diff --git a/morphocut/installation.txt b/morphocut/README.md
similarity index 100%
rename from morphocut/installation.txt
rename to morphocut/README.md
diff --git a/scripts/mqtt_pump_focus_image.py b/scripts/mqtt_pump_focus_image.py
deleted file mode 100644
index d2d3b81..0000000
--- a/scripts/mqtt_pump_focus_image.py
+++ /dev/null
@@ -1,439 +0,0 @@
-import paho.mqtt.client as mqtt
-from picamera import PiCamera
-from datetime import datetime, timedelta
-from adafruit_motor import stepper
-from adafruit_motorkit import MotorKit
-from time import sleep
-import json
-
-import os
-import subprocess
-
-from skimage.util import img_as_ubyte
-
-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, FilterVariables
-
-from skimage.feature import canny
-from skimage.color import rgb2gray, label2rgb
-from skimage.morphology import disk
-from skimage.morphology import erosion, dilation, closing
-from skimage.measure import label, regionprops
-import cv2, shutil
-
-import smbus
-#fan
-bus = smbus.SMBus(1)
-################################################################################
-kit = MotorKit()
-pump_stepper = kit.stepper1
-pump_stepper.release()
-focus_stepper = kit.stepper2
-focus_stepper.release()
-
-################################################################################
-
-camera = PiCamera()
-camera.resolution = (3280, 2464)
-camera.iso = 60
-camera.shutter_speed = 500
-camera.exposure_mode = 'fixedfps'
-
-################################################################################
-message = ''
-topic = ''
-count=''
-
-################################################################################
-
-def on_connect(client, userdata, flags, rc):
- print("Connected! - " + str(rc))
- client.subscribe("actuator/#")
- rgb(0,255,0)
-def on_subscribe(client, obj, mid, granted_qos):
- print("Subscribed! - "+str(mid)+" "+str(granted_qos))
-
-def on_message(client, userdata, msg):
- print(msg.topic+" "+str(msg.qos)+" "+str(msg.payload))
- global message
- global topic
- global count
- message=str(msg.payload.decode())
- topic=msg.topic.split("/")[1]
- count=0
-
-def on_log(client, obj, level, string):
- print(string)
-
-def rgb(R,G,B):
- bus.write_byte_data(0x0d, 0x00, 0)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
-
- bus.write_byte_data(0x0d, 0x00, 1)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
-
- bus.write_byte_data(0x0d, 0x00, 2)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
- cmd="i2cdetect -y 1"
- subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)
-
-################################################################################
-client = mqtt.Client()
-client.connect("127.0.0.1",1883,60)
-client.on_connect = on_connect
-client.on_subscribe = on_subscribe
-client.on_message = on_message
-client.on_log = on_log
-client.loop_start()
-
-
-################################################################################
-while True:
-
-################################################################################
- if (topic=="pump"):
- rgb(0,0,255)
- direction=message.split(" ")[0]
- delay=float(message.split(" ")[1])
- nb_step=int(message.split(" ")[2])
-
- client.publish("receiver/pump", "Start");
-
-
- while True:
-
- if direction == "BACKWARD":
- direction=stepper.BACKWARD
- if direction == "FORWARD":
- direction=stepper.FORWARD
- count+=1
-# print(count,nb_step)
- pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)
- sleep(delay)
-
- if topic!="pump":
- pump_stepper.release()
- print("The pump has been interrompted.")
- client.publish("receiver/pump", "Interrompted");
- rgb(0,255,0)
- break
-
- if count>nb_step:
- pump_stepper.release()
- print("The pumping is done.")
- topic="wait"
- client.publish("receiver/pump", "Done");
- rgb(0,255,0)
- break
-
-################################################################################
-
- elif (topic=="focus"):
-
- rgb(255,255,0)
- direction=message.split(" ")[0]
- nb_step=int(message.split(" ")[1])
- client.publish("receiver/focus", "Start");
-
-
- while True:
-
- if direction == "FORWARD":
- direction=stepper.FORWARD
- if direction == "BACKWARD":
- direction=stepper.BACKWARD
- count+=1
-# print(count,nb_step)
- focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)
-
- if topic!="focus":
- focus_stepper.release()
- print("The stage has been interrompted.")
