From 19af98736d80731dd7e010fbf5ca3abf4e2e4771 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 11:55:39 +0000
Subject: [PATCH 1/7] Draft of new semantics

---
 openflexure_microscope/api/microscope.py      |  29 ---
 openflexure_microscope/api/v2/views/state.py  |   4 +-
 openflexure_microscope/camera/base.py         |  35 +++-
 openflexure_microscope/camera/mock.py         |  22 ++-
 openflexure_microscope/camera/pi.py           |  56 ++++--
 openflexure_microscope/config.py              |  35 ++--
 openflexure_microscope/microscope.py          | 176 ++++++++++--------
 .../microscope_configuration.default.json     |  17 ++
 .../microscope_settings.default.json          |   6 +-
 openflexure_microscope/paths.py               |  11 +-
 openflexure_microscope/stage/base.py          |  16 +-
 openflexure_microscope/stage/mock.py          |  18 +-
 openflexure_microscope/stage/sanga.py         |  14 +-
 13 files changed, 252 insertions(+), 187 deletions(-)
 create mode 100644 openflexure_microscope/microscope_configuration.default.json

diff --git a/openflexure_microscope/api/microscope.py b/openflexure_microscope/api/microscope.py
index 04053892..2f534b49 100644
--- a/openflexure_microscope/api/microscope.py
+++ b/openflexure_microscope/api/microscope.py
@@ -3,38 +3,9 @@ from openflexure_microscope.camera.capture import build_captures_from_exif
 
 import logging
 
-# Import device modules
-# NB this will eventually be handled by the RC file, so you can choose what device
-# class should be attached.
-try:
-    from openflexure_microscope.camera.pi import PiCameraStreamer
-except ImportError:
-    logging.warning("Unable to import PiCameraStreamer")
-from openflexure_microscope.camera.mock import MockStreamer
-
-from openflexure_microscope.stage.sanga import SangaStage
-from openflexure_microscope.stage.mock import MockStage
 
 default_microscope = Microscope()
 
-# Initialise camera
-logging.debug("Creating camera object...")
-try:
-    api_camera = PiCameraStreamer()
-except Exception as e:
-    logging.error(e)
-    logging.warning("No valid camera hardware found. Falling back to mock camera!")
-    api_camera = MockStreamer()
-
-# Initialise stage
-logging.debug("Creating stage object...")
-
-api_stage = MockStage()
-
-# Attach devices to microscope
-logging.debug("Attaching devices to microscope...")
-default_microscope.attach(api_camera, api_stage)
-
 # Restore loaded capture array to camera object
 logging.debug("Restoring captures...")
 default_microscope.camera.images = build_captures_from_exif(
diff --git a/openflexure_microscope/api/v2/views/state.py b/openflexure_microscope/api/v2/views/state.py
index aa59ffdf..34637754 100644
--- a/openflexure_microscope/api/v2/views/state.py
+++ b/openflexure_microscope/api/v2/views/state.py
@@ -30,7 +30,7 @@ class SettingsProperty(View):
         logging.debug("Updating settings from PUT request:")
         logging.debug(payload.json)
 
-        microscope.apply_settings(payload.json)
+        microscope.update_settings(payload.json)
         microscope.save_settings()
 
         return self.get()
@@ -65,7 +65,7 @@ class NestedSettingsProperty(View):
         dictionary = create_from_path(keys)
         set_by_path(dictionary, keys, payload.json)
 
-        microscope.apply_settings(dictionary)
+        microscope.update_settings(dictionary)
         microscope.save_settings()
 
         return self.get(route)
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index e6395e1f..e823cfd0 100644
--- a/openflexure_microscope/camera/base.py
+++ b/openflexure_microscope/camera/base.py
@@ -121,7 +121,8 @@ class BaseCamera(metaclass=ABCMeta):
         self.stream_timeout = 20
         self.stream_timeout_enabled = False
 
-        self.status = {"board": None}
+        self.stream_active = False
+        self.record_active = False
 
         self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
 
@@ -129,8 +130,24 @@ class BaseCamera(metaclass=ABCMeta):
         self.images = []
         self.videos = []
 
+    @property
     @abstractmethod
-    def apply_settings(self, config: dict):
+    def configuration(self):
+        """The current camera configuration."""
+        pass
+
+    @property
+    @abstractmethod
+    def state(self):
+        """The current read-only camera state."""
+        pass
+
+    @property
+    def settings(self):
+        return self.read_settings()
+
+    @abstractmethod
+    def update_settings(self, config: dict):
         """Update settings from a config dictionary"""
         with self.lock:
             # Apply valid config params to camera object
@@ -187,7 +204,7 @@ class BaseCamera(metaclass=ABCMeta):
         self.last_access = time.time()
         self.stop = False
 
-        if not self.status["stream_active"]:
+        if not self.stream_active:
             # start background frame thread
             self.thread = threading.Thread(target=self._thread)
             self.thread.daemon = True
@@ -207,12 +224,12 @@ class BaseCamera(metaclass=ABCMeta):
         logging.debug("Stopping worker thread")
         timeout_time = time.time() + timeout
 
-        if self.status["stream_active"]:
+        if self.stream_active:
             self.stop = True
             self.thread.join()  # Wait for stream thread to exit
             logging.debug("Waiting for stream thread to exit.")
 
-        while self.status["stream_active"]:
+        while self.stream_active:
             if time.time() > timeout_time:
                 logging.debug("Timeout waiting for worker thread close.")
                 raise TimeoutError("Timeout waiting for worker thread close.")
@@ -352,7 +369,7 @@ class BaseCamera(metaclass=ABCMeta):
         self.frames_iterator = self.frames()
         logging.debug("Entering worker thread.")
 
-        self.status["stream_active"] = True
+        self.stream_active = True
 
         for frame in self.frames_iterator:
             self.frame = frame
@@ -365,9 +382,7 @@ class BaseCamera(metaclass=ABCMeta):
                 and (  # If using timeout
                     time.time() - self.last_access > self.stream_timeout
                 )
-                and not self.status[  # And timeout time
-                    "preview_active"
-                ]  # And GPU preview is not active
+                and not self.preview_active  # And GPU preview is not active
             ):
                 self.frames_iterator.close()
                 break
@@ -383,4 +398,4 @@ class BaseCamera(metaclass=ABCMeta):
 
         logging.debug("BaseCamera worker thread exiting...")
         # Set stream_activate state
-        self.status["stream_active"] = False
+        self.stream_active = False
diff --git a/openflexure_microscope/camera/mock.py b/openflexure_microscope/camera/mock.py
index abffb221..322bae58 100644
--- a/openflexure_microscope/camera/mock.py
+++ b/openflexure_microscope/camera/mock.py
@@ -26,17 +26,13 @@ We override the logging settings in api.app by setting a level for PIL here.
 pil_logger = logging.getLogger("PIL")
 pil_logger.setLevel(logging.INFO)
 
+
 # MAIN CLASS
-class MockStreamer(BaseCamera):
+class MissingCamera(BaseCamera):
     def __init__(self):
         # Run BaseCamera init
         BaseCamera.__init__(self)
 
-        # Store state of PiCameraStreamer
-        self.status.update(
-            {"stream_active": False, "record_active": False, "board": None}
-        )
-
         # Update config properties
         self.image_resolution = (1312, 976)
         self.stream_resolution = (640, 480)
@@ -71,6 +67,16 @@ class MockStreamer(BaseCamera):
 
         image.save(self.stream, format="JPEG")
 
+    @property
+    def configuration(self):
+        """The current camera configuration."""
+        return {}
+
+    @property
+    def state(self):
+        """The current read-only camera state."""
+        return {}
+
     def initialisation(self):
         """Run any initialisation code when the frame iterator starts."""
         pass
@@ -101,7 +107,7 @@ class MockStreamer(BaseCamera):
 
         return conf_dict
 
-    def apply_settings(self, config: dict):
+    def update_settings(self, config: dict):
         """
         Write a config dictionary to the PiCameraStreamer config.
 
@@ -117,7 +123,7 @@ class MockStreamer(BaseCamera):
         with self.lock:
 
             # Apply valid config params to camera object
-            if not self.status["record_active"]:  # If not recording a video
+            if not self.record_active:  # If not recording a video
 
                 for key, value in config.items():  # For each provided setting
                     if hasattr(self, key):
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 5cafb045..bbd04e44 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -47,6 +47,7 @@ from .base import BaseCamera, CaptureObject
 from .set_picamera_gain import set_analog_gain, set_digital_gain
 
 from openflexure_microscope.paths import settings_file_path
+from openflexure_microscope.utilities import serialise_array_b64
 
 
 # MAIN CLASS
@@ -85,14 +86,7 @@ class PiCameraStreamer(BaseCamera):
         )  #: :py:class:`picamera.PiCamera`: Picamera object
 
         # Store status of PiCameraStreamer
-        self.status.update(
-            {
-                "stream_active": False,
-                "record_active": False,
-                "preview_active": False,
-                "board": f"picamera_{self.camera.revision}",
-            }
-        )
+        self.preview_active = False
 
         # Reset variable states
         self.set_zoom(1.0)
@@ -116,15 +110,37 @@ class PiCameraStreamer(BaseCamera):
             "picamera_lst.npy"
         )  #: str: Path of .npy lens shading table file
 
-        # Update board identifier
-        self.status.update({})
-
         # Create an empty stream
         self.stream = io.BytesIO()
 
         # Start streaming
         self.start_worker()
 
+    @property
+    def configuration(self):
+        """The current camera configuration."""
+        config = {
+            "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):
+        """The current read-only camera state."""
+        return {}
+
     def initialisation(self):
         """Run any initialisation code when the frame iterator starts."""
         pass
@@ -176,7 +192,7 @@ class PiCameraStreamer(BaseCamera):
         logging.info("Saving picamera_lst to {}".format(self.picamera_lst_path))
         self.save_lens_shading_table()
 
-    def apply_settings(self, config: dict):
+    def update_settings(self, config: dict):
         """
         Write a config dictionary to the PiCameraStreamer config.
 
@@ -194,10 +210,10 @@ class PiCameraStreamer(BaseCamera):
         with self.lock:
 
             # Apply valid config params to Picamera object
-            if not self.status["record_active"]:  # If not recording a video
+            if not self.record_active:  # If not recording a video
 
                 # Pause stream while changing settings
-                if self.status["stream_active"]:  # If stream is active
+                if self.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
@@ -365,7 +381,7 @@ class PiCameraStreamer(BaseCamera):
                     self.camera.preview.window = window
                 if fullscreen:
                     self.camera.preview.fullscreen = fullscreen
-            self.status["preview_active"] = True
+            self.preview_active = True
         except picamera.exc.PiCameraMMALError as e:
             logging.error(
                 "Suppressed a MMALError in start_preview. Exception: {}".format(e)
@@ -380,7 +396,7 @@ class PiCameraStreamer(BaseCamera):
     def stop_preview(self):
         """Stop the on board GPU camera preview."""
         self.camera.stop_preview()
-        self.status["preview_active"] = False
+        self.preview_active = False
 
     def start_recording(self, output, fmt: str = "h264", quality: int = 15):
         """Start recording.
@@ -398,7 +414,7 @@ class PiCameraStreamer(BaseCamera):
         """
         with self.lock:
             # Start recording method only if a current recording is not running
-            if not self.status["record_active"]:
+            if not self.record_active:
 
                 # Start the camera video recording on port 2
                 logging.info("Recording to {}".format(output))
@@ -412,7 +428,7 @@ class PiCameraStreamer(BaseCamera):
                 )
 
                 # Update status dictionary
-                self.status["record_active"] = True
+                self.record_active = True
 
                 return output
 
@@ -432,7 +448,7 @@ class PiCameraStreamer(BaseCamera):
             logging.info("Recording stopped")
 
             # Update status dictionary
-            self.status["record_active"] = False
+            self.record_active = False
 
     def stop_stream_recording(
         self, splitter_port: int = 1, resolution: Tuple[int, int] = None
@@ -500,7 +516,7 @@ class PiCameraStreamer(BaseCamera):
                 self.camera.resolution = resolution
 
             # If the stream should be active
-            if self.status["stream_active"]:
+            if self.stream_active:
                 try:
                     # Start recording on stream port
                     self.camera.start_recording(
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 8e613574..cfc458a1 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -7,7 +7,7 @@ from uuid import UUID
 import numpy as np
 from fractions import Fraction
 
-from .paths import CONFIG_FILE_PATH, DEFAULT_CONFIG_FILE_PATH
+from .paths import SETTINGS_FILE_PATH, DEFAULT_SETTINGS_FILE_PATH, CONFIGURATION_FILE_PATH, DEFAULT_CONFIGURATION_FILE_PATH
 
 
 class OpenflexureSettingsFile:
@@ -19,21 +19,21 @@ class OpenflexureSettingsFile:
         expand (bool): Expand paths to valid auxillary config files.
     """
 
-    def __init__(self, config_path: str = None):
-        global DEFAULT_CONFIG, CONFIG_FILE_PATH
+    def __init__(self, path: str, defaults: dict = {}):
+        global DEFAULT_SETTINGS
 
         # Set arguments
-        self.config_path = config_path or CONFIG_FILE_PATH
+        self.path = path
 
         # Initialise basic config file with defaults if it doesn't exist
-        initialise_file(self.config_path, populate=DEFAULT_CONFIG)
+        initialise_file(self.path, populate=defaults)
 
     def load(self) -> dict:
         """
         Loads settings from a file on-disk.
         """
         # Unexpanded config dictionary (used at load/save time)
-        loaded_config = load_json_file(self.config_path)
+        loaded_config = load_json_file(self.path)
 
         logging.debug("Reading settings from disk")
         return loaded_config
@@ -50,11 +50,11 @@ class OpenflexureSettingsFile:
         save_settings = config
 
         if backup:
-            if os.path.isfile(self.config_path):
-                shutil.copyfile(self.config_path, self.config_path + ".bk")
+            if os.path.isfile(self.path):
+                shutil.copyfile(self.path, self.path + ".bk")
 
         logging.debug("Saving settings dictionary to disk")
-        save_json_file(self.config_path, save_settings)
+        save_json_file(self.path, save_settings)
 
     def merge(self, config: dict) -> dict:
         """
@@ -178,10 +178,17 @@ def initialise_file(config_path, populate: str = "{}\n"):
             outfile.write(populate)
 
 
-# Load the default config
-with open(DEFAULT_CONFIG_FILE_PATH, "r") as default_rc:
-    DEFAULT_CONFIG = default_rc.read()
-
+# Load the default settings
+with open(DEFAULT_SETTINGS_FILE_PATH, "r") as default_settings:
+    DEFAULT_SETTINGS = default_settings.read()
 
 #: Default user settings object
-user_settings = OpenflexureSettingsFile(config_path=CONFIG_FILE_PATH)
+user_settings = OpenflexureSettingsFile(path=SETTINGS_FILE_PATH, defaults=DEFAULT_SETTINGS)
+
+
+# Load the default configuration
+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)
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index 31ea505c..2f52c6d9 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -6,15 +6,20 @@ import logging
 import pkg_resources
 import uuid
 
