diff --git a/docs/mqtt_messages.md b/docs/mqtt_messages.md
index edde1d0..9b51c06 100644
--- a/docs/mqtt_messages.md
+++ b/docs/mqtt_messages.md
@@ -68,13 +68,13 @@ This topic controls the camera and capture. The message allowed is a JSON messag
```json
{
"action": "image",
- "sleep": 5,
+ "pump_direction": "FORWARD",
"volume": 1,
"nb_frame": 200
}
```
-Sleep in seconds and volume in mL.
+Volume is in mL.
This topic can also receive a config update message:
```json
diff --git a/flows/main.json b/flows/main.json
index 395da46..f29a74b 100644
--- a/flows/main.json
+++ b/flows/main.json
@@ -80,6 +80,17 @@
"env": [],
"color": "#DDAA99"
},
+ {
+ "id": "4ed15f63.9d1468",
+ "type": "subflow",
+ "name": "MQTT Receive",
+ "info": "",
+ "category": "",
+ "in": [],
+ "out": [],
+ "env": [],
+ "color": "#DDAA99"
+ },
{
"id": "da2c279f.cbe318",
"type": "ui_group",
@@ -286,11 +297,12 @@
{
"id": "36739a35.7cce36",
"type": "ui_tab",
+ "z": "",
"name": "Gallery",
"icon": "fa fa-file-image-o",
"order": 6,
- "disabled": false,
- "hidden": false
+ "disabled": true,
+ "hidden": true
},
{
"id": "c0ebfc57.42527",
@@ -473,10 +485,11 @@
{
"id": "b5d61bc7.54fe48",
"type": "ui_group",
- "name": "Config",
+ "z": "",
+ "name": "Statistics",
"tab": "c9194f02.9d5e9",
"order": 5,
- "disp": false,
+ "disp": true,
"width": "10",
"collapse": false
},
@@ -552,15 +565,6 @@
"willQos": "0",
"willPayload": ""
},
- {
- "id": "c669e9d3.b5cfd",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "4248342d.e55fac",
- "order": 7,
- "width": 10,
- "height": 1
- },
{
"id": "abeb6dad.635a2",
"type": "ui_group",
@@ -572,60 +576,6 @@
"width": 12,
"collapse": false
},
- {
- "id": "a3de84cd.c01b6",
- "type": "ui_tab",
- "name": "Management",
- "icon": "dashboard",
- "order": 2,
- "disabled": false,
- "hidden": false
- },
- {
- "id": "6d0a997.393d868",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "567a49a4.244cb8",
- "order": 4,
- "width": 10,
- "height": 1
- },
- {
- "id": "f03eb9bf.839b88",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "4322c187.e73e5",
- "order": 3,
- "width": 10,
- "height": 1
- },
- {
- "id": "ba8b3166.35cf5",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "4322c187.e73e5",
- "order": 5,
- "width": 1,
- "height": 1
- },
- {
- "id": "e86b3059.c9a53",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "4322c187.e73e5",
- "order": 7,
- "width": 10,
- "height": 1
- },
- {
- "id": "9e9d9991.80e7e8",
- "type": "ui_spacer",
- "name": "spacer",
- "group": "b7919ae2.c01788",
- "order": 2,
- "width": 5,
- "height": 1
- },
{
"id": "cf5d9f0e.d57e7",
"type": "ui_group",
@@ -710,23 +660,89 @@
"collapse": false
},
{
- "id": "2ccfcb49.5e95cc",
+ "id": "70de8209.68416c",
"type": "ui_group",
- "name": "Object metadata",
- "tab": "a2259300.ec17d",
- "order": 2,
+ "z": "",
+ "name": "Status",
+ "tab": "c9194f02.9d5e9",
+ "order": 7,
"disp": true,
- "width": "24",
- "collapse": true
+ "width": 10,
+ "collapse": false
},
{
- "id": "a2259300.ec17d",
- "type": "ui_tab",
- "name": "Acquisition",
- "icon": "fa-eyedropper",
- "order": 1,
- "disabled": false,
- "hidden": false
+ "id": "46be9c86.dea684",
+ "type": "ui_group",
+ "z": "",
+ "name": "Status",
+ "tab": "8d16beb8.9b3fb",
+ "order": 3,
+ "disp": true,
+ "width": "12",
+ "collapse": false
+ },
+ {
+ "id": "e764dcc5.9e55c8",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "4248342d.e55fac",
+ "order": 7,
+ "width": 10,
+ "height": 1
+ },
+ {
+ "id": "60e1ee82.b706e8",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "4322c187.e73e5",
+ "order": 4,
+ "width": 10,
+ "height": 1
+ },
+ {
+ "id": "cf7da2b1.3c81b",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "4322c187.e73e5",
+ "order": 7,
+ "width": 10,
+ "height": 1
+ },
+ {
+ "id": "2e29ff58.977b88",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "b5d61bc7.54fe48",
+ "order": 2,
+ "width": 6,
+ "height": 1
+ },
+ {
+ "id": "86d29a27.55d4e",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "b5d61bc7.54fe48",
+ "order": 3,
+ "width": 1,
+ "height": 1
+ },
+ {
+ "id": "9b6d3ed4.6dfcc",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "b5d61bc7.54fe48",
+ "order": 5,
+ "width": 1,
+ "height": 1
+ },
+ {
+ "id": "7d4d95a.48907ec",
+ "type": "ui_spacer",
+ "name": "spacer",
+ "group": "b7919ae2.c01788",
+ "order": 2,
+ "width": 5,
+ "height": 1
},
{
"id": "4e78af2d.90be7",
@@ -877,9 +893,9 @@
"height": 0,
"gtype": "gage",
"title": "CPU Temperature",
