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{
"id": "cbb8afed.0a026",
"type": "rpi-gpio out",
"z": "bccd1f23.87219",
"name": "LED Output",
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"set": true,
"level": "0",
"freq": "",
"out": "out",
+ "bcm": true,
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"y": 120,
"wires": []
@@ -2926,791 +3693,6 @@
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- "passthru": true,
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- "tooltip": "",
- "color": "",
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- "group": "4322c187.e73e5",
- "order": 12,
- "width": 5,
- "height": 1,
- "passthru": false,
- "label": "Start Acquisition",
- "tooltip": "",
- "color": "",
- "bgcolor": "",
- "icon": "camera",
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- "payloadType": "str",
- "topic": "imager/image",
- "x": 460,
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- "name": "Image control",
- "func": "// Reset the number of images taken\nflow.set('img_counter', 0);\n\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 imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar acq_id = global.get(\"acq_id\");\nvar nb_frame = global.get(\"nb_frame\");\nvar pump_direction = global.get(\"pump_direction\");\nvar sleep_before = global.get(\"sleep_before\");\nvar object_date = global.get(\"object_date\");\n\nif (acq_celltype === undefined || acq_celltype === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Type of the flowcell\";\n return [null, msg];\n} else if (acq_minimum_mesh === undefined || acq_minimum_mesh === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Lower fraction size\";\n return [null, msg];\n} else if (acq_maximum_mesh === undefined || acq_maximum_mesh === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Upper fraction size\";\n return [null, msg];\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 return [null, msg];\n} else if (acq_id === undefined || acq_id === \"\") {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Acquisition ID\";\n return [null, msg];\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 return [null, msg];\n} else if (pump_direction === undefined || pump_direction === \"\" || pump_direction === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Pump direction\";\n return [null, msg];\n} else if (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Delay before image\";\n return [null, msg];\n}else if (object_date === undefined || object_date === \"\" || object_date === null) {\n msg.topic = \"Missing entry :\";\n msg.payload = \"Object date\";\n return [null, msg];\n}\n\nmsg.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\nreturn [msg, null];",
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- "cancel": "",
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- "name": "",
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- "group": "4322c187.e73e5",
- "order": 11,
- "width": 5,
- "height": 1,
- "passthru": true,
- "label": "STOP ACQUISITION",
- "tooltip": "",
- "color": "",
- "bgcolor": "#AD1625",
- "icon": "cancel",
- "payload": "{\"action\":\"stop\"}",
- "payloadType": "json",
- "topic": "imager/image",
- "x": 460,
- "y": 520,
- "wires": [
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- "d74210ef.edc15"
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- "type": "ui_switch",
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- "label": "Pump direction",
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- "group": "4322c187.e73e5",
- "order": 9,
- "width": 5,
- "height": 1,
- "passthru": true,
- "decouple": "false",
- "topic": "pump_direction",
- "style": "",
- "onvalue": "FORWARD",
- "onvalueType": "str",
- "onicon": "",
- "oncolor": "",
- "offvalue": "BACKWARD",
- "offvalueType": "str",
- "officon": "",
- "offcolor": "",
- "x": 460,
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- "wires": [
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- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "Encapsulate config",
- "func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n \t\"description\": {\n \t\t\"sample_project\": \"Project's name\",\n \t\t\"sample_id\": \"Sample ID\",\n \t\t\"sample_uuid\": \"Sample UUID (Autogenerated)\",\n \t\t\"sample_ship\": \"Ship's name\",\n \t\t\"sample_operator\": \"Operator's name\",\n \t\t\"sample_sampling_gear\": \"Sampling gear used\",\n \t\t\"sample_concentrated_sample_volume\": \"Volume of concentrated sample, in mL\",\n \t\t\"sample_total_volume\": \"Total volume filtered by the net used, in L\",\n \t\t\"sample_dilution_factor\": \"Dilution factor of the sample, 0.5 if diluted by 2, 2 if concentrated by 2\",\n \t\t\"sample_speed_through_water\": \"Speed of the boat through water when sampling, in kts\",\n \t\t\"acq_id\": \"Acquisition ID\",\n \t\t\"acq_uuid\": \"Acquisition UUID (Autogenerated)\",\n \t\t\"acq_instrument\": \"Instrument type\",\n \t\t\"acq_instrument_id\": \"Instrument ID\",\n \t\t\"acq_celltype\": \"Flow cell dimension thickness, in µm\",\n \t\t\"acq_minimum_mesh\": \"Minimum filtration mesh size, in µm\",\n \t\t\"acq_maximum_mesh\": \"Maximum filtration mesh size, in µm\",\n \t\t\"acq_min_esd\": \"\",\n \t\t\"acq_max_esd\": \"\",\n \t\t\"acq_volume\": \"Pumped volume, in mL\",\n\t\t \"acq_imaged_volume\": \"Total imaged volume, in mL\",\n \t\t\"acq_magnification\": \"Optical magnification\",\n \t\t\"acq_fnumber_objective\": \"Focal length of the objective, in mm\",\n \t\t\"acq_camera_name\": \"Name of the camera used\",\n \t\t\"acq_nb_frame\": \"Number of picture taken\",\n \"acq_local_datetime\": \"Instrument local datetime\",\n \"acq_camera_resolution\": \"Resolution of the images\",\n \"acq_camera_iso\": \"ISO Number of