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = new Date();\n//get weekday\nvar weekday = new Array(7);\nweekday[0] = \"Sun\";\nweekday[1] = \"Mon\";\nweekday[2] = \"Tue\";\nweekday[3] = \"Wed\";\nweekday[4] = \"Thu\";\nweekday[5] = \"Fri\";\nweekday[6] = \"Sat\";\nvar w = weekday[d.getUTCDay()];\n//get Month\nvar month = new Array(12);\nmonth[0] = \"Jan\";\nmonth[1] = \"Feb\";\nmonth[2] = \"Mar\";\nmonth[3] = \"Apr\";\nmonth[4] = \"May\";\nmonth[5] = \"Jun\";\nmonth[6] = \"Jul\";\nmonth[7] = \"Aug\";\nmonth[8] = \"Sep\";\nmonth[9] = \"Oct\";\nmonth[10] = \"Nov\";\nmonth[11] = \"Dec\";\nvar n = month[d.getUTCMonth()];\n \n//get day\nvar day = d.getUTCDay()\n\n//get Hours\nvar Hours = d.getUTCHours();\n//get Minutes\nvar Minutes = d.getUTCMinutes();\n//get Seconds\nvar Seconds = d.getUTCSeconds();\n//get FullYear\nvar FullYear = d.getUTCFullYear();\n\n//Thu Aug 09 2012 23:34:04 GMT+0200 (GMT+02:00)\n\n//Thu Aug 9 21:31:26 UTC 2012\n\n//msg.payload = \"Thu Aug 9 21:31:26 UTC 2012\"\n\nmsg.payload = '\"'+w+\" \"+n+\" \"+day+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+\" UTC \"+FullYear+'\"';\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 40, + "wires": [ + [ + "a1db5dbb.32c998" + ] + ] + }, + { + "id": "a1db5dbb.32c998", + "type": "ui_template", + "z": "c10e968b.87e488", + "group": "9c86b3b7.54841", + "name": "", + "order": 1, + "width": 0, + "height": 0, + "format": "
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+ "wrap": false, + "passthru": true, + "topic": "tmp_minute", + "format": "{{value}}", + "min": "0", + "max": "59", + "step": 1, + "x": 650, + "y": 240, + "wires": [ + [ + "8de4b398.3c755" + ] + ] + }, + { + "id": "5b200123.04ec98", + "type": "ui_numeric", + "z": "c10e968b.87e488", + "name": "tmp_second", + "label": "Second", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 7, + "width": 3, + "height": 1, + "wrap": false, + "passthru": true, + "topic": "tmp_second", + "format": "{{value}}", + "min": "0", + "max": "59", + "step": 1, + "x": 650, + "y": 280, + "wires": [ + [ + "8de4b398.3c755" + ] + ] + }, + { + "id": "d8f0f8d1.0550d", + "type": "interval", + "z": "c10e968b.87e488", + "name": "interval", + "interval": "1", + "onstart": false, + "msg": "ping", + "showstatus": true, + "unit": "seconds", + "statusformat": "YYYY-MM-D HH:mm:ss", + "x": 310, + "y": 40, + "wires": [ + [ + "68aace8d.6bf5" + ] + ] + }, + { + "id": "eb163e1c.a7b97", + "type": "ui_button", + "z": "c10e968b.87e488", + "name": "", + "group": "9c86b3b7.54841", + "order": 8, + "width": 4, + "height": 1, + "passthru": false, + "label": "Update", + "tooltip": "", + "color": "black", + "bgcolor": "white", + "icon": "", + "payload": "", + "payloadType": "str", + "topic": "", + "x": 640, + "y": 320, + "wires": [ + [ + "aa948c91.3895a" + ] + ] + }, + { + "id": "aa948c91.3895a", + "type": "function", + "z": "c10e968b.87e488", + "name": "update datetime", + "func": "var FullYear= global.get(\"year\");\nvar Month= global.get(\"month\");\nvar day= global.get(\"day\");\nvar Hours= global.get(\"hour\");\nvar Minutes= global.get(\"minute\");\nvar Seconds= global.get(\"second\");\n\nmsg.payload = new Date();\n//get Month\nvar month = new Array(12);\nmonth[1] = \"Jan\";\nmonth[2] = \"Feb\";\nmonth[3] = \"Mar\";\nmonth[4] = \"Apr\";\nmonth[5] = \"May\";\nmonth[6] = \"Jun\";\nmonth[7] = \"Jul\";\nmonth[8] = \"Aug\";\nmonth[9] = \"Sep\";\nmonth[10] = \"Oct\";\nmonth[11] = \"Nov\";\nmonth[12] = \"Dec\";\nvar n = month[Month];\n \nmsg.payload = '\"'+day+\" \"+n+\" \"+FullYear+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+'\"';\n\n\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 800, + "y": 320, + "wires": [ + [ + "3b7403cb.d33394", + "b60669a0.b480d8" + ] + ] + }, + { + "id": "8de4b398.3c755", + "type": "function", + "z": "c10e968b.87e488", + "name": "set global", + "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 840, + "y": 60, + "wires": [ + [] + ] + }, + { + "id": "3b7403cb.d33394", + "type": "debug", + "z": "c10e968b.87e488", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "false", + "x": 1010, "y": 300, + "wires": [] + }, + { + "id": "315c5aa3.fdf5d6", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCFullYear();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 80, "wires": [ [ - "82696634.821678" + "b3b03af9.8edae8" ] ] }, { - "id": "ec028844.198c98", - "type": "ui_button", - "z": "7f885510.6173fc", + "id": "93b9f3cd.759688", + "type": "function", + "z": "c10e968b.87e488", "name": "", - "group": "10d36e29.c78b42", - "order": 1, - "width": 12, - "height": 6, - "passthru": false, - "label": "Fluidic Acquisition", + "func": "d = new Date();\nmsg.payload = d\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 310, + "y": 80, + "wires": [ + [ + "315c5aa3.fdf5d6", + "922cecc2.dc7f68", + "c2aa11f2.0fdee8", + "915b7162.7a73e", + "b57fe145.320d28", + "d3f45b98.f05a58" + ] + ] + }, + { + "id": "922cecc2.dc7f68", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCMonth();\n\nmsg.payload = val+1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 120, + "wires": [ + [ + "ed1f72c4.e136e" + ] + ] + }, + { + "id": "c2aa11f2.0fdee8", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCDay();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 160, + "wires": [ + [ + "be55a4d1.4d5fa8" + ] + ] + }, + { + "id": "915b7162.7a73e", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCHours();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 200, + "wires": [ + [ + "ee1e92f8.a01bb8" + ] + ] + }, + { + "id": "b57fe145.320d28", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCMinutes();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 240, + "wires": [ + [ + "c532a0cd.b0a47" + ] + ] + }, + { + "id": "d3f45b98.f05a58", + "type": "function", + "z": "c10e968b.87e488", + "name": "", + "func": "d = msg.payload;\n\nvar val = d.getUTCSeconds();\n\nmsg.payload = val;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 490, + "y": 280, + "wires": [ + [ + "5b200123.04ec98" + ] + ] + }, + { + "id": "c4527705.33a84", + "type": "ui_text_input", + "z": "863e8384.56889", + "name": "custom_nb_step", + "label": "Number of steps in between two images", "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Fluidic Acquisition", - "x": 210, - "y": 340, - "wires": [ - [ - "82696634.821678" - ] - ] - }, - { - "id": "47a9f575.dc2c8c", - "type": "ui_button", - "z": "7f885510.6173fc", - "name": "", - "group": "edb89598.853498", - "order": 1, - "width": 12, - "height": 6, - "passthru": false, - "label": "Dashboard Control", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Dashboard Control", - "x": 270, - "y": 380, - "wires": [ - [ - "82696634.821678" - ] - ] - }, - { - "id": "c0f2a501.1677c8", - "type": "ui_ui_control", - "z": "7f885510.6173fc", - "name": "", - "events": "change", + "group": "48649115.fcd01", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_nb_step", "x": 540, - "y": 260, + "y": 80, "wires": [ [] ] }, { - "id": "c52be0d9.e6412", - "type": "ui_button", - "z": "55a31f5b.d4ec5", - "name": "", - "group": "498d73e3.d1c94c", - "order": 0, + "id": "582e21b2.ad67a8", + "type": "ui_text_input", + "z": "863e8384.56889", + "name": "custom_nb_frame", + "label": "Number of images per acquisition", + "tooltip": "", + "group": "48649115.fcd01", + "order": 3, "width": 0, "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "66e609a2.2d57d8" - ] - ] - }, - { - "id": "82696634.821678", - "type": "function", - "z": "7f885510.6173fc", - "name": "swtich tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", - "outputs": 1, - "noerr": 0, - "x": 400, - "y": 260, - "wires": [ - [ - "c0f2a501.1677c8" - ] - ] - }, - { - "id": "8059df68.0963c", - "type": "ui_ui_control", - "z": "55a31f5b.d4ec5", - "name": "", - "events": "change", - "x": 380, - "y": 40, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_nb_frame", + "x": 530, + "y": 120, "wires": [ [] ] }, { - "id": "66e609a2.2d57d8", + "id": "3eaf4c98.d94b54", "type": "function", - "z": "55a31f5b.d4ec5", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", + "z": "863e8384.56889", + "name": "get custom_nb_step", + "func": "msg.payload = msg.payload.custom_nb_step;\nreturn msg;", "outputs": 1, "noerr": 0, "x": 220, - "y": 40, + "y": 80, "wires": [ [ - "8059df68.0963c" + "c4527705.33a84" ] ] }, { - "id": "f8c2a4c7.928f88", - "type": "ui_button", - "z": "c04dcc2a.47862", - "name": "", - "group": "72fe0cc7.df9fd4", - "order": 0, + "id": "8eeb9e9e.a50d7", + "type": "function", + "z": "863e8384.56889", + "name": "get custom_nb_frame", + "func": "msg.payload = msg.payload.custom_nb_frame;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 120, + "wires": [ + [ + "582e21b2.ad67a8" + ] + ] + }, + { + "id": "e4e16eb9.5296c", + "type": "function", + "z": "863e8384.56889", + "name": "get custom_segmentation", + "func": "msg.payload = msg.payload.custom_segmentation;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 160, + "wires": [ + [ + "f9705bc.3d322a8" + ] + ] + }, + { + "id": "e50aa637.59ac68", + "type": "function", + "z": "863e8384.56889", + "name": "get custom_sleep_before", + "func": "msg.payload = msg.payload.custom_sleep_before;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 40, + "wires": [ + [ + "f648e44.94e3998" + ] + ] + }, + { + "id": "f648e44.94e3998", + "type": "ui_text_input", + "z": "863e8384.56889", + "name": "custom_sleep_before", + "label": "Duration before the acquisition (s)", + "tooltip": "", + "group": "48649115.fcd01", + "order": 1, "width": 0, "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", - "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, - "wires": [ - [ - "6715b713.0ea1e8" - ] - ] - }, - { - "id": "16edbf14.c67bb1", - "type": "ui_ui_control", - "z": "c04dcc2a.47862", - "name": "", - "events": "change", - "x": 380, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "custom_sleep_before", + "x": 520, "y": 40, "wires": [ [] ] }, { - "id": "6715b713.0ea1e8", + "id": "11b31baf.95996c", + "type": "ui_text_input", + "z": "5a287804.a10e2", + "name": "process_id", + "label": "Id of the process", + "tooltip": "", + "group": "beeb994e.b67688", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "process_id", + "x": 550, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "dfb4b682.601e1", "type": "function", - "z": "c04dcc2a.47862", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", + "z": "5a287804.a10e2", + "name": "get process_id", + "func": "msg.payload = msg.payload.process_id+1;\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 220, - "y": 40, + "x": 200, + "y": 80, "wires": [ [ - "16edbf14.c67bb1" + "11b31baf.95996c" ] ] }, { - "id": "e46b58fd.671568", - "type": "ui_button", - "z": "300f077.33624f8", + "id": "3777e513.35c3fa", + "type": "mqtt in", + "z": "a8ad6dec.1a393", "name": "", - "group": "54c8e6e0.223fc8", - "order": 0, + "topic": "receiver/#", + "qos": "0", + "datatype": "auto", + "broker": "84801dc0.193d88", + "x": 80, + "y": 40, + "wires": [ + [ + "9886f960.4b6268", + "589fbae2.8ff914" + ] + ] + }, + { + "id": "9886f960.4b6268", + "type": "switch", + "z": "a8ad6dec.1a393", + "name": "", + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "receiver/pump", + "vt": "str" + }, + { + "t": "eq", + "v": "receiver/focus", + "vt": "str" + }, + { + "t": "eq", + "v": "receiver/image", + "vt": "str" + }, + { + "t": "cont", + "v": "receiver/segmentation", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 4, + "x": 230, + "y": 40, + "wires": [ + [ + "c90e948f.2f7348" + ], + [ + "1d54f7b3.db7ac8" + ], + [ + "d02a7968.b8874" + ], + [ + "11e60fef.079d38" + ] + ] + }, + { + "id": "c90e948f.2f7348", + "type": "switch", + "z": "a8ad6dec.1a393", + "name": "", + "property": "payload", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "Start", + "vt": "str" + }, + { + "t": "eq", + "v": "Done", + "vt": "str" + }, + { + "t": "eq", + "v": "Interrompted", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 3, + "x": 470, + "y": 40, + "wires": [ + [ + "e16b8120.403e8" + ], + [ + "4ea155a3.d8531c" + ], + [ + "3d35b841.e6596" + ] + ] + }, + { + "id": "e16b8120.403e8", + "type": "change", + "z": "a8ad6dec.1a393", + 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"removeOlderUnit": "3600", + "cutout": 0, + "useOneColor": false, + "colors": [ + "#1f77b4", + "#aec7e8", + "#ff7f0e", + "#2ca02c", + "#98df8a", + "#d62728", + "#ff9896", + "#9467bd", + "#c5b0d5" + ], + "useOldStyle": false, + "outputs": 1, + "x": 950, + "y": 760, + "wires": [ + [] + ] + }, + { + "id": "e50c9bb6.397a08", + "type": "ui_chart", + "z": "a8ad6dec.1a393", + "name": "", + "group": "eb610eb9.84fae8", + "order": 8, + "width": 0, + "height": 0, + "label": "chart", + "chartType": "line", + "legend": "false", + "xformat": "HH:mm:ss", + "interpolate": "linear", + "nodata": "", + "dot": true, + "ymin": "", + "ymax": "", + "removeOlder": 1, + "removeOlderPoints": "1000", + "removeOlderUnit": "3600", + "cutout": 0, + "useOneColor": false, + "colors": [ + "#1f77b4", + "#aec7e8", + "#ff7f0e", + "#2ca02c", + "#98df8a", + "#d62728", + "#ff9896", + "#9467bd", + "#c5b0d5" + ], + "useOldStyle": false, + "outputs": 1, + "x": 970, + "y": 700, + "wires": [ + [] + ] + }, + { + "id": "1597b08f.5bce8f", + "type": "ui_toast", + "z": "a8ad6dec.1a393", + "position": "top right", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 0, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 1220, + "y": 360, + "wires": [] + }, + { + "id": "85ced3a9.8bc898", + "type": "exec", + "z": "9882c53a.0ccc8", + "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", + "addpay": false, + "append": "", + "useSpawn": "", + "timer": "", + "name": "RPi Temp.", + "x": 350, + "y": 80, + "wires": [ + [ + "8715b9fb.194438" + ], + [], + [] + ] + }, + { + "id": "3bb0ef9d.258af8", + "type": "inject", + "z": "9882c53a.0ccc8", + "name": "", + "topic": "", + "payload": "", + "payloadType": "date", + "repeat": "10", + "crontab": "", + "once": false, + "onceDelay": "", + "x": 190, + "y": 80, + "wires": [ + [ + "85ced3a9.8bc898" + ] + ] + }, + { + "id": "8715b9fb.194438", + "type": "python3-function", + "z": "9882c53a.0ccc8", + "name": "fan.py", + "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", + "outputs": 1, + "x": 530, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "7bdf69d9.8f98e", + "type": "ui_button", + "z": "fbe9590f.bd63b8", + "name": "", + "group": "82b3caaa.0518", + "order": 1, "width": 0, "height": 0, "passthru": false, - "label": "Home", + "label": "Reboot", "tooltip": "", "color": "", - "bgcolor": "", + "bgcolor": "#AD1625", "icon": "", - "payload": "", + "payload": "off", "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, + "topic": "reboot", + "x": 220, + "y": 80, "wires": [ [ - "5c885d69.f82f74" + "c55ff479.c166a8" ] ] }, { - "id": "c492a6c.3ff6558", - "type": "ui_ui_control", - "z": "300f077.33624f8", + "id": "f400fb5a.9bc108", + "type": "exec", + "z": "fbe9590f.bd63b8", + "command": "sudo", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "2", + "oldrc": false, + "name": "cmd", + "x": 530, + "y": 80, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "867e9bed.e2a298", + "type": "ui_button", + "z": "fbe9590f.bd63b8", "name": "", - "events": "change", - "x": 380, + "group": "82b3caaa.0518", + "order": 2, + "width": 0, + "height": 0, + "passthru": false, + "label": "Shutdown", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "shutdown", + "x": 220, + "y": 140, + "wires": [ + [ + "c55ff479.c166a8" + ] + ] + }, + { + "id": "c55ff479.c166a8", + "type": "python3-function", + "z": "fbe9590f.bd63b8", + "name": "action", + "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", + "outputs": 1, + "x": 390, + "y": 100, + "wires": [ + [ + "46f85d17.08fa54", + "f400fb5a.9bc108" + ] + ] + }, + { + "id": "46f85d17.08fa54", + "type": "exec", + "z": "fbe9590f.bd63b8", + "command": "i2cdetect -y 1", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "1", + "oldrc": false, + "name": "i2c update", + "x": 550, + "y": 140, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "cf0b247b.e3e7c", + "type": "ui_numeric", + "z": "b45c6fb6.f6dfa8", + "name": "object_depth_min", + "label": "Minimum depth (m)", + "tooltip": "", + "group": "f377d75b.32d27", + "order": 3, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "object_depth_min", + "format": "{{value}}", + "min": "0", + "max": "2000", + "step": "1", + "x": 610, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "1675637a.1d762d", + "type": "ui_numeric", + "z": "b45c6fb6.f6dfa8", + "name": "object_depth_max", + "label": "Maximum depth (m)", + "tooltip": "", + "group": "f377d75b.32d27", + "order": 2, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "object_depth_max", + "format": "{{value}}", + "min": "0", + "max": "2000", + "step": "1", + "x": 610, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "8a61177.8eaa1e8", + "type": "function", + "z": "b45c6fb6.f6dfa8", + "name": "get object_depth_min", + "func": "msg.payload = msg.payload.object_depth_min;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 304, + "y": 120, + "wires": [ + [ + "cf0b247b.e3e7c" + ] + ] + }, + { + "id": "3893c81e.a9b9e", + "type": "function", + "z": "b45c6fb6.f6dfa8", + "name": "get object_depth_max", + "func": "msg.payload = msg.payload.object_depth_max;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 304, + "y": 160, + "wires": [ + [ + "1675637a.1d762d" + ] + ] + }, 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+ "outputs": 1, + "noerr": 0, + "x": 320, + "y": 200, + "wires": [ + [ + "ca169437.bb25e8" + ] + ] + }, + { + "id": "d485fec3.802e", + "type": "function", + "z": "b45c6fb6.f6dfa8", + "name": "set object_time", + "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute;\nglobal.set('object_time',time_UTC);\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 804, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "5196107b.a5eae8", + "type": "function", + "z": "b45c6fb6.f6dfa8", + "name": "set object_date", + "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 804, "y": 40, "wires": [ [] ] }, { - "id": "5c885d69.f82f74", + "id": "edee5fda.673ae", + "type": "debug", + "z": "b45c6fb6.f6dfa8", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 280, + "y": 360, + "wires": [] + }, + { + "id": "5a5fcc9a.9ede14", "type": "function", - "z": "300f077.33624f8", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", + "z": "6ca1a253.126bb4", + "name": "set optical config", + "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"acq_magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"acq_magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"acq_magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"acq_magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"acq_magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 220, - "y": 40, + "x": 750, + "y": 360, "wires": [ - [ - "c492a6c.3ff6558" - ] + [] ] }, { - "id": "cb7440f4.3efff", - "type": "ui_button", - "z": "121f01ae.4c4abe", - "name": "", - "group": "5841eafd.95e5e4", - "order": 0, + "id": "3d3aafbf.e907a8", + "type": "ui_dropdown", + "z": "6ca1a253.126bb4", + "name": "acq_fnumber_objective", + "label": "M12 Lens*", + "tooltip": "", + "place": "Select option", + "group": "60b93a5.a032344", + "order": 3, "width": 0, "height": 0, - "passthru": false, - "label": "Home", - "tooltip": "", - "color": "", - "bgcolor": "", - "icon": "", + "passthru": true, + "options": [ + { + "label": "f 25mm 1/2\" 5MP IR", + "value": 25, + "type": "num" + }, + { + "label": "f 16mm 1/2.5\" 5MP IR", + "value": 16, + "type": "num" + }, + { + "label": "f 12mm 1/2.5\" 5MP IR", + "value": 12, + "type": "num" + }, + { + "label": "f 8mm 1/2.5\" 5MP IR", + "value": 8, + "type": "num" + }, + { + "label": "f 6mm 1/2.5\" 5MP IR", + "value": 6, + "type": "num" + } + ], "payload": "", - "payloadType": "str", - "topic": "Home", - "x": 70, - "y": 40, + "topic": "acq_fnumber_objective", + "x": 526, + "y": 360, "wires": [ [ - "b0b1ec9.5371e1" + "5a5fcc9a.9ede14" ] ] }, { - "id": "a4505700.60eb18", - "type": "ui_ui_control", - "z": "121f01ae.4c4abe", - "name": "", - "events": "change", - "x": 380, + "id": "12e818fa.b7301f", + "type": "ui_numeric", + "z": "6ca1a253.126bb4", + "name": "acq_minimum_mesh", + "label": "Min fraction size (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 8, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_minimum_mesh", + "format": "{{value}}", + "min": 0, + "max": "300", + "step": "10", + "x": 536, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "b577dcd2.8d2c88", + "type": "ui_numeric", + "z": "6ca1a253.126bb4", + "name": "acq_maximum_mesh", + "label": "Max fraction size (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 4, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_maximum_mesh", + "format": "{{value}}", + "min": "200", + "max": "2000", + "step": "100", + "x": 536, + "y": 200, + "wires": [ + [] + ] + }, + { + "id": "21b35429.fe43a4", + "type": "ui_text_input", + "z": "6ca1a253.126bb4", + "name": "acq_id", + "label": "Acquisition unique ID*", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "acq_id", + "x": 586, "y": 40, "wires": [ [] ] }, { - "id": "b0b1ec9.5371e1", + "id": "c4e69883.a0f3d", + "type": "ui_dropdown", + "z": "6ca1a253.126bb4", + "name": "acq_celltype", + "label": "Thickness flowcell*", + "tooltip": "", + "place": "Select option", + "group": "60b93a5.a032344", + "order": 7, + "width": 0, + "height": 0, + "passthru": true, + "options": [ + { + "label": "200 μm µ-Slide I Luer", + "value": 200, + "type": "num" + }, + { + "label": "400 μm µ-Slide I Luer", + "value": 400, + "type": "num" + }, + { + "label": "600 μm µ-Slide I Luer", + "value": 600, + "type": "num" + }, + { + "label": "800 μm µ-Slide I Luer", + "value": 800, + "type": "num" + } + ], + "payload": "", + "topic": "acq_celltype", + "x": 566, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "f7f5ccc1.29a41", + "type": "ui_text_input", + "z": "6ca1a253.126bb4", + "name": "acq_volume", + "label": "Volume to pass (ml)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "acq_volume", + "x": 566, + "y": 240, + "wires": [ + [] + ] + }, + { + "id": "f0595ff1.c4d568", + "type": "ui_text_input", + "z": "6ca1a253.126bb4", + "name": "acq_instrument", + "label": "Acquisition instrument", + "tooltip": "PlanktonScope V2.1", + "group": "60b93a5.a032344", + "order": 6, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "acq_instrument", + "x": 556, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "93a3fd29.c55938", "type": "function", - "z": "121f01ae.4c4abe", - "name": "change tab", - "func": "\nmsg.payload={\"tab\":msg.topic};\nreturn msg;", + "z": "6ca1a253.126bb4", + "name": "get acq_id", + "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;", "outputs": 1, "noerr": 0, - "x": 220, + "x": 210, "y": 40, "wires": [ [ - "a4505700.60eb18" + "21b35429.fe43a4" ] ] + }, + { + "id": "9e9e7f8a.b66d4", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_instrument", + "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 80, + "wires": [ + [ + "f0595ff1.c4d568" + ] + ] + }, + { + "id": "b1105180.b4b78", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_celltype", + "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 120, + "wires": [ + [ + "c4e69883.a0f3d" + ] + ] + }, + { + "id": "ec403304.e34c58", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_minimum_mesh", + "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 160, + "wires": [ + [ + "12e818fa.b7301f" + ] + ] + }, + { + "id": "7aac5c46.0669ec", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_maximum_mesh", + "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 200, + "wires": [ + [ + "b577dcd2.8d2c88" + ] + ] + }, + { + "id": "c491cf7.36957b", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_volume", + "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 240, + "wires": [ + [ + "f7f5ccc1.29a41" + ] + ] + }, + { + "id": "31d58fcd.ede758", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_fnumber_objective", + "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 260, + "y": 360, + "wires": [ + [ + "3d3aafbf.e907a8" + ] + ] + }, + { + "id": "bd733bef.7efd08", + "type": "ui_numeric", + "z": "6ca1a253.126bb4", + "name": "acq_min_esd", + "label": "Minimum size to segment (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 9, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_min_esd", + "format": "{{value}}", + "min": 0, + "max": "300", + "step": "5", + "x": 566, + "y": 280, + "wires": [ + [] + ] + }, + { + "id": "a6057924.bc14", + "type": "ui_numeric", + "z": "6ca1a253.126bb4", + "name": "acq_max_esd", + "label": "Maximum size to segment (μm)", + "tooltip": "", + "group": "60b93a5.a032344", + "order": 5, + "width": 0, + "height": 0, + "wrap": false, + "passthru": true, + "topic": "acq_max_esd", + "format": "{{value}}", + "min": "100", + "max": "2000", + "step": "5", + "x": 556, + "y": 320, + "wires": [ + [] + ] + }, + { + "id": "e0644195.305068", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_min_esd", + "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 280, + "wires": [ + [ + "bd733bef.7efd08" + ] + ] + }, + { + "id": "e3fe6242.bfaf18", + "type": "function", + "z": "6ca1a253.126bb4", + "name": "get acq_max_esd", + "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 320, + "wires": [ + [ + "a6057924.bc14" + ] + ] + }, + { + "id": "edfb5b10.95636", + "type": "function", + "z": "626459d2.f9c98", + "name": "pump.js", + "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"pump_manual_volume\");\nvar flowrate= global.get(\"pump_flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"pump_manual_volume\");\n nb_step=volume*507\n msg.volume = volume;\n flowrate = global.get(\"pump_flowrate\");\n duration=(volume*60)/flowrate\n delay=(duration/nb_step)-0.005\n msg.topic = \"actuator/pump\";\n \n if(msg.payload === \"FORWARD\" & state===\"free\"){\n msg.payload='FORWARD '+delay+' '+nb_step;\n }\n if(msg.payload === \"BACKWARD\" & state===\"free\"){\n msg.payload='BACKWARD '+delay+' '+nb_step;\n }\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 640, + "y": 140, + "wires": [ + [ + "fb35e49.f64de18" + ] + ], + "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" + }, + { + "id": "26686514.749b4a", + "type": "ui_button", + "z": "626459d2.f9c98", + "name": "BACKWARD", + "group": "4153382f.45437", + "order": 2, + "width": 6, + "height": 1, + "passthru": false, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_back", + "payload": "BACKWARD", + "payloadType": "str", + "topic": "actuator/pump", + "x": 470, + "y": 120, + "wires": [ + [ + "edfb5b10.95636" + ] + ] + }, + { + "id": "bee2fd6d.cffb28", + "type": "ui_button", + "z": "626459d2.f9c98", + "name": "FORWARD", + "group": "4153382f.45437", + "order": 4, + "width": 6, + "height": 1, + "passthru": true, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_forward", + "payload": "FORWARD", + "payloadType": "str", + "topic": "actuator/pump", + "x": 470, + "y": 160, + "wires": [ + [ + "edfb5b10.95636" + ] + ] + }, + { + "id": "fb35e49.f64de18", + "type": "switch", + "z": "626459d2.f9c98", + "name": "", + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "actuator/pump", + "vt": "str" + }, + { + "t": "eq", + "v": "Missing entry :", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 2, + "x": 770, + "y": 140, + "wires": [ + [ + "f6aa3e03.85018" + ], + [ + "f6dcda51.633398" + ] + ] + }, + { + "id": "f6dcda51.633398", + "type": "ui_toast", + "z": "626459d2.f9c98", + "position": "dialog", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 1, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 930, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "c3edd9e7.1ac36", + "type": "ui_button", + "z": "626459d2.f9c98", + "name": "stop pump", + "group": "4153382f.45437", + "order": 5, + "width": 4, + "height": 1, + "passthru": true, + "label": "STOP PUMP", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "actuator/wait", + "x": 470, + "y": 200, + "wires": [ + [ + "2521ba15.88a58e" + ] + ] + }, + { + "id": "f6aa3e03.85018", + "type": "mqtt out", + "z": "626459d2.f9c98", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 910, + "y": 120, + "wires": [] + }, + { + "id": "2521ba15.88a58e", + "type": "mqtt out", + "z": "626459d2.f9c98", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 610, + "y": 200, + "wires": [] + }, + { + "id": "2f9ec1a6.d5fb66", + "type": "ui_text_input", + "z": "626459d2.f9c98", + "name": "pump_manual_volume", + "label": "Volume to pass (ml)", + "tooltip": "", + "group": "4153382f.45437", + "order": 3, + "width": 8, + "height": 1, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "pump_manual_volume", + "x": 480, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "50093f5.8e35ec", + "type": "function", + "z": "626459d2.f9c98", + "name": "get pump_manual_volume", + "func": "msg.payload = msg.payload.pump_manual_volume;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 220, + "y": 80, + "wires": [ + [ + "2f9ec1a6.d5fb66" + ] + ] + }, + { + "id": "fa485315.928ae", + "type": "ui_slider", + "z": "626459d2.f9c98", + "name": "pump_flowrate", + "label": "Flowrate (ml/min)*", + "tooltip": "", + "group": "4153382f.45437", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "outs": "end", + "topic": "pump_flowrate", + "min": 0, + "max": "20", + "step": "0.1", + "x": 500, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "f7b6f5e7.7b7ca", + "type": "function", + "z": "626459d2.f9c98", + "name": "get pump_flowrate", + "func": "msg.payload = msg.payload.pump_flowrate;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 190, + "y": 40, + "wires": [ + [ + "fa485315.928ae" + ] + ] + }, + { + "id": "7297e2f7.dce564", + "type": "ui_text_input", + "z": "5c516299.73e054", + "name": "focus_nb_step", + "label": "Number of step(s)", + "tooltip": "", + "group": "69433259.f306fc", + "order": 2, + "width": 8, + "height": 1, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "focus_nb_step", + "x": 540, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "60dc5851.6962b", + "type": "function", + "z": "5c516299.73e054", + "name": "get focus_nb_step", + "func": "msg.payload = msg.payload.focus_nb_step;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 230, + "y": 40, + "wires": [ + [ + "7297e2f7.dce564" + ] + ] + }, + { + "id": "7200408d.a1be4", + "type": "ui_button", + "z": "5c516299.73e054", + "name": "DOWN", + "group": "69433259.f306fc", + "order": 3, + "width": 6, + "height": 1, + "passthru": true, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_downward", + "payload": "DOWN", + "payloadType": "str", + "topic": "actuator/focus", + "x": 520, + "y": 120, + "wires": [ + [ + "2e2a455b.5ff4fa" + ] + ] + }, + { + "id": "7f823e6.d3bcfc", + "type": "ui_button", + "z": "5c516299.73e054", + "name": "UP", + "group": "69433259.f306fc", + "order": 1, + "width": 6, + "height": 1, + "passthru": false, + "label": "", + "tooltip": "", + "color": "", + "bgcolor": "", + "icon": "arrow_upwards", + "payload": "UP", + "payloadType": "str", + "topic": "actuator/focus", + "x": 530, + "y": 81, + "wires": [ + [ + "2e2a455b.5ff4fa" + ] + ] + }, + { + "id": "54482c7a.a384ac", + "type": "switch", + "z": "5c516299.73e054", + "name": "", + "property": "topic", + "propertyType": "msg", + "rules": [ + { + "t": "eq", + "v": "actuator/focus", + "vt": "str" + }, + { + "t": "eq", + "v": "Missing entry :", + "vt": "str" + } + ], + "checkall": "true", + "repair": false, + "outputs": 2, + "x": 810, + "y": 100, + "wires": [ + [ + "2a7a3d34.08e2a2" + ], + [ + "4277442b.04d1b4" + ] + ] + }, + { + "id": "4277442b.04d1b4", + "type": "ui_toast", + "z": "5c516299.73e054", + "position": "dialog", + "displayTime": "3", + "highlight": "", + "sendall": true, + "outputs": 1, + "ok": "OK", + "cancel": "", + "raw": false, + "topic": "", + "name": "", + "x": 970, + "y": 140, + "wires": [ + [] + ] + }, + { + "id": "2e2a455b.5ff4fa", + "type": "function", + "z": "5c516299.73e054", + "name": "focus.js", + "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"focus_nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"focus_nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 660, + "y": 100, + "wires": [ + [ + "54482c7a.a384ac" + ] + ], + "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" + }, + { + "id": "73e0d0c.c07ab3", + "type": "ui_button", + "z": "5c516299.73e054", + "name": "stop focus", + "group": "69433259.f306fc", + "order": 4, + "width": 4, + "height": 1, + "passthru": true, + "label": "STOP FOCUS", + "tooltip": "", + "color": "", + "bgcolor": "#AD1625", + "icon": "", + "payload": "off", + "payloadType": "str", + "topic": "actuator/wait", + "x": 510, + "y": 160, + "wires": [ + [ + "8e86348d.69657" + ] + ] + }, + { + "id": "2a7a3d34.08e2a2", + "type": "mqtt out", + "z": "5c516299.73e054", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 950, + "y": 80, + "wires": [] + }, + { + "id": "8e86348d.69657", + "type": "mqtt out", + "z": "5c516299.73e054", + "name": "", + "topic": "", + "qos": "", + "retain": "", + "broker": "e8ab36cc.74d77", + "x": 650, + "y": 160, + "wires": [] + }, + { + "id": "10f1e5c1.3cb69a", + "type": "ui_text_input", + "z": "efeebffd.34c7e", + "name": "sample_ship", + "label": "Name of the ship", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 2, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_ship", + "x": 590, + "y": 120, + "wires": [ + [] + ] + }, + { + "id": "da0c5a96.74c0e", + "type": "ui_dropdown", + "z": "efeebffd.34c7e", + "name": "sample_sampling_gear", + "label": "Sampling gear", + "tooltip": "", + "place": "Select", + "group": "417f91c9.193ab", + "order": 4, + "width": 0, + "height": 0, + "passthru": true, + "options": [ + { + "label": "Plankton net", + "value": "net", + "type": "str" + }, + { + "label": "Niskin bottle 12L", + "value": "niskin_12L", + "type": "str" + }, + { + "label": "Niskin bottle 24L", + "value": "niskin_24L", + "type": "str" + }, + { + "label": "Pass Hull", + "value": "pass_hull", + "type": "str" + }, + { + "label": "Flask", + "value": "flask", + "type": "str" + } + ], + "payload": "", + "topic": "sample_sampling_gear", + "x": 550, + "y": 200, + "wires": [ + [] + ] + }, + { + "id": "aa90b06d.ca78e", + "type": "ui_text_input", + "z": "efeebffd.34c7e", + "name": "sample_operator", + "label": "Name of the operator", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 3, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_operator", + "x": 570, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "1cb896c7.6dfc11", + "type": "ui_text_input", + "z": "efeebffd.34c7e", + "name": "sample_project", + "label": "Name of the project*", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 1, + "width": 0, + "height": 0, + "passthru": true, + "mode": "text", + "delay": 300, + "topic": "sample_project", + "x": 580, + "y": 40, + "wires": [ + [] + ] + }, + { + "id": "288ba4b3.a9a2cc", + "type": "ui_text_input", + "z": "efeebffd.34c7e", + "name": "sample_id", + "label": "ID of the station*", + "tooltip": "", + "group": "417f91c9.193ab", + "order": 5, + "width": 0, + "height": 0, + "passthru": true, + "mode": "number", + "delay": 300, + "topic": "sample_id", + "x": 590, + "y": 80, + "wires": [ + [] + ] + }, + { + "id": "78f5791d.946bd8", + "type": "function", + "z": "efeebffd.34c7e", + "name": "get sample_projet", + "func": "msg.payload = msg.payload.sample_project;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 250, + "y": 40, + "wires": [ + [ + "1cb896c7.6dfc11" + ] + ] + }, + { + "id": "2a09d440.119154", + "type": "function", + "z": "efeebffd.34c7e", + "name": "get sample_ship", + "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 240, + "y": 120, + "wires": [ + [ + "10f1e5c1.3cb69a" + ] + ] + }, + { + "id": "346d141f.ebab3c", + "type": "function", + "z": "efeebffd.34c7e", + "name": "get sample_id", + "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 240, + "y": 80, + "wires": [ + [ + "288ba4b3.a9a2cc" + ] + ] + }, + { + "id": "2d438355.ed942c", + "type": "function", + "z": "efeebffd.34c7e", + "name": "get sample_operator", + "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 260, + "y": 160, + "wires": [ + [ + "aa90b06d.ca78e" + ] + ] + }, + { + "id": "ac4a71a.c35309", + "type": "function", + "z": "efeebffd.34c7e", + "name": "get sample_sampling_gear", + "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 280, + "y": 200, + "wires": [ + [ + "da0c5a96.74c0e" + ] + ] + }, + { + "id": "45482528.43f93c", + "type": "function", + "z": "ff9251a5.9c5e18", + "name": "get global", + "func": "msg.payload={\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"custom_nb_frame\":global.get(\"custom_nb_frame\"),\n \"custom_nb_step\":global.get(\"custom_nb_step\"),\n \"custom_segmentation\":global.get(\"custom_segmentation\"),\n \"custom_sleep_before\":global.get(\"custom_sleep_before\"),\n \"focus_nb_step\":global.get(\"focus_nb_step\"),\n \"pump_flowrate\":global.get(\"pump_flowrate\"),\n \"pump_manual_volume\":global.get(\"pump_manual_volume\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n \n};\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 1260, + "y": 160, + "wires": [ + [ + "fe81be99.6859e8" + ] + ] + }, + { + "id": "a5f18550.68466", + "type": "file", + "z": "ff9251a5.9c5e18", + "name": "", + "filename": "/home/pi/PlanktonScope/config.json", + "appendNewline": true, + "createDir": true, + "overwriteFile": "true", + "encoding": "none", + "x": 1640, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "fe81be99.6859e8", + "type": "json", + "z": "ff9251a5.9c5e18", + "name": "config.json", + "property": "payload", + "action": "str", + "pretty": true, + "x": 1410, + "y": 160, + "wires": [ + [ + "a5f18550.68466" + ] + ] + }, + { + "id": "b24cc280.5a59b", + "type": "file in", + "z": "ff9251a5.9c5e18", + "name": "", + "filename": "/home/pi/PlanktonScope/config.json", + "format": "utf8", + "chunk": false, + "sendError": false, + "encoding": "none", + "x": 360, + "y": 80, + "wires": [ + [ + "11e5237b.e558c5" + ] + ], + "info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n" + }, + { + "id": "4c6084c.1b7bb7c", + "type": "inject", + "z": "ff9251a5.9c5e18", + "name": "on_load", + "topic": "", + "payload": "", + "payloadType": "date", + "repeat": "", + "crontab": "", + "once": true, + "onceDelay": 0.1, + "x": 120, + "y": 80, + "wires": [ + [ + "b24cc280.5a59b", + "845bb10c.d99208", + "a01c8373.701628" + ] + ], + "info": "# PlanktonScope Help\nWhen the **Pi** is booting, **Node-RED** will be initiated and this node will be activated once and execute the following nodes." + }, + { + "id": "11e5237b.e558c5", + "type": "json", + "z": "ff9251a5.9c5e18", + "name": "config.json", + "property": "payload", + "action": "", + "pretty": false, + "x": 610, + "y": 80, + "wires": [ + [ + "9dc8498a.4a36b", + "9b67b810.97a618", + "32282348.35c09c", + "fe7c0e45.ee983", + "3e6ceaa0.5fad56", + "9e577327.d9a1f", + "c50792f5.6b5148" + ] + ] + }, + { + "id": "f72f54db.590c9", + "type": "function", + "z": "ff9251a5.9c5e18", + "name": "set global", + "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 1080, + "y": 80, + "wires": [ + [ + "45482528.43f93c" + ] + ] + }, + { + "id": "2372125a.7f69d6", + "type": "rpi-gpio out", + "z": "ff9251a5.9c5e18", + "name": "", + "pin": "40", + "set": "", + "level": "0", + "freq": "", + "out": "out", + "x": 440, + "y": 120, + "wires": [] + }, + { + "id": "bae08e6f.11bc28", + "type": "ui_template", + "z": "ff9251a5.9c5e18", + "group": "dc721eb.9ef51e", + "name": "Stream Pi Camera", + "order": 1, + "width": 24, + "height": 11, + "format": "
