Code formatting

openflexure_microscope/api/app.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
+import atexit
+import logging
+import logging.handlers
 import sys
 import time
-import atexit
-import logging, logging.handlers
 
 # Look for debug flag
 if "-d" in sys.argv or "--debug" in sys.argv:
@@ -17,33 +18,27 @@ root_log.setLevel(log_level)
 
 
 import os
-import pkg_resources
-
-from flask import Flask, send_file, abort
-
 from datetime import datetime
 
+import pkg_resources
+from flask import Flask, abort, send_file
 from flask_cors import CORS, cross_origin
-
-from openflexure_microscope.api.utilities import list_routes, init_default_extensions
-
-from openflexure_microscope.config import JSONEncoder
-from openflexure_microscope.paths import (
-    OPENFLEXURE_VAR_PATH,
-    OPENFLEXURE_EXTENSIONS_PATH,
-    settings_file_path,
-    logs_file_path,
-)
-
 from labthings import create_app
 from labthings.extensions import find_extensions
 
 from openflexure_microscope.api.microscope import default_microscope as api_microscope
-
+from openflexure_microscope.api.utilities import init_default_extensions, list_routes
 from openflexure_microscope.api.v2 import views
+from openflexure_microscope.config import JSONEncoder
+from openflexure_microscope.paths import (
+    OPENFLEXURE_EXTENSIONS_PATH,
+    OPENFLEXURE_VAR_PATH,
+    logs_file_path,
+    settings_file_path,
+)
 
 # Handle logging
-access_log = logging.getLogger('werkzeug')
+access_log = logging.getLogger("werkzeug")
 # Block the access logs from propagating up to the root logger
 access_log.propagate = False
 
@@ -207,6 +202,7 @@ atexit.register(cleanup)
 # Start the app
 if __name__ == "__main__":
     from labthings import Server
+
     logging.info("Starting OpenFlexure Microscope Server...")
     server = Server(app)
     server.run(host="0.0.0.0", port=5000, debug=False, zeroconf=True)

openflexure_microscope/api/default_extensions/autofocus.py

@@ -1,18 +1,16 @@
-from labthings import fields, find_component, current_action
-from labthings.extensions import BaseExtension
-from labthings.views import View, ActionView, PropertyView
-
-from openflexure_microscope.devel import JsonResponse, request, abort
-from openflexure_microscope.utilities import set_properties
-
-import time
-import numpy as np
-
 import logging
-from scipy import ndimage
+import time
 from contextlib import contextmanager
+from threading import Event, Thread
 
-from threading import Thread, Event
+import numpy as np
+from labthings import current_action, fields, find_component
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, PropertyView, View
+from scipy import ndimage
+
+from openflexure_microscope.devel import JsonResponse, abort, request
+from openflexure_microscope.utilities import set_properties
 
 ### Autofocus utilities
 
@@ -447,4 +445,3 @@ autofocus_extension_v2.add_view(
 autofocus_extension_v2.add_view(
     MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
 )
-

openflexure_microscope/api/default_extensions/autostorage.py

@@ -1,21 +1,18 @@
-from labthings.extensions import BaseExtension
-from labthings.views import View, PropertyView
-from labthings import fields, find_component
-
-from openflexure_microscope.paths import settings_file_path, check_rw
-from openflexure_microscope.config import OpenflexureSettingsFile
-from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
-from openflexure_microscope.captures.capture import build_captures_from_exif
-
-from openflexure_microscope.api.utilities.gui import build_gui
-
-from flask import abort
 import logging
 import os
-import psutil
-
 from sys import platform
 
+import psutil
+from flask import abort
+from labthings import fields, find_component
+from labthings.extensions import BaseExtension
+from labthings.views import PropertyView, View
+
+from openflexure_microscope.api.utilities.gui import build_gui
+from openflexure_microscope.captures.capture import build_captures_from_exif
+from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
+from openflexure_microscope.config import OpenflexureSettingsFile
+from openflexure_microscope.paths import check_rw, settings_file_path
 
