386 lines
13 KiB
Python
386 lines
13 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 typing import Tuple
|
|
from expiringdict import ExpiringDict
|
|
|
|
import gevent
|
|
|
|
from openflexure_microscope.captures import CaptureManager
|
|
|
|
from openflexure_microscope.stage.mock import MissingStage
|
|
from openflexure_microscope.camera.mock import MissingCamera
|
|
from openflexure_microscope.stage.sanga import SangaStage
|
|
|
|
try:
|
|
from openflexure_microscope.camera.pi import PiCameraStreamer
|
|
except Exception as e:
|
|
logging.error(e)
|
|
logging.warning("Unable to import PiCameraStreamer")
|
|
from openflexure_microscope.camera.mock import MissingCamera
|
|
|
|
from openflexure_microscope.utilities import serialise_array_b64, Timer
|
|
from openflexure_microscope.config import user_settings, user_configuration
|
|
|
|
from labthings.core.lock import CompositeLock
|
|
|
|
|
|
class Microscope:
|
|
"""
|
|
A basic microscope object.
|
|
|
|
The camera and stage objects may already be initialised, and can be passed as arguments.
|
|
"""
|
|
|
|
def __init__(self, settings=user_settings, configuration=user_configuration):
|
|
self.id = uuid.uuid4()
|
|
self.name = self.id
|
|
|
|
self.captures = CaptureManager()
|
|
|
|
self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
|
|
|
|
# Store settings and configuration files
|
|
self.settings_file = settings
|
|
self.configuration_file = configuration
|
|
|
|
self.extension_settings = {}
|
|
|
|
# Initialise with an empty composite lock
|
|
#: :py:class:`labthings.lock.CompositeLock`: Composite lock for locking both camera and stage
|
|
self.lock = CompositeLock([])
|
|
|
|
self.camera = None #: Currently connected camera object
|
|
self.stage = None #: Currently connected stage object
|
|
|
|
self.setup(self.configuration_file.load()) # Attach components
|
|
|
|
# Apply settings loaded from file
|
|
self.update_settings(self.settings_file.load())
|
|
|
|
# Data cache
|
|
self.configuration_cache = ExpiringDict(max_len=100, max_age_seconds=3600)
|
|
self.metadata_cache = ExpiringDict(max_len=100, max_age_seconds=3600)
|
|
|
|
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:
|
|
try:
|
|
self.camera.close()
|
|
except TimeoutError as e:
|
|
logging.error(e)
|
|
if self.stage:
|
|
try:
|
|
self.stage.close()
|
|
except TimeoutError as e:
|
|
logging.error(e)
|
|
self.captures.close()
|
|
logging.info("Closed {}".format(self))
|
|
|
|
def setup(self, configuration):
|
|
"""
|
|
Attach microscope components based on initially passed configuration file
|
|
"""
|
|
|
|
### Detector
|
|
logging.info("Creating camera")
|
|
if configuration.get("camera"):
|
|
camera_type = configuration["camera"].get("type")
|
|
if camera_type in ("PiCamera", "PiCameraStreamer"):
|
|
try:
|
|
self.camera = PiCameraStreamer()
|
|
except Exception as e:
|
|
logging.error(e)
|
|
logging.warning("No compatible camera hardware found.")
|
|
|
|
### Stage
|
|
logging.info("Creating stage")
|
|
if configuration.get("stage"):
|
|
stage_type = configuration["stage"].get("type")
|
|
stage_port = configuration["stage"].get("port")
|
|
if stage_type in ("SangaBoard", "SangaStage"):
|
|
try:
|
|
self.stage = SangaStage(port=stage_port)
|
|
except Exception as e:
|
|
logging.error(e)
|
|
logging.warning("No compatible Sangaboard hardware found.")
|
|
|
|
logging.info("Handling fallbacks")
|
|
### Fallbacks
|
|
if not self.camera:
|
|
self.camera = MissingCamera()
|
|
if not self.stage:
|
|
self.stage = MissingStage()
|
|
|
|
### Locks
|
|
logging.info("Creating locks")
|
|
if hasattr(self.camera, "lock"):
|
|
self.lock.locks.append(self.camera.lock)
|
|
if hasattr(self.stage, "lock"):
|
|
self.lock.locks.append(self.stage.lock)
|
|
|
|
def has_real_stage(self) -> bool:
|
|
"""
|
|
Check if a real (non-mock) stage is currently attached.