- client.publish("receiver/focus", "Interrompted");
- rgb(0,255,0)
- break
-
- if count>nb_step:
- focus_stepper.release()
- print("The focusing is done.")
- topic="wait"
- client.publish("receiver/focus", "Done");
- rgb(0,255,0)
- break
-
-################################################################################
-
- elif (topic=="image"):
-
- camera.start_preview(fullscreen=False, window = (160, 0, 640, 480))
-
- sleep_before=int(message.split(" ")[0])
-
- nb_step=int(message.split(" ")[1])
-
- path=str(message.split(" ")[2])
-
- nb_frame=int(message.split(" ")[3])
-
- sleep_during=int(message.split(" ")[4])
-
- #sleep a duration before to start
- sleep(sleep_before)
-
- client.publish("receiver/image", "Start");
-
- #flushing before to begin
-
- rgb(0,0,255)
- for i in range(nb_step):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- rgb(0,255,0)
-
- directory = os.path.join(path, "PlanktonScope")
- os.makedirs(directory, exist_ok=True)
-
- export = os.path.join(directory, "export")
- os.makedirs(export, exist_ok=True)
-
- date=datetime.now().strftime("%m_%d_%Y")
- time=datetime.now().strftime("%H_%M")
-
- path_date = os.path.join(directory, date)
- os.makedirs(path_date, exist_ok=True)
-
- path_time = os.path.join(path_date,time)
- os.makedirs(path_time, exist_ok=True)
- while True:
-
- count+=1
-# print(count,nb_frame)
-
- filename = os.path.join(path_time,datetime.now().strftime("%M_%S_%f")+".jpg")
-
- rgb(0,255,255)
- camera.capture(filename)
- rgb(0,255,0)
-
- client.publish("receiver/image", datetime.now().strftime("%M_%S_%f")+".jpg has been imaged.");
-
- rgb(0,0,255)
- for i in range(10):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- sleep(0.5)
- rgb(0,255,0)
-
- if(count>nb_frame):
-
- camera.stop_preview()
-
- client.publish("receiver/image", "Completed");
- # Meta data that is added to every object
- local_metadata = {
- "process_datetime": datetime.now(),
- "acq_camera_resolution" : camera.resolution,
- "acq_camera_iso" : camera.iso,
- "acq_camera_shutter_speed" : camera.shutter_speed
- }
- global_metadata = None
- config_txt = None
- RAW = None
- CLEAN = None
- ANNOTATED = None
- OBJECTS = None
- archive_fn = None
-
- config_txt = open('/home/pi/PlanktonScope/config.txt','r')
- node_red_metadata = json.loads(config_txt.read())
-
- global_metadata = {**local_metadata, **node_red_metadata}
-
- RAW = os.path.join(path_time, "RAW")
- os.makedirs(RAW, exist_ok=True)
-
- os.system("mv "+str(path_time)+"/*.jpg "+str(RAW))
-
- CLEAN = os.path.join(path_time, "CLEAN")
- os.makedirs(CLEAN, exist_ok=True)
-
- ANNOTATED = os.path.join(path_time, "ANNOTATED")
- os.makedirs(ANNOTATED, exist_ok=True)
-
- OBJECTS = os.path.join(path_time, "OBJECTS")
- os.makedirs(OBJECTS, exist_ok=True)
-
- archive_fn = os.path.join(directory,"export", str(date)+"_"+str(time)+"_ecotaxa_export.zip")
-
- client.publish("receiver/segmentation", "Start");
- # Define processing pipeline
- # Define processing pipeline
- with Pipeline() as p:
- # Recursively find .jpg files in import_path.
- # Sort to get consective frames.
- abs_path = Find(RAW, [".jpg"], sort=True, verbose=True)
-
- FilterVariables(abs_path)
-
- # Extract name from abs_path
- name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
-
- Call(rgb, 0,255,0)
- # Read image
- img = ImageReader(abs_path)
-
- # Show progress bar for frames
- #TQDM(Format("Frame {name}", name=name))
-
- # Apply running median to approximate the background image
- flat_field = RunningMedian(img, 5)
-
- # Correct image
- img = img / flat_field
-
- FilterVariables(name,img)
-
- # Rescale intensities and convert to uint8 to speed up calculations
- img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
-
- frame_fn = Format(os.path.join(CLEAN, "{name}.jpg"), name=name)
-
- ImageWriter(frame_fn, img)
-
- FilterVariables(name,img)
-
- # Convert image to uint8 gray
- img_gray = RGB2Gray(img)
-
- # ?