the images\",\n \"acq_camera_shutter_speed\": \"Shutter speed of the images, in µs\",\n \"acq_software\": \"Software version number\",\n \t\t\"object_date\": \"Sample collection date (or beginning if using a net)\",\n \t\t\"object_time\": \"Sample collection time (or beginning if using a net)\",\n \t\t\"object_lat\": \"Sample collection latitude (or beginning if using a net)\",\n \t\t\"object_lon\": \"Sample collection longitude (or beginning if using a net)\",\n \t\t\"object_depth_min\": \"Sample collection minimal depth, in m\",\n \t\t\"object_depth_max\": \"Sample collection maximum depth, in m\",\n \t\t\"process_pixel\": \"Pixel imaging resolution, in µm/pixel\",\n \t\t\"process_datetime\": \"Segmentation timestamp\",\n \t\t\"process_id\": \"Segmentation ID\",\n \t\t\"process_uuid\": \"Segmentation UUID (Autogenerated)\",\n \t\t\"process_source\": \"Code source link of the executed code\",\n \t\t\"process_commit\": \"Version reference of the executed code\",\n \t\t\"sample_gear_net_opening\": \"Sample mouth opening dimension, in mm\",\n \t\t\"object_date_end\": \"Sample end collection date when using a net\",\n \t\t\"object_time_end\": \"Sample end collection time when using a net\",\n \t\t\"object_lat_end\": \"Sample end collection latitude when using a net\",\n \t\t\"object_lon_end\": \"Sample end collection longitude when using a net\",\n \t},\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_project\") + \"_\" + 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\t\t\"sample_dilution_factor\": global.get(\"sample_dilution_factor\"),\n\t\t\"sample_speed_through_water\": global.get(\"sample_speed_through_water\"),\n\n\t\t\"acq_id\": global.get(\"sample_project\") + \"_\" + global.get(\"sample_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_imaged_volume\": global.get(\"acq_imaged_volume\"),\n\t\t\"acq_magnification\": global.get(\"acq_magnification\"),\n\t\t\"acq_fnumber_objective\": global.get(\"acq_fnumber_objective\"),\n\t\t\"acq_camera\": global.get(\"acq_camera\"),\n\t\t\"acq_nb_frame\": global.get(\"nb_frame\"),\n\t\t\"acq_software\": global.get(\"acq_software\"),\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_source\": 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- "noerr": 0,
- "initialize": "",
- "finalize": "",
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- "type": "delay",
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- "pauseType": "delay",
- "timeout": "1",
- "timeoutUnits": "seconds",
- "rate": "1",
- "nbRateUnits": "1",
- "rateUnits": "second",
- "randomFirst": "1",
- "randomLast": "5",
- "randomUnits": "seconds",
- "drop": false,
- "x": 940,
- "y": 480,
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- "order": 10,
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- "passthru": false,
- "label": "Update config",
- "tooltip": "",
- "color": "",
- "bgcolor": "",
- "icon": "save",
- "payload": "",
- "payloadType": "str",
- "topic": "imager/image",
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- "wires": [
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- "type": "python3-function",
- "z": "1371dec5.76e671",
- "name": "Get MachineName",
- "func": "import sys\nsys.path.append('/home/pi/PlanktoScope/scripts')\nimport planktoscope.uuidName\n\nmsg['payload'] = planktoscope.uuidName.machineName(machine=planktoscope.uuidName.getSerial())\nmsg['topic'] = \"acq_instrument_id\";\nreturn msg",
- "outputs": 1,
- "x": 350,
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- "name": "set global",
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- "x": 580,
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- "outputs": 1,
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- "name": "get sample_ship",
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- "name": "get sample_sampling_gear",
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- "type": "file in",
- "z": "1c24ad9c.bebec2",
- "name": "",
- "filename": "/home/pi/PlanktoScope/config.json",
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- "x": 480,
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- "wires": [
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- ],
- "info": "# PlanktoScope 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",
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- "name": "Global Set",
- "func": "global.set(\"config_keys\", Object.keys(msg.payload));\n\nfor (const key in msg.payload) {\n global.set(key, msg.payload[key]);\n}\n\nreturn msg;",
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@@ -3737,1278 +3719,6 @@
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- "name": "",
- "x": 1340,
- "y": 680,
- "wires": []
- },
- {
- "id": "458cd82e.03d258",
- "type": "ui_chart",
- "z": "cb95299c.2817c8",
- "name": "Area chart",
- "group": "46be9c86.dea684",
- "order": 9,
- "width": 10,
- "height": 6,
- "label": "",
- "chartType": "line",
- "legend": "false",
- "xformat": "HH:mm:ss",
- "interpolate": "linear",
- "nodata": "Objects area will be shown here once the segmentation is started",
- "dot": true,
- "ymin": "",
- "ymax": "",
- "removeOlder": 1,
- "removeOlderPoints": "1000",
- "removeOlderUnit": "3600",
- "cutout": 0,
- "useOneColor": false,
- "useUTC": true,
- "colors": [
- "#1f77b4",
- "#aec7e8",
- "#ff7f0e",
- "#2ca02c",
- "#98df8a",
- "#d62728",
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- "#9467bd",
- "#c5b0d5"
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- "outputs": 1,
- "x": 1320,
- "y": 920,
- "wires": [
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- ]
- },
- {
- "id": "49af3d24.1799e4",
- "type": "debug",
- "z": "cb95299c.2817c8",
- "name": "segmentation name",
- "active": true,
- "tosidebar": true,
- "console": false,
