Code formatting

docs/source/extensions/example_extension/01_basic_structure.py

@@ -1,5 +1,5 @@
-from labthings.extensions import BaseExtension
 from labthings import find_component
+from labthings.extensions import BaseExtension
 
 
 def identify():

docs/source/extensions/example_extension/01b_basic_structure_subclass.py

@@ -1,5 +1,5 @@
-from labthings.extensions import BaseExtension
 from labthings import find_component
+from labthings.extensions import BaseExtension
 
 
 # Create the extension class

docs/source/extensions/example_extension/02_adding_views.py

@@ -1,5 +1,5 @@
+from labthings import fields, find_component
 from labthings.extensions import BaseExtension
-from labthings import find_component, fields
 from labthings.views import View
 
 ## Extension methods
@@ -41,7 +41,7 @@ class ExampleIdentifyView(View):
 
 
 class ExampleRenameView(View):
-    # Expect a request parameter called "name", which is a string. 
+    # Expect a request parameter called "name", which is a string.
     # Passed to the argument "args".
     args = fields.String(required=True, example="My Example Microscope")
 

docs/source/extensions/example_extension/03_marshaling_data.py

@@ -1,5 +1,5 @@
+from labthings import Schema, fields, find_component
 from labthings.extensions import BaseExtension
-from labthings import find_component, Schema, fields
 from labthings.views import View
 
 ## Extension methods
@@ -26,6 +26,7 @@ def rename(microscope, new_name):
 
 ## Extension views
 
+
 class ExampleIdentifyView(View):
     # Format our returned object using MicroscopeIdentifySchema
     schema = MicroscopeIdentifySchema()

docs/source/extensions/example_extension/04_properties.py

@@ -1,6 +1,6 @@
+from labthings import Schema, fields, find_component
 from labthings.extensions import BaseExtension
-from labthings import find_component, Schema, fields
+from labthings.views import PropertyView, View
-from labthings.views import View, PropertyView
 
 ## Extension methods
 

docs/source/extensions/example_extension/05_actions.py

@@ -1,9 +1,9 @@
-from labthings.extensions import BaseExtension
+import io  # Used in our capture action
-from labthings import find_component, Schema, fields
-from labthings.views import View, ActionView, PropertyView
 
 from flask import send_file  # Used to send images from our server
-import io  # Used in our capture action
+from labthings import Schema, fields, find_component
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, PropertyView, View
 
 ## Extension methods
 
@@ -46,7 +46,6 @@ class ExampleIdentifyView(PropertyView):
         return microscope
 
 
-
 # We can use a single schema as the input and output will be formatted identically
 # Eg. We always expect a "name" string argument, and always return a "name" string attribute
 class ExampleRenameView(PropertyView):
@@ -83,13 +82,12 @@ class QuickCaptureAPI(ActionView):
     """
     Take an image capture and return it without saving
     """
+
     # Expect a "use_video_port" boolean, which defaults to True if none is given
     args = {"use_video_port": fields.Boolean(missing=True)}
 
     # Our success response (200) returns an image (image/jpeg mimetype)
-    responses = {
+    responses = {200: {"content_type": "image/jpeg"}}
-        200: {"content_type": "image/jpeg"}
-    }
 
     def post(self, args):
         """

docs/source/extensions/example_extension/06_tasks_locks.py

@@ -1,15 +1,20 @@
-from labthings.extensions import BaseExtension
-from labthings import find_component, Schema, fields, update_action_progress, current_action
-from labthings.views import View, ActionView, PropertyView
-
-from flask import send_file  # Used to send images from our server
 import io  # Used in our capture action
 import time  # Used in our timelapse function
 
+from flask import send_file  # Used to send images from our server
+from labthings import (
+    Schema,
+    current_action,
+    fields,
+    find_component,
+    update_action_progress,
+)
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, PropertyView, View
+
 # Used in our timelapse function
 from openflexure_microscope.captures.capture_manager import generate_basename
 
