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try to fix recons

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Ross
2026-06-08 11:41:46 +01:00
parent d89df3d0a6
commit e78a69367f
2 changed files with 215 additions and 28 deletions
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atlas/tasks.py
+37 -15
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@@ -336,6 +336,32 @@ def series_reconstruct_task(
src_y = source_for_patient_axis[1]
src_z = source_for_patient_axis[2]
# Build patient-axis basis vectors expressed in source/world space.
# This preserves source world-frame orientation (including obliquity/sign)
# for derived series instead of hardcoding cardinal axes.
patient_x_vec = np.asarray(source_axis_dirs[src_x], dtype=float) * float(sign_for_patient_axis[0])
patient_y_vec = np.asarray(source_axis_dirs[src_y], dtype=float) * float(sign_for_patient_axis[1])
patient_z_vec = np.asarray(source_axis_dirs[src_z], dtype=float) * float(sign_for_patient_axis[2])
def _norm_vec(vec):
nrm = float(np.linalg.norm(vec))
if nrm == 0:
return np.asarray(vec, dtype=float)
return np.asarray(vec, dtype=float) / nrm
patient_x_vec = _norm_vec(patient_x_vec)
patient_y_vec = _norm_vec(patient_y_vec)
patient_z_vec = _norm_vec(patient_z_vec)
def _orientation_pair(col_vec, row_vec, desired_normal):
col = _norm_vec(col_vec)
row = _norm_vec(row_vec)
desired = _norm_vec(desired_normal)
normal = np.cross(col, row)
if float(np.dot(normal, desired)) < 0:
row = -row
return [float(col[0]), float(col[1]), float(col[2]), float(row[0]), float(row[1]), float(row[2])]
spacing_x = source_axis_spacings[src_x]
spacing_y = source_axis_spacings[src_y]
spacing_z = source_axis_spacings[src_z]
@@ -350,7 +376,7 @@ def series_reconstruct_task(
vol_zyx = np.flip(vol_zyx, axis=2)
def source_indices_from_patient_zyx(iz, iy, ix):
src_indices = [0, 0, 0]
src_indices = [0.0, 0.0, 0.0]
z_index = float(iz)
y_index = float(iy)
@@ -378,10 +404,6 @@ def series_reconstruct_task(
)
return [float(pos[0]), float(pos[1]), float(pos[2])]
spacing_x = source_axis_spacings[src_x]
spacing_y = source_axis_spacings[src_y]
spacing_z = source_axis_spacings[src_z]
def _reduce_slab(slab, reduce_axis=0):
if recon_thickness_mode == "max":
out = np.max(slab, axis=reduce_axis)
@@ -440,8 +462,8 @@ def series_reconstruct_task(
"pixel_spacing_out": [float(spacing_y), float(spacing_x)],
"spacing_between_slices_out": float(plane_spacing),
"slice_thickness_out": float(plane_thickness),
"image_orientation_out": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0],
"plane_normal_out": [0.0, 0.0, 1.0],
"image_orientation_out": _orientation_pair(patient_x_vec, patient_y_vec, patient_z_vec),
"plane_normal_out": [float(patient_z_vec[0]), float(patient_z_vec[1]), float(patient_z_vec[2])],
"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(centers[idx], 0.0, 0.0),
}
elif plane_norm == "coronal":
@@ -452,13 +474,13 @@ def series_reconstruct_task(
)
plane_builders[plane_norm] = {
"count": int(len(slab_indices)),
"slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1)),
"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)],
"spacing_between_slices_out": float(plane_spacing),
"slice_thickness_out": float(plane_thickness),
"image_orientation_out": [1.0, 0.0, 0.0, 0.0, 0.0, -1.0],
"plane_normal_out": [0.0, 1.0, 0.0],
"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), centers[idx], 0.0),
"image_orientation_out": _orientation_pair(patient_x_vec, patient_z_vec, patient_y_vec),
"plane_normal_out": [float(patient_y_vec[0]), float(patient_y_vec[1]), float(patient_y_vec[2])],
"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, centers[idx], 0.0),
}
elif plane_norm == "sagittal":
plane_spacing = float(requested_slice_spacing) if requested_slice_spacing is not None else float(spacing_x)
@@ -468,13 +490,13 @@ def series_reconstruct_task(
)
plane_builders[plane_norm] = {
"count": int(len(slab_indices)),
"slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2)),
"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)],
"spacing_between_slices_out": float(plane_spacing),
"slice_thickness_out": float(plane_thickness),
"image_orientation_out": [0.0, 1.0, 0.0, 0.0, 0.0, -1.0],
"plane_normal_out": [1.0, 0.0, 0.0],
"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), 0.0, centers[idx]),
"image_orientation_out": _orientation_pair(patient_y_vec, patient_z_vec, patient_x_vec),
"plane_normal_out": [float(patient_x_vec[0]), float(patient_x_vec[1]), float(patient_x_vec[2])],
"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, 0.0, centers[idx]),
}
if not plane_builders: