Simplified new configuration and metadata (7458d278) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/app.py

+6 −2

Original line number	Diff line number	Diff line
		@@ -19,7 +19,7 @@ from openflexure_microscope.paths import (
		OPENFLEXURE_VAR_PATH,
		OPENFLEXURE_EXTENSIONS_PATH,
		settings_file_path,
		logs_file_path
		logs_file_path,
		)

		from labthings.server.quick import create_app
		@@ -92,7 +92,7 @@ labthing.add_root_link(views.CaptureList, "captures")
		labthing.add_view(views.CaptureView, f"/captures/<id>")
		labthing.add_view(views.CaptureDownload, f"/captures/<id>/download/<filename>")
		labthing.add_view(views.CaptureTags, f"/captures/<id>/tags")
		labthing.add_view(views.CaptureMetadata, f"/captures/<id>/metadata")
		labthing.add_view(views.CaptureAnnotations, f"/captures/<id>/annotations")

		# Attach settings and status resources
		labthing.add_view(views.SettingsProperty, f"/settings")
		@@ -101,6 +101,10 @@ labthing.add_view(views.NestedSettingsProperty, "/settings/<path:route>")
		labthing.add_view(views.StatusProperty, "/status")
		labthing.add_view(views.NestedStatusProperty, "/status/<path:route>")
		labthing.add_root_link(views.StatusProperty, "status")
		labthing.add_view(views.ConfigurationProperty, "/configuration")
		labthing.add_view(views.NestedConfigurationProperty, "/configuration/<path:route>")
		labthing.add_root_link(views.ConfigurationProperty, "configuration")


		# Attach streams resources
		labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

openflexure_microscope/api/default_extensions/scan.py

+40 −61

Original line number	Diff line number	Diff line
		import itertools
		import logging
		import uuid
		import datetime
		from typing import Tuple
		from functools import reduce

		@@ -71,12 +72,12 @@ def progress():
		def capture(
		microscope,
		basename,
		scan_id,
		temporary: bool = False,
		use_video_port: bool = False,
		resize: Tuple[int, int] = None,
		bayer: bool = False,
		metadata: dict = {},
		annotations: dict = {},
		tags: list = [],
		):

		@@ -94,16 +95,14 @@ def capture(
		output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
		)

		# Affix metadata
		if "scan" not in tags:
		tags.append("scan")

		# Inject system metadata
		output.put_metadata(microscope.metadata, system=True)
		output.put_metadata({"instrument": microscope.metadata})

		# Insert custom metadata
		output.put_metadata(metadata)

		# Insert custom metadata
		output.put_annotations(annotations)
		# Insert custom tags
		output.put_tags(tags)

		@@ -115,7 +114,7 @@ def tile(
		microscope,
		basename: str = None,
		temporary: bool = False,
		step_size: int = [2000, 1500, 100],
		stride_size: int = [2000, 1500, 100],
		grid: list = [3, 3, 5],
		style="raster",
		autofocus_dz: int = 50,
		@@ -124,13 +123,13 @@ def tile(
		bayer: bool = False,
		fast_autofocus=False,
		metadata: dict = {},
		annotations: dict = {},
		tags: list = [],
		):
		global _images_to_be_captured
		global _images_captured_so_far

		# Keep task progress
		# TODO: Make this line not nasty
		_images_to_be_captured = reduce((lambda x, y: x * y), grid)
		_images_captured_so_far = 0

		@@ -138,28 +137,22 @@ def tile(
		if not basename:
		basename = generate_basename()

		# Generate a stack ID
		scan_id = uuid.uuid4()

		# Store initial position
		initial_position = microscope.stage.position

		# Add scan metadata
		if "time" not in metadata:
		metadata["time"] = generate_basename()

		metadata.update(
		{
		"scan_id": scan_id,
		"basename": basename,
		"scan_parameters": {
		"step_size": step_size,
		# Add dataset metadata
		dataset_d = {
		"dataset": {
		"id": uuid.uuid4(),
		"type": "xyzScan",
		"name": basename,
		"acquisitionDate": datetime.datetime.now().isoformat(),
		"strideSize": stride_size,
		"grid": grid,
		"style": style,
		"autofocus_dz": autofocus_dz,
		},
		"autofocusDz": autofocus_dz,
		}
		}
		)

		# Check if autofocus is enabled
		autofocus_extension = find_extension("org.openflexure.autofocus")
		@@ -174,11 +167,11 @@ def tile(
		autofocus_enabled = False

		z_stack_dz = (
		grid[2] * step_size[2] if grid[2] > 1 else 0
		grid[2] * stride_size[2] if grid[2] > 1 else 0
		) # shorthand for Z stack range