-
 ## Extension methods
 
 
@@ -59,6 +64,7 @@ class TimelapseAPI(ActionView):
     """
     Take a series of images in a timelapse
     """
+
     args = {
         "n_images": fields.Integer(
             required=True, example=5, description="Number of images"
@@ -73,9 +79,7 @@ class TimelapseAPI(ActionView):
         microscope = find_component("org.openflexure.microscope")
 
         # Start "timelapse"
-        return timelapse(
+        return timelapse(microscope, args.get("n_images"), args.get("t_between"))
-            microscope, args.get("n_images"), args.get("t_between")
-        )
 
 
 ## Create extension

docs/source/extensions/example_extension/07_ev_gui.py

@@ -1,17 +1,23 @@
-from labthings.extensions import BaseExtension
-from labthings import find_component, Schema, fields, update_action_progress, current_action
-from labthings.views import View, ActionView, PropertyView
-
-from flask import send_file  # Used to send images from our server
 import io  # Used in our capture action
 import time  # Used in our timelapse function
 
-# Used in our timelapse function
+from flask import send_file  # Used to send images from our server
-from openflexure_microscope.captures.capture_manager import generate_basename
+from labthings import (
+    Schema,
+    current_action,
+    fields,
+    find_component,
+    update_action_progress,
+)
+from labthings.extensions import BaseExtension
+from labthings.views import ActionView, PropertyView, View
 
 # Used to convert our GUI dictionary into a complete eV extension GUI
 from openflexure_microscope.api.utilities.gui import build_gui
 
+# Used in our timelapse function
+from openflexure_microscope.captures.capture_manager import generate_basename
+
 ## Extension methods
 
 
@@ -61,6 +67,7 @@ class TimelapseAPI(ActionView):
     """
     Take a series of images in a timelapse, running as a background task
     """
+
     args = {
         "n_images": fields.Integer(
             required=True, example=5, description="Number of images"
@@ -75,9 +82,7 @@ class TimelapseAPI(ActionView):
         microscope = find_component("org.openflexure.microscope")
 
         # Create and start "timelapse", running in a background task
-        return timelapse(
+        return timelapse(microscope, args.get("n_images"), args.get("t_between"))
-            microscope, args.get("n_images"), args.get("t_between")
-        )
 
 
 ## Extension GUI (OpenFlexure eV)

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(
-lst_extension_v2.add_view(DeleteLSTView, "/delete_lens_shading_table", endpoint="delete_lens_shading_table")
+    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(
+        return default_zip_manager.marshaled_build_zip_from_capture_ids(microscope, 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 = {
+    responses = {200: {"content_type": "image/jpeg"}}
-        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
+import logging
-from labthings.views import View, ActionView
-from labthings import find_component, fields
-
-from openflexure_microscope.utilities import axes_to_array, filter_dict
 
 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 = {
+    responses = {200: {"content_type": "image/jpeg"}}
-        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 = {
+    responses = {404: {"description": "Settings key cannot be found"}}
-        404: {"description": "Settings key cannot be found"}
-    }
 
     def get(self, route):
         """
@@ -80,9 +78,7 @@ class StateProperty(PropertyView):
 
 class NestedStateProperty(View):
     tags = ["properties"]
-    responses = {
+    responses = {404: {"description": "Status key cannot be found"}}
-        404: {"description": "Status key cannot be found"}
-    }
 
     def get(self, route):
         """
@@ -110,9 +106,7 @@ class ConfigurationProperty(PropertyView):
 
 class NestedConfigurationProperty(View):
     tags = ["properties"]
-    responses = {
+    responses = {404: {"description": "Status key cannot be found"}}
-        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: {
+    responses = {200: {"content_type": "multipart/x-mixed-replace"}}
-            "content_type": "multipart/x-mixed-replace"
-        }
-    }
 
     def get(self):
         """
@@ -44,12 +40,7 @@ class SnapshotStream(PropertyView):
     Single JPEG snapshot from the camera stream
     """
 