|
|
"""
|
|
if hasattr(self, "stage") and not isinstance(self.stage, MissingStage):
|
|
return True
|
|
else:
|
|
return False
|
|
|
|
def has_real_camera(self):
|
|
"""
|
|
Check if a real (non-mock) camera is currently attached.
|
|
"""
|
|
if hasattr(self, "camera") and not isinstance(self.camera, MissingCamera):
|
|
return True
|
|
else:
|
|
return False
|
|
|
|
# Create unified state
|
|
@property
|
|
def state(self):
|
|
"""Dictionary of the basic microscope state.
|
|
|
|
Return:
|
|
dict: Dictionary containing complete microscope state
|
|
"""
|
|
with self.lock:
|
|
state = {"camera": self.camera.state, "stage": self.stage.state}
|
|
return state
|
|
|
|
def update_settings(self, settings: dict):
|
|
"""
|
|
Applies a settings dictionary to the microscope. Missing parameters will be left untouched.
|
|
"""
|
|
with self.lock:
|
|
logging.debug("Microscope: Applying settings: {}".format(settings))
|
|
|
|
# If attached to a camera
|
|
if ("camera" in settings) and self.camera:
|
|
self.camera.update_settings(settings.get("camera", {}))
|
|
|
|
# If attached to a stage
|
|
if ("stage" in settings) and self.stage:
|
|
self.stage.update_settings(settings.get("stage", {}))
|
|
|
|
# Capture manager
|
|
self.captures.update_settings(settings.get("captures", {}))
|
|
|
|
# Microscope settings
|
|
if "id" in settings:
|
|
self.id = settings["id"]
|
|
if "name" in settings:
|
|
self.name = settings["name"]
|
|
if "fov" in settings:
|
|
self.fov = settings["fov"]
|
|
|
|
# Extension settings
|
|
if "extensions" in settings:
|
|
self.extension_settings.update(settings["extensions"])
|
|
|
|
# TODO: warn if there are settings that we silently ignore
|
|
|
|
def read_settings(self, full: bool = True):
|
|
"""
|
|
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,
|
|
"extensions": self.extension_settings,
|
|
}
|
|
|
|
with self.lock:
|
|
# If attached to a camera
|
|
if self.camera:
|
|
settings_current_camera = self.camera.read_settings()
|
|
settings_current["camera"] = settings_current_camera
|
|
|
|
# Store an encoded copy of the PiCamera lens shading table, if it exists
|
|
if hasattr(self.camera, "read_lens_shading_table"):
|
|
# Read LST. Returns None if no LST is active
|
|
lst_arr = self.camera.read_lens_shading_table()
|
|
|
|
if lst_arr is not None:
|
|
b64_string, dtype, shape = serialise_array_b64(lst_arr)
|
|
|
|
settings_current["camera"]["lens_shading_table"] = {
|
|
"@type": "ndarray",
|
|
"b64_string": b64_string,
|
|
"dtype": dtype,
|
|
"shape": shape,
|
|
}
|
|
|
|
# If attached to a stage
|
|
if self.stage:
|
|
settings_current_stage = self.stage.read_settings()
|
|
settings_current["stage"] = settings_current_stage
|
|
|
|
# Capture manager
|
|
settings_current_captures = self.captures.read_settings()
|
|
settings_current["captures"] = settings_current_captures
|
|
|
|
settings_full = self.settings_file.merge(settings_current)
|
|
|
|
if full:
|
|
return settings_full
|
|
else:
|
|
return settings_current
|
|
|
|
def save_settings(self):
|
|
"""
|
|
Merges the current settings back to disk
|
|
"""
|
|
# Read curent config
|
|
current_config = self.read_settings()
|
|
# Save config to file
|
|
self.settings_file.save(current_config, backup=True)
|
|
|
|
def force_get_configuration(self):
|
|
with self.lock:
|
|
