diff --git a/.codespellignore b/.codespellignore new file mode 100644 index 0000000..cd0c3b4 --- /dev/null +++ b/.codespellignore @@ -0,0 +1,2 @@ +src/simbids/data/**/*.yaml +src/simbids/data/**/*.yml \ No newline at end of file diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml index ae7833e..48ec10c 100644 --- a/.github/workflows/contrib.yml +++ b/.github/workflows/contrib.yml @@ -38,3 +38,6 @@ jobs: uses: actions/checkout@v4 - name: Codespell uses: codespell-project/actions-codespell@v2 + with: + skip: "src/simbids/data/**/*.yaml,src/simbids/data/**/*.yml" + ignore_words_list: ND diff --git a/data b/data new file mode 120000 index 0000000..acaebac --- /dev/null +++ b/data @@ -0,0 +1 @@ +../ds004146 \ No newline at end of file diff --git a/src/simbids/data/bids-mri/ds002278_configs.yaml b/src/simbids/data/bids-mri/ds002278_configs.yaml new file mode 100644 index 0000000..cc1912c --- /dev/null +++ b/src/simbids/data/bids-mri/ds002278_configs.yaml @@ -0,0 +1,56762 @@ +"Blossom": +- "func": + - 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Dec 19 2017 11:00:25 by eja" + "run": "01" + "suffix": "bold" + "task": "restPA" + - "extension": ".json" + "metadata": {} + "run": "02" + "suffix": "bold" + "task": "restPA" + - "extension": ".nii.gz" + "metadata": + "AcquisitionMatrixPE": "104" + "AcquisitionNumber": "1" + "AcquisitionTime": "17:00:4.942500" + "BandwidthPerPixelPhaseEncode": 16.578 + "BaseResolution": "104" + "BodyPartExamined": "BRAIN" + "ConsistencyInfo": "N4_VE11C_LATEST_20160120" + "ConversionSoftware": "dcm2niix" + "ConversionSoftwareVersion": "v1.0.20171215 (OpenJPEG build) GCC4.8.4" + "DerivedVendorReportedEchoSpacing": 0.000580009 + "DeviceSerialNumber": "166095" + "DwellTime": 2.1e-06 + "EchoTime": 0.037 + "EchoTrainLength": "104" + "EffectiveEchoSpacing": 0.000580009 + "FlipAngle": "52" + "ImageComments": "Unaliased_MB8_PE3_LB" + "ImageOrientationPatientDICOM": + - 0.996068 + - 0.017245 + - -0.0868961 + - -0.0471477 + - 0.933615 + - -0.355161 + "ImageType": + - "ORIGINAL" + - "PRIMARY" + - "M" + - "MB" + - "ND" + - "MOSAIC" + "InPlanePhaseEncodingDirectionDICOM": "COL" + "InstitutionAddress": "Hillhouse_Ave._10_New_Haven_Northeast_US_06519" + "InstitutionName": "Yale_University_-_Dunham_Lab._Bldg." + "InstitutionalDepartmentName": "Department" + "MRAcquisitionType": "2D" + "MagneticFieldStrength": "3" + "Manufacturer": "Siemens" + "ManufacturersModelName": "Prisma" + "Modality": "MR" + "MultibandAccelerationFactor": "8" + "PartialFourier": "1" + "PatientPosition": "HFS" + "PercentPhaseFOV": "100" + "PhaseEncodingDirection": "j" + "PhaseEncodingSteps": "104" + "PhaseResolution": "1" + "PixelBandwidth": "2290" + "ProcedureStepDescription": "PCY" + "ProtocolName": "rfMRI_REST_PA" + "PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_bold" + "ReceiveCoilActiveElements": "HC1-7;NC1,2" + "ReceiveCoilName": "HeadNeck_64" + "ReconMatrixPE": "104" + "RepetitionTime": 0.8 + "SAR": 0.0545566 + "ScanOptions": "FS_EXT" + "ScanningSequence": "EP" + "SequenceName": "epfid2d1_104" + "SequenceVariant": "SK_SS" + "SeriesDescription": "rfMRI_REST_PA" + "SeriesNumber": "38" + "ShimSetting": + - -2143 + - -607 + - -4006 + - 431 + - 10 + - -325 + - -32 + - 64 + "SliceThickness": "2" + "SliceTiming": + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + - 0 + - 0.4325 + - 0.0875 + - 0.52 + - 0.1725 + - 0.6075 + - 0.26 + - 0.6925 + - 0.3475 + "SoftwareVersions": "syngo_MR_E11" + "SpacingBetweenSlices": "2" + "StationName": "AWP166095" + "TaskName": "restPA" + "TotalReadoutTime": 