Renamed LabThing plugins to extensions (2a245185) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/app.py

+8 −8

Original line number	Diff line number	Diff line
		@@ -11,16 +11,16 @@ from datetime import datetime

		from flask_cors import CORS

		from openflexure_microscope.api.utilities import list_routes, init_default_plugins
		from openflexure_microscope.api.utilities import list_routes, init_default_extensions

		from openflexure_microscope.config import (
		settings_file_path,
		JSONEncoder,
		USER_PLUGINS_PATH,
		USER_EXTENSIONS_PATH,
		)

		from openflexure_microscope.common.flask_labthings.labthing import LabThing
		from openflexure_microscope.common.flask_labthings.plugins import find_plugins
		from openflexure_microscope.common.flask_labthings.extensions import find_extensions

		from openflexure_microscope.api.microscope import default_microscope as api_microscope

		@@ -73,11 +73,11 @@ labthing.title = f"OpenFlexure Microscope {api_microscope.name}"
		# Attach lab devices
		labthing.register_device(api_microscope, "openflexure_microscope")

		# Attach plugins
		if not os.path.isfile(USER_PLUGINS_PATH):
		init_default_plugins(USER_PLUGINS_PATH)
		for plugin in find_plugins(USER_PLUGINS_PATH):
		labthing.register_plugin(plugin)
		# Attach extensions
		if not os.path.isfile(USER_EXTENSIONS_PATH):
		init_default_extensions(USER_EXTENSIONS_PATH)
		for extension in find_extensions(USER_EXTENSIONS_PATH):
		labthing.register_extension(extension)

		# Attach captures resources
		labthing.add_resource(views.CaptureList, f"/captures")

openflexure_microscope/api/default_plugins/init.py→openflexure_microscope/api/default_extensions/init.py

+0 −0

File moved.

openflexure_microscope/api/default_plugins/autofocus.py→openflexure_microscope/api/default_extensions/autofocus.py

+10 −10

Original line number	Diff line number	Diff line
		from openflexure_microscope.common.flask_labthings.find import find_device
		from openflexure_microscope.common.flask_labthings.plugins import BasePlugin
		from openflexure_microscope.common.flask_labthings.extensions import BaseExtension
		from openflexure_microscope.common.flask_labthings.resource import Resource

		from openflexure_microscope.devel import JsonResponse, request, jsonify, taskify, abort
		@@ -139,7 +139,7 @@ def sharpness_edge(image):
		)


		### Autofocus plugin
		### Autofocus extension


		def measure_sharpness(microscope, metric_fn=sharpness_sum_lap2):
		@@ -353,15 +353,15 @@ class FastAutofocusAPI(Resource):
		abort(503, "No stage connected. Unable to autofocus.")


		autofocus_plugin_v2 = BasePlugin("autofocus")
		autofocus_extension_v2 = BaseExtension("autofocus")

		autofocus_plugin_v2.add_method(fast_autofocus, "fast_autofocus")
		autofocus_plugin_v2.add_method(autofocus, "autofocus")
		autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")
		autofocus_extension_v2.add_method(autofocus, "autofocus")

		autofocus_plugin_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")
		autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")

		autofocus_plugin_v2.add_view(AutofocusAPI, "/autofocus")
		autofocus_plugin_v2.register_action(AutofocusAPI)
		autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus")
		autofocus_extension_v2.register_action(AutofocusAPI)

		autofocus_plugin_v2.add_view(FastAutofocusAPI, "/fast_autofocus")
		autofocus_plugin_v2.register_action(FastAutofocusAPI)
		autofocus_extension_v2.add_view(FastAutofocusAPI, "/fast_autofocus")
		autofocus_extension_v2.register_action(FastAutofocusAPI)

openflexure_microscope/api/default_plugins/scan.py→openflexure_microscope/api/default_extensions/scan.py