- img_gray = Call(img_as_ubyte, img_gray)
-
- #Canny edge detection
- img_canny = Call(cv2.Canny, img_gray, 50,100)
-
- #Dilate
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
- img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)
-
- #Close
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))
- img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)
-
- #Erode
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
- mask = Call(cv2.erode, img_close, kernel, iterations=2)
-
- FilterVariables(name,img,img_gray,mask)
-
- # Find objects
- regionprops = FindRegions(
- mask, img_gray, min_area=1000, padding=10, warn_empty=name
- )
-
- Call(rgb, 255,0,255)
- # For an object, extract a vignette/ROI from the image
- roi_orig = ExtractROI(img, regionprops, bg_color=255)
-
- # Generate an object identifier
- i = Enumerate()
- #Call(print,i)
-
- object_id = Format("{name}_{i:d}", name=name, i=i)
- #Call(print,object_id)
-
- object_fn = Format(os.path.join(OBJECTS, "{name}.jpg"), name=object_id)
-
- ImageWriter(object_fn, roi_orig)
-
- # 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
- )
- json_meta = Call(json.dumps,meta, sort_keys=True, default=str)
-
- Call(client.publish, "receiver/segmentation/metric", json_meta)
-
- # Add object_id to the metadata dictionary
- meta["object_id"] = object_id
-
- # Generate object filenames
- orig_fn = Format("{object_id}.jpg", object_id=object_id)
-
- FilterVariables(orig_fn,roi_orig,meta,object_id)
- # 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))
-
- Call(client.publish, "receiver/segmentation/object_id", object_id)
-
- meta=None
- FilterVariables(meta)
-
-
- p.run()
-
- #remove directory
- #shutil.rmtree(import_path)
-
- client.publish("receiver/segmentation", "Completed");
-
- rgb(255,255,255)
- sleep(sleep_during)
- rgb(0,255,0)
-
- date=datetime.now().strftime("%m_%d_%Y")
- time=datetime.now().strftime("%H_%M")
-
- path_date = os.path.join(directory, date)
- os.makedirs(path_date, exist_ok=True)
-
- path_time = os.path.join(path_date,time)
- os.makedirs(path_time, exist_ok=True)
-
- rgb(0,0,255)
- for i in range(nb_step):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- rgb(0,255,0)
-
- os.makedirs(path_time, exist_ok=True)
- count=0
-
- if topic!="image":
- pump_stepper.release()
- print("The imaging has been interrompted.")
- client.publish("receiver/image", "Interrompted");
- rgb(0,255,0)
- count=0
- break
-
- else:
-# print("Waiting")
- sleep(1)
-
-
diff --git a/scripts/mqtt_pump_focus_image_segment_strem.py b/scripts/mqtt_pump_focus_image_segment_strem.py
deleted file mode 100644
index c1e7a27..0000000
--- a/scripts/mqtt_pump_focus_image_segment_strem.py
+++ /dev/null
@@ -1,529 +0,0 @@
-################################################################################
-#Actuator Libraries
-################################################################################
-
-#Library for exchaning messages with Node-RED
-import paho.mqtt.client as mqtt
-
-#Library to control the PiCamera
-from picamera import PiCamera
-
-#Libraries to control the steppers for focusing and pumping
-from adafruit_motor import stepper
-from adafruit_motorkit import MotorKit
-
-#Library to send command over I2C for the light module on the fan
-import smbus
-
-################################################################################
-#Practical Libraries
-################################################################################
-
-#Library to get date and time for folder name and filename
-from datetime import datetime, timedelta
-
-#Library to be able to sleep for a duration
-from time import sleep
-
-#Libraries manipulate json format, execute bash commands
-import json, shutil, os, subprocess
-
-################################################################################
-#Morphocut Libraries
-################################################################################
-
-from skimage.util import img_as_ubyte
-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, FilterVariables
-
-################################################################################
-#Other image processing Libraries
-################################################################################
-
-from skimage.feature import canny
-from skimage.color import rgb2gray, label2rgb
-from skimage.morphology import disk
-from skimage.morphology import erosion, dilation, closing
-from skimage.measure import label, regionprops
-#pip3 install opencv-python