0.0597409 + "TxRefAmp": 228.804 + "run": "02" + "suffix": "bold" + "task": "restPA" + - "extension": ".json" + "metadata": {} + "run": "01" + "suffix": "bold" + "task": "stroopAP" + - "extension": ".nii.gz" + "metadata": + "AcquisitionMatrixPE": "104" + "AcquisitionNumber": "1" + "AcquisitionTime": "16:29:58.562500" + "BandwidthPerPixelPhaseEncode": 16.578 + "BaseResolution": "104" + "BodyPartExamined": "BRAIN" + "ConsistencyInfo": "N4_VE11C_LATEST_20160120" + "ConversionSoftware": "dcm2niix" + "ConversionSoftwareVersion": "v1.0.20210317" + "DerivedVendorReportedEchoSpacing": 0.000580009 + "DeviceSerialNumber": "166095" + "DwellTime": 2.1e-06 + "EchoTime": 0.037 + "EchoTrainLength": "104" + "EffectiveEchoSpacing": 0.000580009 + "FlipAngle": "52" + "ImageComments": "Unaliased MB8/PE3/LB" + "ImageOrientationPatientDICOM": + - 0.996068 + - 0.017245 + - -0.0868961 + - -0.0471477 + - 0.933615 + - -0.355161 + "ImageType": + - "ORIGINAL" + - "PRIMARY" + - "M" + - "MB" + - "ND" + - "MOSAIC" + "ImagingFrequency": 123.261 + "InPlanePhaseEncodingDirectionDICOM": "COL" + "InstitutionAddress": "Hillhouse Ave. 10,New Haven ,Northeast,US,06519" + "InstitutionName": "Yale University - Dunham Lab. 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Bldg." + "InstitutionalDepartmentName": "Department" + "MRAcquisitionType": "2D" + "MagneticFieldStrength": "3" + "Manufacturer": "Siemens" + "ManufacturersModelName": "Prisma" + "Modality": "MR" + "MultibandAccelerationFactor": "8" + "PartialFourier": "1" + "PatientPosition": "HFS" + "PercentPhaseFOV": "100" + "PercentSampling": "100" + "PhaseEncodingDirection": "j" + "PhaseEncodingSteps": "104" + "PhaseResolution": "1" + "PixelBandwidth": "2290" + "ProcedureStepDescription": "PCY" + "ProtocolName": "Stroop_Bl2_PA" + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold" + "ReceiveCoilActiveElements": "HC1-7;NC1,2" + "ReceiveCoilName": "HeadNeck_64" + "ReconMatrixPE": "104" + "RepetitionTime": 0.8 + "SAR": 0.0545828 + "ScanOptions": "FS\\EXT" + "ScanningSequence": "EP" + "SequenceName": "epfid2d1_104" + "SequenceVariant": "SK\\SS" + "SeriesDescription": "Stroop_Bl2_PA" + "SeriesNumber": "29" + "ShimSetting": + - -2143 + - -607 + - -4006 + - 431 + - 10 + - -325 + - -32 + - 64 + "SliceThickness": "2" + "SliceTiming": + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + - 0 + - 0.4325 + - 0.085 + - 0.5175 + - 0.1725 + - 0.605 + - 0.26 + - 0.6925 + - 0.345 + "SoftwareVersions": "syngo MR E11" + "SpacingBetweenSlices": "2" + "StationName": "AWP166095" + "TaskName": "stroopPA" + "TotalReadoutTime": 0.0597409 + "TxRefAmp": 228.804 + "WipMemBlock": "16a80915-fd50-478b-9a9f-d8536f2cf147||Sequence: R016 ve11c/master\ + \ r/e634e98; Dec 19 2017 11:00:25 by eja" + "run": "01" + "suffix": "bold" + "task": "stroopPA" diff --git a/src/simbids/data/multi_ses_qsiprep.yaml b/src/simbids/data/bids-mri/multi_ses_qsiprep.yaml similarity index 100% rename from src/simbids/data/multi_ses_qsiprep.yaml rename to src/simbids/data/bids-mri/multi_ses_qsiprep.yaml diff --git a/src/simbids/data/no_ses_qsiprep.yaml b/src/simbids/data/bids-mri/no_ses_qsiprep.yaml similarity index 100% rename from src/simbids/data/no_ses_qsiprep.yaml rename to src/simbids/data/bids-mri/no_ses_qsiprep.yaml diff --git a/src/simbids/data/smriprep_outputs.yaml b/src/simbids/data/bids-mri/smriprep_outputs.yaml similarity index 100% rename from src/simbids/data/smriprep_outputs.yaml rename to src/simbids/data/bids-mri/smriprep_outputs.yaml diff --git a/src/simbids/utils/utils.py