Blackened everything

openflexure_microscope/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ['Microscope', 'config', 'task', 'lock', 'utilities']
+__all__ = ["Microscope", "config", "task", "lock", "utilities"]
 __version__ = "0.1.0"
 
 from .microscope import Microscope

openflexure_microscope/api/__init__.py

@@ -1,3 +1,3 @@
-__all__ = ['utilities']
+__all__ = ["utilities"]
 
 from . import utilities

openflexure_microscope/api/app.py

@@ -6,8 +6,7 @@ import logging
 import sys
 import os
 
-from flask import (
-    Flask, jsonify, send_file)
+from flask import Flask, jsonify, send_file
 
 from serial import SerialException
 from datetime import datetime
@@ -39,7 +38,7 @@ from openflexure_microscope.stage.mock import MockStage
 # Handle logging
 is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
 
-DEFAULT_LOGFILE = os.path.join(USER_CONFIG_DIR, 'openflexure_microscope.log')
+DEFAULT_LOGFILE = os.path.join(USER_CONFIG_DIR, "openflexure_microscope.log")
 
 if (__name__ == "__main__") or (not is_gunicorn):
     # If imported, but not by gunicorn
@@ -48,18 +47,15 @@ if (__name__ == "__main__") or (not is_gunicorn):
 else:
     # Direct standard Python logging to file and console
     root = logging.getLogger()
-    error_formatter = logging.Formatter("[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s")
-
-    rotating_logfile = logging.handlers.RotatingFileHandler(
-        DEFAULT_LOGFILE, 
-        maxBytes=1000000, 
-        backupCount=7
+    error_formatter = logging.Formatter(
+        "[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
     )
 
-    error_handlers = [
-        rotating_logfile,
-        logging.StreamHandler()
-    ]
+    rotating_logfile = logging.handlers.RotatingFileHandler(
+        DEFAULT_LOGFILE, maxBytes=1000000, backupCount=7
+    )
+
+    error_handlers = [rotating_logfile, logging.StreamHandler()]
 
     for handler in error_handlers:
         handler.setFormatter(error_formatter)
@@ -88,7 +84,7 @@ def uri(suffix, api_version, base=None):
 app = Flask(__name__)
 app.url_map.strict_slashes = False
 
-CORS(app, resources=r'/api/*')
+CORS(app, resources=r"/api/*")
 
 # Make errors more API friendly
 handler = JSONExceptionHandler(app)
@@ -121,10 +117,7 @@ def attach_microscope():
 
     # Attach devices to microscope
     logging.debug("Attaching devices to microscope...")
-    api_microscope.attach(
-        api_camera,
-        api_stage
-    )
+    api_microscope.attach(api_camera, api_stage)
 
     # Restore loaded capture array to camera object
     logging.debug("Restoring captures...")
@@ -140,26 +133,26 @@ def attach_microscope():
 
 # Base routes
 base_blueprint = blueprints.base.construct_blueprint(api_microscope)
-app.register_blueprint(base_blueprint, url_prefix=uri('', 'v1'))
+app.register_blueprint(base_blueprint, url_prefix=uri("", "v1"))
 
 # Stage routes
 stage_blueprint = blueprints.stage.construct_blueprint(api_microscope)
-app.register_blueprint(stage_blueprint, url_prefix=uri('/stage', 'v1'))
+app.register_blueprint(stage_blueprint, url_prefix=uri("/stage", "v1"))
 
 # Camera routes
 camera_blueprint = blueprints.camera.construct_blueprint(api_microscope)
-app.register_blueprint(camera_blueprint, url_prefix=uri('/camera', 'v1'))
+app.register_blueprint(camera_blueprint, url_prefix=uri("/camera", "v1"))
 
 # Plugin routes
 plugin_blueprint = blueprints.plugins.construct_blueprint(api_microscope)
-app.register_blueprint(plugin_blueprint, url_prefix=uri('/plugin', 'v1'))
+app.register_blueprint(plugin_blueprint, url_prefix=uri("/plugin", "v1"))
 
 # Task routes
 task_blueprint = blueprints.task.construct_blueprint(api_microscope)
-app.register_blueprint(task_blueprint, url_prefix=uri('/task', 'v1'))
+app.register_blueprint(task_blueprint, url_prefix=uri("/task", "v1"))
 
 
-@app.route('/routes')
+@app.route("/routes")
 def routes():
     """
     List of all connected API routes
@@ -173,7 +166,7 @@ def routes():
     return jsonify(list_routes(app))
 
 
-@app.route('/log')
+@app.route("/log")
 def err_log():
     """
     Most recent 1mb of log output
@@ -186,9 +179,9 @@ def err_log():
     """
     timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
     return send_file(
-        DEFAULT_LOGFILE, 
-        as_attachment=True, 
-        attachment_filename='openflexure_microscope_{}.log'.format(timestamp)
+        DEFAULT_LOGFILE,
+        as_attachment=True,
+        attachment_filename="openflexure_microscope_{}.log".format(timestamp),
     )
 
 
@@ -219,4 +212,4 @@ def cleanup():
 atexit.register(cleanup)
 
 if __name__ == "__main__":
-    app.run(host='0.0.0.0', port="5000", threaded=True, debug=True, use_reloader=False)
+    app.run(host="0.0.0.0", port="5000", threaded=True, debug=True, use_reloader=False)

openflexure_microscope/api/exceptions.py

@@ -17,17 +17,14 @@ class JSONExceptionHandler(object):
     def std_handler(self, error):
         if isinstance(error, HTTPException):
             message = error.description
-        elif hasattr(error, 'message'):
+        elif hasattr(error, "message"):
             message = error.message
         else:
             message = str(error)
 
         status_code = error.code if isinstance(error, HTTPException) else 500
 
-        response = {
-            'status_code': status_code,
-            'message': escape(message)
-        }
+        response = {"status_code": status_code, "message": escape(message)}
         return jsonify(response), status_code
 
     def init_app(self, app):

openflexure_microscope/api/utilities.py

@@ -10,7 +10,9 @@ class JsonResponse:
         """
         # Try to load as json
         try:
-            self.json = request.get_json()  #: dict: Dictionary representation of request JSON
+            self.json = (
+                request.get_json()
+            )  #: dict: Dictionary representation of request JSON
         # If malformed JSON is passed, make an empty dictionary
         except BadRequest as e:
             logging.error(e)
@@ -55,15 +57,12 @@ def gen(camera):
         # the obtained frame is a jpeg
         frame = camera.get_frame()
 
-        yield (b'--frame\r\n'
-               b'Content-Type: image/jpeg\r\n\r\n' + frame + b'\r\n')
+        yield (b"--frame\r\n" b"Content-Type: image/jpeg\r\n\r\n" + frame + b"\r\n")
 
 
 def get_bool(get_arg):
     """Convert GET request argument string to a Python bool"""
-    if (get_arg == 'true' or
-            get_arg == 'True' or
-            get_arg == '1'):
+    if get_arg == "true" or get_arg == "True" or get_arg == "1":
         return True
     else:
         return False
@@ -80,10 +79,7 @@ def list_routes(app):
         endpoint = rule.endpoint
         methods = list(rule.methods)
         url = url_for(rule.endpoint, **options)
-        line = {
-            'endpoint': endpoint,
-            'methods': methods
-        }
+        line = {"endpoint": endpoint, "methods": methods}
         output[url] = line
-    
-    return output
+
+    return output

openflexure_microscope/api/v1/blueprints/base.py

@@ -6,7 +6,6 @@ import logging
 
 
 class StreamAPI(MicroscopeView):
-
     def get(self):
         """
         Real-time MJPEG stream from the microscope camera
@@ -22,11 +21,11 @@ class StreamAPI(MicroscopeView):
 
         return Response(
             gen(self.microscope.camera),
-            mimetype='multipart/x-mixed-replace; boundary=frame')
+            mimetype="multipart/x-mixed-replace; boundary=frame",
+        )
 
 
 class StateAPI(MicroscopeView):
-
     def get(self):
         """
         JSON representation of the microscope object.
@@ -77,7 +76,6 @@ class StateAPI(MicroscopeView):
 
 
 class ConfigAPI(MicroscopeView):
-
     def get(self):
         """
         JSON representation of the microscope config.
@@ -216,21 +214,18 @@ class ConfigAPI(MicroscopeView):
 
 def construct_blueprint(microscope_obj):
 
-    blueprint = Blueprint('base_blueprint', __name__)
+    blueprint = Blueprint("base_blueprint", __name__)
 
     blueprint.add_url_rule(
-        '/stream',
-        view_func=StreamAPI.as_view('stream', microscope=microscope_obj)
+        "/stream", view_func=StreamAPI.as_view("stream", microscope=microscope_obj)
     )
 
     blueprint.add_url_rule(
-        '/state',
-        view_func=StateAPI.as_view('state', microscope=microscope_obj)
+        "/state", view_func=StateAPI.as_view("state", microscope=microscope_obj)
     )
 
     blueprint.add_url_rule(
-        '/config',
-        view_func=ConfigAPI.as_view('config', microscope=microscope_obj)
+        "/config", view_func=ConfigAPI.as_view("config", microscope=microscope_obj)
     )
 
     return blueprint

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

@@ -7,51 +7,70 @@ from . import capture, record, preview, function
 
 def construct_blueprint(microscope_obj):
 
-    blueprint = Blueprint('camera_blueprint', __name__)
+    blueprint = Blueprint("camera_blueprint", __name__)
 
     # Metadata routes
     blueprint.add_url_rule(
-        '/capture/<capture_id>/metadata/<filename>',
-        view_func=capture.MetadataAPI.as_view('metadata_download', microscope=microscope_obj))
+        "/capture/<capture_id>/metadata/<filename>",
+        view_func=capture.MetadataAPI.as_view(
+            "metadata_download", microscope=microscope_obj
+        ),
+    )
 
     blueprint.add_url_rule(
-        '/capture/<capture_id>/metadata',
-        view_func=capture.MetadataRedirectAPI.as_view('metadata_download_redirect', microscope=microscope_obj))
+        "/capture/<capture_id>/metadata",
+        view_func=capture.MetadataRedirectAPI.as_view(
+            "metadata_download_redirect", microscope=microscope_obj
+        ),
+    )
 
     # Tag routes
     blueprint.add_url_rule(
-        '/capture/<capture_id>/tags',
-        view_func=capture.TagsAPI.as_view('capture_tags', microscope=microscope_obj))
+        "/capture/<capture_id>/tags",
+        view_func=capture.TagsAPI.as_view("capture_tags", microscope=microscope_obj),
+    )
 
     # Capture routes
     blueprint.add_url_rule(
-        '/capture/<capture_id>/download/<filename>',
-        view_func=capture.DownloadAPI.as_view('capture_download', microscope=microscope_obj))
+        "/capture/<capture_id>/download/<filename>",
+        view_func=capture.DownloadAPI.as_view(
+            "capture_download", microscope=microscope_obj
+        ),
+    )
 
     blueprint.add_url_rule(
-        '/capture/<capture_id>/download',
-        view_func=capture.DownloadRedirectAPI.as_view('capture_download_redirect', microscope=microscope_obj))
+        "/capture/<capture_id>/download",
+        view_func=capture.DownloadRedirectAPI.as_view(
+            "capture_download_redirect", microscope=microscope_obj
+        ),
+    )
 
     blueprint.add_url_rule(
-        '/capture/<capture_id>/',
-        view_func=capture.CaptureAPI.as_view('capture', microscope=microscope_obj))
+        "/capture/<capture_id>/",
+        view_func=capture.CaptureAPI.as_view("capture", microscope=microscope_obj),
+    )
 
     blueprint.add_url_rule(
-        '/capture/', 
-        view_func=capture.ListAPI.as_view('capture_list', microscope=microscope_obj))
+        "/capture/",
+        view_func=capture.ListAPI.as_view("capture_list", microscope=microscope_obj),
+    )
 
     # Preview routes
     blueprint.add_url_rule(
-        '/preview/<string:operation>', 
-        view_func=preview.GPUPreviewAPI.as_view('gpu_preview', microscope=microscope_obj))
+        "/preview/<string:operation>",
+        view_func=preview.GPUPreviewAPI.as_view(
+            "gpu_preview", microscope=microscope_obj
+        ),
+    )
 
     # Function routes
     blueprint.add_url_rule(
-        '/overlay', 
-        view_func=function.OverlayAPI.as_view('overlay', microscope=microscope_obj))
+        "/overlay",
+        view_func=function.OverlayAPI.as_view("overlay", microscope=microscope_obj),
+    )
 
     blueprint.add_url_rule(
-        '/zoom', 
-        view_func=function.ZoomAPI.as_view('zoom', microscope=microscope_obj))
+        "/zoom", view_func=function.ZoomAPI.as_view("zoom", microscope=microscope_obj)
+    )
 
-    return(blueprint)
+    return blueprint

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

@@ -6,7 +6,6 @@ from flask import Response, jsonify, request, abort, url_for, redirect, send_fil
 
 
 class ListAPI(MicroscopeView):
-
     def get(self):
         """
         Get list of image captures.
@@ -30,12 +29,16 @@ class ListAPI(MicroscopeView):
         :status 200: capture found
         :status 404: no capture found with that id
         """
-        include_unavailable = get_bool(request.args.get('include_unavailable'))
+        include_unavailable = get_bool(request.args.get("include_unavailable"))
 
         if include_unavailable:
             captures = [image.state for image in self.microscope.camera.images]
         else:
-            captures = [image.state for image in self.microscope.camera.images if image.state['available']]
+            captures = [
+                image.state
+                for image in self.microscope.camera.images
+                if image.state["available"]
+            ]
 
         return jsonify(captures)
 
@@ -100,38 +103,40 @@ class ListAPI(MicroscopeView):
         """
         payload = JsonResponse(request)
 
-        filename = payload.param('filename')
-        temporary = payload.param('temporary', default=False, convert=bool)
-        use_video_port = payload.param('use_video_port', default=False, convert=bool)
-        bayer = payload.param('bayer', default=True, convert=bool)
-        metadata = payload.param('metadata', default={}, convert=dict)
-        tags = payload.param('tags', default=[], convert=list)
+        filename = payload.param("filename")
+        temporary = payload.param("temporary", default=False, convert=bool)
+        use_video_port = payload.param("use_video_port", default=False, convert=bool)
+        bayer = payload.param("bayer", default=True, convert=bool)
+        metadata = payload.param("metadata", default={}, convert=dict)
+        tags = payload.param("tags", default=[], convert=list)
 
-        resize = payload.param('size', default=None)
+        resize = payload.param("size", default=None)
         if resize:
-            if ('width' in resize) and ('height' in resize):
-                resize = (int(resize['width']), int(resize['height']))  # Convert dict to tuple
+            if ("width" in resize) and ("height" in resize):
+                resize = (
+                    int(resize["width"]),
+                    int(resize["height"]),
+                )  # Convert dict to tuple
             else:
                 abort(404)
 
         # Explicitally acquire lock (prevents empty files being created if lock is unavailable)
         with self.microscope.camera.lock:
             output = self.microscope.camera.new_image(
-                write_to_file=True,
-                temporary=temporary,
-                filename=filename)
+                write_to_file=True, temporary=temporary, filename=filename
+            )
 
             self.microscope.camera.capture(
-                output,
-                use_video_port=use_video_port,
-                resize=resize,
-                bayer=bayer)
+                output, use_video_port=use_video_port, resize=resize, bayer=bayer
+            )
 
-            metadata.update({
-                'position': self.microscope.state['stage']['position'],
-                'microscope_id': self.microscope.id,
-                'microscope_name': self.microscope.name
-            })
+            metadata.update(
+                {
+                    "position": self.microscope.state["stage"]["position"],
+                    "microscope_id": self.microscope.id,
+                    "microscope_name": self.microscope.name,
+                }
+            )
 
             output.put_metadata(metadata)
             output.put_tags(tags)
@@ -140,7 +145,6 @@ class ListAPI(MicroscopeView):
 
 
 class CaptureAPI(MicroscopeView):
-
     def get(self, capture_id):
         """
         Get JSON representation of a capture
@@ -200,14 +204,15 @@ class CaptureAPI(MicroscopeView):
 
         # Add API routes to returned state
         uri_dict = {
-            'uri': {'state': '{}'.format(url_for('.capture', capture_id=capture_obj.id))}
+            "uri": {
+                "state": "{}".format(url_for(".capture", capture_id=capture_obj.id))
+            }
         }
 
         # If available, also add download link
-        if capture_metadata['available']:
-            uri_dict['uri']['download'] = '{}download/{}'.format(
-                url_for('.capture', capture_id=capture_obj.id),
-                capture_obj.filename
+        if capture_metadata["available"]:
+            uri_dict["uri"]["download"] = "{}download/{}".format(
+                url_for(".capture", capture_id=capture_obj.id), capture_obj.filename
             )
 
         capture_metadata.update(uri_dict)
@@ -257,7 +262,7 @@ class CaptureAPI(MicroscopeView):
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
-        
+
         data_dict = JsonResponse(request).json
 
         capture_obj.put_metadata(data_dict)
@@ -299,17 +304,20 @@ class DownloadRedirectAPI(MicroscopeView):
         """
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
 
-        thumbnail = get_bool(request.args.get('thumbnail'))
+        thumbnail = get_bool(request.args.get("thumbnail"))
 
-        return redirect(url_for(
-            '.capture_download',
-            capture_id=capture_id,
-            filename=capture_obj.filename,
-            thumbnail=thumbnail
-        ), code=307)
+        return redirect(
+            url_for(
+                ".capture_download",
+                capture_id=capture_id,
+                filename=capture_obj.filename,
+                thumbnail=thumbnail,
+            ),
+            code=307,
+        )
 
 
 class DownloadAPI(MicroscopeView):
@@ -317,19 +325,22 @@ class DownloadAPI(MicroscopeView):
 
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
 
-        thumbnail = get_bool(request.args.get('thumbnail'))
+        thumbnail = get_bool(request.args.get("thumbnail"))
 
         # If no filename is specified, redirect to the capture's currently set filename
         if not filename:
-            return redirect(url_for(
-                'capture_download',
-                capture_id=capture_id,
-                filename=capture_obj.filename,
-                thumbnail=thumbnail
-            ), code=307)
+            return redirect(
+                url_for(
+                    "capture_download",
+                    capture_id=capture_id,
+                    filename=capture_obj.filename,
+                    thumbnail=thumbnail,
+                ),
+                code=307,
+            )
 
         # Download the image data using the requested filename
         if thumbnail:
@@ -337,9 +348,7 @@ class DownloadAPI(MicroscopeView):
         else:
             img = capture_obj.data
 
-        return send_file(
-            img,
-            mimetype='image/jpeg')
+        return send_file(img, mimetype="image/jpeg")
 
 
 class MetadataRedirectAPI(MicroscopeView):
@@ -374,14 +383,17 @@ class MetadataRedirectAPI(MicroscopeView):
         """
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
 
-        return redirect(url_for(
-            '.metadata_download',
-            capture_id=capture_id,
-            filename=capture_obj.metadataname
-        ), code=307)
+        return redirect(
+            url_for(
+                ".metadata_download",
+                capture_id=capture_id,
+                filename=capture_obj.metadataname,
+            ),
+            code=307,
+        )
 
 
 class MetadataAPI(MicroscopeView):
@@ -389,23 +401,24 @@ class MetadataAPI(MicroscopeView):
 
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
 
         # If no filename is specified, redirect to the capture's currently set filename
         if not filename:
-            return redirect(url_for(
-                'capture_download',
-                capture_id=capture_id,
-                filename=capture_obj.metadataname
-            ), code=307)
+            return redirect(
+                url_for(
+                    "capture_download",
+                    capture_id=capture_id,
+                    filename=capture_obj.metadataname,
+                ),
+                code=307,
+            )
 
         # Download the metadata using the requested filename
         data = capture_obj.yaml
 
-        return Response(
-            data,
-            mimetype="text/yaml")
+        return Response(data, mimetype="text/yaml")
 
 
 class TagsAPI(MicroscopeView):
@@ -430,13 +443,13 @@ class TagsAPI(MicroscopeView):
         """
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
 
-        metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
+        metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
 
         return jsonify(metadata_tags)
-    
+
     def put(self, capture_id):
         """
         Add tags to the capture
@@ -460,9 +473,9 @@ class TagsAPI(MicroscopeView):
 
         capture_obj = self.microscope.camera.image_from_id(capture_id)
 
-        if not capture_obj or not capture_obj.state['available']:
+        if not capture_obj or not capture_obj.state["available"]:
             return abort(404)  # 404 Not Found
-        
+
         data_dict = JsonResponse(request).json
 
         if type(data_dict) != list:
@@ -470,7 +483,7 @@ class TagsAPI(MicroscopeView):
 
         capture_obj.put_tags(data_dict)
 
-        metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
+        metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
 
         return jsonify(metadata_tags)
 
@@ -507,6 +520,6 @@ class TagsAPI(MicroscopeView):
         for tag in data_dict:
             capture_obj.delete_tag(str(tag))
 
-        metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
+        metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
 
         return jsonify(metadata_tags)

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

@@ -5,7 +5,6 @@ from flask import jsonify, request
 
 
 class ZoomAPI(MicroscopeView):
-
     def get(self):
         """
         Get the current zoom value
@@ -17,9 +16,9 @@ class ZoomAPI(MicroscopeView):
         :<header Content-Type: application/json
         :status 200: preview started/stopped
         """
-        zoom_value = self.microscope.camera.state['zoom_value']
+        zoom_value = self.microscope.camera.state["zoom_value"]
 
-        return jsonify({'zoom_value': zoom_value})
+        return jsonify({"zoom_value": zoom_value})
 
     def post(self):
         """
@@ -44,7 +43,7 @@ class ZoomAPI(MicroscopeView):
         :status 200: preview started/stopped
         """
         payload = JsonResponse(request)
-        zoom_value = payload.param('zoom_value', default=1.0, convert=float)
+        zoom_value = payload.param("zoom_value", default=1.0, convert=float)
 
         self.microscope.camera.set_zoom(zoom_value)
 
@@ -52,7 +51,6 @@ class ZoomAPI(MicroscopeView):
 
 
 class OverlayAPI(MicroscopeView):
-
     def get(self):
         """
         Get overlay text
@@ -67,7 +65,7 @@ class OverlayAPI(MicroscopeView):
         text = self.microscope.camera.camera.annotate_text
         size = self.microscope.camera.camera.annotate_text_size
 
-        return jsonify({'text': text, 'size': size})
+        return jsonify({"text": text, "size": size})
 
     def post(self):
         """
@@ -94,10 +92,10 @@ class OverlayAPI(MicroscopeView):
         """
 
         payload = JsonResponse(request)
-        text = payload.param('text', default="", convert=str)
-        size = payload.param('size', default=50, convert=int)
+        text = payload.param("text", default="", convert=str)
+        size = payload.param("size", default=50, convert=int)
 
         self.microscope.camera.camera.annotate_text = text
         self.microscope.camera.camera.annotate_text_size = size
 
-        return jsonify({'text': text, 'size': size})
+        return jsonify({"text": text, "size": size})

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

@@ -6,7 +6,6 @@ import logging
 
 
 class GPUPreviewAPI(MicroscopeView):
-
     def post(self, operation):
         """
         Start or stop the onboard GPU preview. 
@@ -39,7 +38,7 @@ class GPUPreviewAPI(MicroscopeView):
         if operation == "start":
             payload = JsonResponse(request)
 
-            window = payload.param('window', default=[])
+            window = payload.param("window", default=[])
             logging.debug(window)
 
             if len(window) != 4:

openflexure_microscope/api/v1/blueprints/plugins.py

@@ -6,6 +6,7 @@ from openflexure_microscope.api.v1.views import MicroscopeView
 import logging
 import warnings
 
+
 class PluginFormAPI(MicroscopeView):
     def get(self):
         """
@@ -26,12 +27,12 @@ class PluginFormAPI(MicroscopeView):
 
 def construct_blueprint(microscope_obj):
 
-    blueprint = Blueprint('plugin_blueprint', __name__)
+    blueprint = Blueprint("plugin_blueprint", __name__)
 
     # Create a base route to return plugin API forms, if any exist
     blueprint.add_url_rule(
-        '/',
-        view_func=PluginFormAPI.as_view('plugin_api_form', microscope=microscope_obj)
+        "/",
+        view_func=PluginFormAPI.as_view("plugin_api_form", microscope=microscope_obj),
     )
 
     all_routes = []
@@ -40,7 +41,7 @@ def construct_blueprint(microscope_obj):
     for plugin_name, plugin_obj in microscope_obj.plugin.plugins:
 
         # If plugin contains valid endpoints
-        if hasattr(plugin_obj, 'api_views') and isinstance(plugin_obj.api_views, dict):
+        if hasattr(plugin_obj, "api_views") and isinstance(plugin_obj.api_views, dict):
 
             # We'll keep a record of how each route was expanded
             expanded_routes = {}
@@ -50,7 +51,7 @@ def construct_blueprint(microscope_obj):
 
                 # Remove all leading slashes from view route
                 cleaned_route = view_route
-                while cleaned_route[0] == '/':
+                while cleaned_route[0] == "/":
                     cleaned_route = cleaned_route[1:]
 
                 # Construct a full view route from the plugin name
@@ -61,12 +62,16 @@ def construct_blueprint(microscope_obj):
                 expanded_routes[view_route] = full_view_route
 
                 # Check if endpoint name clashes
-                if full_view_route not in all_routes and issubclass(view_class, MicroscopeViewPlugin):
+                if full_view_route not in all_routes and issubclass(
+                    view_class, MicroscopeViewPlugin
+                ):
                     # Add route to main route dictionary
                     all_routes.append(full_view_route)
 
                     # Create a Python-safe name for the route
-                    plugin_route_id = 'plugin{}'.format(full_view_route).replace('/', '_')
+                    plugin_route_id = "plugin{}".format(full_view_route).replace(
+                        "/", "_"
+                    )
 
                     # Add route to the plugins blueprint
                     blueprint.add_url_rule(
@@ -74,30 +79,37 @@ def construct_blueprint(microscope_obj):
                         view_func=view_class.as_view(
                             plugin_route_id,
                             microscope=microscope_obj,
-                            plugin=plugin_obj
-                        )
+                            plugin=plugin_obj,
+                        ),
                     )
 
                 else:
                     warnings.warn(
                         "An endpoint /{} has already been loaded. Skipping {}.".format(
-                            full_view_route,
-                            view_class
+                            full_view_route, view_class
                         )
                     )
 
             # If plugin includes an API form
-            if hasattr(plugin_obj, 'api_form') and isinstance(plugin_obj.api_form, dict):
+            if hasattr(plugin_obj, "api_form") and isinstance(
+                plugin_obj.api_form, dict
+            ):
                 api_form_info = plugin_obj.api_form
                 # TODO: Validate form? We need to make sure no single plugin can break all plugins.
-                api_form_info['id'] = plugin_name
-                if 'forms' in api_form_info and isinstance(api_form_info['forms'], list):
-                    for form in api_form_info['forms']:
-                        if 'route' in form and form['route'] in expanded_routes.keys():
-                            form['route'] = expanded_routes[form['route']]
+                api_form_info["id"] = plugin_name
+                if "forms" in api_form_info and isinstance(
+                    api_form_info["forms"], list
+                ):
+                    for form in api_form_info["forms"]:
+                        if "route" in form and form["route"] in expanded_routes.keys():
+                            form["route"] = expanded_routes[form["route"]]
                         else:
-                            logging.warn("No valid expandable route found for {}".format(form['route']))
-                
+                            logging.warn(
+                                "No valid expandable route found for {}".format(
+                                    form["route"]
+                                )
+                            )
+
                 # Store the complete form in Microscope().plugin.form
                 microscope_obj.plugin.forms.append(api_form_info)
                 print(microscope_obj.plugin.forms)

openflexure_microscope/api/v1/blueprints/stage.py

@@ -8,7 +8,6 @@ import logging
 
 
 class PositionAPI(MicroscopeView):
-
     def get(self):
         """
         Return current x, y and z positions of the stage. 
@@ -42,7 +41,7 @@ class PositionAPI(MicroscopeView):
           }
 
         """
-        out = filter_dict(self.microscope.state, ['stage', 'position'])
+        out = filter_dict(self.microscope.state, ["stage", "position"])
         return jsonify(out)
 
     def post(self):
@@ -67,15 +66,19 @@ class PositionAPI(MicroscopeView):
         position = [0, 0, 0]
 
         # Handle absolute positioning (calculate a relative move from current position and target)
-        if (payload.param('absolute') is True) and (self.microscope.stage):  # Only if stage exists
-            target_position = axes_to_array(payload.json, ['x', 'y', 'z'])
+        if (payload.param("absolute") is True) and (
+            self.microscope.stage
+        ):  # Only if stage exists
+            target_position = axes_to_array(payload.json, ["x", "y", "z"])
             logging.debug("TARGET: {}".format(target_position))
-            position = [target_position[i] - self.microscope.stage.position[i] for i in range(3)]
+            position = [
+                target_position[i] - self.microscope.stage.position[i] for i in range(3)
+            ]
             logging.debug("DELTA: {}".format(position))
 
         else:
             # Get coordinates from payload
-            position = axes_to_array(payload.json, ['x', 'y', 'z'], [0, 0, 0])
+            position = axes_to_array(payload.json, ["x", "y", "z"], [0, 0, 0])
 
         logging.debug(position)
 
@@ -85,18 +88,18 @@ class PositionAPI(MicroscopeView):
             with self.microscope.stage.lock:
                 self.microscope.stage.move_rel(position)
 
-        out = filter_dict(self.microscope.state, ['stage', 'position'])
+        out = filter_dict(self.microscope.state, ["stage", "position"])
 
         return jsonify(out)
 
 
 def construct_blueprint(microscope_obj):
 
-    blueprint = Blueprint('stage_blueprint', __name__)
+    blueprint = Blueprint("stage_blueprint", __name__)
 
     blueprint.add_url_rule(
-        '/position',
-        view_func=PositionAPI.as_view('position', microscope=microscope_obj)
+        "/position",
+        view_func=PositionAPI.as_view("position", microscope=microscope_obj),
     )
 
     return blueprint

openflexure_microscope/api/v1/blueprints/task.py

@@ -3,7 +3,6 @@ from flask import jsonify, abort, Blueprint
 
 
 class TaskListAPI(MicroscopeView):
-
     def get(self):
         """
         Get list of long-running tasks.
@@ -66,7 +65,6 @@ class TaskListAPI(MicroscopeView):
 
 
 class TaskAPI(MicroscopeView):
-
     def get(self, task_id):
         """
         Get JSON representation of a task
@@ -123,14 +121,11 @@ class TaskAPI(MicroscopeView):
         success = self.microscope.task.delete(task_id)
 
         if success:
-            data = {
-                'status': 'success',
-                'message': 'task successfully deleted'
-            }
+            data = {"status": "success", "message": "task successfully deleted"}
         else:
             data = {
-                'status': 'fail',
-                'message': 'task could not be deleted, as it is currently running or does not exist'
+                "status": "fail",
+                "message": "task could not be deleted, as it is currently running or does not exist",
             }
 
         return jsonify(data)
@@ -138,16 +133,14 @@ class TaskAPI(MicroscopeView):
 
 def construct_blueprint(microscope_obj):
 
-    blueprint = Blueprint('task_blueprint', __name__)
+    blueprint = Blueprint("task_blueprint", __name__)
 
     blueprint.add_url_rule(
-        '/',
-        view_func=TaskListAPI.as_view('task_list', microscope=microscope_obj)
+        "/", view_func=TaskListAPI.as_view("task_list", microscope=microscope_obj)
     )
 
     blueprint.add_url_rule(
-        '/<task_id>/',
-        view_func=TaskAPI.as_view('task', microscope=microscope_obj)
+        "/<task_id>/", view_func=TaskAPI.as_view("task", microscope=microscope_obj)
     )
 
     return blueprint

openflexure_microscope/api/v1/views.py

@@ -6,6 +6,7 @@ class MicroscopeView(MethodView):
     Create a generic MethodView with a globally available
     microscope object passed as an argument.
     """
+
     def __init__(self, microscope, **kwargs):
 
         self.microscope = microscope
@@ -19,6 +20,7 @@ class MicroscopeViewPlugin(MicroscopeView):
     microscope object passed as an argument, and a plugin
     reference stored in 'self'. Initially None.
     """
+
     def __init__(self, microscope, plugin=None, **kwargs):
 
         self.plugin = plugin

openflexure_microscope/camera/base.py

@@ -56,6 +56,7 @@ class CameraEvent(object):
 
     An event-like class that signals all active clients when a new frame is available.
     """
+
     def __init__(self):
         self.events = {}
 
@@ -112,9 +113,10 @@ class BaseCamera(metaclass=ABCMeta):
         images (list): List of image capture objects
         videos (list): List of video capture objects
     """
+
     def __init__(self):
         self.thread = None
-        self.camera = None 
+        self.camera = None
 
         self.lock = StrictLock(timeout=1)
 
@@ -128,11 +130,11 @@ class BaseCamera(metaclass=ABCMeta):
 
         self.state = {}
         self.paths = {
-            'image': BASE_CAPTURE_PATH,
-            'video': BASE_CAPTURE_PATH,
-            'image_tmp': TEMP_CAPTURE_PATH,
-            'video_tpm': TEMP_CAPTURE_PATH
-        } 
+            "image": BASE_CAPTURE_PATH,
+            "video": BASE_CAPTURE_PATH,
+            "image_tmp": TEMP_CAPTURE_PATH,
+            "video_tpm": TEMP_CAPTURE_PATH,
+        }
 
         # Capture data
         self.images = []
@@ -176,7 +178,7 @@ class BaseCamera(metaclass=ABCMeta):
         self.last_access = time.time()
         self.stop = False
 
-        if not self.state['stream_active']:
+        if not self.state["stream_active"]:
             # start background frame thread
             self.thread = threading.Thread(target=self._thread)
             self.thread.daemon = True
@@ -196,12 +198,12 @@ class BaseCamera(metaclass=ABCMeta):
         logging.debug("Stopping worker thread")
         timeout_time = time.time() + timeout
 
-        if self.state['stream_active']:
+        if self.state["stream_active"]:
             self.stop = True
             self.thread.join()  # Wait for stream thread to exit
             logging.debug("Waiting for stream thread to exit.")
 
