planktoscope/flows/main.json

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        "func": "state = global.get(\"state\");\nglobal.set('img_counter',0)\nglobal.set('obj_counter',0)\nif (state == null){state=\"free\"}\n\nvar sleep_before= global.get(\"custom_sleep_before\");\nvar nb_step= global.get(\"custom_nb_step\");\nvar nb_frame= global.get(\"custom_nb_frame\");\nvar segmentation= global.get(\"custom_segmentation\");\n\nif (sleep_before === undefined || sleep_before === \"\" || sleep_before === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Duration before the acquisition\";\n    \n}else if (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Number of step in between two frames\";\n    \n}else if (nb_frame === undefined || nb_frame === \"\" || nb_frame === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Number of image to save\";\n    \n}else if (segmentation === undefined || segmentation === \"\" || segmentation === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Realize or not the segmentation\";\n    \n}else {\n    nb_frame=nb_frame-1\n    \n    msg.payload=sleep_before+' '+nb_step+' '+nb_frame+' '+segmentation;\n}\nreturn msg;",
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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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        "width": 4,
        "height": 1,
        "passthru": false,
        "label": "Update",
        "tooltip": "",
        "color": "black",
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        "payloadType": "str",
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        "x": 640,
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        "noerr": 0,
        "x": 800,
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        "x": 840,
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    },
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    },
    {
        "id": "d3875217.e3b668",
        "type": "function",
        "z": "506e9090.6e905",
        "name": "set object_time",
        "func": "var time = new Date(msg.payload);\n\nvar hour = time.getUTCHours();\nif (hour<10){hour = \"0\"+hour;}\nvar minute = time.getUTCMinutes();\nif (minute<10){minute = \"0\"+minute;}\n\nvar time_UTC = \"\"+hour+minute;\nglobal.set('object_time',time_UTC);\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 804,
        "y": 80,
        "wires": [
            []
        ]
    },
    {
        "id": "82fef572.49b5f",
        "type": "function",
        "z": "506e9090.6e905",
        "name": "set object_date",
        "func": "var date = new Date(msg.payload);\n\nvar year = date.getUTCFullYear();\nvar month = date.getUTCMonth()+1;\nif (month<10){month = \"0\"+month;}\nvar day = date.getUTCDate();\nif (day<10){day = \"0\"+day;}\n\nvar date_UTC = \"\"+year+month+day;\nglobal.set('object_date',date_UTC);\n\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 804,
        "y": 40,
        "wires": [
            []
        ]
    },
    {
        "id": "ab40705d.43a5d",
        "type": "debug",
        "z": "506e9090.6e905",
        "name": "",
        "active": true,
        "tosidebar": true,
        "console": false,
        "tostatus": false,
        "complete": "true",
        "targetType": "full",
        "x": 280,
        "y": 360,
        "wires": []
    },
    {
        "id": "f377d75b.32d27",
        "type": "ui_group",
        "z": "",
        "name": "Object metadata",
        "tab": "2b97fe34.a699fa",
        "order": 6,
        "disp": true,
        "width": "24",
        "collapse": false
    },
    {
        "id": "97d77aeb.75afd8",
        "type": "subflow",
        "name": "Acquisition metadata",
        "info": "",
        "category": "",
        "in": [
            {
                "x": 50,
                "y": 30,
                "wires": [
                    {
                        "id": "282cae65.749e9a"
                    },
                    {
                        "id": "cc899daf.a8d5d8"
                    },
                    {
                        "id": "9873f1c8.6cb608"
                    },
                    {
                        "id": "e53df171.eed68"
                    },
                    {
                        "id": "5f728563.cf6214"
                    },
                    {
                        "id": "c1a5eaf5.8691c"
                    },
                    {
                        "id": "86c63d98.eb21"
                    },
                    {
                        "id": "3707a612.b8619a"
                    },
                    {
                        "id": "b2d20d5d.fd9e38"
                    }
                ]
            }
        ],
        "out": [
            {
                "x": 740,
                "y": 40,
                "wires": [
                    {
                        "id": "3b267291.1eee26",
                        "port": 0
                    },
                    {
                        "id": "435a2dcf.a1a60c",
                        "port": 0
                    },
                    {
                        "id": "cc6cb58d.b2dbe8",
                        "port": 0