-from openflexure_microscope.stage.base import BaseStage
-from openflexure_microscope.stage.mock import MockStage
-from openflexure_microscope.camera.base import BaseCamera
-from openflexure_microscope.camera.mock import MockStreamer
+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:
+    logging.warning("Unable to import PiCameraStreamer")
+from openflexure_microscope.camera.mock import MissingCamera
 
 from openflexure_microscope.utilities import serialise_array_b64
-from openflexure_microscope.config import user_settings
+from openflexure_microscope.config import user_settings, user_configuration
 
 from labthings.core.lock import CompositeLock
+from labthings.core.utilities import rupdate
 
 
 class Microscope:
@@ -24,20 +29,32 @@ class Microscope:
     The camera and stage objects may already be initialised, and can be passed as arguments.
     """
 
-    def __init__(self):
-        # Initial attributes
-        self.id = uuid.uuid4()  #: Microscope UUID
-        self.name = self.id  #: Microscope name (modifiable)
-        self.fov = [0, 0]  #: Microscope field-of-view in stage motor steps
-        self.camera = None  #: Currently connected camera object
-        self.stage = None  #: Currently connected stage object
+    def __init__(self, settings = user_settings, configuration = user_configuration):
+        # Store settings and configuration files
+        self.settings_file = settings
+        self.configuration_file = configuration
 
         # Initialise with an empty composite lock
         #: :py:class:`labthings.lock.CompositeLock`: Composite lock for locking both camera and stage
         self.lock = CompositeLock([])
 
+        self.camera = None  #: Currently connected camera object
+        self.stage = None  #: Currently connected stage object
+        self.setup(self.configuration_file.load())  # Attach components
+
         # Apply settings loaded from file
-        self.apply_settings(user_settings.load())
+        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."""
@@ -56,58 +73,49 @@ class Microscope:
             self.stage.close()
         logging.info("Closed {}".format(self))
 
-    def attach(self, camera: BaseCamera, stage: BaseStage):
+    def setup(self, configuration):
         """
-        Retroactively attaches a camera and stage to the microscope object.
-
-        Allows the microscope to be created as a "dummy", with hardware communications
-        opened at a later time.
-
-        Args:
-            camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): camera object
-            stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): stage object
+        Attach microscope components based on initially passed configuration file
         """
 
-        settings_full = self.read_settings()
+        ### Detector
+        if configuration.get("detector"):
+            detector_type = configuration["detector"].get("type")
+            if detector_type == "PiCamera" or detector_type == "PiCameraStreamer":
+                try:
+                    self.camera = PiCameraStreamer()
+                except Exception as e:
+                    logging.error(e)
+                    logging.warning("No compatible camera hardware found.")
 
-        logging.debug("Attaching camera...")
-        self.camera = (
-            camera
-        )  #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
+        ### Stage
+        if configuration.get("stage"):
+            stage_type = configuration["stage"].get("type")
+            stage_port = configuration["stage"].get("port")
+            if stage_type == "SangaBoard" or detector_type == "SangaStage":
+                try:
+                    self.stage = SangaStage(port=stage_port)
+                except Exception as e:
+                    logging.error(e)
+                    logging.warning("No compatible stage hardware found.")
+
+        ### Fallbacks
         if not self.camera:
-            logging.info("No camera attached.")
-        else:
-            logging.info("Attached camera {}".format(camera))
-
-            if hasattr(self.camera, "lock"):  # If camera has a lock
-                logging.info("Attaching {} to composite lock.".format(self.camera.lock))
-                # Add the lock to the microscope composite lock
-                self.lock.locks.append(self.camera.lock)
-
-        logging.debug("Attaching stage...")
-        self.stage = (
-            stage
-        )  #: :py:class:`openflexure_microscope.stage.base.BaseStage`: OpenFlexure stage object
+            self.camera = MissingCamera()
         if not self.stage:
-            logging.info("No stage attached.")
-        else:
-            logging.info("Attached stage {}".format(stage))
+            self.stage = MissingStage()
 
-            if hasattr(self.stage, "lock"):  # If stage object has a lock
-                logging.info(
-                    "Attaching lock {} to composite lock.".format(self.stage.lock)
-                )
-                # Add the lock to the microscope composite lock
-                self.lock.locks.append(self.stage.lock)
-
-        logging.info("Reapplying settings to newly attached devices")
-        self.apply_settings(settings_full)
+        ### Locks
+        if hasattr(self.camera, "lock"):
+            self.lock.locks.append(self.camera.lock)
+        if hasattr(self.stage, "lock"):
+            self.lock.locks.append(self.stage.lock)
 
     def has_real_stage(self) -> bool:
         """
         Check if a real (non-mock) stage is currently attached.
         """
-        if hasattr(self, "stage") and not isinstance(self.stage, MockStage):
+        if hasattr(self, "stage") and not isinstance(self.stage, MissingStage):
             return True
         else:
             return False
@@ -116,27 +124,26 @@ class Microscope:
         """
         Check if a real (non-mock) camera is currently attached.
         """
-        if hasattr(self, "camera") and not isinstance(self.camera, MockStreamer):
+        if hasattr(self, "camera") and not isinstance(self.camera, MissingCamera):
             return True
         else:
             return False
 
     # Create unified status
     @property
-    def status(self):
+    def state(self):
         """Dictionary of the basic microscope status.
 
         Return:
             dict: Dictionary containing complete microscope status
         """
         state = {
-            "camera": self.camera.status,
-            "stage": self.stage.status,
-            "version": pkg_resources.get_distribution("openflexure_microscope").version,
+            "camera": self.camera.state,
+            "stage": self.stage.state,
         }
         return state
 
-    def apply_settings(self, config: dict):
+    def update_settings(self, config: dict):
         """
         Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
         """
@@ -144,21 +151,19 @@ class Microscope:
 
         # If attached to a camera
         if ("camera_settings" in config) and self.camera:
-            self.camera.apply_settings(config["camera_settings"])
+            self.camera.update_settings(config["camera_settings"])
 
         # If attached to a stage
         if ("stage_settings" in config) and self.stage:
-            self.stage.apply_settings(config["stage_settings"])
+            self.stage.update_settings(config["stage_settings"])
 
         # Todo: tidy up with some loopy goodness
-        if "id" in config:
-            self.id = config["id"]
         if "name" in config:
             self.name = config["name"]
         if "fov" in config:
             self.fov = config["fov"]
 
-    def read_settings(self, json_safe=False):
+    def read_settings(self, full: bool=True):
         """
         Get an updated settings dictionary.
 
@@ -169,7 +174,7 @@ class Microscope:
         don't get removed from the settings file.
         """
 
-        settings_current = {"id": self.id, "name": self.name, "fov": self.fov}
+        settings_current = {"name": self.name, "fov": self.fov}
 
         # If attached to a camera
         if self.camera:
@@ -181,9 +186,12 @@ class Microscope:
             settings_current_stage = self.stage.read_settings()
             settings_current["stage_settings"] = settings_current_stage
 
-        settings_full = user_settings.merge(settings_current)
+        settings_full = self.settings_file.merge(settings_current)
 
-        return settings_full
+        if full:
+            return settings_full
+        else:
+            return settings_current
 
     def save_settings(self):
         """
@@ -196,7 +204,7 @@ class Microscope:
             self.camera.save_settings()
         if self.stage:
             self.stage.save_settings()
-        user_settings.save(current_config, backup=True)
+        self.settings_file.save(current_config, backup=True)
 
     @property
     def metadata(self):
@@ -204,10 +212,10 @@ class Microscope:
         Microscope system metadata, to be applied to basically all captures
         """
         system_metadata = {
-            "microscope_settings": self.read_settings(),
-            "microscope_state": self.status,
-            "microscope_id": self.id,
-            "microscope_name": self.name,
+            "@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
@@ -217,10 +225,32 @@ class Microscope:
 
             b64_string, dtype, shape = serialise_array_b64(lst_arr)
 