- "tostatus": false,
- "complete": "true",
- "targetType": "full",
- "statusVal": "",
- "statusType": "auto",
- "x": 830,
- "y": 760,
- "wires": []
- },
- {
- "id": "7088a5be.0c79a4",
- "type": "template",
- "z": "cb95299c.2817c8",
- "name": "Create sentence",
- "field": "payload",
- "fieldType": "msg",
- "format": "handlebars",
- "syntax": "mustache",
- "template": "The {{topic}} is {{payload.status}}",
- "output": "str",
- "x": 1100,
- "y": 680,
- "wires": [
- [
- "a4f0f0d1.3aca88"
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- ]
- },
- {
- "id": "b9a23b91.93638",
- "type": "change",
- "z": "cb95299c.2817c8",
- "name": "Remove high-level topic",
- "rules": [
- {
- "t": "change",
- "p": "topic",
- "pt": "msg",
- "from": "status/",
- "fromt": "str",
- "to": "",
- "tot": "str"
- }
- ],
- "action": "",
- "property": "",
- "from": "",
- "to": "",
- "reg": false,
- "x": 850,
- "y": 680,
- "wires": [
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- },
- {
- "id": "6919465f.332e5",
- "type": "ui_text",
- "z": "cb95299c.2817c8",
- "group": "46be9c86.dea684",
- "order": 1,
- "width": 10,
- "height": 1,
- "name": "segmenter",
- "label": "Segmenter status:",
- "format": "{{msg.payload.status}}",
- "layout": "row-spread",
- "x": 810,
- "y": 720,
- "wires": []
- },
- {
- "id": "fa3b7929.ac7da8",
- "type": "ui_text",
- "z": "cb95299c.2817c8",
- "group": "46be9c86.dea684",
- "order": 5,
- "width": 4,
- "height": 1,
- "name": "counter",
- "label": "",
- "format": "{{msg.payload}}",
- "layout": "col-center",
- "x": 1320,
- "y": 800,
- "wires": []
- },
- {
- "id": "640ece83.88cab",
- "type": "inject",
- "z": "cb95299c.2817c8",
- "name": "Init graphs",
- "props": [
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- "p": "payload"
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- "p": "topic",
- "vt": "str"
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- ],
- "repeat": "",
- "crontab": "",
- "once": true,
- "onceDelay": 0.1,
- "topic": "object count",
- "payload": "0",
- "payloadType": "num",
- "x": 810,
- "y": 880,
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- {
- "id": "25867454.a8e334",
- "type": "link in",
- "z": "cb95299c.2817c8",
- "name": "Segmenter module status",
- "links": [
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- "x": 295,
- "y": 740,
- "wires": [
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- {
- "id": "dcf5bd45.16a8d",
- "type": "link out",
- "z": "9a22e67a.378818",
- "name": "Segmenter module status",
- "links": [
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- "x": 795,
- "y": 360,
- "wires": []
- },
- {
- "id": "52af9ac0.60eb24",
- "type": "link out",
- "z": "b771c342.49603",
- "name": "Sample Operator",
- "links": [
- "35eb925e.5f8016"
- ],
- "x": 815,
- "y": 160,
- "wires": []
- },
- {
- "id": "9bd72495.a8a098",
- "type": "ui_text",
- "z": "baa1e3d9.cb29d",
- "group": "4322c187.e73e5",
- "order": 5,
- "width": 5,
- "height": 1,
- "name": "Total imaged volume",
- "label": "Total imaged volume",
- "format": "{{msg.payload}}",
- "layout": "col-center",
- "x": 1200,
- "y": 140,
- "wires": []
- },
- {
- "id": "99b11fe4.2795d",
- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "imaged volume calc",
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- "noerr": 0,
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- "libs": [],
- "x": 950,
- "y": 140,
- "wires": [
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- {
- "id": "8e16aa2f.e40398",
- "type": "ui_text",
- "z": "baa1e3d9.cb29d",
- "group": "4322c187.e73e5",
- "order": 7,
- "width": 5,
- "height": 1,
- "name": "Total pumped volume",
- "label": "Total pumped volume",
- "format": "{{msg.payload}} mL",
- "layout": "col-center",
- "x": 1200,
- "y": 300,
- "wires": []
- },
- {
- "id": "67091ac0.8f9f6c",
- "type": "function",
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- "func": "var imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar nb_frame = global.get(\"nb_frame\");\nvar acq_volume = 0\n\nacq_volume = (Number(nb_frame)*Number(imaging_pump_volume)).toFixed(2)\nglobal.set(\"acq_volume\", acq_volume)\n\nmsg.payload = acq_volume\nreturn msg;",
- "outputs": 1,
- "noerr": 0,
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- "finalize": "",
- "x": 940,
- "y": 300,
- "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/PlanktoScope/scripts/focus.py 650 up\n"
- },
- {
- "id": "2b9d6988.d84836",
- "type": "switch",
- "z": "baa1e3d9.cb29d",
- "name": "",
- "property": "payload",
- "propertyType": "msg",
- "rules": [
- {
- "t": "hask",
- "v": "status",
- "vt": "str"
- },
- {
- "t": "hask",
- "v": "camera_name",
- "vt": "str"
- }
- ],
- "checkall": "true",
- "repair": false,
- "outputs": 2,
- "x": 650,
- "y": 760,
- "wires": [
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- {
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- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "set camera name",
- "func": "global.set(\"acq_camera\", msg.payload.camera_name);\n\nmsg.payload = msg.payload.camera_name;\n\nreturn msg;",
- "outputs": 1,
- "noerr": 0,
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- "x": 810,
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- },
- {
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- "type": "link out",
- "z": "baa1e3d9.cb29d",
- "name": "Camera Name",
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- "x": 965,
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- "wires": []
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- {
- "id": "30067f35.532f2",
- "type": "link in",
- "z": "1371dec5.76e671",
- "name": "Camera Name",
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- "x": 875,
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- {