- "label": "C",
+ "label": "°C",
"format": "{{value}}",
- "min": "35",
+ "min": "30",
"max": "55",
"colors": [
"#00b500",
@@ -930,13 +946,14 @@
"interpolate": "linear",
"nodata": "",
"dot": false,
- "ymin": "",
- "ymax": "",
+ "ymin": "30",
+ "ymax": "60",
"removeOlder": "20",
"removeOlderPoints": "200",
"removeOlderUnit": "60",
"cutout": 0,
"useOneColor": false,
+ "useUTC": false,
"colors": [
"#1f77b4",
"#aec7e8",
@@ -981,7 +998,7 @@
"id": "c2b8d8b.0d90328",
"type": "exec",
"z": "1371dec5.76e671",
- "command": "free | grep Mem | awk '{print 100*($3)/$2}' | awk -F \".\" '{print $1}' | tr -d \"\\n\"",
+ "command": "free | grep Mem | awk '{print 100*($2-$7)/$2}' | awk '{print int($1+0.5)}' | tr -d \"\\n\"",
"addpay": false,
"append": "",
"useSpawn": "",
@@ -1009,7 +1026,7 @@
"height": 0,
"gtype": "gage",
"title": "Processor",
- "label": "CPU",
+ "label": "%",
"format": "{{value}}",
"min": 0,
"max": "100",
@@ -1020,7 +1037,7 @@
],
"seg1": "",
"seg2": "",
- "x": 520,
+ "x": 580,
"y": 180,
"wires": []
},
@@ -1035,7 +1052,7 @@
"height": 0,
"gtype": "gage",
"title": "Memory",
- "label": "RAM",
+ "label": "%",
"format": "{{value}}",
"min": 0,
"max": "100",
@@ -1046,7 +1063,7 @@
],
"seg1": "",
"seg2": "",
- "x": 520,
+ "x": 580,
"y": 280,
"wires": []
},
@@ -1054,7 +1071,7 @@
"id": "3910d662.fa1f7a",
"type": "exec",
"z": "1371dec5.76e671",
- "command": "df -h | grep /dev/root | awk -F ' ' '{print $3}' | tr -d G | tr \"\\n$\" \"\\ \" | sed 's/,/./' | tr -d \" \" ",
+ "command": "df -h | grep /dev/root | awk -F ' ' '{print $5}' | tr -d % | tr \"\\n$\" \"\\ \" | sed 's/,/./' | tr -d \" \"",
"addpay": false,
"append": "",
"useSpawn": "",
@@ -1082,10 +1099,10 @@
"height": 0,
"gtype": "gage",
"title": "Disk",
- "label": "Go",
+ "label": "%",
"format": "{{value}}",
"min": 0,
- "max": "256",
+ "max": "100",
"colors": [
"#00b500",
"#e6e600",
@@ -1093,7 +1110,7 @@
],
"seg1": "",
"seg2": "",
- "x": 510,
+ "x": 570,
"y": 380,
"wires": []
},
@@ -1133,7 +1150,7 @@
],
"useOldStyle": true,
"outputs": 1,
- "x": 510,
+ "x": 570,
"y": 220,
"wires": [
[]
@@ -1176,7 +1193,7 @@
],
"useOldStyle": true,
"outputs": 1,
- "x": 510,
+ "x": 570,
"y": 320,
"wires": [
[]
@@ -1198,10 +1215,10 @@
"interpolate": "linear",
"nodata": "",
"dot": false,
- "ymin": "",
- "ymax": "",
+ "ymin": "0",
+ "ymax": "100",
"removeOlder": "4",
- "removeOlderPoints": "",
+ "removeOlderPoints": "200",
"removeOlderUnit": "3600",
"cutout": 0,
"useOneColor": false,
@@ -1219,7 +1236,7 @@
],
"useOldStyle": true,
"outputs": 1,
- "x": 510,
+ "x": 570,
"y": 420,
"wires": [
[]
@@ -1229,20 +1246,17 @@
"id": "1cd5b4c0.46af9b",
"type": "inject",
"z": "1371dec5.76e671",
- "name": "",
+ "name": "update: 15s",
"props": [
{
- "p": "payload",
- "v": "",
- "vt": "date"
+ "p": "payload"
},
{
"p": "topic",
- "v": "",
- "vt": "string"
+ "vt": "str"
}
],
- "repeat": "60",
+ "repeat": "5",
"crontab": "",
"once": false,
"onceDelay": "",
@@ -1420,7 +1434,7 @@
"rules": [
{
"t": "gt",
- "v": "45",
+ "v": "50",
"vt": "num"
},
{
@@ -1447,7 +1461,7 @@
"id": "5d4f3e71.1bad4",
"type": "change",
"z": "1371dec5.76e671",
- "name": "",
+ "name": "Set OFF",
"rules": [
{
"t": "set",
@@ -1462,7 +1476,7 @@
"from": "",
"to": "",
"reg": false,
- "x": 740,
+ "x": 720,
"y": 60,
"wires": [
[
@@ -1474,7 +1488,7 @@
"id": "a25d6486.e1ce28",
"type": "change",
"z": "1371dec5.76e671",
- "name": "",
+ "name": "Set ON",
"rules": [
{
"t": "set",
@@ -1489,7 +1503,7 @@
"from": "",
"to": "",
"reg": false,
- "x": 740,
+ "x": 720,
"y": 20,
"wires": [
[
@@ -1593,7 +1607,7 @@
"label": "Acquisition unique ID*",
"tooltip": "",
"group": "4322c187.e73e5",
- "order": 2,
+ "order": 1,
"width": 5,
"height": 1,
"passthru": true,
@@ -1753,7 +1767,7 @@
"tooltip": "",
"group": "707d9797.c8e798",
"order": 3,
- "width": 4,
+ "width": 3,
"height": 1,
"passthru": true,
"mode": "number",
@@ -2008,7 +2022,7 @@
"noerr": 0,
"initialize": "",
"finalize": "",
- "x": 960,
+ "x": 1100,
"y": 520,
"wires": [
[]
@@ -2194,7 +2208,7 @@
"z": "b771c342.49603",
"name": "object_lat",
"label": "Latitude of throw",
- "tooltip": "In decimal degrees",
+ "tooltip": "36°57'9\" N",
"group": "cef1e703.bcf3c8",
"order": 1,
"width": 12,
@@ -2207,7 +2221,7 @@
"y": 520,
"wires": [
[
- "9f501f49.45645"
+ "42795da1.0ee104"
]
]
},
@@ -2217,7 +2231,7 @@
"z": "b771c342.49603",
"name": "object_lon",
"label": "Longitude of throw",
- "tooltip": "",
+ "tooltip": "110°4'21\" W",