-            system_metadata["lens_shading_table"] = {
+            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()
+
+        current_configuration = {
+            "@application": {
+                "name": "openflexure_microscope",
+                "version": pkg_resources.get_distribution("openflexure_microscope").version
+            },
+            "stage": {
+                "type": self.stage.__class__.__name__,
+                **self.stage.configuration
+            },
+            "detector": {
+                "type": self.camera.__class__.__name__,
+                **self.camera.configuration
+            }
+        }
+
+        initial_configuration.update(current_configuration)
+        return initial_configuration
diff --git a/openflexure_microscope/microscope_configuration.default.json b/openflexure_microscope/microscope_configuration.default.json
new file mode 100644
index 00000000..d7129bc8
--- /dev/null
+++ b/openflexure_microscope/microscope_configuration.default.json
@@ -0,0 +1,17 @@
+{
+  "microscope": {
+    "stepsPerView": [4100, 3146]
+  },
+  "detector": {
+    "type": "PiCamera"
+  },
+  "stage": {
+    "type": "SangaStage",
+    "port": null
+  },
+  "lightSource": {
+    "type": "LED"
+  },
+  "objective": {
+  }
+}
\ No newline at end of file
diff --git a/openflexure_microscope/microscope_settings.default.json b/openflexure_microscope/microscope_settings.default.json
index bde62f47..fa0fcb28 100644
--- a/openflexure_microscope/microscope_settings.default.json
+++ b/openflexure_microscope/microscope_settings.default.json
@@ -1,7 +1,3 @@
 {
-  "fov": [
-    4100,
-    3146
-  ],
-  "jpeg_quality": 75
+  "jpeg_quality": 100
 }
\ No newline at end of file
diff --git a/openflexure_microscope/paths.py b/openflexure_microscope/paths.py
index a261d618..8fbf9b55 100644
--- a/openflexure_microscope/paths.py
+++ b/openflexure_microscope/paths.py
@@ -32,8 +32,9 @@ def logs_file_path(filename: str):
 HERE = os.path.abspath(os.path.dirname(__file__))
 
 #: Path of default (first-run) microscope settings
-DEFAULT_CONFIG_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
-
+DEFAULT_SETTINGS_FILE_PATH = os.path.join(HERE, "microscope_settings.default.json")
+#: Path of default (first-run) microscope configuration
+DEFAULT_CONFIGURATION_FILE_PATH = os.path.join(HERE, "microscope_configuration.default.json")
 
 # BASE PATHS
 
@@ -60,7 +61,9 @@ else:
 
 # SERVER PATHS
 
-#: Path of microscope settings directory
-CONFIG_FILE_PATH = settings_file_path("microscope_settings.json")
+#: Path of microscope settings file
+SETTINGS_FILE_PATH = settings_file_path("microscope_settings.json")
+#: Path of microscope configuration file
+CONFIGURATION_FILE_PATH = settings_file_path("microscope_configuration.json")
 #: Path of microscope extensions directory
 OPENFLEXURE_EXTENSIONS_PATH = extensions_file_path("microscope_extensions")
diff --git a/openflexure_microscope/stage/base.py b/openflexure_microscope/stage/base.py
index d5ef31f3..564ba1a6 100644
--- a/openflexure_microscope/stage/base.py
+++ b/openflexure_microscope/stage/base.py
@@ -14,7 +14,7 @@ class BaseStage(metaclass=ABCMeta):
         self.lock = StrictLock(timeout=5)
 
     @abstractmethod
-    def apply_settings(self, config: dict):
+    def update_settings(self, config: dict):
         """Update settings from a config dictionary"""
         pass
 
@@ -29,12 +29,14 @@ class BaseStage(metaclass=ABCMeta):
 
     @property
     @abstractmethod
-    def status(self):
-        """The general state dictionary of the board.
-        Should at least contain 'position', and 'board' keys.
-        Note: A None/Null value for 'board' will disable stage
-        movement in the OpenFlexure eV client software,
-        """
+    def state(self):
+        """The general state dictionary of the board."""
+        pass
+
+    @property
+    @abstractmethod
+    def configuration(self):
+        """The general stage configuration."""
         pass
 
     @property
diff --git a/openflexure_microscope/stage/mock.py b/openflexure_microscope/stage/mock.py
index e85fa43b..e4810f3c 100644
--- a/openflexure_microscope/stage/mock.py
+++ b/openflexure_microscope/stage/mock.py
@@ -7,7 +7,7 @@ import time
 import logging
 
 
-class MockStage(BaseStage):
+class MissingStage(BaseStage):
     def __init__(self, port=None, **kwargs):
         BaseStage.__init__(self)
         self._position = [0, 0, 0]
@@ -17,19 +17,17 @@ class MockStage(BaseStage):
         self.axis_names = ["x", "y", "z"]  # Assume all sangaboards are 3 axis
 
     @property
-    def status(self):
+    def state(self):
         """The general status dictionary of the board."""
-        status = {
-            "position": self.position_map,
-            "board": None,
-            "firmware": None,
-            "version": None,
-        }
+        status = {"position": self.position_map}
         return status
 
-    def apply_settings(self, config: dict):
-        """Update settings from a config dictionary"""
+    @property
+    def configuration(self):
+        return {}
 
+    def update_settings(self, config: dict):
+        """Update settings from a config dictionary"""
         # Set backlash. Expects a dictionary with axis labels
         if "backlash" in config:
             # Construct backlash array
diff --git a/openflexure_microscope/stage/sanga.py b/openflexure_microscope/stage/sanga.py
index 2c4fa6d9..11ffbbc6 100644
--- a/openflexure_microscope/stage/sanga.py
+++ b/openflexure_microscope/stage/sanga.py
@@ -23,6 +23,7 @@ class SangaStage(BaseStage):
         """Class managing serial communications with the motors for an Openflexure stage"""
         BaseStage.__init__(self)
 
+        self.port = port
         self.board = Sangaboard(port, **kwargs)
 
         self._backlash = (
@@ -31,14 +32,17 @@ class SangaStage(BaseStage):
         self.axis_names = ["x", "y", "z"]  # Assume all sangaboards are 3 axis
 
     @property
-    def status(self):
+    def state(self):
         """The general status dictionary of the board."""
-        status = {
-            "position": self.position_map,
+        return {"position": self.position_map}
+
+    @property
+    def configuration(self):
+        return {
+            "port": self.port,
             "board": self.board.board,
             "firmware": self.board.firmware,
         }
-        return status
 
     @property
     def n_axes(self):
@@ -81,7 +85,7 @@ class SangaStage(BaseStage):
         else:
             self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
 
-    def apply_settings(self, config: dict):
+    def update_settings(self, config: dict):
         """Update settings from a config dictionary"""
 
         # Set backlash. Expects a dictionary with axis labels

From 5d65c62001ce7cd4717f5982f9aa9838d108d86a Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 15:36:46 +0000
Subject: [PATCH 2/7] Updated dependencies

---
 poetry.lock    | 537 ++++++++-----------------------------------------
 pyproject.toml |   1 +
 2 files changed, 82 insertions(+), 456 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 603d03f8..923babf7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,14 +14,6 @@ optional = false
 python-versions = ">=3.5"
 version = "3.2.0"
 
-[package.extras]
-dev = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"]
-docs = ["marshmallow (>=2.19.2)", "pyyaml (5.2)", "sphinx (2.3.0)", "sphinx-issues (1.2.0)", "sphinx-rtd-theme (0.4.3)"]
-lint = ["flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"]
-tests = ["PyYAML (>=3.10)", "prance (>=0.11)", "marshmallow (>=2.19.2)", "pytest", "mock"]
-validation = ["prance (>=0.11)"]
-yaml = ["PyYAML (>=3.10)"]
-
 [[package]]
 category = "dev"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
@@ -55,12 +47,6 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "19.3.0"
 
