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Preserve map shape and dtype when a map is merged #341

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merged 4 commits into from
Apr 21, 2023
Merged

Preserve map shape and dtype when a map is merged #341

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5653bd5
preserve map shape and dtype when a map is merged
AhmetNSimsek Apr 19, 2023
919b4aa
Merge_nifti voxdim is always of int type
AhmetNSimsek Apr 20, 2023
60fe544
chore: remove unnecessary dtype
AhmetNSimsek Apr 20, 2023
3bf2547
Fix map shape and dtpye in neuroglancer._merge_fragments
AhmetNSimsek Apr 21, 2023
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7 changes: 3 additions & 4 deletions siibra/volumes/nifti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,6 @@ def loader(url):
self._img_loaders = {lbl: loader(url) for lbl, url in src.items()}
else:
raise ValueError(f"Invalid source specification for {self.__class__}: {src}")

if not isinstance(src, nib.Nifti1Image):
self._init_url = src

Expand Down Expand Up @@ -95,9 +94,9 @@ def _merge_fragments(self) -> nib.Nifti1Image:
s0 = np.identity(4)
s0[:3, -1] = list(bbox.minpoint.transform(np.linalg.inv(img.affine)))
result_affine = np.dot(img.affine, s0) # adjust global bounding box offset to get global affine
voxdims = np.dot(np.linalg.inv(result_affine), np.r_[bbox.shape, 1])[:3]
result_arr = np.zeros((voxdims + .5).astype('int'))
result = nib.Nifti1Image(dataobj=result_arr, affine=result_affine)
voxdims = np.r_[bbox.transform(result_affine).shape].astype(img.dataobj.dtype)
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result_arr = np.zeros(voxdims, dtype=img.dataobj.dtype)
result = nib.Nifti1Image(dataobj=result_arr, affine=result_affine, dtype=img.dataobj.dtype)
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arr = np.asanyarray(img.dataobj)
Xs, Ys, Zs = np.where(arr != 0)
Expand Down