Blackened

openflexure_microscope/api/v1/blueprints/camera/capture.py

@@ -132,11 +132,11 @@ class ListAPI(MicroscopeView):
 
             # Inject system metadata
             system_metadata = {
-                    "microscope_settings": self.microscope.read_settings(),
-                    "microscope_state": self.microscope.state,
-                    "microscope_id": self.microscope.id,
-                    "microscope_name": self.microscope.name,
-                }
+                "microscope_settings": self.microscope.read_settings(),
+                "microscope_state": self.microscope.state,
+                "microscope_id": self.microscope.id,
+                "microscope_name": self.microscope.name,
+            }
             output.system_metadata.update(system_metadata)
 
             # Insert custom metadata

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

@@ -8,38 +8,38 @@ _actions = {
         "rule": "/camera/capture/",
         "view_class": camera.CaptureAPI,
         "description": "Take a single still capture",
-        "conditions": True
+        "conditions": True,
     },
     "preview_start": {
         "rule": "/camera/preview/start",
         "view_class": camera.GPUPreviewStartAPI,
         "description": "Start the on-board GPU preview",
-        "conditions": True
+        "conditions": True,
     },
     "preview_stop": {
         "rule": "/camera/preview/stop",
         "view_class": camera.GPUPreviewStopAPI,
         "description": "Stop the on-board GPU preview",
-        "conditions": True
+        "conditions": True,
     },
     "move": {
         "rule": "/stage/move/",
         "view_class": stage.MoveStageAPI,
         "description": "Move the microscope stage",
-        "conditions": True
+        "conditions": True,
     },
     "shutdown": {
         "rule": "/system/shutdown/",
         "view_class": system.ShutdownAPI,
         "description": "Shutdown the device",
-        "conditions": (platform == "linux")
+        "conditions": (platform == "linux"),
     },
     "reboot": {
         "rule": "/system/reboot/",
         "view_class": system.RebootAPI,
         "description": "Reboot the device",
-        "conditions": (platform == "linux")
-    }
+        "conditions": (platform == "linux"),
+    },
 }
 
 
@@ -57,7 +57,7 @@ def actions_representation():
             "links": {"self": url_for(f".{name}")},
             "description": action["description"],
             "rule": action["rule"],
-            "view_class": str(action["view_class"])
+            "view_class": str(action["view_class"]),
         }
 
         actions[name] = d

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

@@ -84,11 +84,11 @@ class CaptureAPI(MicroscopeView):
 
             # Inject system metadata
             system_metadata = {
-                    "microscope_settings": self.microscope.read_settings(),
-                    "microscope_state": self.microscope.state,
-                    "microscope_id": self.microscope.id,
-                    "microscope_name": self.microscope.name,
-                }
+                "microscope_settings": self.microscope.read_settings(),
+                "microscope_state": self.microscope.state,
+                "microscope_id": self.microscope.id,
+                "microscope_name": self.microscope.name,
+            }
             output.system_metadata.update(system_metadata)
 
             # Insert custom metadata

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

@@ -11,7 +11,7 @@ class ShutdownAPI(MicroscopeView):
         .. :quickref: Actions; Shutdown
 
         """
-        subprocess.Popen(['shutdown', '-h', 'now'])
+        subprocess.Popen(["shutdown", "-h", "now"])
 
         return "{}", 201
 
@@ -24,6 +24,6 @@ class RebootAPI(MicroscopeView):
         .. :quickref: Actions; Shutdown
 
         """
-        subprocess.Popen(['sudo', 'shutdown', '-r', 'now'])
+        subprocess.Popen(["sudo", "shutdown", "-r", "now"])
 
         return "{}", 201

openflexure_microscope/api/v2/blueprints/captures.py

@@ -20,14 +20,22 @@ def captures_representation(capture_list: list, include_unavailable: bool = Fals
     if include_unavailable:
         captures = {image.id: image.state for image in capture_list}
     else:
-        captures = {image.id: image.state for image in capture_list if image.state["available"]}
+        captures = {
+            image.id: image.state for image in capture_list if image.state["available"]
+        }
 
     for capture_key, capture_repr in captures.items():
         # Add API routes to returned representations
         extra_state = {
             "links": {
                 "self": "{}".format(url_for(".capture", capture_id=capture_key)),
-                "download": "{}".format(url_for(".capture_download", capture_id=capture_key, filename=capture_repr["filename"])),
+                "download": "{}".format(
+                    url_for(
+                        ".capture_download",
+                        capture_id=capture_key,
+                        filename=capture_repr["filename"],
+                    )
+                ),
                 "tags": "{}".format(url_for(".capture_tags", capture_id=capture_key)),
             }
         }
@@ -131,7 +139,9 @@ class CaptureAPI(MicroscopeView):
         """
 
         try:
-            representation = captures_representation(self.microscope.camera.images)[capture_id]
+            representation = captures_representation(self.microscope.camera.images)[
+                capture_id
+            ]
         except KeyError:
             return abort(404)  # 404 Not Found
 
