def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins: bool=True):
"""
Performs a bidscoin installation test
:param bidsmapfile: The bidsmap or the full pathname / basename of the bidsmap yaml-file
:param options: The bidscoin options. If empty, the default options are used
:return: True if the test was successful
"""
if not bidsmapfile:
return
LOGGER.info('--------- Testing the BIDScoin tools and settings ---------')
# Test loading the template bidsmap
if isinstance(bidsmapfile, (str, Path)):
try:
try: # Include the import in the test + moving the import to the top of this module will cause circular import issues
from bidscoin import bids
except ImportError:
import bids # This should work if bidscoin was not pip-installed
bidsmap, _ = bids.load_bidsmap(Path(bidsmapfile))
if not options:
options = bidsmap['Options']
success = True
except Exception as bidsmaperror:
LOGGER.error(f'{bidsmaperror}')
success = False
else:
if not options:
options = bidsmapfile['Options']
success = True
# Show an overview of the bidscoin tools. TODO: test the entry points?
if not options['plugins']:
LOGGER.warning('No plugins found in the bidsmap (BIDScoin will likely not do anything)')
list_executables(True)
# Test the plugins
if testplugins:
# Show an overview of the plugins and show the test results
list_plugins(True)
for plugin in (bidscoinfolder/'plugins').glob('*.py'):
if plugin.stem != '__init__':
success = test_plugin(plugin.stem, options['plugins'].get(plugin.stem,{})) and success
return success
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 bidscoiner(rawfolder: str,
bidsfolder: str,
subjects: list = (),
force: bool = False,
participants: bool = False,
bidsmapfile: str = 'bidsmap.yaml',
subprefix: str = 'sub-',
sesprefix: str = 'ses-') -> None:
"""
Main function that processes all the subjects and session in the sourcefolder and uses the
bidsmap.yaml file in bidsfolder/code/bidscoin to cast the data into the BIDS folder.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param subjects: List of selected subjects / participants (i.e. sub-# names / folders) to be processed (the sub- prefix can be removed). Otherwise all subjects in the sourcefolder will be selected
:param force: If True, subjects will be processed, regardless of existing folders in the bidsfolder. Otherwise existing folders will be skipped
:param participants: If True, subjects in particpants.tsv will not be processed (this could be used e.g. to protect these subjects from being reprocessed), also when force=True
:param bidsmapfile: The name of the bidsmap YAML-file. If the bidsmap pathname is relative (i.e. no "/" in the name) then it is assumed to be located in bidsfolder/code/bidscoin
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:return: Nothing
"""
# Input checking & defaults
rawfolder = Path(rawfolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
bidsmapfile = Path(bidsmapfile)
# Start logging
bids.setup_logging(bidsfolder / 'code' / 'bidscoin' / 'bidscoiner.log')
LOGGER.info('')
LOGGER.info(
f"-------------- START BIDScoiner {bids.version()}: BIDS {bids.bidsversion()} ------------"
)
LOGGER.info(
f">>> bidscoiner sourcefolder={rawfolder} bidsfolder={bidsfolder} subjects={subjects} force={force}"
f" participants={participants} bidsmap={bidsmapfile} subprefix={subprefix} sesprefix={sesprefix}"
)
# Create a code/bidscoin subfolder
(bidsfolder / 'code' / 'bidscoin').mkdir(parents=True, exist_ok=True)
# Create a dataset description file if it does not exist
dataset_file = bidsfolder / 'dataset_description.json'
if not dataset_file.is_file():
dataset_description = {
"Name":
"REQUIRED. Name of the dataset",
"BIDSVersion":
str(bids.bidsversion()),
"DatasetType":
"raw",
"License":
"RECOMMENDED. The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license. The corresponding full license text MAY be specified in an additional LICENSE file",
"Authors": [
"OPTIONAL. List of individuals who contributed to the creation/curation of the dataset"
],
"Acknowledgements":
"OPTIONAL. Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding",
"HowToAcknowledge":
"OPTIONAL. Instructions how researchers using this dataset should acknowledge the original authors. This field can also be used to define a publication that should be cited in publications that use the dataset",
"Funding":
["OPTIONAL. List of sources of funding (grant numbers)"],
"EthicsApprovals": [
"OPTIONAL. List of ethics committee approvals of the research protocols and/or protocol identifiers"
],
"ReferencesAndLinks": [
"OPTIONAL. List of references to publication that contain information on the dataset, or links",
"https://github.com/Donders-Institute/bidscoin"
],
"DatasetDOI":
"OPTIONAL. The Document Object Identifier of the dataset (not the corresponding paper)"
}
LOGGER.info(f"Creating dataset description file: {dataset_file}")
with open(dataset_file, 'w') as fid:
json.dump(dataset_description, fid, indent=4)
# Create a README file if it does not exist
readme_file = bidsfolder / 'README'
if not readme_file.is_file():
LOGGER.info(f"Creating README file: {readme_file}")
with open(readme_file, 'w') as fid:
fid.write(
f"A free form text ( README ) describing the dataset in more details that SHOULD be provided\n\n"
f"The raw BIDS data was created using BIDScoin {bids.version()}\n"
