def rename_reshape_pdt2_scans(quar_dir, is_whicap_V1=False, is_whicap_V2=False , is_whicap_V3=False):
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if is_whicap_V2:
for path in nifti_paths:
if os.path.basename(path).startswith('x'):
os.unlink(path)
continue
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if len(nifti_paths) == 1:
shape = getshape(nifti_paths[0])
if shape[3] != 2:
raise Bad_Nifti_Error(path, "DWI Nifti has {} timepoints but should have 2".format(shape[3]))
split = fslsplit()
split.split(nifti_paths[0], os.path.join(quar_dir, 'pdt2sp_'))
splits1 = [os.path.join(quar_dir, "pdt2sp_{0:04d}.nii.gz".format(x)) for x in range(0, 30)]
os.unlink(nifti_paths[0])
return
elif len(nifti_paths) == 3:
sizes = [(x, os.stat(x).st_size) for x in nifti_paths]
sizes.sort(key=lambda x :x[1])
os.unlink(sizes[2][0])
elif len(nifti_paths) == 2:
return
else:
raise Wrong_Number_Of_Files_Error(quar_dir, "Wrong number of DWI files left after pruning stage, expected 1, got {}".format(len(nifti_paths)))
def rename_reshape_asl_scans(quar_dir, is_whicap_V2=False):
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if len(nifti_paths) == 2:
if is_whicap_V2:
return
else:
raise Wrong_Number_Of_Files_Error(
series_folder.path,
"Wrong number of ASL files to reshape and not whicap, expected 1, got {}"
.format(len(nifti_paths)))
elif len(nifti_paths) == 1:
if is_whicap_V2:
shape = getshape(nifti_paths[0])
if shape[3] > 60:
raise Bad_Nifti_Error(
quar_dir,
"nifti has {} timepoints, expected 60".format(shape[3]))
if shape[2] == 15:
reshapeASL(nifti_paths[0], z_voxel_size_multiplier=0.5)
os.unlink(nifti_paths[0])
else:
split = fslsplit()
merge = fslmerge()
split.split(nifti_paths[0], os.path.join(quar_dir, 'aslsp_'))
splits1 = [
os.path.join(quar_dir, "aslsp_{0:04d}.nii.gz".format(x))
for x in range(0, 30)
]
splits2 = [
os.path.join(quar_dir, "aslsp_{0:04d}.nii.gz".format(x))
for x in range(30, 60)
]
merge.merge(os.path.join(quar_dir, 'ASLOne.nii.gz'), splits1)
merge.merge(os.path.join(quar_dir, 'ASLTwo.nii.gz'), splits2)
[os.unlink(file) for file in splits1]
[os.unlink(file) for file in splits2]
os.unlink(nifti_paths[0])
else:
reshapeASL(nifti_paths[0], z_voxel_size_multiplier=1)
os.unlink(nifti_paths[0])
else:
raise Wrong_Number_Of_Files_Error(
quar_dir,
"dcm2nii produced {} nifti paths, expected 1 or 2".format(
len(nifti_paths)))
def rename_reshape_pdt2_scans(quar_dir,
is_whicap_V1=False,
is_whicap_V2=False,
is_whicap_V3=False):
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if is_whicap_V2:
for path in nifti_paths:
if os.path.basename(path).startswith('x'):
os.unlink(path)
continue
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if len(nifti_paths) == 1:
shape = getshape(nifti_paths[0])
if shape[3] != 2:
raise Bad_Nifti_Error(
path,
"DWI Nifti has {} timepoints but should have 2".format(
shape[3]))
split = fslsplit()
split.split(nifti_paths[0], os.path.join(quar_dir, 'pdt2sp_'))
splits1 = [
os.path.join(quar_dir, "pdt2sp_{0:04d}.nii.gz".format(x))
for x in range(0, 30)
]
os.unlink(nifti_paths[0])
return
elif len(nifti_paths) == 3:
sizes = [(x, os.stat(x).st_size) for x in nifti_paths]
sizes.sort(key=lambda x: x[1])
os.unlink(sizes[2][0])
elif len(nifti_paths) == 2:
return
else:
raise Wrong_Number_Of_Files_Error(
quar_dir,
"Wrong number of DWI files left after pruning stage, expected 1, got {}"
.format(len(nifti_paths)))
def rename_reshape_asl_scans(quar_dir, is_whicap_V2=False):
files = os.listdir(quar_dir)
nifti_paths = [os.path.join(quar_dir, x) for x in files if is_nifti(x)]
if len(nifti_paths) == 2:
if is_whicap_V2:
return
else:
raise Wrong_Number_Of_Files_Error(
series_folder.path,
"Wrong number of ASL files to reshape and not whicap, expected 1, got {}".format(len(nifti_paths)),
)
elif len(nifti_paths) == 1:
if is_whicap_V2:
shape = getshape(nifti_paths[0])
if shape[3] > 60:
raise Bad_Nifti_Error(quar_dir, "nifti has {} timepoints, expected 60".format(shape[3]))
if shape[2] == 15:
reshapeASL(nifti_paths[0], z_voxel_size_multiplier=0.5)
os.unlink(nifti_paths[0])
else:
split = fslsplit()
merge = fslmerge()
split.split(nifti_paths[0], os.path.join(quar_dir, "aslsp_"))
splits1 = [os.path.join(quar_dir, "aslsp_{0:04d}.nii.gz".format(x)) for x in range(0, 30)]
splits2 = [os.path.join(quar_dir, "aslsp_{0:04d}.nii.gz".format(x)) for x in range(30, 60)]
merge.merge(os.path.join(quar_dir, "ASLOne.nii.gz"), splits1)
merge.merge(os.path.join(quar_dir, "ASLTwo.nii.gz"), splits2)
[os.unlink(file) for file in splits1]
[os.unlink(file) for file in splits2]
os.unlink(nifti_paths[0])
else:
reshapeASL(nifti_paths[0], z_voxel_size_multiplier=1)
os.unlink(nifti_paths[0])
else:
raise Wrong_Number_Of_Files_Error(
quar_dir, "dcm2nii produced {} nifti paths, expected 1 or 2".format(len(nifti_paths))
)