", + "storeOutMessages": true, + "fwdInMessages": true, + "templateScope": "local", + "x": 850, + "y": 320, + "wires": [ + [] + ] + }, + { + "id": "845bb10c.d99208", + "type": "function", + "z": "ff9251a5.9c5e18", + "name": "init LED", + "func": "msg.payload=1;\nreturn msg;", + "outputs": 1, + "noerr": 0, + "x": 280, + "y": 120, + "wires": [ + [ + "2372125a.7f69d6" + ] + ] + }, + { + "id": "9dc8498a.4a36b", + "type": "subflow:efeebffd.34c7e", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 830, + "y": 80, + "wires": [ + [ + "f72f54db.590c9" + ] + ] + }, + { + "id": "9e577327.d9a1f", + "type": "subflow:5c516299.73e054", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 846, + "y": 242, + "wires": [ + [ + "f72f54db.590c9" + ] + ] + }, + { + "id": "c50792f5.6b5148", + "type": "subflow:626459d2.f9c98", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 846, + "y": 282, + "wires": [ + [ + "f72f54db.590c9" + ] + ] + }, + { + "id": "9b67b810.97a618", + "type": "subflow:6ca1a253.126bb4", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 840, + "y": 120, + "wires": [ + [ + "f72f54db.590c9" + ], + [ + "45482528.43f93c" + ] + ] + }, + { + "id": "32282348.35c09c", + "type": "subflow:b45c6fb6.f6dfa8", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 820, + "y": 160, + "wires": [ + [ + "f72f54db.590c9" + ], + [ + "45482528.43f93c" + ] + ] + }, + { + "id": "8e1d0d8d.fc54d8", + "type": "subflow:fbe9590f.bd63b8", + "z": "ff9251a5.9c5e18", + "name": "System commands", + "env": [], + "x": 850, + "y": 500, + "wires": [] + }, + { + "id": "f8a906b3.a2c81", + "type": "subflow:9882c53a.0ccc8", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 320, + "y": 280, + "wires": [] + }, + { + "id": "b1be7e1e.9ec3c8", + "type": "subflow:a8ad6dec.1a393", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 850, + "y": 420, + "wires": [] + }, + { + "id": "fe7c0e45.ee983", + "type": "subflow:5a287804.a10e2", + "z": "ff9251a5.9c5e18", + "name": "process metadata", + "env": [], + "x": 830, + "y": 200, + "wires": [ + [ + "f72f54db.590c9" + ] + ] + }, + { + "id": "3e6ceaa0.5fad56", + "type": "subflow:863e8384.56889", + "z": "ff9251a5.9c5e18", + "name": "Acquisition inputs", + "env": [], + "x": 836, + "y": 362, + "wires": [ + [ + "f72f54db.590c9" + ] + ], + "icon": "node-red-dashboard/ui_switch.png" + }, + { + "id": "a01c8373.701628", + "type": "subflow:c10e968b.87e488", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 300, + "y": 200, + "wires": [] + }, + { + "id": "1924ce1c.0459f2", + "type": "subflow:c1d3ff7c.4384f", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 290, + "y": 240, + "wires": [] + }, + { + "id": "d3892f94.428a28", + "type": "subflow:bba19d97.b32b1", + "z": "ff9251a5.9c5e18", + "name": "", + "env": [], + "x": 850, + "y": 460, + "wires": [] + }, + { + "id": "e73525a.1103158", + "type": "ui_switch", + "z": "ff9251a5.9c5e18", + "name": "", + "label": "LED", + "tooltip": "", + "group": "9c86b3b7.54841", + "order": 10, + "width": 0, + "height": 0, + "passthru": true, + "decouple": "false", + "topic": "", + "style": "", + "onvalue": "true", + "onvalueType": "bool", + "onicon": "", + "oncolor": "", + "offvalue": "false", + "offvalueType": "bool", + "officon": "", + "offcolor": "", + "x": 270, + "y": 160, + "wires": [ + [ + "2372125a.7f69d6" + ] + ] + }, + { + "id": "be37d12f.0898f", + "type": "file", + "z": "c1d3ff7c.4384f", + "name": "", + "filename": "/home/pi/PlanktonScope/script/main.py", + "appendNewline": false, + "createDir": true, + "overwriteFile": "true", + "encoding": "none", + "x": 530, + "y": 100, + "wires": [ + [ + "23f3e613.20ad82" + ] + ] + }, + { + "id": "49e31e85.7ac51", + "type": "template", + "z": "c1d3ff7c.4384f", + "name": "main.py", + "field": "payload", + "fieldType": "msg", + "format": "python", + "syntax": "plain", + "template": "################################################################################\n#Actuator Libraries\n################################################################################\n\n#Library for exchaning messages with Node-RED\nimport paho.mqtt.client as mqtt\n\n#Library to control the PiCamera\nfrom picamera import PiCamera\n\n#Libraries to control the steppers for focusing and pumping\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\n\n#Library to send command over I2C for the light module on the fan\nimport smbus\n\n################################################################################\n#Practical Libraries\n################################################################################\n\n#Library to get date and time for folder name and filename\nfrom datetime import datetime, timedelta\n\n#Library to be able to sleep for a duration\nfrom time import sleep\n\n#Libraries manipulate json format, execute bash commands\nimport json, shutil, os, subprocess\n\n################################################################################\n#Morphocut Libraries\n################################################################################\n\nfrom skimage.util import img_as_ubyte\nfrom morphocut import Call\nfrom morphocut.contrib.ecotaxa import EcotaxaWriter\nfrom morphocut.contrib.zooprocess import CalculateZooProcessFeatures\nfrom morphocut.core import Pipeline\nfrom morphocut.file import Find\nfrom morphocut.image import (ExtractROI,\n FindRegions,\n ImageReader,\n ImageWriter,\n RescaleIntensity,\n RGB2Gray\n)\nfrom morphocut.stat import RunningMedian\nfrom morphocut.str import Format\nfrom morphocut.stream import TQDM, Enumerate, FilterVariables\n\n################################################################################\n#Other image processing Libraries\n################################################################################\n\nfrom skimage.feature import canny\nfrom skimage.color import rgb2gray, label2rgb\nfrom skimage.morphology import disk\nfrom skimage.morphology import erosion, dilation, closing\nfrom skimage.measure import label, regionprops\nimport cv2\n\n################################################################################\n#Streaming PiCamera over server\n################################################################################\nimport io\nimport picamera\nimport logging\nimport socketserver\nfrom threading import Condition\nfrom http import server\nimport threading\n\n################################################################################\n#Creation of the webpage containing the PiCamera Streaming\n################################################################################\n\nPAGE=\"\"\"\\\n\n\nPlanktonScope v2 | PiCamera Streaming\n\n\n\n\n\n\"\"\"\n\n################################################################################\n#Classes for the PiCamera Streaming\n################################################################################\n\nclass StreamingOutput(object):\n def __init__(self):\n self.frame = None\n self.buffer = io.BytesIO()\n self.condition = Condition()\n\n def write(self, buf):\n if buf.startswith(b'\\xff\\xd8'):\n # New frame, copy the existing buffer's content and notify all\n # clients it's available\n self.buffer.truncate()\n with self.condition:\n self.frame = self.buffer.getvalue()\n self.condition.notify_all()\n self.buffer.seek(0)\n return self.buffer.write(buf)\n\nclass StreamingHandler(server.BaseHTTPRequestHandler):\n def do_GET(self):\n if self.path == '/':\n self.send_response(301)\n self.send_header('Location', '/index.html')\n self.end_headers()\n elif self.path == '/index.html':\n content = PAGE.encode('utf-8')\n self.send_response(200)\n self.send_header('Content-Type', 'text/html')\n self.send_header('Content-Length', len(content))\n self.end_headers()\n self.wfile.write(content)\n elif self.path == '/stream.mjpg':\n self.send_response(200)\n self.send_header('Age', 0)\n self.send_header('Cache-Control', 'no-cache, private')\n self.send_header('Pragma', 'no-cache')\n self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')\n self.end_headers()\n try:\n while True:\n with output.condition:\n output.condition.wait()\n frame = output.frame\n self.wfile.write(b'--FRAME\\r\\n')\n self.send_header('Content-Type', 'image/jpeg')\n self.send_header('Content-Length', len(frame))\n self.end_headers()\n self.wfile.write(frame)\n self.wfile.write(b'\\r\\n')\n except Exception as e:\n logging.warning(\n 'Removed streaming client %s: %s',\n self.client_address, str(e))\n else:\n self.send_error(404)\n self.end_headers()\n\nclass StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):\n allow_reuse_address = True\n daemon_threads = True\n\n################################################################################\n#MQTT core functions\n################################################################################\n\n#Run this function in order to connect to the client (Node-RED)\ndef on_connect(client, userdata, flags, rc):\n #Print when connected\n print(\"Connected! - \" + str(rc))\n #When connected, run subscribe()\n client.subscribe(\"actuator/#\")\n #Turn green the light module\n rgb(0,255,0)\n\n#Run this function in order to subscribe to all the topics begining by actuator\ndef on_subscribe(client, obj, mid, granted_qos):\n #Print when subscribed\n print(\"Subscribed! - \"+str(mid)+\" \"+str(granted_qos))\n\n#Run this command when Node-RED is sending a message on the subscribed topic\ndef on_message(client, userdata, msg):\n #Print the topic and the message\n print(msg.topic+\" \"+str(msg.qos)+\" \"+str(msg.payload))\n #Update the global variables command, args and counter\n global command\n global args\n global counter\n #Parse the topic to find the command. ex : actuator/pump -> pump\n command=msg.topic.split(\"/\")[1]\n #Decode the message to find the arguments\n args=str(msg.payload.decode())\n #Reset the counter to 0\n counter=0\n\n################################################################################\n#LEDs Actuation\n################################################################################\ndef rgb(R,G,B):\n #Update LED n1\n bus.write_byte_data(0x0d, 0x00, 0)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n2\n bus.write_byte_data(0x0d, 0x00, 1)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n3\n bus.write_byte_data(0x0d, 0x00, 2)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update the I2C Bus in order to really update the LEDs new values\n cmd=\"i2cdetect -y 1\"\n subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)\n\n################################################################################\n#Init function - executed only once\n################################################################################\n\n#define the bus used to actuate the light module on the fan\nbus = smbus.SMBus(1)\n\n#define the names for the 2 exsting steppers\nkit = MotorKit()\npump_stepper = kit.stepper1\nfocus_stepper = kit.stepper2\n#Make sure the steppers are release and do not use any power\npump_stepper.release()\nfocus_stepper.release()\n\n#Precise the settings of the PiCamera\ncamera = PiCamera()\ncamera.resolution = (3280, 2464)\ncamera.iso = 60\ncamera.shutter_speed = 500\ncamera.exposure_mode = 'fixedfps'\n\n#Declare the global variables command, args and counter\ncommand = ''\nargs = ''\ncounter=''\n\n#MQTT Client functions definition\nclient = mqtt.Client()\nclient.connect(\"192.168.4.1\",1883,60)\nclient.on_connect = on_connect\nclient.on_subscribe = on_subscribe\nclient.on_message = on_message\nclient.loop_start()\n\n################################################################################\n#Definition of the few important metadata\n################################################################################\n\nlocal_metadata = {\n \"process_datetime\": datetime.now(),\n \"acq_camera_resolution\" : camera.resolution,\n \"acq_camera_iso\" : camera.iso,\n \"acq_camera_shutter_speed\" : camera.shutter_speed\n}\n\n#Read the content of config.json containing the metadata defined on Node-RED\nconfig_json = open('/home/pi/PlanktonScope/config.json','r')\nnode_red_metadata = json.loads(config_json.read())\n\n#Concat the local metadata and the metadata from Node-RED\nglobal_metadata = {**local_metadata, **node_red_metadata}\n\n#Define the name of the .zip file that will contain the images and the .tsv table for EcoTaxa\narchive_fn = os.path.join(\"/home/pi/PlanktonScope/\",\"export\", \"ecotaxa_export.zip\")\n\n################################################################################\n#MorphoCut Script\n################################################################################\n\n#Define processing pipeline\nwith Pipeline() as p:\n\n #Recursively find .jpg files in import_path.\n #Sort to get consective frames.\n abs_path = Find(\"/home/pi/PlanktonScope/tmp\", [\".jpg\"], sort=True, verbose=True)\n\n #Extract name from abs_path\n name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n #Read image\n img = ImageReader(abs_path)\n\n #Show progress bar for frames\n TQDM(Format(\"Frame {name}\", name=name))\n\n #Apply running median to approximate the background image\n flat_field = RunningMedian(img, 5)\n\n #Correct image\n img = img / flat_field\n\n #Rescale intensities and convert to uint8 to speed up calculations\n img = RescaleIntensity(img, in_range=(0, 1.1), dtype=\"uint8\")\n\n #Filter variable to reduce memory load\n FilterVariables(name,img)\n\n #Save cleaned images\n #frame_fn = Format(os.path.join(\"/home/pi/PlanktonScope/tmp\",\"CLEAN\", \"{name}.jpg\"), name=name)\n #ImageWriter(frame_fn, img)\n\n #Convert image to uint8 gray\n img_gray = RGB2Gray(img)\n\n #?\n img_gray = Call(img_as_ubyte, img_gray)\n\n #Canny edge detection using OpenCV\n img_canny = Call(cv2.Canny, img_gray, 50,100)\n\n #Dilate using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)\n\n #Close using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))\n img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)\n\n #Erode using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n mask = Call(cv2.erode, img_close, kernel, iterations=2)\n\n #Find objects\n regionprops = FindRegions(\n mask, img_gray, min_area=1000, padding=10, warn_empty=name\n )\n\n #Set the LEDs as Purple\n Call(rgb, 255,0,255)\n\n # For an object, extract a vignette/ROI from the image\n roi_orig = ExtractROI(img, regionprops, bg_color=255)\n\n # Generate an object identifier\n i = Enumerate()\n\n #Call(print,i)\n\n #Define the ID of each object\n object_id = Format(\"{name}_{i:d}\", name=name, i=i)\n\n #Call(print,object_id)\n\n #Define the name of each object\n object_fn = Format(os.path.join(\"/home/pi/PlanktonScope/\",\"OBJECTS\", \"{name}.jpg\"), name=object_id)\n\n #Save the image of the object with its name\n ImageWriter(object_fn, roi_orig)\n\n #Calculate features. The calculated features are added to the global_metadata.\n #Returns a Variable representing a dict for every object in the stream.\n meta = CalculateZooProcessFeatures(\n regionprops, prefix=\"object_\", meta=global_metadata\n )\n\n #Get all the metadata\n json_meta = Call(json.dumps,meta, sort_keys=True, default=str)\n\n #Publish the json containing all the metadata to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/metric\", json_meta)\n\n #Add object_id to the metadata dictionary\n meta[\"object_id\"] = object_id\n\n #Generate object filenames\n orig_fn = Format(\"{object_id}.jpg\", object_id=object_id)\n\n #Write objects to an EcoTaxa archive:\n #roi image in original color, roi image in grayscale, metadata associated with each object\n EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)\n\n #Progress bar for objects\n TQDM(Format(\"Object {object_id}\", object_id=object_id))\n\n #Publish the object_id to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/object_id\", object_id)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n################################################################################\n#While loop for capting commands from Node-RED\n################################################################################\n\noutput = StreamingOutput()\naddress = ('192.168.4.1', 8000)\nserver = StreamingServer(address, StreamingHandler)\nthreading.Thread(target=server.serve_forever).start()\ncamera.start_recording(output, format='mjpeg', resize=(640, 480))\n\nwhile True:\n\n ############################################################################\n #Pump Event\n ############################################################################\n\n #If the command is \"pump\"\n if (command==\"pump\"):\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get delay (in between steps) from the different received arguments\n delay=float(args.split(\" \")[1])\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[2])\n\n #Print status\n print(\"The pump has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the pump\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n #Actuate the pump for one step in the right direction\n pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)\n\n #Increment the counter\n counter+=1\n\n #Wait during the delay to pump at the right flowrate\n sleep(delay)\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pumping is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"pump\":\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pump has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Focus Event\n ############################################################################\n\n #If the command is \"focus\"\n elif (command==\"focus\"):\n\n #Set the LEDs as Yellow\n rgb(255,255,0)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Print status\n print(\"The focus has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the focus\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n #Actuate the focus for one microstep in the right direction\n focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)\n\n #Increment the counter\n counter+=1\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The focusing is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"focus\":\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The stage has been interrompted.\")\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Image Event\n ############################################################################\n\n elif (command==\"image\"):\n \n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Will do my best dude\");\n\n #Get duration to wait before an image from the different received arguments\n sleep_before=int(args.split(\" \")[0])\n\n #Get number of step in between two images from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Get the number of frames to image from the different received arguments\n nb_frame=int(args.split(\" \")[2])\n\n #Get the segmentation status (true/false) from the different received arguments\n segmentation=str(args.split(\" \")[3])\n\n #Sleep a duration before to start acquisition\n sleep(sleep_before)\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Start\");\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump duing a given number of steps (in between each image)\n for i in range(nb_step):\n\n #If the command is still image - pump a defined nb of steps\n if (command==\"image\"):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #If the command isn't image anymore - break\n else:\n\n break\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n while True:\n\n #Set the LEDs as Cyan\n rgb(0,255,255)\n\n #Increment the counter\n counter+=1\n\n #Get datetime\n datetime_tmp=datetime.now().strftime(\"%H_%M_%S_%f\")\n\n #Print datetime\n print(datetime_tmp)\n\n #Define the filename of the image\n filename = os.path.join(\"/home/pi/PlanktonScope/tmp\",datetime_tmp+\".jpg\")\n\n #Capture an image with the proper filename\n camera.capture(filename)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Publish the name of the image to via MQTT to Node-RED\n\n client.publish(\"receiver/image\", datetime_tmp+\".jpg has been imaged.\");\n \n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump during a given nb of steps\n for i in range(nb_step):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #Wait a fixed delay which set the framerate as < than 2 imag/sec\n sleep(0.5)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n ####################################################################\n #If counter reach the number of frame, break\n if(counter>nb_frame):\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Completed\");\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n if(segmentation == \"True\"):\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Start\");\n\n #Start the MorphoCut Pipeline\n p.run()\n\n #remove directory\n #shutil.rmtree(import_path)\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Completed\");\n\n #Set the LEDs as White\n rgb(255,255,255)\n\n #cmd = os.popen(\"rm -rf /home/pi/PlanktonScope/tmp/*.jpg\")\n\n #Let it happen\n sleep(1)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #End if(segmentation == \"True\"):\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n \n #Set the LEDs as Green\n rgb(0,255,255)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"image\", break this while loop\n if command!