248 lines
8.4 KiB
Python
248 lines
8.4 KiB
Python
# -*- coding: utf-8 -*-
|
|
"""
|
|
Defines a microscope object, binding a camera and stage with basic functionality.
|
|
"""
|
|
import logging
|
|
import pkg_resources
|
|
import uuid
|
|
|
|
from .stage.base import BaseStage
|
|
|
|
from .camera.base import BaseCamera
|
|
|
|
from .plugins import PluginMount
|
|
from .utilities import axes_to_array
|
|
from .task import TaskOrchestrator
|
|
from .lock import CompositeLock
|
|
from .config import OpenflexureSettingsFile, settings_to_json
|
|
|
|
|
|
class Microscope:
|
|
"""
|
|
A basic microscope object.
|
|
|
|
The camera and stage should already be initialised, and passed as arguments.
|
|
|
|
Attributes:
|
|
settings_file (:py:class:`openflexure_microscope.config.OpenflexureSettingsFile`): Runtime-config object,
|
|
automatically created if None.
|
|
lock (:py:class:`openflexure_microscope.lock.CompositeLock`): Composite lock controlling thread access
|
|
to multiple pieces of hardware.
|
|
camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): Camera object
|
|
stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): Stage object
|
|
task: (:py:class:`openflexure_microscope.task.TaskOrchestrator`): Threaded ask orchestrator for managing
|
|
background tasks using microscope hardware
|
|
plugin (:py:class:`openflexure_microscope.plugins.PluginMount`): Mounting point for all microscope plugins
|
|
"""
|
|
|
|
def __init__(self):
|
|
# Initial attributes
|
|
self.id = uuid.uuid4().hex
|
|
self.name = self.id
|
|
self.fov = [0, 0]
|
|
self.plugin_maps = []
|
|
self.camera = None
|
|
self.stage = None
|
|
|
|
# Initialise with an empty composite lock
|
|
self.lock = CompositeLock([])
|
|
|
|
# Create a task orchestrator
|
|
self.task = TaskOrchestrator()
|
|
|
|
# Attach to a settings file
|
|
self.settings_file = OpenflexureSettingsFile(expand=True)
|
|
# Apply settings loaded from file
|
|
self.apply_config(self.settings_file.load())
|
|
|
|
# Create plugin mount-point and attach plugins from maps
|
|
self.plugin = PluginMount(self)
|
|
self.attach_plugins(self.plugin_maps)
|
|
|
|
def __enter__(self):
|
|
"""Create microscope on context enter."""
|
|
return self
|
|
|
|
def __exit__(self, exc_type, exc_value, traceback):
|
|
"""Close microscope on context exit."""
|
|
self.close()
|
|
|
|
def close(self):
|
|
"""Shut down the microscope hardware."""
|
|
logging.info("Closing {}".format(self))
|
|
if self.camera:
|
|
self.camera.close()
|
|
if self.stage:
|
|
self.stage.close()
|
|
logging.info("Closed {}".format(self))
|
|
|
|
def attach(self, camera: BaseCamera, stage: BaseStage):
|
|
"""
|
|
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
|
|
"""
|
|
|
|
settings_full = self.read_config()
|
|
|
|
logging.debug("Attaching camera...")
|
|
self.camera = (
|
|
camera
|
|
) #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
|
|
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
|
|
if not self.stage:
|
|
logging.info("No stage attached.")
|
|
else:
|
|
logging.info("Attached stage {}".format(stage))
|
|
|
|
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_config(settings_full)
|
|
|
|
def attach_plugins(self, plugin_maps: list):
|
|
"""
|
|
Automatically search for plugin maps in config, and attach.
|
|
"""
|
|
if plugin_maps:
|
|
for plugin_map in plugin_maps:
|
|
self.plugin.attach(plugin_map)
|
|
else:
|
|
logging.warning("No plugins specified. Skipping.")
|
|
|
|
def reload_plugins(self):
|
|
"""
|
|
Empty the plugin mount and re-attach from config.
|
|
"""
|
|
logging.info("Tearing down existing PluginMount...")
|
|
self.plugin = PluginMount(self)
|
|
logging.info("Repopulating PluginMount...")
|
|
self.attach_plugins(self.plugin_maps)
|
|
|
|
# Create unified state
|
|
@property
|
|
def state(self):
|
|
"""Dictionary of the basic microscope state.
|
|
|
|
Return:
|
|
dict: Dictionary containing position data,
|
|
and :py:attr:`openflexure_microscope.camera.base.BaseCamera.state`
|
|
"""
|
|
state = {
|
|
"camera": self.camera.state,
|
|
"stage": self.stage.state,
|
|
"plugin": self.plugin.state,
|
|
"version": pkg_resources.get_distribution("openflexure_microscope").version,
|
|
}
|
|
return state
|
|
|
|
def apply_config(self, config: dict):
|
|
"""
|
|
Applies a config dictionary. Missing parameters will be left untouched.
|
|
"""
|
|
logging.debug("Microscope: Applying config: {}".format(config))
|
|
|
|
# If attached to a camera
|
|
if ("camera_settings" in config) and self.camera:
|
|
self.camera.apply_config(config["camera_settings"])
|
|
|
|
# If attached to a stage
|
|
if ("stage_settings" in config) and self.stage:
|
|
self.stage.apply_config(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"]
|
|
if "plugins" in config:
|
|
self.plugin_maps = config["plugins"]
|
|
|
|
def read_config(self, json_safe=False):
|
|
"""
|
|
Get an updated settings dictionary.
|
|
|
|
Reads current attributes and properties from connected hardware,
|
|
then merges those with the currently saved settings.
|
|
|
|
This is to ensure that settings for currently disconnected hardware
|
|
don't get removed from the settings file.
|
|
"""
|
|
|
|
settings_current = {
|
|
"id": self.id,
|
|
"name": self.name,
|
|
"fov": self.fov,
|
|
"plugins": self.plugin_maps,
|
|
}
|
|
|
|
# If attached to a camera
|
|
if self.camera:
|
|
settings_current_camera = self.camera.read_config()
|
|
settings_current["camera_settings"] = settings_current_camera
|
|
|
|
# If attached to a stage
|
|
if self.stage:
|
|
settings_current_stage = self.stage.read_config()
|
|
settings_current["stage_settings"] = settings_current_stage
|
|
|
|
settings_full = self.settings_file.merge(settings_current)
|
|
|
|
if json_safe:
|
|
settings_full = settings_to_json(settings_full)
|
|
|
|
return settings_full
|
|
|
|
def save_config(self, backup: bool = True):
|
|
"""
|
|
Merges the current settings back to disk
|
|
"""
|
|
# Read curent config
|
|
current_config = self.read_config()
|
|
# Merge in server version responsible for saving the config file
|
|
current_config["server_version"] = pkg_resources.get_distribution(
|
|
"openflexure_microscope"
|
|
).version
|
|
# Save config to file
|
|
self.settings_file.save(current_config, backup=True)
|
|
|
|
@property
|
|
def config(self) -> dict:
|
|
logging.warn(
|
|
"Reading microscope through config property is deprecated.\
|
|
Please use read_config method instead."
|
|
)
|
|
return self.read_config()
|
|
|
|
@config.setter
|
|
def config(self, config: dict) -> None:
|
|
logging.warn(
|
|
"Setting microscope through config property is deprecated.\
|
|
Please use apply_config method instead."
|
|
)
|
|
self.apply_config(config)
|