1851 lines
51 KiB
JSON
1851 lines
51 KiB
JSON
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"func": "global.set(msg.topic,msg.payload);\nvar acq_fnumber_objective = String(global.get(msg.topic));\n\nswitch(acq_fnumber_objective) {\n case \"25\":\n global.set(\"magnification\",0.6);\n global.set(\"process_pixel\",1.86);\n global.set(\"sug_min\",60);\n global.set(\"sug_max\",670);\n global.set(\"flowrate\",3);\n break;\n case \"16\":\n global.set(\"magnification\",0.94);\n global.set(\"process_pixel\",1.19);\n global.set(\"sug_min\",40);\n global.set(\"sug_max\",430);\n global.set(\"flowrate\",2.4);\n break;\n case \"12\":\n global.set(\"magnification\",1.20);\n global.set(\"process_pixel\",0.94);\n global.set(\"sug_min\",30);\n global.set(\"sug_max\",340);\n global.set(\"flowrate\",1.25);\n break;\n case \"8\":\n global.set(\"magnification\",1.78);\n global.set(\"process_pixel\",0.63);\n global.set(\"sug_min\",20);\n global.set(\"sug_max\",230);\n global.set(\"flowrate\",0.42);\n break;\n case \"6\":\n global.set(\"magnification\",2.36);\n global.set(\"process_pixel\",0.48);\n global.set(\"sug_min\",15);\n global.set(\"sug_max\",170);\n global.set(\"flowrate\",0.32);\n break;\n}\nreturn msg;",
|
|
"outputs": 1,
|
|
"noerr": 0,
|
|
"x": 1220,
|
|
"y": 40,
|
|
"wires": [
|
|
[
|
|
"c83fc403.8ba2d8",
|
|
"48d9cc9c.852214",
|
|
"44969aec.4e87e4",
|
|
"a1201a.dc3f8fe8",
|
|
"89b9399b.9389a8"
|
|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "f3aa18d.65f0de8",
|
|
"type": "ui_dropdown",
|
|
"z": "7f885510.6173fc",
|
|
"name": "acq_celltype",
|
|
"label": "Thickness flowcell*",
|
|
"tooltip": "",
|
|
"place": "Select option",
|
|
"group": "a72a9ec6.bb144",
|
|
"order": 1,
|
|
"width": 0,
|
|
"height": 0,
|
|
"passthru": true,
|
|
"options": [
|
|
{
|
|
"label": "200 μm µ-Slide I Luer",
|
|
"value": 200,
|
|
"type": "num"
|
|
},
|
|
{
|
|
"label": "400 μm µ-Slide I Luer",
|
|
"value": 400,
|
|
"type": "num"
|
|
},
|
|
{
|
|
"label": "600 μm µ-Slide I Luer",
|
|
"value": 600,
|
|
"type": "num"
|
|
},
|
|
{
|
|
"label": "800 μm µ-Slide I Luer",
|
|
"value": 800,
|
|
"type": "num"
|
|
}
|
|
],
|
|
"payload": "",
|
|
"topic": "acq_celltype",
|
|
"x": 170,
|
|
"y": 280,
|
|
"wires": [
|
|
[
|
|
"8861710f.55b92"
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|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "45568fe8.67759",
|
|
"type": "ui_numeric",
|
|
"z": "7f885510.6173fc",
|
|
"name": "acq_minimum_mesh",
|
|
"label": "Min fraction size (μm)",
|
|
"tooltip": "",
|
|
"group": "a72a9ec6.bb144",
|
|
"order": 2,
|
|
"width": 0,
|
|
"height": 0,
|
|
"wrap": false,
|
|
"passthru": true,
|
|
"topic": "acq_minimum_mesh",
|
|
"format": "{{value}}",
|
|
"min": 0,
|
|
"max": "300",
|
|
"step": "10",
|
|
"x": 140,
|
|
"y": 320,
|
|
"wires": [
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[
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"8861710f.55b92"
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]
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]
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},
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{
|
|
"id": "918b69e2.7e6e88",
|
|
"type": "ui_numeric",
|
|
"z": "7f885510.6173fc",
|
|
"name": "acq_maximum_mesh",
|
|
"label": "Max fraction size (μm)",
|
|
"tooltip": "",
|
|
"group": "a72a9ec6.bb144",
|
|
"order": 3,
|
|
"width": 0,
|
|
"height": 0,
|
|
"wrap": false,
|
|
"passthru": true,
|
|
"topic": "acq_maximum_mesh",
|
|
"format": "{{value}}",
|
|
"min": "200",
|
|
"max": "2000",
|
|
"step": "100",
|
|
"x": 140,
|
|
"y": 360,
|
|
"wires": [
|
|
[
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|
"8861710f.55b92"
|
|
]
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]
|
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},
|
|
{
|
|
"id": "86d762dc.47911",
|
|
"type": "ui_switch",
|
|
"z": "7f885510.6173fc",
|
|
"name": "light_state",
|
|
"label": "Light",
|
|
"tooltip": "",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 1,
|
|
"width": 2,
|
|
"height": 1,
|
|
"passthru": true,
|
|
"decouple": "false",
|
|
"topic": "",
|
|
"style": "",
|
|
"onvalue": "true",
|
|
"onvalueType": "bool",
|
|
"onicon": "",
|
|
"oncolor": "",
|
|
"offvalue": "false",
|
|
"offvalueType": "bool",
|
|
"officon": "",
|
|
"offcolor": "",
|
|
"x": 510,
|
|
"y": 160,
|
|
"wires": [
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[
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"b5a366b4.cb6918"
|
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]
|
|
]
|
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},
|
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{
|
|
"id": "b5a366b4.cb6918",
|
|
"type": "exec",
|
|
"z": "7f885510.6173fc",
|
|
"command": "python3.7 $HOME/PlanktonScope/scripts/light.py",
|
|
"addpay": true,
|
|
"append": "",
|
|
"useSpawn": "false",
|
|
"timer": "",
|
|
"oldrc": false,
|
|
"name": "light.py",
|
|
"x": 820,
|
|
"y": 160,
|
|
"wires": [
|
|
[],
|
|
[],
|
|
[]
|
|
],
|
|
"icon": "node-red/light.svg"
|
|
},
|
|
{
|
|
"id": "5ea28a70.42ae14",