-        while self.state['stream_active']:
+        while self.state["stream_active"]:
             if time.time() > timeout_time:
                 logging.debug("Timeout waiting for worker thread close.")
                 raise TimeoutError("Timeout waiting for worker thread close.")
@@ -249,12 +251,13 @@ class BaseCamera(metaclass=ABCMeta):
     # CREATING NEW CAPTURES
 
     def new_image(
-            self,
-            write_to_file: bool = True,
-            temporary: bool = True,
-            filename: str = None,
-            folder: str = "",
-            fmt: str = 'jpeg'):
+        self,
+        write_to_file: bool = True,
+        temporary: bool = True,
+        filename: str = None,
+        folder: str = "",
+        fmt: str = "jpeg",
+    ):
 
         """
         Create a new image capture object. Adds to the image list, and shunt all others.
@@ -275,7 +278,7 @@ class BaseCamera(metaclass=ABCMeta):
         filename = "{}.{}".format(filename, fmt)
 
         # Generate folder
-        base_folder = self.paths['image_tmp'] if temporary else self.paths['image']
+        base_folder = self.paths["image_tmp"] if temporary else self.paths["image"]
         folder = os.path.join(base_folder, folder)
 
         # Generate file path
@@ -283,9 +286,8 @@ class BaseCamera(metaclass=ABCMeta):
 
         # Create capture object
         output = CaptureObject(
-            write_to_file=write_to_file,
-            temporary=temporary,
-            filepath=filepath)
+            write_to_file=write_to_file, temporary=temporary, filepath=filepath
+        )
 
         # Update capture list
         shunt_captures(self.images)
@@ -294,12 +296,13 @@ class BaseCamera(metaclass=ABCMeta):
         return output
 
     def new_video(
-            self,
-            write_to_file: bool = True,
-            temporary: bool = False,
-            filename: str = None,
-            folder: str = "",
-            fmt: str = 'h264'):
+        self,
+        write_to_file: bool = True,
+        temporary: bool = False,
+        filename: str = None,
+        folder: str = "",
+        fmt: str = "h264",
+    ):
 
         """
         Create a new video capture object. Adds to the image list, and shunt all others.
@@ -320,7 +323,7 @@ class BaseCamera(metaclass=ABCMeta):
         filename = "{}.{}".format(filename, fmt)
 
         # Generate folder
-        base_folder = self.paths['video_tmp'] if temporary else self.paths['video']
+        base_folder = self.paths["video_tmp"] if temporary else self.paths["video"]
         folder = os.path.join(base_folder, folder)
 
         # Generate file path
@@ -328,9 +331,8 @@ class BaseCamera(metaclass=ABCMeta):
 
         # Create capture object
         output = CaptureObject(
-            write_to_file=write_to_file,
-            temporary=temporary,
-            filepath=filepath)
+            write_to_file=write_to_file, temporary=temporary, filepath=filepath
+        )
 
         # Update capture list
         shunt_captures(self.videos)
@@ -345,7 +347,7 @@ class BaseCamera(metaclass=ABCMeta):
         self.frames_iterator = self.frames()
         logging.debug("Entering worker thread.")
 
-        self.state['stream_active'] = True
+        self.state["stream_active"] = True
 
         for frame in self.frames_iterator:
             self.frame = frame
@@ -354,9 +356,13 @@ class BaseCamera(metaclass=ABCMeta):
 
             # Handle timeout
             if (
-                self.stream_timeout_enabled and  # If using timeout
-                (time.time() - self.last_access > self.stream_timeout) and  # And timeout time
-                not self.state['preview_active']  # And GPU preview is not active
+                self.stream_timeout_enabled
+                and (  # If using timeout
+                    time.time() - self.last_access > self.stream_timeout
+                )
+                and not self.state[  # And timeout time
+                    "preview_active"
+                ]  # And GPU preview is not active
             ):
                 self.frames_iterator.close()
                 break
@@ -372,4 +378,4 @@ class BaseCamera(metaclass=ABCMeta):
 
         logging.debug("BaseCamera worker thread exiting...")
         # Set stream_activate state
-        self.state['stream_active'] = False
+        self.state["stream_active"] = False

openflexure_microscope/camera/capture.py

@@ -18,12 +18,12 @@ Attributes:
     TEMP_CAPTURE_PATH (str): Base path to store all temporary captures (automatically emptied)
 """
 
-PIL_FORMATS = ['JPG', 'JPEG', 'PNG', 'TIF', 'TIFF']
-EXIF_FORMATS = ['JPG', 'JPEG', 'TIF', 'TIFF']
+PIL_FORMATS = ["JPG", "JPEG", "PNG", "TIF", "TIFF"]
+EXIF_FORMATS = ["JPG", "JPEG", "TIF", "TIFF"]
 THUMBNAIL_SIZE = (200, 150)
 
-BASE_CAPTURE_PATH = os.path.join(os.path.expanduser('~'), 'micrographs')
-TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, 'tmp')
+BASE_CAPTURE_PATH = os.path.join(os.path.expanduser("~"), "micrographs")
+TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")
 
 
 # TODO: Move these methods to a camera utilities module?
@@ -50,8 +50,8 @@ def pull_usercomment_dict(filepath):
     except InvalidImageDataError:
         logging.error("Invalid data at {}. Skipping.".format(filepath))
         return None
-    if 'Exif' in exif_dict and 37510 in exif_dict['Exif']:
-        return yaml.load(exif_dict['Exif'][37510].decode())
+    if "Exif" in exif_dict and 37510 in exif_dict["Exif"]:
+        return yaml.load(exif_dict["Exif"][37510].decode())
     else:
         return None
 
@@ -59,7 +59,9 @@ def pull_usercomment_dict(filepath):
 def make_file_list(directory, formats):
     files = []
     for fmt in formats:
-        files.extend(glob.glob('{}/**/*.{}'.format(directory, fmt.lower()), recursive=True))
+        files.extend(
+            glob.glob("{}/**/*.{}".format(directory, fmt.lower()), recursive=True)
+        )
 
     logging.info("{} capture files found on disk".format(len(files)))
 
@@ -98,21 +100,19 @@ def capture_from_exif(path, exif_dict):
     """
 
     # Create a placeholder capture
-    capture = CaptureObject(
-        filepath=path
-    ) 
+    capture = CaptureObject(filepath=path)
 
     # Build file path information
     capture.split_file_path(capture.file)
 
     # Populate capture parameters
-    capture.id = exif_dict['id']
-    
-    capture.timestring = exif_dict['time']
-    capture.format = exif_dict['format']
+    capture.id = exif_dict["id"]
 
-    capture._metadata = exif_dict['custom']
-    capture.tags = exif_dict['tags']
+    capture.timestring = exif_dict["time"]
+    capture.format = exif_dict["format"]
+
+    capture._metadata = exif_dict["custom"]
+    capture.tags = exif_dict["tags"]
 
     return capture
 
@@ -138,10 +138,8 @@ class CaptureObject(object):
     """
 
     def __init__(
-            self,
-            write_to_file: bool = False,
-            temporary: bool = False,
-            filepath: str = '') -> None:
+        self, write_to_file: bool = False, temporary: bool = False, filepath: str = ""
+    ) -> None:
         """Create a new StreamObject, to manage capture data."""
 
         # Store a nice ID
@@ -184,7 +182,9 @@ class CaptureObject(object):
         """Create StreamObject in context, to auto-clean disk data."""
         logging.debug(
             "Entering context for {}. Stored files will be cleaned up automatically regardless of location.".format(
-                self.id))
+                self.id
+            )
+        )
         self.temporary = True  # Flag file to be removed on close.
         self.context_manager = True  # Used in metadata
 
@@ -203,12 +203,14 @@ class CaptureObject(object):
         Construct a full file path, based on filename, folder, and file format.
         Defaults to UUID.
         """
-        global TEMP_CAPTURE_PATH, BASE_CAPTURE_PATH 
+        global TEMP_CAPTURE_PATH, BASE_CAPTURE_PATH
         if self.temporary:
             base_dir = TEMP_CAPTURE_PATH
         else:
             base_dir = BASE_CAPTURE_PATH
-        return os.path.join(base_dir, self.filename)  # Full file name by joining given folder to given name
+        return os.path.join(
+            base_dir, self.filename
+        )  # Full file name by joining given folder to given name
 
     def split_file_path(self, filepath):
         """
@@ -221,7 +223,7 @@ class CaptureObject(object):
         self.filefolder, self.filename = os.path.split(filepath)
         # Split the filename out from it's file extension
         self.basename = os.path.splitext(self.filename)[0]
-        self.format = self.filename.split('.')[-1]
+        self.format = self.filename.split(".")[-1]
 
         # Create folder and file
         if not os.path.exists(self.filefolder):
@@ -298,7 +300,7 @@ class CaptureObject(object):
             # Serialize metadata
             metadata_string = yaml.safe_dump(self.metadata)
             # Insert metadata into exif_dict
-            exif_dict['Exif'][piexif.ExifIFD.UserComment] = metadata_string.encode()
+            exif_dict["Exif"][piexif.ExifIFD.UserComment] = metadata_string.encode()
             # Convert new exif dict to exif bytes
             exif_bytes = piexif.dump(exif_dict)
             # Insert exif into file
@@ -310,8 +312,14 @@ class CaptureObject(object):
         Create basic metadata dictionary from basic capture data, 
         and any added custom metadata and tags.
         """
-        d = {'id': self.id, 'filename': self.filename, 'time': self.timestring,
-             'format': self.format, 'tags': self.tags, 'custom': self._metadata}
+        d = {
+            "id": self.id,
+            "filename": self.filename,
+            "time": self.timestring,
+            "format": self.format,
+            "tags": self.tags,
+            "custom": self._metadata,
+        }
 
         # Add custom metadata to dictionary
         return d
@@ -339,19 +347,19 @@ class CaptureObject(object):
         """
 
         # Create basic state dictionary
-        d = {'path': self.file, 'temporary': self.temporary, 'metadata': self.metadata}
+        d = {"path": self.file, "temporary": self.temporary, "metadata": self.metadata}
 
         # Check bytestream
         if self.stream_exists:
-            d['bytestream'] = True
+            d["bytestream"] = True
         else:
-            d['bytestream'] = False
+            d["bytestream"] = False
 
         # Combined availability of data
         if self.exists:
-            d['available'] = True
+            d["available"] = True
         else:
-            d['available'] = False
+            d["available"] = False
 
         return d
 
@@ -373,7 +381,7 @@ class CaptureObject(object):
         else:  # If data bytestream is empty
             if self.file_exists:  # If data file exists
                 logging.info("Opening from file {}".format(self.file))
-                with open(self.file, 'rb') as f:
+                with open(self.file, "rb") as f:
                     d = io.BytesIO(f.read())  # Load bytes from file
                 d.seek(0)  # Rewind loaded bytestream
                 # Create a copy of the bytestream bytes
@@ -413,7 +421,7 @@ class CaptureObject(object):
     def load_file(self) -> bool:
         """Load data stored on disk to the in-memory bytestream."""
         if self.file_exists:  # If data file exists
-            with open(self.file, 'rb') as f:
+            with open(self.file, "rb") as f:
                 self.bytestream = io.BytesIO(f.read())  # Load bytes from file
             self.bytestream.seek(0)  # Rewind data bytes again
             return True
@@ -423,7 +431,7 @@ class CaptureObject(object):
     def save_file(self) -> bool:
         """Write the StreamObjects bytestream to a file."""
         if self.stream_exists:  # If there's a bytestream to save
-            with open(self.file, 'ab') as f:  # Load file as bytes
+            with open(self.file, "ab") as f:  # Load file as bytes
                 logging.debug("Writing bytestream to file {}".format(self.file))
                 f.seek(0, 0)  # Seek to the start of the file
                 f.write(self.binary)  # Write data bytes to file

openflexure_microscope/camera/pi.py

@@ -36,6 +36,7 @@ import picamera.array
 from typing import Tuple
 
 from .base import BaseCamera, CaptureObject
+
 # Richard's fix gain
 from .set_picamera_gain import set_analog_gain, set_digital_gain
 
@@ -43,30 +44,31 @@ from .set_picamera_gain import set_analog_gain, set_digital_gain
 # MAIN CLASS
 class PiCameraStreamer(BaseCamera):
     """Raspberry Pi camera implementation of PiCameraStreamer."""
+
     picamera_settings_keys = [
-        'exposure_mode',
-        'analog_gain',
-        'digital_gain',
-        'shutter_speed',
-        'awb_gains',
-        'awb_mode',
-        'framerate',
-        'saturation',
-        'lens_shading_table'
+        "exposure_mode",
+        "analog_gain",
+        "digital_gain",
+        "shutter_speed",
+        "awb_gains",
+        "awb_mode",
+        "framerate",
+        "saturation",
+        "lens_shading_table",
     ]
 
     def __init__(self):
         # Run BaseCamera init
         BaseCamera.__init__(self)
         # Attach to Pi camera
-        self.camera = picamera.PiCamera()  #: :py:class:`picamera.PiCamera`: Picamera object
+        self.camera = (
+            picamera.PiCamera()
+        )  #: :py:class:`picamera.PiCamera`: Picamera object
 
         # Store state of PiCameraStreamer
-        self.state.update({
-            'stream_active': False,
-            'record_active': False,
-            'preview_active': False,
-        })
+        self.state.update(
+            {"stream_active": False, "record_active": False, "preview_active": False}
+        )
         # Reset variable states
         self.set_zoom(1.0)
 
@@ -101,11 +103,11 @@ class PiCameraStreamer(BaseCamera):
         """
 
         conf_dict = {
-            'stream_resolution': self.stream_resolution,
-            'image_resolution': self.image_resolution,
-            'numpy_resolution': self.numpy_resolution,
-            'jpeg_quality': self.jpeg_quality,
-            'picamera_settings': {},
+            "stream_resolution": self.stream_resolution,
+            "image_resolution": self.image_resolution,
+            "numpy_resolution": self.numpy_resolution,
+            "jpeg_quality": self.jpeg_quality,
+            "picamera_settings": {},
         }
 
         # PiCamera parameters
@@ -113,7 +115,7 @@ class PiCameraStreamer(BaseCamera):
             try:
                 value = getattr(self.camera, key)
                 logging.debug("Reading PiCamera().{}: {}".format(key, value))
-                conf_dict['picamera_settings'][key] = value
+                conf_dict["picamera_settings"][key] = value
             except AttributeError:
                 logging.debug("Unable to read PiCamera attribute {}".format(key))
 
@@ -138,21 +140,23 @@ class PiCameraStreamer(BaseCamera):
         with self.lock:
 
             # Apply valid config params to Picamera object
-            if not self.state['record_active']:  # If not recording a video
+            if not self.state["record_active"]:  # If not recording a video
 
                 # Pause stream while changing settings
-                if self.state['stream_active']:  # If stream is active
+                if self.state["stream_active"]:  # If stream is active
                     logging.info("Pausing stream to update config.")
                     self.stop_stream_recording()  # Pause stream
                     paused_stream = True  # Remember to unpause stream when done
 
                 # PiCamera parameters
-                if 'picamera_settings' in config:  # If new settings are given
-                    self.apply_picamera_settings(config['picamera_settings'], pause_for_effect=True)
+                if "picamera_settings" in config:  # If new settings are given
+                    self.apply_picamera_settings(
+                        config["picamera_settings"], pause_for_effect=True
+                    )
 
                 # PiCameraStreamer parameters
                 for key, value in config.items():  # For each provided setting
-                    if (key != 'picamera_settings') and hasattr(self, key):
+                    if (key != "picamera_settings") and hasattr(self, key):
                         setattr(self, key, value)
 
                 # If stream was paused to update config, unpause
@@ -162,67 +166,84 @@ class PiCameraStreamer(BaseCamera):
 
             else:
                 raise Exception(
-                    "Cannot update camera config while recording is active.")
+                    "Cannot update camera config while recording is active."
+                )
 
-    def apply_picamera_settings(self, settings_dict: dict, pause_for_effect: bool=True):
+    def apply_picamera_settings(
+        self, settings_dict: dict, pause_for_effect: bool = True
+    ):
         # Set exposure mode
-        if 'exposure_mode' in settings_dict:
-            logging.debug("Applying exposure_mode: {}".format(settings_dict['exposure_mode']))
-            self.camera.exposure_mode = settings_dict['exposure_mode']
+        if "exposure_mode" in settings_dict:
+            logging.debug(
+                "Applying exposure_mode: {}".format(settings_dict["exposure_mode"])
+            )
+            self.camera.exposure_mode = settings_dict["exposure_mode"]
 
         # Apply gains and let them settle
-        if 'analog_gain' in settings_dict:
-            logging.debug("Applying analog_gain: {}".format(settings_dict['analog_gain']))
-            set_analog_gain(self.camera, float(settings_dict['analog_gain']))
-        if 'digital_gain' in settings_dict:
-            logging.debug("Applying digital_gain: {}".format(settings_dict['digital_gain']))
-            set_digital_gain(self.camera, float(settings_dict['digital_gain']))
-        
+        if "analog_gain" in settings_dict:
+            logging.debug(
+                "Applying analog_gain: {}".format(settings_dict["analog_gain"])
+            )
+            set_analog_gain(self.camera, float(settings_dict["analog_gain"]))
+        if "digital_gain" in settings_dict:
+            logging.debug(
+                "Applying digital_gain: {}".format(settings_dict["digital_gain"])
+            )
+            set_digital_gain(self.camera, float(settings_dict["digital_gain"]))
+
         # Apply shutter speed
-        if 'shutter_speed' in settings_dict:
-            logging.debug("Applying shutter_speed: {}".format(settings_dict['shutter_speed']))
-            self.camera.shutter_speed = int(settings_dict['shutter_speed'])
+        if "shutter_speed" in settings_dict:
+            logging.debug(
+                "Applying shutter_speed: {}".format(settings_dict["shutter_speed"])
+            )
+            self.camera.shutter_speed = int(settings_dict["shutter_speed"])
 
         time.sleep(0.2)  # Let gains settle
 
         # Handle AWB in a half-smart way
-        if 'awb_gains' in settings_dict:
+        if "awb_gains" in settings_dict:
             logging.debug("Applying awb_mode: off")
-            self.camera.awb_mode = 'off'
-            logging.debug("Applying awb_gains: {}".format(settings_dict['awb_gains']))
-            self.camera.awb_gains = settings_dict['awb_gains']
-        elif 'awb_mode' in settings_dict:
-            logging.debug("Applying awb_mode: {}".format(settings_dict['awb_mode']))
-            self.camera.awb_mode = settings_dict['awb_mode']
+            self.camera.awb_mode = "off"
+            logging.debug("Applying awb_gains: {}".format(settings_dict["awb_gains"]))
+            self.camera.awb_gains = settings_dict["awb_gains"]
+        elif "awb_mode" in settings_dict:
+            logging.debug("Applying awb_mode: {}".format(settings_dict["awb_mode"]))
+            self.camera.awb_mode = settings_dict["awb_mode"]
 
         # Handle some properties that can be quickly applied
-        batched_keys = ['framerate', 'saturation']
+        batched_keys = ["framerate", "saturation"]
         for key in batched_keys:
             if (key in settings_dict) and hasattr(self.camera, key):
                 logging.debug("Applying {}: {}".format(key, settings_dict[key]))
                 setattr(self.camera, key, settings_dict[key])
 
         # Handle lens shading if camera supports it
-        if ('lens_shading_table' in settings_dict) and hasattr(self.camera, 'lens_shading_table'):
-            logging.debug("Applying lens_shading_table: {}".format(settings_dict['lens_shading_table']))
-            self.camera.lens_shading_table = settings_dict['lens_shading_table']
+        if ("lens_shading_table" in settings_dict) and hasattr(
+            self.camera, "lens_shading_table"
+        ):
+            logging.debug(
+                "Applying lens_shading_table: {}".format(
+                    settings_dict["lens_shading_table"]
+                )
+            )
+            self.camera.lens_shading_table = settings_dict["lens_shading_table"]
 
         # Final optional pause to settle
         if pause_for_effect:
             time.sleep(0.2)
 
-    def set_zoom(self, zoom_value: float = 1.) -> None:
+    def set_zoom(self, zoom_value: float = 1.0) -> None:
         """
         Change the camera zoom, handling re-centering and scaling.
         """
         with self.lock:
-            self.state['zoom_value'] = float(zoom_value)
-            if self.state['zoom_value'] < 1:
-                self.state['zoom_value'] = 1
+            self.state["zoom_value"] = float(zoom_value)
+            if self.state["zoom_value"] < 1:
+                self.state["zoom_value"] = 1
             # Richard's code for zooming !
             fov = self.camera.zoom
             centre = np.array([fov[0] + fov[2] / 2.0, fov[1] + fov[3] / 2.0])
-            size = 1.0 / self.state['zoom_value']
+            size = 1.0 / self.state["zoom_value"]
             # If the new zoom value would be invalid, move the centre to
             # keep it within the camera's sensor (this is only relevant
             # when zooming out, if the FoV is not centred on (0.5, 0.5)
@@ -252,22 +273,24 @@ class PiCameraStreamer(BaseCamera):
                     self.camera.preview.window = window
                 if fullscreen:
                     self.camera.preview.fullscreen = fullscreen
-            self.state['preview_active'] = True
+            self.state["preview_active"] = True
         except picamera.exc.PiCameraMMALError as e:
-            logging.error("Suppressed a MMALError in start_preview. Exception: {}".format(e))
+            logging.error(
+                "Suppressed a MMALError in start_preview. Exception: {}".format(e)
+            )
         except picamera.exc.PiCameraValueError as e:
-            logging.error("Suppressed a ValueError exception in start_preview. Exception: {}".format(e))
+            logging.error(
+                "Suppressed a ValueError exception in start_preview. Exception: {}".format(
+                    e
+                )
+            )
 
     def stop_preview(self):
         """Stop the on board GPU camera preview."""
         self.camera.stop_preview()
-        self.state['preview_active'] = False
+        self.state["preview_active"] = False
 
-    def start_recording(
-            self,
-            output,
-            fmt: str = 'h264',
-            quality: int = 15):
+    def start_recording(self, output, fmt: str = "h264", quality: int = 15):
         """Start recording.
 
         Start a new video recording, writing to a output object.
@@ -283,7 +306,7 @@ class PiCameraStreamer(BaseCamera):
         """
         with self.lock:
             # Start recording method only if a current recording is not running
-            if not self.state['record_active']:
+            if not self.state["record_active"]:
 
                 # If output is a StreamObject
                 if isinstance(output, CaptureObject):
@@ -300,17 +323,19 @@ class PiCameraStreamer(BaseCamera):
                     format=fmt,
                     splitter_port=2,
                     resize=self.stream_resolution,
-                    quality=quality)
+                    quality=quality,
+                )
 
                 # Update state dictionary
-                self.state['record_active'] = True
+                self.state["record_active"] = True
 
                 return output
 
             else:
                 logging.error(
                     "Cannot start a new recording\
-                    until the current recording has stopped.")
+                    until the current recording has stopped."
+                )
                 return None
 
     def stop_recording(self):
@@ -322,12 +347,11 @@ class PiCameraStreamer(BaseCamera):
             logging.info("Recording stopped")
 
             # Update state dictionary
-            self.state['record_active'] = False
+            self.state["record_active"] = False
 
     def stop_stream_recording(
-            self,
-            splitter_port: int = 1,
-            resolution: Tuple[int, int] = None) -> None:
+        self, splitter_port: int = 1, resolution: Tuple[int, int] = None
+    ) -> None:
         """
         Sets the camera resolution to the still-image resolution, and stops recording if the stream is active.
 
@@ -346,16 +370,21 @@ class PiCameraStreamer(BaseCamera):
             except picamera.exc.PiCameraNotRecording:
                 logging.info("Not recording on splitter_port {}".format(splitter_port))
             else:
-                logging.info("Stopped MJPEG stream on port {1}. Switching to {0}.".format(resolution, splitter_port))
+                logging.info(
+                    "Stopped MJPEG stream on port {1}. Switching to {0}.".format(
+                        resolution, splitter_port
+                    )
+                )
 
             # Increase the resolution for taking an image
-            time.sleep(0.2)  # Sprinkled a sleep to prevent camera getting confused by rapid commands
+            time.sleep(
+                0.2
+            )  # Sprinkled a sleep to prevent camera getting confused by rapid commands
             self.camera.resolution = resolution
 
     def start_stream_recording(
-            self,
-            splitter_port: int = 1,
-            resolution: Tuple[int, int] = None) -> None:
+        self, splitter_port: int = 1, resolution: Tuple[int, int] = None
+    ) -> None:
         """
         Sets the camera resolution to the video/stream resolution, and starts recording if the stream should be active.
 
@@ -366,45 +395,57 @@ class PiCameraStreamer(BaseCamera):
         """
         with self.lock:
             # If stream object was destroyed
-            if not hasattr(self, 'stream'):
+            if not hasattr(self, "stream"):
                 self.stream = io.BytesIO()  # Create a stream object
 
             # If no explicit resolution is passed
             if not resolution:
-                resolution = self.stream_resolution  # Default to video recording resolution
+                resolution = (
+                    self.stream_resolution
+                )  # Default to video recording resolution
 
             # Reduce the resolution for video streaming
             try:
                 self.camera._check_recording_stopped()
             except picamera.exc.PiCameraRuntimeError:
-                logging.info("Error while changing resolution: Recording already running.")
+                logging.info(
+                    "Error while changing resolution: Recording already running."
+                )
             else:
                 self.camera.resolution = resolution
 
             # If the stream should be active
-            if self.state['stream_active']:
+            if self.state["stream_active"]:
                 try:
                     # Start recording on stream port
                     self.camera.start_recording(
                         self.stream,
-                        format='mjpeg',
+                        format="mjpeg",
                         quality=self.jpeg_quality,
-                        bitrate=-1,  # RWB: disable bitrate control 
+                        bitrate=-1,  # RWB: disable bitrate control
                         # (bitrate control makes JPEG size less good as a focus
                         # metric)
-                        splitter_port=splitter_port)
+                        splitter_port=splitter_port,
+                    )
                 except picamera.exc.PiCameraAlreadyRecording:
-                    logging.info("Error while starting preview: Recording already running.")
+                    logging.info(
+                        "Error while starting preview: Recording already running."
+                    )
                 else:
-                    logging.debug("Started MJPEG stream at {} on port {}".format(resolution, splitter_port))
+                    logging.debug(
+                        "Started MJPEG stream at {} on port {}".format(
+                            resolution, splitter_port
+                        )
+                    )
 
     def capture(
-            self,
-            output,
-            fmt: str = 'jpeg',
-            use_video_port: bool = False,
-            resize: Tuple[int, int] = None,
-            bayer: bool = True):
+        self,
+        output,
+        fmt: str = "jpeg",
+        use_video_port: bool = False,
+        resize: Tuple[int, int] = None,
+        bayer: bool = True,
+    ):
         """
         Capture a still image to a StreamObject.
 
@@ -439,7 +480,8 @@ class PiCameraStreamer(BaseCamera):
                 quality=100,
                 resize=resize,
                 bayer=(not use_video_port) and bayer,
-                use_video_port=use_video_port)
+                use_video_port=use_video_port,
+            )
 
             # Set resolution and start stream recording if necessary
             if not use_video_port:
@@ -448,9 +490,8 @@ class PiCameraStreamer(BaseCamera):
             return output
 
     def yuv(
-            self,
-            use_video_port: bool = True,
-            resize: Tuple[int, int] = None) -> np.ndarray:
+        self, use_video_port: bool = True, resize: Tuple[int, int] = None
+    ) -> np.ndarray:
         """Capture an uncompressed still YUV image to a Numpy array.
 
         Args:
@@ -477,10 +518,8 @@ class PiCameraStreamer(BaseCamera):
                 logging.info("Capturing to {}".format(output))
 
                 self.camera.capture(
-                    output,
-                    resize=size,
-                    format='yuv',
-                    use_video_port=use_video_port)
+                    output, resize=size, format="yuv", use_video_port=use_video_port
+                )
 
                 if not use_video_port:
                     self.start_stream_recording()
@@ -488,9 +527,8 @@ class PiCameraStreamer(BaseCamera):
                 return output.array
 
     def array(
-            self,
-            use_video_port: bool = True,
-            resize: Tuple[int, int] = None) -> np.ndarray:
+        self, use_video_port: bool = True, resize: Tuple[int, int] = None
+    ) -> np.ndarray:
         """Capture an uncompressed still RGB image to a Numpy array.
 