=\"image\":\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The imaging has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n else:\n #Set the LEDs as Black\n rgb(0,0,0)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n #Set the LEDs as White\n rgb(255,255,255)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n", + "output": "str", + "x": 300, + "y": 100, + "wires": [ + [ + "be37d12f.0898f" + ] + ] + }, + { + "id": "f9705bc.3d322a8", + "type": "ui_switch", + "z": "863e8384.56889", + "name": "custom_segmentation", + "label": "Realize the segmentation", + "tooltip": "", + "group": "48649115.fcd01", + "order": 6, + "width": 0, + "height": 0, + "passthru": true, + "decouple": "false", + "topic": "custom_segmentation", + "style": "", + "onvalue": "True", + "onvalueType": "str", + "onicon": "", + "oncolor": "", + "offvalue": "False", + "offvalueType": "str", + "officon": "", + "offcolor": "", + "x": 520, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "2de12b49.050f44", + "type": "debug", + "z": "c1d3ff7c.4384f", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 1230, + "y": 200, + "wires": [] + }, + { + "id": "5079cccb.298d14", + "type": "exec", + "z": "c1d3ff7c.4384f", + "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 430, + "y": 40, + "wires": [ + [ + "c47c2122.5eea38" + ], + [], + [] + ] + }, + { + "id": "c47c2122.5eea38", + "type": "exec", + "z": "c1d3ff7c.4384f", + "command": "kill", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 910, + "y": 40, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "197215b2.165f22", + "type": "delay", + "z": "c1d3ff7c.4384f", + "name": "", + "pauseType": "delay", + "timeout": "1", + "timeoutUnits": "seconds", + "rate": "1", + "nbRateUnits": "1", + "rateUnits": "second", + "randomFirst": "1", + "randomLast": "5", + "randomUnits": "seconds", + "drop": false, + "x": 160, + "y": 100, + "wires": [ + [ + "49e31e85.7ac51" + ] + ] + }, + { + "id": "589fbae2.8ff914", + "type": "debug", + "z": "a8ad6dec.1a393", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 240, + "y": 140, + "wires": [] } ] From ea602ede24e49f0d456df0cb97ead3dea531803d Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:27:49 +0200 Subject: [PATCH 15/17] Update flows.json --- flows/flows.json | 3139 +++++++++++++++++++--------------------------- 1 file changed, 1286 insertions(+), 1853 deletions(-) diff --git a/flows/flows.json b/flows/flows.json index 84e7f3f..4106b23 100644 --- a/flows/flows.json +++ b/flows/flows.json @@ -1,13 +1,6 @@ [ { - "id": "ff9251a5.9c5e18", - "type": "tab", - "label": "Main", - "disabled": false, - "info": "" - }, - { - "id": "bba19d97.b32b1", + "id": "97600dff.93378", "type": "subflow", "name": "Acquisition actuation", "info": "", @@ -18,1139 +11,9 @@ "color": "#A6BBCF" }, { - "id": "c1d3ff7c.4384f", - "type": "subflow", - "name": "MQQT Cmds", - "info": "", - "category": "", - "in": [ - { - "x": 40, - "y": 40, - "wires": [ - { - "id": "5079cccb.298d14" - }, - { - "id": "197215b2.165f22" - } - ] - } - ], - "out": [], - "env": [], - "color": "#DDAA99" - }, - { - "id": "c10e968b.87e488", - "type": "subflow", - "name": "Datetime update", - "info": "", - "category": "", - "in": [ - { - "x": 140, - "y": 80, - "wires": [ - { - "id": "93b9f3cd.759688" - } - ] - } - ], - "out": [], - "env": [], - "color": "#DDAA99", - "icon": "font-awesome/fa-clock-o" - }, - { - "id": "863e8384.56889", - "type": "subflow", - "name": "Acquisition inputs", - "info": "", - 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"width": "24", - "collapse": false - }, - { - "id": "2b97fe34.a699fa", - "type": "ui_tab", - "z": "", - "name": "GUI", - "icon": "fa-eyedropper", - "order": 2, - "disabled": false, - "hidden": false - }, - { - "id": "dc721eb.9ef51e", - "type": "ui_group", - "z": "", - "name": "Streaming camera", - "tab": "2b97fe34.a699fa", - "order": 3, - "disp": true, - "width": 24, - "collapse": false - }, - { - "id": "853e90d6.4afd1", + "id": "604c996b.1a8428", "type": "ui_button", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "", "group": "cdb72118.692578", "order": 1, @@ -1169,14 +32,14 @@ "y": 100, "wires": [ [ - "6e46e66c.654ff8" + "b854ad48.5869e8" ] ] }, { - "id": "6e46e66c.654ff8", + "id": "b854ad48.5869e8", "type": "function", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "image.js", "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar sleep_before= global.get(\"custom_sleep_before\");\nvar nb_step= global.get(\"custom_nb_step\");\nvar nb_frame= global.get(\"custom_nb_frame\");\nvar segmentation= global.get(\"custom_segmentation\");\n\nif (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Duration before the acquisition\";\n \n}else if (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of step in between two frames\";\n \n}else if (nb_frame === undefined || nb_frame === \"\" || nb_frame === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of image to save\";\n \n}else if (segmentation === undefined || segmentation === \"\" || segmentation === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Realize or not the segmentation\";\n \n}else {\n nb_frame=nb_frame-1\n \n msg.payload=sleep_before+' '+nb_step+' '+nb_frame+' '+segmentation;\n}\nreturn msg;", "outputs": 1, @@ -1185,15 +48,15 @@ "y": 100, "wires": [ [ - "5a37b9e6.6e3e58" + "84505b75.883a48" ] ], "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" }, { - "id": "5a37b9e6.6e3e58", + "id": "84505b75.883a48", "type": "switch", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "", "property": "topic", "propertyType": "msg", @@ -1216,17 +79,17 @@ "y": 100, "wires": [ [ - "75233be8.98e6f4" + "715a8f15.dc211" ], [ - "bee35f80.112d" + "3173806b.bb0c7" ] ] }, { - "id": "bee35f80.112d", + "id": "3173806b.bb0c7", "type": "ui_toast", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "position": "dialog", "displayTime": "3", "highlight": "", @@ -1244,9 +107,9 @@ ] }, { - "id": "75233be8.98e6f4", + "id": "715a8f15.dc211", "type": "mqtt out", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "", "topic": "", "qos": "", @@ -1257,9 +120,9 @@ "wires": [] }, { - "id": "75d00421.d31e1c", + "id": "ed689faa.3a3e08", "type": "ui_button", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "Stop Acquisition", "group": "cdb72118.692578", "order": 2, @@ -1278,14 +141,14 @@ "y": 140, "wires": [ [ - "f2ce7a07.d3eff8" + "f6bd3440.60d5a" ] ] }, { - "id": "f2ce7a07.d3eff8", + "id": "f6bd3440.60d5a", "type": "mqtt out", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "", "topic": "", "qos": "", @@ -1296,9 +159,9 @@ "wires": [] }, { - "id": "977270e2.b70738", + "id": "3b827bf5.c7bc64", "type": "mqtt out", - "z": "bba19d97.b32b1", + "z": "97600dff.93378", "name": "", "topic": "", "qos": "", @@ -1309,9 +172,44 @@ "wires": [] }, { - "id": "23f3e613.20ad82", + "id": "cdb72118.692578", + "type": "ui_group", + "z": "", + "name": "Acquisition actuation", + "tab": "2b97fe34.a699fa", + "order": 10, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "e8320d42.9a3ad8", + "type": "subflow", + "name": "MQQT Cmds", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "cf9e02a2.3feff" + }, + { + "id": "18da28e6.7b000f" + } + ] + } + ], + "out": [], + "env": [], + "color": "#DDAA99" + }, + { + "id": "a7301ba5.d56d48", "type": "exec", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "command": "python3.7 /home/pi/PlanktonScope/script/main.py", "addpay": false, "append": "", @@ -1323,23 +221,23 @@ "y": 140, "wires": [ [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ], [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ], [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ] ] }, { - "id": "1ef92011.66439", + "id": "62b9a3b1.74dbc4", "type": "exec", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", "addpay": false, "append": "", @@ -1351,16 +249,16 @@ "y": 200, "wires": [ [ - "c1fd2bf6.fa7198" + "66fb9ed2.8ecd3" ], [], [] ] }, { - "id": "c1fd2bf6.fa7198", + "id": "66fb9ed2.8ecd3", "type": "exec", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "command": "kill", "addpay": true, "append": "", @@ -1372,23 +270,23 @@ "y": 200, "wires": [ [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ], [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ], [ - "87b835dc.107c6", - "2de12b49.050f44" + "87558394.4e589", + "a11158b1.b7649" ] ] }, { - "id": "9a6e378b.5ea938", + "id": "5df162d7.08eb34", "type": "ui_button", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "name": "", "group": "9c86b3b7.54841", "order": 9, @@ -1407,14 +305,14 @@ "y": 200, "wires": [ [ - "1ef92011.66439" + "62b9a3b1.74dbc4" ] ] }, { - "id": "e74e7b3d.2ba678", + "id": "d16389e5.3bc67", "type": "ui_button", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "name": "", "group": "9c86b3b7.54841", "order": 10, @@ -1433,14 +331,14 @@ "y": 140, "wires": [ [ - "23f3e613.20ad82" + "a7301ba5.d56d48" ] ] }, { - "id": "87b835dc.107c6", + "id": "87558394.4e589", "type": "ui_toast", - "z": "c1d3ff7c.4384f", + "z": "e8320d42.9a3ad8", "position": "top right", "displayTime": "3", "highlight": "", @@ -1456,9 +354,146 @@ "wires": [] }, { - "id": "b60669a0.b480d8", + "id": "500abffa.c7a788", + "type": "file", + "z": "e8320d42.9a3ad8", + "name": "", + "filename": "/home/pi/PlanktonScope/script/main.py", + "appendNewline": false, + "createDir": true, + "overwriteFile": "true", + "encoding": "none", + "x": 530, + "y": 100, + "wires": [ + [ + "a7301ba5.d56d48" + ] + ] + }, + { + "id": "985c65de.0801b", + "type": "template", + "z": "e8320d42.9a3ad8", + "name": "main.py", + "field": "payload", + "fieldType": "msg", + "format": "python", + "syntax": "plain", + "template": "################################################################################\n#Actuator Libraries\n################################################################################\n\n#Library for exchaning messages with Node-RED\nimport paho.mqtt.client as mqtt\n\n#Library to control the PiCamera\nfrom picamera import PiCamera\n\n#Libraries to control the steppers for focusing and pumping\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\n\n#Library to send command over I2C for the light module on the fan\nimport smbus\n\n################################################################################\n#Practical Libraries\n################################################################################\n\n#Library to get date and time for folder name and filename\nfrom datetime import datetime, timedelta\n\n#Library to be able to sleep for a duration\nfrom time import sleep\n\n#Libraries manipulate json format, execute bash commands\nimport json, shutil, os, subprocess\n\n################################################################################\n#Morphocut Libraries\n################################################################################\n\nfrom skimage.util import img_as_ubyte\nfrom morphocut import Call\nfrom morphocut.contrib.ecotaxa import EcotaxaWriter\nfrom morphocut.contrib.zooprocess import CalculateZooProcessFeatures\nfrom morphocut.core import Pipeline\nfrom morphocut.file import Find\nfrom morphocut.image import (ExtractROI,\n FindRegions,\n ImageReader,\n ImageWriter,\n RescaleIntensity,\n RGB2Gray\n)\nfrom morphocut.stat import RunningMedian\nfrom morphocut.str import Format\nfrom morphocut.stream import TQDM, Enumerate, FilterVariables\n\n################################################################################\n#Other image processing Libraries\n################################################################################\n\nfrom skimage.feature import canny\nfrom skimage.color import rgb2gray, label2rgb\nfrom skimage.morphology import disk\nfrom skimage.morphology import erosion, dilation, closing\nfrom skimage.measure import label, regionprops\nimport cv2\n\n################################################################################\n#Streaming PiCamera over server\n################################################################################\nimport io\nimport picamera\nimport logging\nimport socketserver\nfrom threading import Condition\nfrom http import server\nimport threading\n\n################################################################################\n#Creation of the webpage containing the PiCamera Streaming\n################################################################################\n\nPAGE=\"\"\"\\\n\n\nPlanktonScope v2 | PiCamera Streaming\n\n\n\n\n\n\"\"\"\n\n################################################################################\n#Classes for the PiCamera Streaming\n################################################################################\n\nclass StreamingOutput(object):\n def __init__(self):\n self.frame = None\n self.buffer = io.BytesIO()\n self.condition = Condition()\n\n def write(self, buf):\n if buf.startswith(b'\\xff\\xd8'):\n # New frame, copy the existing buffer's content and notify all\n # clients it's available\n self.buffer.truncate()\n with self.condition:\n self.frame = self.buffer.getvalue()\n self.condition.notify_all()\n self.buffer.seek(0)\n return self.buffer.write(buf)\n\nclass StreamingHandler(server.BaseHTTPRequestHandler):\n def do_GET(self):\n if self.path == '/':\n self.send_response(301)\n self.send_header('Location', '/index.html')\n self.end_headers()\n elif self.path == '/index.html':\n content = PAGE.encode('utf-8')\n self.send_response(200)\n self.send_header('Content-Type', 'text/html')\n self.send_header('Content-Length', len(content))\n self.end_headers()\n self.wfile.write(content)\n elif self.path == '/stream.mjpg':\n self.send_response(200)\n self.send_header('Age', 0)\n self.send_header('Cache-Control', 'no-cache, private')\n self.send_header('Pragma', 'no-cache')\n self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')\n self.end_headers()\n try:\n while True:\n with output.condition:\n output.condition.wait()\n frame = output.frame\n self.wfile.write(b'--FRAME\\r\\n')\n self.send_header('Content-Type', 'image/jpeg')\n self.send_header('Content-Length', len(frame))\n self.end_headers()\n self.wfile.write(frame)\n self.wfile.write(b'\\r\\n')\n except Exception as e:\n logging.warning(\n 'Removed streaming client %s: %s',\n self.client_address, str(e))\n else:\n self.send_error(404)\n self.end_headers()\n\nclass StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):\n allow_reuse_address = True\n daemon_threads = True\n\n################################################################################\n#MQTT core functions\n################################################################################\n\n#Run this function in order to connect to the client (Node-RED)\ndef on_connect(client, userdata, flags, rc):\n #Print when connected\n print(\"Connected! - \" + str(rc))\n #When connected, run subscribe()\n client.subscribe(\"actuator/#\")\n #Turn green the light module\n rgb(0,255,0)\n\n#Run this function in order to subscribe to all the topics begining by actuator\ndef on_subscribe(client, obj, mid, granted_qos):\n #Print when subscribed\n print(\"Subscribed! - \"+str(mid)+\" \"+str(granted_qos))\n\n#Run this command when Node-RED is sending a message on the subscribed topic\ndef on_message(client, userdata, msg):\n #Print the topic and the message\n print(msg.topic+\" \"+str(msg.qos)+\" \"+str(msg.payload))\n #Update the global variables command, args and counter\n global command\n global args\n global counter\n #Parse the topic to find the command. ex : actuator/pump -> pump\n command=msg.topic.split(\"/\")[1]\n #Decode the message to find the arguments\n args=str(msg.payload.decode())\n #Reset the counter to 0\n counter=0\n\n################################################################################\n#LEDs Actuation\n################################################################################\ndef rgb(R,G,B):\n #Update LED n1\n bus.write_byte_data(0x0d, 0x00, 0)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n2\n bus.write_byte_data(0x0d, 0x00, 1)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n3\n bus.write_byte_data(0x0d, 0x00, 2)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update the I2C Bus in order to really update the LEDs new values\n cmd=\"i2cdetect -y 1\"\n subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)\n\n################################################################################\n#Init function - executed only once\n################################################################################\n\n#define the bus used to actuate the light module on the fan\nbus = smbus.SMBus(1)\n\n#define the names for the 2 exsting steppers\nkit = MotorKit()\npump_stepper = kit.stepper1\nfocus_stepper = kit.stepper2\n#Make sure the steppers are release and do not use any power\npump_stepper.release()\nfocus_stepper.release()\n\n#Precise the settings of the PiCamera\ncamera = PiCamera()\ncamera.resolution = (3280, 2464)\ncamera.iso = 60\ncamera.shutter_speed = 500\ncamera.exposure_mode = 'fixedfps'\n\n#Declare the global variables command, args and counter\ncommand = ''\nargs = ''\ncounter=''\n\n#MQTT Client functions definition\nclient = mqtt.Client()\nclient.connect(\"192.168.4.1\",1883,60)\nclient.on_connect = on_connect\nclient.on_subscribe = on_subscribe\nclient.on_message = on_message\nclient.loop_start()\n\n################################################################################\n#Definition of the few important metadata\n################################################################################\n\nlocal_metadata = {\n \"process_datetime\": datetime.now(),\n \"acq_camera_resolution\" : camera.resolution,\n \"acq_camera_iso\" : camera.iso,\n \"acq_camera_shutter_speed\" : camera.shutter_speed\n}\n\n#Read the content of config.json containing the metadata defined on Node-RED\nconfig_json = open('/home/pi/PlanktonScope/config.json','r')\nnode_red_metadata = json.loads(config_json.read())\n\n#Concat the local metadata and the metadata from Node-RED\nglobal_metadata = {**local_metadata, **node_red_metadata}\n\n#Define the name of the .zip file that will contain the images and the .tsv table for EcoTaxa\narchive_fn = os.path.join(\"/home/pi/PlanktonScope/\",\"export\", \"ecotaxa_export.zip\")\n\n################################################################################\n#MorphoCut Script\n################################################################################\n\n#Define processing pipeline\nwith Pipeline() as p:\n\n #Recursively find .jpg files in import_path.\n #Sort to get consective frames.\n abs_path = Find(\"/home/pi/PlanktonScope/tmp\", [\".jpg\"], sort=True, verbose=True)\n\n #Extract name from abs_path\n name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n #Read image\n img = ImageReader(abs_path)\n\n #Show progress bar for frames\n TQDM(Format(\"Frame {name}\", name=name))\n\n #Apply running median to approximate the background image\n flat_field = RunningMedian(img, 5)\n\n #Correct image\n img = img / flat_field\n\n #Rescale intensities and convert to uint8 to speed up calculations\n img = RescaleIntensity(img, in_range=(0, 1.1), dtype=\"uint8\")\n\n #Filter variable to reduce memory load\n FilterVariables(name,img)\n\n #Save cleaned images\n #frame_fn = Format(os.path.join(\"/home/pi/PlanktonScope/tmp\",\"CLEAN\", \"{name}.jpg\"), name=name)\n #ImageWriter(frame_fn, img)\n\n #Convert image to uint8 gray\n img_gray = RGB2Gray(img)\n\n #?\n img_gray = Call(img_as_ubyte, img_gray)\n\n #Canny edge detection using OpenCV\n img_canny = Call(cv2.Canny, img_gray, 50,100)\n\n #Dilate using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)\n\n #Close using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))\n img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)\n\n #Erode using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n mask = Call(cv2.erode, img_close, kernel, iterations=2)\n\n #Find objects\n regionprops = FindRegions(\n mask, img_gray, min_area=1000, padding=10, warn_empty=name\n )\n\n #Set the LEDs as Purple\n Call(rgb, 255,0,255)\n\n # For an object, extract a vignette/ROI from the image\n roi_orig = ExtractROI(img, regionprops, bg_color=255)\n\n # Generate an object identifier\n i = Enumerate()\n\n #Call(print,i)\n\n #Define the ID of each object\n object_id = Format(\"{name}_{i:d}\", name=name, i=i)\n\n #Call(print,object_id)\n\n #Define the name of each object\n object_fn = Format(os.path.join(\"/home/pi/PlanktonScope/\",\"OBJECTS\", \"{name}.jpg\"), name=object_id)\n\n #Save the image of the object with its name\n ImageWriter(object_fn, roi_orig)\n\n #Calculate features. The calculated features are added to the global_metadata.\n #Returns a Variable representing a dict for every object in the stream.