"group": "cef1e703.bcf3c8",
"order": 2,
"width": 12,
@@ -2226,11 +2240,11 @@
"mode": "number",
"delay": 300,
"topic": "object_lon",
- "x": 660,
+ "x": 650,
"y": 560,
"wires": [
[
- "9f501f49.45645"
+ "42795da1.0ee104"
]
]
},
@@ -2377,7 +2391,7 @@
"name": "Backward",
"group": "707d9797.c8e798",
"order": 2,
- "width": 5,
+ "width": 4,
"height": 1,
"passthru": false,
"label": "",
@@ -2838,7 +2852,7 @@
"label": "Volume to pass (ml)",
"tooltip": "",
"group": "4322c187.e73e5",
- "order": 1,
+ "order": 2,
"width": 5,
"height": 1,
"passthru": true,
@@ -2989,7 +3003,7 @@
"label": "Comment",
"tooltip": "",
"group": "567a49a4.244cb8",
- "order": 5,
+ "order": 1,
"width": 0,
"height": 0,
"passthru": true,
@@ -3004,528 +3018,6 @@
]
]
},
- {
- "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": [
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- "addpay": false,
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"type": "exec",
"z": "1371dec5.76e671",
- "command": "git --git-dir /home/pi/PlanktonScope/.git/ stash",
+ "command": "/home/pi/PlanktoScope/scripts/bash/update.sh",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "2",
"oldrc": false,
- "name": "git stash",
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- "wires": [
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"name": "Python soft kill",
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"x": 130,
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"id": "c9f510c0.7d1328",
"type": "function",
"z": "baa1e3d9.cb29d",
- "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 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 if (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 {\n msg.payload={\"action\":\"image\", \n \"sleep\":sleep_before,\n \"volume\":nb_step,\n \"nb_frame\":nb_frame,\n }\n}\n\nreturn msg;",
+ "name": "Image control",
+ "func": "state = global.get(\"state\");\nglobal.set('img_counter',0);\nglobal.set('obj_counter',0);\nif (state === null){state=\"free\"}\n\nvar nb_frame= global.get(\"nb_frame\");\nvar 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\");\nvar pump_direction= global.get(\"pump_direction\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Type of the flowcell\"\n}else if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Lower fraction size\"\n}else if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Upper fraction size\"\n}else if (acq_volume === undefined || acq_volume === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume to image\"\n}else if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Acquisition ID\"\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 (pump_direction === undefined || pump_direction === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Pump direction\";\n \n}else {\n msg.payload={\"action\":\"image\", \n \"sleep\":1,\n \"pump_direction\": pump_direction,\n \"volume\":acq_volume/nb_frame,\n \"nb_frame\":nb_frame,\n }\n}\n\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
- "x": 880,
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"wires": [
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+ "52ea7d01.711034",
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"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"
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"repair": false,
"outputs": 2,
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"topic": "",
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+ "x": 1230,
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"broker": "8dc3722c.06efa8",
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+ "x": 1210,
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@@ -4865,24 +4319,24 @@
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
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{
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"type": "ui_switch",
"z": "baa1e3d9.cb29d",
- "name": "",
- "label": "Pump FORWARD/BACKWARD",
- "tooltip": "",
+ "name": "Pump direction",
+ "label": "Pump direction",
+ "tooltip": "BACKWARD / FORWARD",
"group": "4322c187.e73e5",
- "order": 4,
- "width": 3,
+ "order": 5,
+ "width": 5,
"height": 1,
"passthru": true,
"decouple": "false",
- "topic": "",
+ "topic": "pump_direction",
"style": "",
"onvalue": "FORWARD",
"onvalueType": "str",
@@ -4892,10 +4346,13 @@
"offvalueType": "str",
"officon": "",
"offcolor": "",
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+ "x": 520,