initial_configuration = self.configuration_file.load()
|
|
|
|
current_configuration = {
|
|
"application": {
|
|
"name": "openflexure-microscope-server",
|
|
"version": pkg_resources.get_distribution(
|
|
"openflexure-microscope-server"
|
|
).version,
|
|
},
|
|
"stage": {
|
|
"type": self.stage.__class__.__name__,
|
|
**self.stage.configuration,
|
|
},
|
|
"camera": {
|
|
"type": self.camera.__class__.__name__,
|
|
**self.camera.configuration,
|
|
},
|
|
}
|
|
|
|
initial_configuration.update(current_configuration)
|
|
return initial_configuration
|
|
|
|
def get_configuration(self, cache_key=None):
|
|
if cache_key:
|
|
cached_config = self.configuration_cache.get(cache_key, None)
|
|
if cached_config:
|
|
return cached_config
|
|
else:
|
|
full_config = self.force_get_configuration()
|
|
self.configuration_cache[cache_key] = full_config
|
|
return full_config
|
|
return self.force_get_configuration()
|
|
|
|
@property
|
|
def configuration(self):
|
|
return self.get_configuration()
|
|
|
|
def force_get_metadata(self):
|
|
"""
|
|
Read cachable bits of microscope metadata.
|
|
Currently ID, settings, and configuration can be cached
|
|
"""
|
|
system_metadata = {
|
|
"id": self.id,
|
|
"settings": self.read_settings(full=False),
|
|
"configuration": self.get_configuration(),
|
|
}
|
|
|
|
return system_metadata
|
|
|
|
def get_metadata(self, cache_key=None):
|
|
"""
|
|
Read microscope metadata, with partial caching
|
|
"""
|
|
metadata = {}
|
|
|
|
# Load cached bits of metadata
|
|
if cache_key:
|
|
logging.debug(f"Reading cached microscope metadata: {cache_key}")
|
|
metadata = self.metadata_cache.get(cache_key, None)
|
|
if not metadata:
|
|
logging.debug(f"Building and caching microscope metadata: {cache_key}")
|
|
metadata = self.force_get_metadata()
|
|
self.metadata_cache[cache_key] = metadata
|
|
else:
|
|
logging.debug(f"Building microscope metadata: {cache_key}")
|
|
metadata = self.force_get_metadata()
|
|
|
|
# Keys that should never be cached
|
|
metadata.update({
|
|
"state": self.state,
|
|
})
|
|
|
|
return metadata
|
|
|
|
@property
|
|
def metadata(self):
|
|
return self.get_metadata()
|
|
|
|
def capture(
|
|
self,
|
|
filename: str = None,
|
|
folder: str = "",
|
|
temporary: bool = False,
|
|
use_video_port: bool = False,
|
|
resize: Tuple[int, int] = None,
|
|
bayer: bool = True,
|
|
fmt: str = "jpeg",
|
|
annotations: dict = None,
|
|
tags: list = None,
|
|
metadata: dict = None,
|
|
cache_key: str = None
|
|
):
|
|
logging.debug(f"Microscope capturing to {filename}")
|
|
if not annotations:
|
|
annotations = {}
|
|
if not metadata:
|
|
metadata = {}
|
|
if not tags:
|
|
tags = []
|
|
|
|
# Read metadata for capture
|
|
full_metadata = {"instrument": self.get_metadata(cache_key), **metadata}
|
|
|
|
# Do capture
|
|
with self.camera.lock:
|
|
# Create output object
|
|
output = self.captures.new_image(
|
|
temporary=temporary, filename=filename, folder=folder, fmt=fmt
|
|
)
|
|
|
|
# Capture to output object
|
|
logging.info(f"Starting microscope capture {filename}")
|
|
self.camera.capture(
|
|
output,
|
|
use_video_port=use_video_port,
|
|
resize=resize,
|
|
bayer=bayer,
|
|
fmt=fmt,
|
|
)
|
|
|
|
output.put_and_save(tags, annotations, full_metadata)
|
|
logging.debug(f"Finished capture to {output.file}")
|
|
|
|
return output
|