Close #166 (1c0cc32b) · Commits · OpenFlexure / openflexure-microscope-server

openflexure_microscope/api/default_extensions/scan.py

+44 −30

Original line number	Diff line number	Diff line
		@@ -56,9 +56,20 @@ def flatten_grid(grid):
		### Capturing





		class ScanExtension(BaseExtension):
		def __init__(self):
		self._images_to_be_captured: int = 1
		self._images_captured_so_far: int = 0
		BaseExtension.__init__(self, "org.openflexure.scan", version="2.0.0")

		def capture(
		self,
		microscope,
		basename,
		namemode: str = "coordinates",
		temporary: bool = False,
		use_video_port: bool = False,
		resize: Tuple[int, int] = None,
		@@ -69,7 +80,10 @@ def capture(
		):

		# Construct a tile filename
		if namemode == "coordinates":
		filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
		else:
		filename = "{}_{}".format(basename, str(self._images_captured_so_far).zfill(len(str(self._images_to_be_captured))))
		folder = "SCAN_{}".format(basename)

		# Do capture
		@@ -86,13 +100,6 @@ def capture(
		cache_key=folder
		)


		class ScanExtension(BaseExtension):
		def __init__(self):
		self._images_to_be_captured: int = 1
		self._images_captured_so_far: int = 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
		logging.info(progress)
		@@ -103,6 +110,7 @@ class ScanExtension(BaseExtension):
		self,
		microscope,
		basename: str = None,
		namemode: str = "coordinates",
		temporary: bool = False,
		stride_size: int = [2000, 1500, 100],
		grid: list = [3, 3, 5],
		@@ -198,6 +206,7 @@ class ScanExtension(BaseExtension):
		capture(
		microscope,
		basename,
		namemode=namemode,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		@@ -214,6 +223,7 @@ class ScanExtension(BaseExtension):
		self.stack(
		microscope=microscope,
		basename=basename,
		namemode=namemode,
		temporary=temporary,
		step_size=stride_size[2],
		steps=grid[2],
		@@ -240,6 +250,7 @@ class ScanExtension(BaseExtension):
		self,
		microscope,
		basename: str = None,
		namemode: str = "coordinates",
		temporary: bool = False,
		step_size: int = 100,
		steps: int = 5,
		@@ -265,9 +276,10 @@ class ScanExtension(BaseExtension):
		for i in range(steps):
		time.sleep(0.1)
		logging.debug(f"Capturing from position {microscope.stage.position}")
		capture(
		self.capture(
		microscope,
		basename,
		namemode=namemode,
		temporary=temporary,
		use_video_port=use_video_port,
		resize=resize,
		@@ -295,6 +307,7 @@ scan_extension_v2 = ScanExtension()
		class TileScanAPI(ActionView):
		args = {
		"filename": fields.String(missing=None, example=None),
		"namemode": fields.String(missing="coordinates", example="coordinates"),
		"temporary": fields.Boolean(missing=False),
		"stride_size": fields.List(
		fields.Integer, missing=[2000, 1500, 100], example=[2000, 1500, 100]
		@@ -338,6 +351,7 @@ class TileScanAPI(ActionView):
		return scan_extension_v2.tile(
		microscope,
		basename=args.get("filename"),
		namemode=args.get("namemode"),
		temporary=args.get("temporary"),
		stride_size=args.get("stride_size"),
		grid=args.get("grid"),

openflexure_microscope/api/static/src/components/controlComponents/paneCapture.vue

+13 −0

Original line number	Diff line number	Diff line
		@@ -227,6 +227,17 @@
		<option>Snake</option>
		</select>
		</div>

		<div class="uk-margin-small uk-margin-remove-bottom">
		<label class="uk-form-label" for="form-stacked-text"
		>Naming style</label
		>
		<select v-model="namingStyle" class="uk-select">
		<option>Coordinates</option>
		<option>Number</option>
		</select>
		</div>

		</div>
		</div>
		</li>
		@@ -284,6 +295,7 @@ export default {
		scanCapture: false,
		scanDeltaZ: "Fast",
		scanStyle: "Raster",
		namingStyle: "Coordinates",
		scanStepSize: {
		x: 0,
		y: 0,
		@@ -364,6 +376,7 @@ export default {
		this.scanStepSize.z
		];
		payload.style = this.scanStyle.toLowerCase();
		payload.namemode = this.namingStyle.toLowerCase();

		// Convert AF selector to dz
		var afDeltas = {