Updated default extensions to subclass structure (8d0759e9) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/default_extensions/init.py

+22 −6

Original line number	Diff line number	Diff line
		@@ -2,6 +2,8 @@ import logging
		import traceback
		from contextlib import contextmanager

		LABTHINGS_EXTENSIONS = []


		@contextmanager
		def handle_extension_error(extension_name):
		@@ -17,14 +19,28 @@ def handle_extension_error(extension_name):


		with handle_extension_error("autofocus"):
		from .autofocus import autofocus_extension_v2
		from .autofocus import AutofocusExtension

		LABTHINGS_EXTENSIONS.append(AutofocusExtension)
		with handle_extension_error("scan"):
		from .scan import scan_extension_v2
		from .scan import ScanExtension

		LABTHINGS_EXTENSIONS.append(ScanExtension)
		with handle_extension_error("zip builder"):
		from .zip_builder import zip_extension_v2
		from .zip_builder import ZipBuilderExtension

		LABTHINGS_EXTENSIONS.append(ZipBuilderExtension)
		with handle_extension_error("autostorage"):
		from .autostorage import autostorage_extension_v2
		from .autostorage import AutostorageExtension

		LABTHINGS_EXTENSIONS.append(AutostorageExtension)

		with handle_extension_error("lens shading calibration"):
		from .picamera_autocalibrate import LSTExtension

		LABTHINGS_EXTENSIONS.append(LSTExtension)

		with handle_extension_error("camera stage mapping"):
		from camera_stage_mapping.ofm_extension import csm_extension
		with handle_extension_error("lens shading calibration"):
		from .picamera_autocalibrate import lst_extension_v2

		LABTHINGS_EXTENSIONS.append(csm_extension)

openflexure_microscope/api/default_extensions/autofocus.py

+196 −206

Original line number	Diff line number	Diff line
		@@ -109,6 +109,16 @@ class JPEGSharpnessMonitor:
		return data


		@contextmanager
		def monitor_sharpness(microscope: Microscope):
		m = JPEGSharpnessMonitor(microscope)
		m.start()
		try:
		yield m
		finally:
		m.stop()


		def sharpness_sum_lap2(rgb_image: np.ndarray):
		"""Return an image sharpness metric: sum(laplacian(image)**")"""
		image_bw = np.mean(rgb_image, 2)
		@@ -129,7 +139,29 @@ def sharpness_edge(image: np.ndarray):
		### Autofocus extension


		def measure_sharpness(microscope: Microscope, metric_fn: Callable = sharpness_sum_lap2):
		class AutofocusExtension(BaseExtension):
		def __init__(self):
		super().__init__(
		"org.openflexure.autofocus",
		version="2.0.0",
		description="Actions to move the microscope in Z and pick the point with the sharpest image.",
		)
		self.add_view(
		MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness"
		)
		self.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus")
		self.add_view(FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus")
		self.add_view(
		UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
		)

		self.add_view(
		MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
		)

		def measure_sharpness(
		self, microscope: Microscope, metric_fn: Callable = sharpness_sum_lap2
		):
		"""Measure the sharpness of the camera's current view."""

		if hasattr(microscope.camera, "array") and callable(
		@@ -139,8 +171,8 @@ def measure_sharpness(microscope: Microscope, metric_fn: Callable = sharpness_su
		else:
		raise RuntimeError(f"Object {microscope.camera} has no method `array`")


		def autofocus(
		self,
		microscope: Microscope,
		dz: List[int],
		settle: float = 0.5,
		@@ -169,39 +201,26 @@ def autofocus(
		return
		positions.append(stage.position[2])
		time.sleep(settle)
		sharpnesses.append(measure_sharpness(microscope, metric_fn))
		sharpnesses.append(self.measure_sharpness(microscope, metric_fn))

		newposition = positions[np.argmax(sharpnesses)]
		stage.move_rel((0, 0, newposition - stage.position[2]))

		return positions, sharpnesses


		@contextmanager
		def monitor_sharpness(microscope: Microscope):
		m = JPEGSharpnessMonitor(microscope)
		m.start()
		try:
		yield m
		finally:
		m.stop()


		def move_and_find_focus(microscope: Microscope, dz: int):
		def move_and_find_focus(self, microscope: Microscope, dz: int):
		"""Make a relative Z move and return the peak sharpness position"""
		with monitor_sharpness(microscope) as m:
		m.focus_rel(dz)
		return m.sharpest_z_on_move(0)


		def move_and_measure(microscope: Microscope, dz: int):
		def move_and_measure(self, microscope: Microscope, dz: int):
		"""Make a relative Z move and return the sharpness data"""
		with monitor_sharpness(microscope) as m:
		m.focus_rel(dz)
		return m.data_dict()


		def fast_autofocus(microscope: Microscope, dz: int = 2000):
		def fast_autofocus(self, microscope: Microscope, dz: int = 2000):
		"""Perform a down-up-down-up autofocus"""
		with microscope.camera.lock, microscope.stage.lock:
		with monitor_sharpness(microscope) as m:
		@@ -222,8 +241,8 @@ def fast_autofocus(microscope: Microscope, dz: int = 2000):
		# Return all focus data
		return m.data_dict()


		def fast_up_down_up_autofocus(
		self,
		microscope: Microscope,
		dz: int = 2000,
		target_z: int = 0,
		@@ -316,7 +335,7 @@ class MeasureSharpnessAPI(View):
		if not microscope:
		abort(503, "No microscope connected. Unable to measure sharpness.")