		# Construct an x-y grid (worry about z later)
		x_y_grid = construct_grid(initial_position, step_size[:2], grid[:2], style=style)
		x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)

		# Keep the initial Z position the same as our current position
		next_z = initial_position[2]
		@@ -209,26 +202,25 @@ def tile(
		target_z=-z_stack_dz / 2.0, # Finish below the focus
		initial_move_up=False, # We're already at the top of the scan
		)
		# TODO: save the focus data for future reference? Use it for diagnostics?
		else:
		logging.debug("Running autofocus")
		autofocus_extension.autofocus(
		range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
		)
		logging.debug("Finished autofocus")
		time.sleep(1) # TODO: Remove
		time.sleep(1)

		# If we're not doing a z-stack, just capture
		if grid[2] <= 1:
		capture(
		microscope,
		basename,
		scan_id,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		metadata=metadata,
		metadata=dataset_d,
		annotations=annotations,
		tags=tags,
		)
		# Update task progress
		@@ -240,15 +232,14 @@ def tile(
		microscope=microscope,
		basename=basename,
		temporary=temporary,
		scan_id=scan_id,
		step_size=step_size[2],
		step_size=stride_size[2],
		steps=grid[2],
		center=not fast_autofocus, # fast_autofocus does this for us!
		return_to_start=not fast_autofocus,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		metadata=metadata,
		metadata=dataset_d,
		annotations=annotations,
		tags=tags,
		)
		# Make sure we use our current best estimate of focus (i.e. the current position) next point
		@@ -259,7 +250,7 @@ def tile(
		) # Fast autofocus requires us to start at the top of the range
		if grid[2] > 1:
		next_z -= int(
		grid[2] / 2.0 * step_size[2]
		grid[2] / 2.0 * stride_size[2]
		) # Z stacking means we're higher up to start with

		logging.debug("Returning to {}".format(initial_position))
		@@ -270,37 +261,23 @@ def stack(
		microscope,
		basename: str = None,
		temporary: bool = False,
		scan_id: str = None,
		step_size: int = 100,
		steps: int = 5,
		center: bool = True,
		return_to_start: bool = True,
		use_video_port: bool = False,
		resize: Tuple[int, int] = None,
		bayer: bool = False,
		metadata: dict = {},
		annotations: dict = {},
		tags: list = [],
		):
		global _images_captured_so_far

		# Generate a basename if none given
		if not basename:
		basename = generate_basename()

		# Generate a stack ID
		if not scan_id:
		scan_id = uuid.uuid4()

		# Add scan metadata
		if not "time" in metadata:
		metadata["time"] = generate_basename()

		# Store initial position
		initial_position = microscope.stage.position

		with microscope.lock:
		# Move to center scan
		if center:
		logging.debug("Moving to starting position")
		microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])

		@@ -310,12 +287,12 @@ def stack(
		capture(
		microscope,
		basename,
		scan_id,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		metadata=metadata,
		annotations=annotations,
		tags=tags,
		)
		# Update task progress
		@@ -337,16 +314,18 @@ def stack(
		class TileScanAPI(View):
		@use_args(
		{
		"filename": fields.String(),
		"filename": fields.String(missing=None, example=None),
		"temporary": fields.Boolean(missing=False),
		"step_size": fields.List(fields.Integer, missing=[2000, 1500, 100]),
		"grid": fields.List(fields.Integer, missing=[3, 3, 5]),
		"stride_size": fields.List(
		fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
		),
		"grid": fields.List(fields.Integer, missing=[3, 3, 3], example=[3, 3, 3]),
		"style": fields.String(missing="raster"),
		"autofocus_dz": fields.Integer(missing=50),
		"fast_autofocus": fields.Boolean(missing=False),
		"use_video_port": fields.Boolean(missing=False),
		"bayer": fields.Boolean(missing=False),
		"metadata": fields.Dict(missing={}),
		"annotations": fields.Dict(missing={}, example={"Foo": "Bar"}),
		"tags": fields.List(fields.String, missing=[]),
		"resize": fields.Dict(missing=None), # TODO: Validate keys
		}
		@@ -373,7 +352,7 @@ class TileScanAPI(View):
		microscope,
		basename=args.get("filename"),
		temporary=args.get("temporary"),
		step_size=args.get("step_size"),
		stride_size=args.get("stride_size"),
		grid=args.get("grid"),
		style=args.get("style"),
		autofocus_dz=args.get("autofocus_dz"),
		@@ -381,7 +360,7 @@ class TileScanAPI(View):
		resize=resize,
		bayer=args.get("bayer"),
		fast_autofocus=args.get("fast_autofocus"),
		metadata=args.get("metadata"),
		annotations=args.get("annotations"),
		tags=args.get("tags"),
		)

