119 lines
4.1 KiB
Python
119 lines
4.1 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 os
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import numpy as np
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from openflexure_stage import OpenFlexureStage
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from .camera.pi import StreamingCamera
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from .plugins import PluginMount, load_plugin, search_plugin_dirs
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from .config import load_config, save_config, convert_config
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class Microscope(object):
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"""
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A basic microscope object.
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The camera and stage should already be initialised, and passed as arguments.
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Args:
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camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
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microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
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load_config (bool): Should a config file be automatically loaded on init?
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config_path (str): Path to the config YAML file to be loaded. If None, defaults to USER_CONFIG_PATH.
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"""
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def __init__(self, camera: StreamingCamera, stage: OpenFlexureStage):
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self.attach(camera, stage)
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# Create plugin mountpoint
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self.plugin = PluginMount(self) #: :py:class:`openflexure_microscope.plugins.PluginMount`: Mounting point for all microscope plugins
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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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if self.camera:
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self.camera.close()
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if self.stage:
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self.stage.close()
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def attach(self, camera: StreamingCamera, stage: OpenFlexureStage, apply_config: bool=True):
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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.pi.StreamingCamera`): camera object
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microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
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apply_config (bool): Should the microscope config dictionary be applied to the attached hardware?
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"""
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self.camera = camera #: :py:class:`openflexure_microscope.camera.pi.StreamingCamera`: Picamera object
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if isinstance(camera, StreamingCamera):
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logging.info("Attached camera {}".format(camera))
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self.stage = stage #: :py:class:`openflexure_stage.stage.OpenFlexureStage`: OpenFlexure stage object
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if isinstance(self.stage, OpenFlexureStage): # If a stage object has been attached
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logging.info("Attached stage {}".format(stage))
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self.stage.backlash = np.zeros(3, dtype=np.int)
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def find_plugins(self, plugin_paths=[], include_default=True):
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"""
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Automatically search for plugins, and attach to self.
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Args:
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plugin_paths (list): List of strings of plugin directories.
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include_default (bool): Also load plugins from the module default directory (DEFAULT_PLUGIN_PATH)
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"""
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# TODO: Get paths from rc file
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plugins_list = search_plugin_dirs(plugin_paths, include_default=include_default)
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for i in plugins_list:
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module = load_plugin(i)
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self.plugin.attach(module)
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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 position data, and :py:attr:`openflexure_microscope.camera.base.BaseCamera.state`
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"""
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state = {
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'camera': {},
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'stage': {},
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'plugin': {}
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}
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# Add stage position
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position = self.stage.position
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state['stage']['position'] = {
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'x': position[0],
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'y': position[1],
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'z': position[2],
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}
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backlash = self.stage.backlash.tolist()
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state['stage']['backlash'] = {
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'x': backlash[0],
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'y': backlash[1],
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'z': backlash[2],
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}
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# Add camera state
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state['camera'] = self.camera.state
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return state
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