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"type": "tab",
"label": "Home",
"disabled": false,
"info": ""
},
{
"id": "b771c342.49603",
"type": "tab",
"label": "Sample",
"disabled": false,
"info": ""
},
{
"id": "bccd1f23.87219",
"type": "tab",
"label": "Optic Configuration",
"disabled": false,
"info": ""
},
{
"id": "baa1e3d9.cb29d",
"type": "tab",
"label": "Fluidic Acquisition",
"disabled": false,
"info": ""
},
{
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"type": "tab",
"label": "Segmentation",
"disabled": false,
"info": ""
},
{
"id": "1371dec5.76e671",
"type": "tab",
"label": "Settings",
"disabled": false,
"info": ""
},
{
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"type": "tab",
"label": "Gallery",
"disabled": false,
"info": ""
},
{
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"type": "tab",
"label": "MQTT Receive",
"disabled": false,
"info": ""
},
{
"id": "1c24ad9c.bebec2",
"type": "subflow",
"name": "Config",
"info": "An input to this subflow will get the configuration to be saved to disk.\n\nOn startup, this node outputs the loaded configuration",
"category": "",
"in": [
{
"x": 440,
"y": 860,
"wires": [
{
"id": "cdc75496.45f748"
}
]
}
],
"out": [
{
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"wires": [
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}
]
}
],
"env": [],
"color": "#DDAA99"
},
{
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"type": "subflow",
"name": "Get global for config.json",
"info": "",
"category": "",
"in": [
{
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"y": 80,
"wires": [
{
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}
]
}
],
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{
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}
]
}
],
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"color": "#DDAA99"
},
{
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"type": "ui_group",
"z": "",
"name": "Preview",
"tab": "181bb236.1e94be",
"order": 1,
"disp": true,
"width": 18,
"collapse": false
},
{
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"type": "ui_tab",
"name": "Home",
"icon": "home",
"order": 1,
"disabled": false,
"hidden": false
},
{
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"name": "Optic Configuration",
"icon": "fa-eye",
"order": 3,
"disabled": false,
"hidden": false
},
{
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"type": "ui_tab",
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"disabled": false,
"hidden": false
},
{
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"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,
"width": 10,
"collapse": false
},
{
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"tab": "8d16beb8.9b3fb",
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"disp": false,
"width": "6",
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},
{
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{
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"lightTheme": {
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"baseColor": "#5900ce",
"baseFont": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif",
"edited": false,
"reset": false
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},
"customTheme": {
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"baseColor": "#4B7930",
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},
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"value": "#097479",
"edited": true
},
"page-titlebar-backgroundColor": {
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"edited": false
},
"page-backgroundColor": {
"value": "#111111",
"edited": false
},
"page-sidebar-backgroundColor": {
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"edited": false
},
"group-textColor": {
"value": "#0eb8c0",
"edited": false
},
"group-borderColor": {
"value": "#555555",
"edited": false
},
"group-backgroundColor": {
"value": "#333333",
"edited": false
},
"widget-textColor": {
"value": "#eeeeee",
"edited": false
},
"widget-backgroundColor": {
"value": "#097479",
"edited": false
},
"widget-borderColor": {
"value": "#333333",
"edited": false
},
"base-font": {
"value": "-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Oxygen-Sans,Ubuntu,Cantarell,Helvetica Neue,sans-serif"
}
},
"angularTheme": {
"primary": "indigo",
"accents": "blue",
"warn": "red",
"background": "grey"
}
},
"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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"type": "ui_tab",
"z": "",
"name": "Gallery",
"icon": "fa fa-file-image-o",
"order": 6,
"disabled": true,
"hidden": true
},
{
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"order": 1,
"disp": true,
"width": 24
},
{
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"type": "ui_tab",
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"name": "Sample",
"icon": "fa-eyedropper",
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"disabled": false,
"hidden": false
},
{
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"type": "ui_group",
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"disp": false,
"width": "4",
"collapse": false
},
{
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"disp": true,
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"collapse": false
},
{
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"disp": false,
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"collapse": false
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"order": 3,
"disp": false,
"width": "4",
"collapse": false
},
{
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"type": "ui_group",
"name": "Group 4",