-    responses = {
+    responses = {200: {"content_type": "image/jpeg", "description": "Snapshot taken"}}
-        200: {
-            "content_type": "image/jpeg",
-            "description": "Snapshot taken"
-        }
-    }
 
     def get(self):
         """

openflexure_microscope/camera/base.py

@@ -1,15 +1,13 @@
 # -*- coding: utf-8 -*-
-import time
-import os
-import shutil
 import datetime
 import logging
-
+import os
+import shutil
 import threading
-
+import time
 from abc import ABCMeta, abstractmethod
 
-from labthings import StrictLock, ClientEvent
+from labthings import ClientEvent, StrictLock
 
 
 class BaseCamera(metaclass=ABCMeta):

openflexure_microscope/camera/mock.py

@@ -6,20 +6,19 @@
 from __future__ import division
 
 import io
-import time
-import numpy as np
-from PIL import Image, ImageFont, ImageDraw
-from datetime import datetime
-
 import logging
+import time
+from datetime import datetime
 
 # Type hinting
 from typing import Tuple
 
+import numpy as np
+from PIL import Image, ImageDraw, ImageFont
+
 from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.captures import CaptureObject
 
-
 """
 PIL spams the logger with debug-level information. This is a pain when debugging api.app.
 We override the logging settings in api.app by setting a level for PIL here.

openflexure_microscope/camera/pi.py

@@ -29,31 +29,31 @@ to temporarily increase the capture resolution.
 from __future__ import division
 
 import io
-import time
-import numpy as np
-import os
 import logging
+import os
+import time
+
+# Type hinting
+from typing import Tuple
+
+import numpy as np
 
 # Pi camera
 import picamerax
 import picamerax.array
 
-# Type hinting
-from typing import Tuple
-
 from openflexure_microscope.camera.base import BaseCamera
 from openflexure_microscope.captures import CaptureObject
+from openflexure_microscope.paths import settings_file_path
+from openflexure_microscope.utilities import (
+    json_to_ndarray,
+    ndarray_to_json,
+    serialise_array_b64,
+)
 
 # Richard's fix gain
 from .set_picamera_gain import set_analog_gain, set_digital_gain
 
-from openflexure_microscope.paths import settings_file_path
-from openflexure_microscope.utilities import (
-    serialise_array_b64,
-    ndarray_to_json,
-    json_to_ndarray,
-)
-
 
 # MAIN CLASS
 class PiCameraStreamer(BaseCamera):
@@ -115,7 +115,7 @@ class PiCameraStreamer(BaseCamera):
         self.picamera_lst_path = settings_file_path(
             "picamera_lst.npy"
         )  #: str: Path of .npy lens shading table file
-        
+
         # Start the stream worker on init
         self.start_worker()
 
@@ -348,7 +348,7 @@ class PiCameraStreamer(BaseCamera):
                     "Suppressed a ValueError exception in start_preview. Exception: {}".format(
                         e
                     )
-            )
+                )
 
     def stop_preview(self):
         """Stop the on board GPU camera preview."""
@@ -538,7 +538,7 @@ class PiCameraStreamer(BaseCamera):
                 bayer=(not use_video_port) and bayer,
                 use_video_port=use_video_port,
             )
-            #time.sleep(0.1)
+            # time.sleep(0.1)
 
             # Set resolution and start stream recording if necessary
             if not use_video_port:

openflexure_microscope/camera/piexif/__init__.py

@@ -1,10 +1,9 @@
-from ._remove import remove
-from ._load import load
 from ._dump import dump
-from ._transplant import transplant
-from ._insert import insert
-from ._exif import *
 from ._exceptions import *
-
+from ._exif import *
+from ._insert import insert
+from ._load import load
+from ._remove import remove
+from ._transplant import transplant
 