- "id": "11b51f8f.acd308",
- "type": "python3-function",
- "z": "1371dec5.76e671",
- "d": true,
- "name": "fan temperature",
- "func": "import smbus\nbus = smbus.SMBus(1)\n\naddr = 0x0d\nfan_reg = 0x08\n\ntemp = float( msg[\"payload\"])\n\n# 0x01 full speed, 0x02: 20% speed, ..., 0x09: 90% speed\n\nif temp < 38:\n bus.write_byte_data(addr, fan_reg, 0x00)\nelif temp < 43:\n bus.write_byte_data(addr, fan_reg, 0x02)\nelif temp < 46:\n bus.write_byte_data(addr, fan_reg, 0x04)\nelif temp < 48:\n bus.write_byte_data(addr, fan_reg, 0x06)\nelif temp < 52:\n bus.write_byte_data(addr, fan_reg, 0x08)\nelse:\n bus.write_byte_data(addr, fan_reg, 0x01)\n\nreturn msg",
- "outputs": 1,
- "x": 1440,
- "y": 120,
- "wires": [
- []
- ]
- },
- {
- "id": "cbb123ab.fd3428",
- "type": "ui_ui_control",
- "z": "b771c342.49603",
- "name": "show/hide net groups",
- "events": "change",
- "x": 1320,
- "y": 300,
- "wires": [
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- ]
- },
- {
- "id": "c8749cbb.55254",
- "type": "function",
- "z": "cb95299c.2817c8",
- "name": "set global",
- "func": "global.set(msg.topic, msg.payload);",
- "outputs": 1,
- "noerr": 0,
- "initialize": "",
- "finalize": "",
- "libs": [],
- "x": 960,
- "y": 380,
- "wires": [
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- },
- {
- "id": "d43c3ed9.e6cb1",
- "type": "ui_template",
- "z": "cb95299c.2817c8",
- "group": "46be9c86.dea684",
- "name": "Object counts",
- "order": 3,
- "width": 0,
- "height": 0,
- "format": "\n Sample\nid: \nproject: \nship: \noperator: \nsampling gear: \nconcentrated volume: \ngear net opening: \ntotal volume filtered: \n | \n \n Acquisition\nid: \ninstrument: \ninstrument id: \ncamera: \ncelltype: \nminimum mesh: \nmaximum mesh: \nmin esd: \nmax esd: \nvolume: \nmagnification: \nfnumber objective: \nsoftware: \n | \n
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Object counts
Area chart
Capture progress
| {{row}} | \n
\n
\n",
- "storeOutMessages": true,
- "fwdInMessages": true,
- "resendOnRefresh": true,
- "templateScope": "local",
- "x": 1330,
- "y": 180,
- "wires": [
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- },
- {
- "id": "1f63860d.5f5efa",
- "type": "file in",
- "z": "4ed26b8b.253504",
- "name": "",
- "filename": "/home/pi/PlanktoScope/hardware.json",
- "format": "utf8",
- "chunk": false,
- "sendError": false,
- "encoding": "none",
- "x": 380,
- "y": 80,
- "wires": [
- [
- "8c1fda48.d7d828"
- ]
- ],
- "info": "# PlanktoScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
- },
- {
- "id": "8c1fda48.d7d828",
- "type": "json",
- "z": "4ed26b8b.253504",
- "name": "Parse JSON",
- "property": "payload",
- "action": "",
- "pretty": false,
- "x": 650,
- "y": 80,
- "wires": [
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- "ddb4b136.fc0b78"
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- ]
- },
- {
- "id": "82099021.9ceb08",
- "type": "file",
- "z": "4ed26b8b.253504",
- "name": "",
- "filename": "/home/pi/PlanktoScope/hardware.json",
- "appendNewline": true,
- "createDir": true,
- "overwriteFile": "true",
- "encoding": "none",
- "x": 780,
- "y": 200,
- "wires": [
- []
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- },
- {
- "id": "bb0a8725.a1849",
- "type": "json",
- "z": "4ed26b8b.253504",
- "name": "Create JSON",
- "property": "payload",
- "action": "str",
- "pretty": true,
- "x": 500,
- "y": 200,
- "wires": [
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- ]
- },
- {
- "id": "f748d952.4b6bc8",
- "type": "inject",
- "z": "4ed26b8b.253504",
- "name": "Load config",
- "props": [
- {
- "p": "topic",
- "vt": "str"
- }
- ],
- "repeat": "",
- "crontab": "",
- "once": true,
- "onceDelay": 0.1,
- "topic": "",
- "x": 110,
- "y": 80,
- "wires": [
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- ]
- },
- {
- "id": "ddb4b136.fc0b78",
- "type": "change",
- "z": "4ed26b8b.253504",
- "name": "",
- "rules": [
- {
- "t": "set",
- "p": "hardware_conf",
- "pt": "global",
- "to": "payload",
- "tot": "msg"
- }
- ],
- "action": "",
- "property": "",
- "from": "",
- "to": "",
- "reg": false,
- "x": 870,
- "y": 80,
- "wires": [
- []
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- },
- {
- "id": "44efaeb3.59bf6",
- "type": "subflow:4ed26b8b.253504",
- "z": "1eaf21c8.f7a21e",
- "name": "",
- "env": [],
- "x": 120,
- "y": 440,
- "wires": [
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- },
- {
- "id": "e10f5e55.00b828",
- "type": "change",
- "z": "1eaf21c8.f7a21e",
- "name": "Get stepper_type",
- "rules": [
- {
- "t": "set",
- "p": "payload",
- "pt": "msg",
- "to": "payload.stepper_type",
- "tot": "msg"
- }
- ],
- "action": "",
- "property": "",
- "from": "",
- "to": "",
- "reg": false,
- "x": 350,
- "y": 360,
- "wires": [
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- },
- {
- "id": "dee52a36.2af72",
- "type": "ui_dropdown",
- "z": "1eaf21c8.f7a21e",
- "name": "stepper_type",
- "label": "",
- "tooltip": "",
- "place": "",
- "group": "6be36295.0ab324",
- "order": 4,
- "width": 3,
- "height": 1,
- "passthru": false,
- "multiple": false,
- "options": [
- {
- "label": "",
- "value": "adafruit",
- "type": "str"
- },
- {
- "label": "",
- "value": "waveshare",
- "type": "str"
- },
- {
- "label": "",
- "value": "pscope_hat",
- "type": "str"
- }
- ],
- "payload": "",
- "topic": "stepper_type",
- "topicType": "str",
- "x": 670,
- "y": 360,
- "wires": [
- [
- "2068e7f.f4efb18",
- "8e3b3d3c.955148"
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- },
- {
- "id": "e41870d7.300eb8",
- "type": "link out",
- "z": "1eaf21c8.f7a21e",
- "name": "Stepper config change",
- "links": [
- "45a7b5aa.2ed20c"
- ],
- "x": 1195,
- "y": 380,
- "wires": []
- },
- {
- "id": "2068e7f.f4efb18",
- "type": "delay",
- "z": "1eaf21c8.f7a21e",
- "name": "",