 AS_SETTINGS_PATH = settings_file_path("autostorage_settings.json")
 

openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py

@@ -1,19 +1,18 @@
-from labthings import find_component
-from labthings.views import View, ActionView
-from labthings.extensions import BaseExtension
-
-from flask import abort
-
-from contextlib import contextmanager
 import logging
+from contextlib import contextmanager
 
 # Type hinting
 from typing import Tuple
 
+from flask import abort
+from labthings import find_component
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, View
+
 from .recalibrate_utils import (
-    recalibrate_camera,
     auto_expose_and_freeze_settings,
     flat_lens_shading_table,
+    recalibrate_camera,
 )
 
 
@@ -125,5 +124,9 @@ lst_extension_v2.add_method(
 )
 
 lst_extension_v2.add_view(RecalibrateView, "/recalibrate", endpoint="recalibrate")
-lst_extension_v2.add_view(FlattenLSTView, "/flatten_lens_shading_table", endpoint="flatten_lens_shading_table")
-lst_extension_v2.add_view(DeleteLSTView, "/delete_lens_shading_table", endpoint="delete_lens_shading_table")
+lst_extension_v2.add_view(
+    FlattenLSTView, "/flatten_lens_shading_table", endpoint="flatten_lens_shading_table"
+)
+lst_extension_v2.add_view(
+    DeleteLSTView, "/delete_lens_shading_table", endpoint="delete_lens_shading_table"
+)

openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py

@@ -1,9 +1,9 @@
-import numpy as np
-import time
 import logging
+import time
 
+import numpy as np
 from picamerax import PiCamera
-from picamerax.array import PiRGBArray, PiBayerArray
+from picamerax.array import PiBayerArray, PiRGBArray
 
 
 def rgb_image(camera, resize=None, **kwargs):

openflexure_microscope/api/default_extensions/scan.py

@@ -1,21 +1,24 @@
+import datetime
 import itertools
 import logging
+import time
 import uuid
-import datetime
-from typing import Tuple
 from functools import reduce
+from typing import Tuple
+
+from labthings import (
+    current_action,
+    fields,
+    find_component,
+    find_extension,
+    update_action_progress,
+)
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, View
 
 from openflexure_microscope.captures.capture_manager import generate_basename
-
-from labthings import fields, find_component, find_extension, current_action, update_action_progress
-from labthings.views import View, ActionView
-from labthings.extensions import BaseExtension
-
 from openflexure_microscope.devel import abort
 
-import time
-
-
 ### Grid construction
 
 
@@ -56,9 +59,6 @@ def flatten_grid(grid):
 ### Capturing
 
 
-
-
-
 class ScanExtension(BaseExtension):
     def __init__(self):
         self._images_to_be_captured: int = 1
@@ -83,7 +83,12 @@ class ScanExtension(BaseExtension):
         if namemode == "coordinates":
             filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
         else:
-            filename = "{}_{}".format(basename, str(self._images_captured_so_far).zfill(len(str(self._images_to_be_captured))))
+            filename = "{}_{}".format(
+                basename,
+                str(self._images_captured_so_far).zfill(
+                    len(str(self._images_to_be_captured))
+                ),
+            )
         folder = "SCAN_{}".format(basename)
 
         # Do capture
@@ -97,14 +102,14 @@ class ScanExtension(BaseExtension):
             annotations=annotations,
             tags=tags,
             metadata=metadata,
-            cache_key=folder
+            cache_key=folder,
         )
 
     def progress(self):
         progress = (self._images_captured_so_far / self._images_to_be_captured) * 100
         logging.info(progress)
         return progress
-        
+
     ### Scanning
     def tile(
         self,
@@ -164,7 +169,9 @@ class ScanExtension(BaseExtension):
             autofocus_enabled = False
 
         # Construct an x-y grid (worry about z later)
-        x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)
+        x_y_grid = construct_grid(
+            initial_position, stride_size[:2], grid[:2], style=style
+        )
 