                    },
                    {
                        "id": "8b306bbc.914",
                        "port": 0
                    },
                    {
                        "id": "2a5a2b7a.f218d4",
                        "port": 0
                    },
                    {
                        "id": "28df07d8.d71ba8",
                        "port": 0
                    },
                    {
                        "id": "6cf2c1ac.a0fea8",
                        "port": 0
                    },
                    {
                        "id": "e7c4132f.f4417",
                        "port": 0
                    }
                ]
            },
            {
                "x": 900,
                "y": 360,
                "wires": [
                    {
                        "id": "1e688c91.1b805b",
                        "port": 0
                    }
                ]
            }
        ],
        "env": [],
        "color": "#DDAA99"
    },
    {
        "id": "1e688c91.1b805b",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "set optical config",
        "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(\"acq_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(\"sug_flowrate\",3);\n    break;\n  case \"16\":\n    global.set(\"acq_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(\"sug_flowrate\",2.4);\n    break;\n  case \"12\":\n    global.set(\"acq_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(\"sug_flowrate\",1.25);\n    break;\n  case \"8\":\n    global.set(\"acq_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(\"sug_flowrate\",0.42);\n    break;\n  case \"6\":\n    global.set(\"acq_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(\"sug_flowrate\",0.32);\n    break;\n}\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 750,
        "y": 360,
        "wires": [
            []
        ]
    },
    {
        "id": "2877f2f.211cc8e",
        "type": "ui_dropdown",
        "z": "97d77aeb.75afd8",
        "name": "acq_fnumber_objective",
        "label": "M12 Lens*",
        "tooltip": "",
        "place": "Select option",
        "group": "60b93a5.a032344",
        "order": 3,
        "width": 0,
        "height": 0,
        "passthru": true,
        "options": [
            {
                "label": "f 25mm 1/2\" 5MP IR",
                "value": 25,
                "type": "num"
            },
            {
                "label": "f 16mm 1/2.5\" 5MP IR",
                "value": 16,
                "type": "num"
            },
            {
                "label": "f 12mm 1/2.5\" 5MP IR",
                "value": 12,
                "type": "num"
            },
            {
                "label": "f 8mm 1/2.5\" 5MP IR",
                "value": 8,
                "type": "num"
            },
            {
                "label": "f 6mm 1/2.5\" 5MP IR",
                "value": 6,
                "type": "num"
            }
        ],
        "payload": "",
        "topic": "acq_fnumber_objective",
        "x": 526,
        "y": 360,
        "wires": [
            [
                "1e688c91.1b805b"
            ]
        ]
    },
    {
        "id": "8b306bbc.914",
        "type": "ui_numeric",
        "z": "97d77aeb.75afd8",
        "name": "acq_minimum_mesh",
        "label": "Min fraction size (μm)",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 8,
        "width": 0,
        "height": 0,
        "wrap": false,
        "passthru": true,
        "topic": "acq_minimum_mesh",
        "format": "{{value}}",
        "min": 0,
        "max": "300",
        "step": "10",
        "x": 536,
        "y": 160,
        "wires": [
            []
        ]
    },
    {
        "id": "2a5a2b7a.f218d4",
        "type": "ui_numeric",
        "z": "97d77aeb.75afd8",
        "name": "acq_maximum_mesh",
        "label": "Max fraction size (μm)",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 4,
        "width": 0,
        "height": 0,
        "wrap": false,
        "passthru": true,
        "topic": "acq_maximum_mesh",
        "format": "{{value}}",
        "min": "200",
        "max": "2000",
        "step": "100",
        "x": 536,
        "y": 200,
        "wires": [
            []
        ]
    },
    {
        "id": "3b267291.1eee26",
        "type": "ui_text_input",
        "z": "97d77aeb.75afd8",
        "name": "acq_id",
        "label": "Acquisition unique ID*",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 1,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "number",
        "delay": 300,
        "topic": "acq_id",
        "x": 586,
        "y": 40,
        "wires": [
            []
        ]
    },
    {
        "id": "cc6cb58d.b2dbe8",
        "type": "ui_dropdown",
        "z": "97d77aeb.75afd8",
        "name": "acq_celltype",
        "label": "Thickness flowcell*",
        "tooltip": "",
        "place": "Select option",
        "group": "60b93a5.a032344",
        "order": 7,
        "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": 566,
        "y": 120,
        "wires": [
            []
        ]
    },
    {
        "id": "28df07d8.d71ba8",