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"order": 4,
"disp": false,
"width": "4",
"collapse": false
},
{
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"type": "ui_group",
"name": "Group 5",
"tab": "3a6bb13f.c9703e",
"order": 5,
"disp": false,
"width": "4",
"collapse": false
},
{
"id": "777a7c33.fcd804",
"type": "ui_group",
"name": "Group 6",
"tab": "3a6bb13f.c9703e",
"order": 6,
"disp": false,
"width": "4",
"collapse": false
},
{
"id": "cef1e703.bcf3c8",
"type": "ui_group",
"z": "",
"name": "Sample Location",
"tab": "737ec584.2eea2c",
"order": 2,
"disp": true,
"width": "10",
"collapse": false
},
{
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"type": "ui_group",
"name": "Validation",
"tab": "737ec584.2eea2c",
"order": 4,
"disp": false,
"width": 10,
"collapse": false
},
{
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"type": "ui_group",
"name": "Focus Adjustment",
"tab": "181bb236.1e94be",
"order": 4,
"disp": true,
"width": 10,
"collapse": false
},
{
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"type": "ui_group",
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"disp": true,
"width": 10,
"collapse": false
},
{
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"name": "Navigation",
"tab": "181bb236.1e94be",
"order": 6,
"disp": false,
"width": "10",
"collapse": false
},
{
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"type": "ui_group",
"name": "Fraction size",
"tab": "c9194f02.9d5e9",
"order": 2,
"disp": true,
"width": "10",
"collapse": false
},
{
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"order": 3,
"disp": true,
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},
{
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"disp": false,
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"collapse": false
},
{
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"name": "Statistics",
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"order": 4,
"disp": true,
"width": "10",
"collapse": false
},
{
"id": "1be83144.4fe4bf",
"type": "ui_group",
"name": "Danger Zone (DO NOT TOUCH HERE UNLESS YOU KNOW WHAT YOU ARE DOING)",
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"order": 7,
"disp": true,
"width": 24,
"collapse": false
},
{
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"disp": false,
"width": 10,
"collapse": false
},
{
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"order": 2,
"disp": true,
"width": "6",
"collapse": false
},
{
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"disp": true,
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},
{
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"order": 4,
"disp": true,
"width": "6",
"collapse": false
},
{
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"type": "mqtt-broker",
"name": "",
"broker": "0.0.0.0",
"port": "1883",
"clientid": "Client_node",
"usetls": false,
"compatmode": false,
"keepalive": "60",
"cleansession": true,
"birthTopic": "",
"birthQos": "0",
"birthPayload": "",
"closeTopic": "",
"closeQos": "0",
"closePayload": "",
"willTopic": "",
"willQos": "0",
"willPayload": ""
},
{
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"type": "ui_group",
"z": "",
"name": "Control",
"tab": "8d16beb8.9b3fb",
"order": 1,
"disp": true,
"width": 10,
"collapse": false
},
{
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"name": "Net Metadata",
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"order": 3,
"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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"disp": true,
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},
{
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{
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},
{
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},
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"passthru": false,
"label": "Home",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "home",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
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"x": 410,
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"wires": [
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},
{
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"passthru": false,
"label": "Home",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "home",
"payload": "{\"tab\":\"Home\"}",
"payloadType": "json",
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"x": 130,
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},
{
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},
{
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"name": "",
"group": "b5ba3f26.2e722",
"order": 1,
"width": 0,
"height": 0,
"gtype": "gage",
"title": "CPU Temperature",
"label": "°C",
"format": "{{value}}",
"min": "30",
"max": "55",
"colors": [
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"#e6e600",
"#ca3838"
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"seg1": "",
"seg2": "",
"x": 610,
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"wires": []
},
{
"id": "ddcbbfa5.cd158",
"type": "exec",
"z": "1371dec5.76e671",
"command": "vcgencmd measure_temp | tr -d \"temp=\" | tr -d \"'C\" | tr -d \"\\n\"",
"addpay": false,
"append": "",
"useSpawn": "",
"timer": "",
"name": "RPi Temp.",
"x": 310,
"y": 120,
"wires": [
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"bgcolor": "white",
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"payload": "{\"tab\":\"Optic Configuration\"}",
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{
"id": "29be525e.0c87fe",
"type": "ui_template",
"z": "baa1e3d9.cb29d",
"group": "b5d61bc7.54fe48",
