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"disabled": false,
"info": ""
},
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},
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},
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{
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"disabled": false,
"info": ""
},
{
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"disabled": false,
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},
{
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"disabled": false,
"info": ""
},
{
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"type": "subflow",
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"category": "",
"in": [
{
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"y": 860,
"wires": [
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"disp": true,
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},
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"disp": true,
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"order": 1,
"disabled": false,
"hidden": false
},
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"hidden": false
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{
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"order": 5,
"disabled": false,
"hidden": false
},
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"type": "ui_tab",
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"disabled": false,
"hidden": false
},
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"disp": true,
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"edited": false
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"edited": false
},
"group-textColor": {
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"edited": false
},
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"edited": false
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"edited": false
},
"widget-textColor": {
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"edited": false
},
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"edited": false
},
"widget-borderColor": {
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"edited": false
},
"base-font": {
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}
},
"angularTheme": {
"primary": "indigo",
"accents": "blue",
"warn": "red",
"background": "grey"
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},
"site": {
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"hideToolbar": "false",
"allowSwipe": "false",
"lockMenu": "false",
"allowTempTheme": "true",
"dateFormat": "DD/MM/YYYY",
"sizes": {
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"sy": 56,
"gx": 5,
"gy": 5,
"cx": 5,
"cy": 5,
"px": 5,
"py": 5
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},
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"disp": true,
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"disp": false,
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"collapse": false
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"disp": true,
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"disp": true,
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{
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"disp": true,
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{
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"disp": true,
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},
{
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"type": "mqtt-broker",
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"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": ""
},
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"disp": true,
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},
{
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},
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},
{
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{
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{
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"timer": "",
"name": "RPi Temp.",
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"xformat": "HH:mm:ss",
"interpolate": "linear",
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"dot": false,
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"removeOlder": "20",
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{
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"command": "top -d 0.5 -b -n2 | grep \"Cpu(s)\"|tail -n 1 | awk '{print $2 + $4}' | tr -d \"\\n\"",
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"append": "",
"useSpawn": "",
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"name": "CPU Load",
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"passthru": false,
"label": "Continue",
"tooltip": "",
"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_tab",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
"topic": "",
"x": 500,
"y": 1060,
"wires": [
[
"fe840e05.b46f3"
]
]
},
{
"id": "c72f8fae.23bd4",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
"name": "",
"group": "b7919ae2.c01788",
"order": 1,
"width": 5,
"height": 1,
"passthru": false,
"label": "Previous",
"tooltip": "",
"color": "#097479",
"bgcolor": "white",
"icon": "keyboard_return",
"payload": "{\"tab\":\"Optic Configuration\"}",
"payloadType": "json",
"topic": "",
"x": 880,
"y": 80,
"wires": [
[
"d0c5b57d.590818"
]
]
},
{
"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": 630,
"y": 200,