         Args:
@@ -517,10 +555,8 @@ class PiCameraStreamer(BaseCamera):
                 logging.info("Capturing to {}".format(output))
 
                 self.camera.capture(
-                    output,
-                    resize=size,
-                    format='rgb',
-                    use_video_port=use_video_port)
+                    output, resize=size, format="rgb", use_video_port=use_video_port
+                )
 
                 # Resume stream
                 self.start_stream_recording()

openflexure_microscope/camera/piexif/__init__.py

@@ -7,5 +7,4 @@ from ._exif import *
 from ._exceptions import *
 
 
-
-VERSION = '1.1.2'
+VERSION = "1.1.2"

openflexure_microscope/camera/piexif/_common.py

@@ -12,20 +12,21 @@ def split_into_segments(data):
     head = 2
     segments = [b"\xff\xd8"]
     while 1:
-        if data[head: head + 2] == b"\xff\xda":
+        if data[head : head + 2] == b"\xff\xda":
             segments.append(data[head:])
             break
         else:
-            length = struct.unpack(">H", data[head + 2: head + 4])[0]
+            length = struct.unpack(">H", data[head + 2 : head + 4])[0]
             endPoint = head + length + 2
-            seg = data[head: endPoint]
+            seg = data[head:endPoint]
             segments.append(seg)
             head = endPoint
 
-        if (head >= len(data)):
+        if head >= len(data):
             raise InvalidImageDataError("Wrong JPEG data.")
     return segments
 
+
 def read_exif_from_file(filename):
     """Slices JPEG meta data into a list from JPEG binary data.
     """
@@ -39,11 +40,11 @@ def read_exif_from_file(filename):
     HEAD_LENGTH = 4
     exif = None
     while 1:
-        length = struct.unpack(">H", head[2: 4])[0]
+        length = struct.unpack(">H", head[2:4])[0]
 
         if head[:2] == b"\xff\xe1":
             segment_data = f.read(length - 2)
-            if segment_data[:4] != b'Exif':
+            if segment_data[:4] != b"Exif":
                 head = f.read(HEAD_LENGTH)
                 continue
             exif = head + segment_data
@@ -57,6 +58,7 @@ def read_exif_from_file(filename):
     f.close()
     return exif
 
+
 def get_exif_seg(segments):
     """Returns Exif from JPEG meta data list
     """
@@ -69,9 +71,11 @@ def get_exif_seg(segments):
 def merge_segments(segments, exif=b""):
     """Merges Exif with APP0 and APP1 manipulations.
     """
-    if segments[1][0:2] == b"\xff\xe0" and \
-       segments[2][0:2] == b"\xff\xe1" and \
-       segments[2][4:10] == b"Exif\x00\x00":
+    if (
+        segments[1][0:2] == b"\xff\xe0"
+        and segments[2][0:2] == b"\xff\xe1"
+        and segments[2][4:10] == b"Exif\x00\x00"
+    ):
         if exif:
             segments[2] = exif
             segments.pop(1)
@@ -82,8 +86,7 @@ def merge_segments(segments, exif=b""):
     elif segments[1][0:2] == b"\xff\xe0":
         if exif:
             segments[1] = exif
-    elif segments[1][0:2] == b"\xff\xe1" and \
-         segments[1][4:10] == b"Exif\x00\x00":
+    elif segments[1][0:2] == b"\xff\xe1" and segments[1][4:10] == b"Exif\x00\x00":
         if exif:
             segments[1] = exif
         elif exif is None:

openflexure_microscope/camera/piexif/_dump.py

@@ -31,16 +31,20 @@ def dump(exif_dict_original):
     else:
         zeroth_ifd = {}
 
-    if (("Exif" in exif_dict) and len(exif_dict["Exif"]) or
-          ("Interop" in exif_dict) and len(exif_dict["Interop"]) ):
+    if (
+        ("Exif" in exif_dict)
+        and len(exif_dict["Exif"])
+        or ("Interop" in exif_dict)
+        and len(exif_dict["Interop"])
+    ):
         zeroth_ifd[ImageIFD.ExifTag] = 1
         exif_is = True
         exif_ifd = exif_dict["Exif"]
         if ("Interop" in exif_dict) and len(exif_dict["Interop"]):
-            exif_ifd[ExifIFD. InteroperabilityTag] = 1
+            exif_ifd[ExifIFD.InteroperabilityTag] = 1
             interop_is = True
             interop_ifd = exif_dict["Interop"]
-        elif ExifIFD. InteroperabilityTag in exif_ifd:
+        elif ExifIFD.InteroperabilityTag in exif_ifd:
             exif_ifd.pop(ExifIFD.InteroperabilityTag)
     elif ImageIFD.ExifTag in zeroth_ifd:
         zeroth_ifd.pop(ImageIFD.ExifTag)
@@ -52,17 +56,20 @@ def dump(exif_dict_original):
     elif ImageIFD.GPSTag in zeroth_ifd:
         zeroth_ifd.pop(ImageIFD.GPSTag)
 
-    if (("1st" in exif_dict) and
-            ("thumbnail" in exif_dict) and
-            (exif_dict["thumbnail"] is not None)):
+    if (
+        ("1st" in exif_dict)
+        and ("thumbnail" in exif_dict)
+        and (exif_dict["thumbnail"] is not None)
+    ):
         first_is = True
         exif_dict["1st"][ImageIFD.JPEGInterchangeFormat] = 1
         exif_dict["1st"][ImageIFD.JPEGInterchangeFormatLength] = 1
         first_ifd = exif_dict["1st"]
 
     zeroth_set = _dict_to_bytes(zeroth_ifd, "0th", 0)
-    zeroth_length = (len(zeroth_set[0]) + exif_is * 12 + gps_is * 12 + 4 +
-                     len(zeroth_set[1]))
+    zeroth_length = (
+        len(zeroth_set[0]) + exif_is * 12 + gps_is * 12 + 4 + len(zeroth_set[1])
+    )
 
     if exif_is:
         exif_set = _dict_to_bytes(exif_ifd, "Exif", zeroth_length)
@@ -115,8 +122,7 @@ def dump(exif_dict_original):
     else:
         gps_pointer = b""
     if interop_is:
-        pointer_value = (TIFF_HEADER_LENGTH +
-                         zeroth_length + exif_length + gps_length)
+        pointer_value = TIFF_HEADER_LENGTH + zeroth_length + exif_length + gps_length
         pointer_str = struct.pack(">I", pointer_value)
         key = ExifIFD.InteroperabilityTag
         key_str = struct.pack(">H", key)
@@ -126,33 +132,46 @@ def dump(exif_dict_original):
     else:
         interop_pointer = b""
     if first_is:
-        pointer_value = (TIFF_HEADER_LENGTH + zeroth_length +
-                         exif_length + gps_length + interop_length)
+        pointer_value = (
+            TIFF_HEADER_LENGTH
+            + zeroth_length
+            + exif_length
+            + gps_length
+            + interop_length
+        )
         first_ifd_pointer = struct.pack(">L", pointer_value)
-        thumbnail_pointer = (pointer_value + len(first_set[0]) + 24 +
-                             4 + len(first_set[1]))
-        thumbnail_p_bytes = (b"\x02\x01\x00\x04\x00\x00\x00\x01" +
-                             struct.pack(">L", thumbnail_pointer))
-        thumbnail_length_bytes = (b"\x02\x02\x00\x04\x00\x00\x00\x01" +
-                                  struct.pack(">L", len(thumbnail)))
-        first_bytes = (first_set[0] + thumbnail_p_bytes +
-                       thumbnail_length_bytes + b"\x00\x00\x00\x00" +
-                       first_set[1] + thumbnail)
+        thumbnail_pointer = (
+            pointer_value + len(first_set[0]) + 24 + 4 + len(first_set[1])
+        )
+        thumbnail_p_bytes = b"\x02\x01\x00\x04\x00\x00\x00\x01" + struct.pack(
+            ">L", thumbnail_pointer
+        )
+        thumbnail_length_bytes = b"\x02\x02\x00\x04\x00\x00\x00\x01" + struct.pack(
+            ">L", len(thumbnail)
+        )
+        first_bytes = (
+            first_set[0]
+            + thumbnail_p_bytes
+            + thumbnail_length_bytes
+            + b"\x00\x00\x00\x00"
+            + first_set[1]
+            + thumbnail
+        )
     else:
         first_ifd_pointer = b"\x00\x00\x00\x00"
 
-    zeroth_bytes = (zeroth_set[0] + exif_pointer + gps_pointer +
-                    first_ifd_pointer + zeroth_set[1])
+    zeroth_bytes = (
+        zeroth_set[0] + exif_pointer + gps_pointer + first_ifd_pointer + zeroth_set[1]
+    )
     if exif_is:
         exif_bytes = exif_set[0] + interop_pointer + exif_set[1]
 
-    return (header + zeroth_bytes + exif_bytes + gps_bytes +
-            interop_bytes + first_bytes)
+    return header + zeroth_bytes + exif_bytes + gps_bytes + interop_bytes + first_bytes
 
 
 def _get_thumbnail(jpeg):
     segments = split_into_segments(jpeg)
-    while (b"\xff\xe0" <= segments[1][0:2] <= b"\xff\xef"):
+    while b"\xff\xe0" <= segments[1][0:2] <= b"\xff\xef":
         segments.pop(1)
     thumbnail = b"".join(segments)
     return thumbnail
@@ -161,24 +180,31 @@ def _get_thumbnail(jpeg):
 def _pack_byte(*args):
     return struct.pack("B" * len(args), *args)
 
+
 def _pack_signed_byte(*args):
     return struct.pack("b" * len(args), *args)
 
+
 def _pack_short(*args):
     return struct.pack(">" + "H" * len(args), *args)
 
+
 def _pack_signed_short(*args):
     return struct.pack(">" + "h" * len(args), *args)
 
+
 def _pack_long(*args):
     return struct.pack(">" + "L" * len(args), *args)
 
+
 def _pack_slong(*args):
     return struct.pack(">" + "l" * len(args), *args)
 
+
 def _pack_float(*args):
     return struct.pack(">" + "f" * len(args), *args)
 
+
 def _pack_double(*args):
     return struct.pack(">" + "d" * len(args), *args)
 
@@ -190,16 +216,14 @@ def _value_to_bytes(raw_value, value_type, offset):
     if value_type == TYPES.Byte:
         length = len(raw_value)
         if length <= 4:
-            value_str = (_pack_byte(*raw_value) +
-                            b"\x00" * (4 - length))
+            value_str = _pack_byte(*raw_value) + b"\x00" * (4 - length)
         else:
             value_str = struct.pack(">I", offset)
             four_bytes_over = _pack_byte(*raw_value)
     elif value_type == TYPES.Short:
         length = len(raw_value)
         if length <= 2:
-            value_str = (_pack_short(*raw_value) +
-                            b"\x00\x00" * (2 - length))
+            value_str = _pack_short(*raw_value) + b"\x00\x00" * (2 - length)
         else:
             value_str = struct.pack(">I", offset)
             four_bytes_over = _pack_short(*raw_value)
@@ -241,8 +265,7 @@ def _value_to_bytes(raw_value, value_type, offset):
             new_value = b""
             for n, val in enumerate(raw_value):
                 num, den = val
-                new_value += (struct.pack(">L", num) +
-                                struct.pack(">L", den))
+                new_value += struct.pack(">L", num) + struct.pack(">L", den)
         value_str = struct.pack(">I", offset)
         four_bytes_over = new_value
     elif value_type == TYPES.SRational:
@@ -255,8 +278,7 @@ def _value_to_bytes(raw_value, value_type, offset):
             new_value = b""
             for n, val in enumerate(raw_value):
                 num, den = val
-                new_value += (struct.pack(">l", num) +
-                                struct.pack(">l", den))
+                new_value += struct.pack(">l", num) + struct.pack(">l", den)
         value_str = struct.pack(">I", offset)
         four_bytes_over = new_value
     elif value_type == TYPES.Undefined:
@@ -272,19 +294,17 @@ def _value_to_bytes(raw_value, value_type, offset):
                 value_str = raw_value + b"\x00" * (4 - length)
             except TypeError:
                 raise ValueError("Got invalid type to convert.")
-    elif value_type == TYPES.SByte: # Signed Byte
+    elif value_type == TYPES.SByte:  # Signed Byte
         length = len(raw_value)
         if length <= 4:
-            value_str = (_pack_signed_byte(*raw_value) +
-                            b"\x00" * (4 - length))
+            value_str = _pack_signed_byte(*raw_value) + b"\x00" * (4 - length)
         else:
             value_str = struct.pack(">I", offset)
             four_bytes_over = _pack_signed_byte(*raw_value)
-    elif value_type == TYPES.SShort: # Signed Short
+    elif value_type == TYPES.SShort:  # Signed Short
         length = len(raw_value)
         if length <= 2:
-            value_str = (_pack_signed_short(*raw_value) +
-                            b"\x00\x00" * (2 - length))
+            value_str = _pack_signed_short(*raw_value) + b"\x00\x00" * (2 - length)
         else:
             value_str = struct.pack(">I", offset)
             four_bytes_over = _pack_signed_short(*raw_value)
@@ -295,7 +315,7 @@ def _value_to_bytes(raw_value, value_type, offset):
         else:
             value_str = struct.pack(">I", offset)
             four_bytes_over = _pack_float(*raw_value)
-    elif value_type == TYPES.DFloat: # Double
+    elif value_type == TYPES.DFloat:  # Double
         length = len(raw_value)
         value_str = struct.pack(">I", offset)
         four_bytes_over = _pack_double(*raw_value)
@@ -303,6 +323,7 @@ def _value_to_bytes(raw_value, value_type, offset):
     length_str = struct.pack(">I", length)
     return length_str, value_str, four_bytes_over
 
+
 def _dict_to_bytes(ifd_dict, ifd, ifd_offset):
     tag_count = len(ifd_dict)
     entry_header = struct.pack(">H", tag_count)
@@ -318,7 +339,10 @@ def _dict_to_bytes(ifd_dict, ifd, ifd_offset):
             continue
         elif (ifd == "Exif") and (key == ExifIFD.InteroperabilityTag):
             continue
-        elif (ifd == "1st") and (key in (ImageIFD.JPEGInterchangeFormat, ImageIFD.JPEGInterchangeFormatLength)):
+        elif (ifd == "1st") and (
+            key
+            in (ImageIFD.JPEGInterchangeFormat, ImageIFD.JPEGInterchangeFormatLength)
+        ):
             continue
 
         raw_value = ifd_dict[key]
@@ -332,13 +356,13 @@ def _dict_to_bytes(ifd_dict, ifd, ifd_offset):
         offset = TIFF_HEADER_LENGTH + entries_length + ifd_offset + len(values)
 
         try:
-            length_str, value_str, four_bytes_over = _value_to_bytes(raw_value,
-                                                                     value_type,
-                                                                     offset)
+            length_str, value_str, four_bytes_over = _value_to_bytes(
+                raw_value, value_type, offset
+            )
         except ValueError:
             raise ValueError(
-                '"dump" got wrong type of exif value.\n' +
-                '{0} in {1} IFD. Got as {2}.'.format(key, ifd, type(ifd_dict[key]))
+                '"dump" got wrong type of exif value.\n'
+                + "{0} in {1} IFD. Got as {2}.".format(key, ifd, type(ifd_dict[key]))
             )
 
         entries += key_str + type_str + length_str + value_str

openflexure_microscope/camera/piexif/_exif.py

@@ -14,314 +14,322 @@ class TYPES:
 
