Moved status routes to instrument/state

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

@@ -14,7 +14,7 @@ from labthings.server import fields
 class MicroscopeIdentifySchema(Schema):
     name = fields.String()  # Microscopes name
     id = fields.UUID()  # Microscopes unique ID
-    status = fields.Dict()  # Status dictionary
+    state = fields.Dict()  # Status dictionary
     camera = fields.String()  # Camera object (represented as a string)
     stage = fields.String()  # Stage object (represented as a string)
 

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

@@ -19,7 +19,7 @@ from labthings.server import fields
 class MicroscopeIdentifySchema(Schema):
     name = fields.String()  # Microscopes name
     id = fields.UUID()  # Microscopes unique ID
-    status = fields.Dict()  # Status dictionary
+    state = fields.Dict()  # Status dictionary
     camera = fields.String()  # Camera object (represented as a string)
     stage = fields.String()  # Stage object (represented as a string)
 

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

@@ -24,7 +24,7 @@ import io  # Used in our capture action
 class MicroscopeIdentifySchema(Schema):
     name = fields.String()  # Microscopes name
     id = fields.UUID()  # Microscopes unique ID
-    status = fields.Dict()  # Status dictionary
+    state = fields.Dict()  # Status dictionary
     camera = fields.String()  # Camera object (represented as a string)
     stage = fields.String()  # Stage object (represented as a string)
 

docs/source/extensions/marshaling.rst

@@ -107,7 +107,7 @@ We start by creating a schema to describe how to serialise a :py:class:`openflex
     class MicroscopeIdentifySchema(Schema):
         name = fields.String()  # Microscopes name
         id = fields.UUID()  # Microscopes unique ID
-        status = fields.Dict()  # Status dictionary
+        state = fields.Dict()  # Status dictionary
         camera = fields.String()  # Camera object (represented as a string)
         stage = fields.String()  # Stage object (represented as a string)
 

openflexure_microscope/api/app.py

@@ -94,16 +94,18 @@ labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
 labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
 labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")
 
-# Attach settings and status resources
+# Attach settings and state resources
-labthing.add_view(views.SettingsProperty, f"/settings")
+labthing.add_view(views.SettingsProperty, f"/instrument/settings")
-labthing.add_root_link(views.SettingsProperty, "settings")
+labthing.add_root_link(views.SettingsProperty, "instrumentSettings")
-labthing.add_view(views.NestedSettingsProperty, "/settings/<path:route>")
+labthing.add_view(views.NestedSettingsProperty, "/instrument/settings/<path:route>")
-labthing.add_view(views.StatusProperty, "/status")
+labthing.add_view(views.StateProperty, "/instrument/state")
-labthing.add_view(views.NestedStatusProperty, "/status/<path:route>")
+labthing.add_view(views.NestedStateProperty, "/instrument/state/<path:route>")
-labthing.add_root_link(views.StatusProperty, "status")
+labthing.add_root_link(views.StateProperty, "instrumentState")
-labthing.add_view(views.ConfigurationProperty, "/configuration")
+labthing.add_view(views.ConfigurationProperty, "/instrument/configuration")
-labthing.add_view(views.NestedConfigurationProperty, "/configuration/<path:route>")
+labthing.add_view(
-labthing.add_root_link(views.ConfigurationProperty, "configuration")
+    views.NestedConfigurationProperty, "/instrument/configuration/<path:route>"
+)
+labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
 
 
 # Attach streams resources

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -73,17 +73,15 @@ class ZipManager:
                 # Update task progress
                 update_task_progress(int((index / n_files) * 100))
 
-        session_id = uuid.uuid4()
+        session_id = str(uuid.uuid4())
-        session_key = str(session_id)
+        self.session_zips[session_id] = {
-        # self.session_zips[session_id] = fp
-        self.session_zips[session_key] = {
             "id": session_id,
             "fp": fp,
             "data_size": data_size_megabytes,
             "zip_size": os.path.getsize(fp.name) * 1e-6,
         }
 