-import cv2
-
-
-################################################################################
-#STREAMING
-################################################################################
-import io
-import picamera
-import logging
-import socketserver
-from threading import Condition
-from http import server
-import threading
-
-PAGE="""\
-
-
-picamera MJPEG streaming demo
-
-
-
-
-
-"""
-
-class StreamingOutput(object):
- def __init__(self):
- self.frame = None
- self.buffer = io.BytesIO()
- self.condition = Condition()
-
- def write(self, buf):
- if buf.startswith(b'\xff\xd8'):
- # New frame, copy the existing buffer's content and notify all
- # clients it's available
- self.buffer.truncate()
- with self.condition:
- self.frame = self.buffer.getvalue()
- self.condition.notify_all()
- self.buffer.seek(0)
- return self.buffer.write(buf)
-
-class StreamingHandler(server.BaseHTTPRequestHandler):
- def do_GET(self):
- if self.path == '/':
- self.send_response(301)
- self.send_header('Location', '/index.html')
- self.end_headers()
- elif self.path == '/index.html':
- content = PAGE.encode('utf-8')
- self.send_response(200)
- self.send_header('Content-Type', 'text/html')
- self.send_header('Content-Length', len(content))
- self.end_headers()
- self.wfile.write(content)
- elif self.path == '/stream.mjpg':
- self.send_response(200)
- self.send_header('Age', 0)
- self.send_header('Cache-Control', 'no-cache, private')
- self.send_header('Pragma', 'no-cache')
- self.send_header('Content-Type', 'multipart/x-mixed-replace; boundary=FRAME')
- self.end_headers()
- try:
- while True:
- with output.condition:
- output.condition.wait()
- frame = output.frame
- self.wfile.write(b'--FRAME\r\n')
- self.send_header('Content-Type', 'image/jpeg')
- self.send_header('Content-Length', len(frame))
- self.end_headers()
- self.wfile.write(frame)
- self.wfile.write(b'\r\n')
- except Exception as e:
- logging.warning(
- 'Removed streaming client %s: %s',
- self.client_address, str(e))
- else:
- self.send_error(404)
- self.end_headers()
-
-class StreamingServer(socketserver.ThreadingMixIn, server.HTTPServer):
- allow_reuse_address = True
- daemon_threads = True
-################################################################################
-#MQTT core functions
-################################################################################
-#Run this function in order to connect to the client (Node-RED)
-def on_connect(client, userdata, flags, rc):
- #Print when connected
- print("Connected! - " + str(rc))
- #When connected, run subscribe()
- client.subscribe("actuator/#")
- #Turn green the light module
- rgb(0,255,0)
-
-#Run this function in order to subscribe to all the topics begining by actuator
-def on_subscribe(client, obj, mid, granted_qos):
- #Print when subscribed
- print("Subscribed! - "+str(mid)+" "+str(granted_qos))
-
-#Run this command when Node-RED is sending a message on the subscribed topic
-def on_message(client, userdata, msg):
- #Print the topic and the message
- print(msg.topic+" "+str(msg.qos)+" "+str(msg.payload))
- #Update the global variables command, args and counter
- global command
- global args
- global counter
- #Parse the topic to find the command. ex : actuator/pump -> pump
- command=msg.topic.split("/")[1]
- #Decode the message to find the arguments
- args=str(msg.payload.decode())
- #Reset the counter to 0
- counter=0
-
-################################################################################
-#Actuators core functions
-################################################################################
-def rgb(R,G,B):
- #Update LED n°1
- bus.write_byte_data(0x0d, 0x00, 0)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
-
- #Update LED n°2
- bus.write_byte_data(0x0d, 0x00, 1)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
-
- #Update LED n°3
- bus.write_byte_data(0x0d, 0x00, 2)
- bus.write_byte_data(0x0d, 0x01, R)
- bus.write_byte_data(0x0d, 0x02, G)
- bus.write_byte_data(0x0d, 0x03, B)
-
- #Update the I2C Bus in order to really update the LEDs new values
- cmd="i2cdetect -y 1"
- subprocess.Popen(cmd.split(),stdout=subprocess.PIPE)
-
-
-
-################################################################################
-#Init function - executed only once
-################################################################################
-
-#define the bus used to actuate the light module on the fan
-bus = smbus.SMBus(1)
-
-#define the names for the 2 exsting steppers
