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Complete first pass of capture mode implementation

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This commit is contained in:
Julian Stirling 2026-06-02 16:09:27 +01:00
parent 83ceb82ea8
commit 9ed488e37d
4 changed files with 41 additions and 24 deletions
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14
src/openflexure_microscope_server/things/__init__.py
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@ -64,14 +64,19 @@ class OFMThing(lt.Thing):
)
return self._data_dir
def create_data_path(self, path: str) -> "RelativeDataPath":
def create_data_path(self, path: str, absolute: bool = False) -> "RelativeDataPath":
"""Create a ``RelativeDataPath`` object with this Thing set as the saving Thing.
:param path: The relative path within the data directory of this Thing's data
dir that the data shudl be saved.
:path absolute: Set to True if the current path is absolute. A relative path
will be returned. An validation error will be raised if the absolute path
is not within the data directory.
:return: A ``RelativeDataPath`` object with the saving Thing already set.
"""
if absolute:
path = os.path.relpath(path, self.data_dir)
rel_data_path = RelativeDataPath(path)
rel_data_path.set_saving_thing(self)
return rel_data_path
@ -136,12 +141,15 @@ class RelativeDataPath(RootModel[str]):
:return: A new ``RelativeDataPath`` object with the path appended.
"""
return RelativeDataPath(os.path.join(self.root, sub_path))
new_path = RelativeDataPath(os.path.join(self.root, sub_path))
if self._saving_thing is not None:
new_path.set_saving_thing(self._saving_thing)
return new_path
@property
def abs_data_path(self) -> str:
"""The absolute data directory to save to."""
if self.save_location_set:
if self._saving_thing is None:
raise RuntimeError("The saving Thing for the relative path was never set")
if isinstance(self._saving_thing, TemporaryDirectory):
return os.path.join(self._saving_thing.name, self.root)

2
src/openflexure_microscope_server/things/camera/__init__.py
View file

@ -591,7 +591,7 @@ class BaseCamera(OFMThing, ABC):
self.capture_and_save_to_path(path, capture_mode)
if tmpdir is None:
blob = lt.blob.Blob.from_file(path)
blob = lt.blob.Blob.from_file(path.abs_data_path)
else:
blob = lt.blob.Blob.from_temporary_directory(tmpdir, fname)
blob.media_type = format_info.media_type

35
src/openflexure_microscope_server/things/scan_workflows.py
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@ -111,19 +111,27 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
)
def all_settings(
self, images_dir: str
) -> tuple[SettingModelType, Optional[StitchingSettings]]:
self, images_dir: RelativeDataPath
) -> tuple[SettingModelType, Optional[StitchingSettings], tuple[int, int]]:
"""Return the scan settings and the stitching settings.
- The specific settings for this scan workflow are returned as a Base Model of
the type set when defining the class.
- Stitiching settings are returned either as a StitchingSettings object or None
is returned if it is not possible to stitch the scan.
- The save resolution as determined by a test image.
"""
raise NotImplementedError(
"Each specific ScanWorkflow must implement a `all_settings` method."
)
def _get_save_resolution(self) -> tuple[int, int]:
"""Return the save resolution as determined by a test image."""
# Capture an example image.
image = self._cam._capture_image(capture_mode=self.capture_mode)
# Check side to create a unit faction for downsampling.
return image.size
def pre_scan_routine(self, settings: SettingModelType) -> None:
"""Overload to set the routine that happens before each scan."""
raise NotImplementedError(
@ -268,12 +276,11 @@ class RectGridWorkflow(
)
return y_move_stage["x"], x_move_stage["y"]
def _get_stitching_settings_model(self) -> StitchingSettings:
def _get_stitching_settings_model(
self, save_resolution: tuple[int, int]
) -> StitchingSettings:
"""Return a stitching settings model based on current settings."""
# Use the save resolution and target stitch resolution to choose a unit fraction,
# which makes correlating faster
# TODO Calculate this using a camera method.
width, height = self.save_resolution
width, height = save_resolution
# Target area in pixels
target_area = TARGET_STITCHING_DIMENSION**2
# Find N so that (width/N) * (height/N) ~ target_area
@ -293,24 +300,24 @@ class RectGridWorkflow(
return self._settings_model(**base_kwargs)
def all_settings(
self, images_dir: str
) -> tuple[RectGridSettingModelType, Optional[StitchingSettings]]:
self, images_dir: RelativeDataPath
) -> tuple[RectGridSettingModelType, Optional[StitchingSettings], tuple[int, int]]:
"""Return scan settings and the stitching settings.
:param images_dir: The directory that images are to be written to.
:return: A tuple containing the settings model for this workflow and the
settings model for stitching.
:return: A tuple containing the settings model for this workflow, the
settings model for stitching, and the save resolution.
"""
save_resolution = self._get_save_resolution()
# Developer Note: When subclassing RectGridWorkflow rather than override
# this method first consider overriding _build_scan_settings
stitching_settings = self._get_stitching_settings_model()
stitching_settings = self._get_stitching_settings_model(save_resolution)
dx, dy = self._calc_displacement_from_overlap(self.overlap)
base_kwargs = {
"overlap": self.overlap,
"dx": dx,
"dy": dy,
# TODO set images dir correctly as a RelDataPath
"capture_params": CaptureParams(
images_dir=images_dir, capture_mode=self.capture_mode
),
@ -319,7 +326,7 @@ class RectGridWorkflow(
scan_settings = self._build_scan_settings(base_kwargs)
return scan_settings, stitching_settings
return scan_settings, stitching_settings, save_resolution
@lt.property
def ready(self) -> bool:

14
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -304,8 +304,8 @@ class SmartScanThing(OFMThing):
# Ensure any PreviewStitcher created cannot be reused.
self._preview_stitcher = None
# Remove any scan folders containing zero images.
self.purge_empty_scans()
# Remove any scan folders containing zero images.
self.purge_empty_scans()
@_scan_running
def _move_to_next_point(
@ -343,8 +343,8 @@ class SmartScanThing(OFMThing):
if images_dir is None:
raise RuntimeError("Couldn't run scan, images directory was not created.")
workflow_settings, stitching_settings = workflow.all_settings(
images_dir=images_dir
workflow_settings, stitching_settings, save_resolution = workflow.all_settings(
images_dir=self.create_data_path(images_dir, absolute=True)
)
# If stitching settings is None then this workflow doesn't support stitching.
@ -356,7 +356,7 @@ class SmartScanThing(OFMThing):
starting_position=starting_position,
start_time=datetime.now(),
stitch_automatically=auto_stitch,
save_resolution=workflow.save_resolution,
save_resolution=save_resolution,
workflow=type(workflow).__name__,
workflow_settings=workflow_settings,
stitching_settings=stitching_settings,
@ -392,6 +392,9 @@ class SmartScanThing(OFMThing):
starting x,y,z position.
"""
try:
# Change into streaming mode instantly so mode is correct when collecting
# Scan Data
self._cam.change_streaming_mode(mode="full_resolution")
self._scan_data = self._collect_scan_data(workflow)
images_dir = self.ongoing_scan.images_dir
# Type narrowing
@ -401,7 +404,6 @@ class SmartScanThing(OFMThing):
)
self.ongoing_scan.save_scan_data(self._scan_data)
self._cam.change_streaming_mode(mode="full_resolution")
workflow.pre_scan_routine(self._scan_data.workflow_settings)
# If stitching settings are None then this type of scan can't be stitched