        "type": "ui_text_input",
        "z": "97d77aeb.75afd8",
        "name": "acq_volume",
        "label": "Volume to pass (ml)",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 2,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "number",
        "delay": 300,
        "topic": "acq_volume",
        "x": 566,
        "y": 240,
        "wires": [
            []
        ]
    },
    {
        "id": "435a2dcf.a1a60c",
        "type": "ui_text_input",
        "z": "97d77aeb.75afd8",
        "name": "acq_instrument",
        "label": "Acquisition instrument",
        "tooltip": "PlanktonScope V2.1",
        "group": "60b93a5.a032344",
        "order": 6,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "text",
        "delay": 300,
        "topic": "acq_instrument",
        "x": 556,
        "y": 80,
        "wires": [
            []
        ]
    },
    {
        "id": "282cae65.749e9a",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_id",
        "func": "msg.payload = msg.payload.acq_id+1;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 210,
        "y": 40,
        "wires": [
            [
                "3b267291.1eee26"
            ]
        ]
    },
    {
        "id": "cc899daf.a8d5d8",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_instrument",
        "func": "msg.payload = msg.payload.acq_instrument;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 230,
        "y": 80,
        "wires": [
            [
                "435a2dcf.a1a60c"
            ]
        ]
    },
    {
        "id": "9873f1c8.6cb608",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_celltype",
        "func": "msg.payload = msg.payload.acq_celltype;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 220,
        "y": 120,
        "wires": [
            [
                "cc6cb58d.b2dbe8"
            ]
        ]
    },
    {
        "id": "e53df171.eed68",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_minimum_mesh",
        "func": "msg.payload = msg.payload.acq_minimum_mesh;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 250,
        "y": 160,
        "wires": [
            [
                "8b306bbc.914"
            ]
        ]
    },
    {
        "id": "5f728563.cf6214",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_maximum_mesh",
        "func": "msg.payload = msg.payload.acq_maximum_mesh;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 250,
        "y": 200,
        "wires": [
            [
                "2a5a2b7a.f218d4"
            ]
        ]
    },
    {
        "id": "c1a5eaf5.8691c",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_volume",
        "func": "msg.payload = msg.payload.acq_volume;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 220,
        "y": 240,
        "wires": [
            [
                "28df07d8.d71ba8"
            ]
        ]
    },
    {
        "id": "b2d20d5d.fd9e38",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_fnumber_objective",
        "func": "msg.payload = msg.payload.acq_fnumber_objective;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 260,
        "y": 360,
        "wires": [
            [
                "2877f2f.211cc8e"
            ]
        ]
    },
    {
        "id": "6cf2c1ac.a0fea8",
        "type": "ui_numeric",
        "z": "97d77aeb.75afd8",
        "name": "acq_min_esd",
        "label": "Minimum size to segment (μm)",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 9,
        "width": 0,
        "height": 0,
        "wrap": false,
        "passthru": true,
        "topic": "acq_min_esd",
        "format": "{{value}}",
        "min": 0,
        "max": "300",
        "step": "5",
        "x": 566,
        "y": 280,
        "wires": [
            []
        ]
    },
    {
        "id": "e7c4132f.f4417",
        "type": "ui_numeric",
        "z": "97d77aeb.75afd8",
        "name": "acq_max_esd",
        "label": "Maximum size to segment (μm)",
        "tooltip": "",
        "group": "60b93a5.a032344",
        "order": 5,
        "width": 0,
        "height": 0,
        "wrap": false,
        "passthru": true,
        "topic": "acq_max_esd",
        "format": "{{value}}",
        "min": "100",
        "max": "2000",
        "step": "5",
        "x": 556,
        "y": 320,
        "wires": [
            []
        ]
    },
    {
        "id": "86c63d98.eb21",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_min_esd",
        "func": "msg.payload = msg.payload.acq_min_esd;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 230,
        "y": 280,
        "wires": [
            [
                "6cf2c1ac.a0fea8"
            ]
        ]
    },
    {
        "id": "3707a612.b8619a",
        "type": "function",
        "z": "97d77aeb.75afd8",
        "name": "get acq_max_esd",
        "func": "msg.payload = msg.payload.acq_max_esd;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 230,
        "y": 320,
        "wires": [
            [
                "e7c4132f.f4417"
            ]
        ]
    },
    {
        "id": "60b93a5.a032344",
        "type": "ui_group",
        "z": "",
        "name": "Acquisition metadata",
        "tab": "2b97fe34.a699fa",
