341 lines
11 KiB
Python
341 lines
11 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 typing import Tuple
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import gevent
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from openflexure_microscope.captures import CaptureManager
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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 Exception as e:
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logging.error(e)
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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, Timer
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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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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.captures = CaptureManager()
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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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self.extension_settings = {}
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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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try:
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self.camera.close()
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except TimeoutError as e:
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logging.error(e)
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if self.stage:
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try:
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self.stage.close()
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except TimeoutError as e:
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logging.error(e)
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self.captures.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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logging.info("Creating camera")
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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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logging.info("Creating 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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try:
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self.stage = SangaStage(port=stage_port)
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except Exception as e:
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logging.error(e)
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logging.warning("No compatible Sangaboard hardware found.")
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logging.info("Handling fallbacks")
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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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logging.info("Creating 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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with self.lock:
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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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with self.lock:
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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.get("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.get("stage", {}))
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# Capture manager
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self.captures.update_settings(settings.get("captures", {}))
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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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# Extension settings
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if "extensions" in settings:
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self.extension_settings.update(settings["extensions"])
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# TODO: warn if there are settings that we silently ignore
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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 = {
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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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"extensions": self.extension_settings,
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}
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with self.lock:
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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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# 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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# Capture manager
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settings_current_captures = self.captures.read_settings()
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settings_current["captures"] = settings_current_captures
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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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self.settings_file.save(current_config, backup=True)
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@property
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def configuration(self):
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with self.lock:
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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-server",
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"version": pkg_resources.get_distribution(
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"openflexure-microscope-server"
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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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with Timer("Reading settings:"):
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settings = self.read_settings(full=False)
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with Timer("Reading state:"):
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state = self.state
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with Timer("Reading configuration:"):
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configuration = self.configuration
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system_metadata = {
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"id": self.id,
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"settings": settings,
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"state": state,
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"configuration": configuration,
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}
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return system_metadata
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def add_metadata_to_capture(self, output, metadata, annotations, tags):
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logging.debug(f"Waiting for {output.file}")
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# Wait for the file to be written to disk
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with Timer("Waiting for file:"):
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output.file_ready.wait()
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with Timer("Building metadata"):
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full_metadata = {"instrument": self.metadata, **metadata}
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with Timer("Writing metadata to file"):
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output.put_and_save(tags, annotations, full_metadata)
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logging.info(f"Finished injecting EXIF data into {output.file}")
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def capture(
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self,
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filename: str = None,
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folder: str = "",
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temporary: bool = False,
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use_video_port: bool = False,
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resize: Tuple[int, int] = None,
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bayer: bool = True,
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fmt: str = "jpeg",
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annotations: dict = None,
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tags: list = None,
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metadata: dict = None,
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):
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logging.debug(f"Microscope capturing to {filename}")
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if not annotations:
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annotations = {}
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if not metadata:
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metadata = {}
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if not tags:
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tags = []
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with self.camera.lock:
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# Create output object
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output = self.captures.new_image(
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temporary=temporary, filename=filename, folder=folder, fmt=fmt
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)
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# Capture to output object
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logging.info("Starting microscope capture...")
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self.camera.capture(
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output,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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fmt=fmt,
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)
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# Gether metadata from hardware in a greenlet
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#gevent.get_hub().threadpool.spawn(self.add_metadata_to_capture, output, metadata, annotations, tags)
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gevent.spawn(self.add_metadata_to_capture, output, metadata, annotations, tags)
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#self.add_metadata_to_capture(output, metadata, annotations, tags)
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logging.info(f"Finished capture to {output.file}")
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return output
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