259 lines
8.8 KiB
Python
259 lines
8.8 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.base import BaseStage
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from openflexure_microscope.stage.mock import MockStage
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from openflexure_microscope.camera.base import BaseCamera
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from openflexure_microscope.camera.mock import MockStreamer
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from openflexure_microscope.utilities import serialise_array_b64
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from openflexure_microscope.plugins import PluginLoader
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from openflexure_microscope.common.lock import CompositeLock
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from openflexure_microscope.config import user_settings
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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 should already be initialised, and passed as arguments.
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Attributes:
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lock (:py:class:`openflexure_microscope.common.lock.CompositeLock`): Composite lock controlling thread access
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to multiple pieces of hardware.
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camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): Camera object
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stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): Stage object
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task: (:py:class:`openflexure_microscope.task.TaskOrchestrator`): Threaded ask orchestrator for managing
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background tasks using microscope hardware
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plugins (:py:class:`openflexure_microscope.plugins.PluginLoader`): Mounting point for all microscope plugins
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"""
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def __init__(self):
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# Initial attributes
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self.id = uuid.uuid4().hex
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self.name = self.id
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self.fov = [0, 0]
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self.plugin_maps = []
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self.camera = None
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self.stage = None
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# Initialise with an empty composite lock
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self.lock = CompositeLock([])
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# Apply settings loaded from file
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self.apply_settings(user_settings.load())
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# Create plugin mount-point and attach plugins from maps
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self.plugins = PluginLoader(self)
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self.attach_plugins(self.plugin_maps)
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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 attach(self, camera: BaseCamera, stage: BaseStage):
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"""
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Retroactively attaches a camera and stage to the microscope object.
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Allows the microscope to be created as a "dummy", with hardware communications
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opened at a later time.
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Args:
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camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): camera object
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stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): stage object
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"""
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settings_full = self.read_settings()
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logging.debug("Attaching camera...")
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self.camera = (
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camera
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) #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
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if not self.camera:
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logging.info("No camera attached.")
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else:
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logging.info("Attached camera {}".format(camera))
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if hasattr(self.camera, "lock"): # If camera has a lock
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logging.info("Attaching {} to composite lock.".format(self.camera.lock))
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# Add the lock to the microscope composite lock
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self.lock.locks.append(self.camera.lock)
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logging.debug("Attaching stage...")
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self.stage = (
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stage
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) #: :py:class:`openflexure_microscope.stage.base.BaseStage`: OpenFlexure stage object
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if not self.stage:
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logging.info("No stage attached.")
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else:
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logging.info("Attached stage {}".format(stage))
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if hasattr(self.stage, "lock"): # If stage object has a lock
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logging.info(
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"Attaching lock {} to composite lock.".format(self.stage.lock)
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)
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# Add the lock to the microscope composite lock
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self.lock.locks.append(self.stage.lock)
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logging.info("Reapplying settings to newly attached devices")
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self.apply_settings(settings_full)
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def attach_plugins(self, plugin_maps: list):
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"""
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Automatically search for plugin maps in config, and attach.
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"""
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if plugin_maps:
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for plugin_map in plugin_maps:
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self.plugins.attach(plugin_map)
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else:
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logging.warning("No plugins specified. Skipping.")
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def reload_plugins(self):
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"""
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Empty the plugin mount and re-attach from config.
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"""
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logging.info("Tearing down existing PluginMount...")
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self.plugins = PluginLoader(self)
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logging.info("Repopulating PluginMount...")
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self.attach_plugins(self.plugin_maps)
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def has_real_stage(self):
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if hasattr(self, "stage") and not isinstance(self.stage, MockStage):
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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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if hasattr(self, "camera") and not isinstance(self.camera, MockStreamer):
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return True
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else:
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return False
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# Create unified status
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@property
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def status(self):
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"""Dictionary of the basic microscope status.
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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.status,
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"stage": self.stage.status,
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"version": pkg_resources.get_distribution("openflexure_microscope").version,
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}
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return state
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def apply_settings(self, config: dict):
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"""
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Applies a config dictionary. 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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# If attached to a camera
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if ("camera_settings" in config) and self.camera:
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self.camera.apply_settings(config["camera_settings"])
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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.apply_settings(config["stage_settings"])
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# Todo: tidy up with some loopy goodness
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if "id" in config:
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self.id = config["id"]
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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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if "plugins" in config:
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self.plugin_maps = config["plugins"]
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def read_settings(self, json_safe=False):
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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 = {
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"id": self.id,
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"name": self.name,
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"fov": self.fov,
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"plugins": self.plugin_maps,
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}
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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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# 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_full = user_settings.merge(settings_current)
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return settings_full
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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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user_settings.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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"microscope_settings": self.read_settings(),
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"microscope_state": self.status,
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"microscope_id": self.id,
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"microscope_name": self.name,
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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["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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