"wires": [
[
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]
]
},
{
"id": "b4d324de.a2bd28",
"type": "ui_worldmap",
"z": "b771c342.49603",
"d": true,
"group": "da2c279f.cbe318",
"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": 840,
"y": 920,
"wires": []
},
{
"id": "cf3e1477.25af68",
"type": "function",
"z": "b771c342.49603",
"d": true,
"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": 420,
"y": 960,
"wires": [
[
"105e9b1b.725865"
]
]
},
{
"id": "d7a44df2.0fb29",
"type": "ui_button",
"z": "b771c342.49603",
"d": true,
"name": "",
"group": "da2c279f.cbe318",
"order": 5,
"width": 5,
"height": 1,
"passthru": false,
"label": "Place",
"tooltip": "",
"color": "#333333",
"bgcolor": "white",
"icon": "",
"payload": "",
"payloadType": "str",
"topic": "",
"x": 270,
"y": 960,
"wires": [
[
"cf3e1477.25af68"
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]
},
{
"id": "105e9b1b.725865",
"type": "switch",
"z": "b771c342.49603",
"d": true,
"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": 610,
"y": 960,
"wires": [
[
"b4d324de.a2bd28"
],
[
"10c9c12a.feae6f"
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},
{
"id": "10c9c12a.feae6f",
"type": "ui_toast",
"z": "b771c342.49603",
"d": true,
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 850,
"y": 980,
"wires": [
[]
]
},
{
"id": "f07dec1d.147ce",
"type": "ui_text_input",
"z": "baa1e3d9.cb29d",
"name": "comment",
"label": "Comment",
"tooltip": "",
"group": "567a49a4.244cb8",
"order": 5,
"width": 0,
"height": 0,
"passthru": true,
"mode": "text",
"delay": 300,
"topic": "comment",
"x": 640,
"y": 280,
"wires": [
[
"fb887036.12429"
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]
},
{
"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": [
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},
{
"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": [
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"2bc762dd.1115ce",
"a50134c.ed45ac8",
"f0ef065a.362028"
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"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",
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},
{
"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"
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},
{
"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": [
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},
{
"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": [
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},
{
"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",
"name": "",
"op1": "1",
"op2": "0",
"op1type": "str",
"op2type": "str",
"duration": "-1",
"extend": false,
"units": "s",
"reset": "done",
"bytopic": "all",
"outputs": 1,
"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",
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},
{
"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": [
[
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]
]
},
{
"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": [
[],
[],
[]
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},
{
"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": "29be525e.0c87fe",
"type": "ui_template",
"z": "baa1e3d9.cb29d",
"group": "b5d61bc7.54fe48",
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"order": 2,
"width": 0,
"height": 0,
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"templateScope": "local",
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"wires": [
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},
{
"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 \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_instrument_id\":global.get(\"machine_name\"),\n \"acq_camera\":global.get(\"camera_name\"),\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_software\":global.get(\"acq_software\"),\n \"acq_flowrate\":global.get(\"sug_flowrate\"),\n \n \"object_lat\":global.get(\"object_lat\"),\n \"object_lon\":global.get(\"object_lon\"),\n \"object_lat_end\":global.get(\"object_lat_end\"),\n \"object_lon_end\":global.get(\"object_lon_end\"),\n \"object_date\":global.get(\"object_date\"),\n \"object_time\":global.get(\"object_time\"),\n \"object_date_end\":global.get(\"object_date_end\"),\n \"object_time_end\":global.get(\"object_time_end\"),\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 }\n\nreturn msg;",
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"initialize": "",
"finalize": "",
"x": 720,
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"z": "baa1e3d9.cb29d",
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"active": true,
"tosidebar": true,
"console": false,
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"targetType": "msg",
"statusVal": "",
"statusType": "auto",
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{
"id": "7ca7754c.0f731c",
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"repeat": "",
"crontab": "",
"once": false,
"onceDelay": 0.1,
"topic": "",
"payload": "",
"payloadType": "date",
"x": 120,
"y": 420,
"wires": [
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},
{
"id": "cbb8afed.0a026",
"type": "rpi-gpio out",
"z": "bccd1f23.87219",
"name": "LED Output",
"pin": "40",
"set": true,
"level": "0",
"freq": "",
"out": "out",
"x": 450,
"y": 40,
"wires": []
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{
"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": 280,
"y": 420,
"wires": [
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},