 
 TAGS = {
-    'Image': {11: {'name': 'ProcessingSoftware', 'type': TYPES.Ascii},
-               254: {'name': 'NewSubfileType', 'type': TYPES.Long},
-               255: {'name': 'SubfileType', 'type': TYPES.Short},
-               256: {'name': 'ImageWidth', 'type': TYPES.Long},
-               257: {'name': 'ImageLength', 'type': TYPES.Long},
-               258: {'name': 'BitsPerSample', 'type': TYPES.Short},
-               259: {'name': 'Compression', 'type': TYPES.Short},
-               262: {'name': 'PhotometricInterpretation', 'type': TYPES.Short},
-               263: {'name': 'Threshholding', 'type': TYPES.Short},
-               264: {'name': 'CellWidth', 'type': TYPES.Short},
-               265: {'name': 'CellLength', 'type': TYPES.Short},
-               266: {'name': 'FillOrder', 'type': TYPES.Short},
-               269: {'name': 'DocumentName', 'type': TYPES.Ascii},
-               270: {'name': 'ImageDescription', 'type': TYPES.Ascii},
-               271: {'name': 'Make', 'type': TYPES.Ascii},
-               272: {'name': 'Model', 'type': TYPES.Ascii},
-               273: {'name': 'StripOffsets', 'type': TYPES.Long},
-               274: {'name': 'Orientation', 'type': TYPES.Short},
-               277: {'name': 'SamplesPerPixel', 'type': TYPES.Short},
-               278: {'name': 'RowsPerStrip', 'type': TYPES.Long},
-               279: {'name': 'StripByteCounts', 'type': TYPES.Long},
-               282: {'name': 'XResolution', 'type': TYPES.Rational},
-               283: {'name': 'YResolution', 'type': TYPES.Rational},
-               284: {'name': 'PlanarConfiguration', 'type': TYPES.Short},
-               290: {'name': 'GrayResponseUnit', 'type': TYPES.Short},
-               291: {'name': 'GrayResponseCurve', 'type': TYPES.Short},
-               292: {'name': 'T4Options', 'type': TYPES.Long},
-               293: {'name': 'T6Options', 'type': TYPES.Long},
-               296: {'name': 'ResolutionUnit', 'type': TYPES.Short},
-               301: {'name': 'TransferFunction', 'type': TYPES.Short},
-               305: {'name': 'Software', 'type': TYPES.Ascii},
-               306: {'name': 'DateTime', 'type': TYPES.Ascii},
-               315: {'name': 'Artist', 'type': TYPES.Ascii},
-               316: {'name': 'HostComputer', 'type': TYPES.Ascii},
-               317: {'name': 'Predictor', 'type': TYPES.Short},
-               318: {'name': 'WhitePoint', 'type': TYPES.Rational},
-               319: {'name': 'PrimaryChromaticities', 'type': TYPES.Rational},
-               320: {'name': 'ColorMap', 'type': TYPES.Short},
-               321: {'name': 'HalftoneHints', 'type': TYPES.Short},
-               322: {'name': 'TileWidth', 'type': TYPES.Short},
-               323: {'name': 'TileLength', 'type': TYPES.Short},
-               324: {'name': 'TileOffsets', 'type': TYPES.Short},
-               325: {'name': 'TileByteCounts', 'type': TYPES.Short},
-               330: {'name': 'SubIFDs', 'type': TYPES.Long},
-               332: {'name': 'InkSet', 'type': TYPES.Short},
-               333: {'name': 'InkNames', 'type': TYPES.Ascii},
-               334: {'name': 'NumberOfInks', 'type': TYPES.Short},
-               336: {'name': 'DotRange', 'type': TYPES.Byte},
-               337: {'name': 'TargetPrinter', 'type': TYPES.Ascii},
-               338: {'name': 'ExtraSamples', 'type': TYPES.Short},
-               339: {'name': 'SampleFormat', 'type': TYPES.Short},
-               340: {'name': 'SMinSampleValue', 'type': TYPES.Short},
-               341: {'name': 'SMaxSampleValue', 'type': TYPES.Short},
-               342: {'name': 'TransferRange', 'type': TYPES.Short},
-               343: {'name': 'ClipPath', 'type': TYPES.Byte},
-               344: {'name': 'XClipPathUnits', 'type': TYPES.Long},
-               345: {'name': 'YClipPathUnits', 'type': TYPES.Long},
-               346: {'name': 'Indexed', 'type': TYPES.Short},
-               347: {'name': 'JPEGTables', 'type': TYPES.Undefined},
-               351: {'name': 'OPIProxy', 'type': TYPES.Short},
-               512: {'name': 'JPEGProc', 'type': TYPES.Long},
-               513: {'name': 'JPEGInterchangeFormat', 'type': TYPES.Long},
-               514: {'name': 'JPEGInterchangeFormatLength', 'type': TYPES.Long},
-               515: {'name': 'JPEGRestartInterval', 'type': TYPES.Short},
-               517: {'name': 'JPEGLosslessPredictors', 'type': TYPES.Short},
-               518: {'name': 'JPEGPointTransforms', 'type': TYPES.Short},
-               519: {'name': 'JPEGQTables', 'type': TYPES.Long},
-               520: {'name': 'JPEGDCTables', 'type': TYPES.Long},
-               521: {'name': 'JPEGACTables', 'type': TYPES.Long},
-               529: {'name': 'YCbCrCoefficients', 'type': TYPES.Rational},
-               530: {'name': 'YCbCrSubSampling', 'type': TYPES.Short},
-               531: {'name': 'YCbCrPositioning', 'type': TYPES.Short},
-               532: {'name': 'ReferenceBlackWhite', 'type': TYPES.Rational},
-               700: {'name': 'XMLPacket', 'type': TYPES.Byte},
-               18246: {'name': 'Rating', 'type': TYPES.Short},
-               18249: {'name': 'RatingPercent', 'type': TYPES.Short},
-               32781: {'name': 'ImageID', 'type': TYPES.Ascii},
-               33421: {'name': 'CFARepeatPatternDim', 'type': TYPES.Short},
-               33422: {'name': 'CFAPattern', 'type': TYPES.Byte},
-               33423: {'name': 'BatteryLevel', 'type': TYPES.Rational},
-               33432: {'name': 'Copyright', 'type': TYPES.Ascii},
-               33434: {'name': 'ExposureTime', 'type': TYPES.Rational},
-               34377: {'name': 'ImageResources', 'type': TYPES.Byte},
-               34665: {'name': 'ExifTag', 'type': TYPES.Long},
-               34675: {'name': 'InterColorProfile', 'type': TYPES.Undefined},
-               34853: {'name': 'GPSTag', 'type': TYPES.Long},
-               34857: {'name': 'Interlace', 'type': TYPES.Short},
-               34858: {'name': 'TimeZoneOffset', 'type': TYPES.Long},
-               34859: {'name': 'SelfTimerMode', 'type': TYPES.Short},
-               37387: {'name': 'FlashEnergy', 'type': TYPES.Rational},
-               37388: {'name': 'SpatialFrequencyResponse', 'type': TYPES.Undefined},
-               37389: {'name': 'Noise', 'type': TYPES.Undefined},
-               37390: {'name': 'FocalPlaneXResolution', 'type': TYPES.Rational},
-               37391: {'name': 'FocalPlaneYResolution', 'type': TYPES.Rational},
-               37392: {'name': 'FocalPlaneResolutionUnit', 'type': TYPES.Short},
-               37393: {'name': 'ImageNumber', 'type': TYPES.Long},
-               37394: {'name': 'SecurityClassification', 'type': TYPES.Ascii},
-               37395: {'name': 'ImageHistory', 'type': TYPES.Ascii},
-               37397: {'name': 'ExposureIndex', 'type': TYPES.Rational},
-               37398: {'name': 'TIFFEPStandardID', 'type': TYPES.Byte},
-               37399: {'name': 'SensingMethod', 'type': TYPES.Short},
-               40091: {'name': 'XPTitle', 'type': TYPES.Byte},
-               40092: {'name': 'XPComment', 'type': TYPES.Byte},
-               40093: {'name': 'XPAuthor', 'type': TYPES.Byte},
-               40094: {'name': 'XPKeywords', 'type': TYPES.Byte},
-               40095: {'name': 'XPSubject', 'type': TYPES.Byte},
-               50341: {'name': 'PrintImageMatching', 'type': TYPES.Undefined},
-               50706: {'name': 'DNGVersion', 'type': TYPES.Byte},
-               50707: {'name': 'DNGBackwardVersion', 'type': TYPES.Byte},
-               50708: {'name': 'UniqueCameraModel', 'type': TYPES.Ascii},
-               50709: {'name': 'LocalizedCameraModel', 'type': TYPES.Byte},
-               50710: {'name': 'CFAPlaneColor', 'type': TYPES.Byte},
-               50711: {'name': 'CFALayout', 'type': TYPES.Short},
-               50712: {'name': 'LinearizationTable', 'type': TYPES.Short},
-               50713: {'name': 'BlackLevelRepeatDim', 'type': TYPES.Short},
-               50714: {'name': 'BlackLevel', 'type': TYPES.Rational},
-               50715: {'name': 'BlackLevelDeltaH', 'type': TYPES.SRational},
-               50716: {'name': 'BlackLevelDeltaV', 'type': TYPES.SRational},
-               50717: {'name': 'WhiteLevel', 'type': TYPES.Short},
-               50718: {'name': 'DefaultScale', 'type': TYPES.Rational},
-               50719: {'name': 'DefaultCropOrigin', 'type': TYPES.Short},
-               50720: {'name': 'DefaultCropSize', 'type': TYPES.Short},
-               50721: {'name': 'ColorMatrix1', 'type': TYPES.SRational},
-               50722: {'name': 'ColorMatrix2', 'type': TYPES.SRational},
-               50723: {'name': 'CameraCalibration1', 'type': TYPES.SRational},
-               50724: {'name': 'CameraCalibration2', 'type': TYPES.SRational},
-               50725: {'name': 'ReductionMatrix1', 'type': TYPES.SRational},
-               50726: {'name': 'ReductionMatrix2', 'type': TYPES.SRational},
-               50727: {'name': 'AnalogBalance', 'type': TYPES.Rational},
-               50728: {'name': 'AsShotNeutral', 'type': TYPES.Short},
-               50729: {'name': 'AsShotWhiteXY', 'type': TYPES.Rational},
-               50730: {'name': 'BaselineExposure', 'type': TYPES.SRational},
-               50731: {'name': 'BaselineNoise', 'type': TYPES.Rational},
-               50732: {'name': 'BaselineSharpness', 'type': TYPES.Rational},
-               50733: {'name': 'BayerGreenSplit', 'type': TYPES.Long},
-               50734: {'name': 'LinearResponseLimit', 'type': TYPES.Rational},
-               50735: {'name': 'CameraSerialNumber', 'type': TYPES.Ascii},
-               50736: {'name': 'LensInfo', 'type': TYPES.Rational},
-               50737: {'name': 'ChromaBlurRadius', 'type': TYPES.Rational},
-               50738: {'name': 'AntiAliasStrength', 'type': TYPES.Rational},
-               50739: {'name': 'ShadowScale', 'type': TYPES.SRational},
-               50740: {'name': 'DNGPrivateData', 'type': TYPES.Byte},
-               50741: {'name': 'MakerNoteSafety', 'type': TYPES.Short},
-               50778: {'name': 'CalibrationIlluminant1', 'type': TYPES.Short},
-               50779: {'name': 'CalibrationIlluminant2', 'type': TYPES.Short},
-               50780: {'name': 'BestQualityScale', 'type': TYPES.Rational},
-               50781: {'name': 'RawDataUniqueID', 'type': TYPES.Byte},
-               50827: {'name': 'OriginalRawFileName', 'type': TYPES.Byte},
-               50828: {'name': 'OriginalRawFileData', 'type': TYPES.Undefined},
-               50829: {'name': 'ActiveArea', 'type': TYPES.Short},
-               50830: {'name': 'MaskedAreas', 'type': TYPES.Short},
-               50831: {'name': 'AsShotICCProfile', 'type': TYPES.Undefined},
-               50832: {'name': 'AsShotPreProfileMatrix', 'type': TYPES.SRational},
-               50833: {'name': 'CurrentICCProfile', 'type': TYPES.Undefined},
-               50834: {'name': 'CurrentPreProfileMatrix', 'type': TYPES.SRational},
-               50879: {'name': 'ColorimetricReference', 'type': TYPES.Short},
-               50931: {'name': 'CameraCalibrationSignature', 'type': TYPES.Byte},
-               50932: {'name': 'ProfileCalibrationSignature', 'type': TYPES.Byte},
-               50934: {'name': 'AsShotProfileName', 'type': TYPES.Byte},
-               50935: {'name': 'NoiseReductionApplied', 'type': TYPES.Rational},
-               50936: {'name': 'ProfileName', 'type': TYPES.Byte},
-               50937: {'name': 'ProfileHueSatMapDims', 'type': TYPES.Long},
-               50938: {'name': 'ProfileHueSatMapData1', 'type': TYPES.Float},
-               50939: {'name': 'ProfileHueSatMapData2', 'type': TYPES.Float},
-               50940: {'name': 'ProfileToneCurve', 'type': TYPES.Float},
-               50941: {'name': 'ProfileEmbedPolicy', 'type': TYPES.Long},
-               50942: {'name': 'ProfileCopyright', 'type': TYPES.Byte},
-               50964: {'name': 'ForwardMatrix1', 'type': TYPES.SRational},
-               50965: {'name': 'ForwardMatrix2', 'type': TYPES.SRational},
-               50966: {'name': 'PreviewApplicationName', 'type': TYPES.Byte},
-               50967: {'name': 'PreviewApplicationVersion', 'type': TYPES.Byte},
-               50968: {'name': 'PreviewSettingsName', 'type': TYPES.Byte},
-               50969: {'name': 'PreviewSettingsDigest', 'type': TYPES.Byte},
-               50970: {'name': 'PreviewColorSpace', 'type': TYPES.Long},
-               50971: {'name': 'PreviewDateTime', 'type': TYPES.Ascii},
-               50972: {'name': 'RawImageDigest', 'type': TYPES.Undefined},
-               50973: {'name': 'OriginalRawFileDigest', 'type': TYPES.Undefined},
-               50974: {'name': 'SubTileBlockSize', 'type': TYPES.Long},
-               50975: {'name': 'RowInterleaveFactor', 'type': TYPES.Long},
-               50981: {'name': 'ProfileLookTableDims', 'type': TYPES.Long},
-               50982: {'name': 'ProfileLookTableData', 'type': TYPES.Float},
-               51008: {'name': 'OpcodeList1', 'type': TYPES.Undefined},
-               51009: {'name': 'OpcodeList2', 'type': TYPES.Undefined},
-               51022: {'name': 'OpcodeList3', 'type': TYPES.Undefined},
-               60606: {'name': 'ZZZTestSlong1', 'type': TYPES.SLong},
-               60607: {'name': 'ZZZTestSlong2', 'type': TYPES.SLong},
-               60608: {'name': 'ZZZTestSByte', 'type': TYPES.SByte},
-               60609: {'name': 'ZZZTestSShort', 'type': TYPES.SShort},
-               60610: {'name': 'ZZZTestDFloat', 'type': TYPES.DFloat},},
-    'Exif': {33434: {'name': 'ExposureTime', 'type': TYPES.Rational},
-             33437: {'name': 'FNumber', 'type': TYPES.Rational},
-             34850: {'name': 'ExposureProgram', 'type': TYPES.Short},
-             34852: {'name': 'SpectralSensitivity', 'type': TYPES.Ascii},
-             34855: {'name': 'ISOSpeedRatings', 'type': TYPES.Short},
-             34856: {'name': 'OECF', 'type': TYPES.Undefined},
-             34864: {'name': 'SensitivityType', 'type': TYPES.Short},
-             34865: {'name': 'StandardOutputSensitivity', 'type': TYPES.Long},
-             34866: {'name': 'RecommendedExposureIndex', 'type': TYPES.Long},
-             34867: {'name': 'ISOSpeed', 'type': TYPES.Long},
-             34868: {'name': 'ISOSpeedLatitudeyyy', 'type': TYPES.Long},
-             34869: {'name': 'ISOSpeedLatitudezzz', 'type': TYPES.Long},
-             36864: {'name': 'ExifVersion', 'type': TYPES.Undefined},
-             36867: {'name': 'DateTimeOriginal', 'type': TYPES.Ascii},
-             36868: {'name': 'DateTimeDigitized', 'type': TYPES.Ascii},
-             36880: {'name': 'OffsetTime', 'type': TYPES.Ascii},
-             36881: {'name': 'OffsetTimeOriginal', 'type': TYPES.Ascii},
-             36882: {'name': 'OffsetTimeDigitized', 'type': TYPES.Ascii},
-             37121: {'name': 'ComponentsConfiguration', 'type': TYPES.Undefined},
-             37122: {'name': 'CompressedBitsPerPixel', 'type': TYPES.Rational},
-             37377: {'name': 'ShutterSpeedValue', 'type': TYPES.SRational},
-             37378: {'name': 'ApertureValue', 'type': TYPES.Rational},
-             37379: {'name': 'BrightnessValue', 'type': TYPES.SRational},
-             37380: {'name': 'ExposureBiasValue', 'type': TYPES.SRational},
-             37381: {'name': 'MaxApertureValue', 'type': TYPES.Rational},
-             37382: {'name': 'SubjectDistance', 'type': TYPES.Rational},
-             37383: {'name': 'MeteringMode', 'type': TYPES.Short},
-             37384: {'name': 'LightSource', 'type': TYPES.Short},
-             37385: {'name': 'Flash', 'type': TYPES.Short},
-             37386: {'name': 'FocalLength', 'type': TYPES.Rational},
-             37396: {'name': 'SubjectArea', 'type': TYPES.Short},
-             37500: {'name': 'MakerNote', 'type': TYPES.Undefined},
-             37510: {'name': 'UserComment', 'type': TYPES.Undefined},
-             37520: {'name': 'SubSecTime', 'type': TYPES.Ascii},
-             37521: {'name': 'SubSecTimeOriginal', 'type': TYPES.Ascii},
-             37522: {'name': 'SubSecTimeDigitized', 'type': TYPES.Ascii},
-             37888: {'name': 'Temperature', 'type': TYPES.SRational},
-             37889: {'name': 'Humidity', 'type': TYPES.Rational},
-             37890: {'name': 'Pressure', 'type': TYPES.Rational},
-             37891: {'name': 'WaterDepth', 'type': TYPES.SRational},
-             37892: {'name': 'Acceleration', 'type': TYPES.Rational},
-             37893: {'name': 'CameraElevationAngle', 'type': TYPES.SRational},
-             40960: {'name': 'FlashpixVersion', 'type': TYPES.Undefined},
-             40961: {'name': 'ColorSpace', 'type': TYPES.Short},
-             40962: {'name': 'PixelXDimension', 'type': TYPES.Long},
-             40963: {'name': 'PixelYDimension', 'type': TYPES.Long},
-             40964: {'name': 'RelatedSoundFile', 'type': TYPES.Ascii},
-             40965: {'name': 'InteroperabilityTag', 'type': TYPES.Long},
-             41483: {'name': 'FlashEnergy', 'type': TYPES.Rational},
-             41484: {'name': 'SpatialFrequencyResponse', 'type': TYPES.Undefined},
-             41486: {'name': 'FocalPlaneXResolution', 'type': TYPES.Rational},
-             41487: {'name': 'FocalPlaneYResolution', 'type': TYPES.Rational},
-             41488: {'name': 'FocalPlaneResolutionUnit', 'type': TYPES.Short},
-             41492: {'name': 'SubjectLocation', 'type': TYPES.Short},
-             41493: {'name': 'ExposureIndex', 'type': TYPES.Rational},
-             41495: {'name': 'SensingMethod', 'type': TYPES.Short},
-             41728: {'name': 'FileSource', 'type': TYPES.Undefined},
-             41729: {'name': 'SceneType', 'type': TYPES.Undefined},
-             41730: {'name': 'CFAPattern', 'type': TYPES.Undefined},
-             41985: {'name': 'CustomRendered', 'type': TYPES.Short},
-             41986: {'name': 'ExposureMode', 'type': TYPES.Short},
-             41987: {'name': 'WhiteBalance', 'type': TYPES.Short},
-             41988: {'name': 'DigitalZoomRatio', 'type': TYPES.Rational},
-             41989: {'name': 'FocalLengthIn35mmFilm', 'type': TYPES.Short},
-             41990: {'name': 'SceneCaptureType', 'type': TYPES.Short},
-             41991: {'name': 'GainControl', 'type': TYPES.Short},
-             41992: {'name': 'Contrast', 'type': TYPES.Short},
-             41993: {'name': 'Saturation', 'type': TYPES.Short},
-             41994: {'name': 'Sharpness', 'type': TYPES.Short},
-             41995: {'name': 'DeviceSettingDescription', 'type': TYPES.Undefined},
-             41996: {'name': 'SubjectDistanceRange', 'type': TYPES.Short},
-             42016: {'name': 'ImageUniqueID', 'type': TYPES.Ascii},
-             42032: {'name': 'CameraOwnerName', 'type': TYPES.Ascii},
-             42033: {'name': 'BodySerialNumber', 'type': TYPES.Ascii},
-             42034: {'name': 'LensSpecification', 'type': TYPES.Rational},
-             42035: {'name': 'LensMake', 'type': TYPES.Ascii},
-             42036: {'name': 'LensModel', 'type': TYPES.Ascii},
-             42037: {'name': 'LensSerialNumber', 'type': TYPES.Ascii},
-             42240: {'name': 'Gamma', 'type': TYPES.Rational}},
-    'GPS': {0: {'name': 'GPSVersionID', 'type': TYPES.Byte},
-                1: {'name': 'GPSLatitudeRef', 'type': TYPES.Ascii},
-                2: {'name': 'GPSLatitude', 'type': TYPES.Rational},
-                3: {'name': 'GPSLongitudeRef', 'type': TYPES.Ascii},
-                4: {'name': 'GPSLongitude', 'type': TYPES.Rational},
-                5: {'name': 'GPSAltitudeRef', 'type': TYPES.Byte},
-                6: {'name': 'GPSAltitude', 'type': TYPES.Rational},
-                7: {'name': 'GPSTimeStamp', 'type': TYPES.Rational},
-                8: {'name': 'GPSSatellites', 'type': TYPES.Ascii},
-                9: {'name': 'GPSStatus', 'type': TYPES.Ascii},
-                10: {'name': 'GPSMeasureMode', 'type': TYPES.Ascii},
-                11: {'name': 'GPSDOP', 'type': TYPES.Rational},
-                12: {'name': 'GPSSpeedRef', 'type': TYPES.Ascii},
-                13: {'name': 'GPSSpeed', 'type': TYPES.Rational},
-                14: {'name': 'GPSTrackRef', 'type': TYPES.Ascii},
-                15: {'name': 'GPSTrack', 'type': TYPES.Rational},
-                16: {'name': 'GPSImgDirectionRef', 'type': TYPES.Ascii},
-                17: {'name': 'GPSImgDirection', 'type': TYPES.Rational},
-                18: {'name': 'GPSMapDatum', 'type': TYPES.Ascii},
-                19: {'name': 'GPSDestLatitudeRef', 'type': TYPES.Ascii},
-                20: {'name': 'GPSDestLatitude', 'type': TYPES.Rational},
-                21: {'name': 'GPSDestLongitudeRef', 'type': TYPES.Ascii},
-                22: {'name': 'GPSDestLongitude', 'type': TYPES.Rational},
-                23: {'name': 'GPSDestBearingRef', 'type': TYPES.Ascii},
-                24: {'name': 'GPSDestBearing', 'type': TYPES.Rational},
-                25: {'name': 'GPSDestDistanceRef', 'type': TYPES.Ascii},
-                26: {'name': 'GPSDestDistance', 'type': TYPES.Rational},
-                27: {'name': 'GPSProcessingMethod', 'type': TYPES.Undefined},
-                28: {'name': 'GPSAreaInformation', 'type': TYPES.Undefined},
-                29: {'name': 'GPSDateStamp', 'type': TYPES.Ascii},
-                30: {'name': 'GPSDifferential', 'type': TYPES.Short},
-                31: {'name': 'GPSHPositioningError', 'type': TYPES.Rational}},
-    'Interop': {1: {'name': 'InteroperabilityIndex', 'type': TYPES.Ascii}},
+    "Image": {
+        11: {"name": "ProcessingSoftware", "type": TYPES.Ascii},
+        254: {"name": "NewSubfileType", "type": TYPES.Long},
+        255: {"name": "SubfileType", "type": TYPES.Short},
+        256: {"name": "ImageWidth", "type": TYPES.Long},
+        257: {"name": "ImageLength", "type": TYPES.Long},
+        258: {"name": "BitsPerSample", "type": TYPES.Short},
+        259: {"name": "Compression", "type": TYPES.Short},
+        262: {"name": "PhotometricInterpretation", "type": TYPES.Short},
+        263: {"name": "Threshholding", "type": TYPES.Short},
+        264: {"name": "CellWidth", "type": TYPES.Short},
+        265: {"name": "CellLength", "type": TYPES.Short},
+        266: {"name": "FillOrder", "type": TYPES.Short},
+        269: {"name": "DocumentName", "type": TYPES.Ascii},
+        270: {"name": "ImageDescription", "type": TYPES.Ascii},
+        271: {"name": "Make", "type": TYPES.Ascii},
+        272: {"name": "Model", "type": TYPES.Ascii},
+        273: {"name": "StripOffsets", "type": TYPES.Long},
+        274: {"name": "Orientation", "type": TYPES.Short},
+        277: {"name": "SamplesPerPixel", "type": TYPES.Short},
+        278: {"name": "RowsPerStrip", "type": TYPES.Long},
+        279: {"name": "StripByteCounts", "type": TYPES.Long},
+        282: {"name": "XResolution", "type": TYPES.Rational},
+        283: {"name": "YResolution", "type": TYPES.Rational},
+        284: {"name": "PlanarConfiguration", "type": TYPES.Short},
+        290: {"name": "GrayResponseUnit", "type": TYPES.Short},
+        291: {"name": "GrayResponseCurve", "type": TYPES.Short},
+        292: {"name": "T4Options", "type": TYPES.Long},
+        293: {"name": "T6Options", "type": TYPES.Long},
+        296: {"name": "ResolutionUnit", "type": TYPES.Short},
+        301: {"name": "TransferFunction", "type": TYPES.Short},
+        305: {"name": "Software", "type": TYPES.Ascii},
+        306: {"name": "DateTime", "type": TYPES.Ascii},
+        315: {"name": "Artist", "type": TYPES.Ascii},
+        316: {"name": "HostComputer", "type": TYPES.Ascii},
+        317: {"name": "Predictor", "type": TYPES.Short},
+        318: {"name": "WhitePoint", "type": TYPES.Rational},
+        319: {"name": "PrimaryChromaticities", "type": TYPES.Rational},
+        320: {"name": "ColorMap", "type": TYPES.Short},
+        321: {"name": "HalftoneHints", "type": TYPES.Short},
+        322: {"name": "TileWidth", "type": TYPES.Short},
+        323: {"name": "TileLength", "type": TYPES.Short},
+        324: {"name": "TileOffsets", "type": TYPES.Short},
+        325: {"name": "TileByteCounts", "type": TYPES.Short},
+        330: {"name": "SubIFDs", "type": TYPES.Long},
+        332: {"name": "InkSet", "type": TYPES.Short},
+        333: {"name": "InkNames", "type": TYPES.Ascii},
+        334: {"name": "NumberOfInks", "type": TYPES.Short},
+        336: {"name": "DotRange", "type": TYPES.Byte},
+        337: {"name": "TargetPrinter", "type": TYPES.Ascii},
+        338: {"name": "ExtraSamples", "type": TYPES.Short},
+        339: {"name": "SampleFormat", "type": TYPES.Short},
+        340: {"name": "SMinSampleValue", "type": TYPES.Short},
+        341: {"name": "SMaxSampleValue", "type": TYPES.Short},
+        342: {"name": "TransferRange", "type": TYPES.Short},
+        343: {"name": "ClipPath", "type": TYPES.Byte},
+        344: {"name": "XClipPathUnits", "type": TYPES.Long},
+        345: {"name": "YClipPathUnits", "type": TYPES.Long},
+        346: {"name": "Indexed", "type": TYPES.Short},
+        347: {"name": "JPEGTables", "type": TYPES.Undefined},
+        351: {"name": "OPIProxy", "type": TYPES.Short},
+        512: {"name": "JPEGProc", "type": TYPES.Long},
+        513: {"name": "JPEGInterchangeFormat", "type": TYPES.Long},
+        514: {"name": "JPEGInterchangeFormatLength", "type": TYPES.Long},
+        515: {"name": "JPEGRestartInterval", "type": TYPES.Short},
+        517: {"name": "JPEGLosslessPredictors", "type": TYPES.Short},
+        518: {"name": "JPEGPointTransforms", "type": TYPES.Short},
+        519: {"name": "JPEGQTables", "type": TYPES.Long},
+        520: {"name": "JPEGDCTables", "type": TYPES.Long},
+        521: {"name": "JPEGACTables", "type": TYPES.Long},
+        529: {"name": "YCbCrCoefficients", "type": TYPES.Rational},
+        530: {"name": "YCbCrSubSampling", "type": TYPES.Short},
+        531: {"name": "YCbCrPositioning", "type": TYPES.Short},
+        532: {"name": "ReferenceBlackWhite", "type": TYPES.Rational},
+        700: {"name": "XMLPacket", "type": TYPES.Byte},
+        18246: {"name": "Rating", "type": TYPES.Short},
+        18249: {"name": "RatingPercent", "type": TYPES.Short},
+        32781: {"name": "ImageID", "type": TYPES.Ascii},
+        33421: {"name": "CFARepeatPatternDim", "type": TYPES.Short},
+        33422: {"name": "CFAPattern", "type": TYPES.Byte},
+        33423: {"name": "BatteryLevel", "type": TYPES.Rational},
+        33432: {"name": "Copyright", "type": TYPES.Ascii},
+        33434: {"name": "ExposureTime", "type": TYPES.Rational},
+        34377: {"name": "ImageResources", "type": TYPES.Byte},
+        34665: {"name": "ExifTag", "type": TYPES.Long},
+        34675: {"name": "InterColorProfile", "type": TYPES.Undefined},
+        34853: {"name": "GPSTag", "type": TYPES.Long},
+        34857: {"name": "Interlace", "type": TYPES.Short},
+        34858: {"name": "TimeZoneOffset", "type": TYPES.Long},
+        34859: {"name": "SelfTimerMode", "type": TYPES.Short},
+        37387: {"name": "FlashEnergy", "type": TYPES.Rational},
+        37388: {"name": "SpatialFrequencyResponse", "type": TYPES.Undefined},
+        37389: {"name": "Noise", "type": TYPES.Undefined},
+        37390: {"name": "FocalPlaneXResolution", "type": TYPES.Rational},
+        37391: {"name": "FocalPlaneYResolution", "type": TYPES.Rational},
+        37392: {"name": "FocalPlaneResolutionUnit", "type": TYPES.Short},
+        37393: {"name": "ImageNumber", "type": TYPES.Long},
+        37394: {"name": "SecurityClassification", "type": TYPES.Ascii},
+        37395: {"name": "ImageHistory", "type": TYPES.Ascii},
+        37397: {"name": "ExposureIndex", "type": TYPES.Rational},
+        37398: {"name": "TIFFEPStandardID", "type": TYPES.Byte},
+        37399: {"name": "SensingMethod", "type": TYPES.Short},
+        40091: {"name": "XPTitle", "type": TYPES.Byte},
+        40092: {"name": "XPComment", "type": TYPES.Byte},
+        40093: {"name": "XPAuthor", "type": TYPES.Byte},
+        40094: {"name": "XPKeywords", "type": TYPES.Byte},
+        40095: {"name": "XPSubject", "type": TYPES.Byte},
+        50341: {"name": "PrintImageMatching", "type": TYPES.Undefined},
+        50706: {"name": "DNGVersion", "type": TYPES.Byte},
+        50707: {"name": "DNGBackwardVersion", "type": TYPES.Byte},
+        50708: {"name": "UniqueCameraModel", "type": TYPES.Ascii},
+        50709: {"name": "LocalizedCameraModel", "type": TYPES.Byte},
+        50710: {"name": "CFAPlaneColor", "type": TYPES.Byte},
+        50711: {"name": "CFALayout", "type": TYPES.Short},
+        50712: {"name": "LinearizationTable", "type": TYPES.Short},
+        50713: {"name": "BlackLevelRepeatDim", "type": TYPES.Short},
+        50714: {"name": "BlackLevel", "type": TYPES.Rational},
+        50715: {"name": "BlackLevelDeltaH", "type": TYPES.SRational},
+        50716: {"name": "BlackLevelDeltaV", "type": TYPES.SRational},
+        50717: {"name": "WhiteLevel", "type": TYPES.Short},
+        50718: {"name": "DefaultScale", "type": TYPES.Rational},
+        50719: {"name": "DefaultCropOrigin", "type": TYPES.Short},
+        50720: {"name": "DefaultCropSize", "type": TYPES.Short},
+        50721: {"name": "ColorMatrix1", "type": TYPES.SRational},
+        50722: {"name": "ColorMatrix2", "type": TYPES.SRational},
+        50723: {"name": "CameraCalibration1", "type": TYPES.SRational},
+        50724: {"name": "CameraCalibration2", "type": TYPES.SRational},
+        50725: {"name": "ReductionMatrix1", "type": TYPES.SRational},
+        50726: {"name": "ReductionMatrix2", "type": TYPES.SRational},
+        50727: {"name": "AnalogBalance", "type": TYPES.Rational},
+        50728: {"name": "AsShotNeutral", "type": TYPES.Short},
+        50729: {"name": "AsShotWhiteXY", "type": TYPES.Rational},
+        50730: {"name": "BaselineExposure", "type": TYPES.SRational},
+        50731: {"name": "BaselineNoise", "type": TYPES.Rational},
+        50732: {"name": "BaselineSharpness", "type": TYPES.Rational},
+        50733: {"name": "BayerGreenSplit", "type": TYPES.Long},
+        50734: {"name": "LinearResponseLimit", "type": TYPES.Rational},
+        50735: {"name": "CameraSerialNumber", "type": TYPES.Ascii},
+        50736: {"name": "LensInfo", "type": TYPES.Rational},
+        50737: {"name": "ChromaBlurRadius", "type": TYPES.Rational},
+        50738: {"name": "AntiAliasStrength", "type": TYPES.Rational},
+        50739: {"name": "ShadowScale", "type": TYPES.SRational},
+        50740: {"name": "DNGPrivateData", "type": TYPES.Byte},
+        50741: {"name": "MakerNoteSafety", "type": TYPES.Short},
+        50778: {"name": "CalibrationIlluminant1", "type": TYPES.Short},
+        50779: {"name": "CalibrationIlluminant2", "type": TYPES.Short},
+        50780: {"name": "BestQualityScale", "type": TYPES.Rational},
+        50781: {"name": "RawDataUniqueID", "type": TYPES.Byte},
+        50827: {"name": "OriginalRawFileName", "type": TYPES.Byte},
+        50828: {"name": "OriginalRawFileData", "type": TYPES.Undefined},
+        50829: {"name": "ActiveArea", "type": TYPES.Short},
+        50830: {"name": "MaskedAreas", "type": TYPES.Short},
+        50831: {"name": "AsShotICCProfile", "type": TYPES.Undefined},
+        50832: {"name": "AsShotPreProfileMatrix", "type": TYPES.SRational},
+        50833: {"name": "CurrentICCProfile", "type": TYPES.Undefined},
+        50834: {"name": "CurrentPreProfileMatrix", "type": TYPES.SRational},
+        50879: {"name": "ColorimetricReference", "type": TYPES.Short},
+        50931: {"name": "CameraCalibrationSignature", "type": TYPES.Byte},
+        50932: {"name": "ProfileCalibrationSignature", "type": TYPES.Byte},
+        50934: {"name": "AsShotProfileName", "type": TYPES.Byte},
+        50935: {"name": "NoiseReductionApplied", "type": TYPES.Rational},
+        50936: {"name": "ProfileName", "type": TYPES.Byte},
+        50937: {"name": "ProfileHueSatMapDims", "type": TYPES.Long},
+        50938: {"name": "ProfileHueSatMapData1", "type": TYPES.Float},
+        50939: {"name": "ProfileHueSatMapData2", "type": TYPES.Float},
+        50940: {"name": "ProfileToneCurve", "type": TYPES.Float},
+        50941: {"name": "ProfileEmbedPolicy", "type": TYPES.Long},
+        50942: {"name": "ProfileCopyright", "type": TYPES.Byte},
+        50964: {"name": "ForwardMatrix1", "type": TYPES.SRational},
+        50965: {"name": "ForwardMatrix2", "type": TYPES.SRational},
+        50966: {"name": "PreviewApplicationName", "type": TYPES.Byte},
+        50967: {"name": "PreviewApplicationVersion", "type": TYPES.Byte},
+        50968: {"name": "PreviewSettingsName", "type": TYPES.Byte},
+        50969: {"name": "PreviewSettingsDigest", "type": TYPES.Byte},
+        50970: {"name": "PreviewColorSpace", "type": TYPES.Long},
+        50971: {"name": "PreviewDateTime", "type": TYPES.Ascii},
+        50972: {"name": "RawImageDigest", "type": TYPES.Undefined},
+        50973: {"name": "OriginalRawFileDigest", "type": TYPES.Undefined},
+        50974: {"name": "SubTileBlockSize", "type": TYPES.Long},
+        50975: {"name": "RowInterleaveFactor", "type": TYPES.Long},
+        50981: {"name": "ProfileLookTableDims", "type": TYPES.Long},
+        50982: {"name": "ProfileLookTableData", "type": TYPES.Float},
+        51008: {"name": "OpcodeList1", "type": TYPES.Undefined},
+        51009: {"name": "OpcodeList2", "type": TYPES.Undefined},
+        51022: {"name": "OpcodeList3", "type": TYPES.Undefined},
+        60606: {"name": "ZZZTestSlong1", "type": TYPES.SLong},
+        60607: {"name": "ZZZTestSlong2", "type": TYPES.SLong},
+        60608: {"name": "ZZZTestSByte", "type": TYPES.SByte},
+        60609: {"name": "ZZZTestSShort", "type": TYPES.SShort},
+        60610: {"name": "ZZZTestDFloat", "type": TYPES.DFloat},
+    },
+    "Exif": {
+        33434: {"name": "ExposureTime", "type": TYPES.Rational},
+        33437: {"name": "FNumber", "type": TYPES.Rational},
+        34850: {"name": "ExposureProgram", "type": TYPES.Short},
+        34852: {"name": "SpectralSensitivity", "type": TYPES.Ascii},
+        34855: {"name": "ISOSpeedRatings", "type": TYPES.Short},
+        34856: {"name": "OECF", "type": TYPES.Undefined},
+        34864: {"name": "SensitivityType", "type": TYPES.Short},
+        34865: {"name": "StandardOutputSensitivity", "type": TYPES.Long},
+        34866: {"name": "RecommendedExposureIndex", "type": TYPES.Long},
+        34867: {"name": "ISOSpeed", "type": TYPES.Long},
+        34868: {"name": "ISOSpeedLatitudeyyy", "type": TYPES.Long},
+        34869: {"name": "ISOSpeedLatitudezzz", "type": TYPES.Long},
+        36864: {"name": "ExifVersion", "type": TYPES.Undefined},
+        36867: {"name": "DateTimeOriginal", "type": TYPES.Ascii},
+        36868: {"name": "DateTimeDigitized", "type": TYPES.Ascii},
+        36880: {"name": "OffsetTime", "type": TYPES.Ascii},
+        36881: {"name": "OffsetTimeOriginal", "type": TYPES.Ascii},
+        36882: {"name": "OffsetTimeDigitized", "type": TYPES.Ascii},
+        37121: {"name": "ComponentsConfiguration", "type": TYPES.Undefined},
+        37122: {"name": "CompressedBitsPerPixel", "type": TYPES.Rational},
+        37377: {"name": "ShutterSpeedValue", "type": TYPES.SRational},
+        37378: {"name": "ApertureValue", "type": TYPES.Rational},
+        37379: {"name": "BrightnessValue", "type": TYPES.SRational},
+        37380: {"name": "ExposureBiasValue", "type": TYPES.SRational},
+        37381: {"name": "MaxApertureValue", "type": TYPES.Rational},
+        37382: {"name": "SubjectDistance", "type": TYPES.Rational},
+        37383: {"name": "MeteringMode", "type": TYPES.Short},
+        37384: {"name": "LightSource", "type": TYPES.Short},
+        37385: {"name": "Flash", "type": TYPES.Short},
+        37386: {"name": "FocalLength", "type": TYPES.Rational},
+        37396: {"name": "SubjectArea", "type": TYPES.Short},
+        37500: {"name": "MakerNote", "type": TYPES.Undefined},
+        37510: {"name": "UserComment", "type": TYPES.Undefined},
+        37520: {"name": "SubSecTime", "type": TYPES.Ascii},
+        37521: {"name": "SubSecTimeOriginal", "type": TYPES.Ascii},
+        37522: {"name": "SubSecTimeDigitized", "type": TYPES.Ascii},
+        37888: {"name": "Temperature", "type": TYPES.SRational},
+        37889: {"name": "Humidity", "type": TYPES.Rational},
+        37890: {"name": "Pressure", "type": TYPES.Rational},
+        37891: {"name": "WaterDepth", "type": TYPES.SRational},
+        37892: {"name": "Acceleration", "type": TYPES.Rational},
+        37893: {"name": "CameraElevationAngle", "type": TYPES.SRational},
+        40960: {"name": "FlashpixVersion", "type": TYPES.Undefined},
+        40961: {"name": "ColorSpace", "type": TYPES.Short},
+        40962: {"name": "PixelXDimension", "type": TYPES.Long},
+        40963: {"name": "PixelYDimension", "type": TYPES.Long},
+        40964: {"name": "RelatedSoundFile", "type": TYPES.Ascii},
+        40965: {"name": "InteroperabilityTag", "type": TYPES.Long},
+        41483: {"name": "FlashEnergy", "type": TYPES.Rational},
+        41484: {"name": "SpatialFrequencyResponse", "type": TYPES.Undefined},
+        41486: {"name": "FocalPlaneXResolution", "type": TYPES.Rational},
+        41487: {"name": "FocalPlaneYResolution", "type": TYPES.Rational},
+        41488: {"name": "FocalPlaneResolutionUnit", "type": TYPES.Short},
+        41492: {"name": "SubjectLocation", "type": TYPES.Short},
+        41493: {"name": "ExposureIndex", "type": TYPES.Rational},
+        41495: {"name": "SensingMethod", "type": TYPES.Short},
+        41728: {"name": "FileSource", "type": TYPES.Undefined},
+        41729: {"name": "SceneType", "type": TYPES.Undefined},
+        41730: {"name": "CFAPattern", "type": TYPES.Undefined},
+        41985: {"name": "CustomRendered", "type": TYPES.Short},
+        41986: {"name": "ExposureMode", "type": TYPES.Short},
+        41987: {"name": "WhiteBalance", "type": TYPES.Short},
+        41988: {"name": "DigitalZoomRatio", "type": TYPES.Rational},
+        41989: {"name": "FocalLengthIn35mmFilm", "type": TYPES.Short},
+        41990: {"name": "SceneCaptureType", "type": TYPES.Short},
+        41991: {"name": "GainControl", "type": TYPES.Short},
+        41992: {"name": "Contrast", "type": TYPES.Short},
+        41993: {"name": "Saturation", "type": TYPES.Short},
+        41994: {"name": "Sharpness", "type": TYPES.Short},
+        41995: {"name": "DeviceSettingDescription", "type": TYPES.Undefined},
+        41996: {"name": "SubjectDistanceRange", "type": TYPES.Short},
+        42016: {"name": "ImageUniqueID", "type": TYPES.Ascii},
+        42032: {"name": "CameraOwnerName", "type": TYPES.Ascii},
+        42033: {"name": "BodySerialNumber", "type": TYPES.Ascii},
+        42034: {"name": "LensSpecification", "type": TYPES.Rational},
+        42035: {"name": "LensMake", "type": TYPES.Ascii},
+        42036: {"name": "LensModel", "type": TYPES.Ascii},
+        42037: {"name": "LensSerialNumber", "type": TYPES.Ascii},
+        42240: {"name": "Gamma", "type": TYPES.Rational},
+    },
+    "GPS": {
+        0: {"name": "GPSVersionID", "type": TYPES.Byte},
+        1: {"name": "GPSLatitudeRef", "type": TYPES.Ascii},
+        2: {"name": "GPSLatitude", "type": TYPES.Rational},
+        3: {"name": "GPSLongitudeRef", "type": TYPES.Ascii},
+        4: {"name": "GPSLongitude", "type": TYPES.Rational},
+        5: {"name": "GPSAltitudeRef", "type": TYPES.Byte},
+        6: {"name": "GPSAltitude", "type": TYPES.Rational},
+        7: {"name": "GPSTimeStamp", "type": TYPES.Rational},
+        8: {"name": "GPSSatellites", "type": TYPES.Ascii},
+        9: {"name": "GPSStatus", "type": TYPES.Ascii},
+        10: {"name": "GPSMeasureMode", "type": TYPES.Ascii},
+        11: {"name": "GPSDOP", "type": TYPES.Rational},
+        12: {"name": "GPSSpeedRef", "type": TYPES.Ascii},
+        13: {"name": "GPSSpeed", "type": TYPES.Rational},
+        14: {"name": "GPSTrackRef", "type": TYPES.Ascii},
+        15: {"name": "GPSTrack", "type": TYPES.Rational},
+        16: {"name": "GPSImgDirectionRef", "type": TYPES.Ascii},
+        17: {"name": "GPSImgDirection", "type": TYPES.Rational},
+        18: {"name": "GPSMapDatum", "type": TYPES.Ascii},
+        19: {"name": "GPSDestLatitudeRef", "type": TYPES.Ascii},
+        20: {"name": "GPSDestLatitude", "type": TYPES.Rational},
+        21: {"name": "GPSDestLongitudeRef", "type": TYPES.Ascii},
+        22: {"name": "GPSDestLongitude", "type": TYPES.Rational},
+        23: {"name": "GPSDestBearingRef", "type": TYPES.Ascii},
+        24: {"name": "GPSDestBearing", "type": TYPES.Rational},
+        25: {"name": "GPSDestDistanceRef", "type": TYPES.Ascii},
+        26: {"name": "GPSDestDistance", "type": TYPES.Rational},
+        27: {"name": "GPSProcessingMethod", "type": TYPES.Undefined},
+        28: {"name": "GPSAreaInformation", "type": TYPES.Undefined},
+        29: {"name": "GPSDateStamp", "type": TYPES.Ascii},
+        30: {"name": "GPSDifferential", "type": TYPES.Short},
+        31: {"name": "GPSHPositioningError", "type": TYPES.Rational},
+    },
+    "Interop": {1: {"name": "InteroperabilityIndex", "type": TYPES.Ascii}},
 }
 
 TAGS["0th"] = TAGS["Image"]
 TAGS["1st"] = TAGS["Image"]
 
+
 class ImageIFD:
     """Exif tag number reference - 0th IFD"""
+
     ProcessingSoftware = 11
     NewSubfileType = 254
     SubfileType = 255
@@ -516,6 +524,7 @@ class ImageIFD:
 
 class ExifIFD:
     """Exif tag number reference - Exif IFD"""
+
     ExposureTime = 33434
     FNumber = 33437
     ExposureProgram = 34850
@@ -599,6 +608,7 @@ class ExifIFD:
 
 class GPSIFD:
     """Exif tag number reference - GPS IFD"""
+
     GPSVersionID = 0
     GPSLatitudeRef = 1
     GPSLatitude = 2
@@ -635,4 +645,5 @@ class GPSIFD:
 
 class InteropIFD:
     """Exif tag number reference - Interoperability IFD"""
+
     InteroperabilityIndex = 1

openflexure_microscope/camera/piexif/_insert.py

@@ -6,6 +6,7 @@ from ._common import *
 from ._exceptions import InvalidImageDataError
 from . import _webp
 
+
 def insert(exif, image, new_file=None):
     """
     py:function:: piexif.insert(exif_bytes, filename)
@@ -20,7 +21,7 @@ def insert(exif, image, new_file=None):
 
     output_file = False
     # Prevents "UnicodeWarning: Unicode equal comparison failed" warnings on Python 2
-    maybe_image = sys.version_info >= (3,0,0) or isinstance(image, str)
+    maybe_image = sys.version_info >= (3, 0, 0) or isinstance(image, str)
 
     if maybe_image and image[0:2] == b"\xff\xd8":
         image_data = image
@@ -29,7 +30,7 @@ def insert(exif, image, new_file=None):
         image_data = image
         file_type = "webp"
     else:
-        with open(image, 'rb') as f:
+        with open(image, "rb") as f:
             image_data = f.read()
         if image_data[0:2] == b"\xff\xd8":
             file_type = "jpeg"
@@ -57,4 +58,4 @@ def insert(exif, image, new_file=None):
         with open(image, "wb+") as f:
             f.write(new_data)
     else:
-        raise ValueError("Give a 3rd argument to 'insert' to output file")
+        raise ValueError("Give a 3rd argument to 'insert' to output file")

openflexure_microscope/camera/piexif/_load.py

@@ -19,12 +19,14 @@ def load(input_data, key_is_name=False):
     :return: Exif data({"0th":dict, "Exif":dict, "GPS":dict, "Interop":dict, "1st":dict, "thumbnail":bytes})
     :rtype: dict
     """
-    exif_dict = {"0th":{},
-                 "Exif":{},
-                 "GPS":{},
-                 "Interop":{},
-                 "1st":{},
-                 "thumbnail":None}
+    exif_dict = {
+        "0th": {},
+        "Exif": {},
+        "GPS": {},
+        "Interop": {},
+        "1st": {},
+        "thumbnail": None,
+    }
     exifReader = _ExifReader(input_data)
     if exifReader.tiftag is None:
         return exif_dict
@@ -34,8 +36,7 @@ def load(input_data, key_is_name=False):
     else:
         exifReader.endian_mark = ">"
 
