Introduced apply_config and read_config methods (5471ffa6) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/camera/pi.py

+23 −37

Original line number	Diff line number	Diff line
		@@ -25,13 +25,7 @@ from __future__ import division

		import io
		import time
		import datetime
		import sys
		import os
		import yaml
		import copy
		import numpy as np
		from PIL import Image
		import logging

		# Used for conversion only
		@@ -44,9 +38,6 @@ import picamera.array
		# Type hinting
		from typing import Tuple

		# Threading
		import threading

		from .base import BaseCamera, CaptureObject
		# Richard's fix gain
		from .set_picamera_gain import set_analog_gain, set_digital_gain
		@@ -70,9 +61,9 @@ CONFIG_KEYS = {
		},
		}


		# Useful methods

		# TODO: Remove this
		def fractions_to_floats(value):
		"""Deal with horrible, horrible PiCamera fractions"""
		result = value
		@@ -85,15 +76,15 @@ def fractions_to_floats(value):
		result = float(value)
		return result

		# MAIN CLASS

		# MAIN CLASS
		class StreamingCamera(BaseCamera):
		"""Raspberry Pi camera implementation of StreamingCamera.

		Args:
		config (dict): Dictionary of config parameters to apply on init. If None, will default to basic config.
		"""
		def __init__(self, config: dict=None, picamera_settings: dict=None):
		def __init__(self, config: dict = None):
		global CONFIG_KEYS

		# Run BaseCamera init
		@@ -111,11 +102,14 @@ class StreamingCamera(BaseCamera):
		self.set_zoom(1.0)

		# Populate config and settings with all available keys
		self._config.update(CONFIG_KEYS)
		self.config.update(CONFIG_KEYS)

		# Load config dictionary if passed
		if config:
		self.config = config
		self.apply_config(config)

		# Create an empty stream
		self.stream = io.BytesIO()

		# Start streaming
		self.start_worker()
		@@ -128,7 +122,7 @@ class StreamingCamera(BaseCamera):
		"""Close the Raspberry Pi StreamingCamera."""
		# Run BaseCamera close method
		BaseCamera.close(self)
		# Detatch Pi camera
		# Detach Pi camera
		if self.camera:
		self.camera.close()

		@@ -146,8 +140,7 @@ class StreamingCamera(BaseCamera):
		"""
		return hasattr(self.camera, "lens_shading_table")

		@property
		def config(self):
		def read_config(self):
		"""
		Return config dictionary of the StreamingCamera.
		"""
		@@ -156,7 +149,7 @@ class StreamingCamera(BaseCamera):
		}

		# PiCamera parameters (obtained directly from PiCamera object)
		for key, _ in self._config['picamera_settings'].items():
		for key, _ in self.config['picamera_settings'].items():
		try:
		value = getattr(self.camera, key)
		value = fractions_to_floats(value)
		@@ -166,13 +159,12 @@ class StreamingCamera(BaseCamera):

		# StreamingCamera parameters (obtained from StreamingCamera _config)
		for key in CONFIG_KEYS:
		if (key != 'picamera_settings') and (key in self._config):
		conf_dict[key] = self._config[key]
		if (key != 'picamera_settings') and (key in self.config):
		conf_dict[key] = self.config[key]

		return conf_dict

		@config.setter
		def config(self, config: dict) -> None:
		def apply_config(self, config: dict) -> None:
		"""
		Write a config dictionary to the StreamingCamera config.

		@@ -202,7 +194,7 @@ class StreamingCamera(BaseCamera):
		# PiCamera parameters (applied directly to PiCamera object)
		if 'picamera_settings' in config: # If new settings are given
		for key, value in config['picamera_settings'].items(): # For each given setting
		self._config['picamera_settings'][key] = None # Add the key to the list of returned settings
		self.config['picamera_settings'][key] = None # Add the key to the list of returned settings
		logging.debug("Setting parameter {}: {}".format(key, config['picamera_settings'][key]))

