Initial 0.7.0 conversion (e6cb9f6b) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/default_extensions/autofocus.py

+13 −9

Original line number	Diff line number	Diff line
		from labthings.server.find import find_component
		from labthings.server.extensions import BaseExtension
		from labthings.server.view import View, ActionView, PropertyView
		from labthings.server.decorators import ThingAction, ThingProperty
		from labthings.server import fields

		from openflexure_microscope.devel import JsonResponse, request, abort
		from openflexure_microscope.utilities import set_properties
		@@ -336,7 +336,9 @@ class AutofocusAPI(ActionView):
		"""
		Run a standard autofocus
		"""
		def post(self):
		args = {"dz": fields.List(fields.Int())}

		def post(self, args):
		payload = JsonResponse(request)
		microscope = find_component("org.openflexure.microscope")

		@@ -344,7 +346,7 @@ class AutofocusAPI(ActionView):
		abort(503, "No microscope connected. Unable to autofocus.")

		# Figure out the range of z values to use
		dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
		dz = np.array(args.get("dz", np.linspace(-300, 300, 7)))

		if microscope.has_real_stage():
		logging.debug("Running autofocus...")
		@@ -360,18 +362,20 @@ class FastAutofocusAPI(ActionView):
		"""
		Run a fast autofocus
		"""
		def post(self):
		payload = JsonResponse(request)
		args = {
		"dz": fields.Int(default=2000),
		"backlash": fields.Int(default=25, minimum=0)
		}

		def post(self, args):
		microscope = find_component("org.openflexure.microscope")

		if not microscope:
		abort(503, "No microscope connected. Unable to autofocus.")

		# Figure out the parameters to use
		dz = payload.param("dz", default=2000, convert=int)
		backlash = payload.param("backlash", default=25, convert=int)
		if backlash < 0:
		backlash = 0
		dz = args.get("dz")
		backlash = args.get("backlash")

		if microscope.has_real_stage():
		logging.debug("Running autofocus...")

openflexure_microscope/api/default_extensions/autostorage.py

+4 −3

Original line number	Diff line number	Diff line
		from labthings.server.extensions import BaseExtension
		from labthings.server.view import View, PropertyView
		from labthings.server.decorators import ThingProperty, PropertySchema, use_args
		from labthings.server import fields
		from labthings.server.find import find_component

		@@ -198,8 +197,9 @@ class GetLocationsView(PropertyView):
		return autostorage_extension_v2.get_locations()


		@PropertySchema(fields.String(required=True, example="Default"))
		class PreferredLocationView(PropertyView):
		schema = fields.String(required=True, example="Default")

		def get(self):
		global autostorage_extension_v2

		@@ -219,7 +219,8 @@ class PreferredLocationView(PropertyView):


		class PreferredLocationGUIView(View):
		@use_args({"new_path_title": fields.String(required=True)})
		args = {"new_path_title": fields.String(required=True)}

		def post(self, args):
		global autostorage_extension_v2

openflexure_microscope/api/default_extensions/scan.py

+18 −20

Original line number	Diff line number	Diff line
		@@ -8,7 +8,6 @@ from functools import reduce
		from openflexure_microscope.captures.capture_manager import generate_basename
		from labthings.server.find import find_component, find_extension
		from labthings.server.extensions import BaseExtension
		from labthings.server.decorators import use_args
		from labthings.server import fields

		from openflexure_microscope.devel import abort, update_task_progress
		@@ -91,7 +90,7 @@ class ScanExtension(BaseExtension):
		def __init__(self):
		self._images_to_be_captured: int = 1
		self._images_captured_so_far: int = 0
		return BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")
		BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")

		def progress(self):
		progress = (self._images_captured_so_far / self._images_to_be_captured) * 100
		@@ -289,8 +288,7 @@ class ScanExtension(BaseExtension):
		scan_extension_v2 = ScanExtension()

		class TileScanAPI(ActionView):
		@use_args(
		{
		args = {
		"filename": fields.String(missing=None, example=None),
		"temporary": fields.Boolean(missing=False),
		"stride_size": fields.List(
		@@ -306,7 +304,7 @@ class TileScanAPI(ActionView):
		"tags": fields.List(fields.String, missing=[]),
		"resize": fields.Dict(missing=None), # TODO: Validate keys
		}
		)

		def post(self, args):
		microscope = find_component("org.openflexure.microscope")

openflexure_microscope/api/default_extensions/zip_builder.py

+3 −9

Original line number	Diff line number	Diff line
		@@ -14,16 +14,10 @@ import logging

		from labthings.server.find import find_component
		from labthings.server.view import View, ActionView, PropertyView
		from labthings.server.schema import Schema
		from labthings.server.schema import Schema, pre_dump
		from labthings.server import fields
		from labthings.server.extensions import BaseExtension
		from labthings.server.utilities import description_from_view
		from labthings.server.decorators import (
		ThingAction,
		ThingProperty,
		marshal_with,
		pre_dump,
		)


		class ZipObjectSchema(Schema):
		@@ -140,7 +134,6 @@ default_zip_manager = ZipManager()

		class ZipBuilderAPIView(ActionView):
		def post(self):

		ids = list(JsonResponse(request).json)
		microscope = find_component("org.openflexure.microscope")

		@@ -151,7 +144,8 @@ class ZipBuilderAPIView(ActionView):


		class ZipListAPIView(PropertyView):
		@marshal_with(ZipObjectSchema(many=True))
		schema = ZipObjectSchema(many=True)

		def get(self):
		return default_zip_manager.session_zips.values()

openflexure_microscope/api/v2/views/actions/init.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -58,7 +58,6 @@ def enabled_root_actions():
		return {k: v for k, v in _actions.items() if v["conditions"]}


		# @Tag("actions")
		class ActionsView(View):
		def get(self):
		"""