         # Keep the initial Z position the same as our current position
         initial_z = initial_position[2]
@@ -245,7 +252,6 @@ class ScanExtension(BaseExtension):
         end = time.time()
         logging.info(f"Scan took {end - start} seconds")
 
-
     def stack(
         self,
         microscope,
@@ -304,6 +310,7 @@ class ScanExtension(BaseExtension):
 
 scan_extension_v2 = ScanExtension()
 
+
 class TileScanAPI(ActionView):
     args = {
         "filename": fields.String(missing=None, example=None),
@@ -365,4 +372,5 @@ class TileScanAPI(ActionView):
                 tags=args.get("tags"),
             )
 
+
 scan_extension_v2.add_view(TileScanAPI, "/tile", endpoint="tile")

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -1,21 +1,17 @@
-from openflexure_microscope.devel import (
-    JsonResponse,
-    request,
-)
-
-from flask import send_file, abort, url_for
-
-import uuid
-import os
-import zipfile
-import tempfile
 import logging
+import os
+import tempfile
+import uuid
+import zipfile
 
+from flask import abort, send_file, url_for
 from labthings import fields, find_component, update_action_progress
-from labthings.views import View, ActionView, PropertyView
-from labthings.schema import Schema, pre_dump
 from labthings.extensions import BaseExtension
+from labthings.schema import Schema, pre_dump
 from labthings.utilities import description_from_view
+from labthings.views import ActionView, PropertyView, View
+
+from openflexure_microscope.devel import JsonResponse, request
 
 
 class ZipObjectSchema(Schema):
@@ -137,9 +133,7 @@ class ZipBuilderAPIView(ActionView):
         microscope = find_component("org.openflexure.microscope")
 
         # Return a handle on the autofocus task
-        return default_zip_manager.marshaled_build_zip_from_capture_ids(
-            microscope, ids
-        )
+        return default_zip_manager.marshaled_build_zip_from_capture_ids(microscope, ids)
 
 
 class ZipListAPIView(PropertyView):
@@ -191,7 +185,9 @@ zip_extension_v2 = BaseExtension(
     description="Build and download capture collections as ZIP files",
 )
 
-zip_extension_v2.add_view(ZipGetterAPIView, "/get/<string:session_id>", endpoint="get_id")
+zip_extension_v2.add_view(
+    ZipGetterAPIView, "/get/<string:session_id>", endpoint="get_id"
+)
 zip_extension_v2.add_view(ZipListAPIView, "/get", endpoint="get")
 
 zip_extension_v2.add_view(ZipBuilderAPIView, "/build", endpoint="build")

openflexure_microscope/api/dev_extensions/__init__.py

@@ -1 +1 @@
-from .tools import devtools_extension_v2
+from .tools import devtools_extension_v2

openflexure_microscope/api/dev_extensions/tools.py

@@ -1,14 +1,16 @@
+import logging
+import time
+
 from labthings import fields
 from labthings.extensions import BaseExtension
 from labthings.views import ActionView
 
-import logging
-import time
 
 class RaiseException(ActionView):
     def post(self):
         raise Exception("The developer raised an exception")
 
+
 class SleepFor(ActionView):
     schema = {"TimeAsleep": fields.Float()}
     args = {"time": fields.Float(description="Time to sleep, in seconds", example=0.5)}
@@ -22,6 +24,7 @@ class SleepFor(ActionView):
         logging.info("Waking up!")
         return {"TimeAsleep": (end - start)}
 
+
 devtools_extension_v2 = BaseExtension(
     "org.openflexure.dev.tools",
     version="0.1.0",
@@ -29,4 +32,4 @@ devtools_extension_v2 = BaseExtension(
 )
 
 devtools_extension_v2.add_view(RaiseException, "/raise")
-devtools_extension_v2.add_view(SleepFor, "/sleep")
+devtools_extension_v2.add_view(SleepFor, "/sleep")

openflexure_microscope/api/microscope.py

@@ -1,7 +1,6 @@
-from openflexure_microscope.microscope import Microscope
-
 import logging
 