 VERSION = "1.1.2"

openflexure_microscope/camera/piexif/_dump.py

@@ -5,7 +5,6 @@ import struct
 from ._common import *
 from ._exif import *
 
-
 TIFF_HEADER_LENGTH = 8
 
 

openflexure_microscope/camera/piexif/_insert.py

@@ -2,9 +2,9 @@ import io
 import struct
 import sys
 
+from . import _webp
 from ._common import *
 from ._exceptions import InvalidImageDataError
-from . import _webp
 
 
 def insert(exif, image, new_file=None):

openflexure_microscope/camera/piexif/_load.py

@@ -1,10 +1,10 @@
 import struct
 import sys
 
+from . import _webp
 from ._common import *
 from ._exceptions import InvalidImageDataError
 from ._exif import *
-from . import _webp
 
 LITTLE_ENDIAN = b"\x49\x49"
 

openflexure_microscope/camera/piexif/_remove.py

@@ -1,7 +1,7 @@
 import io
 
-from ._common import *
 from . import _webp
+from ._common import *
 
 
 def remove(src, new_file=None):

openflexure_microscope/camera/set_picamera_gain.py

@@ -1,10 +1,11 @@
 from __future__ import print_function
 
-import picamerax
-from picamerax import mmal, mmalobj, exc
-from picamerax.mmalobj import to_rational
-import time
 import logging
+import time
+
+import picamerax
+from picamerax import exc, mmal, mmalobj
+from picamerax.mmalobj import to_rational
 
 MMAL_PARAMETER_ANALOG_GAIN = mmal.MMAL_PARAMETER_GROUP_CAMERA + 0x59
 MMAL_PARAMETER_DIGITAL_GAIN = mmal.MMAL_PARAMETER_GROUP_CAMERA + 0x5A

openflexure_microscope/captures/__init__.py

@@ -1,3 +1,3 @@
-from .capture_manager import CaptureManager
+from . import capture, capture_manager
 from .capture import CaptureObject
-from . import capture_manager, capture
+from .capture_manager import CaptureManager

openflexure_microscope/captures/capture.py

@@ -1,17 +1,17 @@
-import uuid
+import atexit
-import io
-import os
-import shutil
-import glob
 import datetime
+import glob
+import io
 import json
 import logging
-from PIL import Image
+import os
-import dateutil.parser
+import shutil
-import atexit
+import uuid
-
 from collections import OrderedDict
 
+import dateutil.parser
+from PIL import Image
+
 from openflexure_microscope.camera import piexif
 from openflexure_microscope.camera.piexif._exceptions import InvalidImageDataError
 from openflexure_microscope.config import JSONEncoder
@@ -156,7 +156,7 @@ class CaptureObject(object):
 
     def flush(self):
         logging.info(f"Writing to disk {self.file}")
-        with open(self.file, "wb")  as outfile:
+        with open(self.file, "wb") as outfile:
             outfile.write(self.stream.getbuffer())
         self.stream.close()
         logging.info(f"Finished writing to disk {self.file}")
@@ -233,7 +233,9 @@ class CaptureObject(object):
         self._metadata.update(data)
         self.save_metadata()
 
-    def put_and_save(self, tags: list = None, annotations: dict = None, metadata: dict = None):
+    def put_and_save(
+        self, tags: list = None, annotations: dict = None, metadata: dict = None
+    ):
         """
         Batch-write tags, metadata, and annotations in a single disk operation
         """
@@ -243,7 +245,7 @@ class CaptureObject(object):
             annotations = {}
         if not metadata:
             metadata = {}
-        
+
         # Tags
         for tag in tags:
             if tag not in self.tags:

openflexure_microscope/captures/capture_manager.py

@@ -1,13 +1,13 @@
-import os
 import datetime
-import shutil
 import logging
+import os
+import shutil
 from collections import OrderedDict
 
 from labthings import StrictLock
 
-from openflexure_microscope.utilities import entry_by_uuid
 from openflexure_microscope.paths import data_file_path
+from openflexure_microscope.utilities import entry_by_uuid
 
 from .capture import CaptureObject, build_captures_from_exif
 

openflexure_microscope/config.py

@@ -1,20 +1,20 @@
-import json
-import flask
-import os
 import errno
+import json
 import logging
+import os
 import shutil
-from uuid import UUID
-import numpy as np
 from fractions import Fraction
+from uuid import UUID
 