        "order": 7,
        "disp": true,
        "width": "24",
        "collapse": false
    },
    {
        "id": "9a45991b.365bc8",
        "type": "subflow",
        "name": "Pump actuation",
        "info": "",
        "category": "",
        "in": [
            {
                "x": 40,
                "y": 40,
                "wires": [
                    {
                        "id": "eb7c01ae.d00358"
                    },
                    {
                        "id": "642ae1f3.cf7d28"
                    }
                ]
            }
        ],
        "out": [
            {
                "x": 700,
                "y": 40,
                "wires": [
                    {
                        "id": "4485759b.52ee74",
                        "port": 0
                    },
                    {
                        "id": "3283f063.31c548",
                        "port": 0
                    }
                ]
            }
        ],
        "env": [],
        "color": "#A6BBCF",
        "icon": "font-awesome/fa-recycle"
    },
    {
        "id": "6246d9ef.156bd",
        "type": "function",
        "z": "9a45991b.365bc8",
        "name": "pump.js",
        "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar manual_volume= global.get(\"pump_manual_volume\");\nvar flowrate= global.get(\"pump_flowrate\");\n\nif (manual_volume === undefined || manual_volume === \"\" || manual_volume === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Volume to pass\";\n    \n}else if (flowrate === undefined || flowrate === \"\" || flowrate === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Flowrate\";\n    \n}else {\n    volume = global.get(\"pump_manual_volume\");\n    nb_step=volume*507\n    msg.volume = volume;\n    flowrate = global.get(\"pump_flowrate\");\n    duration=(volume*60)/flowrate\n    delay=(duration/nb_step)-0.005\n    msg.topic = \"actuator/pump\";\n    \n    if(msg.payload === \"FORWARD\" & state===\"free\"){\n        msg.payload='FORWARD '+delay+' '+nb_step;\n    }\n    if(msg.payload === \"BACKWARD\" & state===\"free\"){\n        msg.payload='BACKWARD '+delay+' '+nb_step;\n    }\n}\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 640,
        "y": 140,
        "wires": [
            [
                "53bef09a.8102e"
            ]
        ],
        "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": "2374d55d.a3e3a2",
        "type": "ui_button",
        "z": "9a45991b.365bc8",
        "name": "BACKWARD",
        "group": "4153382f.45437",
        "order": 2,
        "width": 6,
        "height": 1,
        "passthru": false,
        "label": "",
        "tooltip": "",
        "color": "",
        "bgcolor": "",
        "icon": "arrow_back",
        "payload": "BACKWARD",
        "payloadType": "str",
        "topic": "actuator/pump",
        "x": 470,
        "y": 120,
        "wires": [
            [
                "6246d9ef.156bd"
            ]
        ]
    },
    {
        "id": "c8aa9753.f51c08",
        "type": "ui_button",
        "z": "9a45991b.365bc8",
        "name": "FORWARD",
        "group": "4153382f.45437",
        "order": 4,
        "width": 6,
        "height": 1,
        "passthru": true,
        "label": "",
        "tooltip": "",
        "color": "",
        "bgcolor": "",
        "icon": "arrow_forward",
        "payload": "FORWARD",
        "payloadType": "str",
        "topic": "actuator/pump",
        "x": 470,
        "y": 160,
        "wires": [
            [
                "6246d9ef.156bd"
            ]
        ]
    },
    {
        "id": "53bef09a.8102e",
        "type": "switch",
        "z": "9a45991b.365bc8",
        "name": "",
        "property": "topic",
        "propertyType": "msg",
        "rules": [
            {
                "t": "eq",
                "v": "actuator/pump",
                "vt": "str"
            },
            {
                "t": "eq",
                "v": "Missing entry :",
                "vt": "str"
            }
        ],
        "checkall": "true",
        "repair": false,
        "outputs": 2,
        "x": 770,
        "y": 140,
        "wires": [
            [
                "4d3bf3c2.6a380c"
            ],
            [
                "d943e58a.e85fc"
            ]
        ]
    },
    {
        "id": "d943e58a.e85fc",
        "type": "ui_toast",
        "z": "9a45991b.365bc8",
        "position": "dialog",
        "displayTime": "3",
        "highlight": "",
        "sendall": true,
        "outputs": 1,
        "ok": "OK",
        "cancel": "",
        "raw": false,
        "topic": "",
        "name": "",
        "x": 930,
        "y": 160,
        "wires": [
            []
        ]
    },
    {
        "id": "eaa22490.6843d",
        "type": "ui_button",
        "z": "9a45991b.365bc8",
        "name": "stop pump",
        "group": "4153382f.45437",
        "order": 5,
        "width": 4,
        "height": 1,
        "passthru": true,
        "label": "STOP PUMP",
        "tooltip": "",
        "color": "",
        "bgcolor": "#AD1625",
        "icon": "",
        "payload": "off",
        "payloadType": "str",
        "topic": "actuator/wait",