{
"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": 640,
"y": 420,
"wires": [
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{
"id": "3cd4bf1e.11ae3",
"type": "debug",
"z": "eaae323a.31b3",
"name": "",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "false",
"x": 870,
"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": 430,
"y": 420,
"wires": [
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},
{
"id": "3cb96380.e575ec",
"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(\"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 msg.volume = volume;\n flowrate = global.get(\"pump_flowrate\");\n msg.topic = \"actuator/pump\";\n \n if(state===\"free\"){\n // msg.payload is FORWARD or BACKWARD here\n msg.payload={\"action\":\"move\", \n \"direction\":msg.payload,\n \"volume\":volume,\n \"flowrate\":flowrate};\n }\n}\nreturn msg;",
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"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 240,
"wires": [
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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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"type": "switch",
"z": "bccd1f23.87219",
"name": "",
"property": "topic",
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{
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{
"t": "eq",
"v": "Missing entry :",
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],
"checkall": "true",
"repair": false,
"outputs": 2,
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"y": 240,
"wires": [
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"type": "ui_toast",
"z": "bccd1f23.87219",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 650,
"y": 260,
"wires": [
[]
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{
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 630,
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"wires": []
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{
"id": "3d31ee98.a7d6fa",
"type": "ui_text_input",
"z": "bccd1f23.87219",
"name": "focus_distance",
"label": "Distance in µm",
"tooltip": "This will be rounded to the nearest 25µm",
"group": "fbd92986.1028c8",
"order": 4,
"width": 0,
"height": 0,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "focus_distance",
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{
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"name": "",
"property": "topic",
"propertyType": "msg",
"rules": [
{
"t": "eq",
"v": "actuator/focus",
"vt": "str"
},
{
"t": "eq",
"v": "Missing entry :",
"vt": "str"
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],
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 470,
"y": 620,
"wires": [
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"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
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"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 650,
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"wires": [
[]
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},
{
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"noerr": 0,
"initialize": "",
"finalize": "",
"x": 320,
"y": 620,
"wires": [
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{
"id": "1962d999.4a97e6",
"type": "ui_button",
"z": "bccd1f23.87219",
"name": "stop focus",
"group": "fbd92986.1028c8",
"order": 7,
"width": 0,
"height": 0,
"passthru": true,
"label": "STOP FOCUS",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "",
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 180,
"y": 680,
"wires": [
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},
{
"id": "62030521.88317c",
"type": "mqtt out",
"z": "bccd1f23.87219",
"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 630,
"y": 560,
"wires": []
},
{
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"broker": "8dc3722c.06efa8",
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},
{
"id": "dbd6bde.99db64",
"type": "function",
"z": "bccd1f23.87219",
"name": "round distance",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 620,
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"group": "fbd92986.1028c8",
"order": 2,
"width": 0,
"height": 0,
"passthru": false,
"label": "UP 1mm",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "{\"action\":\"move\",\"direction\":\"UP\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 180,
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"group": "fbd92986.1028c8",
"order": 6,
"width": 0,
"height": 0,
"passthru": false,
"label": "DOWN 1mm",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "{\"action\":\"move\",\"direction\":\"DOWN\",\"distance\":1}",
"payloadType": "json",
"topic": "actuator/focus",
"x": 170,
"y": 560,
"wires": [
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{
"id": "69d4ea6c.4c1e2c",
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"z": "bccd1f23.87219",
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"label": "",
"tooltip": "in µm",
"group": "fbd92986.1028c8",
"order": 3,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "focus_distance",
"min": "25",
"max": "2000",
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},
{
"id": "71f55a58.d7eaf4",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 500µm",
"props": [
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}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "500",
"payloadType": "num",
"x": 120,