		return {"sharpness": measure_sharpness(microscope)}
		return {"sharpness": self.extension.measure_sharpness(microscope)}


		class MoveAndMeasureAPI(ActionView):
		@@ -335,7 +354,7 @@ class MoveAndMeasureAPI(ActionView):
		if microscope.has_real_stage():
		# Acquire microscope lock with 1s timeout
		with microscope.camera.lock, microscope.stage.lock:
		return move_and_measure(microscope, dz=args.get("dz"))
		return self.extension.move_and_measure(microscope, dz=args.get("dz"))

		else:
		abort(503, "No stage connected. Unable to autofocus.")
		@@ -361,7 +380,7 @@ class AutofocusAPI(ActionView):
		logging.debug("Running autofocus...")

		# return a handle on the autofocus task
		return autofocus(microscope, dz)
		return self.extension.autofocus(microscope, dz)

		else:
		abort(503, "No stage connected. Unable to autofocus.")
		@@ -385,7 +404,7 @@ class FastAutofocusAPI(ActionView):
		# Acquire microscope lock with 1s timeout
		with microscope.lock(timeout=1):
		# Run fast_autofocus
		return fast_autofocus(microscope, dz=args.get("dz"))
		return self.extension.fast_autofocus(microscope, dz=args.get("dz"))

		else:
		abort(503, "No stage connected. Unable to autofocus.")
		@@ -417,38 +436,9 @@ class UpDownUpAutofocusAPI(ActionView):
		# Acquire microscope lock with 1s timeout
		with microscope.lock(timeout=1):
		# Run fast_up_down_up_autofocus
		return fast_up_down_up_autofocus(
		return self.extension.fast_up_down_up_autofocus(
		microscope, dz=dz, mini_backlash=backlash
		)

		else:
		abort(503, "No stage connected. Unable to autofocus.")


		autofocus_extension_v2 = BaseExtension(
		"org.openflexure.autofocus",
		version="2.0.0",
		description="Actions to move the microscope in Z and pick the point with the sharpest image.",
		)

		autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")
		autofocus_extension_v2.add_method(
		fast_up_down_up_autofocus, "fast_up_down_up_autofocus"
		)
		autofocus_extension_v2.add_method(autofocus, "autofocus")
		autofocus_extension_v2.add_method(move_and_measure, "move_and_measure")

		autofocus_extension_v2.add_view(
		MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness"
		)
		autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus")
		autofocus_extension_v2.add_view(
		FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
		)
		autofocus_extension_v2.add_view(
		UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
		)

		autofocus_extension_v2.add_view(
		MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
		)

openflexure_microscope/api/default_extensions/autostorage.py

+40 −47

Original line number	Diff line number	Diff line
		@@ -93,12 +93,43 @@ class AutostorageExtension(BaseExtension):

		# We'll store a reference to a CaptureManager object, who's capture paths will be modified
		self.capture_manager: Optional[CaptureManager] = None

		self.initial_location: str = get_default_location()

		# Register the on_microscope function to run when the microscope is attached
		self.on_component("org.openflexure.microscope", self.on_microscope)

		self.add_view(GetLocationsView, "/list-locations")
		self.add_view(PreferredLocationView, "/location")
		self.add_view(PreferredLocationGUIView, "/location-from-title")
		self.add_meta("gui", build_gui(self.dynamic_form, self))

		def dynamic_form(self):
		self.check_location()
		return {
		"icon": "sd_storage",
		"title": "Storage",
		"viewPanel": "gallery",
		"forms": [
		{
		"name": "Autostorage",
		"isCollapsible": False,
		"isTask": False,
		"route": "/location-from-title",
		"emitOnResponse": "globalUpdateCaptures",
		"submitLabel": "Set path",
		"schema": [
		{
		"fieldType": "selectList",
		"name": "new_path_title",
		"label": "Capture storage path",
		"options": self.get_titles(),
		"value": self.get_preferred_title(),
		}
		],
		}
		],
		}

		def on_microscope(self, microscope_obj: Microscope):
		"""Function to automatically call when the parent LabThing has a microscope attached."""
		logging.debug("Autostorage extension found microscope %s", microscope_obj)
		@@ -204,12 +235,9 @@ class AutostorageExtension(BaseExtension):
		return self.key_to_title(self.get_preferred_key())


		autostorage_extension_v2 = AutostorageExtension()


		class GetLocationsView(PropertyView):
		def get(self):
		autostorage_extension_v2.check_location()
		self.extension.check_location()
		return autostorage_extension_v2.get_locations()