        "x": 470,
        "y": 200,
        "wires": [
            [
                "9e71b7a5.28dff8"
            ]
        ]
    },
    {
        "id": "4d3bf3c2.6a380c",
        "type": "mqtt out",
        "z": "9a45991b.365bc8",
        "name": "",
        "topic": "",
        "qos": "",
        "retain": "",
        "broker": "e8ab36cc.74d77",
        "x": 910,
        "y": 120,
        "wires": []
    },
    {
        "id": "9e71b7a5.28dff8",
        "type": "mqtt out",
        "z": "9a45991b.365bc8",
        "name": "",
        "topic": "",
        "qos": "",
        "retain": "",
        "broker": "e8ab36cc.74d77",
        "x": 610,
        "y": 200,
        "wires": []
    },
    {
        "id": "3283f063.31c548",
        "type": "ui_text_input",
        "z": "9a45991b.365bc8",
        "name": "pump_manual_volume",
        "label": "Volume to pass (ml)",
        "tooltip": "",
        "group": "4153382f.45437",
        "order": 3,
        "width": 8,
        "height": 1,
        "passthru": true,
        "mode": "number",
        "delay": 300,
        "topic": "pump_manual_volume",
        "x": 480,
        "y": 80,
        "wires": [
            []
        ]
    },
    {
        "id": "642ae1f3.cf7d28",
        "type": "function",
        "z": "9a45991b.365bc8",
        "name": "get pump_manual_volume",
        "func": "msg.payload = msg.payload.pump_manual_volume;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 220,
        "y": 80,
        "wires": [
            [
                "3283f063.31c548"
            ]
        ]
    },
    {
        "id": "4485759b.52ee74",
        "type": "ui_slider",
        "z": "9a45991b.365bc8",
        "name": "pump_flowrate",
        "label": "Flowrate (ml/min)*",
        "tooltip": "",
        "group": "4153382f.45437",
        "order": 1,
        "width": 0,
        "height": 0,
        "passthru": true,
        "outs": "end",
        "topic": "pump_flowrate",
        "min": 0,
        "max": "20",
        "step": "0.1",
        "x": 500,
        "y": 40,
        "wires": [
            []
        ]
    },
    {
        "id": "eb7c01ae.d00358",
        "type": "function",
        "z": "9a45991b.365bc8",
        "name": "get pump_flowrate",
        "func": "msg.payload = msg.payload.pump_flowrate;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 190,
        "y": 40,
        "wires": [
            [
                "4485759b.52ee74"
            ]
        ]
    },
    {
        "id": "4153382f.45437",
        "type": "ui_group",
        "z": "",
        "name": "Pump actuation",
        "tab": "2b97fe34.a699fa",
        "order": 5,
        "disp": true,
        "width": "24",
        "collapse": false
    },
    {
        "id": "ac806d39.1682a8",
        "type": "subflow",
        "name": "Focus actuation",
        "info": "",
        "category": "",
        "in": [
            {
                "x": 40,
                "y": 40,
                "wires": [
                    {
                        "id": "c631467a.569ba"
                    }
                ]
            }
        ],
        "out": [
            {
                "x": 800,
                "y": 200,
                "wires": [
                    {
                        "id": "97bf666e.4d3ad",
                        "port": 0
                    }
                ]
            }
        ],
        "env": [],
        "color": "#A6BBCF",
        "icon": "node-red/sort.svg"
    },
    {
        "id": "97bf666e.4d3ad",
        "type": "ui_text_input",
        "z": "ac806d39.1682a8",
        "name": "focus_nb_step",
        "label": "Number of step(s)",
        "tooltip": "",
        "group": "69433259.f306fc",
        "order": 2,
        "width": 8,
        "height": 1,
        "passthru": true,
        "mode": "number",
        "delay": 300,
        "topic": "focus_nb_step",
        "x": 540,
        "y": 40,
        "wires": [
            []
        ]
    },
    {
        "id": "c631467a.569ba",
        "type": "function",
        "z": "ac806d39.1682a8",
        "name": "get focus_nb_step",
        "func": "msg.payload = msg.payload.focus_nb_step;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 230,
        "y": 40,
        "wires": [
            [
                "97bf666e.4d3ad"
            ]
        ]
    },
    {
        "id": "8346f4af.5c0978",
        "type": "ui_button",
        "z": "ac806d39.1682a8",
        "name": "DOWN",
        "group": "69433259.f306fc",
        "order": 3,
        "width": 6,
        "height": 1,
        "passthru": true,
        "label": "",
        "tooltip": "",
        "color": "",
        "bgcolor": "",
        "icon": "arrow_downward",
        "payload": "DOWN",
        "payloadType": "str",
        "topic": "actuator/focus",
        "x": 520,
        "y": 120,
        "wires": [
            [
                "350c388d.12cd28"
            ]
        ]
    },
    {
        "id": "7ee30e1c.691bd",
        "type": "ui_button",
        "z": "ac806d39.1682a8",
        "name": "UP",
        "group": "69433259.f306fc",
        "order": 1,
        "width": 6,
        "height": 1,
        "passthru": false,
        "label": "",
