From cf69721b9284b3255a59ebbbecd5188ac711e539 Mon Sep 17 00:00:00 2001 From: dorfmanrobert Date: Tue, 19 Nov 2024 13:44:19 +0000 Subject: [PATCH 1/3] correct pixdim application in mask to polygon --- darwin/importer/formats/nifti.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/darwin/importer/formats/nifti.py b/darwin/importer/formats/nifti.py index 3d6a32d17..a66a1f461 100644 --- a/darwin/importer/formats/nifti.py +++ b/darwin/importer/formats/nifti.py @@ -376,7 +376,7 @@ def adjust_for_pixdims(x, y, pixdims): else: return {"x": y, "y": x} else: - return {"x": y * pixdims[1], "y": x * pixdims[0]} + return {"x": y * pixdims[0], "y": x * pixdims[1]} _labels, external_paths, _internal_paths = find_contours(mask) if len(external_paths) > 1: From c72bec793731c59230e44ff266fb8ab1a8a4fee8 Mon Sep 17 00:00:00 2001 From: dorfmanrobert Date: Tue, 19 Nov 2024 14:47:38 +0000 Subject: [PATCH 2/3] update process_nifti to allow arbitrary oriented outputs --- darwin/importer/formats/nifti.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/darwin/importer/formats/nifti.py b/darwin/importer/formats/nifti.py index a66a1f461..834dd00f7 100644 --- a/darwin/importer/formats/nifti.py +++ b/darwin/importer/formats/nifti.py @@ -515,12 +515,12 @@ def process_nifti( ornt: Optional[List[List[float]]] = [[0.0, -1.0], [1.0, -1.0], [2.0, -1.0]], ) -> Tuple[np.ndarray, Tuple[float]]: """ - Function that converts a nifti object to the RAS orientation, then converts to the passed ornt orientation. + Converts a nifti object of any orientation to the passed ornt orientation. The default ornt is LPI. Args: input_data: nibabel nifti object. - ornt: (n,2) orientation array. + ornt: (n,2) orientation array. It defines a transformation from RAS. ornt[N,1] is a flip of axis N of the array, where 1 means no flip and -1 means flip. ornt[:,0] is the transpose that needs to be done to the implied array, as in arr.transpose(ornt[:,0]). @@ -529,9 +529,14 @@ def process_nifti( pixdims: tuple of nifti header zoom values. """ img = correct_nifti_header_if_necessary(input_data) - img = nib.funcs.as_closest_canonical(img) - data_array = nib.orientations.apply_orientation(img.get_fdata(), ornt) - pixdims = img.header.get_zooms() + orig_ax_codes = nib.orientations.aff2axcodes(img.affine) + orig_ornt = nib.orientations.axcodes2ornt(orig_ax_codes) + transform = nib.orientations.ornt_transform(orig_ornt, ornt) + reoriented_img = img.as_reoriented(transform) + + data_array = reoriented_img.get_fdata() + pixdims = reoriented_img.header.get_zooms() + return data_array, pixdims From 6d859db750107413b69dc981281533d67b534ac1 Mon Sep 17 00:00:00 2001 From: dorfmanrobert Date: Tue, 19 Nov 2024 15:02:22 +0000 Subject: [PATCH 3/3] update test --- .../no-legacy/BRAINIX_NIFTI_ROI.nii.json | 436 +++++++++--------- 1 file changed, 218 insertions(+), 218 deletions(-) diff --git a/tests/darwin/data/nifti/no-legacy/BRAINIX_NIFTI_ROI.nii.json b/tests/darwin/data/nifti/no-legacy/BRAINIX_NIFTI_ROI.nii.json index 363aadffb..384ff58c6 100644 --- a/tests/darwin/data/nifti/no-legacy/BRAINIX_NIFTI_ROI.nii.json +++ b/tests/darwin/data/nifti/no-legacy/BRAINIX_NIFTI_ROI.nii.json @@ -5,17 +5,17 @@ "name": "BRAINIX_NIFTI_ROI.nii.gz", "path": "/", "source_info": { - 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