Simplified new configuration and metadata

openflexure_microscope/api/app.py

@@ -19,7 +19,7 @@ from openflexure_microscope.paths import (
     OPENFLEXURE_VAR_PATH,
     OPENFLEXURE_EXTENSIONS_PATH,
     settings_file_path,
-    logs_file_path
+    logs_file_path,
 )
 
 from labthings.server.quick import create_app
@@ -92,7 +92,7 @@ labthing.add_root_link(views.CaptureList, "captures")
 labthing.add_view(views.CaptureView, f"/captures/<id>")
 labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
 labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
-labthing.add_view(views.CaptureMetadata, f"/captures/<id>/metadata")
+labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")
 
 # Attach settings and status resources
 labthing.add_view(views.SettingsProperty, f"/settings")
@@ -101,6 +101,10 @@ labthing.add_view(views.NestedSettingsProperty, "/settings/<path:route>")
 labthing.add_view(views.StatusProperty, "/status")
 labthing.add_view(views.NestedStatusProperty, "/status/<path:route>")
 labthing.add_root_link(views.StatusProperty, "status")
+labthing.add_view(views.ConfigurationProperty, "/configuration")
+labthing.add_view(views.NestedConfigurationProperty, "/configuration/<path:route>")
+labthing.add_root_link(views.ConfigurationProperty, "configuration")
+
 
 # Attach streams resources
 labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

openflexure_microscope/api/default_extensions/scan.py

@@ -1,6 +1,7 @@
 import itertools
 import logging
 import uuid
+import datetime
 from typing import Tuple
 from functools import reduce
 
@@ -71,12 +72,12 @@ def progress():
 def capture(
     microscope,
     basename,
-    scan_id,
     temporary: bool = False,
     use_video_port: bool = False,
     resize: Tuple[int, int] = None,
     bayer: bool = False,
     metadata: dict = {},
+    annotations: dict = {},
     tags: list = [],
 ):
 
@@ -94,16 +95,14 @@ def capture(
         output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
     )
 
-    # Affix metadata
-    if "scan" not in tags:
-        tags.append("scan")
-
     # Inject system metadata
-    output.put_metadata(microscope.metadata, system=True)
+    output.put_metadata({"instrument": microscope.metadata})
 
     # Insert custom metadata
     output.put_metadata(metadata)
 
+    # Insert custom metadata
+    output.put_annotations(annotations)
     # Insert custom tags
     output.put_tags(tags)
 
@@ -115,7 +114,7 @@ def tile(
     microscope,
     basename: str = None,
     temporary: bool = False,
-    step_size: int = [2000, 1500, 100],
+    stride_size: int = [2000, 1500, 100],
     grid: list = [3, 3, 5],
     style="raster",
     autofocus_dz: int = 50,
@@ -124,13 +123,13 @@ def tile(
     bayer: bool = False,
     fast_autofocus=False,
     metadata: dict = {},
+    annotations: dict = {},
     tags: list = [],
 ):
     global _images_to_be_captured
     global _images_captured_so_far
 
     # Keep task progress
-    # TODO: Make this line not nasty
     _images_to_be_captured = reduce((lambda x, y: x * y), grid)
     _images_captured_so_far = 0
 
@@ -138,28 +137,22 @@ def tile(
     if not basename:
         basename = generate_basename()
 
-    # Generate a stack ID
-    scan_id = uuid.uuid4()
-
     # Store initial position
     initial_position = microscope.stage.position
 
-    # Add scan metadata
+    # Add dataset metadata
-    if "time" not in metadata:
+    dataset_d = {
-        metadata["time"] = generate_basename()
+        "dataset": {
-
+            "id": uuid.uuid4(),
-    metadata.update(
+            "type": "xyzScan",
-        {
+            "name": basename,
-            "scan_id": scan_id,
+            "acquisitionDate": datetime.datetime.now().isoformat(),
-            "basename": basename,
+            "strideSize": stride_size,
-            "scan_parameters": {
+            "grid": grid,
-                "step_size": step_size,
+            "style": style,
-                "grid": grid,
+            "autofocusDz": autofocus_dz,
-                "style": style,
-                "autofocus_dz": autofocus_dz,
-            },
         }
-    )
+    }
 
     # Check if autofocus is enabled
     autofocus_extension = find_extension("org.openflexure.autofocus")
@@ -174,11 +167,11 @@ def tile(
         autofocus_enabled = False
 
     z_stack_dz = (
-        grid[2] * step_size[2] if grid[2] > 1 else 0
+        grid[2] * stride_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)
+    x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)
 
     # Keep the initial Z position the same as our current position
     next_z = initial_position[2]
@@ -209,26 +202,25 @@ def tile(
                         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")
                     autofocus_extension.autofocus(
                         range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
                     )
                     logging.debug("Finished autofocus")
-                    time.sleep(1)  # TODO: Remove
+                    time.sleep(1)
 
             # If we're not doing a z-stack, just capture
             if grid[2] <= 1:
                 capture(
                     microscope,
                     basename,
-                    scan_id,
                     temporary=temporary,
                     use_video_port=use_video_port,
                     resize=resize,
                     bayer=bayer,
-                    metadata=metadata,
+                    metadata=dataset_d,
+                    annotations=annotations,
                     tags=tags,
                 )
                 # Update task progress
@@ -240,15 +232,14 @@ def tile(
                     microscope=microscope,
                     basename=basename,
                     temporary=temporary,
-                    scan_id=scan_id,
+                    step_size=stride_size[2],
-                    step_size=step_size[2],
                     steps=grid[2],
-                    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,
+                    metadata=dataset_d,
+                    annotations=annotations,
                     tags=tags,
                 )
             # Make sure we use our current best estimate of focus (i.e. the current position) next point
@@ -259,7 +250,7 @@ def tile(
                 )  # 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]
+                        grid[2] / 2.0 * stride_size[2]
                     )  # Z stacking means we're higher up to start with
 
     logging.debug("Returning to {}".format(initial_position))
@@ -270,39 +261,25 @@ def stack(
     microscope,
     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 = {},
+    annotations: dict = {},
     tags: list = [],
 ):
     global _images_captured_so_far
 
-    # Generate a basename if none given
-    if not basename:
-        basename = generate_basename()
-
-    # Generate a stack ID
-    if not scan_id:
-        scan_id = uuid.uuid4()
-
-    # Add scan metadata
-    if not "time" in metadata:
-        metadata["time"] = generate_basename()
-
     # Store initial position
     initial_position = microscope.stage.position
 
     with microscope.lock:
         # Move to center scan
-        if center:
+        logging.debug("Moving to starting position")
-            logging.debug("Moving to starting position")
+        microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
-            microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
 
         for i in range(steps):
             time.sleep(0.1)
@@ -310,12 +287,12 @@ def stack(
             capture(
                 microscope,
                 basename,
-                scan_id,
                 temporary=temporary,
                 use_video_port=use_video_port,
                 resize=resize,
                 bayer=bayer,
                 metadata=metadata,
+                annotations=annotations,
                 tags=tags,
             )
             # Update task progress
@@ -337,16 +314,18 @@ def stack(
 class TileScanAPI(View):
     @use_args(
         {
-            "filename": fields.String(),
+            "filename": fields.String(missing=None, example=None),
             "temporary": fields.Boolean(missing=False),
-            "step_size": fields.List(fields.Integer, missing=[2000, 1500, 100]),
+            "stride_size": fields.List(
-            "grid": fields.List(fields.Integer, missing=[3, 3, 5]),
+                fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
+            ),
+            "grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
             "style": fields.String(missing="raster"),
             "autofocus_dz": fields.Integer(missing=50),
             "fast_autofocus": fields.Boolean(missing=False),
             "use_video_port": fields.Boolean(missing=False),
             "bayer": fields.Boolean(missing=False),
-            "metadata": fields.Dict(missing={}),
+            "annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
             "tags": fields.List(fields.String, missing=[]),
             "resize": fields.Dict(missing=None),  # TODO: Validate keys
         }
@@ -373,7 +352,7 @@ class TileScanAPI(View):
             microscope,
             basename=args.get("filename"),
             temporary=args.get("temporary"),
-            step_size=args.get("step_size"),
+            stride_size=args.get("stride_size"),
             grid=args.get("grid"),
             style=args.get("style"),
             autofocus_dz=args.get("autofocus_dz"),
@@ -381,7 +360,7 @@ class TileScanAPI(View):
             resize=resize,
             bayer=args.get("bayer"),
             fast_autofocus=args.get("fast_autofocus"),
-            metadata=args.get("metadata"),
+            annotations=args.get("annotations"),
             tags=args.get("tags"),
         )
 

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

@@ -36,7 +36,7 @@ class CaptureAPI(View):
             "bayer": fields.Boolean(
                 missing=False, description="Store raw bayer data in file"
             ),
-            "metadata": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
+            "annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
             "tags": fields.List(fields.String, missing=[], example=["docs"]),
             "resize": fields.Dict(
                 missing=None, example={"width": 640, "height": 480}
@@ -75,11 +75,10 @@ class CaptureAPI(View):
             )
 
             # Inject system metadata
-            output.put_metadata(microscope.metadata, system=True)
+            output.put_metadata({"instrument": microscope.metadata})
 
             # Insert custom metadata
-            output.put_metadata(args.get("metadata"))
+            output.put_annotations(args.get("annotations"))
-
             # Insert custom tags
             output.put_tags(args.get("tags"))
 

openflexure_microscope/api/v2/views/captures.py

@@ -39,10 +39,12 @@ class CaptureSchema(Schema):
                 "mimetype": "application/json",
                 **description_from_view(CaptureTags),
             },
-            "metadata": {
+            "annotations": {
-                "href": url_for(CaptureMetadata.endpoint, id=data.id, _external=True),
+                "href": url_for(
+                    CaptureAnnotations.endpoint, id=data.id, _external=True
+                ),
                 "mimetype": "application/json",
-                **description_from_view(CaptureMetadata),
+                **description_from_view(CaptureAnnotations),
             },
             "download": {
                 "href": url_for(
@@ -62,6 +64,9 @@ capture_schema = CaptureSchema()
 capture_list_schema = CaptureSchema(many=True)
 
 
+from pprint import pprint
+
+
 @ThingProperty
 @Tag("captures")
 class CaptureList(View):
@@ -197,10 +202,10 @@ class CaptureTags(View):
 
 
 @Tag("captures")
-class CaptureMetadata(View):
+class CaptureAnnotations(View):
     def get(self, id):
         """
-        Get metadata associated with a single image capture
+        Get annotations associated with a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
         capture_obj = microscope.camera.image_from_id(id)
@@ -208,7 +213,7 @@ class CaptureMetadata(View):
         if not capture_obj:
             return abort(404)  # 404 Not Found
 
-        return jsonify(capture_obj.metadata)
+        return jsonify(capture_obj.annotations)
 
     def put(self, id):
         """
@@ -226,7 +231,6 @@ class CaptureMetadata(View):
         if type(data_dict) != dict:
             return abort(400)
 
-        # TODO: Allow putting system metadata maybe?
+        capture_obj.put_annotations(data_dict)
-        capture_obj.put_metadata(data_dict)
 
-        return jsonify(capture_obj.metadata)
+        return jsonify(capture_obj.annotations)

openflexure_microscope/api/v2/views/state.py

@@ -78,7 +78,7 @@ class StatusProperty(View):
         Show current read-only state of the microscope
         """
         microscope = find_component("org.openflexure.microscope")
-        return jsonify(microscope.status)
+        return jsonify(microscope.state)
 