        "tooltip": "",
        "color": "",
        "bgcolor": "",
        "icon": "arrow_upwards",
        "payload": "UP",
        "payloadType": "str",
        "topic": "actuator/focus",
        "x": 530,
        "y": 81,
        "wires": [
            [
                "350c388d.12cd28"
            ]
        ]
    },
    {
        "id": "a2f04fac.5a338",
        "type": "switch",
        "z": "ac806d39.1682a8",
        "name": "",
        "property": "topic",
        "propertyType": "msg",
        "rules": [
            {
                "t": "eq",
                "v": "actuator/focus",
                "vt": "str"
            },
            {
                "t": "eq",
                "v": "Missing entry :",
                "vt": "str"
            }
        ],
        "checkall": "true",
        "repair": false,
        "outputs": 2,
        "x": 810,
        "y": 100,
        "wires": [
            [
                "9fd904e.d1cbcf8"
            ],
            [
                "ccd4fa1e.152"
            ]
        ]
    },
    {
        "id": "ccd4fa1e.152",
        "type": "ui_toast",
        "z": "ac806d39.1682a8",
        "position": "dialog",
        "displayTime": "3",
        "highlight": "",
        "sendall": true,
        "outputs": 1,
        "ok": "OK",
        "cancel": "",
        "raw": false,
        "topic": "",
        "name": "",
        "x": 970,
        "y": 140,
        "wires": [
            []
        ]
    },
    {
        "id": "350c388d.12cd28",
        "type": "function",
        "z": "ac806d39.1682a8",
        "name": "focus.js",
        "func": "state = global.get(\"state\");\n\nif (state == null){state=\"free\"}\n\nvar nb_step= global.get(\"focus_nb_step\");\n\nif (nb_step === undefined || nb_step === \"\" || nb_step === null) {\n    msg.topic = \"Missing entry :\"\n    msg.payload = \"Number of steps\";\n    \n}else {\n    nb_step= global.get(\"focus_nb_step\");\n    if(msg.payload === \"UP\" & state===\"free\"){\n        msg.payload=\"FORWARD \"+nb_step;\n    }\n    if(msg.payload === \"DOWN\" & state===\"free\"){\n        msg.payload=\"BACKWARD \"+nb_step;\n    }\n}\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 660,
        "y": 100,
        "wires": [
            [
                "a2f04fac.5a338"
            ]
        ],
        "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": "da904b2b.4a1d68",
        "type": "ui_button",
        "z": "ac806d39.1682a8",
        "name": "stop focus",
        "group": "69433259.f306fc",
        "order": 4,
        "width": 4,
        "height": 1,
        "passthru": true,
        "label": "STOP FOCUS",
        "tooltip": "",
        "color": "",
        "bgcolor": "#AD1625",
        "icon": "",
        "payload": "off",
        "payloadType": "str",
        "topic": "actuator/wait",
        "x": 510,
        "y": 160,
        "wires": [
            [
                "8bb9c09d.bc8178"
            ]
        ]
    },
    {
        "id": "9fd904e.d1cbcf8",
        "type": "mqtt out",
        "z": "ac806d39.1682a8",
        "name": "",
        "topic": "",
        "qos": "",
        "retain": "",
        "broker": "e8ab36cc.74d77",
        "x": 950,
        "y": 80,
        "wires": []
    },
    {
        "id": "8bb9c09d.bc8178",
        "type": "mqtt out",
        "z": "ac806d39.1682a8",
        "name": "",
        "topic": "",
        "qos": "",
        "retain": "",
        "broker": "e8ab36cc.74d77",
        "x": 650,
        "y": 160,
        "wires": []
    },
    {
        "id": "69433259.f306fc",
        "type": "ui_group",
        "z": "",
        "name": "Focus actuation",
        "tab": "2b97fe34.a699fa",
        "order": 4,
        "disp": true,
        "width": "24",
        "collapse": false
    },
    {
        "id": "e8ab36cc.74d77",
        "type": "mqtt-broker",
        "z": "",
        "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": ""
    },
    {
        "id": "5c6dd7ee.546fa8",
        "type": "subflow",
        "name": "Sample metadata",
        "info": "",
        "category": "",
        "in": [
            {
                "x": 40,
                "y": 40,
                "wires": [
                    {
                        "id": "730e3aa0.75f6dc"
                    },
                    {
                        "id": "b49441ee.07b358"
                    },
                    {
                        "id": "77454044.f47e88"
                    },
                    {
                        "id": "203e3416.6c480c"
                    },
                    {
                        "id": "3555467a.6ba1ea"
                    }
                ]
            }
        ],
        "out": [
            {
                "x": 840,
                "y": 40,
                "wires": [
                    {
                        "id": "419967b7.b9b5f",
                        "port": 0
                    },
                    {
                        "id": "9b3f7b46.107718",
                        "port": 0
                    },
                    {
                        "id": "6f24740b.fbae5c",
                        "port": 0
                    },