+from openflexure_microscope.microscope import Microscope
 
 default_microscope = Microscope()
 

openflexure_microscope/api/utilities/__init__.py

@@ -1,8 +1,9 @@
+import errno
 import logging
 import os
-import errno
+
+from flask import Blueprint, current_app, url_for
 from werkzeug.exceptions import BadRequest
-from flask import url_for, Blueprint, current_app
 
 from . import gui
 

openflexure_microscope/api/v2/views/__init__.py

@@ -1,5 +1,5 @@
 from .actions import enabled_root_actions
 from .captures import *
 from .instrument import *
-from .streams import *
 from .stage import *
+from .streams import *

openflexure_microscope/api/v2/views/actions/__init__.py

@@ -2,11 +2,11 @@
 Top-level representation of enabled actions
 """
 from flask import url_for
-from . import camera, stage, system
-
 from labthings import current_labthing
-from labthings.views import View
 from labthings.utilities import description_from_view
+from labthings.views import View
+
+from . import camera, stage, system
 
 _actions = {
     "capture": {

openflexure_microscope/api/v2/views/actions/camera.py

@@ -1,14 +1,13 @@
-from openflexure_microscope.api.utilities import get_bool, JsonResponse
-from labthings.views import View, ActionView
-from labthings import find_component, fields
-
-from openflexure_microscope.utilities import filter_dict
-
-from openflexure_microscope.api.v2.views.captures import CaptureSchema
-
-import logging
 import io
-from flask import request, abort, url_for, redirect, send_file
+import logging
+
+from flask import abort, redirect, request, send_file, url_for
+from labthings import fields, find_component
+from labthings.views import ActionView, View
+
+from openflexure_microscope.api.utilities import JsonResponse, get_bool
+from openflexure_microscope.api.v2.views.captures import CaptureSchema
+from openflexure_microscope.utilities import filter_dict
 
 
 class CaptureAPI(ActionView):
@@ -58,11 +57,10 @@ class CaptureAPI(ActionView):
                 resize=resize,
                 bayer=args.get("bayer"),
                 annotations=args.get("annotations"),
-                tags=args.get("tags")
+                tags=args.get("tags"),
             )
 
 
-
 class RAMCaptureAPI(ActionView):
     """
     Take a non-persistant image capture.
@@ -77,12 +75,8 @@ class RAMCaptureAPI(ActionView):
             missing=None, example={"width": 640, "height": 480}
         ),  # TODO: Validate keys
     }
-    
-    responses = {
-        200: {
-            "content_type": "image/jpeg"
-        }
-    }
+
+    responses = {200: {"content_type": "image/jpeg"}}
 
     def post(self, args):
         """

openflexure_microscope/api/v2/views/actions/stage.py

@@ -1,12 +1,11 @@
-from openflexure_microscope.api.utilities import JsonResponse
-from labthings.views import View, ActionView
-from labthings import find_component, fields
-
-from openflexure_microscope.utilities import axes_to_array, filter_dict
+import logging
 
 from flask import Blueprint, request
+from labthings import fields, find_component
+from labthings.views import ActionView, View
 
-import logging
+from openflexure_microscope.api.utilities import JsonResponse
+from openflexure_microscope.utilities import axes_to_array, filter_dict
 
 
 class MoveStageAPI(ActionView):
@@ -65,5 +64,3 @@ class ZeroStageAPI(ActionView):
 
         # TODO: Make schema for microscope state
         return microscope.state["stage"]
-
-

openflexure_microscope/api/v2/views/actions/system.py

@@ -1,8 +1,9 @@
-from labthings.views import View, ActionView
-import subprocess
 import os
+import subprocess
 from sys import platform
 
+from labthings.views import ActionView, View
+
 
 def is_raspberrypi(raise_on_errors=False):
     """

openflexure_microscope/api/v2/views/captures.py

@@ -1,15 +1,14 @@
 import logging
-from flask import abort, request, redirect, url_for, send_file
-
-from openflexure_microscope.api.utilities import get_bool, JsonResponse
 