- "pauseType": "delay",
- "timeout": "1",
- "timeoutUnits": "seconds",
- "rate": "1",
- "nbRateUnits": "1",
- "rateUnits": "second",
- "randomFirst": "1",
- "randomLast": "5",
- "randomUnits": "seconds",
- "drop": false,
- "x": 880,
- "y": 380,
- "wires": [
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- "e41870d7.300eb8"
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- ]
- },
- {
- "id": "45a7b5aa.2ed20c",
- "type": "link in",
- "z": "9daf9e2b.019fc",
- "name": "Python restart",
- "links": [
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- "x": 175,
- "y": 560,
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- },
- {
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- "type": "function",
- "z": "4ed26b8b.253504",
- "name": "Update and retrieve hardware_conf",
- "func": "// change global\nhardware_conf = global.get(\"hardware_conf\");\n\nif (msg.topic == \"process_pixel_fixed\" && msg.payload == 0){\n delete hardware_conf[msg.topic]\n delete msg.topic\n}\n\nif (msg.topic !== null && msg.topic !== undefined){\n hardware_conf[msg.topic] = msg.payload;\n global.set(\"hardware_conf\", hardware_conf);\n}\n\nreturn {\"payload\": hardware_conf};",
- "outputs": 1,
- "noerr": 0,
- "initialize": "",
- "finalize": "",
- "libs": [],
- "x": 240,
- "y": 200,
- "wires": [
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- "z": "1eaf21c8.f7a21e",
- "name": "",
- "env": [],
- "x": 900,
- "y": 420,
- "wires": [
- []
- ]
- },
- {
- "id": "c534fd26.13741",
- "type": "change",
- "z": "1eaf21c8.f7a21e",
- "name": "Get stepper_reverse",
- "rules": [
- {
- "t": "set",
- "p": "payload",
- "pt": "msg",
- "to": "payload.stepper_reverse",
- "tot": "msg"
- }
- ],
- "action": "",
- "property": "",
- "from": "",
- "to": "",
- "reg": false,
- "x": 360,
- "y": 440,
- "wires": [
- [
- "cd1987c7.027f58"
- ]
- ]
- },
- {
- "id": "cd1987c7.027f58",
- "type": "ui_switch",
- "z": "1eaf21c8.f7a21e",
- "name": "stepper_reverse",
- "label": "Invert stepper output",
- "tooltip": "Stepper 1 is controlled by output 1 or the other way around",
- "group": "6be36295.0ab324",
- "order": 5,
- "width": 0,
- "height": 0,
- "passthru": false,
- "decouple": "false",
- "topic": "stepper_reverse",
- "style": "",
- "onvalue": "true",
- "onvalueType": "bool",
- "onicon": "",
- "oncolor": "",
- "offvalue": "false",
- "offvalueType": "bool",
- "officon": "",
- "offcolor": "",
- "x": 660,
- "y": 440,
- "wires": [
- [
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@@ -7477,621 +3747,6 @@
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- "func": "country_code = flow.get(\"country_code\")\n\nvar template = `sudo tee /etc/wpa_supplicant/wpa_supplicant.conf <Changing one of these values will make the python back-end to restart.
\nIf you are not sure, you probably should not be touching anything here!
\n\nRemember to first unlock the shutdown button.\n
The segmentation is run recursively in all folders. So if you select a top level folder, the segmentation will be run in all subfolders.\n
Also, you will be able to chose wether for force the segmentation for folders in which it has run already.
\n Objective lens aperture: \n \n mm\n
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+ "type": "link in",
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+ "field": "payload",
+ "fieldType": "msg",
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+ "syntax": "mustache",
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\n
",
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+ "group": "4322c187.e73e5",
+ "order": 12,
+ "width": 5,
+ "height": 1,
+ "passthru": false,
+ "label": "Start Acquisition",
+ "tooltip": "",
+ "color": "",
+ "bgcolor": "",
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+ "displayTime": "3",
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+ "name": "",
+ "x": 950,
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+ {
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+ "type": "mqtt out",
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+ "qos": "",
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+ "broker": "8dc3722c.06efa8",
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+ "wires": []
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+ {
+ "id": "3a4450b1.4459a8",
+ "type": "ui_button",
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+ "height": 1,
+ "passthru": true,
+ "label": "STOP ACQUISITION",
+ "tooltip": "",
+ "color": "",
+ "bgcolor": "#AD1625",
+ "icon": "cancel",
+ "payload": "{\"action\":\"stop\"}",
+ "payloadType": "json",
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+ "y": 520,
+ "wires": [
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+ "type": "ui_switch",
+ "z": "baa1e3d9.cb29d",
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+ "width": 5,
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+ "style": "",
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+ "onvalueType": "str",
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+ "offvalueType": "str",
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+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "Encapsulate config",