		# Handle special attributes:
		@@ -217,7 +209,7 @@ class StreamingCamera(BaseCamera):
		for key, value in config.items(): # For each provided setting
		if key != 'picamera_settings': # We already handled this
		logging.debug("Setting parameter {}: {}".format(key, value))
		self._config[key] = value
		self.config[key] = value

		# If stream was paused to update config, unpause
		if paused_stream:
		@@ -230,7 +222,7 @@ class StreamingCamera(BaseCamera):

		def set_zoom(self, zoom_value: float = 1.) -> None:
		"""
		Change the camera zoom, handling recentering and scaling.
		Change the camera zoom, handling re-centering and scaling.
		"""
		with self.lock:
		self.state['zoom_value'] = float(zoom_value)
		@@ -275,9 +267,8 @@ class StreamingCamera(BaseCamera):

		Args:
		output (CaptureObject/str): Output object to write data bytes to.
		write_to_file (bool/NoneType): Should the StreamObject write to a file?
		filename (str): Name of the stored file. Defaults to timestamp.
		fmt (str): Format of the capture.
		quality (int): Video recording quality.

		Returns:
		output_object (str/BytesIO): Target object.
		@@ -317,7 +308,7 @@ class StreamingCamera(BaseCamera):
		until the current recording has stopped.")
		return None

		def stop_recording(self) -> bool:
		def stop_recording(self):
		"""Stop the last started video recording on splitter port 2."""
		with self.lock:
		# Stop the camera video recording on port 2
		@@ -364,7 +355,7 @@ class StreamingCamera(BaseCamera):
		splitter_port (int): Splitter port to start recording on
		resolution ((int, int)): Resolution to set the camera to, before starting recording. Defaults to `self.config['video_resolution']`.
		"""
		# If no stream object exists
		# If stream object was destroyed
		if not hasattr(self, 'stream'):
		self.stream = io.BytesIO() # Create a stream object

		@@ -404,6 +395,7 @@ class StreamingCamera(BaseCamera):
		use_video_port (bool): Capture from the video port used for streaming. Lower resolution, faster.
		fmt (str): Format of the capture.
		resize ((int, int)): Resize the captured image.
		bayer (bool): Store raw bayer data in capture
		"""

		with self.lock:
		@@ -416,7 +408,7 @@ class StreamingCamera(BaseCamera):

		logging.info("Capturing to {}".format(output))

		# Set resolution and stop stream recording if necesarry
		# Set resolution and stop stream recording if necessary
		if not use_video_port:
		self.stop_stream_recording()

		@@ -428,7 +420,7 @@ class StreamingCamera(BaseCamera):
		bayer=(not use_video_port) and bayer,
		use_video_port=use_video_port)

		# Set resolution and start stream recording if necesarry
		# Set resolution and start stream recording if necessary
		if not use_video_port:
		self.start_stream_recording()

		@@ -436,7 +428,6 @@ class StreamingCamera(BaseCamera):

		def yuv(
		self,
		rgb=False,
		use_video_port: bool = True,
		resize: Tuple[int, int] = None) -> np.ndarray:
		"""Capture an uncompressed still YUV image to a Numpy array.
		@@ -473,10 +464,6 @@ class StreamingCamera(BaseCamera):
		if not use_video_port:
		self.start_stream_recording()

		if rgb:
		logging.debug("Converting to RGB")
		return output.rgb_array
		else:
		return output.array

		def array(
		@@ -537,7 +524,6 @@ class StreamingCamera(BaseCamera):

		# Update state
		logging.debug("STREAM ACTIVE")
		#self.state['stream_active'] = True

		# While the iterator is not closed
		try:

openflexure_microscope/microscope.py

+50 −34

Original line number	Diff line number	Diff line
		@@ -25,22 +25,29 @@ class Microscope(object):

		Args:
		camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
		microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
		config (dict): Dictionary of the runtime config to apply to the microscope. Does not automatically apply to camera and stage.
		stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
		config_path (str): Path to a microscoperc.yaml runtime-config file
		attach_plugins (bool): Should the microscope attach plugins listen in 'config' immediately.
		"""
		def __init__(self, camera: StreamingCamera, stage: OpenFlexureStage, config_path: str=None, attach_plugins: bool=True):
		def __init__(
		self,
		camera: StreamingCamera,
		stage: OpenFlexureStage,
		config_path: str = None,
		attach_plugins: bool = True):

