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[FIX] Deprecation exceptions with nibabel and pandas #175

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[FIX] Deprecation exceptions with nibabel and pandas #175

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ee2c6c4
[FIX] Update references to nibabel's getArraysFromIntent
DESm1th Nov 3, 2022
2caa837
[FIX] Set based indexing is deprecated by pandas
DESm1th Nov 3, 2022
997474f
[FIX] Update deprecated references to nibabel's .get_header() and .ge…
DESm1th Nov 4, 2022
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2 changes: 1 addition & 1 deletion ciftify/bin/ciftify_PINT_vertices.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,7 +404,7 @@ def pint_move_vertex(df, idx, vertex_incol, vertex_outcol,

# loop through each time series, calculating r
if pcorr:
o_networks = set(netmeants.columns.tolist()) - {network}
o_networks = list(set(netmeants.columns.tolist()) - {network})
seed_corrs[idx_mask] = mass_partial_corr(meants,
func_data[idx_mask, :],
netmeants.loc[:,o_networks].values)
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4 changes: 2 additions & 2 deletions ciftify/bin/ciftify_peaktable.py
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Expand Up @@ -232,7 +232,7 @@ def load_hemisphere_labels(filename, wb_structure, map_number = 1):

# loads label table as dict and data as numpy array
gifti_img = nibabel.gifti.giftiio.read(labels_gii)
atlas_data = gifti_img.getArraysFromIntent('NIFTI_INTENT_LABEL')[map_number - 1].data
atlas_data = gifti_img.get_arrays_from_intent('NIFTI_INTENT_LABEL')[map_number - 1].data

atlas_dict = gifti_img.get_labeltable().get_labels_as_dict()
atlas_df = pd.DataFrame.from_dict(atlas_dict, orient = "index")
Expand Down Expand Up @@ -321,7 +321,7 @@ def build_hemi_results_df(surf_settings, atlas_settings,
clust_array = load_hemisphere_data(clusters_dscalar, surf_settings['wb_structure'])

## load the coordinates
coords = nibabel.gifti.giftiio.read(surf_settings['surface']).getArraysFromIntent('NIFTI_INTENT_POINTSET')[0].data
coords = nibabel.gifti.giftiio.read(surf_settings['surface']).get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0].data
surf_va = ciftify.niio.load_gii_data(surf_settings['vertex_areas'])

## put all this info together into one pandas dataframe
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12 changes: 6 additions & 6 deletions ciftify/niio.py
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Expand Up @@ -97,8 +97,8 @@ def load_nifti(filename):
logger.error("Cannot read {}".format(filename))
sys.exit(1)

affine = nifti.get_affine()
header = nifti.get_header()
affine = nifti.affine
header = nifti.header
dims = list(nifti.shape)

# if smaller than 3D
Expand Down Expand Up @@ -183,15 +183,15 @@ def load_gii_data(filename, intent='NIFTI_INTENT_NORMAL'):

## read all arrays and concatenate in numpy
try:
array1 = surf_dist_nib.getArraysFromIntent(intent)[0]
array1 = surf_dist_nib.get_arrays_from_intent(intent)[0]
except IndexError:
logger.error("Invalid intent: {}".format(intent))
sys.exit(1)

data = array1.data
if numDA >= 1:
for DA in range(1,numDA):
data = np.vstack((data, surf_dist_nib.getArraysFromIntent(intent)[
data = np.vstack((data, surf_dist_nib.get_arrays_from_intent(intent)[
DA].data))

## transpose the data so that it is vertices by TR
Expand Down Expand Up @@ -267,7 +267,7 @@ def get_surf_distances(surf, orig_vertex, radius_search=100,

def load_surf_coords(surf):
'''load the coordinates from a surface file'''
coords = nibabel.gifti.giftiio.read(surf).getArraysFromIntent('NIFTI_INTENT_POINTSET')[0].data
coords = nibabel.gifti.giftiio.read(surf).get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0].data
return coords


Expand All @@ -282,7 +282,7 @@ def load_hemisphere_labels(filename, wb_structure, map_number = 1):

# loads label table as dict and data as numpy array
gifti_img = nibabel.gifti.giftiio.read(labels_gii)
atlas_data = gifti_img.getArraysFromIntent('NIFTI_INTENT_LABEL')[map_number - 1].data
atlas_data = gifti_img.get_arrays_from_intent('NIFTI_INTENT_LABEL')[map_number - 1].data

atlas_dict = gifti_img.get_labeltable().get_labels_as_dict()

Expand Down