 
 @Tag("properties")
@@ -92,7 +92,35 @@ class NestedStatusProperty(View):
         keys = route.split("/")
 
         try:
-            value = get_by_path(microscope.status, keys)
+            value = get_by_path(microscope.state, keys)
+        except KeyError:
+            return abort(404)
+
+        return jsonify(value)
+
+
+@ThingProperty
+class ConfigurationProperty(View):
+    def get(self):
+        """
+        Show current read-only state of the microscope
+        """
+        microscope = find_component("org.openflexure.microscope")
+        return jsonify(microscope.configuration)
+
+
+@Tag("properties")
+class NestedConfigurationProperty(View):
+    @doc_response(404, description="Configuration key cannot be found")
+    def get(self, route):
+        """
+        Show a nested section of the current microscope state
+        """
+        microscope = find_component("org.openflexure.microscope")
+        keys = route.split("/")
+
+        try:
+            value = get_by_path(microscope.configuration, keys)
         except KeyError:
             return abort(404)
 

openflexure_microscope/camera/capture.py

@@ -8,6 +8,7 @@ import yaml
 import json
 import logging
 from PIL import Image
+import dateutil.parser
 import atexit
 
 from openflexure_microscope.camera import piexif
@@ -93,18 +94,18 @@ def capture_from_exif(path, exif_dict):
     # Build file path information
     capture.split_file_path(capture.file)
 
-    # Populate capture parameters
+    # Image metadata
-    capture.id = exif_dict["id"]
+    image_metadata = exif_dict.pop("image")
-    capture.timestring = exif_dict["time"]
-    capture.format = exif_dict["format"]
 
-    capture.custom_metadata = (
+    # Populate capture parameters
-        exif_dict["custom"] if "custom" in exif_dict.keys() else {}
+    capture.id = image_metadata.get("id")
-    )
+    capture.datetime = dateutil.parser.isoparse(image_metadata.get("acquisitionDate"))
-    capture.system_metadata = (
+    capture.format = image_metadata.get("format")
-        exif_dict["system"] if "system" in exif_dict.keys() else {}
+    capture.tags = image_metadata.get("tags")
-    )
+    capture.annotations = image_metadata.get("annotations")
-    capture.tags = exif_dict["tags"]
+
+    # Since we popped the "image" key, we dump whatever is left in _metadata
+    capture._metadata = exif_dict
 
     return capture
 
@@ -113,16 +114,6 @@ class CaptureObject(object):
     """
     StreamObject used to store and process on-disk capture data, and metadata.
     Serves to simplify modifying properties of on-disk capture data.
-
-    Attributes:
-        timestring (str): Timestring of capture creation time
-        custom_metadata (dict): Dictionary of custom metadata to be included in metadata file
-        tags (list): List of tags. Essentially just as extra custom metadata field, but useful for quick organisation
-        filefolder (str): Folder in which the capture file will be stored
-        filename (str): Full name of the capture file
-        basename (str): Filename of the capture, without a file extension
-        format (str): Format of the capture data
-
     """
 
     def __init__(self, filepath) -> None:
@@ -131,17 +122,20 @@ class CaptureObject(object):
         # Store a nice ID
         self.id = uuid.uuid4()  #: str: Unique capture ID
         logging.debug("Created StreamObject {}".format(self.id))
-        self.timestring = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+        self.datetime = datetime.datetime.now()
 
         # Create file name. Default to UUID
         self.file = filepath
         self.split_file_path(self.file)
 
-        # Dictionary for storing custom metadata
+        if not os.path.exists(self.filefolder):
-        self.custom_metadata = {}
+            os.makedirs(self.filefolder)
-        # Dictionary for adding top-level metadata (cannmot be accessed through web API)
-        self.system_metadata = {}
 
+        # Dictionary for adding top-level metadata (cannmot be accessed through web API)
+        self._metadata = {}
+
+        # Dictionary for storing custom annotations
+        self.annotations = {}
         # List for storing tags
         self.tags = []
 
@@ -164,10 +158,6 @@ class CaptureObject(object):
         self.basename = os.path.splitext(self.filename)[0]
         self.format = self.filename.split(".")[-1]
 