+ "y": 660,
"wires": [
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"z": "baa1e3d9.cb29d",
"name": "Encapsulate config",
- "func": "msg.payload = {\n \"action\":\"update_config\", \n \"config\":{\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 \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n \"acq_nb_frame\":global.get(\"custom_nb_frame\"),\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;",
+ "func": "msg.payload = {\n \"action\":\"update_config\", \n \"config\":{\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 \"acq_camera_name\":global.get(\"acq_camera_name\"),\n \"acq_nb_frame\":global.get(\"nb_frame\"),\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,
"initialize": "",
"finalize": "",
- "x": 750,
- "y": 420,
+ "x": 950,
+ "y": 540,
"wires": [
[
"c3e50240.82aa58"
@@ -4931,11 +4388,11 @@
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
- "x": 720,
- "y": 460,
+ "x": 920,
+ "y": 580,
"wires": [
[
- "c9f510c0.7d1328"
+ "d6ebaa2.ea21d58"
]
]
},
@@ -4946,7 +4403,7 @@
"name": "",
"group": "4322c187.e73e5",
"order": 6,
- "width": 6,
+ "width": 5,
"height": 1,
"passthru": false,
"label": "Update config",
@@ -4958,7 +4415,7 @@
"payloadType": "str",
"topic": "imager/image",
"x": 520,
- "y": 420,
+ "y": 540,
"wires": [
[
"52ea7d01.711034",
@@ -5290,7 +4747,7 @@
"z": "b771c342.49603",
"name": "object_lat_end",
"label": "Latitude of retrieval",
- "tooltip": "",
+ "tooltip": "36°57'9\" N",
"group": "cf5d9f0e.d57e7",
"order": 1,
"width": 12,
@@ -5303,7 +4760,7 @@
"y": 700,
"wires": [
[
- "9f501f49.45645"
+ "42795da1.0ee104"
]
]
},
@@ -5313,7 +4770,7 @@
"z": "b771c342.49603",
"name": "object_lon_end",
"label": "Longitude of retrieval",
- "tooltip": "",
+ "tooltip": "110°4'21\" W",
"group": "cf5d9f0e.d57e7",
"order": 2,
"width": 12,
@@ -5326,7 +4783,7 @@
"y": 740,
"wires": [
[
- "9f501f49.45645"
+ "42795da1.0ee104"
]
]
},
@@ -5432,7 +4889,7 @@
"type": "function",
"z": "1371dec5.76e671",
"name": "store git rev",
- "func": "msg.payload = \"PlanktoScope v2.2-\"+msg.payload\n\nglobal.set(\"acq_software\",msg.payload);\n\nreturn msg\n",
+ "func": "msg.payload = \"PlanktoScope v2.2-\"+msg.payload.trim()\n\nglobal.set(\"acq_software\",msg.payload);\n\nreturn msg\n",
"outputs": 1,
"noerr": 0,
"initialize": "",
@@ -5481,8 +4938,8 @@
"type": "subflow:1c24ad9c.bebec2",
"z": "baa1e3d9.cb29d",
"name": "",
- "x": 80,
- "y": 120,
+ "x": 90,
+ "y": 160,
"wires": [
[
"f3658d30.b8448",
@@ -5498,10 +4955,12 @@
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_id",
- "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;",
+ "func": "msg.payload = msg.payload.acq_id;\nreturn msg;",
"outputs": 1,
"noerr": 0,
- "x": 310,
+ "initialize": "",
+ "finalize": "",
+ "x": 300,
"y": 240,
"wires": [
[
@@ -5579,6 +5038,8 @@
"func": "msg.payload = msg.payload.acq_volume;\nreturn msg;",
"outputs": 1,
"noerr": 0,
+ "initialize": "",
+ "finalize": "",
"x": 320,
"y": 200,
"wires": [
@@ -5671,20 +5132,20 @@
"id": "a0e2d78c.a587e",
"type": "inject",
"z": "1371dec5.76e671",
- "name": "ON",
+ "name": "Default: ON",
"props": [
{
"p": "payload"
}
],
- "repeat": "60",
+ "repeat": "",
"crontab": "",
"once": true,
"onceDelay": "",
"topic": "",
"payload": "true",
"payloadType": "bool",
- "x": 130,
+ "x": 110,
"y": 620,
"wires": [
[
@@ -5740,5 +5201,833 @@
"wires": [
[]
]
+ },
+ {
+ "id": "48879182.6fd718",
+ "type": "inject",
+ "z": "baa1e3d9.cb29d",
+ "name": "Default: 10",
+ "props": [
+ {
+ "p": "payload"
+ },
+ {
+ "p": "topic",
+ "vt": "str"
+ }
+ ],
+ "repeat": "",
+ "crontab": "",
+ "once": true,
+ "onceDelay": 0.1,
+ "topic": "",
+ "payload": "10",
+ "payloadType": "num",
+ "x": 310,
+ "y": 320,
+ "wires": [
+ [
+ "d657f11c.c9f07"
+ ]
+ ]
+ },
+ {
+ "id": "25d449c7.eaa3ee",
+ "type": "mqtt in",
+ "z": "4ed15f63.9d1468",
+ "name": "",
+ "topic": "status/#",
+ "qos": "0",
+ "datatype": "json",
+ "broker": "8dc3722c.06efa8",
+ "x": 170,
+ "y": 320,
+ "wires": [
+ [
+ "8470d39.987ef3"
+ ]
+ ]
+ },
+ {
+ "id": "5ba11465.0cd9a4",
+ "type": "switch",
+ "z": "4ed15f63.9d1468",
+ "name": "topic filter",
+ "property": "topic",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "eq",
+ "v": "status/pump",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/focus",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/imager",
+ "vt": "str"
+ },
+ {
+ "t": "cont",
+ "v": "status/segmenter",
+ "vt": "str"
+ }
+ ],
+ "checkall": "true",