-kit = MotorKit()
-pump_stepper = kit.stepper1
-pump_stepper.release()
-focus_stepper = kit.stepper2
-focus_stepper.release()
-
-#Precise the settings of the PiCamera
-camera = PiCamera()
-camera.resolution = (3280, 2464)
-camera.iso = 60
-camera.shutter_speed = 500
-camera.exposure_mode = 'fixedfps'
-
-#Declare the global variables command, args and counter
-command = ''
-args = ''
-counter=''
-
-client = mqtt.Client()
-client.connect("127.0.0.1",1883,60)
-client.on_connect = on_connect
-client.on_subscribe = on_subscribe
-client.on_message = on_message
-client.loop_start()
-
-################################################################################
-
-local_metadata = {
- "process_datetime": datetime.now(),
- "acq_camera_resolution" : camera.resolution,
- "acq_camera_iso" : camera.iso,
- "acq_camera_shutter_speed" : camera.shutter_speed
-}
-
-config_txt = open('/home/pi/PlanktonScope/config.txt','r')
-node_red_metadata = json.loads(config_txt.read())
-
-global_metadata = {**local_metadata, **node_red_metadata}
-
-archive_fn = os.path.join("/home/pi/PlanktonScope/","export", "ecotaxa_export.zip")
-# Define processing pipeline
-
-with Pipeline() as p:
- # Recursively find .jpg files in import_path.
- # Sort to get consective frames.
- abs_path = Find("/home/pi/PlanktonScope/tmp", [".jpg"], sort=True, verbose=True)
-
-
- # Extract name from abs_path
- name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
-
- Call(rgb, 0,255,0)
-
- # Read image
- img = ImageReader(abs_path)
-
- # Show progress bar for frames
- TQDM(Format("Frame {name}", name=name))
-
- # Apply running median to approximate the background image
- flat_field = RunningMedian(img, 5)
-
- # Correct image
- img = img / flat_field
-
- # Rescale intensities and convert to uint8 to speed up calculations
- img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
-
- FilterVariables(name,img)
-# frame_fn = Format(os.path.join("/home/pi/PlanktonScope/tmp","CLEAN", "{name}.jpg"), name=name)
-
-# ImageWriter(frame_fn, img)
-
- # Convert image to uint8 gray
- img_gray = RGB2Gray(img)
-
- # ?
- img_gray = Call(img_as_ubyte, img_gray)
-
- #Canny edge detection
- img_canny = Call(cv2.Canny, img_gray, 50,100)
-
- #Dilate
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
- img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)
-
- #Close
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))
- img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)
-
- #Erode
- kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
- mask = Call(cv2.erode, img_close, kernel, iterations=2)
-
- # Find objects
- regionprops = FindRegions(
- mask, img_gray, min_area=1000, padding=10, warn_empty=name
- )
-
- Call(rgb, 255,0,255)
- # For an object, extract a vignette/ROI from the image
- roi_orig = ExtractROI(img, regionprops, bg_color=255)
-
- # Generate an object identifier
- i = Enumerate()
- #Call(print,i)
-
- object_id = Format("{name}_{i:d}", name=name, i=i)
- #Call(print,object_id)
- object_fn = Format(os.path.join("/home/pi/PlanktonScope/","OBJECTS", "{name}.jpg"), name=object_id)
-
- ImageWriter(object_fn, roi_orig)
-
- # 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
- )
-
- json_meta = Call(json.dumps,meta, sort_keys=True, default=str)
-
- Call(client.publish, "receiver/segmentation/metric", json_meta)
-
- # Add object_id to the metadata dictionary
- meta["object_id"] = object_id
-
- # Generate object filenames
- orig_fn = Format("{object_id}.jpg", object_id=object_id)
-
- # 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))
-
- Call(client.publish, "receiver/segmentation/object_id", object_id)
-
-
-output = StreamingOutput()
-address = ('', 8000)
-server = StreamingServer(address, StreamingHandler)
-
-threading.Thread(target=server.serve_forever).start()
-################################################################################
-
-camera.start_recording(output, format='mjpeg', resize=(640, 480))
-while True:
-
- if (command=="pump"):
- rgb(0,0,255)
- direction=args.split(" ")[0]
- delay=float(args.split(" ")[1])
- nb_step=int(args.split(" ")[2])
-
- client.publish("receiver/pump", "Start");
-
-
- while True:
-
- if direction == "BACKWARD":
- direction=stepper.BACKWARD
- if direction == "FORWARD":
- direction=stepper.FORWARD
- pump_stepper.onestep(direction=direction, style=stepper.DOUBLE)
- counter+=1
- sleep(delay)
-
- if command!="pump":
- pump_stepper.release()
- print("The pump has been interrompted.")