+ "func": "msg.payload = {\n\t\"action\": \"update_config\",\n\t\"config\": {\n \t\"description\": {\n \t\t\"sample_project\": \"Project's name\",\n \t\t\"sample_id\": \"Sample ID\",\n \t\t\"sample_uuid\": \"Sample UUID (Autogenerated)\",\n \t\t\"sample_ship\": \"Ship's name\",\n \t\t\"sample_operator\": \"Operator's name\",\n \t\t\"sample_sampling_gear\": \"Sampling gear used\",\n \t\t\"sample_concentrated_sample_volume\": \"Volume of concentrated sample, in mL\",\n \t\t\"sample_total_volume\": \"Total volume filtered by the net used, in L\",\n \t\t\"sample_dilution_factor\": \"Dilution factor of the sample, 0.5 if diluted by 2, 2 if concentrated by 2\",\n \t\t\"sample_speed_through_water\": \"Speed of the boat through water when sampling, in kts\",\n \t\t\"acq_id\": \"Acquisition ID\",\n \t\t\"acq_uuid\": \"Acquisition UUID (Autogenerated)\",\n \t\t\"acq_instrument\": \"Instrument type\",\n \t\t\"acq_instrument_id\": \"Instrument ID\",\n \t\t\"acq_celltype\": \"Flow cell dimension 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using a net)\",\n \t\t\"object_lat\": \"Sample collection latitude (or beginning if using a net)\",\n \t\t\"object_lon\": \"Sample collection longitude (or beginning if using a net)\",\n \t\t\"object_depth_min\": \"Sample collection minimal depth, in m\",\n \t\t\"object_depth_max\": \"Sample collection maximum depth, in m\",\n \t\t\"process_pixel\": \"Pixel imaging resolution, in µm/pixel\",\n \t\t\"process_datetime\": \"Segmentation timestamp\",\n \t\t\"process_id\": \"Segmentation ID\",\n \t\t\"process_uuid\": \"Segmentation UUID (Autogenerated)\",\n \t\t\"process_source\": \"Code source link of the executed code\",\n \t\t\"process_commit\": \"Version reference of the executed code\",\n \t\t\"sample_gear_net_opening\": \"Sample mouth opening dimension, in mm\",\n \t\t\"object_date_end\": \"Sample end collection date when using a net\",\n \t\t\"object_time_end\": \"Sample end collection time when using a net\",\n \t\t\"object_lat_end\": \"Sample end collection latitude when using a net\",\n \t\t\"object_lon_end\": \"Sample end collection longitude when using a net\",\n \t},\n\t\t\"sample_project\": global.get(\"sample_project\"),\n\t\t\"sample_id\": global.get(\"sample_project\") + \"_\" + 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\t\t\"sample_dilution_factor\": global.get(\"sample_dilution_factor\"),\n\t\t\"sample_speed_through_water\": global.get(\"sample_speed_through_water\"),\n\n\t\t\"acq_id\": global.get(\"sample_project\") + \"_\" + global.get(\"sample_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\": 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+ "f948151ab4031df4",
+ "5e3dec55.881074",
+ "d3ca8847.4d1ae"
+ ]
+ ]
+ },
+ {
+ "id": "f3658d30.b8448",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "get acq_id",
+ "func": "msg.payload = msg.payload.acq_id;\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 330,
+ "y": 240,
+ "wires": [
+ [
+ "6b34c456.83178c"
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+ },
+ {
+ "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,
+ "initialize": "",
+ "finalize": "",
+ "libs": [],
+ "x": 340,
+ "y": 80,
+ "wires": [
+ [
+ "cc0ca68b.4263a8"
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+ ]
+ },
+ {
+ "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": 370,
+ "y": 160,
+ "wires": [
+ [
+ "f59a2f0d.5e9af"
+ ]
+ ]
+ },
+ {
+ "id": "d3ca8847.4d1ae",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "get acq_maximum_mesh",
+ "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "x": 370,
+ "y": 200,
+ "wires": [
+ [
+ "6008a8bb.259f08"
+ ]
+ ]
+ },
+ {
+ "id": "b402f719.55bc98",
+ "type": "inject",
+ "z": "baa1e3d9.cb29d",
+ "name": "Default: FORWARD",
+ "props": [
+ {
+ "p": "payload"
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+ {
+ "p": "topic",
+ "vt": "str"
+ }
+ ],
+ "repeat": "",
+ "crontab": "",
+ "once": true,
+ "onceDelay": 0.1,
+ "topic": "pump_direction",
+ "payload": "FORWARD",
+ "payloadType": "str",
+ "x": 220,
+ "y": 560,
+ "wires": [
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+ "id": "6b2239f3.41fa3",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "set global",
+ "func": "global.set(msg.topic, msg.payload);",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 660,
+ "y": 560,
+ "wires": [
+ []
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+ {
+ "id": "51b4d0df.d70a88",
+ "type": "ui_text_input",
+ "z": "baa1e3d9.cb29d",
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+ "label": "Number of images to acquire",
+ "tooltip": "",
+ "group": "4322c187.e73e5",
+ "order": 2,
+ "width": 5,
+ "height": 1,
+ "passthru": true,
+ "mode": "number",
+ "delay": 300,
+ "topic": "nb_frame",
+ "x": 680,
+ "y": 280,
+ "wires": [
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+ {
+ "id": "999065ca.27edb8",
+ "type": "switch",
+ "z": "baa1e3d9.cb29d",
+ "name": "topic filter",
+ "property": "topic",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "eq",
+ "v": "status/pump",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/focus",
+ "vt": "str"
+ },
+ {
+ "t": "eq",
+ "v": "status/imager",
+ "vt": "str"
+ }
+ ],
+ "checkall": "true",
+ "repair": false,
+ "outputs": 3,
+ "x": 320,
+ "y": 800,
+ "wires": [
+ [
+ "a46a1e7f.88a92",
+ "6742014e.1bb238"
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+ "type": "ui_text",
+ "z": "baa1e3d9.cb29d",
+ "group": "70de8209.68416c",
+ "order": 3,
+ "width": 10,
+ "height": 2,
+ "name": "imager",
+ "label": "Imager status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 770,
+ "y": 740,
+ "wires": []
+ },
+ {
+ "id": "c516d9ea.f7f6e",
+ "type": "ui_text",
+ "z": "baa1e3d9.cb29d",
+ "group": "70de8209.68416c",
+ "order": 1,
+ "width": 5,
+ "height": 1,
+ "name": "focus",
+ "label": "Focus status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 770,
+ "y": 700,
+ "wires": []
+ },
+ {
+ "id": "a46a1e7f.88a92",
+ "type": "ui_text",
+ "z": "baa1e3d9.cb29d",
+ "group": "70de8209.68416c",
+ "order": 2,
+ "width": 5,
+ "height": 1,
+ "name": "pump",
+ "label": "Pump status:",
+ "format": "{{msg.payload.status}}",
+ "layout": "col-center",
+ "x": 770,
+ "y": 660,
+ "wires": []
+ },
+ {
+ "id": "bb628f8d.98f108",
+ "type": "link in",
+ "z": "baa1e3d9.cb29d",
+ "name": "Status for fluidic module",
+ "links": [