+ "repair": false,
+ "outputs": 4,
+ "x": 460,
+ "y": 320,
+ "wires": [
+ [
+ "6a152db4.21e354",
+ "d0f14512.fea9c8"
+ ],
+ [
+ "6a152db4.21e354",
+ "46a63eb6.be3948"
+ ],
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+ "18045f2c.7335c1",
+ "61e3060c.62ccf8"
+ ],
+ [
+ "f5b2279.156d358"
+ ]
+ ]
+ },
+ {
+ "id": "18045f2c.7335c1",
+ "type": "switch",
+ "z": "4ed15f63.9d1468",
+ "name": "Imaging state",
+ "property": "payload",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "else"
+ },
+ {
+ "t": "jsonata_exp",
+ "v": "$contains(msg.payload.status, \"jpg\")\t",
+ "vt": "jsonata"
+ }
+ ],
+ "checkall": "true",
+ "repair": false,
+ "outputs": 2,
+ "x": 740,
+ "y": 360,
+ "wires": [
+ [
+ "6a152db4.21e354"
+ ],
+ [
+ "cdf762d8.f081f8"
+ ]
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+ {
+ "id": "cdf762d8.f081f8",
+ "type": "function",
+ "z": "4ed15f63.9d1468",
+ "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,
+ "initialize": "",
+ "finalize": "",
+ "x": 1000,
+ "y": 400,
+ "wires": [
+ [
+ "333763e6.02dd44",
+ "e8c2e01c.5f4148"
+ ]
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+ "id": "3ff0a45a.f00bd4",
+ "type": "function",
+ "z": "4ed15f63.9d1468",
+ "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,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 1000,
+ "y": 520,
+ "wires": [
+ [
+ "51ea0aaf.ef328c",
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+ "id": "f5b2279.156d358",
+ "type": "switch",
+ "z": "4ed15f63.9d1468",
+ "name": "Segmenter",
+ "property": "topic",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "eq",
+ "v": "status/segmenter",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/segmenter/name",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/segmenter/object_id",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/segmenter/metric",
+ "vt": "str"
+ }
+ ],
+ "checkall": "true",
+ "repair": false,
+ "outputs": 4,
+ "x": 730,
+ "y": 500,
+ "wires": [
+ [
+ "6a152db4.21e354",
+ "8ef827ad.d1832"
+ ],
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+ "id": "51ea0aaf.ef328c",
+ "type": "ui_chart",
+ "z": "4ed15f63.9d1468",
+ "name": "obj_counter",
+ "group": "46be9c86.dea684",
+ "order": 3,
+ "width": "12",
+ "height": 2,
+ "label": "obj_counter",
+ "chartType": "horizontalBar",
+ "legend": "false",
+ "xformat": "HH:mm:ss",
+ "interpolate": "linear",
+ "nodata": "Objects count will be shown here once the segmentation is started",
+ "dot": false,
+ "ymin": "",
+ "ymax": "",
+ "removeOlder": 1,
+ "removeOlderPoints": "",
+ "removeOlderUnit": "3600",
+ "cutout": 0,
+ "useOneColor": true,
+ "useUTC": false,
+ "colors": [
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+ "#aec7e8",
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+ "#98df8a",
+ "#d62728",
+ "#ff9896",
+ "#9467bd",
+ "#c5b0d5"
+ ],
+ "useOldStyle": false,
+ "outputs": 1,
+ "x": 1470,
+ "y": 560,
+ "wires": [
+ []
+ ]
+ },
+ {
+ "id": "68f3b16.5beabd",
+ "type": "function",
+ "z": "4ed15f63.9d1468",
+ "name": "ex : area",
+ "func": "msg.payload=msg.payload.object_area\nmsg.topic=\"area\"\n\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 980,
+ "y": 560,
+ "wires": [
+ [
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+ ]
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+ },
+ {
+ "id": "5d3095bd.37df6c",
+ "type": "ui_toast",
+ "z": "4ed15f63.9d1468",
+ "position": "top right",
+ "displayTime": "5",
+ "highlight": "",
+ "sendall": true,
+ "outputs": 0,
+ "ok": "OK",
+ "cancel": "",
+ "raw": false,
+ "topic": "",
+ "name": "",
+ "x": 1490,
+ "y": 300,
+ "wires": []
+ },
+ {
+ "id": "e299b4f3.c55ce",
+ "type": "ui_chart",
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+ "name": "chart area",
+ "group": "46be9c86.dea684",
+ "order": 5,
+ "width": "12",
+ "height": 7,
+ "label": "chart area",
+ "chartType": "line",
+ "legend": "false",
+ "xformat": "HH:mm:ss",
+ "interpolate": "linear",
+ "nodata": "Objects area will be shown here once the segmentation is started",
+ "dot": true,
+ "ymin": "",
+ "ymax": "",
+ "removeOlder": 1,
+ "removeOlderPoints": "1000",
+ "removeOlderUnit": "3600",
+ "cutout": 0,
+ "useOneColor": false,
+ "useUTC": true,
+ "colors": [
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+ "#aec7e8",
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+ "#c5b0d5"
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+ "useOldStyle": false,