-        return self.session_zips[session_key]
+        return self.session_zips[session_id]
 
     def zip_from_id(self, session_id):
         return self.session_zips[session_id]["fp"]
@@ -103,13 +101,13 @@ class ZipBuilderAPIView(View):
         task = taskify(default_zip_manager.build_zip_from_capture_ids)(microscope, ids)
 
         # Return a handle on the autofocus task
-        return jsonify(task.state), 201
+        return task.state, 201
 
 
 @ThingProperty
 class ZipListAPIView(View):
     def get(self):
-        return jsonify(default_zip_manager.session_zips)
+        return default_zip_manager.session_zips
 
 
 class ZipGetterAPIView(View):
@@ -141,7 +139,7 @@ class ZipGetterAPIView(View):
 
         del default_zip_manager.session_zips[session_id]
 
-        return jsonify({"return": session_id})
+        return {"return": session_id}
 
 
 zip_extension_v2 = BaseExtension("org.openflexure.zipbuilder", version="2.0.0-beta.1")

openflexure_microscope/api/v2/views/__init__.py

@@ -1,4 +1,4 @@
 from .actions import enabled_root_actions
 from .captures import *
-from .state import *
+from .instrument import *
 from .streams import *

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

@@ -163,8 +163,8 @@ class GPUPreviewStartAPI(View):
 
         microscope.camera.start_preview(fullscreen=fullscreen, window=window)
 
-        # TODO: Make schema for microscope status
+        # TODO: Make schema for microscope state
-        return jsonify(microscope.status)
+        return jsonify(microscope.state)
 
 
 @ThingAction
@@ -175,5 +175,5 @@ class GPUPreviewStopAPI(View):
         """
         microscope = find_component("org.openflexure.microscope")
         microscope.camera.stop_preview()
-        # TODO: Make schema for microscope status
+        # TODO: Make schema for microscope state
-        return jsonify(microscope.status)
+        return jsonify(microscope.state)

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

@@ -52,7 +52,7 @@ class MoveStageAPI(View):
         else:
             logging.warning("Unable to move. No stage found.")
 
-        # TODO: Make schema for microscope status
+        # TODO: Make schema for microscope state
         return jsonify(microscope.state["stage"]["position"])
 
 
@@ -66,5 +66,5 @@ class ZeroStageAPI(View):
         microscope = find_component("org.openflexure.microscope")
         microscope.stage.zero_position()
 
-        # TODO: Make schema for microscope status
+        # TODO: Make schema for microscope state
-        return jsonify(microscope.status["stage"])
+        return jsonify(microscope.state["stage"])

openflexure_microscope/api/v2/views/instrument.py

@@ -72,7 +72,7 @@ class NestedSettingsProperty(View):
 
 
 @ThingProperty
-class StatusProperty(View):
+class StateProperty(View):
     def get(self):
         """
         Show current read-only state of the microscope
@@ -82,7 +82,7 @@ class StatusProperty(View):
 
 
 @Tag("properties")
-class NestedStatusProperty(View):
+class NestedStateProperty(View):
     @doc_response(404, description="Status key cannot be found")
     def get(self, route):
         """

openflexure_microscope/camera/base.py

@@ -91,20 +91,6 @@ class CameraEvent(object):
 class BaseCamera(metaclass=ABCMeta):
     """
     Base implementation of StreamingCamera.
-
-    Attributes:
-        thread: Background thread reading frames from camera
-        camera: Camera object
-        lock (:py:class:`labthings.lock.StrictLock`): Strict lock controlling thread
-            access to stage hardware
-        frame (bytes): Current frame is stored here by background thread
-        last_access (time): Time of last client access to the camera
-        stream_timeout (int): Number of inactive seconds before timing out the stream
-        stream_timeout_enabled (bool): Enable or disable timing out the stream
-        status (dict): Dictionary for capture state
-        paths (dict): Dictionary of capture paths
-        images (list): List of image capture objects
-        videos (list): List of video capture objects
     """
 
     def __init__(self):

openflexure_microscope/camera/pi.py

@@ -85,7 +85,7 @@ class PiCameraStreamer(BaseCamera):
             picamera.PiCamera()
         )  #: :py:class:`picamera.PiCamera`: Picamera object
 
