Initial support for SBv3 and MockStage (ff534e6a) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/app.py

+8 −6

Original line number	Diff line number	Diff line
		@@ -13,7 +13,8 @@ from openflexure_microscope.api.utilities import list_routes

		from openflexure_microscope import Microscope
		from openflexure_microscope.camera.pi import StreamingCamera
		from openflexure_microscope.stage.openflexure import Stage
		from openflexure_microscope.stage.sanga import SangaStage
		from openflexure_microscope.stage.mock import MockStage

		import atexit
		import logging
		@@ -71,11 +72,12 @@ def attach_microscope():

		logging.debug("Creating stage object...")
		try:
		api_stage = Stage("/dev/ttyUSB0")
		except SerialException as e:
		api_camera.close()
		raise e
		else:
		api_stage = SangaStage()
		except (SerialException, OSError) as e:
		logging.error(e)
		logging.warning("No valid stage hardware found. Falling back to mock stage!")
		api_stage = MockStage()
		finally:
		logging.debug("Attaching devices to microscope...")
		api_microscope.attach(
		api_camera,

+2 −2

Original line number	Diff line number	Diff line
		from flask import jsonify
		from flask import jsonify, escape
		from werkzeug.exceptions import default_exceptions
		from werkzeug.exceptions import HTTPException

		@@ -21,7 +21,7 @@ class JSONExceptionHandler(object):

		response = {
		'status_code': status_code,
		'message': message
		'message': escape(message)
		}
		return jsonify(response), status_code

+7 −20

Original line number	Diff line number	Diff line
		@@ -163,26 +163,10 @@ class Microscope(object):
		dict: Dictionary containing position data, and :py:attr:`openflexure_microscope.camera.base.BaseCamera.state`
		"""
		state = {
		'camera': {},
		'stage': {},
		'plugin': {}
		'camera': self.camera.state,
		'stage': self.stage.state,
		'plugin': self.plugin.state
		}

		# Add stage position
		if self.stage: # If stage exists, populate with real values
		position = self.stage.position
		else: # Else, zero
		position = [0, 0, 0]

		state['stage']['position'] = {
		'x': position[0],
		'y': position[1],
		'z': position[2],
		}

		# Add camera state
		state['camera'] = self.camera.state

		return state

		def write_config(self, config: dict):
		@@ -216,7 +200,10 @@ class Microscope(object):

		# If attached to a stage
		if self.stage:
		if hasattr(self.stage.backlash, 'tolist'):
		backlash = self.stage.backlash.tolist()
		else:
		backlash = self.stage.backlash
		else:
		backlash = [0, 0, 0]

+6 −1

Original line number	Diff line number	Diff line
		@@ -131,11 +131,16 @@ class PluginMount(object):
		self.plugins = []
		print("Creating plugin mount")

		@property
		def state(self):
		return [m[0] for m in self.members]

		@property
		def members(self):
		ignores = ['state', 'members', 'attach']
		plugin_array = []
		for obj_name in dir(self):
		if not obj_name == "plugins" and not obj_name[:2] == '__':
		if not obj_name in ignores and not obj_name[:2] == '__':
		obj = getattr(self, obj_name)
		if isinstance(obj, MicroscopePlugin):
		plugin_members = [member for member in inspect.getmembers(obj) if not member[0][:2] == '__']

0 → 100644

+58 −0

Original line number	Diff line number	Diff line
		from abc import ABCMeta, abstractmethod
		from openflexure_microscope.lock import StrictLock

		class BaseStage(metaclass=ABCMeta):
		def __init__(self):
		self.lock = StrictLock(timeout=5) #: :py:class:`openflexure_microscope.lock.StrictLock`: Strict lock controlling thread access to camera hardware

		@property
		@abstractmethod
		def state(self):
		"""The general state dictionary of the board.
		Should at least contain 'position', and 'board' keys.
		Note: A None/Null value for 'board' will disable stage
		movement in the OpenFlexure eV client software,
		"""
		pass

		@property
		@abstractmethod
		def n_axes(self):
		"""The number of axes this stage has."""
		pass

		@property
		@abstractmethod
		def position(self):
		"""The current position, as a list"""
		pass

		@property
		@abstractmethod
		def backlash(self):
		"""Get the distance used for backlash compensation."""
		pass

		@backlash.setter
		@abstractmethod
		def backlash(self):
		"""Set the distance used for backlash compensation."""
		pass

		@abstractmethod
		def move_rel(self, displacement, backlash=True):
		"""Make a relative move, optionally correcting for backlash.
		displacement: integer or array/list of 3 integers
		backlash: (default: True) whether to correct for backlash.
		"""
		pass

		@abstractmethod
		def move_abs(self, final, **kwargs):
		"""Make an absolute move to a position"""
		pass

		@abstractmethod
		def close(self):
		"""Cleanly close communication with the stage"""
		pass