-    pointer = struct.unpack(exifReader.endian_mark + "L",
-                            exifReader.tiftag[4:8])[0]
+    pointer = struct.unpack(exifReader.endian_mark + "L", exifReader.tiftag[4:8])[0]
     exif_dict["0th"] = exifReader.get_ifd_dict(pointer, "0th")
     first_ifd_pointer = exif_dict["0th"].pop("first_ifd_pointer")
     if ImageIFD.ExifTag in exif_dict["0th"]:
@@ -48,14 +49,19 @@ def load(input_data, key_is_name=False):
         pointer = exif_dict["Exif"][ExifIFD.InteroperabilityTag]
         exif_dict["Interop"] = exifReader.get_ifd_dict(pointer, "Interop")
     if first_ifd_pointer != b"\x00\x00\x00\x00":
-        pointer = struct.unpack(exifReader.endian_mark + "L",
-                                first_ifd_pointer)[0]
+        pointer = struct.unpack(exifReader.endian_mark + "L", first_ifd_pointer)[0]
         exif_dict["1st"] = exifReader.get_ifd_dict(pointer, "1st")
-        if (ImageIFD.JPEGInterchangeFormat in exif_dict["1st"] and
-            ImageIFD.JPEGInterchangeFormatLength in exif_dict["1st"]):
-            end = (exif_dict["1st"][ImageIFD.JPEGInterchangeFormat] +
-                   exif_dict["1st"][ImageIFD.JPEGInterchangeFormatLength])
-            thumb = exifReader.tiftag[exif_dict["1st"][ImageIFD.JPEGInterchangeFormat]:end]
+        if (
+            ImageIFD.JPEGInterchangeFormat in exif_dict["1st"]
+            and ImageIFD.JPEGInterchangeFormatLength in exif_dict["1st"]
+        ):
+            end = (
+                exif_dict["1st"][ImageIFD.JPEGInterchangeFormat]
+                + exif_dict["1st"][ImageIFD.JPEGInterchangeFormatLength]
+            )
+            thumb = exifReader.tiftag[
+                exif_dict["1st"][ImageIFD.JPEGInterchangeFormat] : end
+            ]
             exif_dict["thumbnail"] = thumb
 
     if key_is_name:
@@ -66,7 +72,7 @@ def load(input_data, key_is_name=False):
 class _ExifReader(object):
     def __init__(self, data):
         # Prevents "UnicodeWarning: Unicode equal comparison failed" warnings on Python 2
-        maybe_image = sys.version_info >= (3,0,0) or isinstance(data, str)
+        maybe_image = sys.version_info >= (3, 0, 0) or isinstance(data, str)
 
         if maybe_image and data[0:2] == b"\xff\xd8":  # JPEG
             segments = split_into_segments(data)
@@ -82,7 +88,7 @@ class _ExifReader(object):
         elif maybe_image and data[0:4] == b"Exif":  # Exif
             self.tiftag = data[6:]
         else:
-            with open(data, 'rb') as f:
+            with open(data, "rb") as f:
                 magic_number = f.read(2)
             if magic_number == b"\xff\xd8":  # JPEG
                 app1 = read_exif_from_file(data)
@@ -91,13 +97,13 @@ class _ExifReader(object):
                 else:
                     self.tiftag = None
             elif magic_number in (b"\x49\x49", b"\x4d\x4d"):  # TIFF
-                with open(data, 'rb') as f:
+                with open(data, "rb") as f:
                     self.tiftag = f.read()
             else:
-                with open(data, 'rb') as f:
+                with open(data, "rb") as f:
                     header = f.read(12)
-                if header[0:4] == b"RIFF"and header[8:12] == b"WEBP":
-                    with open(data, 'rb') as f:
+                if header[0:4] == b"RIFF" and header[8:12] == b"WEBP":
+                    with open(data, "rb") as f:
                         file_data = f.read()
                     self.tiftag = _webp.get_exif(file_data)
                 else:
@@ -105,8 +111,9 @@ class _ExifReader(object):
 
     def get_ifd_dict(self, pointer, ifd_name, read_unknown=False):
         ifd_dict = {}
-        tag_count = struct.unpack(self.endian_mark + "H",
-                                  self.tiftag[pointer: pointer+2])[0]
+        tag_count = struct.unpack(
+            self.endian_mark + "H", self.tiftag[pointer : pointer + 2]
+        )[0]
         offset = pointer + 2
         if ifd_name in ["0th", "1st"]:
             t = "Image"
@@ -115,26 +122,28 @@ class _ExifReader(object):
         p_and_value = []
         for x in range(tag_count):
             pointer = offset + 12 * x
-            tag = struct.unpack(self.endian_mark + "H",
-                       self.tiftag[pointer: pointer+2])[0]
-            value_type = struct.unpack(self.endian_mark + "H",
-                         self.tiftag[pointer + 2: pointer + 4])[0]
-            value_num = struct.unpack(self.endian_mark + "L",
-                                      self.tiftag[pointer + 4: pointer + 8]
-                                      )[0]
-            value = self.tiftag[pointer+8: pointer+12]
+            tag = struct.unpack(
+                self.endian_mark + "H", self.tiftag[pointer : pointer + 2]
+            )[0]
+            value_type = struct.unpack(
+                self.endian_mark + "H", self.tiftag[pointer + 2 : pointer + 4]
+            )[0]
+            value_num = struct.unpack(
+                self.endian_mark + "L", self.tiftag[pointer + 4 : pointer + 8]
+            )[0]
+            value = self.tiftag[pointer + 8 : pointer + 12]
             p_and_value.append((pointer, value_type, value_num, value))
             v_set = (value_type, value_num, value, tag)
             if tag in TAGS[t]:
                 ifd_dict[tag] = self.convert_value(v_set)
             elif read_unknown:
                 ifd_dict[tag] = (v_set[0], v_set[1], v_set[2], self.tiftag)
-            #else:
+            # else:
             #    pass
 
         if ifd_name == "0th":
             pointer = offset + 12 * tag_count
-            ifd_dict["first_ifd_pointer"] = self.tiftag[pointer:pointer + 4]
+            ifd_dict["first_ifd_pointer"] = self.tiftag[pointer : pointer + 4]
         return ifd_dict
 
     def convert_value(self, val):
@@ -143,114 +152,148 @@ class _ExifReader(object):
         length = val[1]
         value = val[2]
 
-        if t == TYPES.Byte: # BYTE
+        if t == TYPES.Byte:  # BYTE
             if length > 4:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack("B" * length,
-                                     self.tiftag[pointer: pointer + length])
+                data = struct.unpack(
+                    "B" * length, self.tiftag[pointer : pointer + length]
+                )
             else:
                 data = struct.unpack("B" * length, value[0:length])
-        elif t == TYPES.Ascii: # ASCII
+        elif t == TYPES.Ascii:  # ASCII
             if length > 4:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = self.tiftag[pointer: pointer+length - 1]
+                data = self.tiftag[pointer : pointer + length - 1]
             else:
-                data = value[0: length - 1]
-        elif t == TYPES.Short: # SHORT
+                data = value[0 : length - 1]
+        elif t == TYPES.Short:  # SHORT
             if length > 2:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack(self.endian_mark + "H" * length,
-                                     self.tiftag[pointer: pointer+length*2])
+                data = struct.unpack(
+                    self.endian_mark + "H" * length,
+                    self.tiftag[pointer : pointer + length * 2],
+                )
             else:
-                data = struct.unpack(self.endian_mark + "H" * length,
-                                     value[0:length * 2])
-        elif t == TYPES.Long: # LONG
+                data = struct.unpack(
+                    self.endian_mark + "H" * length, value[0 : length * 2]
+                )
+        elif t == TYPES.Long:  # LONG
             if length > 1:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack(self.endian_mark + "L" * length,
-                                     self.tiftag[pointer: pointer+length*4])
+                data = struct.unpack(
+                    self.endian_mark + "L" * length,
+                    self.tiftag[pointer : pointer + length * 4],
+                )
             else:
-                data = struct.unpack(self.endian_mark + "L" * length,
-                                     value)
-        elif t == TYPES.Rational: # RATIONAL
+                data = struct.unpack(self.endian_mark + "L" * length, value)
+        elif t == TYPES.Rational:  # RATIONAL
             pointer = struct.unpack(self.endian_mark + "L", value)[0]
             if length > 1:
                 data = tuple(
-                    (struct.unpack(self.endian_mark + "L",
-                                   self.tiftag[pointer + x * 8:
-                                       pointer + 4 + x * 8])[0],
-                     struct.unpack(self.endian_mark + "L",
-                                   self.tiftag[pointer + 4 + x * 8:
-                                       pointer + 8 + x * 8])[0])
+                    (
+                        struct.unpack(
+                            self.endian_mark + "L",
+                            self.tiftag[pointer + x * 8 : pointer + 4 + x * 8],
+                        )[0],
+                        struct.unpack(
+                            self.endian_mark + "L",
+                            self.tiftag[pointer + 4 + x * 8 : pointer + 8 + x * 8],
+                        )[0],
+                    )
                     for x in range(length)
                 )
             else:
-                data = (struct.unpack(self.endian_mark + "L",
-                                      self.tiftag[pointer: pointer + 4])[0],
-                        struct.unpack(self.endian_mark + "L",
-                                      self.tiftag[pointer + 4: pointer + 8]
-                                      )[0])
-        elif t == TYPES.SByte: # SIGNED BYTES
+                data = (
+                    struct.unpack(
+                        self.endian_mark + "L", self.tiftag[pointer : pointer + 4]
+                    )[0],
+                    struct.unpack(
+                        self.endian_mark + "L", self.tiftag[pointer + 4 : pointer + 8]
+                    )[0],
+                )
+        elif t == TYPES.SByte:  # SIGNED BYTES
             if length > 4:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack("b" * length,
-                                     self.tiftag[pointer: pointer + length])
+                data = struct.unpack(
+                    "b" * length, self.tiftag[pointer : pointer + length]
+                )
             else:
                 data = struct.unpack("b" * length, value[0:length])
-        elif t == TYPES.Undefined: # UNDEFINED BYTES
+        elif t == TYPES.Undefined:  # UNDEFINED BYTES
             if length > 4:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = self.tiftag[pointer: pointer+length]
+                data = self.tiftag[pointer : pointer + length]
             else:
                 data = value[0:length]
-        elif t == TYPES.SShort: # SIGNED SHORT
+        elif t == TYPES.SShort:  # SIGNED SHORT
             if length > 2:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack(self.endian_mark + "h" * length,
-                                     self.tiftag[pointer: pointer+length*2])
+                data = struct.unpack(
+                    self.endian_mark + "h" * length,
+                    self.tiftag[pointer : pointer + length * 2],
+                )
             else:
-                data = struct.unpack(self.endian_mark + "h" * length,
-                                     value[0:length * 2])
-        elif t == TYPES.SLong: # SLONG
+                data = struct.unpack(
+                    self.endian_mark + "h" * length, value[0 : length * 2]
+                )
+        elif t == TYPES.SLong:  # SLONG
             if length > 1:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack(self.endian_mark + "l" * length,
-                                     self.tiftag[pointer: pointer+length*4])
+                data = struct.unpack(
+                    self.endian_mark + "l" * length,
+                    self.tiftag[pointer : pointer + length * 4],
+                )
             else:
-                data = struct.unpack(self.endian_mark + "l" * length,
-                                     value)
-        elif t == TYPES.SRational: # SRATIONAL
+                data = struct.unpack(self.endian_mark + "l" * length, value)
+        elif t == TYPES.SRational:  # SRATIONAL
             pointer = struct.unpack(self.endian_mark + "L", value)[0]
             if length > 1:
                 data = tuple(
-                  (struct.unpack(self.endian_mark + "l",
-                   self.tiftag[pointer + x * 8: pointer + 4 + x * 8])[0],
-                   struct.unpack(self.endian_mark + "l",
-                   self.tiftag[pointer + 4 + x * 8: pointer + 8 + x * 8])[0])
-                  for x in range(length)
+                    (
+                        struct.unpack(
+                            self.endian_mark + "l",
+                            self.tiftag[pointer + x * 8 : pointer + 4 + x * 8],
+                        )[0],
+                        struct.unpack(
+                            self.endian_mark + "l",
+                            self.tiftag[pointer + 4 + x * 8 : pointer + 8 + x * 8],
+                        )[0],
+                    )
+                    for x in range(length)
                 )
             else:
-                data = (struct.unpack(self.endian_mark + "l",
-                                      self.tiftag[pointer: pointer + 4])[0],
-                        struct.unpack(self.endian_mark + "l",
-                                      self.tiftag[pointer + 4: pointer + 8]
-                                      )[0])
-        elif t == TYPES.Float: # FLOAT
+                data = (
+                    struct.unpack(
+                        self.endian_mark + "l", self.tiftag[pointer : pointer + 4]
+                    )[0],
+                    struct.unpack(
+                        self.endian_mark + "l", self.tiftag[pointer + 4 : pointer + 8]
+                    )[0],
+                )
+        elif t == TYPES.Float:  # FLOAT
             if length > 1:
                 pointer = struct.unpack(self.endian_mark + "L", value)[0]
-                data = struct.unpack(self.endian_mark + "f" * length,
-                                     self.tiftag[pointer: pointer+length*4])
+                data = struct.unpack(
+                    self.endian_mark + "f" * length,
+                    self.tiftag[pointer : pointer + length * 4],
+                )
             else:
-                data = struct.unpack(self.endian_mark + "f" * length,
-                                     value)
-        elif t == TYPES.DFloat: # DOUBLE
+                data = struct.unpack(self.endian_mark + "f" * length, value)
+        elif t == TYPES.DFloat:  # DOUBLE
             pointer = struct.unpack(self.endian_mark + "L", value)[0]
-            data = struct.unpack(self.endian_mark + "d" * length,
-                                    self.tiftag[pointer: pointer+length*8])
+            data = struct.unpack(
+                self.endian_mark + "d" * length,
+                self.tiftag[pointer : pointer + length * 8],
+            )
         else:
-            raise ValueError("Exif might be wrong. Got incorrect value " +
-                             "type to decode.\n" +
-                             "tag: " + str(val[3]) + "\ntype: " + str(t))
+            raise ValueError(
+                "Exif might be wrong. Got incorrect value "
+                + "type to decode.\n"
+                + "tag: "
+                + str(val[3])
+                + "\ntype: "
+                + str(t)
+            )
 
         if isinstance(data, tuple) and (len(data) == 1):
             return data[0]
@@ -260,11 +303,20 @@ class _ExifReader(object):
 
 def _get_key_name_dict(exif_dict):
     new_dict = {
-        "0th":{TAGS["Image"][n]["name"]:value for n, value in exif_dict["0th"].items()},
-        "Exif":{TAGS["Exif"][n]["name"]:value for n, value in exif_dict["Exif"].items()},
-        "1st":{TAGS["Image"][n]["name"]:value for n, value in exif_dict["1st"].items()},
-        "GPS":{TAGS["GPS"][n]["name"]:value for n, value in exif_dict["GPS"].items()},
-        "Interop":{TAGS["Interop"][n]["name"]:value for n, value in exif_dict["Interop"].items()},
-        "thumbnail":exif_dict["thumbnail"],
+        "0th": {
+            TAGS["Image"][n]["name"]: value for n, value in exif_dict["0th"].items()
+        },
+        "Exif": {
+            TAGS["Exif"][n]["name"]: value for n, value in exif_dict["Exif"].items()
+        },
+        "1st": {
+            TAGS["Image"][n]["name"]: value for n, value in exif_dict["1st"].items()
+        },
+        "GPS": {TAGS["GPS"][n]["name"]: value for n, value in exif_dict["GPS"].items()},
+        "Interop": {
+            TAGS["Interop"][n]["name"]: value
+            for n, value in exif_dict["Interop"].items()
+        },
+        "thumbnail": exif_dict["thumbnail"],
     }
-    return new_dict
+    return new_dict

openflexure_microscope/camera/piexif/_remove.py

@@ -3,6 +3,7 @@ import io
 from ._common import *
 from . import _webp
 
+
 def remove(src, new_file=None):
     """
     py:function:: piexif.remove(filename)
@@ -19,7 +20,7 @@ def remove(src, new_file=None):
         src_data = src
         file_type = "webp"
     else:
-        with open(src, 'rb') as f:
+        with open(src, "rb") as f:
             src_data = f.read()
         output_is_file = True
         if src_data[0:2] == b"\xff\xd8":
@@ -53,4 +54,4 @@ def remove(src, new_file=None):
         with open(src, "wb+") as f:
             f.write(new_data)
     else:
-        raise ValueError("Give a second argument to 'remove' to output file")
+        raise ValueError("Give a second argument to 'remove' to output file")

openflexure_microscope/camera/piexif/_transplant.py

@@ -15,7 +15,7 @@ def transplant(exif_src, image, new_file=None):
     if exif_src[0:2] == b"\xff\xd8":
         src_data = exif_src
     else:
-        with open(exif_src, 'rb') as f:
+        with open(exif_src, "rb") as f:
             src_data = f.read()
     segments = split_into_segments(src_data)
     exif = get_exif_seg(segments)
@@ -26,7 +26,7 @@ def transplant(exif_src, image, new_file=None):
     if image[0:2] == b"\xff\xd8":
         image_data = image
     else:
-        with open(image, 'rb') as f:
+        with open(image, "rb") as f:
             image_data = f.read()
         output_file = True
     segments = split_into_segments(image_data)
@@ -42,4 +42,4 @@ def transplant(exif_src, image, new_file=None):
         with open(image, "wb+") as f:
             f.write(new_data)
     else:
-        raise ValueError("Give a 3rd argument to 'transplant' to output file")
+        raise ValueError("Give a 3rd argument to 'transplant' to output file")

openflexure_microscope/camera/piexif/_webp.py

@@ -1,4 +1,3 @@
-
 import struct
 
 
@@ -18,26 +17,33 @@ def split(data):
 
     chunks = []
     while pointer + CHUNK_FOURCC_LENGTH + LENGTH_BYTES_LENGTH < file_size:
-        fourcc = data[pointer:pointer + CHUNK_FOURCC_LENGTH]
+        fourcc = data[pointer : pointer + CHUNK_FOURCC_LENGTH]
         pointer += CHUNK_FOURCC_LENGTH
-        chunk_length_bytes = data[pointer:pointer + LENGTH_BYTES_LENGTH]
+        chunk_length_bytes = data[pointer : pointer + LENGTH_BYTES_LENGTH]
         chunk_length = struct.unpack("<L", chunk_length_bytes)[0]
         pointer += LENGTH_BYTES_LENGTH
 
-        chunk_data = data[pointer:pointer + chunk_length]
-        chunks.append({"fourcc":fourcc, "length_bytes":chunk_length_bytes, "data":chunk_data})
+        chunk_data = data[pointer : pointer + chunk_length]
+        chunks.append(
+            {"fourcc": fourcc, "length_bytes": chunk_length_bytes, "data": chunk_data}
+        )
 
         padding = 1 if chunk_length % 2 else 0
 
         pointer += chunk_length + padding
     return chunks
 
+
 def merge_chunks(chunks):
-    merged = b"".join([chunk["fourcc"] 
-                       + chunk["length_bytes"]
-                       + chunk["data"]
-                       + (len(chunk["data"]) % 2) * b"\x00"
-                        for chunk in chunks])
+    merged = b"".join(
+        [
+            chunk["fourcc"]
+            + chunk["length_bytes"]
+            + chunk["data"]
+            + (len(chunk["data"]) % 2) * b"\x00"
+            for chunk in chunks
+        ]
+    )
     return merged
 
 
@@ -50,6 +56,7 @@ def _get_size_from_vp8x(chunk):
     height = height_minus_one + 1
     return (width, height)
 
+
 def _get_size_from_vp8(chunk):
     BEGIN_CODE = b"\x9d\x01\x2a"
     begin_index = chunk["data"].find(BEGIN_CODE)
@@ -59,17 +66,21 @@ def _get_size_from_vp8(chunk):
         BEGIN_CODE_LENGTH = len(BEGIN_CODE)
         LENGTH_BYTES_LENGTH = 2
         length_start = begin_index + BEGIN_CODE_LENGTH
-        width_bytes = chunk["data"][length_start:length_start + LENGTH_BYTES_LENGTH]
+        width_bytes = chunk["data"][length_start : length_start + LENGTH_BYTES_LENGTH]
         width = struct.unpack("<H", width_bytes)[0]
-        height_bytes = chunk["data"][length_start + LENGTH_BYTES_LENGTH:length_start + 2 * LENGTH_BYTES_LENGTH]
+        height_bytes = chunk["data"][
+            length_start + LENGTH_BYTES_LENGTH : length_start + 2 * LENGTH_BYTES_LENGTH
+        ]
         height = struct.unpack("<H", height_bytes)[0]
         return (width, height)
 
+
 def _vp8L_contains_alpha(chunk_data):
-    flag = ord(chunk_data[4:5]) >> 5-1 & ord(b"\x01")
+    flag = ord(chunk_data[4:5]) >> 5 - 1 & ord(b"\x01")
     contains = 1 * flag
     return contains
 
+
 def _get_size_from_vp8L(chunk):
     b1 = chunk["data"][1:2]
     b2 = chunk["data"][2:3]
@@ -79,11 +90,14 @@ def _get_size_from_vp8L(chunk):
     width_minus_one = (ord(b2) & ord(b"\x3F")) << 8 | ord(b1)
     width = width_minus_one + 1
 
-    height_minus_one = (ord(b4) & ord(b"\x0F")) << 10 | ord(b3) << 2 | (ord(b2) & ord(b"\xC0")) >> 6
+    height_minus_one = (
+        (ord(b4) & ord(b"\x0F")) << 10 | ord(b3) << 2 | (ord(b2) & ord(b"\xC0")) >> 6
+    )
     height = height_minus_one + 1
 
     return (width, height)
 
+
 def _get_size_from_anmf(chunk):
     width_minus_one_bytes = chunk["data"][6:9] + b"\x00"
     width_minus_one = struct.unpack("<L", width_minus_one_bytes)[0]
@@ -92,12 +106,22 @@ def _get_size_from_anmf(chunk):
     height_minus_one = struct.unpack("<L", height_minus_one_bytes)[0]
     height = height_minus_one + 1
     return (width, height)
-    
+
+
 def set_vp8x(chunks):
 
     width = None
     height = None
-    flags = [b"0", b"0", b"0", b"0", b"0", b"0", b"0", b"0"]  # [0, 0, ICC, Alpha, EXIF, XMP, Anim, 0]
+    flags = [
+        b"0",
+        b"0",
+        b"0",
+        b"0",
+        b"0",
+        b"0",
+        b"0",
+        b"0",
+    ]  # [0, 0, ICC, Alpha, EXIF, XMP, Anim, 0]
 
     for chunk in chunks:
         if chunk["fourcc"] == b"VP8X":
@@ -136,11 +160,16 @@ def set_vp8x(chunks):
 
     data_bytes = flags_bytes + padding_bytes + width_bytes + height_bytes
 
-    vp8x_chunk = {"fourcc":header_bytes, "length_bytes":length_bytes, "data":data_bytes}
+    vp8x_chunk = {
+        "fourcc": header_bytes,
+        "length_bytes": length_bytes,
+        "data": data_bytes,
+    }
     chunks.insert(0, vp8x_chunk)
 
     return chunks
 
+
 def get_file_header(chunks):
     WEBP_HEADER_LENGTH = 4
     FOURCC_LENGTH = 4
@@ -158,7 +187,6 @@ def get_file_header(chunks):
     return file_header
 
 
-
 def get_exif(data):
     if data[0:4] != b"RIFF" or data[8:12] != b"WEBP":
         raise ValueError("Not WebP")
@@ -179,15 +207,15 @@ def get_exif(data):
     chunks = []
     exif = b""
     while pointer < file_size:
-        fourcc = data[pointer:pointer + CHUNK_FOURCC_LENGTH]
+        fourcc = data[pointer : pointer + CHUNK_FOURCC_LENGTH]
         pointer += CHUNK_FOURCC_LENGTH
-        chunk_length_bytes = data[pointer:pointer + LENGTH_BYTES_LENGTH]
+        chunk_length_bytes = data[pointer : pointer + LENGTH_BYTES_LENGTH]
         chunk_length = struct.unpack("<L", chunk_length_bytes)[0]
         if chunk_length % 2:
             chunk_length += 1
         pointer += LENGTH_BYTES_LENGTH
         if fourcc == b"EXIF":
-            return data[pointer:pointer + chunk_length]
+            return data[pointer : pointer + chunk_length]
         pointer += chunk_length
     return None  # if there isn't exif, return None.
 
@@ -195,7 +223,11 @@ def get_exif(data):
 def insert_exif_into_chunks(chunks, exif_bytes):
     EXIF_HEADER = b"EXIF"
     exif_length_bytes = struct.pack("<L", len(exif_bytes))
-    exif_chunk = {"fourcc":EXIF_HEADER, "length_bytes":exif_length_bytes, "data":exif_bytes}
+    exif_chunk = {
+        "fourcc": EXIF_HEADER,
+        "length_bytes": exif_length_bytes,
+        "data": exif_bytes,
+    }
 
     xmp_index = None
     animation_index = None

openflexure_microscope/camera/piexif/helper.py

@@ -2,26 +2,26 @@ class UserComment:
     #
     # Names of encodings that we publicly support.
     #
-    ASCII = 'ascii'
-    JIS = 'jis'
-    UNICODE = 'unicode'
+    ASCII = "ascii"
+    JIS = "jis"
+    UNICODE = "unicode"
     ENCODINGS = (ASCII, JIS, UNICODE)
 
     #
     # The actual encodings accepted by the standard library differ slightly from
     # the above.
     #
-    _JIS = 'shift_jis'
-    _UNICODE = 'utf_16_be'
+    _JIS = "shift_jis"
+    _UNICODE = "utf_16_be"
 
     _PREFIX_SIZE = 8
     #
     # From Table 9: Character Codes and their Designation
     #
-    _ASCII_PREFIX = b'\x41\x53\x43\x49\x49\x00\x00\x00'
-    _JIS_PREFIX = b'\x4a\x49\x53\x00\x00\x00\x00\x00'
-    _UNICODE_PREFIX = b'\x55\x4e\x49\x43\x4f\x44\x45\x00'
-    _UNDEFINED_PREFIX = b'\x00\x00\x00\x00\x00\x00\x00\x00'
+    _ASCII_PREFIX = b"\x41\x53\x43\x49\x49\x00\x00\x00"
+    _JIS_PREFIX = b"\x4a\x49\x53\x00\x00\x00\x00\x00"
+    _UNICODE_PREFIX = b"\x55\x4e\x49\x43\x4f\x44\x45\x00"
+    _UNDEFINED_PREFIX = b"\x00\x00\x00\x00\x00\x00\x00\x00"
 
     @classmethod
     def load(cls, data):
@@ -35,18 +35,20 @@ class UserComment:
         or the encoding is unsupported.
         """
         if len(data) < cls._PREFIX_SIZE:
-            raise ValueError('not enough data to decode UserComment')
-        prefix = data[:cls._PREFIX_SIZE]
-        body = data[cls._PREFIX_SIZE:]
+            raise ValueError("not enough data to decode UserComment")
+        prefix = data[: cls._PREFIX_SIZE]
+        body = data[cls._PREFIX_SIZE :]
         if prefix == cls._UNDEFINED_PREFIX:
-            raise ValueError('prefix is UNDEFINED, unable to decode UserComment')
+            raise ValueError("prefix is UNDEFINED, unable to decode UserComment")
         try:
             encoding = {
-                cls._ASCII_PREFIX: cls.ASCII, cls._JIS_PREFIX: cls._JIS, cls._UNICODE_PREFIX: cls._UNICODE,
+                cls._ASCII_PREFIX: cls.ASCII,
+                cls._JIS_PREFIX: cls._JIS,
+                cls._UNICODE_PREFIX: cls._UNICODE,
             }[prefix]
         except KeyError:
-            raise ValueError('unable to determine appropriate encoding')
-        return body.decode(encoding, errors='replace')
+            raise ValueError("unable to determine appropriate encoding")
+        return body.decode(encoding, errors="replace")
 
     @classmethod
     def dump(cls, data, encoding="ascii"):
@@ -60,7 +62,15 @@ class UserComment:
         :raises: ValueError if the encoding is unsupported.
         """
         if encoding not in cls.ENCODINGS:
-            raise ValueError('encoding %r must be one of %r' % (encoding, cls.ENCODINGS))
-        prefix = {cls.ASCII: cls._ASCII_PREFIX, cls.JIS: cls._JIS_PREFIX, cls.UNICODE: cls._UNICODE_PREFIX}[encoding]
-        internal_encoding = {cls.UNICODE: cls._UNICODE, cls.JIS: cls._JIS}.get(encoding, encoding)
-        return prefix + data.encode(internal_encoding, errors='replace')
+            raise ValueError(
+                "encoding %r must be one of %r" % (encoding, cls.ENCODINGS)
+            )
+        prefix = {
+            cls.ASCII: cls._ASCII_PREFIX,
+            cls.JIS: cls._JIS_PREFIX,
+            cls.UNICODE: cls._UNICODE_PREFIX,
+        }[encoding]
+        internal_encoding = {cls.UNICODE: cls._UNICODE, cls.JIS: cls._JIS}.get(
+            encoding, encoding
+        )
+        return prefix + data.encode(internal_encoding, errors="replace")

openflexure_microscope/camera/set_picamera_gain.py

@@ -20,14 +20,12 @@ def set_gain(camera, gain, value):
     if gain not in [MMAL_PARAMETER_ANALOG_GAIN, MMAL_PARAMETER_DIGITAL_GAIN]:
         raise ValueError("The gain parameter was not valid")
     ret = mmal.mmal_port_parameter_set_rational(
-        camera._camera.control._port, 
-        gain,
-        to_rational(value)
+        camera._camera.control._port, gain, to_rational(value)
     )
     if ret == 4:
         raise exc.PiCameraMMALError(
             ret,
-            "Are you running the latest version of the userland libraries? Gain setting was introduced in late 2017."
+            "Are you running the latest version of the userland libraries? Gain setting was introduced in late 2017.",
         )
     elif ret != 0:
         raise exc.PiCameraMMALError(ret)
@@ -56,21 +54,27 @@ if __name__ == "__main__":
         # fix the shutter speed
         cam.shutter_speed = cam.exposure_speed
 
-        logging.info("Current a/d gains: {}, {}".format(cam.analog_gain, cam.digital_gain))
+        logging.info(
+            "Current a/d gains: {}, {}".format(cam.analog_gain, cam.digital_gain)
+        )
 
         logging.info("Attempting to set analogue gain to 1")
         set_analog_gain(cam, 1)
         logging.info("Attempting to set digital gain to 1")
         set_digital_gain(cam, 1)
         # The old code is left in here in case it is a useful example...
-        # ret = mmal.mmal_port_parameter_set_rational(cam._camera.control._port, 
+        # ret = mmal.mmal_port_parameter_set_rational(cam._camera.control._port,
         #                                            MMAL_PARAMETER_DIGITAL_GAIN,
         #                                            to_rational(1))
         # print("Return code: {}".format(ret))
 
         try:
             while True:
-                logging.info("Current a/d gains: {}, {}".format(cam.analog_gain, cam.digital_gain))
+                logging.info(
+                    "Current a/d gains: {}, {}".format(
+                        cam.analog_gain, cam.digital_gain
+                    )
+                )
                 time.sleep(1)
         except KeyboardInterrupt:
             logging.info("Stopping...")

openflexure_microscope/config.py

@@ -65,7 +65,6 @@ def convert_type_to_json_safe(v):
         return v
 
 
-
 def settings_to_json(data: dict):
     """
     Make a copy of an input dictionary that's safe for JSON return

openflexure_microscope/exceptions.py

@@ -7,8 +7,8 @@ class TaskDeniedException(Exception):
 
 class LockError(ThreadError):
     ERROR_CODES = {
-        'ACQUIRE_ERROR': "Unable to acquire. Lock in use by another thread.",
-        'IN_USE_ERROR': "Lock in use by another thread."
+        "ACQUIRE_ERROR": "Unable to acquire. Lock in use by another thread.",
+        "IN_USE_ERROR": "Lock in use by another thread.",
     }
 
     def __init__(self, code, lock):

openflexure_microscope/lock.py

@@ -14,6 +14,7 @@ class StrictLock(object):
         _lock (:py:class:`threading.RLock`): Parent RLock object
         timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
     """
+
     def __init__(self, timeout=1):
         self._lock = RLock()
         self.timeout = timeout
@@ -29,7 +30,7 @@ class StrictLock(object):
         if result:
             return result
         else:
-            raise LockError('ACQUIRE_ERROR', self)
+            raise LockError("ACQUIRE_ERROR", self)
 
     def __exit__(self, *args):
         self._lock.release()
@@ -51,6 +52,7 @@ class CompositeLock(object):
         locks (list): List of parent RLock objects
         timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
     """
+
     def __init__(self, locks, timeout=1):
         self.locks = locks
         self.timeout = timeout
@@ -63,7 +65,7 @@ class CompositeLock(object):
         if all(result):
             return result
         else:
-            raise LockError('ACQUIRE_ERROR', self)
+            raise LockError("ACQUIRE_ERROR", self)
 
     def __exit__(self, *args):
         for lock in self.locks:

openflexure_microscope/plugins/__init__.py

@@ -1,3 +1,17 @@
-__all__ = ['module_from_file', 'load_plugin_class', 'load_plugin_module', 'class_from_map', 'PluginMount', 'MicroscopePlugin']
+__all__ = [
+    "module_from_file",
+    "load_plugin_class",
+    "load_plugin_module",
+    "class_from_map",
+    "PluginMount",
+    "MicroscopePlugin",
+]
 
