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[WIP] Update deprecated Nibabel calls. #60

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[WIP] Update deprecated Nibabel calls. #60

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16bc2e1
switch to get_fdata for latest versions of nibabel
rwblair Aug 11, 2023
4bc2d3f
fix get_header call, deprecated in nibabel
rwblair Aug 11, 2023
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6 changes: 3 additions & 3 deletions nidmresults/objects/contrast.py
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Original file line number Diff line number Diff line change
Expand Up @@ -254,10 +254,10 @@ def export(self, nidm_version, export_dir):
# Create Contrast Explained Mean Square Map as fstat<num>.nii.gz
# multiplied by sigmasquareds.nii.gz and save it in export_dir
fstat_img = nib.load(self.stat_file)
fstat = fstat_img.get_data()
fstat = fstat_img.get_fdata()

sigma_sq_img = nib.load(self.sigma_sq_file)
sigma_sq = sigma_sq_img.get_data()
sigma_sq = sigma_sq_img.get_fdata()

expl_mean_sq = nib.Nifti1Image(
fstat*sigma_sq, fstat_img.get_qform())
Expand Down Expand Up @@ -320,7 +320,7 @@ def __init__(self, contrast_num, filepath, is_variance, coord_space,

# Create standard error map from contrast variance map
var_cope_img = nib.load(self.file)
contrast_variance = var_cope_img.get_data()
contrast_variance = var_cope_img.get_fdata()

standard_error_img = nib.Nifti1Image(np.sqrt(contrast_variance),
var_cope_img.get_qform())
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4 changes: 2 additions & 2 deletions nidmresults/objects/generic.py
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Expand Up @@ -158,7 +158,7 @@ def __init__(self, coordinate_system, nifti_file=None, vox_to_world=None,
(units is None) and \
(nifti_file is not None):
thresImg = nib.load(nifti_file)
thresImgHdr = thresImg.get_header()
thresImgHdr = thresImg.header

numdim = len(thresImg.shape)
dimensions = np.asarray(thresImg.shape)
Expand Down Expand Up @@ -298,7 +298,7 @@ def is_nifti(self):

def get_sha_sum(self, nifti_file):
nifti_img = nib.load(nifti_file)
data = nifti_img.get_data()
data = nifti_img.get_fdata()
# Fix needed as in https://github.com/pymc-devs/pymc/issues/327
if not data.flags["C_CONTIGUOUS"]:
data = np.ascontiguousarray(data)
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4 changes: 2 additions & 2 deletions nidmresults/objects/modelfitting.py
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Expand Up @@ -964,11 +964,11 @@ def export(self, nidm_version, export_dir):
if self.masked_median is None:
grand_mean_file = self.file.path
grand_mean_img = nib.load(grand_mean_file)
grand_mean_data = grand_mean_img.get_data()
grand_mean_data = grand_mean_img.get_fdata()
grand_mean_data = np.ndarray.flatten(grand_mean_data)

mask_img = nib.load(self.mask_file)
mask_data = mask_img.get_data()
mask_data = mask_img.get_fdata()
mask_data = np.ndarray.flatten(mask_data)

grand_mean_data_in_mask = grand_mean_data[mask_data > 0]
Expand Down