def consistencyCheck(ref_csv,
outputBshellFile=None,
outPutResolutionFile=None):
try:
ref_imgs, _ = read_imgs_masks(ref_csv)
except:
ref_imgs = read_imgs(ref_csv)
if isfile(outputBshellFile) and isfile(outPutResolutionFile):
ref_bvals = read_bvals(outputBshellFile)
ref_res = np.load(outPutResolutionFile)
else:
ref_bshell_img = ref_imgs[0]
print(f'Using {ref_bshell_img} to determine b-shells')
inPrefix = abspath(ref_bshell_img).split('.nii')[0]
ref_bvals = findBShells(inPrefix + '.bval', outputBshellFile)
ref_res = load(ref_bshell_img).header['pixdim'][1:4]
np.save(outPutResolutionFile, ref_res)
print('b-shells are', ref_bvals)
print('\nSite', ref_csv, '\n')
print('Checking consistency of b-shells among subjects')
check_bshells(ref_imgs, ref_bvals)
print('spatial resolution is', ref_res)
print('Checking consistency of spatial resolution among subjects')
check_resolution(ref_imgs, ref_res)
def joinBshells(imgPath, ref_bvals_file=None, ref_bvals=None, sep_prefix=None):
if ref_bvals_file:
print('Reading reference b-shell file ...')
ref_bvals = read_bvals(ref_bvals_file)
print('Joining b-shells for', imgPath)
imgPath = local.path(imgPath)
img = load(imgPath._path)
dim = img.header['dim'][1:5]
inPrefix = abspath(imgPath).split('.nii')[0]
directory = dirname(inPrefix)
prefix = basename(inPrefix)
bvalFile = inPrefix + '.bval'
bvecFile = inPrefix + '.bvec'
if sep_prefix:
harmPrefix = pjoin(directory, sep_prefix + prefix)
else:
harmPrefix = inPrefix
if not isfile(harmPrefix + '.bval'):
copyfile(bvalFile, harmPrefix + '.bval')
if not isfile(harmPrefix + '.bvec'):
copyfile(bvecFile, harmPrefix + '.bvec')
bvals = np.array(read_bvals(inPrefix + '.bval'))
joinedDwi = np.zeros((dim[0], dim[1], dim[2], dim[3]), dtype='float32')
for bval in ref_bvals:
# ind= np.where(bval==bvals)[0]
ind = np.where(abs(bval - bvals) <= BSHELL_MIN_DIST)[0]
if bval == 0.:
b0Img = load(inPrefix + '_b0.nii.gz')
b0 = b0Img.get_data()
for i in ind:
joinedDwi[:, :, :, i] = b0
else:
b0_bshell = load(harmPrefix + f'_b{int(bval)}.nii.gz').get_data()
joinedDwi[:, :, :, ind] = b0_bshell[:, :, :, 1:]
if not isfile(harmPrefix + '.nii.gz'):
save_nifti(harmPrefix + '.nii.gz', joinedDwi, b0Img.affine,
b0Img.header)
else:
print(harmPrefix + '.nii.gz', 'already exists, not overwritten.')
def separateBshells(imgPath, ref_bvals_file=None, ref_bvals=None):
if ref_bvals_file:
print('Reading reference b-shell file ...')
ref_bvals = read_bvals(ref_bvals_file)
print('Separating b-shells for', imgPath)
imgPath = local.path(imgPath)
img = load(imgPath._path)
dwi = img.get_data()
inPrefix = abspath(imgPath).split('.nii')[0]
bvals = np.array(read_bvals(inPrefix + '.bval'))
bvecs = np.array(read_bvecs(inPrefix + '.bvec'))
for bval in ref_bvals:
# ind= np.where(bval==bvals)[0]
ind = np.where(abs(bval - bvals) <= BSHELL_MIN_DIST)[0]
N_b = len(ind)
bPrefix = inPrefix + f'_b{int(bval)}'
if bval == 0.:
b0 = find_b0(dwi, ind)
if isfile(bPrefix + '.nii.gz'):
continue
if bval == 0.:
save_nifti(bPrefix + '.nii.gz', b0, img.affine, img.header)
else:
b0_bshell = np.zeros(
(dwi.shape[0], dwi.shape[1], dwi.shape[2], N_b + 1),
dtype='float32')
b0_bshell[:, :, :, 0] = b0
b0_bshell[:, :, :, 1:] = dwi[:, :, :, ind]
b0_bvals = [0.] + [bval] * N_b
b0_bvecs = np.zeros((N_b + 1, 3), dtype='float32')
b0_bvecs[1:, ] = bvecs[ind, :]
save_nifti(bPrefix + '.nii.gz', b0_bshell, img.affine, img.header)
write_bvals(bPrefix + '.bval', b0_bvals)
write_bvecs(bPrefix + '.bvec', b0_bvecs)
def scan_cases(path):
result = []
# 项目种类
project_kinds = util.safely_list_dir(path)
for project_kind in project_kinds:
projects = util.safely_list_dir(path, project_kind)
# 遍历项目
for project in projects:
versions = util.safely_list_dir(path, project_kind, project)
# 遍历版本
for version in versions:
pycharm_projects = util.safely_list_dir(
path, project_kind, project, version)
# 遍历pycharm工程
for pycharm_project in pycharm_projects:
case_dir = util.join(path, project_kind, project, version,
pycharm_project, 'src', 'cases')
modules = util.safely_list_dir(case_dir)
for m in modules:
# 文件作为模块
if util.isfile(util.join(case_dir, m)):
if util.suffix(m) == '.py':
result.extend(
parsePy2Dict(util.join(case_dir, m),
util.join(path, project),
'cases', '', util.filename(m),
[], None, version,
pycharm_project,
project_kind))
# 目录作为一级模块
else:
# 在目录下的__init__.py里获取模块描述
module_desc = ''
if util.isfile(
util.join(case_dir, m, '__init__.py')):
f = open(util.join(case_dir, m, '__init__.py'))
p = ast.parse(f.read()).body
module_desc = p[0].value.s if p else ''
f.close()
for root, dirs, files in util.walk(
util.join(case_dir, m)):
for file in files:
if util.suffix(file) == '.py':
modules = util.relative(
util.join(root, file),
case_dir)[0:-1]
package = util.relative(
util.join(root, file),
util.dirname(case_dir))[0:-1]
package = '.'.join(package)
result.extend(
parsePy2Dict(
util.join(root, file),
util.join(path,
project), package, m,
util.filename(file), modules,
module_desc, version,
pycharm_project, project_kind))
return result
print('\nSite', ref_csv, '\n')
print('Checking consistency of b-shells among subjects')
check_bshells(ref_imgs, ref_bvals)
print('spatial resolution is', ref_res)
print('Checking consistency of spatial resolution among subjects')
check_resolution(ref_imgs, ref_res)
if __name__ == '__main__':
if len(sys.argv) == 1 or sys.argv[1] == '-h' or sys.argv[1] == '--help':
print(
'''Check consistency of b-shells and spatial resolution among subjects
Usage:
consistencyCheck list.csv/txt ref_bshell_bvalues.txt ref_res_file.npy
Provide a csv/txt file with first column for dwi and 2nd column for mask: dwi1,mask1\\ndwi2,mask2\\n...