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{
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"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: OFF",
"props": [
{
"p": "payload"
}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "false",
"payloadType": "bool",
"x": 110,
"y": 40,
"wires": [
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},
{
"id": "16aa0238.209276",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "Iso slider",
"label": "ISO",
"tooltip": "Possible values are 100, 200, 320, 400, 500, 640, 800. 500 by default.",
"group": "4248342d.e55fac",
"order": 10,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
"min": "100",
"max": "800",
"step": "20",
"x": 360,
"y": 820,
"wires": [
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},
{
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"z": "bccd1f23.87219",
"name": "round iso",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 520,
"y": 820,
"wires": [
[
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"8ea9dc9a.c7d87"
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},
{
"id": "8ea9dc9a.c7d87",
"type": "function",
"z": "bccd1f23.87219",
"name": "Encapsulate settings",
"func": "msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"iso\":msg.payload}\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 720,
"y": 820,
"wires": [
[
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},
{
"id": "5765a825.a595c8",
"type": "ui_slider",
"z": "bccd1f23.87219",
"name": "Shutter speed slider",
"label": "Shutter Speed",
"tooltip": "In microseconds, up to 2500µs, 10µs by default",
"group": "4248342d.e55fac",
"order": 9,
"width": 0,
"height": 0,
"passthru": true,
"outs": "end",
"topic": "imager/image",
"min": "10",
"max": "2500",
"step": "10",
"x": 390,
"y": 880,
"wires": [
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{
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"name": "Encapsulate settings",
"func": "msg.payload = {\n \"action\":\"settings\", \n \"settings\":{\"shutter_speed\":msg.payload}\n}\nmsg.topic = \"imager/image\"\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 720,
"y": 880,
"wires": [
[
"845e06e1.0d812"
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},
{
"id": "845e06e1.0d812",
"type": "mqtt out",
"z": "bccd1f23.87219",
"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 930,
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"wires": []
},
{
"id": "2350e507.d4e302",
"type": "inject",
"z": "bccd1f23.87219",
"name": "Default: 10µs",
"props": [
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}
],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
"payload": "10",
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{
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"name": "Default: ISO 100",
"props": [
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],
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"crontab": "",
"once": true,
"onceDelay": "1",
"topic": "",
"payload": "100",
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"y": 820,
"wires": [
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},
{
"id": "96ff24f0.955f",
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"group": "4248342d.e55fac",
"name": "Camera Settings",
"order": 8,
"width": 0,
"height": 0,
"format": "\nCamera Settings\n",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": false,
"templateScope": "local",
"x": 360,
"y": 780,
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]
},
{
"id": "f782a471.447748",
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"name": "Default: 5mL/min",
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}
],
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"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "5",
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},
{
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"name": "Default: 2mL",
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}
],
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"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
"payload": "2",
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"wires": [
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},
{
"id": "8ec68b82.17e3d8",
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"name": "Start segmentation",
"group": "abeb6dad.635a2",
"order": 1,
"width": 6,
"height": 1,
"passthru": false,
"label": "Start segmentation",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "{\"action\":\"segment\"}",
"payloadType": "json",
"topic": "segmenter/segment",
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},
{
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"passthru": true,
"label": "Stop segmentation",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
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"payload": "{\"action\":\"stop\"}",
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"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
"x": 710,
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"width": 6,
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"passthru": false,
"label": "Update",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "system_update",
"payload": "",
"payloadType": "str",
"topic": "update",
"x": 100,
"y": 520,
"wires": [
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"id": "386ce65d.a15d52",
"type": "exec",
"z": "1371dec5.76e671",
"command": "git",