-from .loader import module_from_file, load_plugin_class, load_plugin_module, class_from_map, PluginMount, MicroscopePlugin
+from .loader import (
+    module_from_file,
+    load_plugin_class,
+    load_plugin_module,
+    class_from_map,
+    PluginMount,
+    MicroscopePlugin,
+)

openflexure_microscope/plugins/default/autofocus/__init__.py

@@ -1,2 +1,2 @@
-__all__ = ['AutofocusPlugin']
-from .plugin import AutofocusPlugin
+__all__ = ["AutofocusPlugin"]
+from .plugin import AutofocusPlugin

openflexure_microscope/plugins/default/autofocus/api.py

@@ -1,18 +1,24 @@
 import numpy as np
 import logging
 
-from openflexure_microscope.devel import MicroscopeViewPlugin, JsonResponse, request, jsonify
+from openflexure_microscope.devel import (
+    MicroscopeViewPlugin,
+    JsonResponse,
+    request,
+    jsonify,
+)
+
 
 class MeasureSharpnessAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonResponse(request)
-        return jsonify({'sharpness': self.plugin.measure_sharpness()})
+        return jsonify({"sharpness": self.plugin.measure_sharpness()})
 
 
 class AutofocusAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonResponse(request)
-        
+
         # Figure out the range of z values to use
         dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
 
@@ -22,10 +28,11 @@ class AutofocusAPI(MicroscopeViewPlugin):
         # return a handle on the autofocus task
         return jsonify(task.state), 202
 
+
 class FastAutofocusAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonResponse(request)
-        
+
         # Figure out the parameters to use
         dz = payload.param("dz", default=2000, convert=int)
         backlash = payload.param("backlash", default=0, convert=int)
@@ -33,7 +40,9 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
             backlash = 0
 
         logging.info("Running autofocus...")
-        task = self.microscope.task.start(self.plugin.fast_autofocus, dz, backlash=backlash)
+        task = self.microscope.task.start(
+            self.plugin.fast_autofocus, dz, backlash=backlash
+        )
 
         # return a handle on the autofocus task
-        return jsonify(task.state), 202
+        return jsonify(task.state), 202

openflexure_microscope/plugins/default/autofocus/focus_utils.py

@@ -4,7 +4,8 @@ import threading
 import logging
 from scipy import ndimage
 
-class JPEGSharpnessMonitor():
+
+class JPEGSharpnessMonitor:
     def __init__(self, microscope, timeout=60):
         self.microscope = microscope
         self.camera = microscope.camera
@@ -17,32 +18,34 @@ class JPEGSharpnessMonitor():
         self.timeout = timeout
         self.keep_alive()
         self.background_thread = None
-            
+
     def is_alive(self):
         if self.background_thread is None:
             return False
         else:
             return self.background_thread.is_alive()
-            
+
     def should_stop(self):
         import time
+
         return time.time() - self.kept_alive > self.timeout
-    
+
     def keep_alive(self):
         import time
+
         self.kept_alive = time.time()
-    
+
     def start(self):
         "Start monitoring sharpness by looking at JPEG size"
         self.background_thread = threading.Thread(target=self._measure_jpegs)
         self.background_thread.start()
         return self
-        
+
     def stop(self):
         "Stop the background thread"
         self.stop_event.set()
         self.background_thread.join()
-        
+
     def _measure_jpegs(self):
         "Function that runs in a background thread to record sharpness"
         logging.info("Starting sharpness measurement in background thread")
@@ -59,7 +62,6 @@ class JPEGSharpnessMonitor():
         """Return the size of a frame from the MJPEG stream"""
         return len(self.camera.get_frame())
 
-
     def focus_rel(self, dz, backlash=False, **kwargs):
         self.keep_alive()
         self.stage_times.append(time.time())
@@ -69,7 +71,7 @@ class JPEGSharpnessMonitor():
         self.stage_positions.append(self.stage.position)
         i = len(self.stage_positions) - 2
         return i, self.stage_positions[-1][2]
-        
+
     def move_data(self, istart, istop=None):
         "Extract sharpness as a function of (interpolated) z"
         global np, logging
@@ -92,18 +94,21 @@ class JPEGSharpnessMonitor():
         """Return the z position of the sharpest image on a given move"""
         jt, jz, js = self.move_data(index)
         return jz[np.argmax(js)]
-    
+
     def data_dict(self):
         """Return the gathered data as a single convenient dictionary"""
         data = {}
-        for k in ['jpeg_times', 'jpeg_sizes', 'stage_times', 'stage_positions']:
+        for k in ["jpeg_times", "jpeg_sizes", "stage_times", "stage_positions"]:
             data[k] = getattr(self, k)
         return data
 
+
 def decimate_to(shape, image):
     """Decimate an image to reduce its size if it's too big."""
-    decimation = np.max(np.ceil(np.array(image.shape, dtype=np.float)[:len(shape)]/np.array(shape)))
-    return image[::int(decimation), ::int(decimation), ...]
+    decimation = np.max(
+        np.ceil(np.array(image.shape, dtype=np.float)[: len(shape)] / np.array(shape))
+    )
+    return image[:: int(decimation), :: int(decimation), ...]
 
 
 def sharpness_sum_lap2(rgb_image):
@@ -111,12 +116,14 @@ def sharpness_sum_lap2(rgb_image):
     # image_bw=np.mean(decimate_to((1000,1000), rgb_image),2)
     image_bw = np.mean(rgb_image, 2)
     image_lap = ndimage.filters.laplace(image_bw)
-    return np.mean(image_lap.astype(np.float)**4)
+    return np.mean(image_lap.astype(np.float) ** 4)
 
 
 def sharpness_edge(image):
     """Return a sharpness metric optimised for vertical lines"""
     gray = np.mean(image.astype(float), 2)
     n = 20
-    edge = np.array([[-1]*n + [1]*n])
-    return np.sum([np.sum(ndimage.filters.convolve(gray, W)**2) for W in [edge, edge.T]])
+    edge = np.array([[-1] * n + [1] * n])
+    return np.sum(
+        [np.sum(ndimage.filters.convolve(gray, W) ** 2) for W in [edge, edge.T]]
+    )

openflexure_microscope/plugins/default/autofocus/plugin.py

@@ -10,15 +10,16 @@ from .api import MeasureSharpnessAPI, AutofocusAPI, FastAutofocusAPI
 
 from openflexure_microscope.devel import MicroscopePlugin
 
+
 class AutofocusPlugin(MicroscopePlugin):
     """
     Basic autofocus plugin
     """
 
     api_views = {
-        '/measure_sharpness': MeasureSharpnessAPI,
-        '/autofocus': AutofocusAPI,
-        '/fast_autofocus': FastAutofocusAPI,
+        "/measure_sharpness": MeasureSharpnessAPI,
+        "/autofocus": AutofocusAPI,
+        "/fast_autofocus": FastAutofocusAPI,
     }
 
     ### SLOW AUTOFOCUS
@@ -70,21 +71,24 @@ class AutofocusPlugin(MicroscopePlugin):
             m.focus_rel(dz)
             return m.sharpest_z_on_move(0)
 
-
     def fast_autofocus(self, dz=2000, backlash=None):
         """Perform a down-up-down-up autofocus"""
         with self.monitor_sharpness() as m:
-            i, z = m.focus_rel(-dz/2)
+            i, z = m.focus_rel(-dz / 2)
             i, z = m.focus_rel(dz)
             fz = m.sharpest_z_on_move(i)
             if backlash is None:
-                i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent
+                i, z = m.focus_rel(
+                    -dz
+                )  # move all the way to the start so it's consistent
             else:
                 i, z = m.focus_rel(fz - z - backlash)
             m.focus_rel(fz - z)
             return m.data_dict()
 
-    def fast_up_down_up_autofocus(self, dz=2000, target_z=0, initial_move_up=True, mini_backlash=150):
+    def fast_up_down_up_autofocus(
+        self, dz=2000, target_z=0, initial_move_up=True, mini_backlash=150
+    ):
         """Autofocus by measuring on the way down, and moving back up with feedback.
 
         This autofocus method is very efficient, as it only passes the peak once.
@@ -124,32 +128,41 @@ class AutofocusPlugin(MicroscopePlugin):
             # Ensure the MJPEG stream has started
             self.microscope.camera.start_stream_recording()
 
-            df = dz #TODO: refactor so I actually use dz in the code below!
+            df = dz  # TODO: refactor so I actually use dz in the code below!
             if initial_move_up:
-                m.focus_rel(df/2)
+                m.focus_rel(df / 2)
             # move down
             i, z = m.focus_rel(-df)
             # now inspect where the sharpest point is, and estimate the sharpness
             # (JPEG size) that we should find at the start of the Z stack
             jt, jz, js = m.move_data(i)
             best_z = jz[np.argmax(js)]
-            target_s = np.interp([best_z+target_z], jz[::-1], js[::-1]) #NB jz is decreasing
+            target_s = np.interp(
+                [best_z + target_z], jz[::-1], js[::-1]
+            )  # NB jz is decreasing
 
             # now move to the start of the z stack
-            i, z = m.focus_rel(best_z + target_z - z + mini_backlash) # takes us to the start of the stack
+            i, z = m.focus_rel(
+                best_z + target_z - z + mini_backlash
+            )  # takes us to the start of the stack
 
             # We've deliberately undershot - figure out how much further we should move based on the curve
             current_js = m.jpeg_size()
-            imax = np.argmax(js) # we want to crop out just the bit below the peak
-            js = js[imax:] # NB z is in DECREASING order
+            imax = np.argmax(js)  # we want to crop out just the bit below the peak
+            js = js[imax:]  # NB z is in DECREASING order
             jz = jz[imax:]
-            inow = np.argmax(js < current_js) # use the curve we recorded to estimate our position
+            inow = np.argmax(
+                js < current_js
+            )  # use the curve we recorded to estimate our position
             # TODO: fancy interpolation stuff
 
             # So, the Z position corresponding to our current sharpness value is zs[inow]
             # That means we should move forwards, by best_z - zs[inow]
             correction_move = best_z + target_z - jz[inow]
-            logging.debug("Fast autofocus scan: correcting backlash by moving {} steps".format(correction_move))
+            logging.debug(
+                "Fast autofocus scan: correcting backlash by moving {} steps".format(
+                    correction_move
+                )
+            )
             m.focus_rel(correction_move)
             return m.data_dict()
-

openflexure_microscope/plugins/default/camera_calibration/__init__.py

@@ -1,2 +1,2 @@
-__all__ = ['Plugin']
+__all__ = ["Plugin"]
 from .plugin import Plugin

openflexure_microscope/plugins/default/camera_calibration/plugin.py

@@ -1,4 +1,10 @@
-from openflexure_microscope.devel import MicroscopePlugin, MicroscopeViewPlugin, JsonResponse, request, jsonify
+from openflexure_microscope.devel import (
+    MicroscopePlugin,
+    MicroscopeViewPlugin,
+    JsonResponse,
+    request,
+    jsonify,
+)
 
 import logging
 
@@ -19,9 +25,7 @@ class Plugin(MicroscopePlugin):
     A set of default plugins
     """
 
-    api_views = {
-        '/recalibrate': RecalibrateAPIView,
-    }
+    api_views = {"/recalibrate": RecalibrateAPIView}
 
     def recalibrate(self):
         """Reset the camera's settings.
@@ -32,8 +36,10 @@ class Plugin(MicroscopePlugin):
         """
         scamera = self.microscope.camera
         with scamera.lock:
-            assert not scamera.state['record_active'], "Can't recalibrate while recording!"
-            streaming = scamera.state['stream_active']
+            assert not scamera.state[
+                "record_active"
+            ], "Can't recalibrate while recording!"
+            streaming = scamera.state["stream_active"]
             if streaming:
                 logging.info("Stopping stream before recalibration")
                 scamera.stop_stream_recording(resolution=(640, 480))

openflexure_microscope/plugins/default/camera_calibration/recalibrate_utils.py

@@ -4,10 +4,11 @@ import time
 from picamera import PiCamera
 from picamera.array import PiRGBArray, PiBayerArray
 
+
 def rgb_image(camera, resize=None, **kwargs):
     """Capture an image and return an RGB numpy array"""
     with PiRGBArray(camera, size=resize) as output:
-        camera.capture(output, format='rgb', resize=resize, **kwargs)
+        camera.capture(output, format="rgb", resize=resize, **kwargs)
         return output.array
 
 
@@ -19,7 +20,9 @@ def flat_lens_shading_table(camera):
     library (with lens shading table support) it will raise an error.
     """
     if not hasattr(PiCamera, "lens_shading_table"):
-        raise ImportError("This program requires the forked picamera library with lens shading support")
+        raise ImportError(
+            "This program requires the forked picamera library with lens shading support"
+        )
     return np.zeros(camera._lens_shading_table_shape(), dtype=np.uint8) + 32
 
 
@@ -28,7 +31,9 @@ def adjust_exposure_to_setpoint(camera, setpoint):
     print("Adjusting shutter speed to hit setpoint {}".format(setpoint), end="")
     for i in range(3):
         print(".", end="")
-        camera.shutter_speed = int(camera.shutter_speed * setpoint / np.max(rgb_image(camera)))
+        camera.shutter_speed = int(
+            camera.shutter_speed * setpoint / np.max(rgb_image(camera))
+        )
         time.sleep(1)
     print("done")
 
@@ -38,7 +43,9 @@ def auto_expose_and_freeze_settings(camera):
     print("Allowing the camera to auto-expose")
     camera.awb_mode = "auto"
     camera.exposure_mode = "auto"
-    camera.iso = 0 # This is important, if it's on a fixed ISO, gain might not set properly.
+    camera.iso = (
+        0
+    )  # This is important, if it's on a fixed ISO, gain might not set properly.
     for i in range(6):
         print(".", end="")
         time.sleep(0.5)
@@ -53,17 +60,26 @@ def auto_expose_and_freeze_settings(camera):
     camera.awb_mode = "off"
     camera.awb_gains = g
     print("Auto white balance disabled, gains are {}".format(g))
-    print("Analogue gain: {}, Digital gain: {}".format(camera.analog_gain, camera.digital_gain))
+    print(
+        "Analogue gain: {}, Digital gain: {}".format(
+            camera.analog_gain, camera.digital_gain
+        )
+    )
     adjust_exposure_to_setpoint(camera, 215)
 
 
 def channels_from_bayer_array(bayer_array):
     """Given the 'array' from a PiBayerArray, return the 4 channels."""
-    bayer_pattern = [(i//2, i % 2) for i in range(4)]
-    channels = np.zeros((4, bayer_array.shape[0]//2, bayer_array.shape[1]//2), dtype=bayer_array.dtype)
+    bayer_pattern = [(i // 2, i % 2) for i in range(4)]
+    channels = np.zeros(
+        (4, bayer_array.shape[0] // 2, bayer_array.shape[1] // 2),
+        dtype=bayer_array.dtype,
+    )
     for i, offset in enumerate(bayer_pattern):
         # We simplify life by dealing with only one channel at a time.
-        channels[i, :, :] = np.sum(bayer_array[offset[0]::2, offset[1]::2, :], axis=2)
+        channels[i, :, :] = np.sum(
+            bayer_array[offset[0] :: 2, offset[1] :: 2, :], axis=2
+        )
 
     return channels
 
@@ -86,25 +102,27 @@ def lst_from_channels(channels):
         # pad the image by copying edge pixels, so that it is exactly 32 times the
         # size of the lens shading table (NB 32 not 64 because each channel is only
         # half the size of the full image - remember the Bayer pattern...  This
-        # should give results very close to 6by9's solution, albeit considerably 
+        # should give results very close to 6by9's solution, albeit considerably
         # less computationally efficient!
-        padded_image_channel = np.pad(image_channel, 
-                                      [(0, lw*32 - iw), (0, lh*32 - ih)],
-                                      mode="edge")  # Pad image to the right and bottom
-        print("Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format(iw,
-                                                                                          ih,
-                                                                                          lw*32,
-                                                                                          lh*32,
-                                                                                          padded_image_channel.shape))
+        padded_image_channel = np.pad(
+            image_channel, [(0, lw * 32 - iw), (0, lh * 32 - ih)], mode="edge"
+        )  # Pad image to the right and bottom
+        print(
+            "Channel shape: {}x{}, shading table shape: {}x{}, after padding {}".format(
+                iw, ih, lw * 32, lh * 32, padded_image_channel.shape
+            )
+        )
         # Next, fill the shading table (except edge pixels).  Please excuse the
         # for loop - I know it's not fast but this code needn't be!
         box = 3  # We average together a square of this side length for each pixel.
         # NB this isn't quite what 6by9's program does - it averages 3 pixels
         # horizontally, but not vertically.
-        for dx in np.arange(box) - box//2:
-            for dy in np.arange(box) - box//2:
-                ls_channel[:, :] += padded_image_channel[16+dx::32, 16+dy::32] - 64
-        ls_channel /= box**2
+        for dx in np.arange(box) - box // 2:
+            for dy in np.arange(box) - box // 2:
+                ls_channel[:, :] += (
+                    padded_image_channel[16 + dx :: 32, 16 + dy :: 32] - 64
+                )
+        ls_channel /= box ** 2
         # The original C code written by 6by9 normalises to the central 64 pixels in each channel.
         # ls_channel /= np.mean(image_channel[iw//2-4:iw//2+4, ih//2-4:ih//2+4])
         # I have had better results just normalising to the maximum:
@@ -114,10 +132,10 @@ def lst_from_channels(channels):
         # For most sensible lenses I'd expect that 1.0 is the maximum value.
         # NB ls_channel should be a "view" of the whole lens shading array, so we don't
         # need to update the big array here.
-     
-    # What we actually want to calculate is the gains needed to compensate for the 
+
+    # What we actually want to calculate is the gains needed to compensate for the
     # lens shading - that's 1/lens_shading_table_float as we currently have it.
-    gains = 32.0/lens_shading  # 32 is unity gain
+    gains = 32.0 / lens_shading  # 32 is unity gain
     gains[gains > 255] = 255  # clip at 255, maximum gain is 255/32
     gains[gains < 32] = 32  # clip at 32, minimum gain is 1 (is this necessary?)
     lens_shading_table = gains.astype(np.uint8)
@@ -145,7 +163,7 @@ def recalibrate_camera(camera):
     # raw_image is a 3D array, with full resolution and 3 colour channels.  No
     # de-mosaicing has been done, so 2/3 of the values are zero (3/4 for R and B
     # channels, 1/2 for green because there's twice as many green pixels).
-    channels = channels_from_bayer_array(raw_image) 
+    channels = channels_from_bayer_array(raw_image)
     lens_shading_table = lst_from_channels(channels)
 
     camera.lens_shading_table = lens_shading_table
@@ -154,8 +172,10 @@ def recalibrate_camera(camera):
     # Fix the AWB gains so the image is neutral
     channel_means = np.mean(np.mean(rgb_image(camera), axis=0, dtype=np.float), axis=0)
     old_gains = camera.awb_gains
-    camera.awb_gains = (channel_means[1]/channel_means[0] * old_gains[0],
-                        channel_means[1]/channel_means[2]*old_gains[1])
+    camera.awb_gains = (
+        channel_means[1] / channel_means[0] * old_gains[0],
+        channel_means[1] / channel_means[2] * old_gains[1],
+    )
     time.sleep(1)
     # Ensure the background is bright but not saturated
     adjust_exposure_to_setpoint(camera, 230)

openflexure_microscope/plugins/default/scan/__init__.py

@@ -1,2 +1,2 @@
-__all__ = ['ScanPlugin']
+__all__ = ["ScanPlugin"]
 from .plugin import ScanPlugin

openflexure_microscope/plugins/default/scan/api.py

@@ -1,36 +1,46 @@
-from openflexure_microscope.devel import MicroscopeViewPlugin, JsonResponse, request, jsonify, abort
+from openflexure_microscope.devel import (
+    MicroscopeViewPlugin,
+    JsonResponse,
+    request,
+    jsonify,
+    abort,
+)
 
 import logging
 
+
 class TileScanAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonResponse(request)
 
         # Get params
-        filename = payload.param('filename')
-        temporary = payload.param('temporary', default=False, convert=bool)
+        filename = payload.param("filename")
+        temporary = payload.param("temporary", default=False, convert=bool)
 
-        step_size = payload.param('step_size', default=[2000, 1500, 100], convert=list)
+        step_size = payload.param("step_size", default=[2000, 1500, 100], convert=list)
         step_size = [int(i) for i in step_size]
 
-        grid = payload.param('grid', default=[3, 3, 5], convert=list)
+        grid = payload.param("grid", default=[3, 3, 5], convert=list)
         grid = [int(i) for i in grid]
 
-        style = payload.param('style', default='raster', convert=str)
-        autofocus_dz = payload.param('autofocus_dz', default=50, convert=int)
-        fast_autofocus = payload.param('fast_autofocus', default=False, convert=bool)
+        style = payload.param("style", default="raster", convert=str)
+        autofocus_dz = payload.param("autofocus_dz", default=50, convert=int)
+        fast_autofocus = payload.param("fast_autofocus", default=False, convert=bool)
 
-        use_video_port = payload.param('use_video_port', default=True, convert=bool)
-        resize = payload.param('size', default=None)
+        use_video_port = payload.param("use_video_port", default=True, convert=bool)
+        resize = payload.param("size", default=None)
         if resize:
-            if ('width' in resize) and ('height' in resize):
-                resize = (int(resize['width']), int(resize['height']))  # Convert dict to tuple
+            if ("width" in resize) and ("height" in resize):
+                resize = (
+                    int(resize["width"]),
+                    int(resize["height"]),
+                )  # Convert dict to tuple
             else:
                 abort(404)
 
-        bayer = payload.param('bayer', default=False, convert=bool)
-        metadata = payload.param('metadata', default={}, convert=dict)
-        tags = payload.param('tags', default=[], convert=list)
+        bayer = payload.param("bayer", default=False, convert=bool)
+        metadata = payload.param("metadata", default={}, convert=dict)
+        tags = payload.param("tags", default=[], convert=list)
 
         logging.info("Running tile scan...")
         task = self.microscope.task.start(
@@ -46,7 +56,7 @@ class TileScanAPI(MicroscopeViewPlugin):
             bayer=bayer,
             fast_autofocus=fast_autofocus,
             metadata=metadata,
-            tags=tags
+            tags=tags,
         )
 
         # return a handle on the autofocus task

openflexure_microscope/plugins/default/scan/plugin.py

@@ -11,29 +11,31 @@ from openflexure_microscope.devel import MicroscopePlugin
 
 from .api import TileScanAPI
 
-def construct_grid(initial, step_sizes, n_steps, style='raster'):
+
+def construct_grid(initial, step_sizes, n_steps, style="raster"):
     """
     Given an initial position, step sizes, and number of steps,
     construct a 2-dimensional list of scan x-y positions.
     """
     arr = []
 
-    for i in range(n_steps[0]): # x axis
+    for i in range(n_steps[0]):  # x axis
         arr.append([])
-        for j in range(n_steps[1]): # y axis
+        for j in range(n_steps[1]):  # y axis
             # Create a coordinate array
-            coord = [initial[ax] + [i, j][ax]*step_sizes[ax] for ax in range(2)]
+            coord = [initial[ax] + [i, j][ax] * step_sizes[ax] for ax in range(2)]
             # Append coordinate array to position grid
             arr[i].append(tuple(coord))
 
     # Style modifiers
-    if style == 'snake':
+    if style == "snake":
         for i, line in enumerate(arr):
             if i % 2 != 0:
                 line.reverse()
 
     return arr
 
+
 def flatten_grid(grid):
     """
     Convert a 3D list of scan positions into a flat list
@@ -43,24 +45,25 @@ def flatten_grid(grid):
     grid = list(itertools.chain(*grid))
     return grid
 
+
 class ScanPlugin(MicroscopePlugin):
     """
     Stack and tile plugin
     """
 
-    api_views = {
-        '/tile': TileScanAPI,
-    }
+    api_views = {"/tile": TileScanAPI}
 
-    def capture(self,
-                basename,
-                scan_id,
-                temporary: bool = False,
-                use_video_port: bool = False,
-                resize: Tuple[int, int] = None,
-                bayer: bool = False,
-                metadata: dict = {},
-                tags: list = []):
+    def capture(
+        self,
+        basename,
+        scan_id,
+        temporary: bool = False,
+        use_video_port: bool = False,
+        resize: Tuple[int, int] = None,
+        bayer: bool = False,
+        metadata: dict = {},
+        tags: list = [],
+    ):
 
         # Construct a tile filename
         filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position)
@@ -68,47 +71,46 @@ class ScanPlugin(MicroscopePlugin):
 
         # Create output object
         output = self.microscope.camera.new_image(
-            write_to_file=True,
-            temporary=temporary,
-            filename=filename,
-            folder=folder)
+            write_to_file=True, temporary=temporary, filename=filename, folder=folder
+        )
 
         # Capture
         self.microscope.camera.capture(
-            output,
-            use_video_port=use_video_port,
-            resize=resize,
-            bayer=bayer)
+            output, use_video_port=use_video_port, resize=resize, bayer=bayer
+        )
 
         # Affix metadata
-        if 'scan' not in tags:
-            tags.append('scan')
+        if "scan" not in tags:
+            tags.append("scan")
 
-        metadata.update({
-            'position': self.microscope.state['stage']['position'],
-            'scan_id': scan_id,
-            'basename': basename,
-            'microscope_id': self.microscope.id,
-            'microscope_name': self.microscope.name
-        })
+        metadata.update(
+            {
+                "position": self.microscope.state["stage"]["position"],
+                "scan_id": scan_id,
+                "basename": basename,
+                "microscope_id": self.microscope.id,
+                "microscope_name": self.microscope.name,
+            }
+        )
 
         output.put_metadata(metadata)
         output.put_tags(tags)
 
     def tile(
-            self,
-            basename: str = None,
-            temporary: bool = False,
-            step_size: int = [2000, 1500, 100],
-            grid: list = [3, 3, 5],
-            style='raster',
-            autofocus_dz: int = 50,
-            use_video_port: bool = False,
-            resize: Tuple[int, int] = None,
-            bayer: bool = False,
-            fast_autofocus = False,
-            metadata: dict = {},
-            tags: list = []):
+        self,
+        basename: str = None,
+        temporary: bool = False,
+        step_size: int = [2000, 1500, 100],
+        grid: list = [3, 3, 5],
+        style="raster",
+        autofocus_dz: int = 50,
+        use_video_port: bool = False,
+        resize: Tuple[int, int] = None,
+        bayer: bool = False,
+        fast_autofocus=False,
+        metadata: dict = {},
+        tags: list = [],
+    ):
 
         # Generate a basename if none given
         if not basename:
@@ -121,42 +123,47 @@ class ScanPlugin(MicroscopePlugin):
         initial_position = self.microscope.stage.position
 
         # Add scan metadata
-        if not 'time' in metadata:
-            metadata['time'] = generate_basename()
+        if not "time" in metadata:
+            metadata["time"] = generate_basename()
 
         # Check if autofocus is enabled
-        if autofocus_dz and hasattr(self.microscope.plugin, 'default_autofocus'):
+        if autofocus_dz and hasattr(self.microscope.plugin, "default_autofocus"):
             autofocus_enabled = True
         else:
             autofocus_enabled = False
 
-        if fast_autofocus and not hasattr(self.microscope.plugin.default_autofocus, 'monitor_sharpness'):
-            logging.error("Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?")
+        if fast_autofocus and not hasattr(
+            self.microscope.plugin.default_autofocus, "monitor_sharpness"
+        ):
+            logging.error(
+                "Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?"
+            )
             fast_autofocus = False
-        z_stack_dz = grid[2] * step_size[2] if grid[2] > 1 else 0 # shorthand for Z stack range
+        z_stack_dz = (
+            grid[2] * step_size[2] if grid[2] > 1 else 0
+        )  # shorthand for Z stack range
 
         # Construct an x-y grid (worry about z later)
         x_y_grid = construct_grid(
-            initial_position, 
-            step_size[:2], 
-            grid[:2],
-            style=style
+            initial_position, step_size[:2], grid[:2], style=style
         )
 
         # Keep the initial Z position the same as our current position
         next_z = initial_position[2]
-        if fast_autofocus:           # If fast autofocus is enabled, make
-            next_z += autofocus_dz/2 # sure we start from the top of the range
-        initial_z = next_z # Save this value for use in raster scans
+        if fast_autofocus:  # If fast autofocus is enabled, make
+            next_z += autofocus_dz / 2  # sure we start from the top of the range
+        initial_z = next_z  # Save this value for use in raster scans
 
         # Now step through each point in the x-y coordinate array
         for line in x_y_grid:
             # If rastering, rather than snake (or eventually spiral)
             # Return focus to initial position
-            if style == 'raster':
+            if style == "raster":
                 next_z = initial_z
                 logging.debug("Returning to initial z position")
-                self.microscope.stage.move_abs([line[0][0], line[0][1], next_z]) #RWB: I think this line is redundant
+                self.microscope.stage.move_abs(
+                    [line[0][0], line[0][1], next_z]
+                )  # RWB: I think this line is redundant
 
             for x_y in line:
                 # Move to new grid position without changing z
@@ -166,20 +173,21 @@ class ScanPlugin(MicroscopePlugin):
                 if autofocus_enabled:
                     if fast_autofocus:
                         self.microscope.plugin.default_autofocus.fast_up_down_up_autofocus(
-                                dz=autofocus_dz,
-                                target_z=-z_stack_dz/2.0, # Finish below the focus
-                                initial_move_up=False, # We're already at the top of the scan
-                                )
-                        #TODO: save the focus data for future reference? Use it for diagnostics?
+                            dz=autofocus_dz,
+                            target_z=-z_stack_dz / 2.0,  # Finish below the focus
+                            initial_move_up=False,  # We're already at the top of the scan
+                        )
+                        # TODO: save the focus data for future reference? Use it for diagnostics?
                     else:
                         logging.debug("Running autofocus")
                         self.microscope.plugin.default_autofocus.autofocus(
-                            range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz))
+                            range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
+                        )
                         logging.debug("Finished autofocus")
                         time.sleep(1)  # TODO: Remove
 
                 # If we're not doing a z-stack, just capture
-                if (grid[2] <= 1):
+                if grid[2] <= 1:
                     self.capture(
                         basename,
                         scan_id,
@@ -188,7 +196,7 @@ class ScanPlugin(MicroscopePlugin):
                         resize=resize,
                         bayer=bayer,
                         metadata=metadata,
-                        tags=tags
+                        tags=tags,
                     )
                 else:
                     logging.debug("Entering z-stack")
@@ -198,38 +206,43 @@ class ScanPlugin(MicroscopePlugin):
                         scan_id=scan_id,
                         step_size=step_size[2],
                         steps=grid[2],
-                        center=not fast_autofocus, # fast_autofocus does this for us!
+                        center=not fast_autofocus,  # fast_autofocus does this for us!
                         return_to_start=not fast_autofocus,
                         use_video_port=use_video_port,
                         resize=resize,
                         bayer=bayer,
                         metadata=metadata,
-                        tags=tags
+                        tags=tags,
                     )
                 # Make sure we use our current best estimate of focus (i.e. the current position) next point
                 next_z = self.microscope.stage.position[2]
                 if fast_autofocus:
-                    next_z += autofocus_dz/2 # Fast autofocus requires us to start at the top of the range
+                    next_z += (
+                        autofocus_dz / 2
+                    )  # Fast autofocus requires us to start at the top of the range
                     if grid[2] > 1:
-                        next_z -= int(grid[2]/2.0*step_size[2]) # Z stacking means we're higher up to start with
+                        next_z -= int(
+                            grid[2] / 2.0 * step_size[2]
+                        )  # Z stacking means we're higher up to start with
 
         logging.debug("Returning to {}".format(initial_position))
         self.microscope.stage.move_abs(initial_position)
 
     def stack(
-            self,
-            basename: str = None,
-            temporary: bool = False,
-            scan_id: str = None,
-            step_size: int = 100,
-            steps: int = 5,
-            center: bool = True,
-            return_to_start: bool = True,
-            use_video_port: bool = False,
-            resize: Tuple[int, int] = None,
-            bayer: bool = False,
-            metadata: dict = {},
-            tags: list = []):
+        self,
+        basename: str = None,
+        temporary: bool = False,
+        scan_id: str = None,
+        step_size: int = 100,
+        steps: int = 5,
+        center: bool = True,
+        return_to_start: bool = True,
+        use_video_port: bool = False,
+        resize: Tuple[int, int] = None,
+        bayer: bool = False,
+        metadata: dict = {},
+        tags: list = [],
+    ):
 