f"All provenance information and settings can be found in ./code/bidscoin\n"
f"For more information see: https://github.com/Donders-Institute/bidscoin"
)
# Get the bidsmap heuristics from the bidsmap YAML-file
bidsmap, _ = bids.load_bidsmap(bidsmapfile,
bidsfolder / 'code' / 'bidscoin')
if not bidsmap:
LOGGER.error(
f"No bidsmap file found in {bidsfolder}. Please run the bidsmapper first and / or use the correct bidsfolder"
)
return
# Save options to the .bidsignore file
bidsignore_items = [
item.strip()
for item in bidsmap['Options']['bidscoin']['bidsignore'].split(';')
]
LOGGER.info(
f"Writing {bidsignore_items} entries to {bidsfolder}.bidsignore")
with (bidsfolder / '.bidsignore').open('w') as bidsignore:
for item in bidsignore_items:
bidsignore.write(item + '\n')
# Get the table & dictionary of the subjects that have been processed
participants_tsv = bidsfolder / 'participants.tsv'
participants_json = participants_tsv.with_suffix('.json')
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t')
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
if participants_json.is_file():
with participants_json.open('r') as json_fid:
participants_dict = json.load(json_fid)
else:
participants_dict = {
'participant_id': {
'Description': 'Unique participant identifier'
}
}
# Get the list of subjects
if not subjects:
subjects = bids.lsdirs(rawfolder, subprefix + '*')
if not subjects:
LOGGER.warning(f"No subjects found in: {rawfolder/subprefix}*")
else:
subjects = [
subprefix + re.sub(f"^{subprefix}", '', subject)
for subject in subjects
] # Make sure there is a "sub-" prefix
subjects = [
rawfolder / subject for subject in subjects
if (rawfolder / subject).is_dir()
]
# Loop over all subjects and sessions and convert them using the bidsmap entries
for n, subject in enumerate(subjects, 1):
LOGGER.info(
f"------------------- Subject {n}/{len(subjects)} -------------------"
)
if participants and subject.name in list(participants_table.index):
LOGGER.info(f"Skipping subject: {subject} ({n}/{len(subjects)})")
continue
personals = dict()
sessions = bids.lsdirs(subject, sesprefix + '*')
if not sessions:
sessions = [subject]
for session in sessions:
# Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
session, unpacked = bids.unpack(session, subprefix, sesprefix)
# See what dataformat we have
dataformat = bids.get_dataformat(session)
if not dataformat:
LOGGER.info(f"Skipping unknown session: {session}")
continue
# Check if we should skip the session-folder
if not force:
subid, sesid = bids.get_subid_sesid(session / 'dum.my',
subprefix=subprefix,
sesprefix=sesprefix)
bidssession = bidsfolder / subid / sesid
if not bidsmap[dataformat]['session']:
bidssession = bidssession.parent
datatypes = []
for datatype in bids.lsdirs(
bidssession
): # See what datatypes we already have in the bids session-folder
if datatype.glob('*') and bidsmap[dataformat].get(
datatype.name
): # See if we are going to add data for this datatype
datatypes.append(datatype.name)
if datatypes:
LOGGER.info(
f"Skipping processed session: {bidssession} already has {datatypes} data (use the -f option to overrule)"
)
continue
LOGGER.info(f"Coining session: {session}")
# Update / append the source data mapping
if dataformat in ('DICOM', 'PAR'):
coin_data2bids(dataformat, session, bidsmap, bidsfolder,
personals, subprefix, sesprefix)
# Update / append the P7 mapping
if dataformat == 'P7':
LOGGER.error(
f"{dataformat} not (yet) supported, skipping session: {session}"
)
continue
# Update / append the nifti mapping
if dataformat == 'Nifti':
coin_nifti(session, bidsmap, bidsfolder, personals)
# Update / append the file-system mapping
if dataformat == 'FileSystem':
coin_filesystem(session, bidsmap, bidsfolder, personals)
# Update / append the plugin mapping
if bidsmap['PlugIns']:
coin_plugin(session, bidsmap, bidsfolder, personals)
# Clean-up the temporary unpacked data
if unpacked:
shutil.rmtree(session)
# Store the collected personals in the participant_table
for key in personals:
# participant_id is the index of the participants_table
assert 'participant_id' in personals
if key == 'participant_id':
continue
# TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
if key not in participants_dict:
participants_dict[key] = dict(
LongName='Long (unabbreviated) name of the column',
Description='Description of the the column',
Levels=dict(
Key=
'Value (This is for categorical variables: a dictionary of possible values (keys) and their descriptions (values))'
),
Units=
'Measurement units. [<prefix symbol>]<unit symbol> format following the SI standard is RECOMMENDED',
TermURL=
'URL pointing to a formal definition of this type of data in an ontology available on the web'
)
participants_table.loc[personals['participant_id'],
key] = personals[key]
# Write the collected data to the participant files
LOGGER.info(f"Writing subject data to: {participants_tsv}")
participants_table.replace('', 'n/a').to_csv(participants_tsv,
sep='\t',
encoding='utf-8',
na_rep='n/a')
LOGGER.info(f"Writing subject data dictionary to: {participants_json}")
with participants_json.open('w') as json_fid:
json.dump(participants_dict, json_fid, indent=4)
LOGGER.info('-------------- FINISHED! ------------')
LOGGER.info('')
bids.reporterrors()
def bidscoiner(rawfolder: str,
bidsfolder: str,
subjects: list = (),
force: bool = False,