"addpay": false,
"append": "stash",
"useSpawn": "false",
"timer": "2",
"oldrc": false,
"name": "git stash",
"x": 260,
"y": 520,
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"z": "1371dec5.76e671",
"command": "git",
"addpay": false,
"append": "pull",
"useSpawn": "false",
"timer": "2",
"oldrc": false,
"name": "git pull",
"x": 430,
"y": 520,
"wires": [
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[]
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},
{
"id": "9998aa86.74bb",
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"z": "1371dec5.76e671",
"command": "python3 /home/pi/PlanktonScope/scripts/main.py",
"addpay": false,
"append": "",
"useSpawn": "true",
"timer": "",
"oldrc": false,
"name": "",
"x": 860,
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},
{
"id": "672d89a8.4e6968",
"type": "exec",
"z": "1371dec5.76e671",
"d": true,
"command": "sudo killall -9 python3",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Hard kill",
"x": 980,
"y": 1020,
"wires": [
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[]
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"id": "afa9f4b.2e77988",
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"pauseType": "delay",
"timeout": "5",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 460,
"y": 940,
"wires": [
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{
"id": "1df370a8.6c70ff",
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"name": "Restart Python",
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"order": 6,
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"height": 1,
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"label": "Restart Python",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "refresh",
"payload": "",
"payloadType": "str",
"topic": "",
"x": 100,
"y": 940,
"wires": [
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"name": "SIGTERM",
"func": "msg.kill = \"SIGTERM\";\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 470,
"y": 900,
"wires": [
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"name": "output",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "payload",
"targetType": "msg",
"statusVal": "",
"statusType": "auto",
"x": 1210,
"y": 900,
"wires": []
},
{
"id": "7aa2e737.e16d98",
"type": "status",
"z": "1371dec5.76e671",
"name": "",
"scope": [
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"x": 980,
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"wires": [
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"name": "status",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "status",
"targetType": "msg",
"statusVal": "",
"statusType": "auto",
"x": 1210,
"y": 1080,
"wires": []
},
{
"id": "35ea3cf0.a398ac",
"type": "exec",
"z": "1371dec5.76e671",
"command": "sudo killall -15 python3",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Python soft kill",
"x": 960,
"y": 860,
"wires": [
[],
[],
[]
]
},
{
"id": "a776b9fc.d542e8",
"type": "delay",
"z": "1371dec5.76e671",
"d": true,
"name": "",
"pauseType": "delay",
"timeout": "4",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 740,
"y": 1020,
"wires": [
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},
{
"id": "569154a.b53182c",
"type": "inject",
"z": "1371dec5.76e671",
"name": "once",
"props": [
{
"p": "topic",
"vt": "str"
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],
"repeat": "60",
"crontab": "",
"once": true,
"onceDelay": "",
"topic": "",
"x": 130,
"y": 840,
"wires": [
[
"afa9f4b.2e77988",
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},
{
"id": "3829adc.ccc87d2",
"type": "exec",
"z": "1371dec5.76e671",
"command": "sudo killall -15 raspimjpeg",
"addpay": true,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "Raspimjpeg soft kill",
"x": 490,
"y": 820,
"wires": [
[],
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[]
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},
{
"id": "b55ed048.2418c8",
"type": "ui_template",
"z": "1371dec5.76e671",
"group": "1be83144.4fe4bf",
"name": "",
"order": 1,
"width": 0,
"height": 0,
"format": "If you want to update to the latest code version of Node-Red and Python, please click here.\n
\nPlease note that all your changes are going to be saved with git stash but are not going to be restored!",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 100,
"y": 460,
"wires": [
[]
]
},
{
"id": "4b489713.ccde5",
"type": "ui_button",
"z": "baa1e3d9.cb29d",
"name": "",
"group": "4322c187.e73e5",
"order": 9,
"width": 5,
"height": 1,
"passthru": false,
"label": "Start Acquisition",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "",
"payloadType": "str",
"topic": "imager/image",
"x": 520,
"y": 460,
"wires": [
[
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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;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 880,
"y": 460,
"wires": [
[
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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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{
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"type": "switch",
"z": "baa1e3d9.cb29d",
"name": "",
"property": "topic",
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{
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"v": "imager/image",
"vt": "str"
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{
"t": "eq",
"v": "Missing entry :",
"vt": "str"
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],