|
|
"type": "ui_button",
|
|
"z": "7f885510.6173fc",
|
|
"name": "up",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 3,
|
|
"width": 1,
|
|
"height": 1,
|
|
"passthru": false,
|
|
"label": "",
|
|
"tooltip": "",
|
|
"color": "",
|
|
"bgcolor": "",
|
|
"icon": "arrow_upwards",
|
|
"payload": "up",
|
|
"payloadType": "str",
|
|
"topic": "up",
|
|
"x": 530,
|
|
"y": 280,
|
|
"wires": [
|
|
[
|
|
"523fdeaa.50c6c"
|
|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "27f16831.dde938",
|
|
"type": "ui_button",
|
|
"z": "7f885510.6173fc",
|
|
"name": "down",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 5,
|
|
"width": 1,
|
|
"height": 1,
|
|
"passthru": true,
|
|
"label": "",
|
|
"tooltip": "",
|
|
"color": "",
|
|
"bgcolor": "",
|
|
"icon": "arrow_downward",
|
|
"payload": "down",
|
|
"payloadType": "str",
|
|
"topic": "down",
|
|
"x": 530,
|
|
"y": 360,
|
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"wires": [
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[
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|
"523fdeaa.50c6c"
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]
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|
]
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},
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{
|
|
"id": "855e9d96.ab869",
|
|
"type": "ui_text_input",
|
|
"z": "7f885510.6173fc",
|
|
"name": "nb_step",
|
|
"label": "nb step (30μm/step)",
|
|
"tooltip": "",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 4,
|
|
"width": 3,
|
|
"height": 1,
|
|
"passthru": false,
|
|
"mode": "number",
|
|
"delay": 300,
|
|
"topic": "nb_step",
|
|
"x": 520,
|
|
"y": 320,
|
|
"wires": [
|
|
[
|
|
"523fdeaa.50c6c"
|
|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "b110542b.5de4f8",
|
|
"type": "ui_button",
|
|
"z": "7f885510.6173fc",
|
|
"name": "kill_focus",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 6,
|
|
"width": 3,
|
|
"height": 1,
|
|
"passthru": false,
|
|
"label": "Cancel focus",
|
|
"tooltip": "",
|
|
"color": "#AD1625",
|
|
"bgcolor": "#333333",
|
|
"icon": "pause",
|
|
"payload": "",
|
|
"payloadType": "str",
|
|
"topic": "",
|
|
"x": 520,
|
|
"y": 400,
|
|
"wires": [
|
|
[
|
|
"d9dea2bc.47097"
|
|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "523fdeaa.50c6c",
|
|
"type": "function",
|
|
"z": "7f885510.6173fc",
|
|
"name": "focus",
|
|
"func": "if(msg.topic === \"nb_step\"){\n nb_step = msg.payload;\n global.set(\"nb_step\",nb_step);\n}\nif(msg.topic === \"up\"){\n\n nb_step = global.get(\"nb_step\");\n\n orientation = \"up\";\n\n msg.payload = String(nb_step).concat(' ', orientation);\n return msg;\n}\nif(msg.topic === \"down\"){\n \n nb_step = global.get(\"nb_step\");\n\n orientation = \"down\";\n msg.payload = String(nb_step).concat(' ', orientation);\n\n return msg;\n}\n\n",
|
|
"outputs": 1,
|
|
"noerr": 0,
|
|
"x": 670,
|
|
"y": 320,
|
|
"wires": [
|
|
[
|
|
"ada728bd.8e7818"
|
|
]
|
|
],
|
|
"info": "### Focusing\n##### focus.py `nb_step` `orientation`\n\n- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step)\n- `orientation` : **string** - orientation of the focus either `up` or `down`\n\nExample:\n\n python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up\n"
|
|
},
|
|
{
|
|
"id": "ada728bd.8e7818",
|
|
"type": "exec",
|
|
"z": "7f885510.6173fc",
|
|
"command": "python3.7 $HOME/PlanktonScope/scripts/focus.py",
|
|
"addpay": true,
|
|
"append": "",
|
|
"useSpawn": "false",
|
|
"timer": "",
|
|
"oldrc": false,
|
|
"name": "focus.py",
|
|
"x": 820,
|
|
"y": 320,
|
|
"wires": [
|
|
[],
|
|
[],
|
|
[]
|
|
],
|
|
"icon": "node-red/sort.svg"
|
|
},
|
|
{
|
|
"id": "d9dea2bc.47097",
|
|
"type": "exec",
|
|
"z": "7f885510.6173fc",
|
|
"command": "bash $HOME/PlanktonScope/scripts/killer.sh focus.py && bash $HOME/PlanktonScope/scripts/killer.sh focus.py",
|
|
"addpay": false,
|
|
"append": "",
|
|
"useSpawn": "false",
|
|
"timer": "",
|
|
"oldrc": false,
|
|
"name": "Kill Focus",
|
|
"x": 820,
|
|
"y": 400,
|
|
"wires": [
|
|
[],
|
|
[],
|
|
[]
|
|
],
|
|
"icon": "font-awesome/fa-stop"
|
|
},
|
|
{
|
|
"id": "2d0f6720.0f92f8",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "832434ce.ebe498",
|
|
"name": "Pi Camera settings",
|
|
"order": 7,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<button style=\"height: 50px;\" class=\"md-raised md-button md-ink-ripple\" type=\"button\" onclick=\"window.location.href = 'http://127.0.0.1/html/';\">Pi Camera settings</button>\n",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 1010,
|
|
"y": 100,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "9599b953.529c28",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "832434ce.ebe498",
|
|
"name": "process_pixel",
|
|
"order": 3,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<div>\n Pixel resolution :\n <span id=\"process_pixel\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 1600,
|
|
"y": 80,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "612e2b9b.ed1684",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "832434ce.ebe498",
