Merge pull request #4 from Glasgow-ICG/new-app

integrate flask web app developments

.gitignore

@@ -1,5 +1,8 @@
 **/local-data/**
+**/period-data/**
 output.log
+**/triggers.png
+**/accuracy.png
 
 # Caches
 **/.ipynb_checkpoints/**

.vscode/settings.json

@@ -1,10 +1,9 @@
 {
-    "python.linting.enabled": false,
     "python.formatting.provider": "black",
     "python.testing.pytestArgs": [
-        "--cov-config=.coveragerc"
-        "--cov=optical_gating_alignment"
-        "--cov-report=xml"
+        "--cov-config=.coveragerc",
+        "--cov=optical_gating_alignment",
+        "--cov-report=xml",
         "tests",
     ],
     "python.testing.unittestEnabled": false,

README.md

@@ -102,7 +102,7 @@ The stage logic in both 'stage_test.py' and 'stage_control_functions.py' might a
 
 5. Ensure the image capture software (QIClick for example) is ready to acquire a stack of images.
 
-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.  
+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.  
 
 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.
 

examples/default_settings.json

@@ -1,20 +1,21 @@
-{"brightfield_framerate": 80,
-"brightfield_resolution":128,
-"analyse_time":1000,
-"awb_mode":"off",
-"exposure_mode":"off",
-"shutter_speed":2500,
-"image_denoise":0,
-"laser_trigger_pin":22,
-"fluorescence_camera_pins":[8,10,12],
-"fluorescence_exposure":1e3,
-"usb_stages":null,
-"frame_buffer_length":100,
-"frame_num":0,
-"live":1,
-"output_mode":"5V_BNC_Only",
-"log":0,
-"predictionLatency":15,
-"updateAfterNTriggers":5
-}
-
+{
+    "brightfield_framerate": "89",
+    "brightfield_resolution": "128",
+    "analyse_time": "1000",
+    "awb_mode": "off",
+    "exposure_mode": "off",
+    "shutter_speed": "2500",
+    "image_denoise": "0",
+    "laser_trigger_pin": "22",
+    "fluorescence_camera_pins": "[8, 10, 12]",
+    "fluorescence_exposure": "1000.0",
+    "usb_stages": null,
+    "frame_buffer_length": "100",
+    "frame_num": "0",
+    "live": "1",
+    "output_mode": "5V_BNC_Only",
+    "log": "0",
+    "period_dir": "period-data/",
+    "predictionLatency": "15",
+    "updateAfterNTriggers": "5"
+}

examples/default_settings_with_stages.json

@@ -1,32 +1,42 @@
-{"brightfield_framerate": 80,
-"brightfield_resolution":128,
-"analyse_time":1000,
-"awb_mode":"off",
-"exposure_mode":"off",
-"shutter_speed":2500,
-"image_denoise":0,
-"laser_trigger_pin":22,
-"fluorescence_camera_pins":[8,10,12],
-"fluorescence_exposure":1e3,
-"usb_stages":{"usb_name":"/dev/tty/USB0",
-"usb_timeout":0.1,
-"usb_baudrate":57600,
-"usb_dataBits":8,
-"usb_parity":"N",
-"usb_XOnOff":1,
-"plane_address":1,
-"encoding":"utf-8",
-"terminators":[13,10],
-"increment":0.0005,
-"negative_limit":0,
-"positive_limit":0.075,
-"current_position":0},
-"frame_buffer_length":100,
-"frame_num":0,
-"live":1,
-"output_mode":"5V_BNC_Only",
-"log":0,
-"predictionLatency":15,
-"updateAfterNTriggers":5
-}
-
+{
+    "analyse_time": 1000,
+    "awb_mode": "off",
+    "brightfield_framerate": 891,
+    "brightfield_resolution": 128,
+    "exposure_mode": "off",
+    "fluorescence_camera_pins": [
+        8,
+        10,
+        12
+    ],
+    "fluorescence_exposure": 1000.0,
+    "frame_buffer_length": 100,
+    "frame_num": 0,
+    "image_denoise": 0,
+    "laser_trigger_pin": 22,
+    "live": 1,
+    "log": 0,
+    "output_mode": "5V_BNC_Only",
+    "period_dir": "period-data/",
+    "predictionLatency": 15,
+    "shutter_speed": 2500,
+    "updateAfterNTriggers": 5,
+    "usb_stages": {
+        "current_position": 0,
+        "encoding": "utf-8",
+        "increment": 0.0005,
+        "negative_limit": 0,
+        "plane_address": 1,
+        "positive_limit": 0.075,
+        "terminators": [
+            13,
+            12
+        ],
+        "usb_XOnOff": 1,
+        "usb_baudrate": 57600,
+        "usb_dataBits": 8,
+        "usb_name": "/dev/tty/USB0",
+        "usb_parity": "Y",
+        "usb_timeout": 0.1
+    }
+}

examples/example_data_settings.json

@@ -1,22 +1,26 @@
-{"brightfield_framerate": 80,
-"brightfield_resolution":128,
-"analyse_time":1000,
-"awb_mode":"off",
-"exposure_mode":"off",
-"shutter_speed":2500,
-"image_denoise":0,
-"laser_trigger_pin":22,
-"fluorescence_camera_pins":[8,10,12],
-"fluorescence_exposure":1e3,
-"usb_stages":null,
-"frame_buffer_length":100,
-"frame_num":0,
-"live":0,
-"output_mode":"5V_BNC_Only",
-"log":0,
-"predictionLatency":15,
-"updateAfterNTriggers":5,
-"usb_stages":null,
-"path":"./examples/example_data.tif"
-}
-
+{
+  "analyse_time": 1000,
+  "awb_mode": "off",
+  "brightfield_framerate": 80,
+  "brightfield_resolution": 115,
+  "exposure_mode": "off",
+  "fluorescence_camera_pins": [
+    8,
+    10,
+    12
+  ],
+  "fluorescence_exposure": 1000.0,
+  "frame_buffer_length": 100,
+  "frame_num": 0,
+  "image_denoise": 0,
+  "laser_trigger_pin": 22,
+  "live": 0,
+  "log": 0,
+  "output_mode": "5V_BNC_Only",
+  "path": "./examples/example_data.tif",
+  "period_dir": "period-data/",
+  "predictionLatency": 15,
+  "shutter_speed": 2500,
+  "updateAfterNTriggers": 500,
+  "usb_stages": null
+}