Draft of new semantics
This commit is contained in:
Joel Collins
parent
b39a0653f2
commit
19af98736d
13 changed files with 252 additions and 187 deletions
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@ -6,15 +6,20 @@ 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.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
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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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@ -24,20 +29,32 @@ 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):
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# Initial attributes
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self.id = uuid.uuid4() #: Microscope UUID
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self.name = self.id #: Microscope name (modifiable)
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self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
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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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def __init__(self, settings = user_settings, configuration = user_configuration):
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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.apply_settings(user_settings.load())
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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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@ -56,58 +73,49 @@ class Microscope:
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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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def setup(self, configuration):
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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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Attach microscope components based on initially passed configuration file
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"""
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settings_full = self.read_settings()
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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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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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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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### 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 == "SangaBoard" or detector_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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logging.error(e)
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logging.warning("No compatible stage hardware found.")
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### Fallbacks
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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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self.camera = MissingCamera()
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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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self.stage = MissingStage()
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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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### 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, MockStage):
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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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@ -116,27 +124,26 @@ class Microscope:
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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, MockStreamer):
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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 status
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@property
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def status(self):
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def state(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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"camera": self.camera.state,
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"stage": self.stage.state,
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}
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return state
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def apply_settings(self, config: dict):
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def update_settings(self, config: 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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@ -144,21 +151,19 @@ class Microscope:
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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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self.camera.update_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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self.stage.update_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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def read_settings(self, json_safe=False):
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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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@ -169,7 +174,7 @@ class Microscope:
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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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settings_current = {"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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@ -181,9 +186,12 @@ class Microscope:
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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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settings_full = self.settings_file.merge(settings_current)
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return settings_full
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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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@ -196,7 +204,7 @@ class Microscope:
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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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self.settings_file.save(current_config, backup=True)
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@property
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def metadata(self):
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@ -204,10 +212,10 @@ class Microscope:
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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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"@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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@ -217,10 +225,32 @@ class Microscope:
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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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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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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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},
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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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"detector": {
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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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