participants: bool = False,
bidsmapfile: str = 'bidsmap.yaml') -> None:
"""
Main function that processes all the subjects and session in the sourcefolder and uses the
bidsmap.yaml file in bidsfolder/code/bidscoin to cast the data into the BIDS folder.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param subjects: List of selected subjects / participants (i.e. sub-# names / folders) to be processed (the sub- prefix can be removed). Otherwise all subjects in the sourcefolder will be selected
:param force: If True, subjects will be processed, regardless of existing folders in the bidsfolder. Otherwise existing folders will be skipped
:param participants: If True, subjects in particpants.tsv will not be processed (this could be used e.g. to protect these subjects from being reprocessed), also when force=True
:param bidsmapfile: The name of the bidsmap YAML-file. If the bidsmap pathname is relative (i.e. no "/" in the name) then it is assumed to be located in bidsfolder/code/bidscoin
:return: Nothing
"""
# Input checking & defaults
rawfolder = Path(rawfolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
bidsmapfile = Path(bidsmapfile)
# Start logging
bidscoin.setup_logging(bidsfolder / 'code' / 'bidscoin' / 'bidscoiner.log')
LOGGER.info('')
LOGGER.info(
f"-------------- START BIDScoiner {localversion}: BIDS {bidscoin.bidsversion()} ------------"
)
LOGGER.info(
f">>> bidscoiner sourcefolder={rawfolder} bidsfolder={bidsfolder} subjects={subjects} force={force} participants={participants} bidsmap={bidsmapfile}"
)
# Create a code/bidscoin subfolder
(bidsfolder / 'code' / 'bidscoin').mkdir(parents=True, exist_ok=True)
# Create a dataset description file if it does not exist
dataset_file = bidsfolder / 'dataset_description.json'
generatedby = [{
"Name": "BIDScoin",
"Version": localversion,
"CodeURL": "https://github.com/Donders-Institute/bidscoin"
}]
if not dataset_file.is_file():
LOGGER.info(f"Creating dataset description file: {dataset_file}")
dataset_description = {
"Name":
"REQUIRED. Name of the dataset",
"GeneratedBy":
generatedby,
"BIDSVersion":
str(bidscoin.bidsversion()),
"DatasetType":
"raw",
"License":
"RECOMMENDED. The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license. The corresponding full license text MAY be specified in an additional LICENSE file",
"Authors": [
"OPTIONAL. List of individuals who contributed to the creation/curation of the dataset"
],
"Acknowledgements":
"OPTIONAL. Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding",
"HowToAcknowledge":
"OPTIONAL. Instructions how researchers using this dataset should acknowledge the original authors. This field can also be used to define a publication that should be cited in publications that use the dataset",
"Funding":
["OPTIONAL. List of sources of funding (grant numbers)"],
"EthicsApprovals": [
"OPTIONAL. List of ethics committee approvals of the research protocols and/or protocol identifiers"
],
"ReferencesAndLinks": [
"OPTIONAL. List of references to publication that contain information on the dataset, or links",
"https://github.com/Donders-Institute/bidscoin"
],
"DatasetDOI":
"OPTIONAL. The Document Object Identifier of the dataset (not the corresponding paper)"
}
else:
with dataset_file.open('r') as fid:
dataset_description = json.load(fid)
if 'BIDScoin' not in [
generatedby_['Name']
for generatedby_ in dataset_description.get('GeneratedBy', [])
]:
LOGGER.info(f"Adding {generatedby} to {dataset_file}")
dataset_description['GeneratedBy'] = dataset_description.get(
'GeneratedBy', []) + generatedby
with dataset_file.open('w') as fid:
json.dump(dataset_description, fid, indent=4)
# Create a README file if it does not exist
readme_file = bidsfolder / 'README'
if not readme_file.is_file():
LOGGER.info(f"Creating README file: {readme_file}")
readme_file.write_text(
f"A free form text ( README ) describing the dataset in more details that SHOULD be provided\n\n"
f"The raw BIDS data was created using BIDScoin {localversion}\n"
f"All provenance information and settings can be found in ./code/bidscoin\n"
f"For more information see: https://github.com/Donders-Institute/bidscoin\n"
)
# Get the bidsmap heuristics from the bidsmap YAML-file
bidsmap, _ = bids.load_bidsmap(bidsmapfile,
bidsfolder / 'code' / 'bidscoin')
dataformats = [
dataformat for dataformat in bidsmap
if dataformat and dataformat not in ('Options', 'PlugIns')
] # Handle legacy bidsmaps (-> 'PlugIns')
if not bidsmap:
LOGGER.error(
f"No bidsmap file found in {bidsfolder}. Please run the bidsmapper first and/or use the correct bidsfolder"
)
return
# Load the data conversion plugins
plugins = [
bidscoin.import_plugin(plugin, ('bidscoiner_plugin', ))
for plugin, options in bidsmap['Options']['plugins'].items()
]
plugins = [plugin for plugin in plugins
if plugin] # Filter the empty items from the list
if not plugins:
LOGGER.warning(
f"The plugins listed in your bidsmap['Options'] did not have a usable `bidscoiner_plugin` function, nothing to do"
)
LOGGER.info('-------------- FINISHED! ------------')
LOGGER.info('')
return
# Append options to the .bidsignore file
bidsignore_items = [
item.strip()
for item in bidsmap['Options']['bidscoin']['bidsignore'].split(';')
]
bidsignore_file = bidsfolder / '.bidsignore'
if bidsignore_items:
LOGGER.info(f"Writing {bidsignore_items} entries to {bidsignore_file}")
