Simplified new configuration and metadata
This commit is contained in:
Joel Collins
parent
5d65c62001
commit
7458d278d8
10 changed files with 214 additions and 216 deletions
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@ -9,6 +9,7 @@ import uuid
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from openflexure_microscope.stage.mock import MissingStage
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from openflexure_microscope.camera.mock import MissingCamera
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from openflexure_microscope.stage.sanga import SangaStage
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try:
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from openflexure_microscope.camera.pi import PiCameraStreamer
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except ImportError:
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@ -29,7 +30,12 @@ class Microscope:
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The camera and stage objects may already be initialised, and can be passed as arguments.
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"""
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def __init__(self, settings = user_settings, configuration = user_configuration):
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def __init__(self, settings=user_settings, configuration=user_configuration):
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self.id = uuid.uuid4()
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self.name = self.id
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self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
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# Store settings and configuration files
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self.settings_file = settings
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self.configuration_file = configuration
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@ -45,17 +51,6 @@ class Microscope:
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# Apply settings loaded from file
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self.update_settings(self.settings_file.load())
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# Initial attributes
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if self.configuration_file.load().get("id"):
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self.id = configuration.get("id")
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else:
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self.id = uuid.uuid4()
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self.configuration_file.save({
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"id": self.id
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})
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self.name = self.id
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def __enter__(self):
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"""Create microscope on context enter."""
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return self
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@ -79,9 +74,9 @@ class Microscope:
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"""
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### Detector
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if configuration.get("detector"):
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detector_type = configuration["detector"].get("type")
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if detector_type == "PiCamera" or detector_type == "PiCameraStreamer":
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if configuration.get("camera"):
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camera_type = configuration["camera"].get("type")
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if camera_type == "PiCamera" or camera_type == "PiCameraStreamer":
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try:
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self.camera = PiCameraStreamer()
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except Exception as e:
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@ -92,7 +87,7 @@ class Microscope:
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if configuration.get("stage"):
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stage_type = configuration["stage"].get("type")
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stage_port = configuration["stage"].get("port")
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if stage_type == "SangaBoard" or detector_type == "SangaStage":
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if stage_type == "SangaBoard" or camera_type == "SangaStage":
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try:
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self.stage = SangaStage(port=stage_port)
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except Exception as e:
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@ -137,33 +132,32 @@ class Microscope:
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Return:
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dict: Dictionary containing complete microscope status
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"""
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state = {
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"camera": self.camera.state,
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"stage": self.stage.state,
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}
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state = {"camera": self.camera.state, "stage": self.stage.state}
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return state
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def update_settings(self, config: dict):
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def update_settings(self, settings: dict):
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"""
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Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
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"""
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logging.debug("Microscope: Applying config: {}".format(config))
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logging.debug("Microscope: Applying settings: {}".format(settings))
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# If attached to a camera
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if ("camera_settings" in config) and self.camera:
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self.camera.update_settings(config["camera_settings"])
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if ("camera" in settings) and self.camera:
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self.camera.update_settings(settings["camera"])
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# If attached to a stage
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if ("stage_settings" in config) and self.stage:
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self.stage.update_settings(config["stage_settings"])
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if ("stage" in settings) and self.stage:
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self.stage.update_settings(settings["stage"])
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# Todo: tidy up with some loopy goodness
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if "name" in config:
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self.name = config["name"]
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if "fov" in config:
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self.fov = config["fov"]
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# Microscope settings
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if "id" in settings:
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self.id = settings["id"]
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if "name" in settings:
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self.name = settings["name"]
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if "fov" in settings:
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self.fov = settings["fov"]
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def read_settings(self, full: bool=True):
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def read_settings(self, full: bool = True):
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"""
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Get an updated settings dictionary.
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@ -174,17 +168,30 @@ class Microscope:
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don't get removed from the settings file.
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"""
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settings_current = {"name": self.name, "fov": self.fov}
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settings_current = {"id": self.id, "name": self.name, "fov": self.fov}
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# If attached to a camera
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if self.camera:
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settings_current_camera = self.camera.read_settings()
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settings_current["camera_settings"] = settings_current_camera
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settings_current["camera"] = settings_current_camera
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# Store an encoded copy of the PiCamera lens shading table, if it exists
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if hasattr(self.camera, "read_lens_shading_table"):
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# Read LST. Returns None if no LST is active
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lst_arr = self.camera.read_lens_shading_table()
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b64_string, dtype, shape = serialise_array_b64(lst_arr)
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settings_current["camera"]["lens_shading_table"] = {
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"b64_string": b64_string,
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"dtype": dtype,
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"shape": shape,
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}
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# If attached to a stage
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if self.stage:
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settings_current_stage = self.stage.read_settings()
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settings_current["stage_settings"] = settings_current_stage
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settings_current["stage"] = settings_current_stage
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settings_full = self.settings_file.merge(settings_current)
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@ -206,33 +213,6 @@ class Microscope:
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self.stage.save_settings()
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self.settings_file.save(current_config, backup=True)
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@property
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def metadata(self):
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"""
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Microscope system metadata, to be applied to basically all captures
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"""
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system_metadata = {
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"@ID": self.id,
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"settings": self.read_settings(full=False),
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"state": self.state,
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"configuration": self.configuration
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}
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# Store an encoded copy of the PiCamera lens shading table, if it exists
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if self.camera and hasattr(self.camera, "read_lens_shading_table"):
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# Read LST. Returns None if no LST is active
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lst_arr = self.camera.read_lens_shading_table()
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b64_string, dtype, shape = serialise_array_b64(lst_arr)
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system_metadata["configuration"]["detector"]["lens_shading_table"] = {
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"b64_string": b64_string,
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"dtype": dtype,
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"shape": shape,
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}
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return system_metadata
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@property
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def configuration(self):
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initial_configuration = self.configuration_file.load()
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@ -240,17 +220,33 @@ class Microscope:
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current_configuration = {
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"@application": {
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"name": "openflexure_microscope",
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"version": pkg_resources.get_distribution("openflexure_microscope").version
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"version": pkg_resources.get_distribution(
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"openflexure_microscope"
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).version,
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},
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"stage": {
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"type": self.stage.__class__.__name__,
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**self.stage.configuration
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**self.stage.configuration,
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},
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"detector": {
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"camera": {
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"type": self.camera.__class__.__name__,
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**self.camera.configuration
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}
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**self.camera.configuration,
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},
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}
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initial_configuration.update(current_configuration)
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return initial_configuration
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@property
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def metadata(self):
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"""
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Microscope system metadata, to be applied to basically all captures
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"""
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system_metadata = {
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"id": self.id,
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"settings": self.read_settings(full=False),
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"state": self.state,
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"configuration": self.configuration,
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}
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return system_metadata
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