+ "outputs": 1,
+ "x": 1470,
+ "y": 600,
+ "wires": [
+ []
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+ },
+ {
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+ "type": "debug",
+ "z": "4ed15f63.9d1468",
+ "name": "segmentation name",
+ "active": true,
+ "tosidebar": true,
+ "console": false,
+ "tostatus": false,
+ "complete": "true",
+ "targetType": "full",
+ "statusVal": "",
+ "statusType": "auto",
+ "x": 1010,
+ "y": 480,
+ "wires": []
+ },
+ {
+ "id": "8470d39.987ef3",
+ "type": "json",
+ "z": "4ed15f63.9d1468",
+ "name": "",
+ "property": "payload",
+ "action": "obj",
+ "pretty": true,
+ "x": 310,
+ "y": 320,
+ "wires": [
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+ "f5d6c42a.3336e"
+ ]
+ ]
+ },
+ {
+ "id": "1002431c.cf5e25",
+ "type": "template",
+ "z": "4ed15f63.9d1468",
+ "name": "Create sentence",
+ "field": "payload",
+ "fieldType": "msg",
+ "format": "handlebars",
+ "syntax": "mustache",
+ "template": "The {{topic}} is {{payload.status}}",
+ "output": "str",
+ "x": 1270,
+ "y": 300,
+ "wires": [
+ [
+ "5d3095bd.37df6c"
+ ]
+ ]
+ },
+ {
+ "id": "6a152db4.21e354",
+ "type": "change",
+ "z": "4ed15f63.9d1468",
+ "name": "Remove high-level topic",
+ "rules": [
+ {
+ "t": "change",
+ "p": "topic",
+ "pt": "msg",
+ "from": "status/",
+ "fromt": "str",
+ "to": "",
+ "tot": "str"
+ }
+ ],
+ "action": "",
+ "property": "",
+ "from": "",
+ "to": "",
+ "reg": false,
+ "x": 1030,
+ "y": 300,
+ "wires": [
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+ "z": "4ed15f63.9d1468",
+ "d": true,
+ "name": "segmenter area",
+ "active": true,
+ "tosidebar": true,
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+ "tostatus": false,
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+ "targetType": "msg",
+ "statusVal": "",
+ "statusType": "auto",
+ "x": 500,
+ "y": 580,
+ "wires": []
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+ "id": "61e3060c.62ccf8",
+ "type": "ui_text",
+ "z": "4ed15f63.9d1468",
+ "group": "70de8209.68416c",
+ "order": 3,
+ "width": 5,
+ "height": 1,
+ "name": "imager",
+ "label": "Imager status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 970,
+ "y": 220,
+ "wires": []
+ },
+ {
+ "id": "8ef827ad.d1832",
+ "type": "ui_text",
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+ "order": 4,
+ "width": 5,
+ "height": 1,
+ "name": "segmenter",
+ "label": "Segmenter status:",
+ "format": "{{msg.payload.status}}",
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+ "x": 990,
+ "y": 440,
+ "wires": []
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+ "order": 1,
+ "width": 5,
+ "height": 1,
+ "name": "focus",
+ "label": "Focus status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 970,
+ "y": 180,
+ "wires": []
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+ {
+ "id": "d0f14512.fea9c8",
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+ "z": "4ed15f63.9d1468",
+ "group": "70de8209.68416c",
+ "order": 2,
+ "width": 5,
+ "height": 1,
+ "name": "pump",
+ "label": "Pump status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 970,
+ "y": 140,
+ "wires": []
+ },
+ {
+ "id": "333763e6.02dd44",
+ "type": "ui_text",
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+ "group": "b5d61bc7.54fe48",
+ "order": 4,
+ "width": 5,
+ "height": 2,
+ "name": "Image Count",
+ "label": "Images count",
+ "format": "{{msg.payload}}",
+ "layout": "col-center",
+ "x": 1470,
+ "y": 380,
+ "wires": []
+ },
+ {
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+ "width": 3,
+ "height": 2,
+ "name": "obj_count",
+ "label": "Objects count",
+ "format": "{{msg.payload}}",
+ "layout": "col-center",
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+ "y": 520,
+ "wires": []
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+ {
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+ "type": "inject",
+ "z": "4ed15f63.9d1468",
+ "name": "Init graphs",
+ "props": [
+ {
+ "p": "payload"
+ },
+ {
+ "p": "topic",
+ "vt": "str"
+ }
+ ],
+ "repeat": "",
+ "crontab": "",
+ "once": true,
+ "onceDelay": 0.1,
+ "topic": "",
+ "payload": "0",
+ "payloadType": "num",
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+ "y": 640,
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+ "type": "function",
+ "z": "4ed15f63.9d1468",
+ "name": "obj_counter init",
+ "func": "obj_counter=0\nglobal.set('obj_counter',obj_counter)\nmsg.payload = obj_counter\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