if bidsignore_file.is_file():
bidsignore_items += bidsignore_file.read_text().splitlines()
with bidsignore_file.open('w') as bidsignore:
for item in set(bidsignore_items):
bidsignore.write(item + '\n')
# Get the table & dictionary of the subjects that have been processed
participants_tsv = bidsfolder / 'participants.tsv'
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t')
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
# Get the list of subjects
subprefix = bidsmap['Options']['bidscoin']['subprefix'].replace('*', '')
sesprefix = bidsmap['Options']['bidscoin']['sesprefix'].replace('*', '')
if not subjects:
subjects = bidscoin.lsdirs(
rawfolder, (subprefix if subprefix != '*' else '') + '*')
if not subjects:
LOGGER.warning(f"No subjects found in: {rawfolder/subprefix}*")
else:
subjects = [
rawfolder / (subprefix + re.sub(f"^{subprefix}", '', subject))
for subject in subjects
] # Make sure there is a sub-prefix
# Loop over all subjects and sessions and convert them using the bidsmap entries
with logging_redirect_tqdm():
for n, subject in enumerate(
tqdm(subjects, unit='subject', leave=False), 1):
LOGGER.info(
f"------------------- Subject {n}/{len(subjects)} -------------------"
)
if participants and subject.name in list(participants_table.index):
LOGGER.info(
f"Skipping subject: {subject} ({n}/{len(subjects)})")
continue
if not subject.is_dir():
LOGGER.warning(
f"The '{subject}' subject folder does not exist")
continue
sessions = bidscoin.lsdirs(
subject, (sesprefix if sesprefix != '*' else '') + '*')
if not sessions or (subject / 'DICOMDIR').is_file():
sessions = [subject]
for session in sessions:
# Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
sesfolders, unpacked = bids.unpack(session)
for sesfolder in sesfolders:
# Check if we should skip the session-folder
datasource = bids.get_datasource(
sesfolder, bidsmap['Options']['plugins'])
if not datasource.dataformat:
LOGGER.info(
f"No coinable datasources found in '{sesfolder}'")
continue
subid = bidsmap[datasource.dataformat]['subject']
sesid = bidsmap[datasource.dataformat]['session']
subid, sesid = datasource.subid_sesid(
subid, sesid if sesid else '')
bidssession = bidsfolder / subid / sesid # TODO: Support DICOMDIR with multiple subjects (as in PYDICOMDIR)
if not force and bidssession.is_dir():
datatypes = []
for dataformat in dataformats:
for datatype in bidscoin.lsdirs(
bidssession
): # See what datatypes we already have in the bids session-folder
if datatype.iterdir(
) and bidsmap[dataformat].get(
datatype.name
): # See if we are going to add data for this datatype
datatypes.append(datatype.name)
if datatypes:
LOGGER.info(
f"Skipping processed session: {bidssession} already has {datatypes} data (you can carefully use the -f option to overrule)"
)
continue
LOGGER.info(f"Coining datasources in: {sesfolder}")
if bidssession.is_dir():
LOGGER.warning(
f"Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure {bidssession} was cleaned-up from old data before (re)running the bidscoiner"
)
bidssession.mkdir(parents=True, exist_ok=True)
# Run the bidscoiner plugins
for module in plugins:
LOGGER.info(
f"Executing plugin: {Path(module.__file__).name}")
module.bidscoiner_plugin(sesfolder, bidsmap,
bidssession)
# Add the special fieldmap metadata (IntendedFor, B0FieldIdentifier, TE, etc)
addmetadata(bidssession, subid, sesid)
# Clean-up the temporary unpacked data
if unpacked:
shutil.rmtree(sesfolder)
# Re-read the participants_table and store the collected personals in the json sidecar-file
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t')
participants_table.set_index(['participant_id'],
verify_integrity=True,
inplace=True)
participants_json = participants_tsv.with_suffix('.json')
participants_dict = {}
if participants_json.is_file():
with participants_json.open('r') as json_fid:
participants_dict = json.load(json_fid)
if not participants_dict.get('participant_id'):
participants_dict['participant_id'] = {
'Description': 'Unique participant identifier'
}
if not participants_dict.get(
'session_id') and 'session_id' in participants_table.columns:
participants_dict['session_id'] = {'Description': 'Session identifier'}
newkey = False
for col in participants_table.columns:
if col not in participants_dict:
newkey = True
participants_dict[col] = dict(
LongName='Long (unabbreviated) name of the column',
Description='Description of the the column',
Levels=dict(
Key=
'Value (This is for categorical variables: a dictionary of possible values (keys) and their descriptions (values))'
),
Units=
'Measurement units. [<prefix symbol>]<unit symbol> format following the SI standard is RECOMMENDED'
)
# Write the collected data to the participant files
if newkey:
LOGGER.info(f"Writing subject meta data to: {participants_json}")
with participants_json.open('w') as json_fid:
json.dump(participants_dict, json_fid, indent=4)
LOGGER.info('-------------- FINISHED! ------------')
LOGGER.info('')
bidscoin.reporterrors()
def bidsmapper(rawfolder: str, bidsfolder: str, bidsmapfile: str, templatefile: str, plugins: list, subprefix: str, sesprefix: str, store: bool=False, noedit: bool=False, force: bool=False) -> None:
"""
Main function that processes all the subjects and session in the sourcefolder
and that generates a maximally filled-in bidsmap.yaml file in bidsfolder/code/bidscoin.