+9 −9

Original line number	Diff line number	Diff line
		@@ -6,8 +6,8 @@ from typing import Tuple
		from functools import reduce

		from openflexure_microscope.camera.base import generate_basename
		from openflexure_microscope.common.flask_labthings.find import find_device, find_plugin
		from openflexure_microscope.common.flask_labthings.plugins import BasePlugin
		from openflexure_microscope.common.flask_labthings.find import find_device, find_extension
		from openflexure_microscope.common.flask_labthings.extensions import BaseExtension

		from openflexure_microscope.devel import (
		JsonResponse,
		@@ -169,10 +169,10 @@ def tile(
		)

		# Check if autofocus is enabled
		autofocus_plugin = find_plugin("autofocus")
		autofocus_extension = find_extension("autofocus")
		if (
		autofocus_dz
		and autofocus_plugin
		and autofocus_extension
		and microscope.has_real_stage()
		and microscope.has_real_camera()
		):
		@@ -211,7 +211,7 @@ def tile(
		# Refocus
		if autofocus_enabled:
		if fast_autofocus:
		autofocus_plugin.fast_autofocus(
		autofocus_extension.fast_autofocus(
		dz=autofocus_dz,
		target_z=-z_stack_dz / 2.0, # Finish below the focus
		initial_move_up=False, # We're already at the top of the scan
		@@ -219,7 +219,7 @@ def tile(
		# TODO: save the focus data for future reference? Use it for diagnostics?
		else:
		logging.debug("Running autofocus")
		autofocus_plugin.autofocus(
		autofocus_extension.autofocus(
		range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
		)
		logging.debug("Finished autofocus")
		@@ -398,7 +398,7 @@ class TileScanAPI(Resource):
		return jsonify(task.state), 201


		scan_plugin_v2 = BasePlugin("scan")
		scan_extension_v2 = BaseExtension("scan")

		scan_plugin_v2.add_view(TileScanAPI, "/tile")
		scan_plugin_v2.register_action(TileScanAPI)
		scan_extension_v2.add_view(TileScanAPI, "/tile")
		scan_extension_v2.register_action(TileScanAPI)

openflexure_microscope/api/utilities.py

+13 −13

Original line number	Diff line number	Diff line
		@@ -108,22 +108,22 @@ def create_file(config_path):
		raise


		def init_default_plugins(plugin_path):
		global _DEFAULT_PLUGIN_INIT
		os.makedirs(os.path.dirname(plugin_path), exist_ok=True)
		def init_default_extensions(extension_path):
		global _DEFAULT_extension_INIT
		os.makedirs(os.path.dirname(extension_path), exist_ok=True)

		if not os.path.exists(plugin_path): # If user plugins file doesn't exist
		logging.warning("No plugin file found at {}. Creating...".format(plugin_path))
		create_file(plugin_path)
		if not os.path.exists(extension_path): # If user extensions file doesn't exist
		logging.warning("No extension file found at {}. Creating...".format(extension_path))
		create_file(extension_path)

		logging.info("Populating {}...".format(plugin_path))
		with open(plugin_path, "w") as outfile:
		outfile.write(_DEFAULT_PLUGIN_INIT)
		logging.info("Populating {}...".format(extension_path))
		with open(extension_path, "w") as outfile:
		outfile.write(_DEFAULT_extension_INIT)


		_DEFAULT_PLUGIN_INIT = """
		from openflexure_microscope.api.default_plugins.autofocus import autofocus_plugin_v2
		from openflexure_microscope.api.default_plugins.scan import scan_plugin_v2
		_DEFAULT_extension_INIT = """
		from openflexure_microscope.api.default_extensions.autofocus import autofocus_extension_v2
		from openflexure_microscope.api.default_extensions.scan import scan_extension_v2

		__plugins__ = [autofocus_plugin_v2, scan_plugin_v2]
		__extensions__ = [autofocus_extension_v2, scan_extension_v2]
		"""