"checkall": "true",
"repair": false,
"outputs": 2,
"x": 1030,
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[
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"type": "ui_toast",
"z": "baa1e3d9.cb29d",
"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1190,
"y": 500,
"wires": [
[]
]
},
{
"id": "c3e50240.82aa58",
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"z": "baa1e3d9.cb29d",
"name": "",
"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
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"y": 420,
"wires": []
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{
"id": "3a4450b1.4459a8",
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"group": "4322c187.e73e5",
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"width": 5,
"height": 1,
"passthru": true,
"label": "STOP ACQUISITION",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "cancel",
"payload": "{\"action\":\"stop\"}",
"payloadType": "json",
"topic": "imager/image",
"x": 520,
"y": 500,
"wires": [
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{
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"broker": "8dc3722c.06efa8",
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"wires": []
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{
"id": "bb62da8a.ebc328",
"type": "ui_switch",
"z": "baa1e3d9.cb29d",
"name": "",
"label": "Pump FORWARD/BACKWARD",
"tooltip": "",
"group": "4322c187.e73e5",
"order": 4,
"width": 3,
"height": 1,
"passthru": true,
"decouple": "false",
"topic": "",
"style": "",
"onvalue": "FORWARD",
"onvalueType": "str",
"onicon": "",
"oncolor": "",
"offvalue": "BACKWARD",
"offvalueType": "str",
"officon": "",
"offcolor": "",
"x": 470,
"y": 540,
"wires": [
[]
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},
{
"id": "52ea7d01.711034",
"type": "function",
"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;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 750,
"y": 420,
"wires": [
[
"c3e50240.82aa58"
]
]
},
{
"id": "40c12463.a1f84c",
"type": "delay",
"z": "baa1e3d9.cb29d",
"name": "",
"pauseType": "delay",
"timeout": "1",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
"x": 720,
"y": 460,
"wires": [
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},
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"id": "4d1b02cb.83b51c",
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"width": 6,
"height": 1,
"passthru": false,
"label": "Update config",
"tooltip": "",
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"payload": "",
"payloadType": "str",
"topic": "imager/image",
"x": 520,
"y": 420,
"wires": [
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},
{
"id": "452af41c.43940c",
"type": "python3-function",
"z": "1371dec5.76e671",
"name": "Get MachineName",
"func": "import sys\nsys.path.append('/home/pi/PlanktonScope/scripts')\nimport planktoscope.uuidName\n\nmsg['payload'] = planktoscope.uuidName.machineName(machine=planktoscope.uuidName.getSerial())\nmsg['topic'] = \"acq_instrument_id\";\nreturn msg",
"outputs": 1,
"x": 490,
"y": 760,
"wires": [
[
"4828d2f4.7c712c",
"e2f39a35.f57298",
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},
{
"id": "4828d2f4.7c712c",
"type": "function",
"z": "1371dec5.76e671",
"name": "set global",
"func": "global.set(msg.topic,msg.payload);\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 780,
"y": 800,
"wires": [
[]
]
},
{
"id": "2200e2ae.0d183e",
"type": "rpi-gpio out",
"z": "1371dec5.76e671",
"name": "Pump Enable",
"pin": "7",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 470,
"y": 600,
"wires": []
},
{
"id": "592c4dac.b8a9dc",
"type": "rpi-gpio out",
"z": "1371dec5.76e671",
"name": "Focus Enable",
"pin": "32",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 480,
"y": 640,
"wires": []
},
{
"id": "d027a6bf.7049e8",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_projet",
"func": "msg.payload = msg.payload.sample_project;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 350,
"y": 300,
"wires": [
[
"9c882b37.fde668"
]
]
},
{
"id": "5a811caf.0f3144",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_ship",
"func": "msg.payload = msg.payload.sample_ship;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 340,
"y": 340,
"wires": [
[
"4557d689.a4fa88"
]
]
},
{
"id": "45911c98.2bd83c",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_id",
"func": "msg.payload = msg.payload.sample_id;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 340,
"y": 380,
"wires": [
[
"94eb4221.9b92c"
]
]
},
{
"id": "1e09a4ab.72996b",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_operator",
"func": "msg.payload = msg.payload.sample_operator;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 420,
"wires": [
[
"82c5fc77.59c97"
]
]
},
{
"id": "a3272681.f271c8",
"type": "function",
"z": "b771c342.49603",
"name": "get sample_sampling_gear",
"func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 380,
"y": 460,
"wires": [
[
"fcfc31ae.af3af"
]
]
},
{
"id": "6465bdd5.15eb8c",
"type": "file in",
"z": "1c24ad9c.bebec2",
"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"format": "utf8",
"chunk": false,
"sendError": false,
"encoding": "none",
"x": 660,
"y": 300,
"wires": [
[
"15ceb135.6628bf"
]
],
"info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
},
{
"id": "15ceb135.6628bf",
"type": "json",
"z": "1c24ad9c.bebec2",
"name": "config.json",
"property": "payload",
"action": "",
"pretty": false,