-[package.extras]
-azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
-dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
-docs = ["sphinx", "zope.interface"]
-tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
-
 [[package]]
 category = "dev"
 description = "Internationalization utilities"
@@ -86,9 +72,6 @@ attrs = ">=17.4.0"
 click = ">=6.5"
 toml = ">=0.9.4"
 
-[package.extras]
-d = ["aiohttp (>=3.3.2)"]
-
 [[package]]
 category = "dev"
 description = "Python package for providing Mozilla's CA Bundle."
@@ -144,11 +127,6 @@ Werkzeug = ">=0.15"
 click = ">=5.1"
 itsdangerous = ">=0.24"
 
-[package.extras]
-dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
-docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
-dotenv = ["python-dotenv"]
-
 [[package]]
 category = "main"
 description = "A Flask extension adding a decorator for CORS support"
@@ -185,12 +163,6 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "4.3.21"
 
-[package.extras]
-pipfile = ["pipreqs", "requirementslib"]
-pyproject = ["toml"]
-requirements = ["pipreqs", "pip-api"]
-xdg_home = ["appdirs (>=1.4.0)"]
-
 [[package]]
 category = "main"
 description = "Various helpers to pass data to untrusted environments and back."
@@ -204,15 +176,12 @@ category = "main"
 description = "A very fast and expressive template engine."
 name = "jinja2"
 optional = false
-python-versions = "*"
-version = "2.10.3"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "2.11.0"
 
 [package.dependencies]
 MarkupSafe = ">=0.23"
 
-[package.extras]
-i18n = ["Babel (>=0.8)"]
-
 [[package]]
 category = "main"
 description = ""
@@ -229,7 +198,7 @@ marshmallow = "^3.3.0"
 webargs = "^5.5.2"
 
 [package.source]
-reference = "23732b17074486367541439a1caa2eb61b9cc22f"
+reference = "cb1ef6a1f8849f4d58601a7a9617ffea12703f39"
 type = "git"
 url = "https://github.com/labthings/python-labthings.git"
 [[package]]
@@ -256,12 +225,6 @@ optional = false
 python-versions = ">=3.5"
 version = "3.3.0"
 
-[package.extras]
-dev = ["pytest", "pytz", "simplejson", "mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)", "tox"]
-docs = ["sphinx (2.2.2)", "sphinx-issues (1.2.0)", "alabaster (0.7.12)", "sphinx-version-warning (1.1.2)"]
-lint = ["mypy (0.750)", "flake8 (3.7.9)", "flake8-bugbear (19.8.0)", "pre-commit (>=1.20,<2.0)"]
-tests = ["pytest", "pytz", "simplejson"]
-
 [[package]]
 category = "dev"
 description = "McCabe checker, plugin for flake8"
@@ -298,11 +261,6 @@ optional = true
 python-versions = "*"
 version = "1.13.1b0"
 
-[package.extras]
-array = ["numpy"]
-doc = ["sphinx"]
-test = ["coverage", "pytest", "mock", "pillow", "numpy"]
-
 [package.source]
 reference = "b39c2b6e42f5f7f57bb46eafcb5c9e2bbdb5d0cb"
 type = "git"
@@ -353,6 +311,17 @@ optional = false
 python-versions = "*"
 version = "3.4"
 
+[[package]]
+category = "main"
+description = "Extensions to the standard Python datetime module"
+name = "python-dateutil"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+version = "2.8.1"
+
+[package.dependencies]
+six = ">=1.5"
+
 [[package]]
 category = "dev"
 description = "World timezone definitions, modern and historical"
@@ -383,10 +352,6 @@ chardet = ">=3.0.2,<3.1.0"
 idna = ">=2.5,<2.9"
 urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26"
 
-[package.extras]
-security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"]
-socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
-
 [[package]]
 category = "dev"
 description = "a python refactoring library..."
@@ -414,6 +379,14 @@ version = "1.3.0"
 [package.dependencies]
 numpy = ">=1.13.3"
 
+[[package]]
+category = "main"
+description = "Simple, fast, extensible JSON encoder/decoder for Python"
+name = "simplejson"
+optional = false
+python-versions = ">=2.5, !=3.0.*, !=3.1.*, !=3.2.*"
+version = "3.17.0"
+
 [[package]]
 category = "main"
 description = "Python 2 and 3 compatibility utilities"
@@ -457,10 +430,6 @@ sphinxcontrib-jsmath = "*"
 sphinxcontrib-qthelp = "*"
 sphinxcontrib-serializinghtml = "*"
 
-[package.extras]
-docs = ["sphinxcontrib-websupport"]
-test = ["pytest", "pytest-cov", "html5lib", "flake8 (>=3.5.0)", "flake8-import-order", "mypy (>=0.761)", "docutils-stubs"]
-
 [[package]]
 category = "dev"
 description = ""
@@ -469,9 +438,6 @@ optional = false
 python-versions = "*"
 version = "1.0.1"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy"]
-
 [[package]]
 category = "dev"
 description = ""
@@ -480,9 +446,6 @@ optional = false
 python-versions = "*"
 version = "1.0.1"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy"]
-
 [[package]]
 category = "dev"
 description = ""
@@ -491,9 +454,6 @@ optional = false
 python-versions = "*"
 version = "1.0.2"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy", "html5lib"]
-
 [[package]]
 category = "dev"
 description = "Sphinx domain for documenting HTTP APIs"
@@ -514,9 +474,6 @@ optional = false
 python-versions = ">=3.5"
 version = "1.0.1"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy"]
-
 [[package]]
 category = "dev"
 description = ""
@@ -525,9 +482,6 @@ optional = false
 python-versions = "*"
 version = "1.0.2"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy"]
-
 [[package]]
 category = "dev"
 description = ""
@@ -536,9 +490,6 @@ optional = false
 python-versions = "*"
 version = "1.1.3"
 
-[package.extras]
-test = ["pytest", "flake8", "mypy"]
-
 [[package]]
 category = "dev"
 description = "Python Library for Tom's Obvious, Minimal Language"
@@ -564,28 +515,17 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 version = "1.25.8"
 
-[package.extras]
-brotli = ["brotlipy (>=0.6.0)"]
-secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
-socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
-
 [[package]]
 category = "main"
 description = "Declarative parsing and validation of HTTP request objects, with built-in support for popular web frameworks, including Flask, Django, Bottle, Tornado, Pyramid, webapp2, Falcon, and aiohttp."
 name = "webargs"
 optional = false
 python-versions = "*"
-version = "5.5.2"
+version = "5.5.3"
 
 [package.dependencies]
 marshmallow = ">=2.15.2"
-
-[package.extras]
-dev = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "tox", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"]
-docs = ["Sphinx (2.2.0)", "sphinx-issues (1.2.0)", "sphinx-typlog-theme (0.7.3)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"]
-frameworks = ["Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "aiohttp (>=3.0.0)"]
-lint = ["flake8 (3.7.8)", "pre-commit (>=1.17,<2.0)", "mypy (0.730)", "flake8-bugbear (19.8.0)"]
-tests = ["pytest", "mock", "webtest (2.0.33)", "Flask (>=0.12.2)", "Django (>=1.11.16)", "bottle (>=0.12.13)", "tornado (>=4.5.2)", "pyramid (>=1.9.1)", "webapp2 (>=3.0.0b1)", "falcon (>=1.4.0,<2.0)", "webtest-aiohttp (2.0.0)", "pytest-aiohttp (>=0.3.0)", "aiohttp (>=3.0.0)"]
+simplejson = ">=2.1.0"
 
 [[package]]
 category = "main"
@@ -593,12 +533,7 @@ description = "The comprehensive WSGI web application library."
 name = "werkzeug"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.16.0"
-
-[package.extras]
-dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
-termcolor = ["termcolor"]
-watchdog = ["watchdog"]
+version = "0.16.1"
 
 [[package]]
 category = "dev"
@@ -612,373 +547,63 @@ version = "1.11.2"
 rpi = ["picamera", "RPi.GPIO"]
 