\n meta = CalculateZooProcessFeatures(\n regionprops, prefix=\"object_\", meta=global_metadata\n )\n\n #Get all the metadata\n json_meta = Call(json.dumps,meta, sort_keys=True, default=str)\n\n #Publish the json containing all the metadata to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/metric\", json_meta)\n\n #Add object_id to the metadata dictionary\n meta[\"object_id\"] = object_id\n\n #Generate object filenames\n orig_fn = Format(\"{object_id}.jpg\", object_id=object_id)\n\n #Write objects to an EcoTaxa archive:\n #roi image in original color, roi image in grayscale, metadata associated with each object\n EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)\n\n #Progress bar for objects\n TQDM(Format(\"Object {object_id}\", object_id=object_id))\n\n #Publish the object_id to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/object_id\", object_id)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n################################################################################\n#While loop for capting commands from Node-RED\n################################################################################\n\noutput = StreamingOutput()\naddress = ('192.168.4.1', 8000)\nserver = StreamingServer(address, StreamingHandler)\nthreading.Thread(target=server.serve_forever).start()\ncamera.start_recording(output, format='mjpeg', resize=(640, 480))\n\nwhile True:\n\n ############################################################################\n #Pump Event\n ############################################################################\n\n #If the command is \"pump\"\n if (command==\"pump\"):\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get delay (in between steps) from the different received arguments\n delay=float(args.split(\" \")[1])\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[2])\n\n #Print status\n print(\"The pump has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the pump\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n #Actuate the pump for one step in the right direction\n pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)\n\n #Increment the counter\n counter+=1\n\n #Wait during the delay to pump at the right flowrate\n sleep(delay)\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pumping is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"pump\":\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pump has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Focus Event\n ############################################################################\n\n #If the command is \"focus\"\n elif (command==\"focus\"):\n\n #Set the LEDs as Yellow\n rgb(255,255,0)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Print status\n print(\"The focus has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the focus\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n #Actuate the focus for one microstep in the right direction\n focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)\n\n #Increment the counter\n counter+=1\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The focusing is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"focus\":\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The stage has been interrompted.\")\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Image Event\n ############################################################################\n\n elif (command==\"image\"):\n \n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Will do my best dude\");\n\n #Get duration to wait before an image from the different received arguments\n sleep_before=int(args.split(\" \")[0])\n\n #Get number of step in between two images from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Get the number of frames to image from the different received arguments\n nb_frame=int(args.split(\" \")[2])\n\n #Get the segmentation status (true/false) from the different received arguments\n segmentation=str(args.split(\" \")[3])\n\n #Sleep a duration before to start acquisition\n sleep(sleep_before)\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Start\");\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump duing a given number of steps (in between each image)\n for i in range(nb_step):\n\n #If the command is still image - pump a defined nb of steps\n if (command==\"image\"):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #If the command isn't image anymore - break\n else:\n\n break\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n while True:\n\n #Set the LEDs as Cyan\n rgb(0,255,255)\n\n #Increment the counter\n counter+=1\n\n #Get datetime\n datetime_tmp=datetime.now().strftime(\"%H_%M_%S_%f\")\n\n #Print datetime\n print(datetime_tmp)\n\n #Define the filename of the image\n filename = os.path.join(\"/home/pi/PlanktonScope/tmp\",datetime_tmp+\".jpg\")\n\n #Capture an image with the proper filename\n camera.capture(filename)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Publish the name of the image to via MQTT to Node-RED\n\n client.publish(\"receiver/image\", datetime_tmp+\".jpg has been imaged.\");\n \n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump during a given nb of steps\n for i in range(nb_step):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #Wait a fixed delay which set the framerate as < than 2 imag/sec\n sleep(0.5)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n ####################################################################\n #If counter reach the number of frame, break\n if(counter>nb_frame):\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Completed\");\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n if(segmentation == \"True\"):\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Start\");\n\n #Start the MorphoCut Pipeline\n p.run()\n\n #remove directory\n #shutil.rmtree(import_path)\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Completed\");\n\n #Set the LEDs as White\n rgb(255,255,255)\n\n #cmd = os.popen(\"rm -rf /home/pi/PlanktonScope/tmp/*.jpg\")\n\n #Let it happen\n sleep(1)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #End if(segmentation == \"True\"):\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n \n #Set the LEDs as Green\n rgb(0,255,255)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"image\", break this while loop\n if command!=\"image\":\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The imaging has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n else:\n #Set the LEDs as Black\n rgb(0,0,0)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n #Set the LEDs as White\n rgb(255,255,255)\n #Its just waiting to receive command from Node-RED\n sleep(1)\n", + "output": "str", + "x": 300, + "y": 100, + "wires": [ + [ + "500abffa.c7a788" + ] + ] + }, + { + "id": "a11158b1.b7649", + "type": "debug", + "z": "e8320d42.9a3ad8", + "name": "", + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 1230, + "y": 200, + "wires": [] + }, + { + "id": "cf9e02a2.3feff", "type": "exec", - "z": "c10e968b.87e488", + "z": "e8320d42.9a3ad8", + "command": "ps -ax | grep \"python3.7 /home/pi/PlanktonScope/script/main.py\"| head -1 | awk -F \" \" '{print$1}' ", + "addpay": false, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 430, + "y": 40, + "wires": [ + [ + "945415c5.01217" + ], + [], + [] + ] + }, + { + "id": "945415c5.01217", + "type": "exec", + "z": "e8320d42.9a3ad8", + "command": "kill", + "addpay": true, + "append": "", + "useSpawn": "false", + "timer": "", + "oldrc": false, + "name": "", + "x": 910, + "y": 40, + "wires": [ + [], + [], + [] + ] + }, + { + "id": "18da28e6.7b000f", + "type": "delay", + "z": "e8320d42.9a3ad8", + "name": "", + "pauseType": "delay", + "timeout": "1", + "timeoutUnits": "seconds", + "rate": "1", + "nbRateUnits": "1", + "rateUnits": "second", + "randomFirst": "1", + "randomLast": "5", + "randomUnits": "seconds", + "drop": false, + "x": 160, + "y": 100, + "wires": [ + [ + "985c65de.0801b" + ] + ] + }, + { + "id": "6384a5e.e34465c", + "type": "subflow", + "name": "Datetime update", + "info": "", + "category": "", + "in": [ + { + "x": 140, + "y": 80, + "wires": [ + { + "id": "42ffcda3.49c30c" + } + ] + } + ], + "out": [], + "env": [], + "color": "#DDAA99", + "icon": "font-awesome/fa-clock-o" + }, + { + "id": "e3824a97.8f2c3", + "type": "exec", + "z": "6384a5e.e34465c", "command": "sudo date -s", "addpay": true, "append": "", @@ -1475,9 +510,9 @@ ] }, { - "id": "68aace8d.6bf5", + "id": "a5a13db6.4c6958", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = new Date();\n//get weekday\nvar weekday = new Array(7);\nweekday[0] = \"Sun\";\nweekday[1] = \"Mon\";\nweekday[2] = \"Tue\";\nweekday[3] = \"Wed\";\nweekday[4] = \"Thu\";\nweekday[5] = \"Fri\";\nweekday[6] = \"Sat\";\nvar w = weekday[d.getUTCDay()];\n//get Month\nvar month = new Array(12);\nmonth[0] = \"Jan\";\nmonth[1] = \"Feb\";\nmonth[2] = \"Mar\";\nmonth[3] = \"Apr\";\nmonth[4] = \"May\";\nmonth[5] = \"Jun\";\nmonth[6] = \"Jul\";\nmonth[7] = \"Aug\";\nmonth[8] = \"Sep\";\nmonth[9] = \"Oct\";\nmonth[10] = \"Nov\";\nmonth[11] = \"Dec\";\nvar n = month[d.getUTCMonth()];\n \n//get day\nvar day = d.getUTCDay()\n\n//get Hours\nvar Hours = d.getUTCHours();\n//get Minutes\nvar Minutes = d.getUTCMinutes();\n//get Seconds\nvar Seconds = d.getUTCSeconds();\n//get FullYear\nvar FullYear = d.getUTCFullYear();\n\n//Thu Aug 09 2012 23:34:04 GMT+0200 (GMT+02:00)\n\n//Thu Aug 9 21:31:26 UTC 2012\n\n//msg.payload = \"Thu Aug 9 21:31:26 UTC 2012\"\n\nmsg.payload = '\"'+w+\" \"+n+\" \"+day+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+\" UTC \"+FullYear+'\"';\nreturn msg;", "outputs": 1, @@ -1486,14 +521,14 @@ "y": 40, "wires": [ [ - "a1db5dbb.32c998" + "bafb69f.a42ea18" ] ] }, { - "id": "a1db5dbb.32c998", + "id": "bafb69f.a42ea18", "type": "ui_template", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "group": "9c86b3b7.54841", "name": "", "order": 1, @@ -1510,9 +545,9 @@ ] }, { - "id": "b3b03af9.8edae8", + "id": "81f9cd4c.8540b", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_year", "label": "Year", "tooltip": "", @@ -1531,14 +566,14 @@ "y": 80, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "ed1f72c4.e136e", + "id": "274f25fc.9e61ba", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_month", "label": "Month", "tooltip": "", @@ -1557,14 +592,14 @@ "y": 120, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "be55a4d1.4d5fa8", + "id": "4ddcb673.905a", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_day", "label": "Day", "tooltip": "", @@ -1583,14 +618,14 @@ "y": 160, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "ee1e92f8.a01bb8", + "id": "248eee4c.238282", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_hour", "label": "Hour", "tooltip": "", @@ -1609,14 +644,14 @@ "y": 200, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "c532a0cd.b0a47", + "id": "a368c4b7.2dc4b8", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_minute", "label": "Minute", "tooltip": "", @@ -1635,14 +670,14 @@ "y": 240, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "5b200123.04ec98", + "id": "96cc9953.9496c8", "type": "ui_numeric", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "tmp_second", "label": "Second", "tooltip": "", @@ -1661,14 +696,14 @@ "y": 280, "wires": [ [ - "8de4b398.3c755" + "8f5a74df.0663f" ] ] }, { - "id": "d8f0f8d1.0550d", + "id": "d6240495.8429c", "type": "interval", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "interval", "interval": "1", "onstart": false, @@ -1680,14 +715,14 @@ "y": 40, "wires": [ [ - "68aace8d.6bf5" + "a5a13db6.4c6958" ] ] }, { - "id": "eb163e1c.a7b97", + "id": "e8d38dc0.c7e84", "type": "ui_button", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "group": "9c86b3b7.54841", "order": 8, @@ -1706,14 +741,14 @@ "y": 320, "wires": [ [ - "aa948c91.3895a" + "581f71d3.bde458" ] ] }, { - "id": "aa948c91.3895a", + "id": "581f71d3.bde458", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "update datetime", "func": "var FullYear= global.get(\"year\");\nvar Month= global.get(\"month\");\nvar day= global.get(\"day\");\nvar Hours= global.get(\"hour\");\nvar Minutes= global.get(\"minute\");\nvar Seconds= global.get(\"second\");\n\nmsg.payload = new Date();\n//get Month\nvar month = new Array(12);\nmonth[1] = \"Jan\";\nmonth[2] = \"Feb\";\nmonth[3] = \"Mar\";\nmonth[4] = \"Apr\";\nmonth[5] = \"May\";\nmonth[6] = \"Jun\";\nmonth[7] = \"Jul\";\nmonth[8] = \"Aug\";\nmonth[9] = \"Sep\";\nmonth[10] = \"Oct\";\nmonth[11] = \"Nov\";\nmonth[12] = \"Dec\";\nvar n = month[Month];\n \nmsg.payload = '\"'+day+\" \"+n+\" \"+FullYear+\" \"+Hours+\":\"+Minutes+\":\"+Seconds+'\"';\n\n\nreturn msg;", "outputs": 1, @@ -1722,15 +757,15 @@ "y": 320, "wires": [ [ - "3b7403cb.d33394", - "b60669a0.b480d8" + "6b023a67.faa104", + "e3824a97.8f2c3" ] ] }, { - "id": "8de4b398.3c755", + "id": "8f5a74df.0663f", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "set global", "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", "outputs": 1, @@ -1742,9 +777,9 @@ ] }, { - "id": "3b7403cb.d33394", + "id": "6b023a67.faa104", "type": "debug", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "active": true, "tosidebar": true, @@ -1756,9 +791,9 @@ "wires": [] }, { - "id": "315c5aa3.fdf5d6", + "id": "4ab089b9.1098", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCFullYear();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, @@ -1767,14 +802,14 @@ "y": 80, "wires": [ [ - "b3b03af9.8edae8" + "81f9cd4c.8540b" ] ] }, { - "id": "93b9f3cd.759688", + "id": "42ffcda3.49c30c", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = new Date();\nmsg.payload = d\nreturn msg;", "outputs": 1, @@ -1783,19 +818,19 @@ "y": 80, "wires": [ [ - "315c5aa3.fdf5d6", - "922cecc2.dc7f68", - "c2aa11f2.0fdee8", - "915b7162.7a73e", - "b57fe145.320d28", - "d3f45b98.f05a58" + "4ab089b9.1098", + "13529b2c.cb9d9d", + "c09bb768.0e7518", + "967b4488.670f08", + "3e3732d.273a04e", + "327729f0.afe466" ] ] }, { - "id": "922cecc2.dc7f68", + "id": "13529b2c.cb9d9d", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCMonth();\n\nmsg.payload = val+1;\nreturn msg;", "outputs": 1, @@ -1804,14 +839,14 @@ "y": 120, "wires": [ [ - "ed1f72c4.e136e" + "274f25fc.9e61ba" ] ] }, { - "id": "c2aa11f2.0fdee8", + "id": "c09bb768.0e7518", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCDay();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, @@ -1820,14 +855,14 @@ "y": 160, "wires": [ [ - "be55a4d1.4d5fa8" + "4ddcb673.905a" ] ] }, { - "id": "915b7162.7a73e", + "id": "967b4488.670f08", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCHours();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, @@ -1836,14 +871,14 @@ "y": 200, "wires": [ [ - "ee1e92f8.a01bb8" + "248eee4c.238282" ] ] }, { - "id": "b57fe145.320d28", + "id": "3e3732d.273a04e", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCMinutes();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, @@ -1852,14 +887,14 @@ "y": 240, "wires": [ [ - "c532a0cd.b0a47" + "a368c4b7.2dc4b8" ] ] }, { - "id": "d3f45b98.f05a58", + "id": "327729f0.afe466", "type": "function", - "z": "c10e968b.87e488", + "z": "6384a5e.e34465c", "name": "", "func": "d = msg.payload;\n\nvar val = d.getUTCSeconds();\n\nmsg.payload = val;\nreturn msg;", "outputs": 1, @@ -1868,14 +903,79 @@ "y": 280, "wires": [ [ - "5b200123.04ec98" + "96cc9953.9496c8" ] ] }, { - "id": "c4527705.33a84", + "id": "9c86b3b7.54841", + "type": "ui_group", + "z": "", + "name": "Datetime", + "tab": "2b97fe34.a699fa", + "order": 1, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "a156df1e.d37178", + "type": "subflow", + "name": "Acquisition inputs", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "2dd27be1.476eac" + }, + { + "id": "3883d084.feb708" + }, + { + "id": "4bf1038f.d36f9c" + }, + { + "id": "ae15c276.ec8c68" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "b996437b.1a45b8", + "port": 0 + }, + { + "id": "d56a51c1.60023", + "port": 0 + }, + { + "id": "229ade87.b1656a", + "port": 0 + }, + { + "id": "5e093b67.a32f9c", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red-contrib-camerapi/photo.png" + }, + { + "id": "b996437b.1a45b8", "type": "ui_text_input", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "custom_nb_step", "label": "Number of steps in between two images", "tooltip": "", @@ -1894,9 +994,9 @@ ] }, { - "id": "582e21b2.ad67a8", + "id": "229ade87.b1656a", "type": "ui_text_input", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "custom_nb_frame", "label": "Number of images per acquisition", "tooltip": "", @@ -1915,9 +1015,9 @@ ] }, { - "id": "3eaf4c98.d94b54", + "id": "2dd27be1.476eac", "type": "function", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "get custom_nb_step", "func": "msg.payload = msg.payload.custom_nb_step;\nreturn msg;", "outputs": 1, @@ -1926,14 +1026,14 @@ "y": 80, "wires": [ [ - "c4527705.33a84" + "b996437b.1a45b8" ] ] }, { - "id": "8eeb9e9e.a50d7", + "id": "4bf1038f.d36f9c", "type": "function", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "get custom_nb_frame", "func": "msg.payload = msg.payload.custom_nb_frame;\nreturn msg;", "outputs": 1, @@ -1942,14 +1042,14 @@ "y": 120, "wires": [ [ - "582e21b2.ad67a8" + "229ade87.b1656a" ] ] }, { - "id": "e4e16eb9.5296c", + "id": "ae15c276.ec8c68", "type": "function", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "get custom_segmentation", "func": "msg.payload = msg.payload.custom_segmentation;\nreturn msg;", "outputs": 1, @@ -1958,14 +1058,14 @@ "y": 160, "wires": [ [ - "f9705bc.3d322a8" + "5e093b67.a32f9c" ] ] }, { - "id": "e50aa637.59ac68", + "id": "3883d084.feb708", "type": "function", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "get custom_sleep_before", "func": "msg.payload = msg.payload.custom_sleep_before;\nreturn msg;", "outputs": 1, @@ -1974,14 +1074,14 @@ "y": 40, "wires": [ [ - "f648e44.94e3998" + "d56a51c1.60023" ] ] }, { - "id": "f648e44.94e3998", + "id": "d56a51c1.60023", "type": "ui_text_input", - "z": "863e8384.56889", + "z": "a156df1e.d37178", "name": "custom_sleep_before", "label": "Duration before the acquisition (s)", "tooltip": "", @@ -2000,9 +1100,81 @@ ] }, { - "id": "11b31baf.95996c", + "id": "5e093b67.a32f9c", + "type": "ui_switch", + "z": "a156df1e.d37178", + "name": "custom_segmentation", + "label": "Realize the segmentation", + "tooltip": "", + "group": "48649115.fcd01", + "order": 6, + "width": 0, + "height": 0, + "passthru": true, + "decouple": "false", + "topic": "custom_segmentation", + "style": "", + "onvalue": "True", + "onvalueType": "str", + "onicon": "", + "oncolor": "", + "offvalue": "False", + "offvalueType": "str", + "officon": "", + "offcolor": "", + "x": 520, + "y": 160, + "wires": [ + [] + ] + }, + { + "id": "48649115.fcd01", + "type": "ui_group", + "z": "", + "name": "Acquisition inputs", + "tab": "2b97fe34.a699fa", + "order": 9, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "99798a85.e62408", + "type": "subflow", + "name": "Process metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 80, + "wires": [ + { + "id": "20414296.54837e" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 80, + "wires": [ + { + "id": "d5ab9061.b06a9", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "d5ab9061.b06a9", "type": "ui_text_input", - "z": "5a287804.a10e2", + "z": "99798a85.e62408", "name": "process_id", "label": "Id of the process", "tooltip": "", @@ -2021,9 +1193,9 @@ ] }, { - "id": "dfb4b682.601e1", + "id": "20414296.54837e", "type": "function", - "z": "5a287804.a10e2", + "z": "99798a85.e62408", "name": "get process_id", "func": "msg.payload = msg.payload.process_id+1;\nreturn msg;", "outputs": 1, @@ -2032,14 +1204,37 @@ "y": 80, "wires": [ [ - "11b31baf.95996c" + "d5ab9061.b06a9" ] ] }, { - "id": "3777e513.35c3fa", + "id": "beeb994e.b67688", + "type": "ui_group", + "z": "", + "name": "Process metadata", + "tab": "2b97fe34.a699fa", + "order": 8, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "246abd43.838a5a", + "type": "subflow", + "name": "MQTT Receive & Plot", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#F3B567", + "icon": "node-red/bridge.svg" + }, + { + "id": "1aeca49c.10b893", "type": "mqtt in", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "topic": "receiver/#", "qos": "0", @@ -2049,15 +1244,15 @@ "y": 40, "wires": [ [ - "9886f960.4b6268", - "589fbae2.8ff914" + "be5de01e.45d56", + "613bee5b.042fe" ] ] }, { - "id": "9886f960.4b6268", + "id": "be5de01e.45d56", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "topic", "propertyType": "msg", @@ -2090,23 +1285,23 @@ "y": 40, "wires": [ [ - "c90e948f.2f7348" + "d39289fb.9f759" ], [ - "1d54f7b3.db7ac8" + "e2ab3af3.e61a8" ], [ - "d02a7968.b8874" + "e43e94c.c297968" ], [ - "11e60fef.079d38" + "b06c80f3.f1642" ] ] }, { - "id": "c90e948f.2f7348", + "id": "d39289fb.9f759", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2134,20 +1329,20 @@ "y": 40, "wires": [ [ - "e16b8120.403e8" + "267bd959.17b856" ], [ - "4ea155a3.d8531c" + "265e58c6.06de38" ], [ - "3d35b841.e6596" + "a433c901.2abd48" ] ] }, { - "id": "e16b8120.403e8", + "id": "267bd959.17b856", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The