- client.publish("receiver/pump", "Interrompted");
- rgb(0,255,0)
- break
-
- if counter>nb_step:
- pump_stepper.release()
- print("The pumping is done.")
- command="wait"
- client.publish("receiver/pump", "Done");
- rgb(0,255,0)
- break
-
-################################################################################
-
- elif (command=="focus"):
-
- rgb(255,255,0)
- direction=args.split(" ")[0]
- nb_step=int(args.split(" ")[1])
- client.publish("receiver/focus", "Start");
-
-
- while True:
-
- if direction == "FORWARD":
- direction=stepper.FORWARD
- if direction == "BACKWARD":
- direction=stepper.BACKWARD
- counter+=1
- focus_stepper.onestep(direction=direction, style=stepper.MICROSTEP)
-
- if command!="focus":
- focus_stepper.release()
- print("The stage has been interrompted.")
- client.publish("receiver/focus", "Interrompted");
- rgb(0,255,0)
- break
-
- if counter>nb_step:
- focus_stepper.release()
- print("The focusing is done.")
- command="wait"
- client.publish("receiver/focus", "Done");
- rgb(0,255,0)
- break
-
-################################################################################
-
- elif (command=="image"):
-
-
- sleep_before=int(args.split(" ")[0])
-
- nb_step=int(args.split(" ")[1])
-
- path=str(args.split(" ")[2])
-
- nb_frame=int(args.split(" ")[3])
-
- sleep_during=int(args.split(" ")[4])
-
- #sleep a duration before to start
- sleep(sleep_before)
-
-
- client.publish("receiver/image", "Start");
-
- #flushing before to begin
-
- rgb(0,0,255)
- for i in range(nb_step):
- if (command=="image"):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- else:
- break
- rgb(0,255,0)
-
- while True:
-
- counter+=1
- print(datetime.now().strftime("%H_%M_%S_%f"))
- filename = os.path.join("/home/pi/PlanktonScope/tmp",datetime.now().strftime("%M_%S_%f")+".jpg")
-
- rgb(0,255,255)
- camera.capture(filename)
- rgb(0,255,0)
-
- client.publish("receiver/image", datetime.now().strftime("%M_%S_%f")+".jpg has been imaged.");
-
- rgb(0,0,255)
- for i in range(10):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- sleep(0.5)
- rgb(0,255,0)
-
- if(counter>nb_frame):
-
-# camera.stop_preview()
-
- client.publish("receiver/image", "Completed");
- # Meta data that is added to every object
-
-
-
- client.publish("receiver/segmentation", "Start");
- # Define processing pipeline
-
-
- p.run()
-
- #remove directory
- #shutil.rmtree(import_path)
-
- client.publish("receiver/segmentation", "Completed");
-
-
- cmd = os.popen("rm -rf /home/pi/PlanktonScope/tmp/*.jpg")
-
- rgb(255,255,255)
- sleep(sleep_during)
- rgb(0,255,0)
-
-
- rgb(0,0,255)
- for i in range(nb_step):
- pump_stepper.onestep(direction=stepper.FORWARD, style=stepper.DOUBLE)
- sleep(0.01)
- rgb(0,255,0)
-
- counter=0
-
-
- if command!="image":
- pump_stepper.release()
- print("The imaging has been interrompted.")
- client.publish("receiver/image", "Interrompted");
- rgb(0,255,0)
- counter=0
- break
-
- else:
-# print("Waiting")
- sleep(1)