Added temporary support to scans (91595888) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/plugins/default/scan/api.py

+2 −40

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ class TileScanAPI(MicroscopeViewPlugin):

		# Get params
		filename = payload.param('filename')
		temporary = payload.param('temporary', default=False, convert=bool)

		step_size = payload.param('step_size', default=[2000, 1500, 100], convert=list)
		step_size = [int(i) for i in step_size]
		@@ -36,6 +37,7 @@ class TileScanAPI(MicroscopeViewPlugin):
		task = self.microscope.task.start(
		self.plugin.tile,
		basename=filename,
		temporary=temporary,
		step_size=step_size,
		grid=grid,
		style=style,
		@@ -49,43 +51,3 @@ class TileScanAPI(MicroscopeViewPlugin):

		# return a handle on the autofocus task
		return jsonify(task.state), 202


		class ZStackAPI(MicroscopeViewPlugin):
		def post(self):
		payload = JsonPayload(request)

		# Get params
		name = payload.param('name')
		step_size = payload.param('step_size', default=100, convert=int)
		steps = payload.param('steps', default=5, convert=int)
		center = payload.param('center', default=True, convert=bool)

		use_video_port = payload.param('use_video_port', default=False, convert=bool)
		resize = payload.param('size', default=None)
		if resize:
		if ('width' in resize) and ('height' in resize):
		resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
		else:
		abort(404)

		bayer = payload.param('bayer', default=True, convert=bool)
		metadata = payload.param('metadata', default={}, convert=dict)
		tags = payload.param('tags', default=[], convert=list)

		print("Running tile scan...")
		task = self.microscope.task.start(
		self.plugin.stack,
		basename=name,
		step_size=step_size,
		steps=steps,
		center=center,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		metadata=metadata,
		tags=tags
		)

		# return a handle on the autofocus task
		return jsonify(task.state), 202

openflexure_microscope/plugins/default/scan/plugin.py

+7 −2

Original line number	Diff line number	Diff line
		@@ -48,12 +48,12 @@ class ScanPlugin(MicroscopePlugin):

		api_views = {
		'/tile': TileScanAPI,
		'/stack': ZStackAPI,
		}

		def capture(self,
		basename,
		scan_id,
		temporary: bool = False,
		use_video_port: bool = False,
		resize: Tuple[int, int] = None,
		bayer: bool = False,
		@@ -67,7 +67,7 @@ class ScanPlugin(MicroscopePlugin):
		# Create output object
		output = self.microscope.camera.new_image(
		write_to_file=True,
		temporary=False,
		temporary=temporary,
		filename=filename,
		folder=foldername)

		@@ -94,6 +94,7 @@ class ScanPlugin(MicroscopePlugin):
		def tile(
		self,
		basename: str = None,
		temporary: bool = False,
		step_size: int = [2000, 1500, 100],
		grid: list = [3, 3, 5],
		style='raster',
		@@ -159,6 +160,7 @@ class ScanPlugin(MicroscopePlugin):
		self.capture(
		basename,
		scan_id,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,
		@@ -169,6 +171,7 @@ class ScanPlugin(MicroscopePlugin):
		logging.debug("Entering z-stack")
		self.stack(
		basename=basename,
		temporary=temporary,
		scan_id=scan_id,
		step_size=step_size[2],
		steps=grid[2],
		@@ -186,6 +189,7 @@ class ScanPlugin(MicroscopePlugin):
		def stack(
		self,
		basename: str = None,
		temporary: bool = False,
		scan_id: str = None,
		step_size: int = 100,
		steps: int = 5,
		@@ -224,6 +228,7 @@ class ScanPlugin(MicroscopePlugin):
		self.capture(
		basename,
		scan_id,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		bayer=bayer,