		# Create RC object
		self.rc = OpenflexureConfig(config_path=config_path, expand=True)

		# Attach initial hardware (may be NoneTypes)
		self.camera = None
		self.stage = None
		self.attach(camera, stage)

		# Create a task orchestrator
		self.task = TaskOrchestrator() #: :py:class:`openflexure_microscope.task.TaskOrchestrator`: Threaded task orchestrator

		# Create plugin mountpoint
		# Create plugin mount-point
		self.plugin = PluginMount(self) #: :py:class:`openflexure_microscope.plugins.PluginMount`: Mounting point for all microscope plugins

		# Attach plugins
		@@ -48,16 +55,15 @@ class Microscope(object):
		self.attach_plugins()

		# Set default parameters
		if not 'name' in self.rc.config:
		self.rc.config['name'] = uuid.uuid4().hex
		if 'name' not in self.rc.config:
		self.rc.update({'name': uuid.uuid4().hex})

		if not 'fov' in self.rc.config:
		self.rc.config['fov'] = [0, 0]
		if 'fov' not in self.rc.config:
		self.rc.update({'fov': [0, 0]})

		# Initialise with an empty composite lock
		self.lock = CompositeLock([]) #: :py:class:`openflexure_microscope.lock.CompositeLock`: Composite lock controlling thread access to multiple pieces of hardware


		def __enter__(self):
		"""Create microscope on context enter."""
		return self
		@@ -82,14 +88,15 @@ class Microscope(object):

		Args:
		camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
		microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
		apply_config (bool): Should the microscope config dictionary be applied to the attached hardware?
		stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
		"""

		logging.debug("Attaching camera...")
		self.camera = camera #: :py:class:`openflexure_microscope.camera.pi.StreamingCamera`: Picamera object
		if isinstance(self.camera, StreamingCamera):
		logging.info("Attached camera {}".format(camera))
		logging.info("Updating camera settings")
		self.apply_config(self.camera.read_config())
		elif not self.camera:
		logging.info("Attached dummy camera.")
		# If camera has a lock
		@@ -173,8 +180,32 @@ class Microscope(object):

		return state

		@property
		def config(self):
		def apply_config(self, config: dict):
		"""
		Updates and applies a config dictionary. Missing parameters will be left untouched.
		"""
		# If attached to a camera
		if self.camera:
		# Update camera config
		self.camera.config = config

		# If attached to a stage
		# TODO: Convert stage settings into a config expansion
		if self.stage:
		if 'backlash' in config:
		# Construct backlash array
		backlash = axes_to_array(config['backlash'], ['x', 'y', 'z'], [0, 0, 0])
		self.stage.backlash = backlash

		# Cache config
		self.rc.update(config)
		# Save to disk
		self.rc.save()

		def read_config(self):
		"""
		Read an updated config including camera settings.
		"""
		# If attached to a camera
		if self.camera:
		# Update camera config params from StreamingCamera object
		@@ -196,27 +227,12 @@ class Microscope(object):

		self.rc.update(backlash)

		return self.rc.config
		return self.rc.asdict()

		@property
		def config(self) -> dict:
		return self.read_config()

		@config.setter
		def config(self, config: dict) -> None:
		"""
		Technically doesn't SET the config, but rather updates it. Missing parameters
		will be left untouched.
		"""
		# If attached to a camera
		if self.camera:
		# Update camera config
		self.camera.config = config

		# If attached to a stage
		if self.stage:
		if 'backlash' in config:
		# Construct backlash array
		backlash = axes_to_array(config['backlash'], ['x', 'y', 'z'], [0, 0, 0])
		self.stage.backlash = backlash

		# Cache config
		self.rc.update(config)
		# Save to disk
		self.rc.save()
		No newline at end of file
		self.apply_config(config)