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Return 3 vars from load_nifti instead of tuple #12

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Return 3 vars from load_nifti instead of tuple #12

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7e41225
Return 3 vars from load_nifti instead of tuple
FelixLiu-SF Jul 22, 2021
800ffd7
Fix argument fa_file and add nifti loading for FA
FelixLiu-SF Jul 29, 2021
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20 changes: 13 additions & 7 deletions run_dipy_gpu.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,10 +85,10 @@
help="default: 0.5")
args = parser.parse_args()

img = load_nifti(args.nifti_file, return_img=True)
img_data, img_affine, img = load_nifti(args.nifti_file, return_img=True)
voxel_order = "".join(aff2axcodes(img.affine))
gtab = gradient_table(args.bvals, args.bvecs)
mask = load_nifti(args.mask_nifti, return_img=True)
mask_data, mask_affine, mask = load_nifti(args.mask_nifti, return_img=True)
data = img.get_fdata()

# resample mask if necessary
Expand All @@ -103,8 +103,14 @@
mask = mask.get_fdata()

# load or compute and save FA file
if (args.fa_numpy is not None) and os.path.isfile(args.fa_numpy):
FA = np.load(args.fa_numpy, allow_pickle=True)
if (args.fa_file is not None) and os.path.isfile(args.fa_file):
_, fa_extension = os.path.splitext(filename)
if fa_extension in ['.npy', '.npz', '.pkl']:
FA = np.load(args.fa_file, allow_pickle=True)
elif fa_extension in ['.nii','.gz']:
FA, FA_affine = load_nifti(args.fa_file)
else:
raise TypeError('FA filename is not one of the supported format (.npy, .npz, .pkl, .nii, .gz).')
else:
# Fit
tenmodel = dti.TensorModel(gtab, fit_method='WLS')
Expand All @@ -114,15 +120,15 @@
FA = tenfit.fa
FA[np.isnan(FA)] = 0

if args.fa_numpy is not None:
np.save(args.fa_numpy, FA)
if args.fa_file is not None:
np.save(args.fa_file, FA)

# Setup tissue_classifier args
metric_map = np.asarray(FA, 'float64')

# resample roi if necessary
if args.roi_nifti is not None:
roi_data, roi = load_nifti(args.roi_nifti,
roi_data, roi_affine, roi = load_nifti(args.roi_nifti,
return_img=True,
as_ndarray=True)
else:
Expand Down