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

+3 −4

Original line number	Diff line number	Diff line
		@@ -36,7 +36,7 @@ class CaptureAPI(View):
		"bayer": fields.Boolean(
		missing=False, description="Store raw bayer data in file"
		),
		"metadata": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
		"annotations": fields.Dict(missing={}, example={"Client": "SwaggerUI"}),
		"tags": fields.List(fields.String, missing=[], example=["docs"]),
		"resize": fields.Dict(
		missing=None, example={"width": 640, "height": 480}
		@@ -75,11 +75,10 @@ class CaptureAPI(View):
		)

		# Inject system metadata
		output.put_metadata(microscope.metadata, system=True)
		output.put_metadata({"instrument": microscope.metadata})

		# Insert custom metadata
		output.put_metadata(args.get("metadata"))

		output.put_annotations(args.get("annotations"))
		# Insert custom tags
		output.put_tags(args.get("tags"))

openflexure_microscope/api/v2/views/captures.py

+13 −9

Original line number	Diff line number	Diff line
		@@ -39,10 +39,12 @@ class CaptureSchema(Schema):
		"mimetype": "application/json",
		**description_from_view(CaptureTags),
		},
		"metadata": {
		"href": url_for(CaptureMetadata.endpoint, id=data.id, _external=True),
		"annotations": {
		"href": url_for(
		CaptureAnnotations.endpoint, id=data.id, _external=True
		),
		"mimetype": "application/json",
		**description_from_view(CaptureMetadata),
		**description_from_view(CaptureAnnotations),
		},
		"download": {
		"href": url_for(
		@@ -62,6 +64,9 @@ capture_schema = CaptureSchema()
		capture_list_schema = CaptureSchema(many=True)


		from pprint import pprint


		@ThingProperty
		@Tag("captures")
		class CaptureList(View):
		@@ -197,10 +202,10 @@ class CaptureTags(View):


		@Tag("captures")
		class CaptureMetadata(View):
		class CaptureAnnotations(View):
		def get(self, id):
		"""
		Get metadata associated with a single image capture
		Get annotations associated with a single image capture
		"""
		microscope = find_component("org.openflexure.microscope")
		capture_obj = microscope.camera.image_from_id(id)
		@@ -208,7 +213,7 @@ class CaptureMetadata(View):
		if not capture_obj:
		return abort(404) # 404 Not Found

		return jsonify(capture_obj.metadata)
		return jsonify(capture_obj.annotations)

		def put(self, id):
		"""
		@@ -226,7 +231,6 @@ class CaptureMetadata(View):
		if type(data_dict) != dict:
		return abort(400)

		# TODO: Allow putting system metadata maybe?
		capture_obj.put_metadata(data_dict)
		capture_obj.put_annotations(data_dict)

		return jsonify(capture_obj.metadata)
		return jsonify(capture_obj.annotations)

openflexure_microscope/api/v2/views/state.py

+30 −2

Original line number	Diff line number	Diff line
		@@ -78,7 +78,7 @@ class StatusProperty(View):
		Show current read-only state of the microscope
		"""
		microscope = find_component("org.openflexure.microscope")
		return jsonify(microscope.status)
		return jsonify(microscope.state)


		@Tag("properties")
		@@ -92,7 +92,35 @@ class NestedStatusProperty(View):
		keys = route.split("/")

		try:
		value = get_by_path(microscope.status, keys)
		value = get_by_path(microscope.state, keys)
		except KeyError:
		return abort(404)

		return jsonify(value)


		@ThingProperty
		class ConfigurationProperty(View):
		def get(self):
		"""
		Show current read-only state of the microscope
		"""
		microscope = find_component("org.openflexure.microscope")
		return jsonify(microscope.configuration)


		@Tag("properties")
		class NestedConfigurationProperty(View):
		@doc_response(404, description="Configuration key cannot be found")
		def get(self, route):
		"""
		Show a nested section of the current microscope state
		"""
		microscope = find_component("org.openflexure.microscope")
		keys = route.split("/")

		try:
		value = get_by_path(microscope.configuration, keys)
		except KeyError:
		return abort(404)