or just one column for dwi1\\ndwi2\\n...
In addition, provide ref_bshell_bvalues and ref_res_file.''')
exit()
ref_csv = abspath(sys.argv[1])
outputBshellFile = abspath(sys.argv[2])
outPutResolutionFile = abspath(sys.argv[3])
if isfile(ref_csv):
consistencyCheck(ref_csv, outputBshellFile, outPutResolutionFile)
else:
raise FileNotFoundError(f'{ref_csv} does not exists.')
def main(self):
if self.N_proc == '-1':
self.N_proc = N_CPU
# check directory existence
check_dir(self.templatePath, self.force)
## check consistency of b-shells and spatial resolution
ref_bvals_file = pjoin(self.templatePath, 'ref_bshell_bvalues.txt')
ref_res_file = pjoin(self.templatePath, 'ref_res_file.npy')
if self.ref_csv:
if isfile(ref_bvals_file) and isfile(ref_res_file):
remove(ref_bvals_file)
remove(ref_res_file)
consistencyCheck(self.ref_csv, ref_bvals_file, ref_res_file)
if self.target_csv:
consistencyCheck(self.target_csv, ref_bvals_file, ref_res_file)
## separate b-shells
if self.ref_csv:
refListOutPrefix = separateShellsWrapper(self.ref_csv,
ref_bvals_file,
self.N_proc)
if self.target_csv:
tarListOutPrefix = separateShellsWrapper(self.target_csv,
ref_bvals_file,
self.N_proc)
## define variables for template creation and data harmonization
# variables common to all ref_bvals
pipeline_vars = [
'--tar_name',
self.target,
'--nshm',
self.N_shm,
'--nproc',
self.N_proc,
'--template',
self.templatePath,
]
if self.reference:
pipeline_vars.append(f'--ref_name {self.reference}')
if self.N_zero:
pipeline_vars.append(f'--nzero {self.N_zero}')
if self.bvalMap:
pipeline_vars.append(f'--bvalMap {self.bvalMap}')
if self.resample:
pipeline_vars.append(f'--resample {self.resample}')
if self.denoise:
pipeline_vars.append('--denoise')
if self.travelHeads:
pipeline_vars.append('--travelHeads')
if self.force:
pipeline_vars.append('--force')
if self.debug:
pipeline_vars.append('--debug')
if self.verbose:
pipeline_vars.append('--verbose')
# the b-shell bvalues are sorted in descending order because we want to perform registration with highest bval
ref_bvals = read_bvals(ref_bvals_file)[::-1]
for bval in ref_bvals[:-1]: # pass the last bval which is 0.
if self.create and not self.process:
print('## template creation ##')
check_call((' ').join([
pjoin(SCRIPTDIR, 'harmonization.py'), '--tar_list',
tarListOutPrefix + f'_b{int(bval)}.csv', '--bshell_b',
str(int(bval)), '--ref_list', refListOutPrefix +
f'_b{int(bval)}.csv', '--create'
] + pipeline_vars),
shell=True)
elif not self.create and self.process:
print('## data harmonization ##')
check_call((' ').join([
pjoin(SCRIPTDIR, 'harmonization.py'), '--tar_list',
tarListOutPrefix + f'_b{int(bval)}.csv',
f'--ref_list {refListOutPrefix}_b{int(bval)}.csv' if self.
ref_csv else '', '--bshell_b',
str(int(bval)), '--process'
] + pipeline_vars),
shell=True)
elif self.create and self.process:
check_call((' ').join([
pjoin(SCRIPTDIR, 'harmonization.py'), '--tar_list',
tarListOutPrefix + f'_b{int(bval)}.csv', '--bshell_b',
str(int(bval)), '--ref_list', refListOutPrefix +
f'_b{int(bval)}.csv', '--create', '--process'
] + pipeline_vars),
shell=True)
if '--force' in pipeline_vars:
pipeline_vars.remove('--force')
## join harmonized data
if self.process:
joinAllBshells(self.target_csv, ref_bvals_file, 'harmonized_',
self.N_proc)
if self.debug and self.ref_csv:
joinAllBshells(self.ref_csv, ref_bvals_file, 'reconstructed_',
self.N_proc)