-        # Create folder and file
-        if not os.path.exists(self.filefolder):
-            os.makedirs(self.filefolder)
-
     @property
     def exists(self) -> bool:
         """Check if capture data file exists on disk."""
@@ -204,17 +194,24 @@ class CaptureObject(object):
 
     # HANDLE METADATA
 
-    def put_metadata(self, data: dict, system: bool = False) -> None:
+    def put_annotations(self, data: dict) -> None:
         """
-        Merge metadata from a passed dictionary into the capture metadata, and saves.
+        Merge annotations from a passed dictionary into the capture metadata, and saves.
 
         Args:
             data (dict): Dictionary of metadata to be added
         """
-        if system:
+        self.annotations.update(data)
-            self.system_metadata.update(data)
+        self.save_metadata()
-        else:
+
-            self.custom_metadata.update(data)
+    def put_metadata(self, data: dict) -> None:
+        """
+        Merge root metadata from a passed dictionary into the capture metadata, and saves.
+
+        Args:
+            data (dict): Dictionary of metadata to be added
+        """
+        self._metadata.update(data)
         self.save_metadata()
 
     def save_metadata(self) -> None:
@@ -244,12 +241,15 @@ class CaptureObject(object):
         and any added custom metadata and tags.
         """
         d = {
-            "id": self.id,
+            "image": {
-            "time": self.timestring,
+                "id": self.id,
-            "format": self.format,
+                "name": self.filename,
-            "tags": self.tags,
+                "acquisitionDate": self.datetime.isoformat(),
-            "custom": self.custom_metadata,
+                "format": self.format,
-            "system": self.system_metadata,
+                "tags": self.tags,
+                "annotations": self.annotations,
+            },
+            **self._metadata,
         }
 
         # Add custom metadata to dictionary

openflexure_microscope/camera/pi.py

@@ -119,22 +119,7 @@ class PiCameraStreamer(BaseCamera):
     @property
     def configuration(self):
         """The current camera configuration."""
-        config = {
+        return {"board": self.camera.revision}
-            "board": self.camera.revision,
-        }
-
-        if self.read_lens_shading_table():
-            b64_string, dtype, shape = serialise_array_b64(self.read_lens_shading_table())
-
-            config.update({
-                "lens_shading_table": {
-                    "b64_string": b64_string,
-                    "dtype": dtype,
-                    "shape": shape,
-                }
-            })
-
-        return config
 
     @property
     def state(self):

openflexure_microscope/config.py

@@ -1,4 +1,5 @@
 import json
+import flask
 import os
 import errno
 import logging
@@ -7,7 +8,12 @@ from uuid import UUID
 import numpy as np
 from fractions import Fraction
 
-from .paths import SETTINGS_FILE_PATH, DEFAULT_SETTINGS_FILE_PATH, CONFIGURATION_FILE_PATH, DEFAULT_CONFIGURATION_FILE_PATH
+from .paths import (
+    SETTINGS_FILE_PATH,
+    DEFAULT_SETTINGS_FILE_PATH,
+    CONFIGURATION_FILE_PATH,
+    DEFAULT_CONFIGURATION_FILE_PATH,
+)
 
 
 class OpenflexureSettingsFile:
@@ -71,7 +77,7 @@ class OpenflexureSettingsFile:
         return settings
 
 
-class JSONEncoder(json.JSONEncoder):
+class JSONEncoder(flask.json.JSONEncoder):
     """
     A custom JSON encoder, with type conversions for PiCamera fractions, Numpy integers, and Numpy arrays
     """
@@ -183,7 +189,9 @@ with open(DEFAULT_SETTINGS_FILE_PATH, "r") as default_settings:
     DEFAULT_SETTINGS = default_settings.read()
 
 #: Default user settings object
-user_settings = OpenflexureSettingsFile(path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS)
+user_settings = OpenflexureSettingsFile(
+    path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS
+)
 
