Code formatting

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")