+import flask
+import numpy as np
 from labthings.json import LabThingsJSONEncoder
 
 from .paths import (
-    SETTINGS_FILE_PATH,
-    DEFAULT_SETTINGS_FILE_PATH,
     CONFIGURATION_FILE_PATH,
     DEFAULT_CONFIGURATION_FILE_PATH,
+    DEFAULT_SETTINGS_FILE_PATH,
+    SETTINGS_FILE_PATH,
 )
 
 

openflexure_microscope/devel/__init__.py

@@ -5,19 +5,15 @@ Here we include some classes used frequently in plugin development,
 as well as some Flask imports to simplify API route development
 """
 
-from openflexure_microscope.api.utilities import JsonResponse
+# Flask things
+from flask import Response, abort, escape, request
 
 # Task management
-from labthings import (
+from labthings import current_action as current_task
-    current_action as current_task,
+from labthings import update_action_data as update_task_data
-    update_action_progress as update_task_progress,
+from labthings import update_action_progress as update_task_progress
-    update_action_data as update_task_data,
-)
-
-
-# Flask things
-from flask import abort, escape, Response, request
 
+from openflexure_microscope.api.utilities import JsonResponse
 
 __all__ = [
     "current_task",

openflexure_microscope/install.py

@@ -1,14 +1,17 @@
+import os
+
 from pynpm import NPMPackage
-import os 
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
 pkg_path = os.path.join(dir_path, "api", "static", "package.json")
 
 pkg = NPMPackage(pkg_path)
 
+
 def install():
     pkg.install()
 
+
 def build():
     pkg.install()
-    pkg.run_script('build')
+    pkg.run_script("build")

openflexure_microscope/microscope.py

@@ -3,29 +3,28 @@
 Defines a microscope object, binding a camera and stage with basic functionality.
 """
 import logging
-import pkg_resources
 import uuid
 from typing import Tuple
+
+import pkg_resources
 from expiringdict import ExpiringDict
 
-from openflexure_microscope.captures import CaptureManager
-
-from openflexure_microscope.stage.mock import MissingStage
 from openflexure_microscope.camera.mock import MissingCamera
-from openflexure_microscope.stage.sanga import SangaStage, SangaDeltaStage
+from openflexure_microscope.captures import CaptureManager
+from openflexure_microscope.stage.mock import MissingStage
+from openflexure_microscope.stage.sanga import SangaDeltaStage, SangaStage
 
 try:
     from openflexure_microscope.camera.pi import PiCameraStreamer
 except Exception as e:
     logging.error(e)
     logging.warning("Unable to import PiCameraStreamer")
-from openflexure_microscope.camera.mock import MissingCamera
-
-from openflexure_microscope.utilities import serialise_array_b64, Timer
-from openflexure_microscope.config import user_settings, user_configuration
-
 from labthings import CompositeLock
 
+from openflexure_microscope.camera.mock import MissingCamera
+from openflexure_microscope.config import user_configuration, user_settings
+from openflexure_microscope.utilities import Timer, serialise_array_b64
+
 
 class Microscope:
     """
@@ -106,7 +105,6 @@ class Microscope:
 