                    {
                        "id": "bf7a47c8.a960b8",
                        "port": 0
                    },
                    {
                        "id": "327afe96.262122",
                        "port": 0
                    }
                ]
            }
        ],
        "env": [],
        "color": "#DDAA99"
    },
    {
        "id": "6f24740b.fbae5c",
        "type": "ui_text_input",
        "z": "5c6dd7ee.546fa8",
        "name": "sample_ship",
        "label": "Name of the ship",
        "tooltip": "",
        "group": "417f91c9.193ab",
        "order": 2,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "text",
        "delay": 300,
        "topic": "sample_ship",
        "x": 590,
        "y": 120,
        "wires": [
            []
        ]
    },
    {
        "id": "327afe96.262122",
        "type": "ui_dropdown",
        "z": "5c6dd7ee.546fa8",
        "name": "sample_sampling_gear",
        "label": "Sampling gear",
        "tooltip": "",
        "place": "Select",
        "group": "417f91c9.193ab",
        "order": 4,
        "width": 0,
        "height": 0,
        "passthru": true,
        "options": [
            {
                "label": "Plankton net",
                "value": "net",
                "type": "str"
            },
            {
                "label": "Niskin bottle 12L",
                "value": "niskin_12L",
                "type": "str"
            },
            {
                "label": "Niskin bottle 24L",
                "value": "niskin_24L",
                "type": "str"
            },
            {
                "label": "Pass Hull",
                "value": "pass_hull",
                "type": "str"
            },
            {
                "label": "Flask",
                "value": "flask",
                "type": "str"
            }
        ],
        "payload": "",
        "topic": "sample_sampling_gear",
        "x": 550,
        "y": 200,
        "wires": [
            []
        ]
    },
    {
        "id": "bf7a47c8.a960b8",
        "type": "ui_text_input",
        "z": "5c6dd7ee.546fa8",
        "name": "sample_operator",
        "label": "Name of the operator",
        "tooltip": "",
        "group": "417f91c9.193ab",
        "order": 3,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "text",
        "delay": 300,
        "topic": "sample_operator",
        "x": 570,
        "y": 160,
        "wires": [
            []
        ]
    },
    {
        "id": "419967b7.b9b5f",
        "type": "ui_text_input",
        "z": "5c6dd7ee.546fa8",
        "name": "sample_project",
        "label": "Name of the project*",
        "tooltip": "",
        "group": "417f91c9.193ab",
        "order": 1,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "text",
        "delay": 300,
        "topic": "sample_project",
        "x": 580,
        "y": 40,
        "wires": [
            []
        ]
    },
    {
        "id": "9b3f7b46.107718",
        "type": "ui_text_input",
        "z": "5c6dd7ee.546fa8",
        "name": "sample_id",
        "label": "ID of the station*",
        "tooltip": "",
        "group": "417f91c9.193ab",
        "order": 5,
        "width": 0,
        "height": 0,
        "passthru": true,
        "mode": "number",
        "delay": 300,
        "topic": "sample_id",
        "x": 590,
        "y": 80,
        "wires": [
            []
        ]
    },
    {
        "id": "730e3aa0.75f6dc",
        "type": "function",
        "z": "5c6dd7ee.546fa8",
        "name": "get sample_projet",
        "func": "msg.payload = msg.payload.sample_project;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 250,
        "y": 40,
        "wires": [
            [
                "419967b7.b9b5f"
            ]
        ]
    },
    {
        "id": "77454044.f47e88",
        "type": "function",
        "z": "5c6dd7ee.546fa8",
        "name": "get sample_ship",
        "func": "msg.payload = msg.payload.sample_ship;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 240,
        "y": 120,
        "wires": [
            [
                "6f24740b.fbae5c"
            ]
        ]
    },
    {
        "id": "b49441ee.07b358",
        "type": "function",
        "z": "5c6dd7ee.546fa8",
        "name": "get sample_id",
        "func": "msg.payload = msg.payload.sample_id+1;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 240,
        "y": 80,
        "wires": [
            [
                "9b3f7b46.107718"
            ]
        ]
    },
    {
        "id": "203e3416.6c480c",
        "type": "function",
        "z": "5c6dd7ee.546fa8",
        "name": "get sample_operator",
        "func": "msg.payload = msg.payload.sample_operator;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 260,
        "y": 160,
        "wires": [
            [
                "bf7a47c8.a960b8"
            ]
        ]
    },
    {
        "id": "3555467a.6ba1ea",
        "type": "function",
        "z": "5c6dd7ee.546fa8",
        "name": "get sample_sampling_gear",
        "func": "msg.payload = msg.payload.sample_sampling_gear;\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 280,
        "y": 200,