pump has started", "rules": [ { @@ -2167,14 +1362,14 @@ "y": 40, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "4ea155a3.d8531c", + "id": "265e58c6.06de38", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The pump has finished.", "rules": [ { @@ -2194,14 +1389,14 @@ "y": 80, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "3d35b841.e6596", + "id": "a433c901.2abd48", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The pump has been stopped.", "rules": [ { @@ -2221,14 +1416,14 @@ "y": 120, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "1d54f7b3.db7ac8", + "id": "e2ab3af3.e61a8", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2256,20 +1451,20 @@ "y": 200, "wires": [ [ - "7ce7cf66.df449" + "bd89c468.5a4f4" ], [ - "8846b607.310e9" + "762ab12c.cc7e88" ], [ - "5a8f4613.c9989" + "ecb1efe6.7cb968" ] ] }, { - "id": "7ce7cf66.df449", + "id": "bd89c468.5a4f4", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The focus has started", "rules": [ { @@ -2289,14 +1484,14 @@ "y": 200, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "8846b607.310e9", + "id": "762ab12c.cc7e88", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The focus has finished.", "rules": [ { @@ -2316,14 +1511,14 @@ "y": 240, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "5a8f4613.c9989", + "id": "ecb1efe6.7cb968", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The focus has been stopped.", "rules": [ { @@ -2343,14 +1538,14 @@ "y": 280, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "d02a7968.b8874", + "id": "e43e94c.c297968", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2383,24 +1578,24 @@ "y": 360, "wires": [ [ - "d7f9086b.728df8" + "87a2aa4d.3590c8" ], [ - "c104db3.a287628" + "da9f9e9b.7c9f5" ], [ - "e99cb81d.b79df" + "1143b916.5047b7" ], [ - "3de45d76.06ab6a", - "1597b08f.5bce8f" + "fa7f2eaf.0e6f1", + "3b6b4fd4.8c3368" ] ] }, { - "id": "90e10524.6709f", + "id": "30c9c4c9.d46e3c", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "payload", "propertyType": "msg", @@ -2423,17 +1618,17 @@ "y": 560, "wires": [ [ - "6c8a5e5c.bf0f5" + "23e5c77c.4f63f" ], [ - "90433a26.6fc278" + "5491334a.93cbfc" ] ] }, { - "id": "c104db3.a287628", + "id": "da9f9e9b.7c9f5", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The acquisition has finished.", "rules": [ { @@ -2453,14 +1648,14 @@ "y": 400, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "e99cb81d.b79df", + "id": "1143b916.5047b7", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The acquisition has been stopped.", "rules": [ { @@ -2480,14 +1675,14 @@ "y": 440, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "d7f9086b.728df8", + "id": "87a2aa4d.3590c8", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The acquisition has started", "rules": [ { @@ -2507,14 +1702,14 @@ "y": 360, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "3de45d76.06ab6a", + "id": "fa7f2eaf.0e6f1", "type": "function", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "img_counter.js", "func": "img_counter=global.get('img_counter')\nimg_counter=img_counter+1\nglobal.set('img_counter',img_counter)\nmsg.payload = img_counter\nreturn msg;", "outputs": 1, @@ -2523,14 +1718,14 @@ "y": 480, "wires": [ [ - "2f2c466d.88c6ba" + "582d7204.ec89fc" ] ] }, { - "id": "aebfa8a2.b4a928", + "id": "498b3d58.58b1a4", "type": "function", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "obj_counter.js", "func": "obj_counter=global.get('obj_counter')\nobj_counter=obj_counter+1\nglobal.set('obj_counter',obj_counter)\nmsg.payload = obj_counter\nreturn msg;", "outputs": 1, @@ -2539,14 +1734,14 @@ "y": 640, "wires": [ [ - "add1bf6d.b7a668" + "67618ae5.b74864" ] ] }, { - "id": "2f2c466d.88c6ba", + "id": "582d7204.ec89fc", "type": "ui_chart", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "img_counter", "group": "eb610eb9.84fae8", "order": 2, @@ -2586,9 +1781,9 @@ ] }, { - "id": "11e60fef.079d38", + "id": "b06c80f3.f1642", "type": "switch", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "topic", "propertyType": "msg", @@ -2616,20 +1811,20 @@ "y": 560, "wires": [ [ - "90e10524.6709f" + "30c9c4c9.d46e3c" ], [ - "aebfa8a2.b4a928" + "498b3d58.58b1a4" ], [ - "7dd159b.6c105a8" + "33094026.f6e8c" ] ] }, { - "id": "90433a26.6fc278", + "id": "5491334a.93cbfc", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The segmentation has finished.", "rules": [ { @@ -2649,14 +1844,14 @@ "y": 600, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "6c8a5e5c.bf0f5", + "id": "23e5c77c.4f63f", "type": "change", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "The segmentation has started", "rules": [ { @@ -2676,14 +1871,14 @@ "y": 560, "wires": [ [ - "1597b08f.5bce8f" + "3b6b4fd4.8c3368" ] ] }, { - "id": "add1bf6d.b7a668", + "id": "67618ae5.b74864", "type": "ui_chart", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "obj_counter", "group": "eb610eb9.84fae8", "order": 5, @@ -2723,9 +1918,9 @@ ] }, { - "id": "6f3399be.761c68", + "id": "3c29eb4.e570414", "type": "function", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "func": "msg.payload=msg.payload.object_area\nmsg.topic=\"area\"\n\nreturn msg;", "outputs": 1, @@ -2734,14 +1929,14 @@ "y": 700, "wires": [ [ - "e50c9bb6.397a08" + "84dfe51a.0e9fd" ] ] }, { - "id": "7dd159b.6c105a8", + "id": "33094026.f6e8c", "type": "json", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "property": "payload", "action": "", @@ -2750,14 +1945,14 @@ "y": 700, "wires": [ [ - "6f3399be.761c68" + "3c29eb4.e570414" ] ] }, { - "id": "b56d820b.9f7b", + "id": "9b672325.568a18", "type": "exec", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "command": "free -m | grep \"Mem\" | awk -F ' ' '{print $3}'", "addpay": false, "append": "", @@ -2768,16 +1963,16 @@ "y": 780, "wires": [ [ - "bb46922a.0aa378" + "76a7ddb6.fbde64" ], [], [] ] }, { - "id": "7c27a4b2.6fe8e4", + "id": "7c9eaef6.142a4", "type": "inject", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "topic": "", "payload": "", @@ -2790,14 +1985,14 @@ "y": 780, "wires": [ [ - "b56d820b.9f7b" + "9b672325.568a18" ] ] }, { - "id": "bb46922a.0aa378", + "id": "76a7ddb6.fbde64", "type": "ui_chart", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "group": "eb610eb9.84fae8", "order": 1, @@ -2837,9 +2032,9 @@ ] }, { - "id": "e50c9bb6.397a08", + "id": "84dfe51a.0e9fd", "type": "ui_chart", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "name": "", "group": "eb610eb9.84fae8", "order": 8, @@ -2879,9 +2074,9 @@ ] }, { - "id": "1597b08f.5bce8f", + "id": "3b6b4fd4.8c3368", "type": "ui_toast", - "z": "a8ad6dec.1a393", + "z": "246abd43.838a5a", "position": "top right", "displayTime": "3", "highlight": "", @@ -2897,62 +2092,69 @@ "wires": [] }, { - "id": "85ced3a9.8bc898", - "type": "exec", - "z": "9882c53a.0ccc8", - "command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"", - "addpay": false, - "append": "", - "useSpawn": "", - "timer": "", - "name": "RPi Temp.", - "x": 350, - "y": 80, - "wires": [ - [ - "8715b9fb.194438" - ], - [], - [] - ] - }, - { - "id": "3bb0ef9d.258af8", - "type": "inject", - "z": "9882c53a.0ccc8", + "id": "613bee5b.042fe", + "type": "debug", + "z": "246abd43.838a5a", "name": "", - "topic": "", - "payload": "", - "payloadType": "date", - "repeat": "10", - "crontab": "", - "once": false, - "onceDelay": "", - "x": 190, - "y": 80, - "wires": [ - [ - "85ced3a9.8bc898" - ] - ] + "active": true, + "tosidebar": true, + "console": false, + "tostatus": false, + "complete": "true", + "targetType": "full", + "x": 240, + "y": 140, + "wires": [] }, { - "id": "8715b9fb.194438", - "type": "python3-function", - "z": "9882c53a.0ccc8", - "name": "fan.py", - "func": "#!/usr/bin/python\nimport smbus\nimport sys\n\ntemp = msg[\"payload\"]\n\ntemp = int(temp.split('.',1)[0])\n\nbus = smbus.SMBus(1)\n\nDEVICE_ADDRESS = 0x0d\n\nif temp < 38:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x00)\nif temp > 42:\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)\n bus.write_byte_data(DEVICE_ADDRESS, 0x08, 0x01)", - "outputs": 1, - "x": 530, - "y": 80, - "wires": [ - [] - ] + "id": "84801dc0.193d88", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "127.0.0.1", + "port": "1883", + "clientid": "test", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" }, { - "id": "7bdf69d9.8f98e", + "id": "eb610eb9.84fae8", + "type": "ui_group", + "z": "", + "name": "MQTT Plots", + "tab": "2b97fe34.a699fa", + "order": 11, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "1273b673.4a35ea", + "type": "subflow", + "name": "System Commands", + "info": "", + "category": "", + "in": [], + "out": [], + "env": [], + "color": "#FFCC66", + "icon": "node-red-dashboard/ui_button.png" + }, + { + "id": "44a78834.e8f8b8", "type": "ui_button", - "z": "fbe9590f.bd63b8", + "z": "1273b673.4a35ea", "name": "", "group": "82b3caaa.0518", "order": 1, @@ -2971,14 +2173,14 @@ "y": 80, "wires": [ [ - "c55ff479.c166a8" + "aba9aac1.c2d198" ] ] }, { - "id": "f400fb5a.9bc108", + "id": "a32bfa65.bc6b9", "type": "exec", - "z": "fbe9590f.bd63b8", + "z": "1273b673.4a35ea", "command": "sudo", "addpay": true, "append": "", @@ -2995,9 +2197,9 @@ ] }, { - "id": "867e9bed.e2a298", + "id": "825c8791.c0bfb", "type": "ui_button", - "z": "fbe9590f.bd63b8", + "z": "1273b673.4a35ea", "name": "", "group": "82b3caaa.0518", "order": 2, @@ -3016,14 +2218,14 @@ "y": 140, "wires": [ [ - "c55ff479.c166a8" + "aba9aac1.c2d198" ] ] }, { - "id": "c55ff479.c166a8", + "id": "aba9aac1.c2d198", "type": "python3-function", - "z": "fbe9590f.bd63b8", + "z": "1273b673.4a35ea", "name": "action", "func": "#!/usr/bin/python\nimport smbus\nimport time\nbus = smbus.SMBus(1)\ntime.sleep(1)\n#turn off fan RGB\nbus.write_byte_data(0x0d, 0x07, 0x00)\nbus.write_byte_data(0x0d, 0x07, 0x00)\n\nmsg[\"payload\"] = str(msg[\"topic\"])+' now'\nreturn msg", "outputs": 1, @@ -3031,15 +2233,15 @@ "y": 100, "wires": [ [ - "46f85d17.08fa54", - "f400fb5a.9bc108" + "72b7368a.abad3", + "a32bfa65.bc6b9" ] ] }, { - "id": "46f85d17.08fa54", + "id": "72b7368a.abad3", "type": "exec", - "z": "fbe9590f.bd63b8", + "z": "1273b673.4a35ea", "command": "i2cdetect -y 1", "addpay": false, "append": "", @@ -3056,9 +2258,76 @@ ] }, { - "id": "cf0b247b.e3e7c", + "id": "82b3caaa.0518", + "type": "ui_group", + "z": "", + "name": "Commands", + "tab": "2b97fe34.a699fa", + "order": 12, + "disp": true, + "width": 24, + "collapse": false + }, + { + "id": "506e9090.6e905", + "type": "subflow", + "name": "Object metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "4ab4976c.eee488" + }, + { + "id": "581c8a23.83fa8c" + }, + { + "id": "52052007.b3d0e" + } + ] + } + ], + "out": [ + { + "x": 1060, + "y": 159, + "wires": [ + { + "id": "26b33a5c.0ef82e", + "port": 0 + }, + { + "id": "9ee0935a.415808", + "port": 0 + } + ] + }, + { + "x": 1060, + "y": 59, + "wires": [ + { + "id": "d3875217.e3b668", + "port": 0 + }, + { + "id": "82fef572.49b5f", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "26b33a5c.0ef82e", "type": "ui_numeric", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "object_depth_min", "label": "Minimum depth (m)", "tooltip": "", @@ -3080,9 +2349,9 @@ ] }, { - "id": "1675637a.1d762d", + "id": "9ee0935a.415808", "type": "ui_numeric", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "object_depth_max", "label": "Maximum depth (m)", "tooltip": "", @@ -3104,9 +2373,9 @@ ] }, { - "id": "8a61177.8eaa1e8", + "id": "4ab4976c.eee488", "type": "function", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "get object_depth_min", "func": "msg.payload = msg.payload.object_depth_min;\nreturn msg;", "outputs": 1, @@ -3115,14 +2384,14 @@ "y": 120, "wires": [ [ - "cf0b247b.e3e7c" + "26b33a5c.0ef82e" ] ] }, { - "id": "3893c81e.a9b9e", + "id": "581c8a23.83fa8c", "type": "function", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "get object_depth_max", "func": "msg.payload = msg.payload.object_depth_max;\nreturn msg;", "outputs": 1, @@ -3131,14 +2400,14 @@ "y": 160, "wires": [ [ - "1675637a.1d762d" + "9ee0935a.415808" ] ] }, { - "id": "f478b054.024158", + "id": "472998cd.45f588", "type": "gpsd", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "", "hostname": "localhost", "port": "2947", @@ -3152,15 +2421,15 @@ "y": 220, "wires": [ [ - "bd643763.2a7768", - "edee5fda.673ae" + "52052007.b3d0e", + "ab40705d.43a5d" ] ] }, { - "id": "ca169437.bb25e8", + "id": "7d5701.1e1981", "type": "ui_worldmap", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "d": true, "group": "f377d75b.32d27", "order": 1, @@ -3187,9 +2456,9 @@ "wires": [] }, { - "id": "bd643763.2a7768", + "id": "52052007.b3d0e", "type": "function", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "get object_lat & object_lon", "func": "\nreturn msg;", "outputs": 1, @@ -3198,14 +2467,14 @@ "y": 200, "wires": [ [ - "ca169437.bb25e8" + "7d5701.1e1981" ] ] }, { - "id": "d485fec3.802e", + "id": "d3875217.e3b668", "type": "function", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "set object_time", "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute;\nglobal.set('object_time',time_UTC);\nreturn msg;", "outputs": 1, @@ -3217,9 +2486,9 @@ ] }, { - "id": "5196107b.a5eae8", + "id": "82fef572.49b5f", "type": "function", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "set object_date", "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;", "outputs": 1, @@ -3231,9 +2500,9 @@ ] }, { - "id": "edee5fda.673ae", + "id": "ab40705d.43a5d", "type": "debug", - "z": "b45c6fb6.f6dfa8", + "z": "506e9090.6e905", "name": "", "active": true, "tosidebar": true, @@ -3246,9 +2515,114 @@ "wires": [] }, { - "id": "5a5fcc9a.9ede14", + "id": "f377d75b.32d27", + "type": "ui_group", + "z": "", + "name": "Object metadata", + "tab": "2b97fe34.a699fa", + "order": 6, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "97d77aeb.75afd8", + "type": "subflow", + "name": "Acquisition metadata", + "info": "", + "category": "", + "in": [ + { + "x": 50, + "y": 30, + "wires": [ + { + "id": "282cae65.749e9a" + }, + { + "id": "cc899daf.a8d5d8" + }, + { + "id": "9873f1c8.6cb608" + }, + { + "id": "e53df171.eed68" + }, + { + "id": "5f728563.cf6214" + }, + { + "id": "c1a5eaf5.8691c" + }, + { + "id": "86c63d98.eb21" + }, + { + "id": "3707a612.b8619a" + }, + { + "id": "b2d20d5d.fd9e38" + } + ] + } + ], + "out": [ + { + "x": 740, + "y": 40, + "wires": [ + { + "id": "3b267291.1eee26", + "port": 0 + }, + { + "id": "435a2dcf.a1a60c", + "port": 0 + }, + { + "id": "cc6cb58d.b2dbe8", + "port": 0 + }, + { + "id": "8b306bbc.914", + "port": 0 + }, + { + "id": "2a5a2b7a.f218d4", + "port": 0 + }, + { + "id": "28df07d8.d71ba8", + "port": 0 + }, + { + "id": "6cf2c1ac.a0fea8", + "port": 0 + }, + { + "id": "e7c4132f.f4417", + "port": 0 + } + ] + }, + { + "x": 900, + "y": 360, + "wires": [ + { + "id": "1e688c91.1b805b", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "1e688c91.1b805b", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "set optical config", "func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"acq_magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"sug_flowrate\",3);\n break;\n case \"16\":\n global.set(\"acq_magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"sug_flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"acq_magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"sug_flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"acq_magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"sug_flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"acq_magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"sug_flowrate\",0.32);\n break;\n}\nreturn msg;", "outputs": 1, @@ -3260,9 +2634,9 @@ ] }, { - "id": "3d3aafbf.e907a8", + "id": "2877f2f.211cc8e", "type": "ui_dropdown", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_fnumber_objective", "label": "M12 Lens*", "tooltip": "", @@ -3305,14 +2679,14 @@ "y": 360, "wires": [ [ - "5a5fcc9a.9ede14" + "1e688c91.1b805b" ] ] }, { - "id": "12e818fa.b7301f", + "id": "8b306bbc.914", "type": "ui_numeric", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_minimum_mesh", "label": "Min fraction size (μm)", "tooltip": "", @@ -3334,9 +2708,9 @@ ] }, { - "id": "b577dcd2.8d2c88", + "id": "2a5a2b7a.f218d4", "type": "ui_numeric", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_maximum_mesh", "label": "Max fraction size (μm)", "tooltip": "", @@ -3358,9 +2732,9 @@ ] }, { - "id": "21b35429.fe43a4", + "id": "3b267291.1eee26", "type": "ui_text_input", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_id", "label": "Acquisition unique ID*", "tooltip": "", @@ -3379,9 +2753,9 @@ ] }, { - "id": "c4e69883.a0f3d", + "id": "cc6cb58d.b2dbe8", "type": "ui_dropdown", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_celltype", "label": "Thickness flowcell*", "tooltip": "", @@ -3422,9 +2796,9 @@ ] }, { - "id": "f7f5ccc1.29a41", + "id": "28df07d8.d71ba8", "type": "ui_text_input", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_volume", "label": "Volume to pass (ml)", "tooltip": "", @@ -3443,9 +2817,9 @@ ] }, { - "id": "f0595ff1.c4d568", + "id": "435a2dcf.a1a60c", "type": "ui_text_input", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_instrument", "label": "Acquisition instrument", "tooltip": "PlanktonScope V2.1", @@ -3464,9 +2838,9 @@ ] }, { - "id": "93a3fd29.c55938", + "id": "282cae65.749e9a", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_id", "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;", "outputs": 1, @@ -3475,14 +2849,14 @@ "y": 40, "wires": [ [ - "21b35429.fe43a4" + "3b267291.1eee26" ] ] }, { - "id": "9e9e7f8a.b66d4", + "id": "cc899daf.a8d5d8", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_instrument", "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;", "outputs": 1, @@ -3491,14 +2865,14 @@ "y": 80, "wires": [ [ - "f0595ff1.c4d568" + "435a2dcf.a1a60c" ] ] }, { - "id": "b1105180.b4b78", + "id": "9873f1c8.6cb608", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_celltype", "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;", "outputs": 1, @@ -3507,14 +2881,14 @@ "y": 120, "wires": [ [ - "c4e69883.a0f3d" + "cc6cb58d.b2dbe8" ] ] }, { - "id": "ec403304.e34c58", + "id": "e53df171.eed68", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_minimum_mesh", "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;", "outputs": 1, @@ -3523,14 +2897,14 @@ "y": 160, "wires": [ [ - "12e818fa.b7301f" + "8b306bbc.914" ] ] }, { - "id": "7aac5c46.0669ec", + "id": "5f728563.cf6214", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_maximum_mesh", "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;", "outputs": 1, @@ -3539,14 +2913,14 @@ "y": 200, "wires": [ [ - "b577dcd2.8d2c88" + "2a5a2b7a.f218d4" ] ] }, { - "id": "c491cf7.36957b", + "id": "c1a5eaf5.8691c", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_volume", "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;", "outputs": 1, @@ -3555,14 +2929,14 @@ "y": 240, "wires": [ [ - "f7f5ccc1.29a41" + "28df07d8.d71ba8" ] ] }, { - "id": "31d58fcd.ede758", + "id": "b2d20d5d.fd9e38", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_fnumber_objective", "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;", "outputs": 1, @@ -3571,14 +2945,14 @@ "y": 360, "wires": [ [ - "3d3aafbf.e907a8" + "2877f2f.211cc8e" ] ] }, { - "id": "bd733bef.7efd08", + "id": "6cf2c1ac.a0fea8", "type": "ui_numeric", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_min_esd", "label": "Minimum size to segment (μm)", "tooltip": "", @@ -3600,9 +2974,9 @@ ] }, { - "id": "a6057924.bc14", + "id": "e7c4132f.f4417", "type": "ui_numeric", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "acq_max_esd", "label": "Maximum size to segment (μm)", "tooltip": "", @@ -3624,9 +2998,9 @@ ] }, { - "id": "e0644195.305068", + "id": "86c63d98.eb21", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_min_esd", "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;", "outputs": 1, @@ -3635,14 +3009,14 @@ "y": 280, "wires": [ [ - "bd733bef.7efd08" + "6cf2c1ac.a0fea8" ] ] }, { - "id": "e3fe6242.bfaf18", + "id": "3707a612.b8619a", "type": "function", - "z": "6ca1a253.126bb4", + "z": "97d77aeb.75afd8", "name": "get acq_max_esd", "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;", "outputs": 1, @@ -3651,14 +3025,65 @@ "y": 320, "wires": [ [ - "a6057924.bc14" + "e7c4132f.f4417" ] ] }, { - "id": "edfb5b10.95636", + "id": "60b93a5.a032344", + "type": "ui_group", + "z": "", + "name": "Acquisition metadata", + "tab": "2b97fe34.a699fa", + "order": 7, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "9a45991b.365bc8", + "type": "subflow", + "name": "Pump actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "eb7c01ae.d00358" + }, + { + "id": "642ae1f3.cf7d28" + } + ] + } + ], + "out": [ + { + "x": 700, + "y": 40, + "wires": [ + { + "id": "4485759b.52ee74", + "port": 0 + }, + { + "id": "3283f063.31c548", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "font-awesome/fa-recycle" + }, + { + "id": "6246d9ef.156bd", "type": "function", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "pump.js", "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"pump_manual_volume\");\nvar flowrate= global.get(\"pump_flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to pass\";\n \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Flowrate\";\n \n}else {\n volume = global.get(\"pump_manual_volume\");\n nb_step=volume*507\n msg.volume = volume;\n flowrate = global.get(\"pump_flowrate\");\n duration=(volume*60)/flowrate\n delay=(duration/nb_step)-0.005\n msg.topic = \"actuator/pump\";\n \n if(msg.payload === \"FORWARD\" & state===\"free\"){\n msg.payload='FORWARD '+delay+' '+nb_step;\n }\n if(msg.payload === \"BACKWARD\" & state===\"free\"){\n msg.payload='BACKWARD '+delay+' '+nb_step;\n }\n}\nreturn msg;", "outputs": 1, @@ -3667,15 +3092,15 @@ "y": 140, "wires": [ [ - "fb35e49.f64de18" + "53bef09a.8102e" ] ], "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" }, { - "id": "26686514.749b4a", + "id": "2374d55d.a3e3a2", "type": "ui_button", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "BACKWARD", "group": "4153382f.45437", "order": 2, @@ -3694,14 +3119,14 @@ "y": 120, "wires": [ [ - "edfb5b10.95636" + "6246d9ef.156bd" ] ] }, { - "id": "bee2fd6d.cffb28", + "id": "c8aa9753.f51c08", "type": "ui_button", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "FORWARD", "group": "4153382f.45437", "order": 4, @@ -3720,14 +3145,14 @@ "y": 160, "wires": [ [ - "edfb5b10.95636" + "6246d9ef.156bd" ] ] }, { - "id": "fb35e49.f64de18", + "id": "53bef09a.8102e", "type": "switch", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "", "property": "topic", "propertyType": "msg", @@ -3750,17 +3175,17 @@ "y": 140, "wires": [ [ - "f6aa3e03.85018" + "4d3bf3c2.6a380c" ], [ - "f6dcda51.633398" + "d943e58a.e85fc" ] ] }, { - "id": "f6dcda51.633398", + "id": "d943e58a.e85fc", "type": "ui_toast", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "position": "dialog", "displayTime": "3", "highlight": "", @@ -3778,9 +3203,9 @@ ] }, { - "id": "c3edd9e7.1ac36", + "id": "eaa22490.6843d", "type": "ui_button", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "stop pump", "group": "4153382f.45437", "order": 5, @@ -3799,14 +3224,14 @@ "y": 200, "wires": [ [ - "2521ba15.88a58e" + "9e71b7a5.28dff8" ] ] }, { - "id": "f6aa3e03.85018", + "id": "4d3bf3c2.6a380c", "type": "mqtt out", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "", "topic": "", "qos": "", @@ -3817,9 +3242,9 @@ "wires": [] }, { - "id": "2521ba15.88a58e", + "id": "9e71b7a5.28dff8", "type": "mqtt out", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "", "topic": "", "qos": "", @@ -3830,9 +3255,9 @@ "wires": [] }, { - "id": "2f9ec1a6.d5fb66", + "id": "3283f063.31c548", "type": "ui_text_input", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "pump_manual_volume", "label": "Volume to pass (ml)", "tooltip": "", @@ -3851,9 +3276,9 @@ ] }, { - "id": "50093f5.8e35ec", + "id": "642ae1f3.cf7d28", "type": "function", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "get pump_manual_volume", "func": "msg.payload = msg.payload.pump_manual_volume;\nreturn msg;", "outputs": 1, @@ -3862,14 +3287,14 @@ "y": 80, "wires": [ [ - "2f9ec1a6.d5fb66" + "3283f063.31c548" ] ] }, { - "id": "fa485315.928ae", + "id": "4485759b.52ee74", "type": "ui_slider", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "pump_flowrate", "label": "Flowrate (ml/min)*", "tooltip": "", @@ -3890,9 +3315,9 @@ ] }, { - "id": "f7b6f5e7.7b7ca", + "id": "eb7c01ae.d00358", "type": "function", - "z": "626459d2.f9c98", + "z": "9a45991b.365bc8", "name": "get pump_flowrate", "func": "msg.payload = msg.payload.pump_flowrate;\nreturn msg;", "outputs": 1, @@ -3901,14 +3326,58 @@ "y": 40, "wires": [ [ - "fa485315.928ae" + "4485759b.52ee74" ] ] }, { - "id": "7297e2f7.dce564", + "id": "4153382f.45437", + "type": "ui_group", + "z": "", + "name": "Pump actuation", + "tab": "2b97fe34.a699fa", + "order": 5, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "ac806d39.1682a8", + "type": "subflow", + "name": "Focus actuation", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "c631467a.569ba" + } + ] + } + ], + "out": [ + { + "x": 800, + "y": 200, + "wires": [ + { + "id": "97bf666e.4d3ad", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#A6BBCF", + "icon": "node-red/sort.svg" + }, + { + "id": "97bf666e.4d3ad", "type": "ui_text_input", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "focus_nb_step", "label": "Number of step(s)", "tooltip": "", @@ -3927,9 +3396,9 @@ ] }, { - "id": "60dc5851.6962b", + "id": "c631467a.569ba", "type": "function", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "get focus_nb_step", "func": "msg.payload = msg.payload.focus_nb_step;\nreturn msg;", "outputs": 1, @@ -3938,14 +3407,14 @@ "y": 40, "wires": [ [ - "7297e2f7.dce564" + "97bf666e.4d3ad" ] ] }, { - "id": "7200408d.a1be4", + "id": "8346f4af.5c0978", "type": "ui_button", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "DOWN", "group": "69433259.f306fc", "order": 3, @@ -3964,14 +3433,14 @@ "y": 120, "wires": [ [ - "2e2a455b.5ff4fa" + "350c388d.12cd28" ] ] }, { - "id": "7f823e6.d3bcfc", + "id": "7ee30e1c.691bd", "type": "ui_button", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "UP", "group": "69433259.f306fc", "order": 1, @@ -3990,14 +3459,14 @@ "y": 81, "wires": [ [ - "2e2a455b.5ff4fa" + "350c388d.12cd28" ] ] }, { - "id": "54482c7a.a384ac", + "id": "a2f04fac.5a338", "type": "switch", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "", "property": "topic", "propertyType": "msg", @@ -4020,17 +3489,17 @@ "y": 100, "wires": [ [ - "2a7a3d34.08e2a2" + "9fd904e.d1cbcf8" ], [ - "4277442b.04d1b4" + "ccd4fa1e.152" ] ] }, { - "id": "4277442b.04d1b4", + "id": "ccd4fa1e.152", "type": "ui_toast", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "position": "dialog", "displayTime": "3", "highlight": "", @@ -4048,9 +3517,9 @@ ] }, { - "id": "2e2a455b.5ff4fa", + "id": "350c388d.12cd28", "type": "function", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "focus.js", "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"focus_nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Number of steps\";\n \n}else {\n nb_step= global.get(\"focus_nb_step\");\n if(msg.payload === \"UP\" & state===\"free\"){\n msg.payload=\"FORWARD \"+nb_step;\n }\n if(msg.payload === \"DOWN\" & state===\"free\"){\n msg.payload=\"BACKWARD \"+nb_step;\n }\n}\nreturn msg;", "outputs": 1, @@ -4059,15 +3528,15 @@ "y": 100, "wires": [ [ - "54482c7a.a384ac" + "a2f04fac.5a338" ] ], "info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n" }, { - "id": "73e0d0c.c07ab3", + "id": "da904b2b.4a1d68", "type": "ui_button", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "stop focus", "group": "69433259.f306fc", "order": 4, @@ -4086,14 +3555,14 @@ "y": 160, "wires": [ [ - "8e86348d.69657" + "8bb9c09d.bc8178" ] ] }, { - "id": "2a7a3d34.08e2a2", + "id": "9fd904e.d1cbcf8", "type": "mqtt out", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "", "topic": "", "qos": "", @@ -4104,9 +3573,9 @@ "wires": [] }, { - "id": "8e86348d.69657", + "id": "8bb9c09d.bc8178", "type": "mqtt out", - "z": "5c516299.73e054", + "z": "ac806d39.1682a8", "name": "", "topic": "", "qos": "", @@ -4117,9 +3586,102 @@ "wires": [] }, { - "id": "10f1e5c1.3cb69a", + "id": "69433259.f306fc", + "type": "ui_group", + "z": "", + "name": "Focus actuation", + "tab": "2b97fe34.a699fa", + "order": 4, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "e8ab36cc.74d77", + "type": "mqtt-broker", + "z": "", + "name": "", + "broker": "0.0.0.0", + "port": "1883", + "clientid": "Client_node", + "usetls": false, + "compatmode": false, + "keepalive": "60", + "cleansession": true, + "birthTopic": "", + "birthQos": "0", + "birthPayload": "", + "closeTopic": "", + "closeQos": "0", + "closePayload": "", + "willTopic": "", + "willQos": "0", + "willPayload": "" + }, + { + "id": "5c6dd7ee.546fa8", + "type": "subflow", + "name": "Sample metadata", + "info": "", + "category": "", + "in": [ + { + "x": 40, + "y": 40, + "wires": [ + { + "id": "730e3aa0.75f6dc" + }, + { + "id": "b49441ee.07b358" + }, + { + "id": "77454044.f47e88" + }, + { + "id": "203e3416.6c480c" + }, + { + "id": "3555467a.6ba1ea" + } + ] + } + ], + "out": [ + { + "x": 840, + "y": 40, + "wires": [ + { + "id": "419967b7.b9b5f", + "port": 0 + }, + { + "id": "9b3f7b46.107718", + "port": 0 + }, + { + "id": "6f24740b.fbae5c", + "port": 0 + }, + { + "id": "bf7a47c8.a960b8", + "port": 0 + }, + { + "id": "327afe96.262122", + "port": 0 + } + ] + } + ], + "env": [], + "color": "#DDAA99" + }, + { + "id": "6f24740b.fbae5c", "type": "ui_text_input", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "sample_ship", "label": "Name of the ship", "tooltip": "", @@ -4138,9 +3700,9 @@ ] }, { - "id": "da0c5a96.74c0e", + "id": "327afe96.262122", "type": "ui_dropdown", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "sample_sampling_gear", "label": "Sampling gear", "tooltip": "", @@ -4186,9 +3748,9 @@ ] }, { - "id": "aa90b06d.ca78e", + "id": "bf7a47c8.a960b8", "type": "ui_text_input", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "sample_operator", "label": "Name of the operator", "tooltip": "", @@ -4207,9 +3769,9 @@ ] }, { - "id": "1cb896c7.6dfc11", + "id": "419967b7.b9b5f", "type": "ui_text_input", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "sample_project", "label": "Name of the project*", "tooltip": "", @@ -4228,9 +3790,9 @@ ] }, { - "id": "288ba4b3.a9a2cc", + "id": "9b3f7b46.107718", "type": "ui_text_input", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "sample_id", "label": "ID of the station*", "tooltip": "", @@ -4249,9 +3811,9 @@ ] }, { - "id": "78f5791d.946bd8", + "id": "730e3aa0.75f6dc", "type": "function", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "get sample_projet", "func": "msg.payload = msg.payload.sample_project;\nreturn msg;", "outputs": 1, @@ -4260,14 +3822,14 @@ "y": 40, "wires": [ [ - "1cb896c7.6dfc11" + "419967b7.b9b5f" ] ] }, { - "id": "2a09d440.119154", + "id": "77454044.f47e88", "type": "function", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "get sample_ship", "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;", "outputs": 1, @@ -4276,14 +3838,14 @@ "y": 120, "wires": [ [ - "10f1e5c1.3cb69a" + "6f24740b.fbae5c" ] ] }, { - "id": "346d141f.ebab3c", + "id": "b49441ee.07b358", "type": "function", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "get sample_id", "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;", "outputs": 1, @@ -4292,14 +3854,14 @@ "y": 80, "wires": [ [ - "288ba4b3.a9a2cc" + "9b3f7b46.107718" ] ] }, { - "id": "2d438355.ed942c", + "id": "203e3416.6c480c", "type": "function", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "get sample_operator", "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;", "outputs": 1, @@ -4308,14 +3870,14 @@ "y": 160, "wires": [ [ - "aa90b06d.ca78e" + "bf7a47c8.a960b8" ] ] }, { - "id": "ac4a71a.c35309", + "id": "3555467a.6ba1ea", "type": "function", - "z": "efeebffd.34c7e", + "z": "5c6dd7ee.546fa8", "name": "get sample_sampling_gear", "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;", "outputs": 1, @@ -4324,14 +3886,42 @@ "y": 200, "wires": [ [ - "da0c5a96.74c0e" + "327afe96.262122" ] ] }, { - "id": "45482528.43f93c", + "id": "417f91c9.193ab", + "type": "ui_group", + "z": "", + "name": "Sample metadata", + "tab": "2b97fe34.a699fa", + "order": 2, + "disp": true, + "width": "24", + "collapse": false + }, + { + "id": "2b97fe34.a699fa", + "type": "ui_tab", + "z": "", + "name": "GUI", + "icon": "fa-eyedropper", + "order": 2, + "disabled": false, + "hidden": false + }, + { + "id": "bb8dbe68.7e20a", + "type": "tab", + "label": "Main", + "disabled": false, + "info": "" + }, + { + "id": "20340bb6.5f923c", "type": "function", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "get global", "func": "msg.payload={\n \n \"sample_project\":global.get(\"sample_project\"),\n \"sample_id\":global.get(\"sample_id\"),\n \"sample_ship\":global.get(\"sample_ship\"),\n \"sample_operator\":global.get(\"sample_operator\"),\n \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n \"acq_celltype\":global.get(\"acq_celltype\"),\n \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n \"acq_min_esd\":global.get(\"acq_min_esd\"),\n \"acq_max_esd\":global.get(\"acq_max_esd\"),\n \"acq_volume\":global.get(\"acq_volume\"),\n \"acq_magnification\":global.get(\"magnification\"),\n \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n \n \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_depth_min\":global.get(\"object_depth_min\"),\n \"object_depth_max\":global.get(\"object_depth_max\"),\n \n \"custom_nb_frame\":global.get(\"custom_nb_frame\"),\n \"custom_nb_step\":global.get(\"custom_nb_step\"),\n \"custom_segmentation\":global.get(\"custom_segmentation\"),\n \"custom_sleep_before\":global.get(\"custom_sleep_before\"),\n \"focus_nb_step\":global.get(\"focus_nb_step\"),\n \"pump_flowrate\":global.get(\"pump_flowrate\"),\n \"pump_manual_volume\":global.get(\"pump_manual_volume\"),\n \n \"process_pixel\":global.get(\"process_pixel\"),\n \"process_id\":global.get(\"process_id\")\n \n \n};\nreturn msg;", "outputs": 1, @@ -4340,14 +3930,14 @@ "y": 160, "wires": [ [ - "fe81be99.6859e8" + "d69f0eb1.d514d" ] ] }, { - "id": "a5f18550.68466", + "id": "aed82ae1.3a7558", "type": "file", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "", "filename": "/home/pi/PlanktonScope/config.json", "appendNewline": true, @@ -4361,9 +3951,9 @@ ] }, { - "id": "fe81be99.6859e8", + "id": "d69f0eb1.d514d", "type": "json", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "config.json", "property": "payload", "action": "str", @@ -4372,14 +3962,14 @@ "y": 160, "wires": [ [ - "a5f18550.68466" + "aed82ae1.3a7558" ] ] }, { - "id": "b24cc280.5a59b", + "id": "b57ab8b0.7bfc4", "type": "file in", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "", "filename": "/home/pi/PlanktonScope/config.json", "format": "utf8", @@ -4390,15 +3980,15 @@ "y": 80, "wires": [ [ - "11e5237b.e558c5" + "5b6059c3.8d4fa8" ] ], "info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n" }, { - "id": "4c6084c.1b7bb7c", + "id": "7880a269.4817ac", "type": "inject", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "on_load", "topic": "", "payload": "", @@ -4411,17 +4001,18 @@ "y": 80, "wires": [ [ - "b24cc280.5a59b", - "845bb10c.d99208", - "a01c8373.701628" + "b57ab8b0.7bfc4", + "10d8393.60498c7", + "dba45961.85d67", + "8231cfcc.0c5dd8" ] ], "info": "# PlanktonScope Help\nWhen the **Pi** is booting, **Node-RED** will be initiated and this node will be activated once and execute the following nodes." }, { - "id": "11e5237b.e558c5", + "id": "5b6059c3.8d4fa8", "type": "json", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "config.json", "property": "payload", "action": "", @@ -4430,20 +4021,20 @@ "y": 80, "wires": [ [ - "9dc8498a.4a36b", - "9b67b810.97a618", - "32282348.35c09c", - "fe7c0e45.ee983", - "3e6ceaa0.5fad56", - "9e577327.d9a1f", - "c50792f5.6b5148" + "9b872b59.667ee", + "67bab5e1.2c7dcc", + "8e5a1fb0.dc878", + "bfc59fc4.be21a8", + "80434aac.22226", + "a3453d30.ca9a28", + "e25e094c.60fb1" ] ] }, { - "id": "f72f54db.590c9", + "id": "1b45a311.c993ed", "type": "function", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "set global", "func": "var value = msg.payload;\nvar key = msg.topic;\n\nglobal.set(key,value);\nreturn msg;", "outputs": 1, @@ -4452,14 +4043,14 @@ "y": 80, "wires": [ [ - "45482528.43f93c" + "20340bb6.5f923c" ] ] }, { - "id": "2372125a.7f69d6", + "id": "1d54c0bf.fbcf07", "type": "rpi-gpio out", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "", "pin": "40", "set": "", @@ -4471,9 +4062,9 @@ "wires": [] }, { - "id": "bae08e6f.11bc28", + "id": "7da863d0.f7d41c", "type": "ui_template", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "group": "dc721eb.9ef51e", "name": "Stream Pi Camera", "order": 1, @@ -4483,16 +4074,16 @@ "storeOutMessages": true, "fwdInMessages": true, "templateScope": "local", - "x": 850, + "x": 830, "y": 320, "wires": [ [] ] }, { - "id": "845bb10c.d99208", + "id": "10d8393.60498c7", "type": "function", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "init LED", "func": "msg.payload=1;\nreturn msg;", "outputs": 1, @@ -4501,149 +4092,139 @@ "y": 120, "wires": [ [ - "2372125a.7f69d6" + "1d54c0bf.fbcf07" ] ] }, { - "id": "9dc8498a.4a36b", - "type": "subflow:efeebffd.34c7e", - "z": "ff9251a5.9c5e18", + "id": "9b872b59.667ee", + "type": "subflow:5c6dd7ee.546fa8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], "x": 830, "y": 80, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ] ] }, { - "id": "9e577327.d9a1f", - "type": "subflow:5c516299.73e054", - "z": "ff9251a5.9c5e18", + "id": "a3453d30.ca9a28", + "type": "subflow:ac806d39.1682a8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], - "x": 846, - "y": 242, + "x": 820, + "y": 240, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ] ] }, { - "id": "c50792f5.6b5148", - "type": "subflow:626459d2.f9c98", - "z": "ff9251a5.9c5e18", + "id": "e25e094c.60fb1", + "type": "subflow:9a45991b.365bc8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], - "x": 846, - "y": 282, + "x": 820, + "y": 280, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ] ] }, { - "id": "9b67b810.97a618", - "type": "subflow:6ca1a253.126bb4", - "z": "ff9251a5.9c5e18", + "id": "67bab5e1.2c7dcc", + "type": "subflow:97d77aeb.75afd8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], "x": 840, "y": 120, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ], [ - "45482528.43f93c" + "20340bb6.5f923c" ] ] }, { - "id": "32282348.35c09c", - "type": "subflow:b45c6fb6.f6dfa8", - "z": "ff9251a5.9c5e18", + "id": "8e5a1fb0.dc878", + "type": "subflow:506e9090.6e905", + "z": "bb8dbe68.7e20a", "name": "", "env": [], "x": 820, "y": 160, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ], [ - "45482528.43f93c" + "20340bb6.5f923c" ] ] }, { - "id": "8e1d0d8d.fc54d8", - "type": "subflow:fbe9590f.bd63b8", - "z": "ff9251a5.9c5e18", + "id": "14b78383.7457bc", + "type": "subflow:1273b673.4a35ea", + "z": "bb8dbe68.7e20a", "name": "System commands", "env": [], - "x": 850, - "y": 500, + "x": 830, + "y": 480, "wires": [] }, { - "id": "f8a906b3.a2c81", - "type": "subflow:9882c53a.0ccc8", - "z": "ff9251a5.9c5e18", + "id": "e6403eaf.54f7e", + "type": "subflow:246abd43.838a5a", + "z": "bb8dbe68.7e20a", "name": "", "env": [], - "x": 320, - "y": 280, + "x": 840, + "y": 400, "wires": [] }, { - "id": "b1be7e1e.9ec3c8", - "type": "subflow:a8ad6dec.1a393", - "z": "ff9251a5.9c5e18", - "name": "", - "env": [], - "x": 850, - "y": 420, - "wires": [] - }, - { - "id": "fe7c0e45.ee983", - "type": "subflow:5a287804.a10e2", - "z": "ff9251a5.9c5e18", + "id": "bfc59fc4.be21a8", + "type": "subflow:99798a85.e62408", + "z": "bb8dbe68.7e20a", "name": "process metadata", "env": [], "x": 830, "y": 200, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ] ] }, { - "id": "3e6ceaa0.5fad56", - "type": "subflow:863e8384.56889", - "z": "ff9251a5.9c5e18", + "id": "80434aac.22226", + "type": "subflow:a156df1e.d37178", + "z": "bb8dbe68.7e20a", "name": "Acquisition inputs", "env": [], - "x": 836, - "y": 362, + "x": 830, + "y": 360, "wires": [ [ - "f72f54db.590c9" + "1b45a311.c993ed" ] ], "icon": "node-red-dashboard/ui_switch.png" }, { - "id": "a01c8373.701628", - "type": "subflow:c10e968b.87e488", - "z": "ff9251a5.9c5e18", + "id": "dba45961.85d67", + "type": "subflow:6384a5e.e34465c", + "z": "bb8dbe68.7e20a", "name": "", "env": [], "x": 300, @@ -4651,9 +4232,9 @@ "wires": [] }, { - "id": "1924ce1c.0459f2", - "type": "subflow:c1d3ff7c.4384f", - "z": "ff9251a5.9c5e18", + "id": "8231cfcc.0c5dd8", + "type": "subflow:e8320d42.9a3ad8", + "z": "bb8dbe68.7e20a", "name": "", "env": [], "x": 290, @@ -4661,19 +4242,19 @@ "wires": [] }, { - "id": "d3892f94.428a28", - "type": "subflow:bba19d97.b32b1", - "z": "ff9251a5.9c5e18", + "id": "557afe0d.33d97", + "type": "subflow:97600dff.93378", + "z": "bb8dbe68.7e20a", "name": "", "env": [], - "x": 850, - "y": 460, + "x": 830, + "y": 