|
|
"name": "min_size",
|
|
"order": 4,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<div>\n Smallest cells to explore :\n <span id=\"min_size\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 1580,
|
|
"y": 120,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "f84ab57a.556df8",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "832434ce.ebe498",
|
|
"name": "max_size",
|
|
"order": 5,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<div>\n Biggest cells to explore :\n <span id=\"max_size\" ng-bind-html=\"msg.payload\"></span>\n μm\n</div>",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 1580,
|
|
"y": 160,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "45f53656.d631e8",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "832434ce.ebe498",
|
|
"name": "flowrate",
|
|
"order": 6,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<div>\n Flowrate :\n <span id=\"max_size\" ng-bind-html=\"msg.payload\"></span>\n ml/min\n</div>",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 1580,
|
|
"y": 200,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "53ec5f97.7567c",
|
|
"type": "ui_template",
|
|
"z": "7f885510.6173fc",
|
|
"group": "3d740a07.4674e6",
|
|
"name": "Stream Pi Camera",
|
|
"order": 1,
|
|
"width": 0,
|
|
"height": 0,
|
|
"format": "<center><iframe id=\"inlineFrameExample\"\n title=\"Inline Frame Example\"\n height=\"384\"\n width=\"512\"\n frameborder=\"0\"\n src=\"http://127.0.0.1/html/min.php\">\n</iframe></center>",
|
|
"storeOutMessages": true,
|
|
"fwdInMessages": true,
|
|
"templateScope": "local",
|
|
"x": 570,
|
|
"y": 40,
|
|
"wires": [
|
|
[]
|
|
]
|
|
},
|
|
{
|
|
"id": "c84f1718.4af6b8",
|
|
"type": "ui_switch",
|
|
"z": "7f885510.6173fc",
|
|
"name": "fan_state",
|
|
"label": "Fan",
|
|
"tooltip": "",
|
|
"group": "c62ffbd3.787ef8",
|
|
"order": 2,
|
|
"width": 2,
|
|
"height": 1,
|
|
"passthru": true,
|
|
"decouple": "false",
|
|
"topic": "",
|
|
"style": "",
|
|
"onvalue": "true",
|
|
"onvalueType": "bool",
|
|
"onicon": "",
|
|
"oncolor": "",
|
|
"offvalue": "false",
|
|
"offvalueType": "bool",
|
|
"officon": "",
|
|
"offcolor": "",
|
|
"x": 520,
|
|
"y": 220,
|
|
"wires": [
|
|
[
|
|
"dec2b84a.6faa18"
|
|
]
|
|
]
|
|
},
|
|
{
|
|
"id": "dec2b84a.6faa18",
|
|
"type": "exec",
|
|
"z": "7f885510.6173fc",
|
|
"command": "python3.7 $HOME/PlanktonScope/scripts/fan.py",
|
|
"addpay": true,
|
|
"append": "",
|
|
"useSpawn": "false",
|
|
"timer": "",
|
|
"oldrc": false,
|
|
"name": "fan.py",
|
|
"x": 810,
|
|
"y": 220,
|
|
"wires": [
|
|
[],
|
|
[],
|
|
[]
|
|
],
|
|
"icon": "font-awesome/fa-spinner"
|
|
},
|
|
{
|
|
"id": "477dc1bd.c3de8",
|
|
"type": "ui_text_input",
|
|
"z": "7f885510.6173fc",
|
|
"name": "acq_id",
|
|
"label": "Acquisition ID*",
|
|
"tooltip": "",
|
|
"group": "a61f7be8.af6418",
|
|
"order": 2,
|
|
"width": "12",
|
|
"height": 1,
|
|
"passthru": true,
|
|
"mode": "text",
|
|
"delay": 300,
|
|
"topic": "acq_id",
|
|
"x": 530,
|
|
"y": 680,
|
|
"wires": [
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"label": "/",
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"tooltip": "",
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"group": "106f0e1b.6478a2",
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"order": 3,
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"width": 2,
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"height": 1,
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"wrap": false,
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"passthru": true,
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"topic": "sample_year",
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"format": "{{value}}",
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"min": "19",
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"order": 2,
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"topic": "sample_month",
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"format": "{{value}}",
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"min": "1",
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"step": 1,
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"x": 1000,
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"group": "106f0e1b.6478a2",
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"order": 4,
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"outputs": 1,
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"x": 680,
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"width": 3,
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"passthru": true,
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"tooltip": "",
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"bgcolor": "",
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"type": "ui_text_input",
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"z": "7f885510.6173fc",
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"name": "volume",
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"label": "Volume (ml)*",
