def subj_data_from_dicoms(ctx, crumb_path, arg_name, verbose=False):
""" Print a list of folder_name -> NUK id. The NUK ID is calculated from
the first DICOM file found in the end of the `dicom_path`.
Parameters
----------
crumb_path: str
Path with Crumbs to the DICOM files, e.g.,
/home/hansel/data/{subj_id}/{session}/{acq}/{dcm_file}
arg_name: str
Name of the argument in `dicom_path` of the subj_id
Returns
-------
subj_data: dict of subj records
A dict with records of the information extracted from the DICOM files
as well as the calculated NUK Pseudonym.
"""
if verbose:
verbose_switch(verbose)
crumb = Crumb(os.path.expanduser(os.path.abspath(crumb_path)), ignore_list=['.*'])
if not crumb.has_crumbs():
raise ValueError('Expected a path with crumb arguments, e.g., '
'"/home/hansel/data/{group}/{sid}/{session}"')
subj_nuks = []
for path in crumb.ls(arg_name):
log.info('Reading DICOMs in {}.'.format(path))
subj_path = path.split()[0]
subj = _read_dcm_until_valid(subj_path)
if subj is None:
log.info('Could not find a valid DICOM in {}.'.format(subj_path))
else:
subj_nuks.append(subj)
return subj_nuks
def _get_plot_file_pairs(
background: hansel.Crumb,
foreground: hansel.Crumb) -> Iterable[Tuple[str, Union[str, None]]]:
if background is None and foreground is not None:
background = foreground
if not foreground:
return ((bg, None) for bg in background.ls(make_crumbs=False))
if not background.has_crumbs() and not foreground.has_crumbs():
return [(background.ls(make_crumbs=False)[0],
foreground.ls(make_crumbs=False)[0])]
if foreground.has_crumbs() and background.has_crumbs():
background_args = tuple(background.open_args())
foreground_args = tuple(foreground.open_args())
if background_args != foreground_args:
raise click.BadParameter(
'Make sure that background and foreground have the same crumb arguments. '
'Got {}, and {}.'.format(background_args, foreground_args))
try:
intersect_values = hansel.intersection(background, foreground)
except KeyError as ke:
raise click.BadParameter(
'Make sure that background and foreground have the same crumb arguments. '
'Got {}, and {}.'.format(background_args,
foreground_args)) from ke
else:
return ((background.build_paths(crumb_args, make_crumbs=False)[0],
foreground.build_paths(crumb_args, make_crumbs=False)[0])
for crumb_args in intersect_values)
bg_files = []
fg_files = []
if background.has_crumbs():
bg_files = list(background.ls(make_crumbs=False))
fg_files = [foreground.ls(make_crumbs=False)[0]] * len(bg_files)
if foreground.has_crumbs():
fg_files = list(foreground.ls(make_crumbs=False))
bg_files = [background.ls(make_crumbs=False)[0]] * len(fg_files)
return zip(bg_files, fg_files)
def dcm2nii(ctx, input_crumb_path, output_dir, regex='fnmatch', ncpus=3):
""" Convert all DICOM files within `input_crumb_path` into NifTI in `output_folder`.
Will copy only the NifTI files reoriented by MRICron's dcm2nii command.
Will rename the NifTI files that are matched with recognized modalities to the short
modality name from config.ACQ_PATTERNS.
Parameters
----------
input_dir: str
A crumb path str indicating the whole path until the DICOM files.
Example: '/home/hansel/data/{group}/{subj_id}/{session_id}/{acquisition}/{dcm_file}
The crumb argument just before the last one will be used as folder container reference
for the DICOM series.
output_dir: str
The root folder path where to save the tree of nifti files.
Example: '/home/hansel/nifti'
This function will create the same tree as the crumbs in input_crumb_path, hence
for the example above the output would have the following structure:
'/home/hansel/nifti/{group}/{subj_id}/{session_id}/{nifti_file}'
Where {nifti_file} will take the name from the {acquisition} or from the
patterns in ACQ_PATTERNS in `config.py` file.
regex: str
The regular expression syntax you may want to set in the Crumbs.
See hansel.Crumb documentation for this.
ncpus: int
this says the number of processes that will be launched for dcm2nii in parallel.