 [metadata]
-content-hash = "cd4e5d59e9a63ae053a05c994a61a46be87a29ec6867bcd47f6ef9b39bb785d3"
+content-hash = "34da76b3341563a0bebfa3e4a3fca90f34b857027e90811fed92b106ad06c2ba"
 python-versions = "^3.6"
 
-[metadata.files]
-alabaster = [
-    {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
-    {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
-]
-apispec = [
-    {file = "apispec-3.2.0-py2.py3-none-any.whl", hash = "sha256:f2ecb3a6534cfb42cf69b5c1222d2c0e695aab5ec3d7edde31b7354670948f05"},
-    {file = "apispec-3.2.0.tar.gz", hash = "sha256:c1625ae910f699c9adb21928693a3245b9faab6843f1b1c94ab2d505549cd78a"},
-]
-appdirs = [
-    {file = "appdirs-1.4.3-py2.py3-none-any.whl", hash = "sha256:d8b24664561d0d34ddfaec54636d502d7cea6e29c3eaf68f3df6180863e2166e"},
-    {file = "appdirs-1.4.3.tar.gz", hash = "sha256:9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92"},
-]
-astroid = [
-    {file = "astroid-2.3.3-py3-none-any.whl", hash = "sha256:840947ebfa8b58f318d42301cf8c0a20fd794a33b61cc4638e28e9e61ba32f42"},
-    {file = "astroid-2.3.3.tar.gz", hash = "sha256:71ea07f44df9568a75d0f354c49143a4575d90645e9fead6dfb52c26a85ed13a"},
-]
-attrs = [
-    {file = "attrs-19.3.0-py2.py3-none-any.whl", hash = "sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c"},
-    {file = "attrs-19.3.0.tar.gz", hash = "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"},
-]
-babel = [
-    {file = "Babel-2.8.0-py2.py3-none-any.whl", hash = "sha256:d670ea0b10f8b723672d3a6abeb87b565b244da220d76b4dba1b66269ec152d4"},
-    {file = "Babel-2.8.0.tar.gz", hash = "sha256:1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38"},
-]
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+urllib3 = ["2f3db8b19923a873b3e5256dc9c2dedfa883e33d87c690d9c7913e1f40673cdc", "87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc"]
+webargs = ["4f04918864c7602886335d8099f9b8960ee698b6b914f022736ed50be6b71235", "871642a2e0c62f21d5b78f357750ac7a87e6bc734c972f633aa5fb6204fbf29a", "fc81c9f9d391acfbce406a319217319fd8b2fd862f7fdb5319ad06944f36ed25"]
+werkzeug = ["1e0dedc2acb1f46827daa2e399c1485c8fa17c0d8e70b6b875b4e7f54bf408d2", "b353856d37dec59d6511359f97f6a4b2468442e454bd1c98298ddce53cac1f04"]
+wrapt = ["565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1"]
diff --git a/pyproject.toml b/pyproject.toml
index fa4bb194..f9ccc42e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,6 +35,7 @@ picamera = { git = "https://github.com/rwb27/picamera.git", branch = "lens-shadi
 pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move to sangaboard pip library
 
 labthings = { git = "https://github.com/labthings/python-labthings.git", branch = "master"} # TODO: Pin to a fixed version before 2.0.0 stable
+python-dateutil = "^2.8"
 
 [tool.poetry.extras]
 rpi = ["picamera", "RPi.GPIO"]

From 7458d278d8ed1c155ef81d651185b9c92965db59 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 15:36:57 +0000
Subject: [PATCH 3/7] Simplified new configuration and metadata

---
 openflexure_microscope/api/app.py             |   8 +-
 .../api/default_extensions/scan.py            | 101 ++++++--------
 .../api/v2/views/actions/camera.py            |   7 +-
 .../api/v2/views/captures.py                  |  22 +--
 openflexure_microscope/api/v2/views/state.py  |  32 ++++-
 openflexure_microscope/camera/capture.py      |  84 +++++------
 openflexure_microscope/camera/pi.py           |  17 +--
 openflexure_microscope/config.py              |  19 ++-
 openflexure_microscope/microscope.py          | 130 +++++++++---------
 .../microscope_configuration.default.json     |  10 +-
 10 files changed, 214 insertions(+), 216 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 7f688fe0..e3aa1404 100644
--- a/openflexure_microscope/api/app.py
+++ b/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")
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 26a7dd6f..261b15b3 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/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
-    if "time" not in metadata:
-        metadata["time"] = generate_basename()
-
-    metadata.update(
-        {
-            "scan_id": scan_id,
-            "basename": basename,
-            "scan_parameters": {
-                "step_size": step_size,
-                "grid": grid,
-                "style": style,
-                "autofocus_dz": autofocus_dz,
-            },
+    # Add dataset metadata
+    dataset_d = {
+        "dataset": {
+            "id": uuid.uuid4(),
+            "type": "xyzScan",
+            "name": basename,
+            "acquisitionDate": datetime.datetime.now().isoformat(),
+            "strideSize": stride_size,
+            "grid": grid,
+            "style": style,
+            "autofocusDz": 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=step_size[2],
+                    step_size=stride_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")
-            microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
+        logging.debug("Moving to starting position")
+        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]),
-            "grid": fields.List(fields.Integer, missing=[3, 3, 5]),
+            "stride_size": fields.List(
+                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"),
         )
 
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index e9912ad9..8b618193 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/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"))
 
diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py
index f4831aa3..c5e00623 100644
--- a/openflexure_microscope/api/v2/views/captures.py
+++ b/openflexure_microscope/api/v2/views/captures.py
@@ -39,10 +39,12 @@ class CaptureSchema(Schema):
                 "mimetype": "application/json",
                 **description_from_view(CaptureTags),
             },
-            "metadata": {
-                "href": url_for(CaptureMetadata.endpoint, id=data.id, _external=True),
+            "annotations": {
+                "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_metadata(data_dict)
+        capture_obj.put_annotations(data_dict)
 
-        return jsonify(capture_obj.metadata)
+        return jsonify(capture_obj.annotations)
diff --git a/openflexure_microscope/api/v2/views/state.py b/openflexure_microscope/api/v2/views/state.py
index 34637754..7f22323c 100644
--- a/openflexure_microscope/api/v2/views/state.py
+++ b/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)
 
diff --git a/openflexure_microscope/camera/capture.py b/openflexure_microscope/camera/capture.py
index 20ec71da..e7264b6c 100644
--- a/openflexure_microscope/camera/capture.py
+++ b/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
-    capture.id = exif_dict["id"]
-    capture.timestring = exif_dict["time"]
-    capture.format = exif_dict["format"]
+    # Image metadata
+    image_metadata = exif_dict.pop("image")
 
-    capture.custom_metadata = (
-        exif_dict["custom"] if "custom" in exif_dict.keys() else {}
-    )
-    capture.system_metadata = (
-        exif_dict["system"] if "system" in exif_dict.keys() else {}
-    )
-    capture.tags = exif_dict["tags"]
+    # Populate capture parameters
+    capture.id = image_metadata.get("id")
+    capture.datetime = dateutil.parser.isoparse(image_metadata.get("acquisitionDate"))
+    capture.format = image_metadata.get("format")
+    capture.tags = image_metadata.get("tags")
+    capture.annotations = image_metadata.get("annotations")
+
+    # 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
-        self.custom_metadata = {}
-        # Dictionary for adding top-level metadata (cannmot be accessed through web API)
-        self.system_metadata = {}
+        if not os.path.exists(self.filefolder):
+            os.makedirs(self.filefolder)
 
