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ChasNelson1990ChasNelson1990
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Merge pull request #4 from Glasgow-ICG/new-app
integrate flask web app developments
2 parents 56e4f29 + 36951a2 commit 60117df

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‎.gitignore

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**/local-data/**
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**/period-data/**
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output.log
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**/triggers.png
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**/accuracy.png
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# Caches
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**/.ipynb_checkpoints/**

‎.vscode/settings.json

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{
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"python.linting.enabled": false,
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"python.formatting.provider": "black",
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"python.testing.pytestArgs": [
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"--cov-config=.coveragerc"
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"--cov=optical_gating_alignment"
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"--cov-report=xml"
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"--cov-config=.coveragerc",
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"--cov=optical_gating_alignment",
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"--cov-report=xml",
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"tests",
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],
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"python.testing.unittestEnabled": false,

‎README.md

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5. Ensure the image capture software (QIClick for example) is ready to acquire a stack of images.
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6. Select a frame from within the period to be used as the target frame (the frames are stored in a folder called 'period_data//' in the same directory as the 'cli.py' program. You can obtain a new reference period by entering -1.
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6. Select a frame from within the period to be used as the target frame (the frames are stored in a folder called 'period-data//' in the same directory as the 'cli.py' program. You can obtain a new reference period by entering -1.
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7. The program will now attempt to capture a 3D gated image of the zebrafish heart (or other period object). The results will be stored with the image capture software.
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‎examples/default_settings.json

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{"brightfield_framerate": 80,
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"brightfield_resolution":128,
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"analyse_time":1000,
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"awb_mode":"off",
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"exposure_mode":"off",
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"shutter_speed":2500,
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"image_denoise":0,
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"laser_trigger_pin":22,
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"fluorescence_camera_pins":[8,10,12],
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"fluorescence_exposure":1e3,
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"usb_stages":null,
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"frame_buffer_length":100,
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"frame_num":0,
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"live":1,
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"output_mode":"5V_BNC_Only",
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"log":0,
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"predictionLatency":15,
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"updateAfterNTriggers":5
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}
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{
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"brightfield_framerate": "89",
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"brightfield_resolution": "128",
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"analyse_time": "1000",
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"awb_mode": "off",
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"exposure_mode": "off",
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"shutter_speed": "2500",
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"image_denoise": "0",
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"laser_trigger_pin": "22",
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"fluorescence_camera_pins": "[8, 10, 12]",
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"fluorescence_exposure": "1000.0",
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"usb_stages": null,
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"frame_buffer_length": "100",
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"frame_num": "0",
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"live": "1",
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"output_mode": "5V_BNC_Only",
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"log": "0",
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"period_dir": "period-data/",
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"predictionLatency": "15",
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"updateAfterNTriggers": "5"
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}

‎examples/default_settings_with_stages.json

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{"brightfield_framerate": 80,
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"brightfield_resolution":128,
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"analyse_time":1000,
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"awb_mode":"off",
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"exposure_mode":"off",
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"shutter_speed":2500,
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"image_denoise":0,
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"laser_trigger_pin":22,
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"fluorescence_camera_pins":[8,10,12],
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"fluorescence_exposure":1e3,
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"usb_stages":{"usb_name":"/dev/tty/USB0",
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"usb_timeout":0.1,
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"usb_baudrate":57600,
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"usb_dataBits":8,
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"usb_parity":"N",
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"usb_XOnOff":1,
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"plane_address":1,
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"encoding":"utf-8",
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"terminators":[13,10],
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"increment":0.0005,
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"negative_limit":0,
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"positive_limit":0.075,
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"current_position":0},
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"frame_buffer_length":100,
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"frame_num":0,
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"live":1,
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"output_mode":"5V_BNC_Only",
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"log":0,
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"predictionLatency":15,
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"updateAfterNTriggers":5
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}
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{
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"analyse_time": 1000,
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"awb_mode": "off",
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"brightfield_framerate": 891,
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"brightfield_resolution": 128,
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"exposure_mode": "off",
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"fluorescence_camera_pins": [
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8,
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],
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"fluorescence_exposure": 1000.0,
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"frame_buffer_length": 100,
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"frame_num": 0,
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"image_denoise": 0,
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"laser_trigger_pin": 22,
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"live": 1,
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"log": 0,
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"output_mode": "5V_BNC_Only",
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"period_dir": "period-data/",
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"predictionLatency": 15,
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"shutter_speed": 2500,
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"updateAfterNTriggers": 5,
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"usb_stages": {
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"current_position": 0,
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"encoding": "utf-8",
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"increment": 0.0005,
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"negative_limit": 0,
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"plane_address": 1,
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"positive_limit": 0.075,
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"terminators": [
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13,
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],
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"usb_XOnOff": 1,
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"usb_baudrate": 57600,
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"usb_dataBits": 8,
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"usb_name": "/dev/tty/USB0",
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"usb_parity": "Y",
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"usb_timeout": 0.1
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}
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}

‎examples/example_data_settings.json

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{"brightfield_framerate": 80,
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"brightfield_resolution":128,
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"analyse_time":1000,
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"awb_mode":"off",
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"exposure_mode":"off",
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"shutter_speed":2500,
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"image_denoise":0,
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"laser_trigger_pin":22,
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"fluorescence_camera_pins":[8,10,12],
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"fluorescence_exposure":1e3,
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"usb_stages":null,
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"frame_buffer_length":100,
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"frame_num":0,
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"live":0,
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"output_mode":"5V_BNC_Only",
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"log":0,
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"predictionLatency":15,
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"updateAfterNTriggers":5,
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"usb_stages":null,
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"path":"./examples/example_data.tif"
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}
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{
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"analyse_time": 1000,
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"awb_mode": "off",
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"brightfield_framerate": 80,
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"brightfield_resolution": 115,
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"exposure_mode": "off",
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"fluorescence_camera_pins": [
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],
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"fluorescence_exposure": 1000.0,
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"frame_buffer_length": 100,
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"frame_num": 0,
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"image_denoise": 0,
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"laser_trigger_pin": 22,
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"live": 0,
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"log": 0,
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"output_mode": "5V_BNC_Only",
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"path": "./examples/example_data.tif",
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"period_dir": "period-data/",
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"predictionLatency": 15,
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"shutter_speed": 2500,
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"updateAfterNTriggers": 500,
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"usb_stages": null
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}

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