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"tooltip": "",
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"group": "c62ffbd3.787ef8",
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"order": 8,
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"width": 3,
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"height": 1,
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"passthru": false,
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"mode": "number",
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"delay": 300,
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"topic": "volume",
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"x": 520,
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"y": 500,
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"id": "83d75b6b.6afa28",
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"type": "ui_button",
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"z": "7f885510.6173fc",
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"name": "kill_pump",
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"group": "c62ffbd3.787ef8",
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"order": 10,
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"width": 3,
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"height": 1,
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"passthru": false,
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"label": "Cancel pump",
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"tooltip": "",
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"color": "#AD1625",
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"bgcolor": "#333333",
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"icon": "pause",
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"payload": "",
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"payloadType": "str",
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"topic": "",
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"x": 520,
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"y": 580,
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"wires": [
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"id": "84fd85fd.426878",
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"type": "function",
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"z": "7f885510.6173fc",
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"name": "pump",
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"func": "if(msg.topic === \"volume\"){\n volume = msg.payload;\n global.set(\"volume\",volume);\n}\nif(msg.topic === \"foward\"){\n\n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" foward\";\n\n msg.payload = String(volume).concat(' ',flowrate, action);\n return msg;\n}\nif(msg.topic === \"backward\"){\n \n volume = global.get(\"volume\");\n flowrate = global.get(\"flowrate\");\n\n action = \" backward\";\n msg.payload = String(volume).concat(' ',flowrate, action);\n\n return msg;\n}\n\n",
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"outputs": 1,
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],
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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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{
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"id": "649f7ec8.06a84",
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"type": "exec",
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"z": "7f885510.6173fc",
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"command": "python3.7 $HOME/PlanktonScope/scripts/pump.py",
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"addpay": true,
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"append": "",
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"useSpawn": "false",
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"timer": "",
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"oldrc": false,
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"name": "pump.py",
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"x": 820,
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],
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"icon": "font-awesome/fa-rotate-left"
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},
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{
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"id": "8fc930df.c7ae6",
|
|
"type": "exec",
|
|
"z": "7f885510.6173fc",
|
|
"command": "bash $HOME/PlanktonScope/scripts/killer.sh pump.py && bash $HOME/PlanktonScope/scripts/killer.sh pump.py",
|
|
"addpay": false,
|
|
"append": "",
|
|
"useSpawn": "false",
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|
"timer": "",
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|
"oldrc": false,
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"name": "Kill Pump",
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"x": 820,
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"y": 580,
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"wires": [