		@@ -217,8 +245,8 @@ class PreferredLocationView(PropertyView):
		schema = fields.String(required=True, example="Default")

		def get(self):
		autostorage_extension_v2.check_location()
		return autostorage_extension_v2.get_preferred_key()
		self.extension.check_location()
		return self.extension.get_preferred_key()

		def post(self, new_path_key):
		microscope = find_component("org.openflexure.microscope")
		@@ -226,8 +254,8 @@ class PreferredLocationView(PropertyView):
		if not microscope:
		abort(503, "No microscope connected. Unable to autofocus.")

		autostorage_extension_v2.check_location()
		autostorage_extension_v2.set_preferred_key(new_path_key)
		self.extension.check_location()
		self.extension.set_preferred_key(new_path_key)
		microscope.save_settings()


		@@ -237,46 +265,11 @@ class PreferredLocationGUIView(View):
		new_path_title = args.get("new_path_title")
		logging.debug(new_path_title)

		new_path_key = autostorage_extension_v2.title_to_key(new_path_title)
		new_path_key = self.extension.title_to_key(new_path_title)
		logging.debug(new_path_key)

		autostorage_extension_v2.check_location()
		autostorage_extension_v2.set_preferred_key(new_path_key)
		self.extension.check_location()
		self.extension.set_preferred_key(new_path_key)

		return new_path_title


		def dynamic_form():
		autostorage_extension_v2.check_location()
		return {
		"icon": "sd_storage",
		"title": "Storage",
		"viewPanel": "gallery",
		"forms": [
		{
		"name": "Autostorage",
		"isCollapsible": False,
		"isTask": False,
		"route": "/location-from-title",
		"emitOnResponse": "globalUpdateCaptures",
		"submitLabel": "Set path",
		"schema": [
		{
		"fieldType": "selectList",
		"name": "new_path_title",
		"label": "Capture storage path",
		"options": autostorage_extension_v2.get_titles(),
		"value": autostorage_extension_v2.get_preferred_title(),
		}
		],
		}
		],
		}


		autostorage_extension_v2.add_view(GetLocationsView, "/list-locations")
		autostorage_extension_v2.add_view(PreferredLocationView, "/location")
		autostorage_extension_v2.add_view(PreferredLocationGUIView, "/location-from-title")
		autostorage_extension_v2.add_meta(
		"gui", build_gui(dynamic_form, autostorage_extension_v2)
		)

openflexure_microscope/api/default_extensions/picamera_autocalibrate/init.py

+1 −1

Original line number	Diff line number	Diff line
		from .extension import lst_extension_v2
		from .extension import LSTExtension

openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py

+38 −37

Original line number	Diff line number	Diff line
		@@ -42,7 +42,27 @@ def pause_stream(scamera: BaseCamera):
		scamera.start_stream()


		def recalibrate(microscope: Microscope):
		class LSTExtension(BaseExtension):
		def __init__(self) -> None:
		super().__init__(
		"org.openflexure.calibration.picamera",
		version="2.0.0-beta.1",
		description="Routines to perform flat-field correction on the camera.",
		)

		self.add_view(RecalibrateView, "/recalibrate", endpoint="recalibrate")
		self.add_view(
		FlattenLSTView,
		"/flatten_lens_shading_table",
		endpoint="flatten_lens_shading_table",
		)
		self.add_view(
		DeleteLSTView,
		"/delete_lens_shading_table",
		endpoint="delete_lens_shading_table",
		)

		def recalibrate(self, microscope: Microscope):
		"""Reset the camera's settings.

		This generates new gains, exposure time, and lens shading
		@@ -70,7 +90,7 @@ class RecalibrateView(ActionView):

		logging.info("Starting microscope recalibration...")

		return recalibrate(microscope)
		return self.extension.recalibrate(microscope)


		class FlattenLSTView(ActionView):
		@@ -102,22 +122,3 @@ class DeleteLSTView(ActionView):
		with pause_stream(microscope.camera) as scamera:
		scamera.camera.lens_shading_table = None
		microscope.save_settings()


		lst_extension_v2 = BaseExtension(
		"org.openflexure.calibration.picamera",
		version="2.0.0-beta.1",
		description="Routines to perform flat-field correction on the camera.",
		)

		lst_extension_v2.add_method(
		recalibrate, "org.openflexure.calibration.picamera.recalibrate"
		)

		lst_extension_v2.add_view(RecalibrateView, "/recalibrate", endpoint="recalibrate")
		lst_extension_v2.add_view(
		FlattenLSTView, "/flatten_lens_shading_table", endpoint="flatten_lens_shading_table"
		)
		lst_extension_v2.add_view(
		DeleteLSTView, "/delete_lens_shading_table", endpoint="delete_lens_shading_table"
		)