Start splitting ScanData into workflow specific data.
This commit is contained in:
Julian Stirling
parent
5ce74cad8a
commit
b6343362b2
4 changed files with 249 additions and 161 deletions
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@ -179,11 +179,11 @@ class SmartScanThing(lt.Thing):
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@lt.action
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def sample_scan(self, scan_name: str = "") -> None:
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"""Move the stage to cover an area, taking images that can be tiled together.
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"""Move the stage to cover an area, taking images.
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The stage will move in a pattern that grows outwards from the starting point,
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stopping once it is surrounded by "background" (as detected by the
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camera Thing) or reaches the "max_range" measured in steps.
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Depending on the way the stage moves depends on the selected worflow.
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If images overlap for a scan workdlow then the images can be stitched together
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into a larger composite image.
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"""
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got_lock = self._scan_lock.acquire(timeout=0.1)
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if not got_lock:
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@ -193,11 +193,13 @@ class SmartScanThing(lt.Thing):
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# the presence of `scan_data` is used during error handling to
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# determine whether the scan started.
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self._scan_data = None
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# probably make workflow a context manager with a lock?
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workflow = self._workflow
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try:
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self._check_background_and_csm_set()
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workflow.check_before_start(scan_name)
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self._ongoing_scan = self._scan_dir_manager.new_scan_dir(scan_name)
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self._latest_scan_name = self.ongoing_scan.name
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self._run_scan()
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self._run_scan(workflow)
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except Exception as e:
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# If _scan_data is set then scan started
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if self._scan_data is not None:
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@ -222,35 +224,6 @@ class SmartScanThing(lt.Thing):
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# Remove any scan folders containing zero images.
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self.purge_empty_scans()
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@_scan_running
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def _check_background_and_csm_set(self) -> None:
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"""Before starting a scan, check that background and camera-stage-mapping are set.
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Raise error if:
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- background is to be skipped but is not set
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- camera stage mapping is not set
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Raise warning if not using background detect that scan will go on until max steps reached
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"""
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self._csm.assert_calibration()
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if self.skip_background:
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if (
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self._cam.background_detector is None
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or not self._cam.background_detector.ready
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):
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raise RuntimeError(
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"Background is not set: you need to calibrate background detection."
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)
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else:
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self.logger.warning(
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"This scan will run in a spiral from the starting point "
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f"until you cancel it, or until it has moved by {self.max_range} steps "
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"in every direction. Make sure you watch it run to stop it leaving "
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"the area of interest, or (worse) leading the microscope's range "
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"of motion."
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)
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@_scan_running
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def _move_to_next_point(
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self, next_point: tuple[int, int], z_estimate: Optional[int] = None
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@ -276,90 +249,26 @@ class SmartScanThing(lt.Thing):
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return (next_point[0], next_point[1], z_estimate)
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@_scan_running
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def _calc_displacement_from_test_image(self, overlap: float) -> tuple[int, int]:
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"""Take a test image and use camera stage mapping to calculate x and y displacement.
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:param overlap: The desired overlap as a fraction of the image. i.e. 0.5 means
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that each image should overlap its nearest neighbour by 50%.
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:returns: (dx, dy) - the x and y displacements in steps
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"""
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if (
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self._csm.image_resolution is None
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or self._csm.image_to_stage_displacement_matrix is None
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):
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raise CSMUncalibratedError("Camera stage mapping is not calibrated")
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test_image = self._cam.grab_as_array()
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test_image_res = list(test_image.shape)
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csm_image_res = [int(i) for i in self._csm.image_resolution]
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# If current stream width is different to csm calibration width,
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# perform the conversion here
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res_ratio = csm_image_res[0] / test_image_res[0]
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# get displacement matrix. note it is for (y, x) not (x, y) coordinates
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csm_disp_matrix = np.array(self._csm.image_to_stage_displacement_matrix)
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csm_disp_matrix *= res_ratio
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# Calculate displacements in image coordinates
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dx_img = test_image.shape[1] * (1 - overlap)
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dy_img = test_image.shape[0] * (1 - overlap)
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# Calculate displacements in steps as vectors using a dot product with the matrix
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dx_vec = np.dot(np.array([0, dx_img]), csm_disp_matrix)
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dy_vec = np.dot(np.array([dy_img, 0]), csm_disp_matrix)
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# Assume no rotation or skew and take only the aligned axis of vector.
