250 lines
8.1 KiB
Python
250 lines
8.1 KiB
Python
# -*- coding: utf-8 -*-
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"""
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Defines a microscope object, binding a camera and stage with basic functionality.
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"""
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import logging
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import pkg_resources
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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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logging.warning("Unable to import PiCameraStreamer")
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from openflexure_microscope.camera.mock import MissingCamera
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from openflexure_microscope.utilities import serialise_array_b64
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from openflexure_microscope.config import user_settings, user_configuration
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from labthings.core.lock import CompositeLock
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from labthings.core.utilities import rupdate
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class Microscope:
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"""
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A basic microscope object.
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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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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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# Initialise with an empty composite lock
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#: :py:class:`labthings.lock.CompositeLock`: Composite lock for locking both camera and stage
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self.lock = CompositeLock([])
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self.camera = None #: Currently connected camera object
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self.stage = None #: Currently connected stage object
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self.setup(self.configuration_file.load()) # Attach components
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# Apply settings loaded from file
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self.update_settings(self.settings_file.load())
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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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def __exit__(self, exc_type, exc_value, traceback):
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"""Close microscope on context exit."""
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self.close()
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def close(self):
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"""Shut down the microscope hardware."""
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logging.info("Closing {}".format(self))
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if self.camera:
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self.camera.close()
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if self.stage:
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self.stage.close()
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logging.info("Closed {}".format(self))
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def setup(self, configuration):
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"""
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Attach microscope components based on initially passed configuration file
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"""
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### Detector
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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 in ("PiCamera", "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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logging.error(e)
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logging.warning("No compatible camera hardware found.")
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### Stage
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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 in ("SangaBoard", "SangaStage"):
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self.stage = SangaStage(port=stage_port)
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### Fallbacks
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if not self.camera:
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self.camera = MissingCamera()
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if not self.stage:
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self.stage = MissingStage()
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### Locks
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if hasattr(self.camera, "lock"):
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self.lock.locks.append(self.camera.lock)
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if hasattr(self.stage, "lock"):
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self.lock.locks.append(self.stage.lock)
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def has_real_stage(self) -> bool:
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"""
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Check if a real (non-mock) stage is currently attached.
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"""
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if hasattr(self, "stage") and not isinstance(self.stage, MissingStage):
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return True
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else:
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return False
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def has_real_camera(self):
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"""
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Check if a real (non-mock) camera is currently attached.
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"""
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if hasattr(self, "camera") and not isinstance(self.camera, MissingCamera):
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return True
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else:
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return False
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# Create unified state
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@property
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def state(self):
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"""Dictionary of the basic microscope state.
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Return:
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dict: Dictionary containing complete microscope 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, 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 settings: {}".format(settings))
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# If attached to a camera
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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" in settings) and self.stage:
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self.stage.update_settings(settings["stage"])
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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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"""
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Get an updated settings dictionary.
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Reads current attributes and properties from connected hardware,
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then merges those with the currently saved settings.
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This is to ensure that settings for currently disconnected hardware
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don't get removed from the settings file.
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"""
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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_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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if lst_arr:
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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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"@type": "ndarray",
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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_current_stage
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settings_full = self.settings_file.merge(settings_current)
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if full:
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return settings_full
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else:
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return settings_current
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def save_settings(self):
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"""
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Merges the current settings back to disk
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"""
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# Read curent config
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current_config = self.read_settings()
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# Save config to file
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if self.camera:
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self.camera.save_settings()
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if self.stage:
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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 configuration(self):
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initial_configuration = self.configuration_file.load()
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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(
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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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},
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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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}
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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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