b/src/simbids/utils/utils.py index 266f444..4a8a9df 100644 --- a/src/simbids/utils/utils.py +++ b/src/simbids/utils/utils.py @@ -23,6 +23,9 @@ """Utility functions for SimBIDS.""" import logging +from pathlib import Path + +import yaml LGR = logging.getLogger(__name__) @@ -43,7 +46,7 @@ def _get_wf_name(bold_fname, prefix): fname = split_filename(bold_fname)[1] fname_nosub = '_'.join(fname.split('_')[1:-1]) - return f"{prefix}_{fname_nosub.replace('-', '_')}_wf" + return f'{prefix}_{fname_nosub.replace("-", "_")}_wf' def update_dict(orig_dict, new_dict): @@ -70,3 +73,216 @@ def update_dict(orig_dict, new_dict): updated_dict[key] = value return updated_dict + + +def _sanitize_value(value): + """Convert PaddedInt values to strings.""" + if hasattr(value, '__class__') and value.__class__.__name__ == 'PaddedInt': + return str(value) + return value + + +def _sanitize_metadata(metadata): + """Convert PaddedInt values to strings in metadata.""" + if not isinstance(metadata, dict): + return metadata + return {k: _sanitize_value(v) for k, v in metadata.items()} + + +def create_skeleton_from_bids(bids_dir, n_subjects, n_sessions): + """Create a skeleton of the BIDS dataset. + + Given an actual BIDS dataset on the file system, this function + will create a BIDS skeleton that mimics the structure of the actual dataset. + + The skeleton can be used by niworkflows.testing.generate_BIDS() + + Parameters + ---------- + bids_dir : str + Path to the BIDS dataset. + n_subjects : int + Number of subjects to create. + n_sessions : int + Number of sessions to create. + + Returns + ------- + dict + A dictionary containing the BIDS skeleton structure. + """ + from bids.layout import BIDSLayout, BIDSLayoutIndexer, parse_file_entities + + # Initialize BIDS layout + indexer = BIDSLayoutIndexer(validate=False, index_metadata=True) + layout = BIDSLayout(bids_dir, indexer=indexer) + + # Get all subjects + subjects = sorted(layout.get_subjects()) + if n_subjects > len(subjects): + n_subjects = len(subjects) + + # Select first n_subjects + selected_subjects = subjects[:n_subjects] + + # Initialize skeleton structure + skeleton = {} + + for subject in selected_subjects: + # Get sessions for this subject + sessions = sorted(layout.get_sessions(subject=subject)) + if n_sessions > len(sessions): + n_sessions = len(sessions) + + # Select first n_sessions + selected_sessions = sessions[:n_sessions] + + if not selected_sessions: + # No sessions case - similar to no_ses_qsiprep.yaml + skeleton[subject] = {} + + # Get anatomical data + anat_files = layout.get( + subject=subject, + datatype='anat', + suffix=['T1w', 'T2w'], + extension=['.nii.gz', '.nii'], + ) + if anat_files: + skeleton[subject]['anat'] = [] + for anat_file in anat_files: + anat_sidecar = _sanitize_metadata(anat_file.get_metadata()) + entities = parse_file_entities(Path(anat_file).name) + anat_entry = { + 'suffix': _sanitize_value(entities.get('suffix', 'T1w')), + 'metadata': anat_sidecar, + } + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + anat_entry[key] = _sanitize_value(value) + skeleton[subject]['anat'].append(anat_entry) + + # Get DWI data + dwi_files = layout.get( + subject=subject, + datatype='dwi', + suffix='dwi', + extension=['.nii.gz', '.nii'], + ) + if dwi_files: + skeleton[subject]['dwi'] = [] + for dwi_file in dwi_files: + dwi_sidecar = _sanitize_metadata(dwi_file.get_metadata()) + entities = parse_file_entities(Path(dwi_file).name) + dwi_entry = {'suffix': 'dwi', 'metadata': dwi_sidecar} + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + dwi_entry[key] = _sanitize_value(value) + skeleton[subject]['dwi'].append(dwi_entry) + + # Get functional data + func_files = layout.get(subject=subject, datatype='func', suffix='bold') + if func_files: + skeleton[subject]['func'] = [] + for func_file in func_files: + func_sidecar = _sanitize_metadata(func_file.get_metadata()) + entities = parse_file_entities(Path(func_file).name) + func_entry = {'suffix': 'bold', 'metadata': func_sidecar} + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + func_entry[key] = _sanitize_value(value) + skeleton[subject]['func'].append(func_entry) + else: + # With sessions case - similar to multi_ses_qsiprep.yaml + skeleton[subject] = [] + for session in selected_sessions: + session_data = {'session': _sanitize_value(session)} + + # Get anatomical data for this session + anat_files = layout.get( + subject=subject, session=session, datatype='anat', suffix=['T1w', 'T2w'] + ) + if anat_files: + session_data['anat'] = [] + for anat_file in anat_files: + anat_sidecar = _sanitize_metadata(anat_file.get_metadata()) + entities = parse_file_entities(Path(anat_file).name) + anat_entry = { + 'suffix': _sanitize_value(entities.get('suffix', 'T1w')), + 'metadata': anat_sidecar, + } + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + anat_entry[key] = _sanitize_value(value) + session_data['anat'].append(anat_entry) + + # Get DWI data for this session + dwi_files = layout.get( + subject=subject, session=session, datatype='dwi', suffix='dwi' + ) + if dwi_files: + session_data['dwi'] = [] + for dwi_file in dwi_files: + dwi_sidecar = _sanitize_metadata(dwi_file.get_metadata()) + entities = parse_file_entities(Path(dwi_file).name) + dwi_entry = {'suffix': 'dwi', 'metadata': dwi_sidecar} + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + dwi_entry[key] = _sanitize_value(value) + session_data['dwi'].append(dwi_entry) + + # Get functional data for this session + func_files = layout.get( + subject=subject, session=session, datatype='func', suffix='bold' + ) + if func_files: + session_data['func'] = [] + for func_file in func_files: + func_sidecar = _sanitize_metadata(func_file.get_metadata()) + entities = parse_file_entities(Path(func_file).name) + func_entry = {'suffix': 'bold', 'metadata': func_sidecar} + # Add all entities except subject and session + for key, value in entities.items(): + if key not in ['subject', 'session', 'suffix']: + func_entry[key] = _sanitize_value(value) + session_data['func'].append(func_entry) + + skeleton[subject].append(session_data) + + return skeleton + + +class BIDSDumper(yaml.Dumper): + """Custom YAML dumper that handles BIDS objects.""" + + def represent_str(self, data): + return self.represent_scalar('tag:yaml.org,2002:str', str(data), style='"') + + def ignore_aliases(self, data): + return True + + def represent_object(self, data): + return self.represent_str(str(data)) + + +# Register the custom dumpers +BIDSDumper.add_representer(str, BIDSDumper.represent_str) +BIDSDumper.add_representer(object, BIDSDumper.represent_object) + + +def _convert_to_serializable(obj): + """Convert BIDS objects to basic Python types for YAML serialization.""" + if hasattr(obj, 'get_metadata'): + return obj.get_metadata() + if isinstance(obj, int | float | str | bool | type(None)): + return obj + if isinstance(obj, list | tuple): + return [_convert_to_serializable(item) for item in obj] + if isinstance(obj, dict): + return {k: _convert_to_serializable(v) for k, v in obj.items()} + return str(obj)