@@ -379,9 +389,7 @@ def construct_blueprint(microscope_obj):
     # Capture routes
     blueprint.add_url_rule(
         "/<capture_id>/download/<filename>",
-        view_func=DownloadAPI.as_view(
-            "capture_download", microscope=microscope_obj
-        ),
+        view_func=DownloadAPI.as_view("capture_download", microscope=microscope_obj),
     )
 
     blueprint.add_url_rule(
@@ -397,7 +405,6 @@ def construct_blueprint(microscope_obj):
     )
 
     blueprint.add_url_rule(
-        "/",
-        view_func=ListAPI.as_view("capture_list", microscope=microscope_obj),
+        "/", view_func=ListAPI.as_view("capture_list", microscope=microscope_obj)
     )
     return blueprint

openflexure_microscope/api/v2/blueprints/plugins.py

@@ -25,7 +25,7 @@ def plugins_representation(plugin_loader_object: PluginLoader):
             "name": plugin["name"],
             "plugin": str(plugin["plugin"]),
             "routes": plugin["routes"],
-            "form": plugin["form"]
+            "form": plugin["form"],
         }
         plugins.append(d)
 
@@ -55,8 +55,7 @@ def construct_blueprint(microscope_obj):
 
     # Create a base route to return plugin API forms, if any exist
     blueprint.add_url_rule(
-        "/",
-        view_func=PluginFormAPI.as_view("plugins", microscope=microscope_obj),
+        "/", view_func=PluginFormAPI.as_view("plugins", microscope=microscope_obj)
     )
 
     all_routes = []

openflexure_microscope/api/v2/blueprints/tasks.py

@@ -16,9 +16,7 @@ def tasks_representation():
     for task_key, task_repr in tasks_dict.items():
         # Add API routes to returned representations
         extra_state = {
-            "links": {
-                "self": "{}".format(url_for(".task", task_id=task_key)),
-            }
+            "links": {"self": "{}".format(url_for(".task", task_id=task_key))}
         }
 
         tasks_dict[task_key].update(extra_state)

openflexure_microscope/camera/capture.py

@@ -35,7 +35,9 @@ def pull_usercomment_dict(filepath):
             return json.loads(exif_dict["Exif"][37510].decode())
         except json.decoder.JSONDecodeError:
             # TODO: Remove YAML support in a later version
-            logging.warning(f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON.")
+            logging.warning(
+                f"Capture {filepath} has metadata stored in YAML format. This is now deprecated in favour of JSON."
+            )
             return yaml.load(exif_dict["Exif"][37510].decode())
     else:
         return None
@@ -227,7 +229,6 @@ class CaptureObject(object):
             # Insert exif into file
             piexif.insert(exif_bytes, self.file)
 
-
     @property
     def metadata(self) -> dict:
         """

openflexure_microscope/camera/pi.py

@@ -68,7 +68,7 @@ class PiCameraStreamer(BaseCamera):
         "sharpness",
         "annotate_text",
         "annotate_text_size",
-        "zoom"
+        "zoom",
     ]
 
     def __init__(self):
@@ -93,13 +93,23 @@ class PiCameraStreamer(BaseCamera):
         self.set_zoom(1.0)
 
         # Set default settings
-        self.image_resolution = tuple(self.camera.MAX_RESOLUTION)  #: tuple: Resolution for image captures
-        self.stream_resolution = (832, 624)  #: tuple: Resolution for stream and video captures
-        self.numpy_resolution = (1312, 976)  #: tuple: Resolution for numpy array captures
+        self.image_resolution = tuple(
+            self.camera.MAX_RESOLUTION
+        )  #: tuple: Resolution for image captures
+        self.stream_resolution = (
+            832,
+            624,
+        )  #: tuple: Resolution for stream and video captures
+        self.numpy_resolution = (
+            1312,
+            976,
+        )  #: tuple: Resolution for numpy array captures
         self.jpeg_quality = 75  #: int: JPEG quality
 
         # Set default lens shading table path
-        self.picamera_lst_path = settings_file_path("picamera_lst.npy")  #: str: Path of .npy lens shading table file
+        self.picamera_lst_path = settings_file_path(
+            "picamera_lst.npy"
+        )  #: str: Path of .npy lens shading table file
 
         # Update board identifier
         self.status.update({})
@@ -138,7 +148,9 @@ class PiCameraStreamer(BaseCamera):
                 "image_resolution": self.image_resolution,
                 "numpy_resolution": self.numpy_resolution,
                 "jpeg_quality": self.jpeg_quality,
-                "picamera_lst_path": self.picamera_lst_path if os.path.isfile(self.picamera_lst_path) else None,
+                "picamera_lst_path": self.picamera_lst_path
+                if os.path.isfile(self.picamera_lst_path)
+                else None,
                 "picamera_settings": {},
             }
         )
@@ -273,7 +285,7 @@ class PiCameraStreamer(BaseCamera):
         """
         Read the current lens shading table as a numpy array, if it exists. Return None otherwise.
         """
-        if hasattr(self.camera, 'lens_shading_table'):
+        if hasattr(self.camera, "lens_shading_table"):
             return self.camera.lens_shading_table
         else:
             return None
@@ -297,13 +309,17 @@ class PiCameraStreamer(BaseCamera):
         elif (type(lst_array_or_path) == str) and os.path.isfile(lst_array_or_path):
             self.camera.lens_shading_table = np.load(lst_array_or_path)
         else:
-            logging.error("Unsupported or missing data for camera lens_shading_table. Must be numpy ndarray, or .npy file path string. Skipping.")
+            logging.error(
+                "Unsupported or missing data for camera lens_shading_table. Must be numpy ndarray, or .npy file path string. Skipping."
+            )
 