"x": 910,
"y": 300,
"wires": [
[
"ad541674.4791c8"
]
]
},
{
"id": "b584292a.24b08",
"type": "function",
"z": "1c24ad9c.bebec2",
"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 \n \"acq_id\":global.get(\"acq_id\"),\n \"acq_instrument\":global.get(\"acq_instrument\"),\n \"acq_instrument_id\":global.get(\"machine_name\"),\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\":global.get(\"camera_name\"),\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};\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 560,
"y": 860,
"wires": [
[
"2e6ddf51.c0dba"
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},
{
"id": "7205d267.36adcc",
"type": "file",
"z": "1c24ad9c.bebec2",
"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"appendNewline": true,
"createDir": true,
"overwriteFile": "true",
"encoding": "none",
"x": 970,
"y": 860,
"wires": [
[]
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},
{
"id": "2e6ddf51.c0dba",
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"id": "ad541674.4791c8",
"type": "function",
"z": "1c24ad9c.bebec2",
"name": "Global Set",
"func": "for (const key in msg.payload) {\n global.set(key, msg.payload[key]);\n}\n\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 1090,
"y": 300,
"wires": [
[]
]
},
{
"id": "3e9a33c.141384c",
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"z": "1c24ad9c.bebec2",
"name": "Load config",
"props": [
{
"p": "topic",
"vt": "str"
}
],
"repeat": "",
"crontab": "",
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"onceDelay": 0.1,
"topic": "",
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},
{
"id": "3cea1f2.20525e",
"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lat_end",
"label": "Latitude of retrieval",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
"order": 1,
"width": 12,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lat_end",
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"type": "ui_text_input",
"z": "b771c342.49603",
"name": "object_lon_end",
"label": "Longitude of retrieval",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
"order": 2,
"width": 12,
"height": 1,
"passthru": true,
"mode": "number",
"delay": 300,
"topic": "object_lon_end",
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"id": "f9d71e4b.2940a",
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"z": "b771c342.49603",
"name": "object_date_end",
"label": "Date",
"group": "cf5d9f0e.d57e7",
"order": 3,
"width": 12,
"height": 1,
"passthru": true,
"topic": "object_date_end",
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"name": "object_time_end",
"label": "Time :",
"tooltip": "",
"group": "cf5d9f0e.d57e7",
"order": 4,
"width": 12,
"height": 1,
"passthru": true,
"mode": "time",
"delay": 300,
"topic": "object_time_end",
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{
"id": "1a945afa.d60aad",
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"z": "b771c342.49603",
"name": "set time global",
"func": "var date = new Date(global.get(msg.topic));\n// From https://stackoverflow.com/a/53752557/2108279\n\n\n// attempt to parse string as time. return js date object\nstring = msg.payload\n\nvar am = null;\n\n// check if \"apm\" or \"pm\" explicitly specified, otherwise null\nif (string.toLowerCase().includes(\"p\")) am = false;\nelse if (string.toLowerCase().includes(\"a\")) am = true;\n\nstring = string.replace(/\\D/g, \"\"); // remove non-digit characters\nstring = string.substring(0, 4); // take only first 4 digits\nif (string.length === 3) string = \"0\" + string; // consider eg \"030\" as \"0030\"\nstring = string.replace(/^00/, \"24\"); // add 24 hours to preserve eg \"0012\" as \"00:12\" instead of \"12:00\", since will be converted to integer\n\nvar time = parseInt(string); // convert to integer\n// default time if all else fails\nvar hours = 12,\nminutes = 0;\n\n// if able to parse as int\nif (Number.isInteger(time)) {\n// treat eg \"4\" as \"4:00pm\" (or \"4:00am\" if \"am\" explicitly specified)\nif (time >= 0 && time <= 12) {\n hours = time;\n minutes = 0;\n // if \"am\" or \"pm\" not specified, establish from number\n if (am === null) {\n if (hours >= 1 && hours <= 12) am = false;\n else am = true;\n }\n}\n// treat eg \"20\" as \"8:00pm\"\nelse if (time >= 13 && time <= 99) {\n hours = time % 24;\n minutes = 0;\n // if \"am\" or \"pm\" not specified, force \"am\"\n if (am === null) am = true;\n}\n// treat eg \"52:95\" as 52 hours 95 minutes \nelse if (time >= 100) {\n hours = Math.floor(time / 100); // take first two digits as hour\n minutes = time % 100; // take last two digits as minute\n // if \"am\" or \"pm\" not specified, establish from number\n if (am === null) {\n if (hours >= 1 && hours <= 12) am = false;\n else am = true;\n }\n}\n\n// add 12 hours if \"pm\"\nif (am === false && hours !== 12) hours += 12;\n// sub 12 hours if \"12:00am\" (midnight), making \"00:00\"\nif (am === true && hours === 12) hours = 0;\n\n// keep hours within 24 and minutes within 60\n// eg 52 hours 95 minutes becomes 4 hours 35 minutes\nhours = hours % 24;\nminutes = minutes % 60;\n}\n\n// convert to js date object\ndate.setHours(hours);\ndate.setMinutes(minutes);\ndate.setSeconds(0);\n\nglobal.set(msg.topic,date.toISOString().split('T')[1].split('.')[0].replace(/:/gi, ''));",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 980,
"y": 740,
"wires": [
[]
]
},
{
"id": "29f2b365.4327ec",
"type": "function",
"z": "b771c342.49603",