         # Generate a basename if none given
         if not basename:
@@ -240,13 +253,12 @@ class ScanPlugin(MicroscopePlugin):
             scan_id = uuid.uuid4().hex
 
         # Add scan metadata
-        if not 'time' in metadata:
-            metadata['time'] = generate_basename()
+        if not "time" in metadata:
+            metadata["time"] = generate_basename()
 
         # Store initial position
         initial_position = self.microscope.stage.position
 
-
         with self.microscope.lock:
             # Move to center scan
             if center:
@@ -264,7 +276,7 @@ class ScanPlugin(MicroscopePlugin):
                     resize=resize,
                     bayer=bayer,
                     metadata=metadata,
-                    tags=tags
+                    tags=tags,
                 )
 
                 if i != steps - 1:

openflexure_microscope/plugins/example/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ['Plugin', 'HelloWorldAPI', 'IdentifyAPI']
+__all__ = ["Plugin", "HelloWorldAPI", "IdentifyAPI"]
 
 from .plugin import Plugin
-from .api import HelloWorldAPI, IdentifyAPI
+from .api import HelloWorldAPI, IdentifyAPI

openflexure_microscope/plugins/example/api.py

@@ -9,11 +9,14 @@ class IdentifyAPI(MicroscopeViewPlugin):
     """
     A simple example API plugin, attached through the main microscope plugin.
     """
+
     def get(self):
         """
         Method to call when an HTTP GET request is made.
         """
-        data = self.plugin.identify()  # Call a method from our plugin, using the MicroscopeViewPlugin.plugin shortcut
+        data = (
+            self.plugin.identify()
+        )  # Call a method from our plugin, using the MicroscopeViewPlugin.plugin shortcut
         return Response(escape(data))
 
 
@@ -28,7 +31,7 @@ class HelloWorldAPI(MicroscopeViewPlugin):
         """
 
         # If the microscope does not already contain our plugin_string attribute
-        if not hasattr(self.microscope, 'plugin_string'):
+        if not hasattr(self.microscope, "plugin_string"):
             # Make a string, using the MicroscopeViewPlugin.plugin shortcut
             self.microscope.plugin_string = self.plugin.hello_world()
 
@@ -43,7 +46,7 @@ class HelloWorldAPI(MicroscopeViewPlugin):
         payload = JsonResponse(request)
 
         # Extract a value from the JSON key 'plugin_string', and convert to a string. If no value is given, default to empty.
-        new_plugin_string = payload.param('plugin_string', default='', convert=str)
+        new_plugin_string = payload.param("plugin_string", default="", convert=str)
 
         if new_plugin_string:  # If not None or empty
             # Set microscope attribute to the specified string
@@ -56,6 +59,7 @@ class LongRunningAPI(MicroscopeViewPlugin):
     """
     An example API plugin that uses a long-running plugin method.
     """
+
     def post(self):
         """
         Method to call when an HTTP POST request is made.
@@ -64,7 +68,7 @@ class LongRunningAPI(MicroscopeViewPlugin):
         payload = JsonResponse(request)
 
         # Extract a values from the JSON payload.
-        time_to_run = payload.param('time', default=10, convert=int)
+        time_to_run = payload.param("time", default=10, convert=int)
 
         # Attach the long-running method as a microscope task
         try:
@@ -79,6 +83,7 @@ class SomeExceptionAPI(MicroscopeViewPlugin):
     """
     An example API plugin that uses a long-running but broken plugin method.
     """
+
     def post(self):
         """
         Method to call when an HTTP POST request is made.

openflexure_microscope/plugins/example/plugin.py

@@ -11,10 +11,10 @@ class Plugin(MicroscopePlugin):
     """
 
     api_views = {
-        '/identify': IdentifyAPI,
-        '/hello': HelloWorldAPI,
-        '/long_running': LongRunningAPI,
-        '/some_exception': SomeExceptionAPI,
+        "/identify": IdentifyAPI,
+        "/hello": HelloWorldAPI,
+        "/long_running": LongRunningAPI,
+        "/some_exception": SomeExceptionAPI,
     }
 
     def identify(self):
@@ -22,7 +22,9 @@ class Plugin(MicroscopePlugin):
         Demonstrate access to Microscope.camera, and Microscope.stage
         """
 
-        response = "My parent camera is {}, and my parent stage is {}.".format(self.microscope.camera, self.microscope.stage)
+        response = "My parent camera is {}, and my parent stage is {}.".format(
+            self.microscope.camera, self.microscope.stage
+        )
         print(response)
         return response
 
@@ -39,7 +41,7 @@ class Plugin(MicroscopePlugin):
         """
         with self.microscope.lock:
             time.sleep(3)
-            result = 15./0
+            result = 15.0 / 0
 
         return result
 

openflexure_microscope/plugins/loader.py

@@ -5,14 +5,14 @@ import logging
 
 
 class ConColors:
-    HEADER = '\033[95m'
-    OKBLUE = '\033[94m'
-    OKGREEN = '\033[92m'
-    WARNING = '\033[93m'
-    FAIL = '\033[91m'
-    ENDC = '\033[0m'
-    BOLD = '\033[1m'
-    UNDERLINE = '\033[4m'
+    HEADER = "\033[95m"
+    OKBLUE = "\033[94m"
+    OKGREEN = "\033[92m"
+    WARNING = "\033[93m"
+    FAIL = "\033[91m"
+    ENDC = "\033[0m"
+    BOLD = "\033[1m"
+    UNDERLINE = "\033[4m"
 
 
 def module_from_file(plugin_path):
@@ -23,7 +23,11 @@ def module_from_file(plugin_path):
 
     # Check if the path is to a file
     if not os.path.isfile(plugin_path):
-        logging.warning(ConColors.FAIL + "No valid plugin found at {}.".format(plugin_path) + ConColors.ENDC)
+        logging.warning(
+            ConColors.FAIL
+            + "No valid plugin found at {}.".format(plugin_path)
+            + ConColors.ENDC
+        )
         return None, None, None
 
     else:
@@ -35,6 +39,7 @@ def module_from_file(plugin_path):
 
         return plugin_spec, plugin_module, plugin_name
 
+
 def check_module(module_path):
     """
     Used to check if a module exists, without ever importing it.
@@ -65,13 +70,13 @@ def check_module(module_path):
 
 
 def name_from_module(plugin_path):
-    path_array = plugin_path.split('.')
+    path_array = plugin_path.split(".")
 
     # Truncate namespace of default plugins
-    if path_array[0:2] == ['openflexure_microscope', 'plugins']:
+    if path_array[0:2] == ["openflexure_microscope", "plugins"]:
         path_array = path_array[2:]
-    
-    return '/'.join(path_array)
+
+    return "/".join(path_array)
 
 
 def load_plugin_module(plugin_path):
@@ -104,7 +109,13 @@ def load_plugin_class(plugin_path, plugin_class_name):
         try:
             plugin_class = getattr(plugin_module, plugin_class_name)
         except AttributeError:
-            logging.warning(ConColors.FAIL + "Class {} does not exist in plugin {}. Skipping.".format(plugin_class_name, plugin_path) + ConColors.ENDC)
+            logging.warning(
+                ConColors.FAIL
+                + "Class {} does not exist in plugin {}. Skipping.".format(
+                    plugin_class_name, plugin_path
+                )
+                + ConColors.ENDC
+            )
             return None, None
         else:
             return plugin_class, plugin_name
@@ -113,10 +124,14 @@ def load_plugin_class(plugin_path, plugin_class_name):
 
 
 def class_from_map(plugin_map):
-    plugin_arr = plugin_map.split(':')
+    plugin_arr = plugin_map.split(":")
 
     if not len(plugin_arr) == 2:
-        logging.warning(ConColors.WARNING + "Malformed plugin map {}. Skipping.".format(plugin_map) + ConColors.ENDC)
+        logging.warning(
+            ConColors.WARNING
+            + "Malformed plugin map {}. Skipping.".format(plugin_map)
+            + ConColors.ENDC
+        )
         return None, None
     else:
         return load_plugin_class(*plugin_arr)
@@ -129,6 +144,7 @@ class PluginMount(object):
     Args:
         parent (:py:class:`openflexure_microscope.microscope.Microscope`): The parent Microscope object to attach to.
     """
+
     def __init__(self, parent):
         self.parent = parent
         self.plugins = []  # List of plugin objects
@@ -141,13 +157,17 @@ class PluginMount(object):
 
     @property
     def members(self):
-        ignores = ['state', 'members', 'attach']
+        ignores = ["state", "members", "attach"]
         plugin_array = []
         for obj_name in dir(self):
-            if not obj_name in ignores and not obj_name[:2] == '__':
+            if not obj_name in ignores and not obj_name[:2] == "__":
                 obj = getattr(self, obj_name)
                 if isinstance(obj, MicroscopePlugin):
-                    plugin_members = [member for member in inspect.getmembers(obj) if not member[0][:2] == '__']
+                    plugin_members = [
+                        member
+                        for member in inspect.getmembers(obj)
+                        if not member[0][:2] == "__"
+                    ]
                     plugin_info = (obj_name, plugin_members)
                     plugin_array.append(plugin_info)
         return plugin_array
@@ -168,10 +188,20 @@ class PluginMount(object):
             if plugin_class and plugin_name:
                 plugin_object = plugin_class()
 
-                if hasattr(self, plugin_name):  # If a plugin with the same name is already attached.
-                    logging.warning(ConColors.WARNING + "A plugin named {} has already been loaded. Skipping {}.".format(plugin_name, plugin_map) + ConColors.ENDC)
+                if hasattr(
+                    self, plugin_name
+                ):  # If a plugin with the same name is already attached.
+                    logging.warning(
+                        ConColors.WARNING
+                        + "A plugin named {} has already been loaded. Skipping {}.".format(
+                            plugin_name, plugin_map
+                        )
+                        + ConColors.ENDC
+                    )
 
-                elif isinstance(plugin_object, MicroscopePlugin):  # If plugin_object is an instance of MicroscopePlugin
+                elif isinstance(
+                    plugin_object, MicroscopePlugin
+                ):  # If plugin_object is an instance of MicroscopePlugin
                     # Attach plugin_object to the plugin mount
                     setattr(self, pythonsafe_plugin_name, plugin_object)
                     self.plugins.append((plugin_name, plugin_object))
@@ -179,11 +209,16 @@ class PluginMount(object):
                     # Grant plugin access to the hardware
                     plugin_object.microscope = self.parent
 
-                    logging.info(ConColors.OKGREEN + "Plugin {} loaded as {}.".format(plugin_map, plugin_name) + ConColors.ENDC)
+                    logging.info(
+                        ConColors.OKGREEN
+                        + "Plugin {} loaded as {}.".format(plugin_map, plugin_name)
+                        + ConColors.ENDC
+                    )
 
         else:
             logging.error(f"Error loading plugin {plugin_map}. Moving on.")
 
+
 class MicroscopePlugin:
     """
     Parent class for all microscope plugins.
@@ -195,4 +230,6 @@ class MicroscopePlugin:
     api_views = {}  # Initially empty dictionary of API views associated with the plugin
 
     def __init__(self):
-        self.microscope = None  #: :py:class:`openflexure_microscope.microscope.Microscope`: Microscope object
+        self.microscope = (
+            None
+        )  #: :py:class:`openflexure_microscope.microscope.Microscope`: Microscope object

openflexure_microscope/plugins/testing/form_example/__init__.py

@@ -1,2 +1,2 @@
 from .plugin import ExamplePlugin
-from . import api
+from . import api

openflexure_microscope/plugins/testing/form_example/api.py

@@ -1,7 +1,16 @@
-from openflexure_microscope.devel import MicroscopeViewPlugin, TaskDeniedException, JsonResponse, Response, request, escape, jsonify
+from openflexure_microscope.devel import (
+    MicroscopeViewPlugin,
+    TaskDeniedException,
+    JsonResponse,
+    Response,
+    request,
+    escape,
+    jsonify,
+)
 
 import logging
 
+
 class DoAPI(MicroscopeViewPlugin):
     """
     A simple example API plugin
@@ -15,27 +24,21 @@ class DoAPI(MicroscopeViewPlugin):
         payload = JsonResponse(request)
 
         # Extract a values from the JSON payload.
-        val_int = payload.param('val_int', default=None, convert=int)
-        val_str = payload.param('val_str', default=None, convert=str)
-        val_radio = payload.param('val_radio', default=None)
-        val_check = payload.param('val_check', default=None)
-        val_select = payload.param('val_select', default=None)
-        val_disposable = payload.param('val_disposable', default=None)
+        val_int = payload.param("val_int", default=None, convert=int)
+        val_str = payload.param("val_str", default=None, convert=str)
+        val_radio = payload.param("val_radio", default=None)
+        val_check = payload.param("val_check", default=None)
+        val_select = payload.param("val_select", default=None)
+        val_disposable = payload.param("val_disposable", default=None)
 
         self.plugin.set_values(
-            val_int,
-            val_str,
-            val_radio,
-            val_check,
-            val_select,
-            val_disposable
+            val_int, val_str, val_radio, val_check, val_select, val_disposable
         )
 
         print(self.plugin.get_values_dict())
 
-        return jsonify({
-            'response': 'completed'
-        })
+        return jsonify({"response": "completed"})
+
 
 class TaskAPI(MicroscopeViewPlugin):
     """
@@ -43,19 +46,19 @@ class TaskAPI(MicroscopeViewPlugin):
     """
 
     def get(self):
-        return jsonify({
-            'run_time': self.plugin.run_time
-        })
+        return jsonify({"run_time": self.plugin.run_time})
 
     def post(self):
         # Get payload JSON
         payload = JsonResponse(request)
 
         # Extract a values from the JSON payload.
-        val_int = payload.param('run_time', default=5, convert=int)
+        val_int = payload.param("run_time", default=5, convert=int)
 
         logging.info("Running task...")
-        task = self.microscope.task.start(self.plugin.generate_random_numbers_for_a_while, val_int)
+        task = self.microscope.task.start(
+            self.plugin.generate_random_numbers_for_a_while, val_int
+        )
 
         # return a handle on the autofocus task
-        return jsonify(task.state), 202
+        return jsonify(task.state), 202

openflexure_microscope/plugins/testing/form_example/plugin.py

@@ -9,19 +9,18 @@ from .api import DoAPI, TaskAPI
 HERE = os.path.dirname(os.path.realpath(__file__))
 FORM_PATH = os.path.join(HERE, "forms.json")
 
+
 class ExamplePlugin(MicroscopePlugin):
     """
     An example plugin using a comprehensive form
     """
+
     global FORM_PATH
 
-    with open(FORM_PATH, 'r') as sc:
+    with open(FORM_PATH, "r") as sc:
         api_form = json.load(sc)
 
-    api_views = {
-        '/do': DoAPI,
-        '/task': TaskAPI
-    }
+    api_views = {"/do": DoAPI, "/task": TaskAPI}
 
     def __init__(self):
         self.val_int = 10
@@ -33,7 +32,9 @@ class ExamplePlugin(MicroscopePlugin):
 
         self.run_time = 5
 
-    def set_values(self, val_int, val_str, val_radio, val_check, val_select, val_disposable):
+    def set_values(
+        self, val_int, val_str, val_radio, val_check, val_select, val_disposable
+    ):
         """
         Demonstrate a plugin with form
         """
@@ -54,12 +55,12 @@ class ExamplePlugin(MicroscopePlugin):
 
     def get_values_dict(self):
         return {
-            'val_int': self.val_int,
-            'val_str': self.val_str,
-            'val_radio': self.val_radio,
-            'val_check': self.val_check,
-            'val_select': self.val_select,
-            'val_unused': self.val_unused
+            "val_int": self.val_int,
+            "val_str": self.val_str,
+            "val_radio": self.val_radio,
+            "val_check": self.val_check,
+            "val_select": self.val_select,
+            "val_unused": self.val_unused,
         }
 
     def generate_random_numbers_for_a_while(self, run_time: int):
@@ -68,5 +69,5 @@ class ExamplePlugin(MicroscopePlugin):
         for _ in range(run_time):
             vals.append(random.random())
             time.sleep(1)
-        
-        return vals
+
+        return vals

openflexure_microscope/stage/__init__.py

@@ -1,3 +1,3 @@
-__all__ = ['base', 'mock', 'sanga']
+__all__ = ["base", "mock", "sanga"]
 
 from . import base, mock, sanga

openflexure_microscope/stage/base.py

@@ -8,6 +8,7 @@ class BaseStage(metaclass=ABCMeta):
         lock (:py:class:`openflexure_microscope.lock.StrictLock`): Strict lock controlling thread
             access to camera hardware
     """
+
     def __init__(self):
         self.lock = StrictLock(timeout=5)
 

openflexure_microscope/stage/mock.py

@@ -4,6 +4,7 @@ from openflexure_microscope.utilities import axes_to_array
 from collections.abc import Iterable
 import numpy as np
 
+
 class MockStage(BaseStage):
     def __init__(self, port=None, **kwargs):
         BaseStage.__init__(self)
@@ -15,13 +16,13 @@ class MockStage(BaseStage):
     def state(self):
         """The general state dictionary of the board."""
         state = {
-            'position': {
-                'x': self.position[0],
-                'y': self.position[1],
-                'z': self.position[2],
+            "position": {
+                "x": self.position[0],
+                "y": self.position[1],
+                "z": self.position[2],
             },
-            'board': None,
-            'version': '0'
+            "board": None,
+            "version": "0",
         }
         return state
 
@@ -29,21 +30,15 @@ class MockStage(BaseStage):
         """Update settings from a config dictionary"""
 
         # Set backlash. Expects a dictionary with axis labels
-        if 'backlash' in config:
+        if "backlash" in config:
             # Construct backlash array
-            backlash = axes_to_array(config['backlash'], ['x', 'y', 'z'], [0, 0, 0])
+            backlash = axes_to_array(config["backlash"], ["x", "y", "z"], [0, 0, 0])
             self.backlash = backlash
 
     def read_config(self) -> dict:
         """Return the current settings as a dictionary"""
         blsh = self.backlash.tolist()
-        config = {
-                'backlash': {
-                    'x': blsh[0],
-                    'y': blsh[1],
-                    'z': blsh[2],
-                }
-            }
+        config = {"backlash": {"x": blsh[0], "y": blsh[1], "z": blsh[2]}}
         return config
 
     @property
@@ -69,7 +64,7 @@ class MockStage(BaseStage):
             assert len(blsh) == self.n_axes
             self._backlash = np.array(blsh)
         else:
-            self._backlash = np.array([int(blsh)]*self.n_axes, dtype=np.int)
+            self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
 
     def move_rel(self, displacement, axis=None, backlash=True):
         pass

openflexure_microscope/stage/sanga.py

@@ -18,26 +18,29 @@ class SangaStage(BaseStage):
         board (:py:class:`openflexure_microscope.stage.sangaboard.Sangaboard`): Parent Sangaboard object.
         _backlash (list): 3-element (element-per-axis) list of backlash compensation in steps.
     """
+
     def __init__(self, port=None, **kwargs):
         """Class managing serial communications with the motors for an Openflexure stage"""
         BaseStage.__init__(self)
 
         self.board = Sangaboard(port, **kwargs)
 
-        self._backlash = None  # Initialise backlash storage, used by property setter/getter
-        self.axis_names = ['x', 'y', 'z']  # Assume all sangaboards are 3 axis
+        self._backlash = (
+            None
+        )  # Initialise backlash storage, used by property setter/getter
+        self.axis_names = ["x", "y", "z"]  # Assume all sangaboards are 3 axis
 
     @property
     def state(self):
         """The general state dictionary of the board."""
         state = {
-            'position': {
-                'x': self.position[0],
-                'y': self.position[1],
-                'z': self.position[2],
+            "position": {
+                "x": self.position[0],
+                "y": self.position[1],
+                "z": self.position[2],
             },
-            'board': self.board.board,
-            'firmware': self.board.firmware
+            "board": self.board.board,
+            "firmware": self.board.firmware,
         }
         return state
 
@@ -80,27 +83,21 @@ class SangaStage(BaseStage):
             assert len(blsh) == self.n_axes
             self._backlash = np.array(blsh)
         else:
-            self._backlash = np.array([int(blsh)]*self.n_axes, dtype=np.int)
+            self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
 
     def apply_config(self, config: dict):
         """Update settings from a config dictionary"""
 
         # Set backlash. Expects a dictionary with axis labels
-        if 'backlash' in config:
+        if "backlash" in config:
             # Construct backlash array
-            backlash = axes_to_array(config['backlash'], ['x', 'y', 'z'], [0, 0, 0])
+            backlash = axes_to_array(config["backlash"], ["x", "y", "z"], [0, 0, 0])
             self.backlash = backlash
 
     def read_config(self) -> dict:
         """Return the current settings as a dictionary"""
         blsh = self.backlash.tolist()
-        config = {
-                'backlash': {
-                    'x': blsh[0],
-                    'y': blsh[1],
-                    'z': blsh[2],
-                }
-            }
+        config = {"backlash": {"x": blsh[0], "y": blsh[1], "z": blsh[2]}}
 
         return config
 
@@ -117,7 +114,9 @@ class SangaStage(BaseStage):
             if axis is not None:
                 # backlash correction is easier if we're always in 3D
                 # so this code just converts single-axis moves into all-axis moves.
-                assert axis in self.axis_names, "axis must be one of {}".format(self.axis_names)
+                assert axis in self.axis_names, "axis must be one of {}".format(
+                    self.axis_names
+                )
                 move = np.zeros(self.n_axes, dtype=np.int)
                 move[np.argmax(np.array(self.axis_names) == axis)] = int(displacement)
                 displacement = move
@@ -134,7 +133,7 @@ class SangaStage(BaseStage):
             initial_move -= np.where(
                 self.backlash * displacement < 0,
                 self.backlash,
-                np.zeros(self.n_axes, dtype=self.backlash.dtype)
+                np.zeros(self.n_axes, dtype=self.backlash.dtype),
             )
             self.board.move_rel(initial_move)
             if np.any(displacement - initial_move != 0):
@@ -160,7 +159,9 @@ class SangaStage(BaseStage):
         """
         starting_position = self.position
         rel_positions = np.array(rel_positions)
-        assert rel_positions.shape[1] == 3, ValueError("Positions should be 3 elements long.")
+        assert rel_positions.shape[1] == 3, ValueError(
+            "Positions should be 3 elements long."
+        )
         try:
             self.move_rel(rel_positions[0], backlash=backlash)
             yield 0
@@ -186,7 +187,7 @@ class SangaStage(BaseStage):
 
     def close(self):
         """Cleanly close communication with the stage"""
-        if hasattr(self, 'board'):
+        if hasattr(self, "board"):
             self.board.close()
 
     # Methods specific to Sangaboard
@@ -205,12 +206,16 @@ class SangaStage(BaseStage):
         need to worry about that here.
         """
         if type is not None:
-            print("An exception occurred inside a with block, resetting position \
-                to its value at the start of the with block")
+            print(
+                "An exception occurred inside a with block, resetting position \
+                to its value at the start of the with block"
+            )
             try:
                 time.sleep(0.5)
                 self.move_abs(self._position_on_enter)
             except Exception as e:
-                print("A further exception occurred when resetting position: {}".format(e))
+                print(
+                    "A further exception occurred when resetting position: {}".format(e)
+                )
             print("Move completed, raising exception...")
             raise value  # Propagate the exception

openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py

@@ -29,6 +29,7 @@ import time
 import logging
 import warnings
 
+
 class ExtensibleSerialInstrument(object):
     """
     An instrument that communicates by sending strings back and forth over serial
@@ -49,8 +50,13 @@ class ExtensibleSerialInstrument(object):
     blocked for a long time.  The lock is reentrant so there's no issue with
     acquiring it twice.
     """
-    termination_character = "\n" #: All messages to or from the instrument end with this character.
-    termination_line = None #: If multi-line responses are recieved, they must end with this string
+
+    termination_character = (
+        "\n"
+    )  #: All messages to or from the instrument end with this character.
+    termination_line = (
+        None
+    )  #: If multi-line responses are recieved, they must end with this string
     ignore_echo = False
     port_settings = {}
 
@@ -61,7 +67,7 @@ class ExtensibleSerialInstrument(object):
         logging.info("Updating ESI port settings")
         self.port_settings.update(kwargs)
         logging.info("Opening ESI connection to port {}".format(port))
-        self.open(port, False) # Eventually this shouldn't rely on init...
+        self.open(port, False)  # Eventually this shouldn't rely on init...
         logging.info("Opened ESI connection to port {}".format(port))
 
     def open(self, port=None, quiet=True):
@@ -71,17 +77,22 @@ class ExtensibleSerialInstrument(object):
         then we don't warn when ports are opened multiple times.
         """
         with self.communications_lock:
-            if hasattr(self,'_ser') and self._ser.isOpen():
-                if not quiet: logging.warning("Attempted to open an already-open port!")
+            if hasattr(self, "_ser") and self._ser.isOpen():
+                if not quiet:
+                    logging.warning("Attempted to open an already-open port!")
                 return
-            if port is None: 
-                port=self.find_port()
-            assert port is not None, "We don't have a serial port to open, meaning you didn't specify a valid port.  Are you sure the instrument is connected?"
-            self._ser = serial.Serial(port,**self.port_settings)
-            #the block above wraps the serial IO layer with a text IO layer
-            #this allows us to read/write in neat lines.  NB the buffer size must
-            #be set to 1 byte for maximum responsiveness.
-            assert self.test_communications(), "The instrument doesn't seem to be responding.  Did you specify the right port?"
+            if port is None:
+                port = self.find_port()
+            assert (
+                port is not None
+            ), "We don't have a serial port to open, meaning you didn't specify a valid port.  Are you sure the instrument is connected?"
+            self._ser = serial.Serial(port, **self.port_settings)
+            # the block above wraps the serial IO layer with a text IO layer
+            # this allows us to read/write in neat lines.  NB the buffer size must
+            # be set to 1 byte for maximum responsiveness.
+            assert (
+                self.test_communications()
+            ), "The instrument doesn't seem to be responding.  Did you specify the right port?"
 
     def close(self):
         """Cleanly close the device. Includes proper logging statements."""
@@ -95,11 +106,12 @@ class ExtensibleSerialInstrument(object):
 
     def __del__(self):
         """Emergency close the device. Try to avoid having to use this."""
-        if hasattr(self, '_ser') and self._ser.isOpen():
+        if hasattr(self, "_ser") and self._ser.isOpen():
             with self.communications_lock:
                 print(
-                    "Closing an open serial communication has been triggered by garbage collection!\n"\
-                    "Please close this device more sensibly in future.")
+                    "Closing an open serial communication has been triggered by garbage collection!\n"
+                    "Please close this device more sensibly in future."
+                )
                 try:
                     self._ser.close()
                 except Exception as e:
@@ -111,30 +123,39 @@ class ExtensibleSerialInstrument(object):
     def __exit__(self, type, value, traceback):
         """Cleanly close down the instrument at end of a with block."""
         self.close()
-        
-    def write(self,query_string):
+
+    def write(self, query_string):
         """Write a string to the serial port"""
         with self.communications_lock:
-            assert self._ser.isOpen(), "Attempted to write to the serial port before it was opened.  Perhaps you need to call the 'open' method first?"
-            #TODO: Check if this code is needed and if not kill it
-#            try:        
-#                if self._ser.outWaiting()>0: self._ser.flushOutput() #ensure there's nothing waiting
-#            except AttributeError:
-#                if self._ser.out_waiting>0: self._ser.flushOutput() #ensure there's nothing waiting
-            data=query_string+self.termination_character
-            data=data.encode()
+            assert (
+                self._ser.isOpen()
+            ), "Attempted to write to the serial port before it was opened.  Perhaps you need to call the 'open' method first?"
+            # TODO: Check if this code is needed and if not kill it
+            #            try:
+            #                if self._ser.outWaiting()>0: self._ser.flushOutput() #ensure there's nothing waiting
+            #            except AttributeError:
+            #                if self._ser.out_waiting>0: self._ser.flushOutput() #ensure there's nothing waiting
+            data = query_string + self.termination_character
+            data = data.encode()
             self._ser.write(data)
 
     def flush_input_buffer(self):
         """Make sure there's nothing waiting to be read, and clear the buffer if there is."""
         with self.communications_lock:
-            if self._ser.inWaiting()>0: self._ser.flushInput()
+            if self._ser.inWaiting() > 0:
+                self._ser.flushInput()
+
     def readline(self, timeout=None):
         """Read one line from the serial port."""
         with self.communications_lock:
-            return self._ser.readline().decode('utf8').replace(self.termination_character,"\n")
+            return (
+                self._ser.readline()
+                .decode("utf8")
+                .replace(self.termination_character, "\n")
+            )
 
     _communications_lock = None
+
     @property
     def communications_lock(self):
         """A lock object used to protect access to the communications bus"""
@@ -143,7 +164,7 @@ class ExtensibleSerialInstrument(object):
         if self._communications_lock is None:
             self._communications_lock = threading.RLock()
         return self._communications_lock
-            
+
     def read_multiline(self, termination_line=None, timeout=None):
         """Read one line from the underlying bus.  Must be overriden.
 
@@ -152,15 +173,19 @@ class ExtensibleSerialInstrument(object):
         with self.communications_lock:
             if termination_line is None:
                 termination_line = self.termination_line
-            assert isinstance(termination_line, str), "If you perform a multiline query, you must specify a termination line either through the termination_line keyword argument or the termination_line property of the NPSerialInstrument."
+            assert isinstance(
+                termination_line, str
+            ), "If you perform a multiline query, you must specify a termination line either through the termination_line keyword argument or the termination_line property of the NPSerialInstrument."
             response = ""
             last_line = "dummy"
-            while termination_line not in last_line and len(last_line) > 0: #read until we get the termination line.
+            while (
+                termination_line not in last_line and len(last_line) > 0
+            ):  # read until we get the termination line.
                 last_line = self.readline(timeout)
                 response += last_line
             return response
-            
-    def query(self,queryString,multiline=False,termination_line=None,timeout=None):
+
+    def query(self, queryString, multiline=False, termination_line=None, timeout=None):
         """
         Write a string to the stage controller and return its response.
 
@@ -170,22 +195,31 @@ class ExtensibleSerialInstrument(object):
         with self.communications_lock:
             self.flush_input_buffer()
             self.write(queryString)
-            if self.ignore_echo == True: # Needs Implementing for a multiline read!
+            if self.ignore_echo == True:  # Needs Implementing for a multiline read!
                 first_line = self.readline(timeout).strip()
                 if first_line == queryString:
                     return self.readline(timeout).strip()
                 else:
-                    logging.info('This command did not echo!!!')
+                    logging.info("This command did not echo!!!")
                     return first_line
-    
+
             if termination_line is not None:
                 multiline = True
             if multiline:
                 return self.read_multiline(termination_line)
             else:
-                return self.readline(timeout).strip() #question: should we strip the final newline?
-            
-    def parsed_query(self, query_string, response_string=r"%d", re_flags=0, parse_function=None, **kwargs):
+                return self.readline(
+                    timeout
+                ).strip()  # question: should we strip the final newline?
+
+    def parsed_query(
+        self,
+        query_string,
+        response_string=r"%d",
+        re_flags=0,
+        parse_function=None,
+        **kwargs
+    ):
         """
         Perform a query, returning a parsed form of the response.
 