         ### Stage
         self.set_stage(configuration=configuration)
-                 
 
         logging.info("Handling fallbacks")
         ### Fallbacks
@@ -131,20 +129,19 @@ class Microscope:
 
         if stage_type:
             if stage_type == configuration["stage"].get("type"):
-                    logging.info("Stage already set to that stage type")
+                logging.info("Stage already set to that stage type")
-                    return
+                return
         else:
             stage_type = configuration["stage"].get("type")
-        
+
         ### Close any existing stages
         if self.stage:
-                stage_port = self.stage.port
+            stage_port = self.stage.port
-                self.stage.close()
+            self.stage.close()
-
 
         logging.info("Setting stage")
-        stage_port = configuration["stage"].get("port")             
+        stage_port = configuration["stage"].get("port")
-                    
+
         if stage_type in ("SangaBoard", "SangaStage"):
             try:
                 logging.info("Trying SangaStage")
@@ -156,17 +153,17 @@ class Microscope:
             try:
                 logging.info("Trying SangaDeltaStage")
                 self.stage = SangaDeltaStage(port=stage_port)
-                
+
             except Exception as e:
                 logging.error(e)
                 logging.warning("No compatible Sangaboard hardware found.")
         else:
-            logging.warning("The stage type is incorrectly defined.")   
+            logging.warning("The stage type is incorrectly defined.")
 
         logging.info("Saving new stage type configuration")
         configuration["stage"]["type"] = stage_type
         self.configuration_file.save(configuration)
-        
+
     def has_real_stage(self) -> bool:
         """
         Check if a real (non-mock) stage is currently attached.
@@ -249,13 +246,13 @@ class Microscope:
         with self.lock:
             # If attached to a camera
             if self.camera:
-                    settings_current_camera = self.camera.read_settings()
+                settings_current_camera = self.camera.read_settings()
-                    settings_current["camera"] = settings_current_camera
+                settings_current["camera"] = settings_current_camera
 
             # If attached to a stage
             if self.stage:
-                    settings_current_stage = self.stage.read_settings()
+                settings_current_stage = self.stage.read_settings()
-                    settings_current["stage"] = settings_current_stage
+                settings_current["stage"] = settings_current_stage
 
             # Capture manager
             settings_current_captures = self.captures.read_settings()
@@ -346,11 +343,9 @@ class Microscope:
         else:
             logging.debug(f"Building microscope metadata: {cache_key}")
             metadata = self.force_get_metadata()
-        
+
         # Keys that should never be cached
-        metadata.update({
+        metadata.update({"state": self.state})
-            "state": self.state,
-        })
 
         return metadata
 
@@ -370,7 +365,7 @@ class Microscope:
         annotations: dict = None,
         tags: list = None,
         metadata: dict = None,
-        cache_key: str = None
+        cache_key: str = None,
     ):
         logging.debug(f"Microscope capturing to {filename}")
         if not annotations:

openflexure_microscope/paths.py

@@ -1,5 +1,5 @@
-import os
 import logging
+import os
 
 # UTILITIES
 

openflexure_microscope/rescue/auto.py

@@ -1,11 +1,12 @@
+import logging
+import os
+
 from openflexure_microscope.paths import (
     FALLBACK_OPENFLEXURE_VAR_PATH,
     PREFERRED_OPENFLEXURE_VAR_PATH,
 )
-import logging
-import os
 
-from . import check_settings, check_capture_reload
+from . import check_capture_reload, check_settings
 
 # Paths for suggestions
 LOGS_PATHS = [

openflexure_microscope/rescue/check_capture_reload.py

@@ -1,10 +1,10 @@
-from openflexure_microscope.rescue.monitor_timeout import launch_timeout_test_process
-from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
-from openflexure_microscope.captures.capture import build_captures_from_exif
-from openflexure_microscope.config import user_settings
-
 import logging
 
+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 user_settings
+from openflexure_microscope.rescue.monitor_timeout import launch_timeout_test_process
+
 
 def check_capture_rebuild(timeout=10):
     logging.info("Loading user settings...")