+        # 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.system_metadata.update(data)
-        else:
-            self.custom_metadata.update(data)
+        self.annotations.update(data)
+        self.save_metadata()
+
+    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,
-            "time": self.timestring,
-            "format": self.format,
-            "tags": self.tags,
-            "custom": self.custom_metadata,
-            "system": self.system_metadata,
+            "image": {
+                "id": self.id,
+                "name": self.filename,
+                "acquisitionDate": self.datetime.isoformat(),
+                "format": self.format,
+                "tags": self.tags,
+                "annotations": self.annotations,
+            },
+            **self._metadata,
         }
 
         # Add custom metadata to dictionary
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index bbd04e44..8f2a4d94 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -119,22 +119,7 @@ class PiCameraStreamer(BaseCamera):
     @property
     def configuration(self):
         """The current camera configuration."""
-        config = {
-            "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
+        return {"board": self.camera.revision}
 
     @property
     def state(self):
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index cfc458a1..5172a07c 100644
--- a/openflexure_microscope/config.py
+++ b/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
+)
+
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index 2f52c6d9..b061bf32 100644
--- a/openflexure_microscope/microscope.py
+++ b/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"):
-            detector_type = configuration["detector"].get("type")
-            if detector_type == "PiCamera" or detector_type == "PiCameraStreamer":
+        if configuration.get("camera"):
+            camera_type = configuration["camera"].get("type")
+            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 = {
-            "camera": self.camera.state,
-            "stage": self.stage.state,
-        }
+        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:
-            self.camera.update_settings(config["camera_settings"])
+        if ("camera" in settings) and self.camera:
+            self.camera.update_settings(settings["camera"])
 
         # If attached to a stage
-        if ("stage_settings" in config) and self.stage:
-            self.stage.update_settings(config["stage_settings"])
+        if ("stage" in settings) and self.stage:
+            self.stage.update_settings(settings["stage"])
 
-        # Todo: tidy up with some loopy goodness
-        if "name" in config:
-            self.name = config["name"]
-        if "fov" in config:
-            self.fov = config["fov"]
+        # Microscope settings
+        if "id" in settings:
+            self.id = settings["id"]
+        if "name" in settings:
+            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
diff --git a/openflexure_microscope/microscope_configuration.default.json b/openflexure_microscope/microscope_configuration.default.json
index d7129bc8..b9cbfdce 100644
--- a/openflexure_microscope/microscope_configuration.default.json
+++ b/openflexure_microscope/microscope_configuration.default.json
@@ -1,17 +1,9 @@
 {
-  "microscope": {
-    "stepsPerView": [4100, 3146]
-  },
-  "detector": {
+  "camera": {
     "type": "PiCamera"
   },
   "stage": {
     "type": "SangaStage",
     "port": null
-  },
-  "lightSource": {
-    "type": "LED"
-  },
-  "objective": {
   }
 }
\ No newline at end of file

From ebdd63f37b2543122504b1027e1ab14d598b4be2 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 15:43:29 +0000
Subject: [PATCH 4/7] Added ndarray type to serialised LST (can be used in
 custom decoder)

---
 openflexure_microscope/microscope.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index b061bf32..d65a8fcb 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -183,6 +183,7 @@ class Microscope:
                 b64_string, dtype, shape = serialise_array_b64(lst_arr)
 
                 settings_current["camera"]["lens_shading_table"] = {
+                    "@type": "ndarray",
                     "b64_string": b64_string,
                     "dtype": dtype,
                     "shape": shape,

From 265eed7bfac79ea03140cca1c540e9f3a9738d84 Mon Sep 17 00:00:00 2001
From: Joel Collins <jc2450@bath.ac.uk>
Date: Wed, 29 Jan 2020 16:16:09 +0000
Subject: [PATCH 5/7] Fixed picamera setup

---
 .../picamera_autocalibrate/extension.py       |  4 ++--
 .../api/v2/views/actions/stage.py             |  2 +-
 openflexure_microscope/camera/pi.py           | 10 ++++----
 openflexure_microscope/microscope.py          | 23 ++++++++-----------
 4 files changed, 18 insertions(+), 21 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 37cbe8cb..343a2c02 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -21,8 +21,8 @@ def recalibrate(microscope):
     """
     scamera = microscope.camera
     with scamera.lock:
-        assert not scamera.status["record_active"], "Can't recalibrate while recording!"
-        streaming = scamera.status["stream_active"]
+        assert not scamera.record_active, "Can't recalibrate while recording!"
+        streaming = scamera.stream_active
         if streaming:
             logging.info("Stopping stream before recalibration")
             scamera.stop_stream_recording(resolution=(640, 480))
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index 8b1020eb..6aa969bb 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -53,7 +53,7 @@ class MoveStageAPI(View):
             logging.warning("Unable to move. No stage found.")
 
         # TODO: Make schema for microscope status
-        return jsonify(microscope.status["stage"]["position"])
+        return jsonify(microscope.state["stage"]["position"])
 
 
 @ThingAction
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 8f2a4d94..d1b71141 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -333,13 +333,13 @@ class PiCameraStreamer(BaseCamera):
         Change the camera zoom, handling re-centering and scaling.
         """
         with self.lock:
-            self.status["zoom_value"] = float(zoom_value)
-            if self.status["zoom_value"] < 1:
-                self.status["zoom_value"] = 1
+            self.zoom_value = float(zoom_value)
+            if self.zoom_value < 1:
+                self.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.status["zoom_value"]
+            size = 1.0 / self.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)
@@ -552,7 +552,7 @@ class PiCameraStreamer(BaseCamera):
         if isinstance(output, CaptureObject):
             target = output.file
         else:
-            target = target
+            target = output
 
         with self.lock:
             logging.info("Capturing to {}".format(output))
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index b061bf32..f1023e13 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -76,7 +76,7 @@ class Microscope:
         ### Detector
         if configuration.get("camera"):
             camera_type = configuration["camera"].get("type")
-            if camera_type == "PiCamera" or camera_type == "PiCameraStreamer":
+            if camera_type in ("PiCamera", "PiCameraStreamer"):
                 try:
                     self.camera = PiCameraStreamer()
                 except Exception as e:
@@ -87,12 +87,8 @@ class Microscope:
         if configuration.get("stage"):
             stage_type = configuration["stage"].get("type")
             stage_port = configuration["stage"].get("port")
-            if stage_type == "SangaBoard" or camera_type == "SangaStage":
-                try:
-                    self.stage = SangaStage(port=stage_port)
-                except Exception as e:
-                    logging.error(e)
-                    logging.warning("No compatible stage hardware found.")
+            if stage_type in ("SangaBoard", "SangaStage"):
+                self.stage = SangaStage(port=stage_port)
 
         ### Fallbacks
         if not self.camera:
@@ -180,13 +176,14 @@ class Microscope:
                 # 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)
+                if lst_arr:
+                    b64_string, dtype, shape = serialise_array_b64(lst_arr)
 
-                settings_current["camera"]["lens_shading_table"] = {
-                    "b64_string": b64_string,
-                    "dtype": dtype,
-                    "shape": shape,
-                }
+                    settings_current["camera"]["lens_shading_table"] = {
+                        "b64_string": b64_string,
+                        "dtype": dtype,
+                        "shape": shape,
+                    }
 
         # If attached to a stage
         if self.stage:

From e9e2419fe4648f3ef8508a63a873b1da18d7f79c Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 16:21:38 +0000
Subject: [PATCH 6/7] Renamed capture.filename to capture.name