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[],
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[],
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"icon": "font-awesome/fa-stop"
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},
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{
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"id": "13ad31b4.5b682e",
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"type": "ui_template",
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"z": "7f885510.6173fc",
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"group": "77a6994b.e3efb8",
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"name": "Device ID",
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|
"order": 4,
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|
"width": 0,
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"height": 0,
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|
"format": "<div>\n Device ID :\n <span id=\"acq_camera_name\">\n Odezenne\n </span>\n</div>",
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|
"storeOutMessages": true,
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|
"fwdInMessages": true,
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|
"templateScope": "local",
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|
"x": 180,
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|
"y": 540,
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"wires": [
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"type": "ui_button",
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"z": "7f885510.6173fc",
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"name": "start",
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"order": 3,
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"bgcolor": "",
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"icon": "play_circle_fill",
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"payload": "",
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"order": 4,
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"passthru": false,
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"label": "Cancel Acquisition",
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"icon": "pause_circle_filled",
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},
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{
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"id": "b0fda998.f0ad48",
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"type": "file",
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"z": "7f885510.6173fc",
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"name": "logs.json",
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|
"filename": "/var/www/logs.json",
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|
"appendNewline": true,
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|
"createDir": false,
|
|
"overwriteFile": "false",
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"format": "<p>In case you forget dude but it's important to read this whenever you are not sure before clicking on any buttons.</p>\n<hr />\n<h3>Focusing :</h3>\n<p>To focus, you need to specify a value for the <strong>number of steps</strong>. Then, you can click <strong>once</strong> but <strong>wait</strong> while the stage is moving.</p>\n<p>To cancel a focusing, click <strong>once</strong> on <strong>CANCEL FOCUS.</strong></p>\n<hr />\n<h3>Pumping manually :</h3>\n<p>To focus, you need to specify a value for the <strong>volume</strong>. Then, you can click <strong>once</strong> in order to pump manually a defined volume in a certain direction.</p>\n<p>To cancel a pumping event, click <strong>once</strong> on <strong>CANCEL PUMP.</strong></p>\n<p><strong>Do not run an acquisition if you are using the pump manually.</strong></p>\n<hr />\n<h3>Start Acquisition :</h3>\n<p>Taking images will requires few inputs :</p>\n<ol>\n<li>Name of the project</li>\n<li>Name of the station</li>\n<li>Directory</li>\n<li>Acquisition ID</li>\n<li>Volume</li>\n<li>M12 Lens</li>\n</ol>\n<p>If any of the previous settings are missing, it's going to be a real mess and delete previous acquisition. <strong>So check twice here !!</strong></p>\n<p><strong>The other inputs are always welcome ;)</strong></p>\n<hr />\n<h3>Cancel Acquisition :</h3>\n<p>I made this button <strong>CANCEL ACQUISITION</strong> to cancel an acquisition which maybe be fucked.</p>\n<p>Image you click it, it's going to delete the folder in which you save this acquisition, meaning execute :</p>\n<p>rm -r Directory/Name_of_the_project/Name_of_the_station/Acquisition_ID</p>\n<p>So if you made a great acquisition, then run a new one with the same input for Acquisition ID and finally click on this button, you are going to delete them both.</p>\n<p>Don't use it if you don't need it and please <strong>never click twice</strong> because the pi might burn.</p>\n<p> </p>",
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