"""
from boyle.dicom.convert import convert_dcm2nii
input_dir = os.path.expanduser(input_crumb_path)
output_dir = os.path.expanduser(output_dir)
if not os.path.exists(output_dir):
log.info('Creating output folder {}.'.format(output_dir))
os.makedirs(output_dir)
else:
log.info('Output folder {} already exists, this will overwrite/merge '
'whatever is inside.'.format(output_dir))
input_dir = Crumb(input_dir, regex=regex, ignore_list=['.*'])
if not input_dir.has_crumbs():
raise ValueError(
'I am almost sure that this cannot work if you do not '
'use crumb arguments in the input path, got {}.'.format(input_dir))
acq_folder_arg, last_in_arg = tuple(input_dir.all_args())[-2:]
out_arg_names = [
'{' + arg + '}' for arg in tuple(input_dir.all_args())[:-1]
]
output_dir = Crumb(os.path.join(output_dir, *out_arg_names),
regex=regex,
ignore_list=['.*'])
src_dst = []
acquisitions = input_dir.ls(acq_folder_arg, make_crumbs=True)
for acq in acquisitions:
out_args = acq.arg_values.copy()
acq_out = output_dir.replace(**out_args)
out_dir = os.path.dirname(acq_out.path)
out_file = os.path.basename(acq_out.path) + '.nii.gz'
os.makedirs(out_dir, exist_ok=True)
src_dst.append((acq.split()[0], out_dir, out_file))
if ncpus > 1:
import multiprocessing as mp
pool = mp.Pool(processes=ncpus)
results = [
pool.apply_async(convert_dcm2nii, args=(dr, ss, dst))
for dr, ss, dst in src_dst
]
_ = [p.get() for p in results]
else:
_ = [convert_dcm2nii(path, sess, dst) for path, sess, dst in src_dst]
def rename_to_nukid(crumb_path, arg_name, subj_data, verbose_only=False):
""" Rename the folders at the `arg_name` level using `subj_data` records.
Will rename from subj_data['DCM Folder'] to subj_data['NUK Pseudonym'].
Parameters
----------
crumb_path: str
Path with Crumbs to the DICOM files, e.g.,
/home/hansel/data/{subj_id}
arg_name: str
Name of the argument in `dicom_path` of the subject identification.
These names should be the same as the ones in 'DCM Folder' value.
outfile: str
verbose_only: bool
Returns
-------
src_dsts: list of 2-tuples of str
"""
def rename_many(src_dsts, verbose_only=False):
""" For each 2-tuple in src_dsts of file/folder paths will rename the first element to the second.
Parameters
----------
src_dsts : list of 2-tuple
verbose_only: bool
Will not perform the operation will only print them.
"""
for (src, dst) in src_dsts:
if not os.path.exists(src):
raise IOError('Could not find source file {}.'.format(src))
if os.path.exists(dst):
if src == dst:
continue
else:
raise IOError('Destination path {} already exists.'.format(dst))
log.info('mv {} -> {}'.format(src, dst))
if not verbose_only:
os.rename(src, dst)
if isinstance(subj_data, pd.DataFrame):
subjs = subj_data.to_records()
else:
subjs = subj_data
if not Crumb.has_crumbs(Crumb(crumb_path)):
raise ValueError('Expected a path with crumb arguments, e.g., '
'"/home/hansel/data/{group}/{sid}/{session}"')
crumb = Crumb(os.path.expanduser(os.path.abspath(crumb_path)), ignore_list=['.*'])
src_dsts = []
for subj in subjs:
src_crs = crumb.replace(**{arg_name: subj['DCM Folder']}).unfold()
for src_cr in src_crs:
dst_args = src_cr.arg_values.copy()
dst_args[arg_name] = subj['nukid']
dst_cr = crumb.replace(**dst_args)
if not os.path.exists(src_cr.path):
raise IOError('Could not find folder {} for subject {}.'.format(src_cr, subj))
if Crumb.has_crumbs(dst_cr.path):
raise KeyError('The destination path should be fully specified, got {}.'.format(dst_cr))
src_dsts.append((src_cr.path, dst_cr.path))
rename_many(src_dsts=src_dsts, verbose_only=verbose_only)
return src_dsts
