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Slice Geometry Pipeline returns annotation points in straightened volume domain #76

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Merged
den-sq merged 1 commit into from
Mar 4, 2026
Merged

Slice Geometry Pipeline returns annotation points in straightened volume domain #76

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5 changes: 3 additions & 2 deletions python/ouroboros/pipeline/pipeline_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,18 +30,19 @@ class PipelineInput(BasePipelineInput):
backproject_options: BackprojectOptions | None = None
source_url: str | None = None
sample_points: np.ndarray | None = None
annotation_points: np.ndarray | None = None
slice_rects: np.ndarray | None = None
volume_cache: VolumeCache | None = None
output_file_path: str | None = None
backprojected_folder_path: str | None = None
config_file_path: str | None = None
backprojection_offset: str | None = None

@field_serializer("sample_points", "slice_rects")
@field_serializer("sample_points", "annotation_points", "slice_rects")
def to_list(self, value) -> list | None:
return value.tolist() if value is not None else None

@field_validator("sample_points", "slice_rects", mode="before")
@field_validator("sample_points", "annotation_points", "slice_rects", mode="before")
@classmethod
def validate_list(cls, value: any) -> np.ndarray | None:
if isinstance(value, list):
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22 changes: 22 additions & 0 deletions python/ouroboros/pipeline/slices_geom_pipeline.py
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Expand Up @@ -65,6 +65,28 @@ def _process(self, input_data: tuple[any]) -> None | str:

equidistant_points = spline(equidistant_params)

# Convert annotation points to straightened-volume coordinates.
# `spline.u` are the fit parameters corresponding to these input points.
annotation_projection_points = spline(spline.u).T

_, normal_vectors, binormal_vectors = spline.calculate_rotation_minimizing_vectors(spline.u)

annotation_offsets = sample_points - annotation_projection_points
lateral_offsets_x = np.einsum("ij,ij->i", annotation_offsets, normal_vectors.T)
lateral_offsets_y = np.einsum("ij,ij->i", annotation_offsets, binormal_vectors.T)

straightened_depth = np.interp(spline.u, equidistant_params,
np.arange(len(equidistant_params), dtype=np.float32))

straightened_annotation_points = np.column_stack(
(
(config.slice_width - 1) / 2.0 + lateral_offsets_x,
(config.slice_height - 1) / 2.0 - lateral_offsets_y,
straightened_depth,
)
)
pipeline_input.annotation_points = straightened_annotation_points

self.update_progress(0.5)

# Calculate the slice rects for each t value
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