        "wires": [
            [
                "327afe96.262122"
            ]
        ]
    },
    {
        "id": "417f91c9.193ab",
        "type": "ui_group",
        "z": "",
        "name": "Sample metadata",
        "tab": "2b97fe34.a699fa",
        "order": 2,
        "disp": true,
        "width": "24",
        "collapse": false
    },
    {
        "id": "2b97fe34.a699fa",
        "type": "ui_tab",
        "z": "",
        "name": "GUI",
        "icon": "fa-eyedropper",
        "order": 2,
        "disabled": false,
        "hidden": false
    },
    {
        "id": "bb8dbe68.7e20a",
        "type": "tab",
        "label": "Main",
        "disabled": false,
        "info": ""
    },
    {
        "id": "20340bb6.5f923c",
        "type": "function",
        "z": "bb8dbe68.7e20a",
        "name": "get global",
        "func": "msg.payload={\n    \n        \"sample_project\":global.get(\"sample_project\"),\n        \"sample_id\":global.get(\"sample_id\"),\n        \"sample_ship\":global.get(\"sample_ship\"),\n        \"sample_operator\":global.get(\"sample_operator\"),\n        \"sample_sampling_gear\":global.get(\"sample_sampling_gear\"),\n        \n        \"acq_id\":global.get(\"acq_id\"),\n        \"acq_instrument\":global.get(\"acq_instrument\"),\n        //\"acq_instrument_id\":global.get(\"acq_instrument_id\"),\n        \"acq_celltype\":global.get(\"acq_celltype\"),\n        \"acq_minimum_mesh\":global.get(\"acq_minimum_mesh\"),\n        \"acq_maximum_mesh\":global.get(\"acq_maximum_mesh\"),\n        \"acq_min_esd\":global.get(\"acq_min_esd\"),\n        \"acq_max_esd\":global.get(\"acq_max_esd\"),\n        \"acq_volume\":global.get(\"acq_volume\"),\n        \"acq_magnification\":global.get(\"magnification\"),\n        \"acq_fnumber_objective\":global.get(\"acq_fnumber_objective\"),\n        \n        \"acq_camera_name\":\"Pi Camera V2.1 - 8MP\",\n        \n        \"object_date\":global.get(\"object_date\"),\n        \"object_time\":global.get(\"object_time\"),\n        \"object_lat\":global.get(\"object_lat\"),\n        \"object_lon\":global.get(\"object_lon\"),\n        \"object_depth_min\":global.get(\"object_depth_min\"),\n        \"object_depth_max\":global.get(\"object_depth_max\"),\n        \n        \"custom_nb_frame\":global.get(\"custom_nb_frame\"),\n        \"custom_nb_step\":global.get(\"custom_nb_step\"),\n        \"custom_segmentation\":global.get(\"custom_segmentation\"),\n        \"custom_sleep_before\":global.get(\"custom_sleep_before\"),\n        \"focus_nb_step\":global.get(\"focus_nb_step\"),\n        \"pump_flowrate\":global.get(\"pump_flowrate\"),\n        \"pump_manual_volume\":global.get(\"pump_manual_volume\"),\n        \n        \"process_pixel\":global.get(\"process_pixel\"),\n        \"process_id\":global.get(\"process_id\")\n        \n        \n};\nreturn msg;",
        "outputs": 1,
        "noerr": 0,
        "x": 1260,
        "y": 160,
        "wires": [
            [
                "d69f0eb1.d514d"
            ]
        ]
    },
    {
        "id": "aed82ae1.3a7558",
        "type": "file",
        "z": "bb8dbe68.7e20a",
        "name": "",
        "filename": "/home/pi/PlanktonScope/config.json",
        "appendNewline": true,
        "createDir": true,
        "overwriteFile": "true",
        "encoding": "none",
        "x": 1640,
        "y": 160,
        "wires": [
            []
        ]
    },
    {
        "id": "d69f0eb1.d514d",
        "type": "json",
        "z": "bb8dbe68.7e20a",
        "name": "config.json",
        "property": "payload",
        "action": "str",
        "pretty": true,
        "x": 1410,
        "y": 160,
        "wires": [
            [
                "aed82ae1.3a7558"
            ]
        ]
    },
    {
        "id": "b57ab8b0.7bfc4",
        "type": "file in",
        "z": "bb8dbe68.7e20a",
        "name": "",
        "filename": "/home/pi/PlanktonScope/config.json",
        "format": "utf8",
        "chunk": false,
        "sendError": false,
        "encoding": "none",
        "x": 360,
        "y": 80,
        "wires": [
            [
                "5b6059c3.8d4fa8"
            ]
        ],
        "info": "# PlanktonScope Help\nThis Node will read the content of the file named **config.txt** containing all the input placeholders.\n"
    },
    {
        "id": "7880a269.4817ac",
        "type": "inject",
        "z": "bb8dbe68.7e20a",
        "name": "on_load",
        "topic": "",
        "payload": "",
        "payloadType": "date",
        "repeat": "",
        "crontab": "",
        "once": true,
        "onceDelay": 0.1,
        "x": 120,
        "y": 80,
        "wires": [
            [
                "b57ab8b0.7bfc4",
                "10d8393.60498c7",
                "dba45961.85d67",
                "8231cfcc.0c5dd8"
            ]
        ],
        "info": "# PlanktonScope Help\nWhen the **Pi** is booting, **Node-RED** will be initiated and this node will be activated once and execute the following nodes."
    },
    {
        "id": "5b6059c3.8d4fa8",
        "type": "json",
        "z": "bb8dbe68.7e20a",
        "name": "config.json",
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