+ "58f2e0f.4e8b12"
+ ],
+ "x": 175,
+ "y": 800,
+ "wires": [
+ [
+ "999065ca.27edb8"
+ ]
+ ]
+ },
+ {
+ "id": "307c851e.fb0f7a",
+ "type": "switch",
+ "z": "baa1e3d9.cb29d",
+ "name": "Imaging state",
+ "property": "payload",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "jsonata_exp",
+ "v": "$contains(msg.payload.status, \"jpg\")\t",
+ "vt": "jsonata"
+ },
+ {
+ "t": "else"
+ }
+ ],
+ "checkall": "false",
+ "repair": false,
+ "outputs": 2,
+ "x": 540,
+ "y": 880,
+ "wires": [
+ [
+ "db8e3dde.44efb8"
+ ],
+ [
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+ {
+ "id": "db8e3dde.44efb8",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "img_counter",
+ "func": "img_counter=flow.get('img_counter')\nif (img_counter === undefined || img_counter === \"\"){\n img_counter = 0\n}\nimg_counter=img_counter+1\nflow.set('img_counter',img_counter)\nmsg.payload = img_counter\nmsg.payload = (100 * img_counter/global.get('nb_frame')).toFixed(2)\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "libs": [],
+ "x": 770,
+ "y": 860,
+ "wires": [
+ [
+ "1a2e721a.f5e876"
+ ]
+ ]
+ },
+ {
+ "id": "59164d65.e7993c",
+ "type": "ui_toast",
+ "z": "baa1e3d9.cb29d",
+ "position": "top right",
+ "displayTime": "5",
+ "highlight": "",
+ "sendall": true,
+ "outputs": 0,
+ "ok": "OK",
+ "cancel": "",
+ "raw": false,
+ "topic": "",
+ "name": "",
+ "x": 1270,
+ "y": 900,
+ "wires": []
+ },
+ {
+ "id": "8c7348aa.1962e8",
+ "type": "template",
+ "z": "baa1e3d9.cb29d",
+ "name": "Create sentence",
+ "field": "payload",
+ "fieldType": "msg",
+ "format": "handlebars",
+ "syntax": "mustache",
+ "template": "The {{topic}} is {{payload.status}}",
+ "output": "str",
+ "x": 1050,
+ "y": 900,
+ "wires": [
+ [
+ "59164d65.e7993c"
+ ]
+ ]
+ },
+ {
+ "id": "6742014e.1bb238",
+ "type": "change",
+ "z": "baa1e3d9.cb29d",
+ "name": "Remove high-level topic",
+ "rules": [
+ {
+ "t": "change",
+ "p": "topic",
+ "pt": "msg",
+ "from": "status/",
+ "fromt": "str",
+ "to": "",
+ "tot": "str"
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+ "action": "",
+ "property": "",
+ "from": "",
+ "to": "",
+ "reg": false,
+ "x": 810,
+ "y": 900,
+ "wires": [
+ [
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+ ]
+ ]
+ },
+ {
+ "id": "1a2e721a.f5e876",
+ "type": "ui_gauge",
+ "z": "baa1e3d9.cb29d",
+ "name": "progress donut",
+ "group": "b5d61bc7.54fe48",
+ "order": 3,
+ "width": 6,
+ "height": 3,
+ "gtype": "donut",
+ "title": "",
+ "label": "%",
+ "format": "{{value}}",
+ "min": 0,
+ "max": "100",
+ "colors": [
+ "#ffa83f",
+ "#e6ff02",
+ "#00dfe9"
+ ],
+ "seg1": "50",
+ "seg2": "75",
+ "x": 1260,
+ "y": 860,
+ "wires": []
+ },
+ {
+ "id": "9bd72495.a8a098",
+ "type": "ui_text",
+ "z": "baa1e3d9.cb29d",
+ "group": "4322c187.e73e5",
+ "order": 5,
+ "width": 5,
+ "height": 1,
+ "name": "Total imaged volume",
+ "label": "Total imaged volume",
+ "format": "{{msg.payload}}",
+ "layout": "col-center",
+ "x": 1200,
+ "y": 140,
+ "wires": []
+ },
+ {
+ "id": "99b11fe4.2795d",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "imaged volume calc",
+ "func": "camera = global.get(\"acq_camera\");\ncell = global.get(\"acq_celltype\");\nnb_frame = global.get(\"nb_frame\");\nprocess_pixel = global.get(\"process_pixel\");\n\nvar volume = 0\nif (camera == \"HQ Camera\"){\n volume = nb_frame * (process_pixel*4056*process_pixel*3040*cell/1000000000) / 1000;\n}\nelse if (camera == \"Camera v2.1\"){\n volume = nb_frame * (process_pixel*3280*process_pixel*2464*cell/1000000000) / 1000;\n}\nelse{\n msg.payload = \"The camera is not known to this system\";\n return msg;\n}\n\nglobal.set(\"acq_imaged_volume\", volume.toFixed(4))\n\nmsg.payload = volume.toFixed(2) + \" mL\"\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "libs": [],
+ "x": 960,
+ "y": 140,
+ "wires": [
+ [
+ "9bd72495.a8a098"
+ ]
+ ],
+ "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/PlanktoScope/scripts/focus.py 650 up\n"
+ },
+ {
+ "id": "8e16aa2f.e40398",
+ "type": "ui_text",
+ "z": "baa1e3d9.cb29d",
+ "group": "4322c187.e73e5",
+ "order": 7,
+ "width": 5,
+ "height": 1,
+ "name": "Total pumped volume",
+ "label": "Total pumped volume",
+ "format": "{{msg.payload}} mL",
+ "layout": "col-center",
+ "x": 1200,
+ "y": 300,
+ "wires": []
+ },
+ {
+ "id": "67091ac0.8f9f6c",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "acq_volume calc",
+ "func": "var imaging_pump_volume = global.get(\"imaging_pump_volume\");\nvar nb_frame = global.get(\"nb_frame\");\nvar acq_volume = 0\n\nacq_volume = (Number(nb_frame)*Number(imaging_pump_volume)).toFixed(2)\nglobal.set(\"acq_volume\", acq_volume)\n\nmsg.payload = acq_volume\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 950,
+ "y": 300,
+ "wires": [
+ [
+ "8e16aa2f.e40398"
+ ]
+ ],
+ "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/PlanktoScope/scripts/focus.py 650 up\n"
+ },
+ {
+ "id": "2b9d6988.d84836",
+ "type": "switch",
+ "z": "baa1e3d9.cb29d",
+ "name": "",
+ "property": "payload",
+ "propertyType": "msg",
+ "rules": [
+ {
+ "t": "hask",
+ "v": "status",
+ "vt": "str"
+ },
+ {
+ "t": "hask",
+ "v": "camera_name",
+ "vt": "str"
+ }
+ ],
+ "checkall": "true",
+ "repair": false,
+ "outputs": 2,
+ "x": 650,
+ "y": 760,
+ "wires": [
+ [
+ "2b009bd7.c07004"
+ ],
+ [
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+ ]
+ },
+ {
+ "id": "3bbb756a.84190a",
+ "type": "function",
+ "z": "baa1e3d9.cb29d",
+ "name": "set camera name",
+ "func": "global.set(\"acq_camera\", msg.payload.camera_name);\n\nmsg.payload = msg.payload.camera_name;\n\nreturn msg;",
+ "outputs": 1,
+ "noerr": 0,
+ "initialize": "",
+ "finalize": "",
+ "x": 810,
+ "y": 780,
+ "wires": [
+ [
+ "559a8085.1d6b9"
+ ]
+ ]
+ },
+ {
+ "id": "559a8085.1d6b9",
+ "type": "link out",
+ "z": "baa1e3d9.cb29d",