@@ -204,46 +238,81 @@ class ExtensibleSerialInstrument(object):
         """
 
         response_regex = response_string
-        noop = lambda x: x #placeholder null parse function
-        placeholders = [ #tuples of (regex matching placeholder, regex to replace it with, parse function)
+        noop = lambda x: x  # placeholder null parse function
+        placeholders = [  # tuples of (regex matching placeholder, regex to replace it with, parse function)
             (r"%c", r".", noop),
-            (r"%(\d+)c", r".{\1}", noop), #TODO support %cn where n is a number of chars
+            (
+                r"%(\d+)c",
+                r".{\1}",
+                noop,
+            ),  # TODO support %cn where n is a number of chars
             (r"%d", r"[-+]?\\d+", int),
             (r"%[eEfg]", r"[-+]?(?:\\d+(?:\.\\d*)?|\.\\d+)(?:[eE][-+]?\\d+)?", float),
-            (r"%i", r"[-+]?(?:0[xX][\\dA-Fa-f]+|0[0-7]*|\\d+)", lambda x: int(x, 0)), #0=autodetect base
-            (r"%o", r"[-+]?[0-7]+", lambda x: int(x, 8)), #8 means octal
+            (
+                r"%i",
+                r"[-+]?(?:0[xX][\\dA-Fa-f]+|0[0-7]*|\\d+)",
+                lambda x: int(x, 0),
+            ),  # 0=autodetect base
+            (r"%o", r"[-+]?[0-7]+", lambda x: int(x, 8)),  # 8 means octal
             (r"%s", r"\\s+", noop),
             (r"%u", r"\\d+", int),
-            (r"%[xX]", r"[-+]?(?:0[xX])?[\\dA-Fa-f]+", lambda x: int(x, 16)), #16 forces hexadecimal
+            (
+                r"%[xX]",
+                r"[-+]?(?:0[xX])?[\\dA-Fa-f]+",
+                lambda x: int(x, 16),
+            ),  # 16 forces hexadecimal
         ]
         matched_placeholders = []
         for placeholder, regex, parse_fun in placeholders:
-            response_regex = re.sub(placeholder, '('+regex+')', response_regex) #substitute regex for placeholder
-            matched_placeholders.extend([(parse_fun, m.start()) for m in re.finditer(placeholder, response_string)]) #save the positions of the placeholders
+            response_regex = re.sub(
+                placeholder, "(" + regex + ")", response_regex
+            )  # substitute regex for placeholder
+            matched_placeholders.extend(
+                [
+                    (parse_fun, m.start())
+                    for m in re.finditer(placeholder, response_string)
+                ]
+            )  # save the positions of the placeholders
         if parse_function is None:
-            parse_function = [f for f, s in sorted(matched_placeholders, key=lambda m: m[1])] #order parse functions by their occurrence in the original string
-        if not hasattr(parse_function,'__iter__'):
-            parse_function = [parse_function] #make sure it's a list.
-            
-        reply = self.query(query_string, **kwargs) #do the query
-        #if match this could be because another response entered the buffer between write and read. Sleep for short while then
-        #check if something is now in the buffer, while the buffer is not empty repeat regex
-        waited=False
-        res=re.search(response_regex, reply, flags=re_flags)
+            parse_function = [
+                f for f, s in sorted(matched_placeholders, key=lambda m: m[1])
+            ]  # order parse functions by their occurrence in the original string
+        if not hasattr(parse_function, "__iter__"):
+            parse_function = [parse_function]  # make sure it's a list.
+
+        reply = self.query(query_string, **kwargs)  # do the query
+        # if match this could be because another response entered the buffer between write and read. Sleep for short while then
+        # check if something is now in the buffer, while the buffer is not empty repeat regex
+        waited = False
+        res = re.search(response_regex, reply, flags=re_flags)
         while res is None:
             if not waited:
-                time.sleep(.1)
-                waited=True
+                time.sleep(0.1)
+                waited = True
                 original_reply = reply
             if self._ser.inWaiting():
                 reply = self.readline().strip()
-                res=re.search(response_regex, reply, flags=re_flags)
+                res = re.search(response_regex, reply, flags=re_flags)
                 if res is not None:
-                    warnings.warn("Query suceeded after initially receieving unmatched response ('%s') to '%s'. Match pattern /%s/ (generated regex /%s/)"%(original_reply, query_string, response_string, response_regex), RuntimeWarning)
+                    warnings.warn(
+                        "Query suceeded after initially receieving unmatched response ('%s') to '%s'. Match pattern /%s/ (generated regex /%s/)"
+                        % (
+                            original_reply,
+                            query_string,
+                            response_string,
+                            response_regex,
+                        ),
+                        RuntimeWarning,
+                    )
             else:
-                raise ValueError("Stage response to '%s' ('%s') wasn't matched by /%s/ (generated regex /%s/)" % (query_string, original_reply, response_string, response_regex))
+                raise ValueError(
+                    "Stage response to '%s' ('%s') wasn't matched by /%s/ (generated regex /%s/)"
+                    % (query_string, original_reply, response_string, response_regex)
+                )
         try:
-            parsed_result= [f(g) for f, g in zip(parse_function, res.groups())] #try to apply each parse function to its argument
+            parsed_result = [
+                f(g) for f, g in zip(parse_function, res.groups())
+            ]  # try to apply each parse function to its argument
             if len(parsed_result) == 1:
                 return parsed_result[0]
             else:
@@ -251,10 +320,15 @@ class ExtensibleSerialInstrument(object):
         except ValueError:
             logging.info("Matched Groups: {}".format(res.groups()))
             logging.info("Parsing Functions {}:".format(parse_function))
-            raise ValueError("Stage response to %s ('%s') couldn't be parsed by the supplied function" % (query_string, reply))
+            raise ValueError(
+                "Stage response to %s ('%s') couldn't be parsed by the supplied function"
+                % (query_string, reply)
+            )
+
     def int_query(self, query_string, **kwargs):
         """Perform a query and return the result(s) as integer(s) (see parsedQuery)"""
         return self.parsed_query(query_string, "%d", **kwargs)
+
     def float_query(self, query_string, **kwargs):
         """Perform a query and return the result(s) as float(s) (see parsedQuery)"""
         return self.parsed_query(query_string, "%f", **kwargs)
@@ -273,7 +347,13 @@ class ExtensibleSerialInstrument(object):
         if our instrument is there."""
         with self.communications_lock:
             success = False
-            for port_name, _, _ in serial.tools.list_ports.comports(): #loop through serial ports, apparently 256 is the limit?!
+            for (
+                port_name,
+                _,
+                _,
+            ) in (
+                serial.tools.list_ports.comports()
+            ):  # loop through serial ports, apparently 256 is the limit?!
                 try:
                     logging.info("Trying port {}".format(port_name))
                     self.open(port_name)
@@ -285,14 +365,15 @@ class ExtensibleSerialInstrument(object):
                     try:
                         self.close()
                     except:
-                        pass #we don't care if there's an error closing the port...
+                        pass  # we don't care if there's an error closing the port...
                 if success:
-                    break #again, make sure this happens *after* closing the port
+                    break  # again, make sure this happens *after* closing the port
             if success:
                 return port_name
             else:
                 return None
 
+
 class OptionalModule(object):
     """This allows a `ExtensibleSerialInstrument` to have optional features.
 
@@ -300,32 +381,42 @@ class OptionalModule(object):
     for interfacing with optional modules which may or may not be included with
     the serial instrument, and can be added or removed at run-time.
     """
-    
-    def __init__(self,available,parent=None,module_type="Undefined",model="Generic"):
-        assert type(available) is bool, 'Option module availablity should be a boolean not a {}'.format(type(available))
-        self._available=available
-        self._parent=parent
-        assert type(module_type) is str, 'Option module type should be a string not a {}'.format(type(module_typ))
-        self.module_type=module_type
+
+    def __init__(
+        self, available, parent=None, module_type="Undefined", model="Generic"
+    ):
+        assert (
+            type(available) is bool
+        ), "Option module availablity should be a boolean not a {}".format(
+            type(available)
+        )
+        self._available = available
+        self._parent = parent
+        assert (
+            type(module_type) is str
+        ), "Option module type should be a string not a {}".format(type(module_typ))
+        self.module_type = module_type
         if available:
-            assert type(model) is str, 'Option module type should be a string not a {}'.format(type(model))
-            self.model=model
+            assert (
+                type(model) is str
+            ), "Option module type should be a string not a {}".format(type(model))
+            self.model = model
         else:
-            self.model=None
-    
+            self.model = None
+
     @property
     def available(self):
         return self._available
-    
+
     def confirm_available(self):
         """Check if module is available, no return, will raise exception if not available!"""
-        assert self._available, "No \"{}\" supported on firmware".format(self.module_type)
-    
+        assert self._available, 'No "{}" supported on firmware'.format(self.module_type)
+
     def describe(self):
         """Consistently spaced desciption for listing modules"""
-        return self.module_type+" "*(25-len(self.module_type))+"- "+self.model
-        
-        
+        return self.module_type + " " * (25 - len(self.module_type)) + "- " + self.model
+
+
 class QueriedProperty(object):
     """A Property interface that reads and writes from the instrument on the bus.
     
@@ -359,8 +450,18 @@ class QueriedProperty(object):
     :ack_writes:
         set to "readline" to discard a line of input after writing.
     """
-    def __init__(self, get_cmd=None, set_cmd=None, validate=None, valrange=None,
-                 fdel=None, doc=None, response_string=None, ack_writes="no"):
+
+    def __init__(
+        self,
+        get_cmd=None,
+        set_cmd=None,
+        validate=None,
+        valrange=None,
+        fdel=None,
+        doc=None,
+        response_string=None,
+        ack_writes="no",
+    ):
         self.response_string = response_string
         self.get_cmd = get_cmd
         self.set_cmd = set_cmd
@@ -369,48 +470,54 @@ class QueriedProperty(object):
         self.fdel = fdel
         self.ack_writes = ack_writes
         self.__doc__ = doc
-        
 
     # TODO: standardise the return (single value only vs parsed result), consider bool
     def __get__(self, obj, objtype=None):
-        if issubclass(type(obj),OptionalModule):
+        if issubclass(type(obj), OptionalModule):
             obj.confirm_available()
-            obj=obj._parent
+            obj = obj._parent
         if obj is None:
             return self
-        assert issubclass(type(obj),ExtensibleSerialInstrument)
+        assert issubclass(type(obj), ExtensibleSerialInstrument)
         if self.get_cmd is None:
             raise AttributeError("unreadable attribute")
         # Allow certain "magic" values to set the response string
-        for key, val in [('float',r"%f"),
-                         ('int',r"%d"),]:
+        for key, val in [("float", r"%f"), ("int", r"%d")]:
             if self.response_string == key:
                 self.response_string = val
-        if self.response_string in ['bool', 'raw', None]:
+        if self.response_string in ["bool", "raw", None]:
             value = obj.query(self.get_cmd)
-            if self.response_string == 'bool':
+            if self.response_string == "bool":
                 value = bool(value)
         else:
             value = obj.parsed_query(self.get_cmd, self.response_string)
         return value
 
     def __set__(self, obj, value):
-        if issubclass(type(obj),OptionalModule):
+        if issubclass(type(obj), OptionalModule):
             obj.confirm_available()
-            obj=obj._parent
-        assert issubclass(type(obj),ExtensibleSerialInstrument)
+            obj = obj._parent
+        assert issubclass(type(obj), ExtensibleSerialInstrument)
         if self.set_cmd is None:
             raise AttributeError("can't set attribute")
         if self.validate is not None:
             if value not in self.validate:
-                raise ValueError('invalid value supplied - value must be one of {}'.format(self.validate))
+                raise ValueError(
+                    "invalid value supplied - value must be one of {}".format(
+                        self.validate
+                    )
+                )
         if self.valrange is not None:
             if value < min(self.valrange) or value > max(self.valrange):
-                raise ValueError('invalid value supplied - value must be in the range {}-{}'.format(*self.valrange))
+                raise ValueError(
+                    "invalid value supplied - value must be in the range {}-{}".format(
+                        *self.valrange
+                    )
+                )
         message = self.set_cmd
-        if '{0' in message:
+        if "{0" in message:
             message = message.format(value)
-        elif '%' in message:
+        elif "%" in message:
             message = message % value
         obj.write(message)
         if self.ack_writes == "readline":

openflexure_microscope/stage/sangaboard/sangaboard.py

@@ -9,12 +9,20 @@ It is (c) Richard Bowman & Julian Stirling 2019 and released under GNU GPL v3
 """
 from __future__ import print_function, division
 import time
-from .extensible_serial_instrument import ExtensibleSerialInstrument, OptionalModule, QueriedProperty, EIGHTBITS, PARITY_NONE, STOPBITS_ONE
+from .extensible_serial_instrument import (
+    ExtensibleSerialInstrument,
+    OptionalModule,
+    QueriedProperty,
+    EIGHTBITS,
+    PARITY_NONE,
+    STOPBITS_ONE,
+)
 import serial, serial.tools.list_ports
 import re
 import warnings
 import logging
 
+
 class Sangaboard(ExtensibleSerialInstrument):
     """Class managing serial communications with a Sangaboard
 
@@ -39,34 +47,45 @@ class Sangaboard(ExtensibleSerialInstrument):
     """
 
     # List of valid and deprecated firmwares, for communication checks
-    valid_firmwares = [
-        (0, 5), 
-        (0, 4)
-    ]
-    deprecated_firmwares = [
-        (0, 4)
-    ]
+    valid_firmwares = [(0, 5), (0, 4)]
+    deprecated_firmwares = [(0, 4)]
 
     # These are the settings for the sangaboards serial port, and can usually be left as default.
-    port_settings = {'baudrate':115200, 'bytesize':EIGHTBITS, 'parity':PARITY_NONE, 'stopbits':STOPBITS_ONE}
-    
+    port_settings = {
+        "baudrate": 115200,
+        "bytesize": EIGHTBITS,
+        "parity": PARITY_NONE,
+        "stopbits": STOPBITS_ONE,
+    }
+
     # position, step time and ramp time are get/set using simple serial commands.
-    position = QueriedProperty(get_cmd="p?", response_string=r"%d %d %d",
-            doc="Get the position of the axes as a tuple of 3 integers.")
-    step_time = QueriedProperty(get_cmd="dt?", set_cmd="dt %d", response_string="minimum step delay %d",
-            doc="Get or set the minimum time between steps of the motors in microseconds.\n\n"
-                "The step time is ``1000000/max speed`` in steps/second.  It is saved to EEPROM on "
-                "the sangaboard, so it will be persistent even if the motor controller is turned off.")
-    ramp_time = QueriedProperty(get_cmd="ramp_time?", set_cmd="ramp_time %d", response_string="ramp time %d",
-            doc="Get or set the acceleration time in microseconds.\n\n"
-                "The motors will accelerate/decelerate between stationary and maximum speed over `ramp_time` "
-                "microseconds.  Zero means the motor runs at full speed initially, with no accleration "
-                "control.  Small moves may last less than `2*ramp_time`, in which case the acceleration "
-                "will be the same, but the motor will never reach full speed.  It is saved to EEPROM on "
-                "the sangaboard, so it will be persistent even if the motor controller is turned off.")
+    position = QueriedProperty(
+        get_cmd="p?",
+        response_string=r"%d %d %d",
+        doc="Get the position of the axes as a tuple of 3 integers.",
+    )
+    step_time = QueriedProperty(
+        get_cmd="dt?",
+        set_cmd="dt %d",
+        response_string="minimum step delay %d",
+        doc="Get or set the minimum time between steps of the motors in microseconds.\n\n"
+        "The step time is ``1000000/max speed`` in steps/second.  It is saved to EEPROM on "
+        "the sangaboard, so it will be persistent even if the motor controller is turned off.",
+    )
+    ramp_time = QueriedProperty(
+        get_cmd="ramp_time?",
+        set_cmd="ramp_time %d",
+        response_string="ramp time %d",
+        doc="Get or set the acceleration time in microseconds.\n\n"
+        "The motors will accelerate/decelerate between stationary and maximum speed over `ramp_time` "
+        "microseconds.  Zero means the motor runs at full speed initially, with no accleration "
+        "control.  Small moves may last less than `2*ramp_time`, in which case the acceleration "
+        "will be the same, but the motor will never reach full speed.  It is saved to EEPROM on "
+        "the sangaboard, so it will be persistent even if the motor controller is turned off.",
+    )
 
     # The names of the sangaboard's axes.  NB this also defines the number of axes
-    axis_names = ('x', 'y', 'z')
+    axis_names = ("x", "y", "z")
 
     # Once initialised, `firmware` is a string that identifies the firmware version
     firmware = None
@@ -88,30 +107,38 @@ class Sangaboard(ExtensibleSerialInstrument):
             # Make absolutely sure that whatever port we're on is valid
             self.check_valid_firmware()
 
-            #Bit messy: Defining all valid modules as not available, then overwriting with available information if available.
+            # Bit messy: Defining all valid modules as not available, then overwriting with available information if available.
             self.light_sensor = LightSensor(False)
 
             for module in self.list_modules():
-                module_type=module.split(':')[0].strip()
-                module_model=module.split(':')[1].strip()
-                if module_type.startswith('Light Sensor'):
+                module_type = module.split(":")[0].strip()
+                module_model = module.split(":")[1].strip()
+                if module_type.startswith("Light Sensor"):
                     if module_model in self.supported_light_sensors:
-                        self.light_sensor = LightSensor(True,parent=self,model=module_model)
+                        self.light_sensor = LightSensor(
+                            True, parent=self, model=module_model
+                        )
                     else:
-                        logging.warning("Light sensor model \"%s\" not recognised."%(module_model))
-                elif module_type.startswith('Endstops'):
+                        logging.warning(
+                            'Light sensor model "%s" not recognised.' % (module_model)
+                        )
+                elif module_type.startswith("Endstops"):
                     self.endstops = Endstops(True, parent=self, model=module_model)
                 else:
-                    logging.warning("Module type \"{}\" not recognised.".format(module_type))
+                    logging.warning(
+                        'Module type "{}" not recognised.'.format(module_type)
+                    )
 
-            self.board = self.query("board",timeout=2).rstrip()
+            self.board = self.query("board", timeout=2).rstrip()
 
         except Exception as e:
             # If an error occurred while setting up (e.g. because the board isn't connected or something)
             # make sure we close the serial port cleanly (otherwise it hangs open).
             self.close()
             logging.error(e)
-            logging.error("You may need to update the firmware running on the Sangaboard.")
+            logging.error(
+                "You may need to update the firmware running on the Sangaboard."
+            )
             raise e
 
     def test_communications(self):
@@ -124,16 +151,22 @@ class Sangaboard(ExtensibleSerialInstrument):
         logging.debug("Running firmware checks")
 
         # Request firmware version from the board
-        self.firmware = self.query("version",timeout=2).rstrip()
+        self.firmware = self.query("version", timeout=2).rstrip()
         logging.info("Firmware response: {}".format(self.firmware))
         # Check for valid firmware string
         if self.firmware:
-            match = re.match(r"Sangaboard Firmware v(([\d]+)(?:\.([\d]+))+)", self.firmware)
+            match = re.match(
+                r"Sangaboard Firmware v(([\d]+)(?:\.([\d]+))+)", self.firmware
+            )
             if not match:
                 # Try old firmware format
-                match = re.match(r"OpenFlexure Motor Board v(([\d]+)(?:\.([\d]+))+)", self.firmware)
+                match = re.match(
+                    r"OpenFlexure Motor Board v(([\d]+)(?:\.([\d]+))+)", self.firmware
+                )
             if not match:
-                logging.error("Version string \"{}\" not recognised.".format(self.firmware))
+                logging.error(
+                    'Version string "{}" not recognised.'.format(self.firmware)
+                )
                 return False
         else:
             logging.error("No firmware version string was returned.")
@@ -146,15 +179,17 @@ class Sangaboard(ExtensibleSerialInstrument):
         self.firmware_version = match.group(1)
 
         if version_tuple not in Sangaboard.valid_firmwares:
-            logging.error("This version of the Python module requires firmware v0.5 (with legacy support for v0.4)")
+            logging.error(
+                "This version of the Python module requires firmware v0.5 (with legacy support for v0.4)"
+            )
             return False
-        
+
         if version_tuple in Sangaboard.deprecated_firmwares:
             logging.warning(
                 "Warning this Sangaboard is using v0.4 of the firmware, this will soon be depreciated! "
                 "Please consider updating the Sangaboard firmware"
             )
-        
+
         return True
 
     def move_rel(self, displacement, axis=None):
@@ -164,10 +199,12 @@ class Sangaboard(ExtensibleSerialInstrument):
         axis: None (for 3-axis moves) or one of 'x','y','z'
         """
         if axis is not None:
-            assert axis in self.axis_names, "axis must be one of {}".format(self.axis_names)
+            assert axis in self.axis_names, "axis must be one of {}".format(
+                self.axis_names
+            )
             self.query("mr{} {}".format(axis, int(displacement)))
         else:
-            #TODO: assert displacement is 3 integers
+            # TODO: assert displacement is 3 integers
             self.query("mr {} {} {}".format(*list(displacement)))
 
     def release_motors(self):
@@ -181,12 +218,12 @@ class Sangaboard(ExtensibleSerialInstrument):
         queries the board for its position, then instructs it to make about
         relative move.
         """
-        rel_mov = [f_pos-i_pos for f_pos,i_pos in zip(final,self.position)]
+        rel_mov = [f_pos - i_pos for f_pos, i_pos in zip(final, self.position)]
         return self.move_rel(rel_mov, **kwargs)
 
     def query(self, message, *args, **kwargs):
         """Send a message and read the response.  See ExtensibleSerialInstrument.query()"""
-        time.sleep(0.001) # This is to protect the stage from us talking too fast!
+        time.sleep(0.001)  # This is to protect the stage from us talking too fast!
         return ExtensibleSerialInstrument.query(self, message, *args, **kwargs)
 
     def list_modules(self):
@@ -194,12 +231,15 @@ class Sangaboard(ExtensibleSerialInstrument):
 
         Each module will correspond to a string of the form ``Module Name: Model``
         """
-        modules =  self.query("list_modules",multiline=True,termination_line="--END--\r\n").split('\r\n')[:-2]
+        modules = self.query(
+            "list_modules", multiline=True, termination_line="--END--\r\n"
+        ).split("\r\n")[:-2]
         return [str(module) for module in modules]
 
     def print_help(self):
         """Print the stage's built-in help message."""
-        print(self.query("help",multiline=True,termination_line="--END--\r\n"))
+        print(self.query("help", multiline=True, termination_line="--END--\r\n"))
+
 
 class LightSensor(OptionalModule):
     """An optional module giving access to the light sensor.
@@ -209,19 +249,25 @@ class LightSensor(OptionalModule):
     module which is an instance of this class.  It can be used to access
     the light sensor (usually via the I2C bus).
     """
+
     valid_gains = None
     _valid_gains_int = None
     integration_time = QueriedProperty(
         get_cmd="light_sensor_integration_time?",
         set_cmd="light_sensor_integration_time %d",
         response_string="light sensor integration time %d ms",
-        doc="Get or set the integration time of the light sensor in milliseconds."
+        doc="Get or set the integration time of the light sensor in milliseconds.",
+    )
+    intensity = QueriedProperty(
+        get_cmd="light_sensor_intensity?",
+        response_string="%d",
+        doc="Read the current intensity measured by the light sensor (arbitrary units).",
     )
-    intensity = QueriedProperty(get_cmd="light_sensor_intensity?", response_string="%d",
-                                doc="Read the current intensity measured by the light sensor (arbitrary units).")
 
-    def __init__(self,available,parent=None,model="Generic"):
-        super(LightSensor, self).__init__(available,parent=parent,module_type="LightSensor",model=model)
+    def __init__(self, available, parent=None, model="Generic"):
+        super(LightSensor, self).__init__(
+            available, parent=parent, module_type="LightSensor", model=model
+        )
         if available:
             self.valid_gains = self.__get_gain_values()
             self._valid_gains_int = [int(g) for g in self.valid_gains]
@@ -232,21 +278,25 @@ class LightSensor(OptionalModule):
 
         Valid gain values are defined in the `valid_gains` property, and should be floating-point numbers."""
         self.confirm_available()
-        gain = self._parent.query('light_sensor_gain?')
-        M = re.search('[0-9\.]+(?=x)',gain)
-        assert M is not None, "Cannot read gain string: \"{}\"".format(gain)
-        #gain is a float as non integer gains exist but are set with floor of value
+        gain = self._parent.query("light_sensor_gain?")
+        M = re.search("[0-9\.]+(?=x)", gain)
+        assert M is not None, 'Cannot read gain string: "{}"'.format(gain)
+        # gain is a float as non integer gains exist but are set with floor of value
         return float(M.group())
 
     @gain.setter
-    def gain(self,val):
+    def gain(self, val):
         self.confirm_available()
-        assert int(val) in self._valid_gains_int, "Gain {} not valid must be one of: {}".format(val,self.valid_gains)
-        gain = self._parent.query('light_sensor_gain %d'%(int(val)))
-        M = re.search('[0-9\.]+(?=x)',gain)
-        assert M is not None, "Cannot read gain string: \"{}\"".format(gain)
-        #gain is a float as non integer gains exist but are set with floor of value
-        assert int(val) == int(float(M.group())), 'Gain of {} set, \"{}\" returned'.format(val,gain)
+        assert (
+            int(val) in self._valid_gains_int
+        ), "Gain {} not valid must be one of: {}".format(val, self.valid_gains)
+        gain = self._parent.query("light_sensor_gain %d" % (int(val)))
+        M = re.search("[0-9\.]+(?=x)", gain)
+        assert M is not None, 'Cannot read gain string: "{}"'.format(gain)
+        # gain is a float as non integer gains exist but are set with floor of value
+        assert int(val) == int(
+            float(M.group())
+        ), 'Gain of {} set, "{}" returned'.format(val, gain)
 
     def __get_gain_values(self):
         """Read the allowable values for the light sensor's gain.
@@ -256,15 +306,16 @@ class LightSensor(OptionalModule):
         values, the list will be of strings.
         """
         self.confirm_available()
-        gains = self._parent.query('light_sensor_gain_values?')
+        gains = self._parent.query("light_sensor_gain_values?")
         try:
-            M = re.findall('[0-9\.]+(?=x)',gains)
+            M = re.findall("[0-9\.]+(?=x)", gains)
             return [float(gain) for gain in M]
         except:
             # Fall back to strings if we don't get floats (unlikely)
             gain_strings = gains[20:].split(", ")
             return gain_strings
 
+
 class Endstops(OptionalModule):
     """An optional module for use with endstops.
 
@@ -273,35 +324,41 @@ class Endstops(OptionalModule):
     the type, state of the endstops, read and write maximum positions, and home.
     """
 
-    installed=[]
+    installed = []
     """List of installed endstop types (min, max, soft)"""
 
-    def __init__(self,available,parent=None,model="min"):
-        super(Endstops, self).__init__(available,parent=parent,model="Endstops")
-        self.installed=model.split(' ')
+    def __init__(self, available, parent=None, model="min"):
+        super(Endstops, self).__init__(available, parent=parent, model="Endstops")
+        self.installed = model.split(" ")
 
-    status = QueriedProperty(get_cmd="endstops?", response_string=r"%d %d %d",
-                            doc="Get endstops status as {-1,0,1} for {min,no,max} endstop triggered for each axis")
-    maxima = QueriedProperty(get_cmd="max_p?", set_cmd="max %d %d %d", response_string="%d %d %d",
-                            doc="Vector of maximum positions, homing to max endstops will measure this, "+
-                                "can be set to a known value for use with max only and min+soft endstops")
+    status = QueriedProperty(
+        get_cmd="endstops?",
+        response_string=r"%d %d %d",
+        doc="Get endstops status as {-1,0,1} for {min,no,max} endstop triggered for each axis",
+    )
+    maxima = QueriedProperty(
+        get_cmd="max_p?",
+        set_cmd="max %d %d %d",
+        response_string="%d %d %d",
+        doc="Vector of maximum positions, homing to max endstops will measure this, "
+        + "can be set to a known value for use with max only and min+soft endstops",
+    )
 
-    def home(self, direction="min", axes=['x','y','z']):
+    def home(self, direction="min", axes=["x", "y", "z"]):
         """ Home given/all axes in the given direction (min/max/both)
 
             :param direction: one of {min,max,both}
             :param axes: list of axes e.g. ['x','y']
         """
-        ax=0
-        if 'x' in axes:
-            ax+=1
-        if 'y' in axes:
-            ax+=2
-        if 'z' in axes:
-            ax+=3
+        ax = 0
+        if "x" in axes:
+            ax += 1
+        if "y" in axes:
+            ax += 2
+        if "z" in axes:
+            ax += 3
 
         if direction == "min" or direction == "both":
-            self._parent.query('home_min {}'.format(ax))
+            self._parent.query("home_min {}".format(ax))
         if direction == "max" or direction == "both":
-            self._parent.query('home_max {}'.format(ax))
-
+            self._parent.query("home_max {}".format(ax))

openflexure_microscope/task.py

@@ -17,6 +17,7 @@ class TaskOrchestrator:
         tasks (list): List of `Task` objects
 
     """
+
     def __init__(self):
         self.tasks = []
 
@@ -106,6 +107,7 @@ class Task:
             `status` will be one of 'idle'', 'running', 'error', or 'success'.
             `return` eventually holds the return value of the task function.
     """
+
     def __init__(self, function, *args, **kwargs):
         # The task long-running method
         self.task = function
@@ -117,39 +119,41 @@ class Task:
         self.id = uuid.uuid4().hex
 
         self.state = {
-            'id': self.id,
-            'status': 'idle',
-            'return': None,
-            'start_time': None,
-            'end_time': None,
+            "id": self.id,
+            "status": "idle",
+            "return": None,
+            "start_time": None,
+            "end_time": None,
         }
 
     def process(self, f):
         """
         Wraps the target function to handle recording `status` and `return` to `state`.
         """
+
         def wrapped(*args, **kwargs):
-            self.state['status'] = 'running'
+            self.state["status"] = "running"
             try:
                 r = f(*args, **kwargs)
-                s = 'success'
+                s = "success"
             except Exception as e:
                 logging.error(e)
                 logging.error(traceback.format_exc())
                 r = str(e)
-                s = 'error'
-            self.state['return'] = r
-            self.state['status'] = s
+                s = "error"
+            self.state["return"] = r
+            self.state["status"] = s
+
         return wrapped
 
     def run(self):
         """
         Records the task start and end times to `state`, and runs the task wrapped in `process`.
         """
-        self.state['start_time'] = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S")
+        self.state["start_time"] = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S")
         self.process(self.task)(*self.args, **self.kwargs)
         self._running = False
-        self.state['end_time'] = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S")
+        self.state["end_time"] = datetime.datetime.now().strftime("%Y-%m-%d %H-%M-%S")
 
     def start(self):  # Start and draw
         """

openflexure_microscope/utilities.py

@@ -17,7 +17,11 @@ def set_properties(obj, **kwargs):
         try:
             saved_properties[k] = getattr(obj, k)
         except AttributeError:
-            print("Warning: could not get {} on {}.  This property will not be restored!".format(k, obj))
+            print(
+                "Warning: could not get {} on {}.  This property will not be restored!".format(
+                    k, obj
+                )
+            )
     for k, v in kwargs.items():
         setattr(obj, k, v)
     try:
@@ -27,12 +31,14 @@ def set_properties(obj, **kwargs):
             setattr(obj, k, v)
 
 
-def axes_to_array(coordinate_dictionary, axis_keys=('x', 'y', 'z'), base_array=None, asint=True):
+def axes_to_array(
+    coordinate_dictionary, axis_keys=("x", "y", "z"), base_array=None, asint=True
+):
     """Takes key-value pairs of a JSON value, and maps onto an array"""
     # If no base array is given
     if not base_array:
         # Create an array of zeros
-        base_array = [0]*len(axis_keys)
+        base_array = [0] * len(axis_keys)
     else:
         # Create a copy of the passed base_array
         base_array = copy.copy(base_array)
@@ -40,7 +46,9 @@ def axes_to_array(coordinate_dictionary, axis_keys=('x', 'y', 'z'), base_array=N
     # Do the mapping
     for axis, key in enumerate(axis_keys):
         if key in coordinate_dictionary:
-            base_array[axis] = int(coordinate_dictionary[key]) if asint else coordinate_dictionary[key]
+            base_array[axis] = (
+                int(coordinate_dictionary[key]) if asint else coordinate_dictionary[key]
+            )
 
     return base_array
 
@@ -84,4 +92,4 @@ def recursively_apply(data, func):
         return [recursively_apply(x, func) for x in data]
     # if the object is neither a map nor iterable
     else:
-        return func(data)
+        return func(data)