---
 openflexure_microscope/api/v2/views/captures.py |  4 ++--
 openflexure_microscope/camera/capture.py        | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py
index c5e00623..097ff665 100644
--- a/openflexure_microscope/api/v2/views/captures.py
+++ b/openflexure_microscope/api/v2/views/captures.py
@@ -20,7 +20,7 @@ class CaptureSchema(Schema):
         data_key="path", description="Path of file on microscope device"
     )
     exists = fields.Bool(data_key="available")
-    filename = fields.String()
+    name = fields.String()
     metadata = fields.Dict()
 
     links = fields.Dict()
@@ -50,7 +50,7 @@ class CaptureSchema(Schema):
                 "href": url_for(
                     CaptureDownload.endpoint,
                     id=data.id,
-                    filename=data.filename,
+                    filename=data.name,
                     _external=True,
                 ),
                 "mimetype": "image/jpeg",
diff --git a/openflexure_microscope/camera/capture.py b/openflexure_microscope/camera/capture.py
index e7264b6c..81edff1a 100644
--- a/openflexure_microscope/camera/capture.py
+++ b/openflexure_microscope/camera/capture.py
@@ -152,11 +152,11 @@ class CaptureObject(object):
         Args:
             filepath (str): String of the full file path, including file format extension
         """
-        # Split the full file path into a folder and a filename
-        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]
+        # Split the full file path into a folder and a name
+        self.filefolder, self.name = os.path.split(filepath)
+        # Split the name out from it's file extension
+        self.basename = os.path.splitext(self.name)[0]
+        self.format = self.name.split(".")[-1]
 
     @property
     def exists(self) -> bool:
@@ -243,7 +243,7 @@ class CaptureObject(object):
         d = {
             "image": {
                 "id": self.id,
-                "name": self.filename,
+                "name": self.name,
                 "acquisitionDate": self.datetime.isoformat(),
                 "format": self.format,
                 "tags": self.tags,
@@ -262,7 +262,7 @@ class CaptureObject(object):
         """
 
         # Create basic state dictionary
-        d = {"path": self.file, "filename": self.filename, "metadata": self.metadata}
+        d = {"path": self.file, "name": self.name, "metadata": self.metadata}
 
         # Combined availability of data
         if self.exists:

From 9b4bf4c8fceb24584e97b767dcbebd666e5f0088 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 29 Jan 2020 17:43:52 +0000
Subject: [PATCH 7/7] Moved status routes to instrument/state

---
 .../example_extension/03_marshaling_data.py   |  2 +-
 .../example_extension/04_properties.py        |  2 +-
 .../example_extension/05_actions.py           |  2 +-
 docs/source/extensions/marshaling.rst         |  2 +-
 openflexure_microscope/api/app.py             | 22 ++++++++++---------
 .../api/default_extensions/zip_builder.py     | 14 +++++-------
 .../api/v2/views/__init__.py                  |  2 +-
 .../api/v2/views/actions/camera.py            |  8 +++----
 .../api/v2/views/actions/stage.py             |  6 ++---
 .../api/v2/views/{state.py => instrument.py}  |  4 ++--
 openflexure_microscope/camera/base.py         | 14 ------------
 openflexure_microscope/camera/pi.py           | 17 +++++++-------
 openflexure_microscope/config.py              |  5 ++++-
 openflexure_microscope/microscope.py          |  8 +++----
 openflexure_microscope/stage/mock.py          |  6 ++---
 openflexure_microscope/stage/sanga.py         |  2 +-
 16 files changed, 52 insertions(+), 64 deletions(-)
 rename openflexure_microscope/api/v2/views/{state.py => instrument.py} (98%)

diff --git a/docs/source/extensions/example_extension/03_marshaling_data.py b/docs/source/extensions/example_extension/03_marshaling_data.py
index f9ad668d..d3179c10 100644
--- a/docs/source/extensions/example_extension/03_marshaling_data.py
+++ b/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)
 
diff --git a/docs/source/extensions/example_extension/04_properties.py b/docs/source/extensions/example_extension/04_properties.py
index 45ee6c18..922270a5 100644
--- a/docs/source/extensions/example_extension/04_properties.py
+++ b/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)
 
diff --git a/docs/source/extensions/example_extension/05_actions.py b/docs/source/extensions/example_extension/05_actions.py
index 027580e8..dc3826a0 100644
--- a/docs/source/extensions/example_extension/05_actions.py
+++ b/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)
 
diff --git a/docs/source/extensions/marshaling.rst b/docs/source/extensions/marshaling.rst
index 10ab188e..1f09162a 100644
--- a/docs/source/extensions/marshaling.rst
+++ b/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)
 
diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index e3aa1404..ce0d1068 100644
--- a/openflexure_microscope/api/app.py
+++ b/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
-labthing.add_view(views.SettingsProperty, f"/settings")
-labthing.add_root_link(views.SettingsProperty, "settings")
-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 settings and state resources
+labthing.add_view(views.SettingsProperty, f"/instrument/settings")
+labthing.add_root_link(views.SettingsProperty, "instrumentSettings")
+labthing.add_view(views.NestedSettingsProperty, "/instrument/settings/<path:route>")
+labthing.add_view(views.StateProperty, "/instrument/state")
+labthing.add_view(views.NestedStateProperty, "/instrument/state/<path:route>")
+labthing.add_root_link(views.StateProperty, "instrumentState")
+labthing.add_view(views.ConfigurationProperty, "/instrument/configuration")
+labthing.add_view(
+    views.NestedConfigurationProperty, "/instrument/configuration/<path:route>"
+)
+labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
 
 
 # Attach streams resources
diff --git a/openflexure_microscope/api/default_extensions/zip_builder.py b/openflexure_microscope/api/default_extensions/zip_builder.py
index 02032c65..a57a3ad1 100644
--- a/openflexure_microscope/api/default_extensions/zip_builder.py
+++ b/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_key = str(session_id)
-        # self.session_zips[session_id] = fp
-        self.session_zips[session_key] = {
+        session_id = str(uuid.uuid4())
+        self.session_zips[session_id] = {
             "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")
diff --git a/openflexure_microscope/api/v2/views/__init__.py b/openflexure_microscope/api/v2/views/__init__.py
index a998c703..3c1fae87 100644
--- a/openflexure_microscope/api/v2/views/__init__.py
+++ b/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 *
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index 8b618193..62f777d7 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/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
-        return jsonify(microscope.status)
+        # TODO: Make schema for microscope state
+        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
-        return jsonify(microscope.status)
+        # TODO: Make schema for microscope state
+        return jsonify(microscope.state)
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index 6aa969bb..5cf4059e 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/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
-        return jsonify(microscope.status["stage"])
+        # TODO: Make schema for microscope state
+        return jsonify(microscope.state["stage"])
diff --git a/openflexure_microscope/api/v2/views/state.py b/openflexure_microscope/api/v2/views/instrument.py
similarity index 98%
rename from openflexure_microscope/api/v2/views/state.py
rename to openflexure_microscope/api/v2/views/instrument.py
index 7f22323c..633d73ff 100644
--- a/openflexure_microscope/api/v2/views/state.py
+++ b/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):
         """
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index e823cfd0..2dd16dc4 100644
--- a/openflexure_microscope/camera/base.py
+++ b/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):
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index d1b71141..85628042 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/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
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 5172a07c..8bbe796a 100644
--- a/openflexure_microscope/config.py
+++ b/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)
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index 19c01be7..1e397339 100644
--- a/openflexure_microscope/microscope.py
+++ b/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"
diff --git a/openflexure_microscope/stage/mock.py b/openflexure_microscope/stage/mock.py
index e4810f3c..fe523c64 100644
--- a/openflexure_microscope/stage/mock.py
+++ b/openflexure_microscope/stage/mock.py
@@ -18,9 +18,9 @@ class MissingStage(BaseStage):
 
     @property
     def state(self):
-        """The general status dictionary of the board."""
-        status = {"position": self.position_map}
-        return status
+        """The general state dictionary of the board."""
+        state = {"position": self.position_map}
+        return state
 
     @property
     def configuration(self):
diff --git a/openflexure_microscope/stage/sanga.py b/openflexure_microscope/stage/sanga.py
index 11ffbbc6..d5ffcf15 100644
--- a/openflexure_microscope/stage/sanga.py
+++ b/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