openflexure_microscope/rescue/check_settings.py

@@ -1,5 +1,5 @@
-import logging
 import json
+import logging
 
 ERROR_SOURCES = []
 

openflexure_microscope/rescue/monitor_service.py

@@ -20,8 +20,8 @@
 # */5 * * * * /root/bin/monitor_service.py prosody > /dev/null 2>&1
 #
 
-import sys
 import subprocess
+import sys
 
 
 class ServiceMonitor(object):

openflexure_microscope/rescue/monitor_timeout.py

@@ -1,7 +1,8 @@
-import multiprocessing
 import logging
+import multiprocessing
 import time
 
+
 # bar
 def test_long_fn():
     for _ in range(100):

openflexure_microscope/stage/base.py

@@ -1,5 +1,6 @@
-import numpy as np
 from abc import ABCMeta, abstractmethod
+
+import numpy as np
 from labthings import StrictLock
 
 

openflexure_microscope/stage/mock.py

@@ -1,11 +1,12 @@
+import logging
+import time
+from collections.abc import Iterable
+
+import numpy as np
+
 from openflexure_microscope.stage.base import BaseStage
 from openflexure_microscope.utilities import axes_to_array
 
-from collections.abc import Iterable
-import numpy as np
-import time
-import logging
-
 
 class MissingStage(BaseStage):
     def __init__(self, port=None, **kwargs):

openflexure_microscope/stage/sanga.py

@@ -1,8 +1,10 @@
-import numpy as np
-import time
 import logging
+import time
 from collections.abc import Iterable
+
+import numpy as np
 from sangaboard import Sangaboard
+
 from openflexure_microscope.stage.base import BaseStage
 from openflexure_microscope.utilities import axes_to_array
 
@@ -189,39 +191,48 @@ class SangaStage(BaseStage):
             print("Move completed, raising exception...")
             raise value  # Propagate the exception
 
+
 class SangaDeltaStage(SangaStage):
-    def __init__(self, port=None, flex_h=80, flex_a=50, flex_b=50, camera_angle=0, **kwargs):
+    def __init__(
+        self, port=None, flex_h=80, flex_a=50, flex_b=50, camera_angle=0, **kwargs
+    ):
         self.flex_h = flex_h
         self.flex_a = flex_a
         self.flex_b = flex_b
 
         # Set up camera rotation relative to stage
-        camera_theta = (camera_angle/180)*np.pi
+        camera_theta = (camera_angle / 180) * np.pi
-        self.R_camera = np.array([
+        self.R_camera = np.array(
-            [np.cos(camera_theta), -np.sin(camera_theta), 0],
+            [
-            [np.sin(camera_theta), np.cos(camera_theta), 0],
+                [np.cos(camera_theta), -np.sin(camera_theta), 0],
-            [0, 0, 1]
+                [np.sin(camera_theta), np.cos(camera_theta), 0],
-        ])
+                [0, 0, 1],
+            ]
+        )
 
         logging.debug(self.R_camera)
 
         # Transformation matrix converting delta into cartesian
-        x_fac = -1 * np.multiply(np.divide(2, np.sqrt(3)), np.divide(self.flex_b, self.flex_h))
+        x_fac = -1 * np.multiply(
+            np.divide(2, np.sqrt(3)), np.divide(self.flex_b, self.flex_h)
+        )
         y_fac = -1 * np.divide(self.flex_b, self.flex_h)
         z_fac = np.multiply(np.divide(1, 3), np.divide(self.flex_b, self.flex_a))
 
-        self.Tvd = np.array([
+        self.Tvd = np.array(
-            [-x_fac, x_fac, 0],
+            [
-            [0.5 * y_fac, 0.5 * y_fac, -y_fac],
+                [-x_fac, x_fac, 0],
-            [z_fac, z_fac, z_fac]
+                [0.5 * y_fac, 0.5 * y_fac, -y_fac],
-        ])
+                [z_fac, z_fac, z_fac],
+            ]
+        )
         logging.debug(self.Tvd)
 
         self.Tdv = np.linalg.inv(self.Tvd)
         logging.debug(self.Tdv)
 