Folders in sourcefolder are assumed to contain a single dataset.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param bidsmapfile: The name of the bidsmap YAML-file
:param templatefile: The name of the bidsmap template YAML-file
:param plugins: Optional list of plugins that should be used (overrules the list in the study/template bidsmaps)
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:param store: If True, the provenance samples will be stored
:param noedit: The bidseditor will not be launched if True
:param force: If True, the previous bidsmap and logfiles will be deleted
:return:
"""
# Input checking
rawfolder = Path(rawfolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
bidsmapfile = Path(bidsmapfile)
templatefile = Path(templatefile)
bidscoinfolder = bidsfolder/'code'/'bidscoin'
# Start logging
if force:
(bidscoinfolder/'bidsmapper.log').unlink(missing_ok=True)
bidscoin.setup_logging(bidscoinfolder/'bidsmapper.log')
LOGGER.info('')
LOGGER.info('-------------- START BIDSmapper ------------')
LOGGER.info(f">>> bidsmapper sourcefolder={rawfolder} bidsfolder={bidsfolder} bidsmap={bidsmapfile} "
f"template={templatefile} plugins={plugins} subprefix={subprefix} sesprefix={sesprefix} store={store} force={force}")
# Get the heuristics for filling the new bidsmap
bidsmap_old, bidsmapfile = bids.load_bidsmap(bidsmapfile, bidscoinfolder, plugins)
template, _ = bids.load_bidsmap(templatefile, bidscoinfolder, plugins)
# Create the new bidsmap as a copy / bidsmap skeleton with no datatype entries (i.e. bidsmap with empty lists)
if force:
bidsmapfile.unlink(missing_ok=True)
bidsmap_old = {}
if bidsmap_old:
bidsmap_new = copy.deepcopy(bidsmap_old)
else:
bidsmap_new = copy.deepcopy(template)
template['Options'] = bidsmap_new['Options'] # Always use the options of the new bidsmap
bidscoindatatypes = bidsmap_new['Options']['bidscoin'].get('datatypes',[])
unknowndatatypes = bidsmap_new['Options']['bidscoin'].get('unknowntypes',[])
ignoredatatypes = bidsmap_new['Options']['bidscoin'].get('ignoretypes',[])
for dataformat in bidsmap_new:
if dataformat in ('Options','PlugIns'): continue # Handle legacy bidsmaps (-> 'PlugIns')
for datatype in bidscoindatatypes + unknowndatatypes + ignoredatatypes:
if bidsmap_new[dataformat].get(datatype):
bidsmap_new[dataformat][datatype] = None
# Store/retrieve the empty or user-defined sub-/ses-prefix
subprefix, sesprefix = setprefix(bidsmap_new, subprefix, sesprefix)
# Start with an empty skeleton if we didn't have an old bidsmap
if not bidsmap_old:
bidsmap_old = copy.deepcopy(bidsmap_new)
bidsmapfile = bidscoinfolder/'bidsmap.yaml'
# Import the data scanning plugins
plugins = [bidscoin.import_plugin(plugin, ('bidsmapper_plugin',)) for plugin in bidsmap_new['Options']['plugins']]
plugins = [plugin for plugin in plugins if plugin] # Filter the empty items from the list
if not plugins:
LOGGER.warning(f"The plugins listed in your bidsmap['Options'] did not have a usable `bidsmapper_plugin` function, nothing to do")
LOGGER.info('-------------- FINISHED! ------------')
LOGGER.info('')
return
# Loop over all subjects and sessions and built up the bidsmap entries
subjects = bidscoin.lsdirs(rawfolder, (subprefix if subprefix!='*' else '') + '*')
if not subjects:
LOGGER.warning(f'No subjects found in: {rawfolder/subprefix}*')
with logging_redirect_tqdm():
for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
sessions = bidscoin.lsdirs(subject, (sesprefix if sesprefix!='*' else '') + '*')
if not sessions or (subject/'DICOMDIR').is_file():
sessions = [subject]
for session in sessions:
LOGGER.info(f"Mapping: {session} (subject {n}/{len(subjects)})")
# Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
sesfolders, unpacked = bids.unpack(session)
for sesfolder in sesfolders:
if store:
store = {'source': sesfolder.parent.parent.parent.parent if unpacked else rawfolder.parent, 'target': bidscoinfolder/'provenance'}
else:
store = {}
# Run the bidsmapper plugins
for module in plugins:
LOGGER.info(f"Executing plugin: {Path(module.__file__).name} -> {sesfolder}")
module.bidsmapper_plugin(sesfolder, bidsmap_new, bidsmap_old, template, store)
# Clean-up the temporary unpacked data
if unpacked:
shutil.rmtree(sesfolder)
# Save the new study bidsmap in the bidscoinfolder or launch the bidseditor UI_MainWindow
if noedit:
bids.save_bidsmap(bidsmapfile, bidsmap_new)
else:
LOGGER.info('Opening the bidseditor')
app = QApplication(sys.argv)
app.setApplicationName(f"{bidsmapfile} - BIDS editor {localversion}")
mainwin = bidseditor.MainWindow(bidsfolder, bidsmap_new, template)
mainwin.show()
messagebox = QMessageBox(mainwin)
messagebox.setText(f"The bidsmapper has finished scanning {rawfolder}\n\n"
f"Please carefully check all the different BIDS output names "
f"and BIDScoin options and (re)edit them to your needs.\n\n"
f"You can always redo this step later by re-running the "
f"bidsmapper or by just running the bidseditor tool\n\n"
f"{versionmessage}")
messagebox.setWindowTitle('About the BIDS-mapping workflow')
messagebox.setIconPixmap(QtGui.QPixmap(str(bidseditor.BIDSCOIN_LOGO)).scaled(150, 150, QtCore.Qt.KeepAspectRatio, QtCore.Qt.SmoothTransformation))
messagebox.setWindowFlags(messagebox.windowFlags() & ~QtCore.Qt.WindowMinMaxButtonsHint)
messagebox.show()
app.exec()
LOGGER.info('-------------- FINISHED! -------------------')
LOGGER.info('')
bidscoin.reporterrors()