+from flask import abort, redirect, request, send_file, url_for
 from labthings import Schema, fields, find_component
-from labthings.views import View, PropertyView
-from labthings.utilities import description_from_view
 from labthings.marshalling import marshal_with
-
+from labthings.utilities import description_from_view
+from labthings.views import PropertyView, View
 from marshmallow import pre_dump
 
+from openflexure_microscope.api.utilities import JsonResponse, get_bool
+
 
 class InstrumentSchema(Schema):
     id = fields.UUID()
@@ -130,11 +129,7 @@ class CaptureView(View):
 
 class CaptureDownload(View):
     tags = ["captures"]
-    responses = {
-        200: {
-            "content_type": "image/jpeg"
-        }
-    }
+    responses = {200: {"content_type": "image/jpeg"}}
 
     def get(self, id, filename):
         """

openflexure_microscope/api/v2/views/instrument.py

@@ -1,12 +1,12 @@
-from openflexure_microscope.api.utilities import JsonResponse
-
-from labthings import find_component
-from labthings.views import View, PropertyView
-from labthings.utilities import get_by_path, set_by_path, create_from_path
-
-from flask import request, abort
 import logging
 
+from flask import abort, request
+from labthings import find_component
+from labthings.utilities import create_from_path, get_by_path, set_by_path
+from labthings.views import PropertyView, View
+
+from openflexure_microscope.api.utilities import JsonResponse
+
 
 class SettingsProperty(PropertyView):
     def get(self):
@@ -34,9 +34,7 @@ class SettingsProperty(PropertyView):
 
 class NestedSettingsProperty(View):
     tags = ["properties"]
-    responses = {
-        404: {"description": "Settings key cannot be found"}
-    }
+    responses = {404: {"description": "Settings key cannot be found"}}
 
     def get(self, route):
         """
@@ -80,9 +78,7 @@ class StateProperty(PropertyView):
 
 class NestedStateProperty(View):
     tags = ["properties"]
-    responses = {
-        404: {"description": "Status key cannot be found"}
-    }
+    responses = {404: {"description": "Status key cannot be found"}}
 
     def get(self, route):
         """
@@ -110,9 +106,7 @@ class ConfigurationProperty(PropertyView):
 
 class NestedConfigurationProperty(View):
     tags = ["properties"]
-    responses = {
-        404: {"description": "Status key cannot be found"}
-    }
+    responses = {404: {"description": "Status key cannot be found"}}
 
     def get(self, route):
         """

openflexure_microscope/api/v2/views/stage.py

@@ -1,8 +1,8 @@
-from labthings import find_component, fields, schema
-from labthings.views import PropertyView
-
 import logging
 
+from labthings import fields, find_component, schema
+from labthings.views import PropertyView
+
 
 class StageTypeProperty(PropertyView):
     """The type of the stage"""

openflexure_microscope/api/v2/views/streams.py

@@ -1,21 +1,17 @@
-from openflexure_microscope.api.utilities import gen, JsonResponse
-
-from labthings import find_component
-from labthings.utilities import get_by_path, set_by_path, create_from_path
-from labthings.views import View, PropertyView
-
 from flask import Response
+from labthings import find_component
+from labthings.utilities import create_from_path, get_by_path, set_by_path
+from labthings.views import PropertyView, View
+
+from openflexure_microscope.api.utilities import JsonResponse, gen
 
 
 class MjpegStream(PropertyView):
     """
     Real-time MJPEG stream from the microscope camera
     """
-    responses = {
-        200: {
-            "content_type": "multipart/x-mixed-replace"
-        }
-    }
+
+    responses = {200: {"content_type": "multipart/x-mixed-replace"}}
 
     def get(self):
         """
@@ -44,12 +40,7 @@ class SnapshotStream(PropertyView):
     Single JPEG snapshot from the camera stream
     """
 
-    responses = {
-        200: {
-            "content_type": "image/jpeg",
-            "description": "Snapshot taken"
-        }
-    }
+    responses = {200: {"content_type": "image/jpeg", "description": "Snapshot taken"}}
 
     def get(self):
         """