-        # Store status of PiCameraStreamer
+        # Store state of PiCameraStreamer
         self.preview_active = False
 
         # Reset variable states
@@ -157,7 +157,7 @@ class PiCameraStreamer(BaseCamera):
                 "picamera_lst_path": self.picamera_lst_path
                 if os.path.isfile(self.picamera_lst_path)
                 else None,
-                "picamera_settings": {},
+                "picamera": {},
             }
         )
 
@@ -166,7 +166,7 @@ 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"][key] = value
             except AttributeError:
                 logging.debug("Unable to read PiCamera attribute {}".format(key))
 
@@ -204,14 +204,14 @@ class PiCameraStreamer(BaseCamera):
                     paused_stream = True  # Remember to unpause stream when done
 
                 # PiCamera parameters
-                if "picamera_settings" in config:  # If new settings are given
+                if "picamera" in config:  # If new settings are given
                     self.apply_picamera_settings(
-                        config["picamera_settings"], pause_for_effect=True
+                        config["picamera"], 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") and hasattr(self, key):
                         setattr(self, key, value)
 
                 # Handle lens shading if camera supports it
@@ -412,7 +412,7 @@ class PiCameraStreamer(BaseCamera):
                     quality=quality,
                 )
 
-                # Update status dictionary
+                # Update state
                 self.record_active = True
 
                 return output
@@ -432,7 +432,7 @@ class PiCameraStreamer(BaseCamera):
             self.camera.stop_recording(splitter_port=2)
             logging.info("Recording stopped")
 
-            # Update status dictionary
+            # Update state
             self.record_active = False
 
     def stop_stream_recording(
@@ -681,7 +681,6 @@ class PiCameraStreamer(BaseCamera):
         # Start stream recording (and set resolution)
         self.start_stream_recording()
 
-        # Update status
         logging.debug("STREAM ACTIVE")
 
         # While the iterator is not closed

openflexure_microscope/config.py

@@ -94,11 +94,14 @@ class JSONEncoder(flask.json.JSONEncoder):
         # Numpy arrays
         elif isinstance(o, np.ndarray):
             return o.tolist()
+        # UUIDs
+        elif isinstance(o, UUID):
+            return str(o)
         else:
             # call base class implementation which takes care of
             # raising exceptions for unsupported types
             try:
-                return json.JSONEncoder.default(self, o)
+                return flask.json.JSONEncoder.default(self, o)
             # if it's some mystery object, just return a string representation
             except TypeError:
                 return str(o)

openflexure_microscope/microscope.py

@@ -120,13 +120,13 @@ class Microscope:
         else:
             return False
 
-    # Create unified status
+    # Create unified state
     @property
     def state(self):
-        """Dictionary of the basic microscope status.
+        """Dictionary of the basic microscope state.
 
         Return:
-            dict: Dictionary containing complete microscope status
+            dict: Dictionary containing complete microscope state
         """
         state = {"camera": self.camera.state, "stage": self.stage.state}
         return state
@@ -216,7 +216,7 @@ class Microscope:
         initial_configuration = self.configuration_file.load()
 
         current_configuration = {
-            "@application": {
+            "application": {
                 "name": "openflexure_microscope",
                 "version": pkg_resources.get_distribution(
                     "openflexure_microscope"

openflexure_microscope/stage/mock.py

@@ -18,9 +18,9 @@ class MissingStage(BaseStage):
 
     @property
     def state(self):
-        """The general status dictionary of the board."""
+        """The general state dictionary of the board."""
-        status = {"position": self.position_map}
+        state = {"position": self.position_map}
-        return status
+        return state
 
     @property
     def configuration(self):

openflexure_microscope/stage/sanga.py

@@ -33,7 +33,7 @@ class SangaStage(BaseStage):
 
     @property
     def state(self):
-        """The general status dictionary of the board."""
+        """The general state dictionary of the board."""
         return {"position": self.position_map}
 
     @property