"name": "set date global",
"func": "var date = new Date(msg.payload);\n\nglobal.set(msg.topic,date.toISOString().split('T')[0].replace(/-/gi, ''));",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 980,
"y": 700,
"wires": [
[]
]
},
{
"id": "b3c21aa9.8c06c",
"type": "exec",
"z": "1371dec5.76e671",
"command": "git --git-dir /home/pi/PlanktonScope/.git/ rev-parse --short master",
"addpay": false,
"append": "",
"useSpawn": "false",
"timer": "",
"oldrc": false,
"name": "git rev",
"x": 450,
"y": 700,
"wires": [
[
"3e64877a.9684b",
"1bdd7f07.616f69"
],
[],
[]
]
},
{
"id": "3e64877a.9684b",
"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",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 790,
"y": 640,
"wires": [
[
"8343fa69.49339"
]
]
},
{
"id": "68fa1227.dbdd5c",
"type": "function",
"z": "bccd1f23.87219",
"name": "get acq_fnumber_objective",
"func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 820,
"y": 100,
"wires": [
[
"cc966678.da8d08"
]
]
},
{
"id": "1c45ea1c.80234e",
"type": "subflow:1c24ad9c.bebec2",
"z": "bccd1f23.87219",
"name": "",
"x": 600,
"y": 100,
"wires": [
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]
},
{
"id": "5921d0d0.a3d568",
"type": "subflow:1c24ad9c.bebec2",
"z": "baa1e3d9.cb29d",
"name": "",
"x": 80,
"y": 120,
"wires": [
[
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"1f133196.96564e",
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},
{
"id": "f3658d30.b8448",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_id",
"func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 310,
"y": 240,
"wires": [
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},
{
"id": "5acd51d4.4ab13",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_instrument",
"func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 370,
"y": 780,
"wires": [
[]
]
},
{
"id": "de2c90cf.b73b08",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_celltype",
"func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 320,
"y": 80,
"wires": [
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"cc0ca68b.4263a8"
]
]
},
{
"id": "5e3dec55.881074",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_minimum_mesh",
"func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 350,
"y": 120,
"wires": [
[
"f59a2f0d.5e9af"
]
]
},
{
"id": "d3ca8847.4d1ae",
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"z": "baa1e3d9.cb29d",
"name": "get acq_maximum_mesh",
"func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 350,
"y": 160,
"wires": [
[
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]
},
{
"id": "1f133196.96564e",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "get acq_volume",
"func": "msg.payload = msg.payload.acq_volume;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"x": 320,
"y": 200,
"wires": [
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]
},
{
"id": "bdc6718a.dd5d48",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 3,
"width": 0,
"height": 0,
"name": "",
"label": "Instrument Type",
"format": "{{msg.payload.acq_instrument}}",
"layout": "row-spread",
"x": 1040,
"y": 700,
"wires": []
},
{
"id": "a400a97e.e333a8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 0,
"width": 0,
"height": 0,
"name": "",
"label": "Instrument Name",
"format": "{{msg.payload}}",
"layout": "row-spread",
"x": 810,
"y": 760,
"wires": []
},
{
"id": "8343fa69.49339",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 1,
"width": 0,
"height": 0,
"name": "",
"label": "Software version",
"format": "{{msg.payload}}",
"layout": "row-spread",
"x": 1040,
"y": 640,
"wires": []
},
{
"id": "f783aefd.c3bfd8",
"type": "ui_text",
"z": "1371dec5.76e671",
"group": "ce9e278.781eed8",
"order": 0,
"width": 0,
"height": 0,
"name": "",
"label": "Camera Name",
"format": "{{msg.payload.acq_camera}}",
"layout": "row-spread",
"x": 1040,
"y": 740,
"wires": []
},
{
"id": "1bdd7f07.616f69",
"type": "debug",
"z": "1371dec5.76e671",
"name": "",
"active": true,
"tosidebar": true,
"console": false,
"tostatus": false,
"complete": "false",
"statusVal": "",
"statusType": "auto",
"x": 790,
"y": 680,
"wires": []
},
{
"id": "a0e2d78c.a587e",
"type": "inject",
"z": "1371dec5.76e671",
"name": "ON",
"props": [
{
"p": "payload"
}
],
"repeat": "60",
"crontab": "",
"once": true,
"onceDelay": "",
"topic": "",
"payload": "true",
"payloadType": "bool",
"x": 130,
"y": 620,
"wires": [
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},
{
"id": "906d9fea.4bab48",
"type": "status",
"z": "b771c342.49603",
"d": true,
"name": "GPS Status",
"scope": [],
"x": 310,
"y": 1320,
"wires": [
[
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},
{
"id": "7116e906.9f50f",
"type": "ui_text",
"z": "b771c342.49603",
"d": true,
"group": "cf5d9f0e.d57e7",
"order": 5,
"width": 6,
"height": 1,
"name": "GPS Status Display",
"label": "GPS Status:",
"format": "{{msg.status.text}}",
"layout": "row-left",
"x": 810,
"y": 1320,
"wires": []
},
{
"id": "3269f55f.05d0d2",
"type": "function",
"z": "b771c342.49603",
"name": "Convert DD to DMS",
"func": "function ConvertDDToDMS(D, lng){\n // from https://stackoverflow.com/a/5786281/2108279\n return {\n dir : D<0?lng?'W':'S':lng?'E':'N',\n deg : 0|(D<0?D=-D:D),\n min : 0|D%1*60,\n sec :(0|D*60%1*6000)/100\n };\n}\n\nmsg.payload = {\n \"lat\":ConvertDDToDMS(msg.payload.lat, false),\n \"lon\":ConvertDDToDMS(msg.payload.lon, true)\n};\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 550,
"y": 1240,
"wires": [
[]
]
}
]