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fix(tasks): Update _reduce_slab function to accept reduce_axis parameter for flexibility in reconstruction

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Ross
2026-05-17 22:20:22 +01:00
parent d5e473d692
commit a9946961f1
1 changed files with 6 additions and 6 deletions
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atlas/tasks.py
+6 -6
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@@ -278,13 +278,13 @@ def series_reconstruct_task(
spacing_y = source_axis_spacings[src_y] spacing_y = source_axis_spacings[src_y]
spacing_z = source_axis_spacings[src_z] spacing_z = source_axis_spacings[src_z]
def _reduce_slab(slab): def _reduce_slab(slab, reduce_axis=0):
if recon_thickness_mode == "max": if recon_thickness_mode == "max":
out = np.max(slab, axis=0) out = np.max(slab, axis=reduce_axis)
elif recon_thickness_mode == "min": elif recon_thickness_mode == "min":
out = np.min(slab, axis=0) out = np.min(slab, axis=reduce_axis)
else: else:
out = np.mean(slab, axis=0) out = np.mean(slab, axis=reduce_axis)
if np.issubdtype(volume.dtype, np.integer): if np.issubdtype(volume.dtype, np.integer):
info = np.iinfo(volume.dtype) info = np.iinfo(volume.dtype)
@@ -348,7 +348,7 @@ def series_reconstruct_task(
) )
plane_builders[plane_norm] = { plane_builders[plane_norm] = {
"count": int(len(slab_indices)), "count": int(len(slab_indices)),
"slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, slabs[idx], :]), "slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1),
"pixel_spacing_out": [float(spacing_z), float(spacing_x)], "pixel_spacing_out": [float(spacing_z), float(spacing_x)],
"spacing_between_slices_out": float(plane_spacing), "spacing_between_slices_out": float(plane_spacing),
"slice_thickness_out": float(plane_thickness), "slice_thickness_out": float(plane_thickness),
@@ -363,7 +363,7 @@ def series_reconstruct_task(
) )
plane_builders[plane_norm] = { plane_builders[plane_norm] = {
"count": int(len(slab_indices)), "count": int(len(slab_indices)),
"slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, :, slabs[idx]]), "slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2),
"pixel_spacing_out": [float(spacing_z), float(spacing_y)], "pixel_spacing_out": [float(spacing_z), float(spacing_y)],
"spacing_between_slices_out": float(plane_spacing), "spacing_between_slices_out": float(plane_spacing),
"slice_thickness_out": float(plane_thickness), "slice_thickness_out": float(plane_thickness),