def is_sourcefile(file: Path) -> str:
"""
This plugin function supports assessing whether the file is a valid sourcefile
:param file: The file that is assessed
:return: The valid dataformat of the file for this plugin
"""
if bids.is_dicomfile(file):
return 'DICOM'
if bids.is_parfile(file):
return 'PAR'
return ''
def bidstrainer(bidsfolder: str, samplefolder: str, bidsmapfile: str,
pattern: str) -> None:
"""
Main function uses all samples in the samplefolder as training / example data to generate a
maximally filled-in bidsmap_sample.yaml file.
:param bidsfolder: The name of the BIDS root folder
:param samplefolder: The name of the root directory of the tree containing the sample files / training data. If left empty, bidsfolder/code/bidscoin/samples is used or such an empty directory tree is created
:param bidsmapfile: The name of the bidsmap YAML-file
:param pattern: The regular expression pattern used in re.match(pattern, dicomfile) to select the dicom files', default='.*\\.(IMA|dcm)$')
:return:
"""
bidsfolder = Path(bidsfolder)
samplefolder = Path(samplefolder)
bidsmapfile = Path(bidsmapfile)
# Start logging
bids.setup_logging(bidsfolder / 'code' / 'bidscoin' / 'bidstrainer.log')
LOGGER.info('------------ START BIDStrainer ------------')
# Get the heuristics for creating the bidsmap
heuristics, _ = bids.load_bidsmap(bidsmapfile,
bidsfolder / 'code' / 'bidscoin')
# Input checking
if not samplefolder:
samplefolder = bidsfolder / 'code' / 'bidscoin' / 'samples'
if not samplefolder.is_dir():
LOGGER.info(
f"Creating an empty samples directory tree: {samplefolder}")
for modality in bids.bidsmodalities + (bids.ignoremodality,
bids.unknownmodality):
for run in heuristics['DICOM'][modality]:
if not run['bids']['suffix']:
run['bids']['suffix'] = ''
(samplefolder / modality / run['bids']['suffix']).mkdir(
parents=True, exist_ok=True)
LOGGER.info(
'Fill the directory tree with example DICOM files and re-run bidstrainer.py'
)
return
# Create a copy / bidsmap skeleton with no modality entries (i.e. bidsmap with empty lists)
bidsmap = copy.deepcopy(heuristics)
for logic in ('DICOM', 'PAR', 'P7', 'Nifti', 'FileSystem'):
for modality in bids.bidsmodalities:
if bidsmap[logic] and modality in bidsmap[logic]:
bidsmap[logic][modality] = None
# Loop over all bidsmodalities and instances and built up the bidsmap entries
files = samplefolder.rglob('*')
samples = [
Path(dcmfile) for dcmfile in files if re.match(pattern, str(dcmfile))
]
for sample in samples:
if not sample.is_file(): continue
LOGGER.info(f"Parsing: {sample}")
# Try to get a dicom mapping
if bids.is_dicomfile(sample) and heuristics['DICOM']:
bidsmap = built_dicommap(sample, bidsmap, heuristics)
# Try to get a PAR/REC mapping
if bids.is_parfile(sample) and heuristics['PAR']:
bidsmap = built_parmap(sample, bidsmap, heuristics)
# Try to get a P7 mapping
if bids.is_p7file(sample) and heuristics['P7']:
bidsmap = built_p7map(sample, bidsmap, heuristics)
# Try to get a nifti mapping
if bids.is_niftifile(sample) and heuristics['Nifti']:
bidsmap = built_niftimap(sample, bidsmap, heuristics)
# Try to get a file-system mapping
if heuristics['FileSystem']:
bidsmap = built_filesystemmap(sample, bidsmap, heuristics)
# Try to get a plugin mapping
if heuristics['PlugIn']:
bidsmap = built_pluginmap(sample, bidsmap)
# Create the bidsmap_sample YAML-file in bidsfolder/code/bidscoin
(bidsfolder / 'code' / 'bidscoin').mkdir(parents=True, exist_ok=True)
bidsmapfile = bidsfolder / 'code' / 'bidscoin' / 'bidsmap_sample.yaml'
# Save the bidsmap to the bidsmap YAML-file
bids.save_bidsmap(bidsmapfile, bidsmap)
LOGGER.info('------------ FINISHED! ------------')
def bidstrainer(bidsfolder, samplefolder='', bidsmapfile='bidsmap_template.yaml'):
"""
Main function uses all samples in the samplefolder as training / example data to generate a
maximally filled-in bidsmap_sample.yaml file.
:param str bidsfolder: The name of the BIDS root folder
:param str samplefolder: The name of the root directory of the tree containing the sample files / training data. If left empty, bidsfolder/code/samples is used or such an empty directory tree is created
:param str bidsmapfile: The name of the bidsmap YAML-file
:return: The name of the new (trained) bidsmap YAML-file that is save in bidsfolder/code
:rtype: str
"""
# Input checking
bidsfolder = os.path.abspath(os.path.expanduser(bidsfolder))
if not samplefolder:
samplefolder = os.path.join(bidsfolder,'code','samples')
if not os.path.isdir(samplefolder):
print('Creating an empty samples directory tree: ' + samplefolder)
shutil.copytree(os.path.join(os.path.dirname(bids.__file__),'..','heuristics','samples'), samplefolder)
print('Fill the directory tree with example DICOM files and re-run bidstrainer.py')
return
samplefolder = os.path.abspath(os.path.expanduser(samplefolder))
# Get the heuristics for creating the bidsmap
heuristics = bids.get_heuristics(bidsmapfile)
# Create a copy / bidsmap skeleton with no modality entries (i.e. bidsmap with empty lists)
bidsmap = copy.deepcopy(heuristics)
for logic in ('DICOM', 'PAR', 'P7', 'Nifti', 'FileSystem'):
for modality in bids.bidsmodalities:
if bidsmap[logic] and modality in bidsmap[logic]:
bidsmap[logic][modality] = None
# Loop over all bidsmodalities and instances and built up the bidsmap entries
samples = glob.glob(os.path.join(samplefolder,'**'), recursive=True)
for sample in samples:
if not os.path.isfile(sample): continue
print('Parsing: ' + sample)
# Try to get a dicom mapping
if bids.is_dicomfile(sample) and heuristics['DICOM']:
bidsmap = built_dicommap(sample, bidsmap, heuristics)
# Try to get a PAR/REC mapping
if bids.is_parfile(sample) and heuristics['PAR']:
bidsmap = built_parmap(sample, bidsmap, heuristics)
# Try to get a P7 mapping
if bids.is_p7file(sample) and heuristics['P7']:
bidsmap = built_p7map(sample, bidsmap, heuristics)
# Try to get a nifti mapping
if bids.is_niftifile(sample) and heuristics['Nifti']:
bidsmap = built_niftimap(sample, bidsmap, heuristics)
# Try to get a file-system mapping
if heuristics['FileSystem']:
bidsmap = built_filesystemmap(sample, bidsmap, heuristics)
# Try to get a plugin mapping
if heuristics['PlugIn']:
bidsmap = built_pluginmap(sample, bidsmap)
# Create the bidsmap_sample YAML-file in bidsfolder/code
os.makedirs(os.path.join(bidsfolder,'code'), exist_ok=True)
bidsmapfile = os.path.join(bidsfolder,'code','bidsmap_sample.yaml')
# Save the bidsmap to the bidsmap YAML-file
print('Writing bidsmap to: ' + bidsmapfile)
with open(bidsmapfile, 'w') as stream:
yaml.dump(bidsmap, stream)
return bidsmapfile