rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Apply suggestions from code review of branch scan-workflows

Browse source 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
This commit is contained in:
Julian Stirling 2026-02-06 13:28:30 +00:00
parent 504a47cbf8
commit 8f30f08bdf
3 changed files with 9 additions and 10 deletions
Download patch file Download diff file Expand all files Collapse all files

5
src/openflexure_microscope_server/scan_directories.py
View file

@ -189,15 +189,14 @@ class HistoricScanData(BaseScanData):
@model_validator(mode="before") @model_validator(mode="before")
@classmethod @classmethod
def coerce_legacy(cls, data: dict) -> dict: def coerce_legacy(cls, data: dict) -> dict:
"""Coerce any legacy data.""" """Coerce any scan data from before version 2 into the version 2 format."""
r"""Coerce any scan data from before version 2 into the version 2 format."""
# Before the current version no schema_version was set # Before the current version no schema_version was set
if "schema_version" in data: if "schema_version" in data:
return data return data
if "correlation_resize" and "overlap" in data: if "correlation_resize" and "overlap" in data:
correlation_resize = data.pop("correlation_resize") correlation_resize = data.pop("correlation_resize")
# Note we don't pop overlap is a setting for the legacy workflow as well # Note we don't pop overlap, as it is a setting for the legacy workflow as well
# as a stitching setting. # as a stitching setting.
# This is done because in future workflows the stitching overlap may be a # This is done because in future workflows the stitching overlap may be a
# directly set setting or something that is calculated from other settings. # directly set setting or something that is calculated from other settings.

10
src/openflexure_microscope_server/things/scan_workflows.py
View file

@ -195,8 +195,8 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
"""The minimum number of images to capture in a stack. """The minimum number of images to capture in a stack.
This many images are captures and tested for focus, if the focus is not central This many images are captures and tested for focus, if the focus is not central
enough more images may be captured. After new images are captured the number sets enough more images may be captured. After new images are captured, this value sets
the number of images used for checking if focus is central. the number of images used for checking if focus is achieved.
Defaults to 9 which balances reliability and speed. Defaults to 9 which balances reliability and speed.
""" """
@ -286,7 +286,7 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
return scan_settings, stitching_settings return scan_settings, stitching_settings
def _calc_displacement_from_overlap(self, overlap: float) -> tuple[int, int]: def _calc_displacement_from_overlap(self, overlap: float) -> tuple[int, int]:
"""Take a test image and use camera stage mapping to calculate x and y displacement. """Use camera stage mapping to calculate x and y displacement.
:param overlap: The desired overlap as a fraction of the image. i.e. 0.5 means :param overlap: The desired overlap as a fraction of the image. i.e. 0.5 means
that each image should overlap its nearest neighbour by 50%. that each image should overlap its nearest neighbour by 50%.
@ -295,7 +295,7 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
""" """
csm_image_res = self._csm.image_resolution csm_image_res = self._csm.image_resolution
if csm_image_res is None: if csm_image_res is None:
raise RuntimeError("CSM not set. Scan shouldn't have progresses this far.") raise RuntimeError("CSM not set. Scan shouldn't have progressed this far.")
# Calculate displacements in image coordinates # Calculate displacements in image coordinates
dx_img = csm_image_res[1] * (1 - overlap) dx_img = csm_image_res[1] * (1 - overlap)
@ -448,7 +448,7 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
imaged = focused or save_on_failure imaged = focused or save_on_failure
if not imaged: if not imaged:
msg = f"Stack failed at {xyz_pos} treating as background." msg = f"Stack failed at {xyz_pos}. Treating as background."
self.logger.info(msg) self.logger.info(msg)
# run_smart_stage always returns a focus height for the sharpest image even # run_smart_stage always returns a focus height for the sharpest image even

4
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -43,7 +43,7 @@ T = TypeVar("T")
P = ParamSpec("P") P = ParamSpec("P")
# This allows ActiveScanData to hold arbitrary workflow settings models during a scan. # This allows ActiveScanData to hold arbitrary workflow settings models during a scan.
AnyModel = Annotated[ AnyModel = Annotated[
BaseModel, BaseModel,
PlainSerializer(lambda value: value.model_dump(), return_type=dict), PlainSerializer(lambda value: value.model_dump(), return_type=dict),
@ -233,7 +233,7 @@ class SmartScanThing(lt.Thing):
def sample_scan(self, scan_name: str = "") -> None: def sample_scan(self, scan_name: str = "") -> None:
"""Move the stage to cover an area, taking images. """Move the stage to cover an area, taking images.
Depending on the way the stage moves depends on the selected workflow. The way the stage moves depends on the selected workflow.
If images overlap for a scan workflow then the images can be stitched together If images overlap for a scan workflow then the images can be stitched together
into a larger composite image. into a larger composite image.
""" """