     def set_zoom(self, zoom_value: float = 1.0) -> None:
         """
         Change the camera zoom, handling re-centering and scaling.
         """
-        logging.warning("set_zoom is deprecated. Please use the 'zoom' property in picamera_settings.")
+        logging.warning(
+            "set_zoom is deprecated. Please use the 'zoom' property in picamera_settings."
+        )
         with self.lock:
             self.status["zoom_value"] = float(zoom_value)
             if self.status["zoom_value"] < 1:

openflexure_microscope/config.py

@@ -21,6 +21,7 @@ class JSONEncoder(json.JSONEncoder):
     """
     A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
     """
+
     def default(self, o, markers=None):
         # PiCamera fractions
         if isinstance(o, Fraction):
@@ -39,6 +40,7 @@ class JSONEncoder(json.JSONEncoder):
 
 # MAIN CONFIG CLASS
 
+
 class OpenflexureSettingsFile:
     """
     An object to handle expansion, conversion, and saving of the microscope configuration.
@@ -164,6 +166,7 @@ class OpenflexureSettingsFile:
 
 # HANDLE BASIC LOADING AND SAVING OF SETTINGS FILES
 
+
 def load_json_file(config_path) -> dict:
     """
     Open a .json config file

openflexure_microscope/microscope.py

@@ -160,7 +160,9 @@ class Microscope:
                 and :py:attr:`openflexure_microscope.camera.base.BaseCamera.status`
         """
         # DEPRECATED
-        logging.warning("Microscope.state is deprecated. Use Microscope.status instead. State will be removed in a future version.")
+        logging.warning(
+            "Microscope.state is deprecated. Use Microscope.status instead. State will be removed in a future version."
+        )
         state = {
             "camera": self.camera.status,
             "stage": self.stage.status,

openflexure_microscope/plugins/default/autofocus/api.py

@@ -32,7 +32,7 @@ class AutofocusAPI(MicroscopeViewPlugin):
             return jsonify(task.state), 202
 
         else:
-            abort(503, 'No stage connected. Unable to autofocus.')
+            abort(503, "No stage connected. Unable to autofocus.")
 
 
 class FastAutofocusAPI(MicroscopeViewPlugin):
@@ -53,4 +53,4 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
             return jsonify(task.state), 202
 
         else:
-            abort(503, 'No stage connected. Unable to autofocus.')
+            abort(503, "No stage connected. Unable to autofocus.")

openflexure_microscope/plugins/default/scan/plugin.py

@@ -147,14 +147,16 @@ class ScanPlugin(MicroscopePlugin):
         if "time" not in metadata:
             metadata["time"] = generate_basename()
 
-        metadata.update({
-            "scan_parameters": {
-                "step_size": step_size,
-                "grid": grid,
-                "style": style,
-                "autofocus_dz": autofocus_dz
+        metadata.update(
+            {
+                "scan_parameters": {
+                    "step_size": step_size,
+                    "grid": grid,
+                    "style": style,
+                    "autofocus_dz": autofocus_dz,
+                }
             }
-        })
+        )
 
         # Check if autofocus is enabled
         if (

openflexure_microscope/plugins/loader.py

@@ -154,7 +154,9 @@ class PluginLoader(object):
     @property
     def state(self):
         # DEPRECATED
-        logging.warning("PluginMount.state is deprecated. Use PluginMount.active instead. State will be removed in a future version.")
+        logging.warning(
+            "PluginMount.state is deprecated. Use PluginMount.active instead. State will be removed in a future version."
+        )
         return [m["python_name"] for m in self._plugins]
 
     @property
@@ -195,13 +197,15 @@ class PluginLoader(object):
                     setattr(self, pythonsafe_plugin_name, plugin_object)
 
                     # Store the plugin object, and it's properties
-                    self._plugins.append({
-                        "name": plugin_name,
-                        "python_name": pythonsafe_plugin_name,
-                        "plugin": plugin_object,
-                        "routes": [],
-                        "form": None
-                    })
+                    self._plugins.append(
+                        {
+                            "name": plugin_name,
+                            "python_name": pythonsafe_plugin_name,
+                            "plugin": plugin_object,
+                            "routes": [],
+                            "form": None,
+                        }
+                    )
 
                     # Grant plugin access to the hardware
                     plugin_object.microscope = self.parent