         SangaStage.__init__(self, port=port, **kwargs)
-    
+
     @property
     def position(self):
         # TODO: Account for camera rotation
@@ -253,4 +264,4 @@ class SangaDeltaStage(SangaStage):
         logging.debug("Delta final: {}".format(final))
 
         # Do the move
-        SangaStage.move_abs(self, final, **kwargs)
+        SangaStage.move_abs(self, final, **kwargs)

openflexure_microscope/utilities.py

@@ -1,22 +1,26 @@
-import re
-import copy
-import operator
 import base64
-from uuid import UUID
+import copy
-import numpy as np
 import logging
+import operator
+import re
 import time
 from collections import abc
-from functools import reduce
 from contextlib import contextmanager
+from functools import reduce
+from uuid import UUID
+
+import numpy as np
+
 
 class Timer(object):
     def __init__(self, name):
         self.name = name
         self.start = None
         self.end = None
+
     def __enter__(self):
         self.start = time.time()
+
     def __exit__(self, type, value, traceback):
         self.end = time.time()
         logging.debug(f"{self.name} time: {self.end - self.start}")

pyproject.toml

@@ -61,3 +61,14 @@ sphinxcontrib-httpdomain = "^1.7"
 rope = "^0.14.0"
 pylint = "^2.3"
 black = {version = "^18.3-alpha.0",allow-prereleases = true}
+
+[tool.black]
+exclude = '(\.eggs|\.git|\.venv)'
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+line_length = 88

tests/api_client.py

@@ -1,7 +1,8 @@
+from io import BytesIO
+
+import numpy as np
 import requests
 from PIL import Image
-from io import BytesIO
-import numpy as np
 
 
 class APIconnection:

tests/test_api.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python
-from api_client import APIconnection
-
-import numpy as np
-import unittest
-
 import logging
 import sys
+import unittest
+
+import numpy as np
+from api_client import APIconnection
 
 logging.basicConfig(stream=sys.stderr, level=logging.INFO)
 

tests/test_camera.py

@@ -1,17 +1,15 @@
 #!/usr/bin/env python
-from openflexure_microscope.camera.pi import PiCameraStreamer, CaptureObject
-
-import os
 import io
+import logging
+import os
+import sys
 import time
-import numpy as np
-
-from PIL import Image
-
 import unittest
 
-import logging
+import numpy as np
-import sys
+from PIL import Image
+
+from openflexure_microscope.camera.pi import CaptureObject, PiCameraStreamer
 
 logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
 
@@ -30,9 +28,7 @@ class TestCaptureMethods(unittest.TestCase):
                 # Capture to a context (auto-deletes files when done)
                 with camera.new_image() as output:
 
-                    camera.capture(
+                    camera.capture(output, use_video_port=use_video_port, resize=resize)
-                        output, use_video_port=use_video_port, resize=resize
-                    )
 
                     # Ensure file deletion fails and returns False
                     self.assertFalse(output.delete_file())

tests/test_plugins.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python
-from openflexure_microscope.camera.pi import PiCameraStreamer
-from openflexure_stage import OpenFlexureStage
-from openflexure_microscope import Microscope, config
-
 import atexit
-
+import logging
+import sys
 import unittest
 
-import logging, sys
+from openflexure_stage import OpenFlexureStage
+
+from openflexure_microscope import Microscope, config
+from openflexure_microscope.camera.pi import PiCameraStreamer
 
 logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
 

tests/test_stage.py

@@ -1,12 +1,10 @@
 #!/usr/bin/env python
-from openflexure_stage import OpenFlexureStage
-
-import numpy as np
-
-import unittest
-
 import logging
 import sys
+import unittest
+
+import numpy as np
+from openflexure_stage import OpenFlexureStage
 
 logging.basicConfig(stream=sys.stderr, level=logging.INFO)