"name": "Show Metadata",
"order": 9,
"width": 0,
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"format": "\n
\n \n \n Sample project: ship: operator: id: sampling gear: concentrated volume: gear net opening: \n \n Acquisition id: instrument: instrument id: camera: celltype: minimum mesh: maximum mesh: min esd: max esd: volume: magnification: fnumber objective: software: flowrate: \n \n \n \n Object latitude: longitude: latitude end: longitude end: date: time: date end: time end: depth min: depth max: \n \n Process pixel: id: \n \n
\n
If you want to update to the latest code version of Node-Red and Python, please click here.\nWe are trying to save your configuration changes with git stash and restore them afterwards, but clearly, things may break!\nIf you have made changes to the flow, you will lose them. Please commit those changes from Node-Red interface, from the Project History tab. ",
"storeOutMessages": true,
"fwdInMessages": true,
"resendOnRefresh": true,
"templateScope": "local",
"x": 130,
"y": 460,
"wires": [
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},
{
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"group": "4322c187.e73e5",
"order": 11,
"width": 5,
"height": 1,
"passthru": false,
"label": "Start Acquisition",
"tooltip": "",
"color": "",
"bgcolor": "",
"icon": "",
"payload": "",
"payloadType": "str",
"topic": "imager/image",
"x": 520,
"y": 580,
"wires": [
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{
"id": "c9f510c0.7d1328",
"type": "function",
"z": "baa1e3d9.cb29d",
"name": "Image control",
"func": "state = global.get(\"state\");\nglobal.set('img_counter', 0);\nglobal.set('obj_counter', 0);\nif (state === null) {\n state = \"free\"\n}\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_id = global.get(\"acq_id\");\nvar pump_direction = global.get(\"pump_direction\");\nvar imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar sleep_before = global.get(\"sleep_before\");\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 (imaging_pump_volume === undefined || imaging_pump_volume === \"\" || imaging_pump_volume === null) {\n msg.topic = \"Missing entry :\"\n msg.payload = \"Volume inbetween images\"\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} else if (pump_direction === undefined || pump_direction === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Pump direction\";\n} else if (sleep_before === undefined || sleep_before === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Delay before image\";\n} else {\n msg.payload = {\n \"action\": \"image\",\n \"sleep\": sleep_before,\n \"pump_direction\": pump_direction,\n \"volume\": imaging_pump_volume,\n \"nb_frame\": nb_frame,\n }\n}\n\nreturn msg;",
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"initialize": "",
"finalize": "",
"x": 730,
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"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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"checkall": "true",
"repair": false,
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"position": "dialog",
"displayTime": "3",
"highlight": "",
"sendall": true,
"outputs": 1,
"ok": "OK",
"cancel": "",
"raw": false,
"topic": "",
"name": "",
"x": 1250,
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"wires": [
[]
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},
{
"id": "c3e50240.82aa58",
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"topic": "",
"qos": "",
"retain": "",
"broker": "8dc3722c.06efa8",
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{
"id": "3a4450b1.4459a8",
"type": "ui_button",
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"group": "4322c187.e73e5",
"order": 10,
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"height": 1,
"passthru": true,
"label": "STOP ACQUISITION",
"tooltip": "",
"color": "",
"bgcolor": "#AD1625",
"icon": "cancel",
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"payloadType": "json",
"topic": "imager/image",
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"retain": "",
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{
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"order": 8,
"width": 5,
"height": 1,
"passthru": true,
"decouple": "false",
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"style": "",
"onvalue": "FORWARD",
"onvalueType": "str",
"onicon": "",
"oncolor": "",
"offvalue": "BACKWARD",
"offvalueType": "str",
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"func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_id\"),\n\t\t\"sample_ship\": global.get(\"sample_ship\"),\n\t\t\"sample_operator\": global.get(\"sample_operator\"),\n\t\t\"sample_sampling_gear\": global.get(\"sample_sampling_gear\"),\n\t\t\"sample_concentrated_sample_volume\": global.get(\"sample_concentrated_sample_volume\"),\n\n\t\t\"acq_id\": global.get(\"acq_id\"),\n\t\t\"acq_instrument\": global.get(\"acq_instrument\"),\n\t\t\"acq_instrument_id\": global.get(\"acq_instrument_id\"),\n\t\t\"acq_celltype\": global.get(\"acq_celltype\"),\n\t\t\"acq_minimum_mesh\": global.get(\"acq_minimum_mesh\"),\n\t\t\"acq_maximum_mesh\": global.get(\"acq_maximum_mesh\"),\n\t\t\"acq_min_esd\": global.get(\"acq_min_esd\"),\n\t\t\"acq_max_esd\": global.get(\"acq_max_esd\"),\n\t\t\"acq_volume\": global.get(\"acq_volume\"),\n\t\t\"acq_magnification\": global.get(\"magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera_name\": global.get(\"acq_camera_name\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\n\t\t\"object_date\": global.get(\"object_date\"),\n\t\t\"object_time\": global.get(\"object_time\"),\n\t\t\"object_lat\": global.get(\"object_lat\"),\n\t\t\"object_lon\": global.get(\"object_lon\"),\n\t\t\"object_depth_min\": global.get(\"object_depth_min\"),\n\t\t\"object_depth_max\": global.get(\"object_depth_max\"),\n\n\t\t\"process_pixel\": global.get(\"process_pixel\"),\n\t\t\"process_id\": global.get(\"process_id\")\n\t}\n};\n\nif (msg.payload.config.sample_sampling_gear == \"net\") {\n\tmsg.payload.config = { ...msg.payload.config ,\n\t\t\t\"sample_gear_net_opening\": global.get(\"sample_gear_net_opening\"),\n\t\t\t\"object_date_end\": global.get(\"object_date_end\"),\n\t\t\t\"object_time_end\": global.get(\"object_time_end\"),\n\t\t\t\"object_lat_end\": global.get(\"object_lat_end\"),\n\t\t\t\"object_lon_end\": global.get(\"object_lon_end\")\n\t};\n}\nreturn msg;",