def bidsparticipants(rawfolder: str, bidsfolder: str, keys: str, bidsmapfile: str='bidsmap.yaml', dryrun: bool=False) -> None:
"""
Main function that processes all the subjects and session in the sourcefolder to (re)generate the particpants.tsv file in the BIDS folder.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param keys: The keys that are extracted fro mthe source data when populating the participants.tsv file
:param bidsmapfile: The name of the bidsmap YAML-file. If the bidsmap pathname is relative (i.e. no "/" in the name) then it is assumed to be located in bidsfolder/code/bidscoin
:param dryrun: Boolean to just display the participants info
:return: Nothing
"""
# Input checking & defaults
rawfolder = Path(rawfolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
# Start logging
if dryrun:
bidscoin.setup_logging()
else:
bidscoin.setup_logging(bidsfolder/'code'/'bidscoin'/'bidsparticipants.log')
LOGGER.info('')
LOGGER.info(f"-------------- START bidsparticipants {bidscoin.version()} ------------")
LOGGER.info(f">>> bidsparticipants sourcefolder={rawfolder} bidsfolder={bidsfolder} bidsmap={bidsmapfile}")
# Get the bidsmap sub-/ses-prefix from the bidsmap YAML-file
bidsmap,_ = bids.load_bidsmap(Path(bidsmapfile), bidsfolder/'code'/'bidscoin')
subprefix = bidsmap['Options']['bidscoin']['subprefix']
sesprefix = bidsmap['Options']['bidscoin']['sesprefix']
# Get the table & dictionary of the subjects that have been processed
participants_tsv = bidsfolder/'participants.tsv'
participants_json = participants_tsv.with_suffix('.json')
if participants_tsv.is_file():
participants_table = pd.read_csv(participants_tsv, sep='\t')
participants_table.set_index(['participant_id'], verify_integrity=True, inplace=True)
else:
participants_table = pd.DataFrame()
participants_table.index.name = 'participant_id'
if participants_json.is_file():
with participants_json.open('r') as json_fid:
participants_dict = json.load(json_fid)
else:
participants_dict = {'participant_id': {'Description': 'Unique participant identifier'}}
# Get the list of subjects
subjects = bidscoin.lsdirs(bidsfolder, 'sub-*')
if not subjects:
LOGGER.warning(f"No subjects found in: {bidsfolder}")
# Remove obsolete participants from the participants table
for participant in participants_table.index:
if participant not in [sub.name for sub in subjects]:
participants_table = participants_table.drop(participant)
# Loop over all subjects in the bids-folder and add them to the participants table
with logging_redirect_tqdm():
for n, subject in enumerate(tqdm(subjects, unit='subject', leave=False), 1):
LOGGER.info(f"------------------- Subject {n}/{len(subjects)} -------------------")
personals = dict()
subject = rawfolder/subject.name.replace('sub-', subprefix.replace('*','')) # TODO: This assumes e.g. that the subject-ids in the rawfolder did not contain BIDS-invalid characters (such as '_')
sessions = bidscoin.lsdirs(subject, (sesprefix if sesprefix!='*' else '') + '*')
if not subject.is_dir():
LOGGER.error(f"Could not find source-folder: {subject}")
continue
if not sessions:
sessions = [subject]
for session in sessions:
# Only take data from the first session -> BIDS specification
subid, sesid = bids.DataSource(session/'dum.my', subprefix='sub-', sesprefix='ses-').subid_sesid()
if sesprefix and sesid and 'session_id' not in personals:
personals['session_id'] = sesid
participants_dict['session_id'] = {'Description': 'Session identifier'}
# Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
sesfolders, unpacked = bids.unpack(session)
for sesfolder in sesfolders:
# Update / append the personal source data
LOGGER.info(f"Scanning session: {sesfolder}")
success = scanpersonals(bidsmap, sesfolder, personals)
# Clean-up the temporary unpacked data
if unpacked:
shutil.rmtree(sesfolder)
if success:
break
# Store the collected personals in the participant_table. TODO: Check that only values that are consistent over sessions go in the participants.tsv file, otherwise put them in a sessions.tsv file
for key in keys:
if key not in participants_dict:
participants_dict[key] = dict(LongName = 'Long (unabbreviated) name of the column',
Description = 'Description of the the column',
Levels = dict(Key='Value (This is for categorical variables: a dictionary of possible values (keys) and their descriptions (values))'),
Units = 'Measurement units. [<prefix symbol>]<unit symbol> format following the SI standard is RECOMMENDED')
participants_table.loc[subid, key] = personals.get(key)
# Write the collected data to the participant files
LOGGER.info(f"Writing subject data to: {participants_tsv}")
if not dryrun:
participants_table.replace('','n/a').to_csv(participants_tsv, sep='\t', encoding='utf-8', na_rep='n/a')
LOGGER.info(f"Writing subject data dictionary to: {participants_json}")
if not dryrun:
with participants_json.open('w') as json_fid:
json.dump(participants_dict, json_fid, indent=4)
print(participants_table)
LOGGER.info('-------------- FINISHED! ------------')
LOGGER.info('')
bidscoin.reporterrors()
def bidsmapper(rawfolder: str,
bidsfolder: str,
bidsmapfile: str,
templatefile: str,
subprefix: str = 'sub-',
sesprefix: str = 'ses-',
interactive: bool = True) -> None:
"""
Main function that processes all the subjects and session in the sourcefolder
and that generates a maximally filled-in bidsmap.yaml file in bidsfolder/code/bidscoin.