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+ "y": 660,
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+ "name": "img_counter init",
+ "func": "img_counter=0\nglobal.set('img_counter',img_counter)\nmsg.payload = img_counter\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 1000,
+ "y": 620,
+ "wires": [
+ [
+ "333763e6.02dd44"
+ ]
+ ]
+ },
+ {
+ "id": "adc98d1c.21c76",
+ "type": "ui_gauge",
+ "z": "4ed15f63.9d1468",
+ "name": "Image Donut",
+ "group": "b5d61bc7.54fe48",
+ "order": 1,
+ "width": 4,
+ "height": 3,
+ "gtype": "donut",
+ "title": "progress",
+ "label": "%",
+ "format": "{{value}}",
+ "min": 0,
+ "max": "100",
+ "colors": [
+ "#ffa83f",
+ "#e6ff02",
+ "#00dfe9"
+ ],
+ "seg1": "50",
+ "seg2": "75",
+ "x": 1470,
+ "y": 420,
+ "wires": []
+ },
+ {
+ "id": "639420d6.1ac248",
+ "type": "subflow:4ed15f63.9d1468",
+ "z": "eaae323a.31b3",
+ "name": "",
+ "x": 150,
+ "y": 520,
+ "wires": []
+ },
+ {
+ "id": "d657f11c.c9f07",
+ "type": "ui_numeric",
+ "z": "baa1e3d9.cb29d",
+ "name": "nb_frame",
+ "label": "Number of images per acquisition",
+ "tooltip": "",
+ "group": "4322c187.e73e5",
+ "order": 3,
+ "width": 0,
+ "height": 0,
+ "wrap": false,
+ "passthru": true,
+ "topic": "nb_frame",
+ "format": "{{value}}",
+ "min": 0,
+ "max": "10000",
+ "step": 1,
+ "x": 580,
+ "y": 320,
+ "wires": [
+ [
+ "fb887036.12429"
+ ]
+ ]
+ },
+ {
+ "id": "e8c2e01c.5f4148",
+ "type": "function",
+ "z": "4ed15f63.9d1468",
+ "name": "percent image",
+ "func": "msg.payload = 100 * msg.payload/global.get('nb_frame')\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 1280,
+ "y": 420,
+ "wires": [
+ [
+ "adc98d1c.21c76"
+ ]
+ ]
+ },
+ {
+ "id": "1fa7fddf.18161a",
+ "type": "ui_toast",
+ "z": "1371dec5.76e671",
+ "position": "dialog",
+ "displayTime": "10",
+ "highlight": "",
+ "sendall": true,
+ "outputs": 1,
+ "ok": "OK",
+ "cancel": "",
+ "raw": false,
+ "topic": "",
+ "name": "Update notif",
+ "x": 570,
+ "y": 500,
+ "wires": [
+ []
+ ]
+ },
+ {
+ "id": "8c3e4a1c.1ebbb",
+ "type": "debug",
+ "z": "1371dec5.76e671",
+ "name": "Update",
+ "active": true,
+ "tosidebar": true,
+ "console": false,
+ "tostatus": false,
+ "complete": "true",
+ "targetType": "full",
+ "statusVal": "",
+ "statusType": "auto",
+ "x": 560,
+ "y": 540,
+ "wires": []
+ },
+ {
+ "id": "6451f991.aaac1",
+ "type": "ui_button",
+ "z": "bccd1f23.87219",
+ "name": "stop pump",
+ "group": "707d9797.c8e798",
+ "order": 5,
+ "width": 2,
+ "height": 1,
+ "passthru": true,
+ "label": "STOP PUMP",
+ "tooltip": "",
+ "color": "",
+ "bgcolor": "#AD1625",
+ "icon": "",
+ "payload": "{\"action\":\"stop\"}",
+ "payloadType": "json",
+ "topic": "actuator/pump",
+ "x": 170,
+ "y": 180,
+ "wires": [
+ [
+ "e2af9066.9c0178"
+ ]
+ ]
+ },
+ {
+ "id": "e2af9066.9c0178",
+ "type": "mqtt out",
+ "z": "bccd1f23.87219",
+ "name": "",
+ "topic": "",
+ "qos": "",
+ "retain": "",
+ "broker": "8dc3722c.06efa8",
+ "x": 310,
+ "y": 180,
+ "wires": []
+ },
+ {
+ "id": "b402f719.55bc98",
+ "type": "inject",
+ "z": "baa1e3d9.cb29d",
+ "name": "Default: FORWARD",
+ "props": [
+ {
+ "p": "payload"
+ },
+ {
+ "p": "topic",
+ "vt": "str"
+ }
+ ],
+ "repeat": "",
+ "crontab": "",
+ "once": true,
+ "onceDelay": 0.1,
+ "topic": "pump_direction",
+ "payload": "FORWARD",
+ "payloadType": "str",
+ "x": 290,
+ "y": 660,
+ "wires": [
+ [
+ "bb62da8a.ebc328"
+ ]
+ ]
+ },
+ {
+ "id": "42795da1.0ee104",
+ "type": "function",
+ "z": "b771c342.49603",
+ "name": "DMS to DD",
+ "func": "// Format 36°57'9\" N, 110°4'21\" W\n// From https://stackoverflow.com/questions/1140189/converting-latitude-and-longitude-to-decimal-values\nfunction ParseDMS(input) {\n var parts = input.split(/[^\\d\\w]+/);\n console.log(parts)\n return ConvertDMSToDD(parts[0], parts[1], parts[2], parts[3]);\n}\n\nfunction ConvertDMSToDD(degrees, minutes, seconds, direction) {\n var dd = Number(degrees) + Number(minutes)/60 + Number(seconds)/(60*60);\n\n if (direction == \"S\" || direction == \"W\") {\n dd = dd * -1;\n } // Don't do anything for N or E\n return dd;\n}\n\nmsg.payload = ParseDMS(msg.payload)\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 910,
+ "y": 540,
+ "wires": [
+ [
+ "9f501f49.45645"
+ ]
+ ]
+ },
+ {
+ "id": "1ba1619e.4aea16",
+ "type": "change",
+ "z": "baa1e3d9.cb29d",
+ "name": "Set pump_direction",
+ "rules": [
+ {
+ "t": "set",
+ "p": "pump_direction",
+ "pt": "global",
+ "to": "payload",