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"noerr": 0,
"initialize": "",
"finalize": "",
"x": 970,
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"pauseType": "delay",
"timeout": "1",
"timeoutUnits": "seconds",
"rate": "1",
"nbRateUnits": "1",
"rateUnits": "second",
"randomFirst": "1",
"randomLast": "5",
"randomUnits": "seconds",
"drop": false,
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{
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"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",
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"wires": [
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"type": "function",
"z": "1371dec5.76e671",
"name": "set global",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 780,
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"wires": [
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},
{
"id": "2200e2ae.0d183e",
"type": "rpi-gpio out",
"z": "1371dec5.76e671",
"name": "Pump Enable",
"pin": "7",
"set": true,
"level": "1",
"freq": "",
"out": "out",
"x": 480,
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"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": [
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{
"id": "5a811caf.0f3144",
"type": "function",
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"name": "get sample_ship",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 340,
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{
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"noerr": 0,
"initialize": "",
"finalize": "",
"x": 340,
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},
{
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"type": "function",
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"name": "get sample_operator",
"func": "msg.payload = msg.payload.sample_operator;\nreturn msg;",
"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 360,
"y": 420,
"wires": [
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},
{
"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": [
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},
{
"id": "6465bdd5.15eb8c",
"type": "file in",
"z": "1c24ad9c.bebec2",
"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"format": "utf8",
"chunk": false,
"sendError": false,
"encoding": "none",
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"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",
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"pretty": false,
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},
{
"id": "b584292a.24b08",
"type": "function",
"z": "20ae9e26.17d73a",
"name": "get global",
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"outputs": 1,
"noerr": 0,
"initialize": "",
"finalize": "",
"x": 200,
"y": 80,
"wires": [
[]
]
},
{
"id": "7205d267.36adcc",
"type": "file",
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"name": "",
"filename": "/home/pi/PlanktonScope/config.json",
"appendNewline": true,
"createDir": true,
"overwriteFile": "true",
"encoding": "none",
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},
{
"id": "2e6ddf51.c0dba",
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{
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"name": "Global Set",
"func": "for (const key in msg.payload) {\n global.set(key, msg.payload[key]);\n}\n\nreturn msg;",
"outputs": 1,
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"initialize": "",
"finalize": "",
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"wires": [
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]
},
{
"id": "3e9a33c.141384c",
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"z": "1c24ad9c.bebec2",
"name": "Load config",
"props": [
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"vt": "str"
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],
"repeat": "",
"crontab": "",
"once": true,
"onceDelay": 0.1,
"topic": "",
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},
{
"id": "e2f39a35.f57298",
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"env": [],
"x": 770,
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{
"id": "b3c21aa9.8c06c",
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"command": "git --git-dir /home/pi/PlanktonScope/.git/ rev-parse --short master",
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"timer": "",
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"initialize": "",
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"x": 820,
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{
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"checkall": "true",
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"outputs": 2,
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"vt": "jsonata"
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"checkall": "false",
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