+ "name": "Camera Name",
+ "links": [
+ "30067f35.532f2",
+ "572a6daa.6004c4",
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+ ],
+ "x": 965,
+ "y": 780,
+ "wires": []
+ },
+ {
+ "id": "49ea1123.ee1768",
+ "type": "ui_numeric",
+ "z": "baa1e3d9.cb29d",
+ "name": "sleep_before",
+ "label": "Delay to stabilize image (s)",
+ "tooltip": "Happens before every capture",
+ "group": "4322c187.e73e5",
+ "order": 4,
+ "width": 5,
+ "height": 1,
+ "wrap": false,
+ "passthru": true,
+ "topic": "sleep_before",
+ "format": "{{value}}",
+ "min": "0.1",
+ "max": "5",
+ "step": "0.1",
+ "x": 670,
+ "y": 120,
+ "wires": [
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+ "links": [
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+ "z": "baa1e3d9.cb29d",
+ "group": "b5d61bc7.54fe48",
+ "name": "progress header",
+ "order": 1,
+ "width": 0,
+ "height": 0,
+ "format": "\n Sample\nid: \nproject: \nship: \noperator: \nsampling gear: \nconcentrated volume: \ngear net opening: \ntotal volume filtered: \n | \n \n Acquisition\nid: \ninstrument: \ninstrument id: \ncamera: \ncelltype: \nminimum mesh: \nmaximum mesh: \nmin esd: \nmax esd: \nvolume: \nmagnification: \nfnumber objective: \nsoftware: \n | \n
\n Object\nlatitude: \nlongitude: \nlatitude end: \nlongitude end: \ndate: \ntime: \ndate end: \ntime end: \ndepth min: \ndepth max: \n | \n \n Process\npixel: \nid: \n | \n
Capture progress
Object counts
Area chart
The segmentation is run recursively in all folders. So if you select a top level folder, the segmentation will be run in all subfolders.\n
Also, you will be able to chose wether for force the segmentation for folders in which it has run already.
\n
| {{row}} | \n
\n
",
+ "storeOutMessages": true,
+ "fwdInMessages": true,
+ "resendOnRefresh": true,
+ "templateScope": "local",
+ "x": 610,
+ "y": 60,
+ "wires": [
+ []
+ ]
+ },
{
"id": "a7e5c7f4.644678",
"type": "ui_dropdown",
@@ -10314,111 +10754,6 @@
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]
},
- {
- "id": "cdd4181922eecf11",
- "type": "ui_text_input",
- "z": "b771c342.49603",
- "name": "sample_speed_through_water",
- "label": "Speed Through Water (kts)",
- "tooltip": "in knots",
- "group": "cf5d9f0e.d57e7",
- "order": 2,
- "width": 10,
- "height": 1,
- "passthru": true,
- "mode": "number",
- "delay": "0",
- "topic": "sample_speed_through_water",
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- "x": 610,
- "y": 520,
- "wires": [
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- "id": "4be09c97f86897d9",
- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "get nb_frame",
- "func": "msg.payload = msg.payload.nb_frame;\nreturn msg;",
- "outputs": 1,
- "noerr": 0,
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- "finalize": "",
- "libs": [],
- "x": 330,
- "y": 280,
- "wires": [
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- },
- {
- "id": "f573206abefa9518",
- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "get imaging_pump_volume",
- "func": "msg.payload = msg.payload.imaging_pump_volume;\nreturn msg;",
- "outputs": 1,
- "noerr": 0,
- "initialize": "",
- "finalize": "",
- "libs": [],
- "x": 380,
- "y": 320,
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- {
- "id": "f948151ab4031df4",
- "type": "function",
- "z": "baa1e3d9.cb29d",
- "name": "get sleep_before",
- "func": "msg.payload = msg.payload.sleep_before;\nreturn msg;",
- "outputs": 1,
- "noerr": 0,
- "initialize": "",
- "finalize": "",
- "libs": [],
- "x": 340,
- "y": 120,
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- "type": "ui_text_input",
- "z": "cb95299c.2817c8",
- "name": "process_id",
- "label": "Process unique ID*",
- "tooltip": "",
- "group": "abeb6dad.635a2",
- "order": 2,
- "width": 10,
- "height": 1,
- "passthru": true,
- "mode": "text",
- "delay": 300,
- "topic": "process_id",
- "topicType": "str",
- "x": 790,
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- "wires": [
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{
"id": "c67c305004f87e39",
"type": "change",
@@ -10462,7 +10797,7 @@
"delay": "1000",
"topic": "process_pixel_fixed",
"topicType": "str",
- "x": 650,
+ "x": 640,
"y": 480,
"wires": [
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@@ -10546,7 +10881,7 @@
"payload": "",
"topic": "acq_fnumber_objective",
"topicType": "str",
- "x": 640,
+ "x": 630,
"y": 520,
"wires": [
[
@@ -10615,329 +10950,5 @@
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- {
- "id": "335a730b9a3830ff",
- "type": "ui_template",
- "z": "bccd1f23.87219",
- "group": "4248342d.e55fac",
- "name": "Lens",
- "order": 3,
- "width": 0,
- "height": 0,
- "format": "Changing one of these values will make the python back-end to restart.
\nIf you are not sure, you probably should not be touching anything here!
\n\n Objective lens aperture: \n \n mm\n
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- "storeOutMessages": true,
- "fwdInMessages": true,
- "resendOnRefresh": false,
- "templateScope": "local",
- "x": 1310,
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- "wires": [
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- {
- "id": "49111a72f4e32740",
- "type": "link out",
- "z": "f21ba04.c26266",
- "name": "IP",
- "links": [
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- },
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- "id": "142bc61a0bde1ba9",
- "type": "link in",
- "z": "bccd1f23.87219",
- "name": "Cam Stream",
- "links": [
- "49111a72f4e32740"
- ],
- "x": 235,
- "y": 40,
- "wires": [
- [
- "3ca8be38ddb269e9"
- ]
- ]
- },
- {
- "id": "3ca8be38ddb269e9",
- "type": "template",
- "z": "bccd1f23.87219",
- "name": "Prepare stream HTML",
- "field": "payload",
- "fieldType": "msg",
- "format": "handlebars",
- "syntax": "mustache",
- "template": "\n