+ "tot": "msg"
+ }
+ ],
+ "action": "",
+ "property": "",
+ "from": "",
+ "to": "",
+ "reg": false,
+ "x": 730,
+ "y": 660,
+ "wires": [
+ []
+ ]
}
-]
+]
\ No newline at end of file
diff --git a/hardware.json b/hardware.json
index bc89ed6..3930582 100644
--- a/hardware.json
+++ b/hardware.json
@@ -5,6 +5,6 @@
"pump_steps_per_ml": 507,
"focus_max_speed": 0.5,
"pump_max_speed": 30,
- "stepper_type": "adafruit",
+ "stepper_type": "waveshare",
"camera_type": "HQ"
}
\ No newline at end of file
diff --git a/scripts/bash/update.sh b/scripts/bash/update.sh
new file mode 100755
index 0000000..c61869c
--- /dev/null
+++ b/scripts/bash/update.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+cd /home/pi/PlanktonScope
+
+git stash
+git pull
+git checkout stash@{0} -- config.json hardware.json
diff --git a/scripts/planktoscope/imager.py b/scripts/planktoscope/imager.py
index 580a8dd..c228eff 100644
--- a/scripts/planktoscope/imager.py
+++ b/scripts/planktoscope/imager.py
@@ -160,6 +160,7 @@ class ImagerProcess(multiprocessing.Process):
self.__img_done = 0
self.__sleep_before = None
self.__pump_volume = None
+ self.__pump_direction = "FORWARD"
self.__img_goal = None
self.imager_client = None
@@ -303,7 +304,12 @@ class ImagerProcess(multiprocessing.Process):
# Get duration to wait before an image from the different received arguments
self.__sleep_before = float(last_message["sleep"])
# Get volume in between two images from the different received arguments
- self.__pump_volume = float(last_message["volume"])
+ # Minimal volume is 0.1mL
+ self.__pump_volume = max(float(last_message["volume"]), 0.1)
+
+ # Get the pump direction message
+ self.__pump_direction = last_message["pump_direction"]
+
# Get the number of frames to image from the different received arguments
self.__img_goal = int(last_message["nb_frame"])
@@ -471,6 +477,21 @@ class ImagerProcess(multiprocessing.Process):
f"We did not understand the received request {action} - {last_message}"
)
+ def __pump_message(self):
+ """Sends a message to the pump process"""
+ # Pump during a given volume
+ self.imager_client.client.publish(
+ "actuator/pump",
+ json.dumps(
+ {
+ "action": "move",
+ "direction": self.__pump_direction,
+ "volume": self.__pump_volume,
+ "flowrate": 2,
+ }
+ ),
+ )
+
def __state_imaging(self):
# TODO we should make sure here that we are not writing to an existing folder
# otherwise we might overwrite the metadata.json file
@@ -516,17 +537,9 @@ class ImagerProcess(multiprocessing.Process):
# Set the LEDs as Blue
planktoscope.light.setRGB(0, 0, 255)
- self.imager_client.client.publish(
- "actuator/pump",
- json.dumps(
- {
- "action": "move",
- "direction": "FORWARD",
- "volume": self.__pump_volume,
- "flowrate": 2,
- }
- ),
- )
+
+ self.__pump_message()
+
# FIXME We should probably update the global metadata here with the current datetime/position/etc...
# Set the LEDs as Green
@@ -610,18 +623,7 @@ class ImagerProcess(multiprocessing.Process):
"status/pump", self.pump_callback
)
- # Pump during a given volume
- self.imager_client.client.publish(
- "actuator/pump",
- json.dumps(
- {
- "action": "move",
- "direction": "BACKWARD",
- "volume": self.__pump_volume,
- "flowrate": 2,
- }
- ),
- )
+ self.__pump_message()
# Set the LEDs as Green
planktoscope.light.setRGB(0, 255, 0)
diff --git a/scripts/planktoscope/light.py b/scripts/planktoscope/light.py
index 8ae0af4..e55c09e 100644
--- a/scripts/planktoscope/light.py
+++ b/scripts/planktoscope/light.py
@@ -92,6 +92,7 @@ def light(state):
## Wait message: Green
## Actuate message: White
## Pumping message: Blue
+## Pumping 2 message: BLue + Green
# This is called if this script is launched directly
if __name__ == "__main__":
diff --git a/scripts/planktoscope/stepper.py b/scripts/planktoscope/stepper.py
index 69ab134..fa7561e 100644
--- a/scripts/planktoscope/stepper.py
+++ b/scripts/planktoscope/stepper.py
@@ -16,7 +16,7 @@ logger.info("planktoscope.stepper is loaded")
class StepperWaveshare:
- """A bipolar stepper motor."""
+ """A bipolar stepper motor using the Waveshare HAT."""
def __init__(self, dir_pin, step_pin, enable_pin):
self.dir_pin = dir_pin
@@ -178,6 +178,7 @@ class StepperProcess(multiprocessing.Process):
def __init__(self, event):
super(StepperProcess, self).__init__()
logger.info("Initialising the stepper process")
+ RPi.GPIO.setup([12, 4], RPi.GPIO.OUT, initial=RPi.GPIO.HIGH)
self.stop_event = event