440, "wires": [] }, { - "id": "e73525a.1103158", + "id": "af4f780b.068368", "type": "ui_switch", - "z": "ff9251a5.9c5e18", + "z": "bb8dbe68.7e20a", "name": "", "label": "LED", "tooltip": "", @@ -4697,167 +4278,19 @@ "y": 160, "wires": [ [ - "2372125a.7f69d6" + "1d54c0bf.fbcf07" ] ] }, { - "id": "be37d12f.0898f", - "type": "file", - "z": "c1d3ff7c.4384f", - "name": "", - "filename": "/home/pi/PlanktonScope/script/main.py", - "appendNewline": false, - "createDir": true, - "overwriteFile": "true", - "encoding": "none", - "x": 530, - "y": 100, - "wires": [ - [ - "23f3e613.20ad82" - ] - ] - }, - { - "id": "49e31e85.7ac51", - "type": "template", - "z": "c1d3ff7c.4384f", - "name": "main.py", - "field": "payload", - "fieldType": "msg", - "format": "python", - "syntax": "plain", - "template": "################################################################################\n#Actuator Libraries\n################################################################################\n\n#Library for exchaning messages with Node-RED\nimport paho.mqtt.client as mqtt\n\n#Library to control the PiCamera\nfrom picamera import PiCamera\n\n#Libraries to control the steppers for focusing and pumping\nfrom adafruit_motor import stepper\nfrom adafruit_motorkit import MotorKit\n\n#Library to send command over I2C for the light module on the fan\nimport smbus\n\n################################################################################\n#Practical Libraries\n################################################################################\n\n#Library to get date and time for folder name and filename\nfrom datetime import datetime, timedelta\n\n#Library to be able to sleep for a duration\nfrom time import sleep\n\n#Libraries manipulate json format, execute bash commands\nimport json, shutil, os, subprocess\n\n################################################################################\n#Morphocut Libraries\n################################################################################\n\nfrom skimage.util import img_as_ubyte\nfrom morphocut import Call\nfrom morphocut.contrib.ecotaxa import EcotaxaWriter\nfrom morphocut.contrib.zooprocess import CalculateZooProcessFeatures\nfrom morphocut.core import Pipeline\nfrom morphocut.file import Find\nfrom morphocut.image import (ExtractROI,\n FindRegions,\n ImageReader,\n ImageWriter,\n RescaleIntensity,\n RGB2Gray\n)\nfrom morphocut.stat import RunningMedian\nfrom morphocut.str import Format\nfrom morphocut.stream import TQDM, Enumerate, FilterVariables\n\n################################################################################\n#Other image processing Libraries\n################################################################################\n\nfrom skimage.feature import canny\nfrom skimage.color import rgb2gray, label2rgb\nfrom skimage.morphology import disk\nfrom skimage.morphology import erosion, dilation, closing\nfrom skimage.measure import label, regionprops\nimport cv2\n\n################################################################################\n#Streaming PiCamera over server\n################################################################################\nimport io\nimport picamera\nimport logging\nimport socketserver\nfrom threading import Condition\nfrom http import server\nimport threading\n\n################################################################################\n#Creation of the webpage containing the PiCamera Streaming\n################################################################################\n\nPAGE=\"\"\"\\\n\n\nPlanktonScope v2 | PiCamera Streaming\n\n\n\n\n\n\"\"\"\n\n################################################################################\n#Classes for the PiCamera Streaming\n################################################################################\n\nclass StreamingOutput(object):\n def __init__(self):\n self.frame = None\n self.buffer = io.BytesIO()\n self.condition = Condition()\n\n def write(self, buf):\n if buf.startswith(b'\\xff\\xd8'):\n # New frame, copy the existing buffer's content and notify all\n # clients it's available\n self.buffer.truncate()\n with self.condition:\n self.frame = self.buffer.getvalue()\n self.condition.notify_all()\n self.buffer.seek(0)\n return self.buffer.write(buf)\n\nclass StreamingHandler(server.BaseHTTPRequestHandler):\n def do_GET(self):\n if self.path == '/':\n self.send_response(301)\n self.send_header('Location', '/index.html')\n self.end_headers()\n elif self.path == '/index.html':\n content = PAGE.encode('utf-8')\n self.send_response(200)\n self.send_header('Content-Type', 'text/html')\n self.send_header('Content-Length', len(content))\n self.end_headers()\n self.wfile.write(content)\n elif self.path == '/stream.mjpg':\n self.send_response(200)\n self.send_header('Age', 0)\n self.send_header('Cache-Control', 'no-cache, private')\n self.send_header('Pragma', 'no-cache')\n self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')\n self.end_headers()\n try:\n while True:\n with output.condition:\n output.condition.wait()\n frame = output.frame\n self.wfile.write(b'--FRAME\\r\\n')\n self.send_header('Content-Type', 'image/jpeg')\n self.send_header('Content-Length', len(frame))\n self.end_headers()\n self.wfile.write(frame)\n self.wfile.write(b'\\r\\n')\n except Exception as e:\n logging.warning(\n 'Removed streaming client %s: %s',\n self.client_address, str(e))\n else:\n self.send_error(404)\n self.end_headers()\n\nclass StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):\n allow_reuse_address = True\n daemon_threads = True\n\n################################################################################\n#MQTT core functions\n################################################################################\n\n#Run this function in order to connect to the client (Node-RED)\ndef on_connect(client, userdata, flags, rc):\n #Print when connected\n print(\"Connected! - \" + str(rc))\n #When connected, run subscribe()\n client.subscribe(\"actuator/#\")\n #Turn green the light module\n rgb(0,255,0)\n\n#Run this function in order to subscribe to all the topics begining by actuator\ndef on_subscribe(client, obj, mid, granted_qos):\n #Print when subscribed\n print(\"Subscribed! - \"+str(mid)+\" \"+str(granted_qos))\n\n#Run this command when Node-RED is sending a message on the subscribed topic\ndef on_message(client, userdata, msg):\n #Print the topic and the message\n print(msg.topic+\" \"+str(msg.qos)+\" \"+str(msg.payload))\n #Update the global variables command, args and counter\n global command\n global args\n global counter\n #Parse the topic to find the command. ex : actuator/pump -> pump\n command=msg.topic.split(\"/\")[1]\n #Decode the message to find the arguments\n args=str(msg.payload.decode())\n #Reset the counter to 0\n counter=0\n\n################################################################################\n#LEDs Actuation\n################################################################################\ndef rgb(R,G,B):\n #Update LED n1\n bus.write_byte_data(0x0d, 0x00, 0)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n2\n bus.write_byte_data(0x0d, 0x00, 1)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update LED n3\n bus.write_byte_data(0x0d, 0x00, 2)\n bus.write_byte_data(0x0d, 0x01, R)\n bus.write_byte_data(0x0d, 0x02, G)\n bus.write_byte_data(0x0d, 0x03, B)\n\n #Update the I2C Bus in order to really update the LEDs new values\n cmd=\"i2cdetect -y 1\"\n subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)\n\n################################################################################\n#Init function - executed only once\n################################################################################\n\n#define the bus used to actuate the light module on the fan\nbus = smbus.SMBus(1)\n\n#define the names for the 2 exsting steppers\nkit = MotorKit()\npump_stepper = kit.stepper1\nfocus_stepper = kit.stepper2\n#Make sure the steppers are release and do not use any power\npump_stepper.release()\nfocus_stepper.release()\n\n#Precise the settings of the PiCamera\ncamera = PiCamera()\ncamera.resolution = (3280, 2464)\ncamera.iso = 60\ncamera.shutter_speed = 500\ncamera.exposure_mode = 'fixedfps'\n\n#Declare the global variables command, args and counter\ncommand = ''\nargs = ''\ncounter=''\n\n#MQTT Client functions definition\nclient = mqtt.Client()\nclient.connect(\"192.168.4.1\",1883,60)\nclient.on_connect = on_connect\nclient.on_subscribe = on_subscribe\nclient.on_message = on_message\nclient.loop_start()\n\n################################################################################\n#Definition of the few important metadata\n################################################################################\n\nlocal_metadata = {\n \"process_datetime\": datetime.now(),\n \"acq_camera_resolution\" : camera.resolution,\n \"acq_camera_iso\" : camera.iso,\n \"acq_camera_shutter_speed\" : camera.shutter_speed\n}\n\n#Read the content of config.json containing the metadata defined on Node-RED\nconfig_json = open('/home/pi/PlanktonScope/config.json','r')\nnode_red_metadata = json.loads(config_json.read())\n\n#Concat the local metadata and the metadata from Node-RED\nglobal_metadata = {**local_metadata, **node_red_metadata}\n\n#Define the name of the .zip file that will contain the images and the .tsv table for EcoTaxa\narchive_fn = os.path.join(\"/home/pi/PlanktonScope/\",\"export\", \"ecotaxa_export.zip\")\n\n################################################################################\n#MorphoCut Script\n################################################################################\n\n#Define processing pipeline\nwith Pipeline() as p:\n\n #Recursively find .jpg files in import_path.\n #Sort to get consective frames.\n abs_path = Find(\"/home/pi/PlanktonScope/tmp\", [\".jpg\"], sort=True, verbose=True)\n\n #Extract name from abs_path\n name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n #Read image\n img = ImageReader(abs_path)\n\n #Show progress bar for frames\n TQDM(Format(\"Frame {name}\", name=name))\n\n #Apply running median to approximate the background image\n flat_field = RunningMedian(img, 5)\n\n #Correct image\n img = img / flat_field\n\n #Rescale intensities and convert to uint8 to speed up calculations\n img = RescaleIntensity(img, in_range=(0, 1.1), dtype=\"uint8\")\n\n #Filter variable to reduce memory load\n FilterVariables(name,img)\n\n #Save cleaned images\n #frame_fn = Format(os.path.join(\"/home/pi/PlanktonScope/tmp\",\"CLEAN\", \"{name}.jpg\"), name=name)\n #ImageWriter(frame_fn, img)\n\n #Convert image to uint8 gray\n img_gray = RGB2Gray(img)\n\n #?\n img_gray = Call(img_as_ubyte, img_gray)\n\n #Canny edge detection using OpenCV\n img_canny = Call(cv2.Canny, img_gray, 50,100)\n\n #Dilate using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)\n\n #Close using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))\n img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)\n\n #Erode using OpenCV\n kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))\n mask = Call(cv2.erode, img_close, kernel, iterations=2)\n\n #Find objects\n regionprops = FindRegions(\n mask, img_gray, min_area=1000, padding=10, warn_empty=name\n )\n\n #Set the LEDs as Purple\n Call(rgb, 255,0,255)\n\n # For an object, extract a vignette/ROI from the image\n roi_orig = ExtractROI(img, regionprops, bg_color=255)\n\n # Generate an object identifier\n i = Enumerate()\n\n #Call(print,i)\n\n #Define the ID of each object\n object_id = Format(\"{name}_{i:d}\", name=name, i=i)\n\n #Call(print,object_id)\n\n #Define the name of each object\n object_fn = Format(os.path.join(\"/home/pi/PlanktonScope/\",\"OBJECTS\", \"{name}.jpg\"), name=object_id)\n\n #Save the image of the object with its name\n ImageWriter(object_fn, roi_orig)\n\n #Calculate features. The calculated features are added to the global_metadata.\n #Returns a Variable representing a dict for every object in the stream.\n meta = CalculateZooProcessFeatures(\n regionprops, prefix=\"object_\", meta=global_metadata\n )\n\n #Get all the metadata\n json_meta = Call(json.dumps,meta, sort_keys=True, default=str)\n\n #Publish the json containing all the metadata to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/metric\", json_meta)\n\n #Add object_id to the metadata dictionary\n meta[\"object_id\"] = object_id\n\n #Generate object filenames\n orig_fn = Format(\"{object_id}.jpg\", object_id=object_id)\n\n #Write objects to an EcoTaxa archive:\n #roi image in original color, roi image in grayscale, metadata associated with each object\n EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)\n\n #Progress bar for objects\n TQDM(Format(\"Object {object_id}\", object_id=object_id))\n\n #Publish the object_id to via MQTT to Node-RED\n Call(client.publish, \"receiver/segmentation/object_id\", object_id)\n\n #Set the LEDs as Green\n Call(rgb, 0,255,0)\n\n################################################################################\n#While loop for capting commands from Node-RED\n################################################################################\n\noutput = StreamingOutput()\naddress = ('192.168.4.1', 8000)\nserver = StreamingServer(address, StreamingHandler)\nthreading.Thread(target=server.serve_forever).start()\ncamera.start_recording(output, format='mjpeg', resize=(640, 480))\n\nwhile True:\n\n ############################################################################\n #Pump Event\n ############################################################################\n\n #If the command is \"pump\"\n if (command==\"pump\"):\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get delay (in between steps) from the different received arguments\n delay=float(args.split(\" \")[1])\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[2])\n\n #Print status\n print(\"The pump has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the pump\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n #Actuate the pump for one step in the right direction\n pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)\n\n #Increment the counter\n counter+=1\n\n #Wait during the delay to pump at the right flowrate\n sleep(delay)\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pumping is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"pump\":\n\n #Release the pump stepper to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The pump has been interrompted.\")\n\n #Publish the status \"Interrompted\" to via MQTT to Node-RED\n client.publish(\"receiver/pump\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Focus Event\n ############################################################################\n\n #If the command is \"focus\"\n elif (command==\"focus\"):\n\n #Set the LEDs as Yellow\n rgb(255,255,0)\n\n #Get direction from the different received arguments\n direction=args.split(\" \")[0]\n\n #Get number of steps from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Print status\n print(\"The focus has been started.\")\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Start\");\n\n ########################################################################\n while True:\n\n #Depending on direction, select the right direction for the focus\n if direction == \"FORWARD\":\n direction=stepper.FORWARD\n\n if direction == \"BACKWARD\":\n direction=stepper.BACKWARD\n\n #Actuate the focus for one microstep in the right direction\n focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)\n\n #Increment the counter\n counter+=1\n\n ####################################################################\n #If counter reach the number of step, break\n if counter>nb_step:\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The focusing is done.\")\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Done\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"pump\", break this while loop\n if command!=\"focus\":\n\n #Release the focus steppers to stop power draw\n focus_stepper.release()\n\n #Print status\n print(\"The stage has been interrompted.\")\n\n #Publish the status \"Done\" to via MQTT to Node-RED\n client.publish(\"receiver/focus\", \"Interrompted\");\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ############################################################################\n #Image Event\n ############################################################################\n\n elif (command==\"image\"):\n \n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Will do my best dude\");\n\n #Get duration to wait before an image from the different received arguments\n sleep_before=int(args.split(\" \")[0])\n\n #Get number of step in between two images from the different received arguments\n nb_step=int(args.split(\" \")[1])\n\n #Get the number of frames to image from the different received arguments\n nb_frame=int(args.split(\" \")[2])\n\n #Get the segmentation status (true/false) from the different received arguments\n segmentation=str(args.split(\" \")[3])\n\n #Sleep a duration before to start acquisition\n sleep(sleep_before)\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Start\");\n\n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump duing a given number of steps (in between each image)\n for i in range(nb_step):\n\n #If the command is still image - pump a defined nb of steps\n if (command==\"image\"):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #If the command isn't image anymore - break\n else:\n\n break\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n while True:\n\n #Set the LEDs as Cyan\n rgb(0,255,255)\n\n #Increment the counter\n counter+=1\n\n #Get datetime\n datetime_tmp=datetime.now().strftime(\"%H_%M_%S_%f\")\n\n #Print datetime\n print(datetime_tmp)\n\n #Define the filename of the image\n filename = os.path.join(\"/home/pi/PlanktonScope/tmp\",datetime_tmp+\".jpg\")\n\n #Capture an image with the proper filename\n camera.capture(filename)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #Publish the name of the image to via MQTT to Node-RED\n\n client.publish(\"receiver/image\", datetime_tmp+\".jpg has been imaged.\");\n \n #Set the LEDs as Blue\n rgb(0,0,255)\n\n #Pump during a given nb of steps\n for i in range(nb_step):\n\n #Actuate the pump for one step in the FORWARD direction\n pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)\n\n #The flowrate is fixed for now.\n sleep(0.01)\n\n #Wait a fixed delay which set the framerate as < than 2 imag/sec\n sleep(0.5)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n ####################################################################\n #If counter reach the number of frame, break\n if(counter>nb_frame):\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/image\", \"Completed\");\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n if(segmentation == \"True\"):\n\n #Publish the status \"Start\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Start\");\n\n #Start the MorphoCut Pipeline\n p.run()\n\n #remove directory\n #shutil.rmtree(import_path)\n\n #Publish the status \"Completed\" to via MQTT to Node-RED\n client.publish(\"receiver/segmentation\", \"Completed\");\n\n #Set the LEDs as White\n rgb(255,255,255)\n\n #cmd = os.popen(\"rm -rf /home/pi/PlanktonScope/tmp/*.jpg\")\n\n #Let it happen\n sleep(1)\n\n #Set the LEDs as Green\n rgb(0,255,0)\n\n #End if(segmentation == \"True\"):\n\n #Change the command to not re-enter in this while loop\n command=\"wait\"\n \n #Set the LEDs as Green\n rgb(0,255,255)\n\n #Reset the counter to 0\n counter=0\n\n break\n\n ####################################################################\n #If a new received command isn't \"image\", break this while loop\n if command!=\"image\":\n\n #Release the pump steppers to stop power draw\n pump_stepper.release()\n\n #Print status\n print(\"The imaging has been interrompted.\")\n\n #Publish the status 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file changed, 0 insertions(+), 0 deletions(-) rename flows/{flows.json => dude.json} (100%) diff --git a/flows/flows.json b/flows/dude.json similarity index 100% rename from flows/flows.json rename to flows/dude.json From 63fc124d534b4928d1220451a7dbc4f14fcf9aea Mon Sep 17 00:00:00 2001 From: tpollina Date: Tue, 14 Jul 2020 18:34:53 +0200 Subject: [PATCH 17/17] Rename dude.json to main.json --- flows/{dude.json => main.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename flows/{dude.json => main.json} (100%) diff --git a/flows/dude.json b/flows/main.json similarity index 100% rename from flows/dude.json rename to flows/main.json