 
 # Load the default configuration
@@ -191,4 +199,7 @@ with open(DEFAULT_CONFIGURATION_FILE_PATH, "r") as default_configuration:
     DEFAULT_CONFIGURATION = default_configuration.read()
 
 #: Default user settings object
-user_configuration = OpenflexureSettingsFile(path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION)
+user_configuration = OpenflexureSettingsFile(
+    path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION
+)
+

openflexure_microscope/microscope.py

@@ -9,6 +9,7 @@ import uuid
 from openflexure_microscope.stage.mock import MissingStage
 from openflexure_microscope.camera.mock import MissingCamera
 from openflexure_microscope.stage.sanga import SangaStage
+
 try:
     from openflexure_microscope.camera.pi import PiCameraStreamer
 except ImportError:
@@ -29,7 +30,12 @@ class Microscope:
     The camera and stage objects may already be initialised, and can be passed as arguments.
     """
 
-    def __init__(self, settings = user_settings, configuration = user_configuration):
+    def __init__(self, settings=user_settings, configuration=user_configuration):
+        self.id = uuid.uuid4()
+        self.name = self.id
+
+        self.fov = [0, 0]  #: Microscope field-of-view in stage motor steps
+
         # Store settings and configuration files
         self.settings_file = settings
         self.configuration_file = configuration
@@ -45,17 +51,6 @@ class Microscope:
         # Apply settings loaded from file
         self.update_settings(self.settings_file.load())
 
-        # Initial attributes
-        if self.configuration_file.load().get("id"):
-            self.id = configuration.get("id")
-        else:
-            self.id = uuid.uuid4()
-            self.configuration_file.save({
-                "id": self.id
-            })
-
-        self.name = self.id
-
     def __enter__(self):
         """Create microscope on context enter."""
         return self
@@ -79,9 +74,9 @@ class Microscope:
         """
 
         ### Detector
-        if configuration.get("detector"):
+        if configuration.get("camera"):
-            detector_type = configuration["detector"].get("type")
+            camera_type = configuration["camera"].get("type")
-            if detector_type == "PiCamera" or detector_type == "PiCameraStreamer":
+            if camera_type == "PiCamera" or camera_type == "PiCameraStreamer":
                 try:
                     self.camera = PiCameraStreamer()
                 except Exception as e:
@@ -92,7 +87,7 @@ class Microscope:
         if configuration.get("stage"):
             stage_type = configuration["stage"].get("type")
             stage_port = configuration["stage"].get("port")
-            if stage_type == "SangaBoard" or detector_type == "SangaStage":
+            if stage_type == "SangaBoard" or camera_type == "SangaStage":
                 try:
                     self.stage = SangaStage(port=stage_port)
                 except Exception as e:
@@ -137,33 +132,32 @@ class Microscope:
         Return:
             dict: Dictionary containing complete microscope status
         """
-        state = {
+        state = {"camera": self.camera.state, "stage": self.stage.state}
-            "camera": self.camera.state,
-            "stage": self.stage.state,
-        }
         return state
 
-    def update_settings(self, config: dict):
+    def update_settings(self, settings: dict):
         """
         Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
         """
-        logging.debug("Microscope: Applying config: {}".format(config))
+        logging.debug("Microscope: Applying settings: {}".format(settings))
 
         # If attached to a camera
-        if ("camera_settings" in config) and self.camera:
+        if ("camera" in settings) and self.camera:
-            self.camera.update_settings(config["camera_settings"])
+            self.camera.update_settings(settings["camera"])
 
         # If attached to a stage
-        if ("stage_settings" in config) and self.stage:
+        if ("stage" in settings) and self.stage:
-            self.stage.update_settings(config["stage_settings"])
+            self.stage.update_settings(settings["stage"])
 
-        # Todo: tidy up with some loopy goodness
+        # Microscope settings
-        if "name" in config:
+        if "id" in settings:
-            self.name = config["name"]
+            self.id = settings["id"]
-        if "fov" in config:
+        if "name" in settings:
-            self.fov = config["fov"]
+            self.name = settings["name"]
+        if "fov" in settings:
+            self.fov = settings["fov"]
 
-    def read_settings(self, full: bool=True):
+    def read_settings(self, full: bool = True):
         """
         Get an updated settings dictionary.
 