Folders in sourcefolder are assumed to contain a single dataset.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param bidsmapfile: The name of the bidsmap YAML-file
:param templatefile: The name of the bidsmap template YAML-file
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:param interactive: If True, the user will be asked for help if an unknown run is encountered
:return:bidsmapfile: The name of the mapped bidsmap YAML-file
"""
# Input checking
rawfolder = Path(rawfolder)
bidsfolder = Path(bidsfolder)
bidsmapfile = Path(bidsmapfile)
templatefile = Path(templatefile)
# Start logging
bids.setup_logging(bidsfolder / 'code' / 'bidscoin' / 'bidsmapper.log')
LOGGER.info('')
LOGGER.info('-------------- START BIDSmapper ------------')
LOGGER.info(
f">>> bidsmapper sourcefolder={rawfolder} bidsfolder={bidsfolder} bidsmap={bidsmapfile} "
f" template={templatefile} subprefix={subprefix} sesprefix={sesprefix} interactive={interactive}"
)
# Get the heuristics for filling the new bidsmap
bidsmap_old, _ = bids.load_bidsmap(bidsmapfile,
bidsfolder / 'code' / 'bidscoin')
template, _ = bids.load_bidsmap(templatefile,
bidsfolder / 'code' / 'bidscoin')
# Create the new bidsmap as a copy / bidsmap skeleton with no modality entries (i.e. bidsmap with empty lists)
if bidsmap_old:
bidsmap_new = copy.deepcopy(bidsmap_old)
else:
bidsmap_new = copy.deepcopy(template)
for logic in ('DICOM', 'PAR', 'P7', 'Nifti', 'FileSystem'):
for modality in bids.bidsmodalities + (bids.unknownmodality,
bids.ignoremodality):
if bidsmap_new[logic] and modality in bidsmap_new[logic]:
bidsmap_new[logic][modality] = None
# Start with an empty skeleton if we didn't have an old bidsmap
if not bidsmap_old:
bidsmap_old = copy.deepcopy(bidsmap_new)
# Start the Qt-application
gui = interactive
if gui:
app = QApplication(sys.argv)
app.setApplicationName('BIDS editor')
mainwin = bidseditor.MainWindow()
gui = bidseditor.Ui_MainWindow()
gui.interactive = interactive
gui.subprefix = subprefix
gui.sesprefix = sesprefix
if gui.interactive == 2:
QMessageBox.information(
mainwin, 'BIDS mapping workflow',
f"The bidsmapper will now scan {bidsfolder} and whenever "
f"it detects a new type of scan it will ask you to identify it.\n\n"
f"It is important that you choose the correct BIDS modality "
f"(e.g. 'anat', 'dwi' or 'func') and suffix (e.g. 'bold' or 'sbref').\n\n"
f"At the end you will be shown an overview of all the "
f"different scan types and BIDScoin options (as in the "
f"bidseditor) that you can then (re)edit to your needs")
# Loop over all subjects and sessions and built up the bidsmap entries
subjects = bids.lsdirs(rawfolder, subprefix + '*')
if not subjects:
LOGGER.warning(f'No subjects found in: {rawfolder/subprefix}*')
gui = None
for n, subject in enumerate(subjects, 1):
sessions = bids.lsdirs(subject, sesprefix + '*')
if not sessions:
sessions = [subject]
for session in sessions:
LOGGER.info(f"Parsing: {session} (subject {n}/{len(subjects)})")
for runfolder in bids.lsdirs(session):
# Update / append the dicom mapping
if bidsmap_old['DICOM']:
bidsmap_new = build_dicommap(runfolder, bidsmap_new,
bidsmap_old, template, gui)
# Update / append the PAR/REC mapping
if bidsmap_old['PAR']:
bidsmap_new = build_parmap(runfolder, bidsmap_new,
bidsmap_old)
# Update / append the P7 mapping
if bidsmap_old['P7']:
bidsmap_new = build_p7map(runfolder, bidsmap_new,
bidsmap_old)
# Update / append the nifti mapping
if bidsmap_old['Nifti']:
bidsmap_new = build_niftimap(runfolder, bidsmap_new,
bidsmap_old)
# Update / append the file-system mapping
if bidsmap_old['FileSystem']:
bidsmap_new = build_filesystemmap(runfolder, bidsmap_new,
bidsmap_old)
# Update / append the plugin mapping
if bidsmap_old['PlugIns']:
bidsmap_new = build_pluginmap(runfolder, bidsmap_new,
bidsmap_old)
# Create the bidsmap YAML-file in bidsfolder/code/bidscoin
bidsmapfile = bidsfolder / 'code' / 'bidscoin' / 'bidsmap.yaml'
bidsmapfile.parent.mkdir(parents=True, exist_ok=True)
# Save the bidsmap to the bidsmap YAML-file
bids.save_bidsmap(bidsmapfile, bidsmap_new)
# (Re)launch the bidseditor UI_MainWindow
if gui:
QMessageBox.information(
mainwin, 'BIDS mapping workflow',
f"The bidsmapper has finished scanning {rawfolder}\n\n"
f"Please carefully check all the different BIDS output names "
f"and BIDScoin options and (re)edit them to your needs.\n\n"
f"You can always redo this step later by re-running the "
f"bidsmapper or by just running the bidseditor tool")
LOGGER.info('Opening the bidseditor')
gui.setupUi(mainwin,
bidsfolder,
rawfolder,
bidsmapfile,
bidsmap_new,
copy.deepcopy(bidsmap_new),
template,
subprefix=subprefix,
sesprefix=sesprefix)
mainwin.show()
app.exec()
LOGGER.info('-------------- FINISHED! -------------------')
LOGGER.info('')
bids.reporterrors()
def bidsmapper(rawfolder: str, bidsfolder: str, bidsmapfile: str, templatefile: str, subprefix: str='sub-', sesprefix: str='ses-', store: bool=False, interactive: bool=True) -> None:
"""
Main function that processes all the subjects and session in the sourcefolder
and that generates a maximally filled-in bidsmap.yaml file in bidsfolder/code/bidscoin.
Folders in sourcefolder are assumed to contain a single dataset.