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# Coerce to positive integer
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dx = int(np.abs(dx_vec[0]))
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dy = int(np.abs(dy_vec[1]))
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return dx, dy
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@_scan_running
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def _collect_scan_data(self) -> scan_directories.ScanData:
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def _collect_scan_data(self, workflow: ScanWorkflow) -> scan_directories.ScanData:
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"""Collect and return the data for this scan so it cannot be changed mid-scan."""
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# Record starting position so it can be returned to at end of scan.
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starting_position = self._stage.position
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overlap = self.overlap
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dx, dy = self._calc_displacement_from_test_image(overlap)
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correlation_resize = stitching.STITCHING_RESOLUTION[0] / self.save_resolution[0]
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self.logger.debug(
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f"Resizing images when correlating by a factor of {correlation_resize}"
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)
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workflow_settings, stitching_settings = workflow.all_settings()
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self.logger.info(
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f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}"
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)
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autofocus_dz = self.autofocus_dz
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if autofocus_dz == 0:
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self.logger.info("Running scan without autofocus")
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elif autofocus_dz <= 200:
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self.logger.warning(
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f"Your autofocus range is {autofocus_dz} steps, which is too short to "
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"attempt to focus. Running without autofocus"
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)
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autofocus_dz = 0
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# If stitching settings is None then this workflow doesn't support stitching.
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auto_stitch = self.stitch_automatically and stitching_settings is not None
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# Fix scan parameters in case UI is updated during scan.
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return scan_directories.ScanData(
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scan_name=self.ongoing_scan.name,
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starting_position=starting_position,
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overlap=overlap,
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max_dist=self.max_range,
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dx=dx,
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dy=dy,
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autofocus_dz=autofocus_dz,
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autofocus_on=bool(autofocus_dz),
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start_time=datetime.now(),
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skip_background=self.skip_background,
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stitch_automatically=self.stitch_automatically,
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correlation_resize=correlation_resize,
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save_resolution=self.save_resolution,
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stitch_automatically=auto_stitch,
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save_resolution=workflow.save_resolution,
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workflow=type(workflow).__name__,
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workflow_settings=workflow_settings,
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stitching_settings=stitching_settings,
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)
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@_scan_running
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@ -381,7 +290,7 @@ class SmartScanThing(lt.Thing):
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self.preview_stitcher.start()
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@_scan_running
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def _run_scan(self) -> None:
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def _run_scan(self, workflow: ScanWorkflow) -> None:
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"""Prepare and run the main scan, and perform final actions on completion.
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The result (or exception) from the main scan loop determines whether the
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@ -389,10 +298,8 @@ class SmartScanThing(lt.Thing):
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starting x,y,z position.
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"""
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try:
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# probably make workflow a context manager with a lock?
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workflow = self._workflow
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self._cam.start_streaming(main_resolution=(3280, 2464))
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self._scan_data = self._collect_scan_data()
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self._scan_data = self._collect_scan_data(workflow)
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workflow.pre_scan_routine(self._scan_data)
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self.ongoing_scan.save_scan_data(self._scan_data)
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images_dir = self.ongoing_scan.images_dir
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@ -572,24 +479,9 @@ class SmartScanThing(lt.Thing):
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raise HTTPException(404, "File not found")
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return FileResponse(preview_path)
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save_resolution: tuple[int, int] = lt.setting(default=(1640, 1232))
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"""A tuple of the image resolution to capture."""
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max_range: int = lt.setting(default=45000)
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"""The maximum distance in steps from the centre of the scan."""
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stitch_tiff: bool = lt.setting(default=False)
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"""Whether or not to also produce a pyramidal tiff at the end of a scan."""
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skip_background: bool = lt.setting(default=True)
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"""Whether to detect and skip empty fields of view.
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This uses the settings from the ``BackgroundDetectThing``.
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"""
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overlap: float = lt.setting(default=0.45)
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"""The fraction (0-1) that adjacent images should overlap in x or y."""
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stitch_automatically: bool = lt.setting(default=True)
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"""Whether to run a final stitch at the end of a successful scan."""
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