@@ -174,17 +168,30 @@ class Microscope:
         don't get removed from the settings file.
         """
 
-        settings_current = {"name": self.name, "fov": self.fov}
+        settings_current = {"id": self.id, "name": self.name, "fov": self.fov}
 
         # If attached to a camera
         if self.camera:
             settings_current_camera = self.camera.read_settings()
-            settings_current["camera_settings"] = settings_current_camera
+            settings_current["camera"] = settings_current_camera
+
+            # Store an encoded copy of the PiCamera lens shading table, if it exists
+            if hasattr(self.camera, "read_lens_shading_table"):
+                # Read LST. Returns None if no LST is active
+                lst_arr = self.camera.read_lens_shading_table()
+
+                b64_string, dtype, shape = serialise_array_b64(lst_arr)
+
+                settings_current["camera"]["lens_shading_table"] = {
+                    "b64_string": b64_string,
+                    "dtype": dtype,
+                    "shape": shape,
+                }
 
         # If attached to a stage
         if self.stage:
             settings_current_stage = self.stage.read_settings()
-            settings_current["stage_settings"] = settings_current_stage
+            settings_current["stage"] = settings_current_stage
 
         settings_full = self.settings_file.merge(settings_current)
 
@@ -206,33 +213,6 @@ class Microscope:
             self.stage.save_settings()
         self.settings_file.save(current_config, backup=True)
 
-    @property
-    def metadata(self):
-        """
-        Microscope system metadata, to be applied to basically all captures
-        """
-        system_metadata = {
-            "@ID": self.id,
-            "settings": self.read_settings(full=False),
-            "state": self.state,
-            "configuration": self.configuration
-        }
-
-        # Store an encoded copy of the PiCamera lens shading table, if it exists
-        if self.camera and hasattr(self.camera, "read_lens_shading_table"):
-            # Read LST. Returns None if no LST is active
-            lst_arr = self.camera.read_lens_shading_table()
-
-            b64_string, dtype, shape = serialise_array_b64(lst_arr)
-
-            system_metadata["configuration"]["detector"]["lens_shading_table"] = {
-                "b64_string": b64_string,
-                "dtype": dtype,
-                "shape": shape,
-            }
-
-        return system_metadata
-
     @property
     def configuration(self):
         initial_configuration = self.configuration_file.load()
@@ -240,17 +220,33 @@ class Microscope:
         current_configuration = {
             "@application": {
                 "name": "openflexure_microscope",
-                "version": pkg_resources.get_distribution("openflexure_microscope").version
+                "version": pkg_resources.get_distribution(
+                    "openflexure_microscope"
+                ).version,
             },
             "stage": {
                 "type": self.stage.__class__.__name__,
-                **self.stage.configuration
+                **self.stage.configuration,
             },
-            "detector": {
+            "camera": {
                 "type": self.camera.__class__.__name__,
-                **self.camera.configuration
+                **self.camera.configuration,
-            }
+            },
         }
 
         initial_configuration.update(current_configuration)
         return initial_configuration
+
+    @property
+    def metadata(self):
+        """
+        Microscope system metadata, to be applied to basically all captures
+        """
+        system_metadata = {
+            "id": self.id,
+            "settings": self.read_settings(full=False),
+            "state": self.state,
+            "configuration": self.configuration,
+        }
+
+        return system_metadata

openflexure_microscope/microscope_configuration.default.json

@@ -1,17 +1,9 @@
 {
-  "microscope": {
+  "camera": {
-    "stepsPerView": [4100, 3146]
-  },
-  "detector": {
     "type": "PiCamera"
   },
   "stage": {
     "type": "SangaStage",
     "port": null
-  },
-  "lightSource": {
-    "type": "LED"
-  },
-  "objective": {
   }
 }