:param rawfolder: The root folder-name of the sub/ses/data/file tree containing the source data files
:param bidsfolder: The name of the BIDS root folder
:param bidsmapfile: The name of the bidsmap YAML-file
:param templatefile: The name of the bidsmap template YAML-file
:param subprefix: The prefix common for all source subject-folders
:param sesprefix: The prefix common for all source session-folders
:param store: If True, the provenance samples will be stored
:param interactive: If True, the user will be asked for help if an unknown run is encountered
:return:bidsmapfile: The name of the mapped bidsmap YAML-file
"""
# Input checking
rawfolder = Path(rawfolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
bidsmapfile = Path(bidsmapfile)
templatefile = Path(templatefile)
bidscoinfolder = bidsfolder/'code'/'bidscoin'
# Start logging
bids.setup_logging(bidscoinfolder/'bidsmapper.log')
LOGGER.info('')
LOGGER.info('-------------- START BIDSmapper ------------')
LOGGER.info(f">>> bidsmapper sourcefolder={rawfolder} bidsfolder={bidsfolder} bidsmap={bidsmapfile} "
f" template={templatefile} subprefix={subprefix} sesprefix={sesprefix} store={store} interactive={interactive}")
# Get the heuristics for filling the new bidsmap
bidsmap_old, _ = bids.load_bidsmap(bidsmapfile, bidscoinfolder)
template, _ = bids.load_bidsmap(templatefile, bidscoinfolder)
# Create the new bidsmap as a copy / bidsmap skeleton with no datatype entries (i.e. bidsmap with empty lists)
if bidsmap_old:
bidsmap_new = copy.deepcopy(bidsmap_old)
else:
bidsmap_new = copy.deepcopy(template)
for logic in ('DICOM', 'PAR', 'P7', 'Nifti', 'FileSystem'):
for datatype in bids.bidsdatatypes + (bids.unknowndatatype, bids.ignoredatatype):
if bidsmap_new.get(logic) and datatype in bidsmap_new[logic]:
bidsmap_new[logic][datatype] = None
# Start with an empty skeleton if we didn't have an old bidsmap
if not bidsmap_old:
bidsmap_old = copy.deepcopy(bidsmap_new)
# Start the Qt-application
gui = interactive
if gui:
app = QApplication(sys.argv)
app.setApplicationName(f"{bidsmapfile} - BIDS editor {bids.version()}")
mainwin = bidseditor.MainWindow()
gui = bidseditor.Ui_MainWindow()
gui.interactive = interactive
gui.subprefix = subprefix
gui.sesprefix = sesprefix
if gui.interactive == 2:
QMessageBox.information(mainwin, 'BIDS mapping workflow',
f"The bidsmapper will now scan {bidsfolder} and whenever "
f"it detects a new type of scan it will ask you to identify it.\n\n"
f"It is important that you choose the correct BIDS datatype "
f"(e.g. 'anat', 'dwi' or 'func') and suffix (e.g. 'bold' or 'sbref').\n\n"
f"At the end you will be shown an overview of all the "
f"different scan types and BIDScoin options (as in the "
f"bidseditor) that you can then (re)edit to your needs")
# Loop over all subjects and sessions and built up the bidsmap entries
dataformat = ''
subjects = bids.lsdirs(rawfolder, subprefix + '*')
if not subjects:
LOGGER.warning(f'No subjects found in: {rawfolder/subprefix}*')
gui = None
for n, subject in enumerate(subjects,1):
sessions = bids.lsdirs(subject, sesprefix + '*')
if not sessions:
sessions = [subject]
for session in sessions:
# Unpack the data in a temporary folder if it is tarballed/zipped and/or contains a DICOMDIR file
session, unpacked = bids.unpack(session, subprefix, sesprefix)
if unpacked:
store = dict(source=unpacked, target=bidscoinfolder/'provenance')
elif store:
store = dict(source=rawfolder, target=bidscoinfolder/'provenance')
else:
store = dict()
# Loop of the different DICOM runs (series) and collect source files
sourcefiles = []
dataformat = bids.get_dataformat(session)
if not dataformat:
LOGGER.info(f"Skipping: {session} (subject {n}/{len(subjects)})")
continue
LOGGER.info(f"Parsing: {session} (subject {n}/{len(subjects)})")
if dataformat=='DICOM':
for sourcedir in bids.lsdirs(session):
sourcefile = bids.get_dicomfile(sourcedir)
if sourcefile.name:
sourcefiles.append(sourcefile)
if dataformat=='PAR':
sourcefiles = bids.get_parfiles(session)
if dataformat=='P7':
sourcefiles = bids.get_p7file(session)
# Update the bidsmap with the info from the source files
for sourcefile in sourcefiles:
bidsmap_new = build_bidsmap(dataformat, sourcefile, bidsmap_new, bidsmap_old, template, store, gui)
# Update / append the nifti mapping
if dataformat=='Nifti':
bidsmap_new = build_niftimap(session, bidsmap_new, bidsmap_old)
# Update / append the file-system mapping
if dataformat=='FileSystem':
bidsmap_new = build_filesystemmap(session, bidsmap_new, bidsmap_old)
# Update / append the plugin mapping
if bidsmap_old['PlugIns']:
bidsmap_new = build_pluginmap(session, bidsmap_new, bidsmap_old)
# Clean-up the temporary unpacked data
if unpacked:
shutil.rmtree(session)
if not dataformat:
LOGGER.warning('Could not determine the dataformat of the source data')
# (Re)launch the bidseditor UI_MainWindow
bidsmapfile = bidscoinfolder/'bidsmap.yaml'
if gui:
if not dataformat:
QMessageBox.information(mainwin, 'BIDS mapping workflow',
'Could not determine the dataformat of the source data.\n'
'You can try running the bidseditor tool yourself')
else:
QMessageBox.information(mainwin, 'BIDS mapping workflow',
f"The bidsmapper has finished scanning {rawfolder}\n\n"
f"Please carefully check all the different BIDS output names "
f"and BIDScoin options and (re)edit them to your needs.\n\n"
f"You can always redo this step later by re-running the "
f"bidsmapper or by just running the bidseditor tool")
LOGGER.info('Opening the bidseditor')
gui.setupUi(mainwin, bidsfolder, bidsmapfile, bidsmap_new, copy.deepcopy(bidsmap_new), template, dataformat, subprefix=subprefix, sesprefix=sesprefix)
mainwin.show()
app.exec()
else:
# Save the bidsmap in the bidscoinfolder
bids.save_bidsmap(bidsmapfile, bidsmap_new)
LOGGER.info('-------------- FINISHED! -------------------')
LOGGER.info('')
bids.reporterrors()
