nipoppy.workflows.base.BaseDatasetWorkflow¶

class nipoppy.workflows.base.BaseDatasetWorkflow(dpath_root, name, fpath_layout=None, verbose=False, dry_run=False, _skip_logfile=False, _validate_layout=True)¶

Base workflow class with awareness of dataset layout and components.

Parameters:

dpath_root (nipoppy.env.StrOrPathLike)
name (str)
fpath_layout (Optional[nipoppy.env.StrOrPathLike])
verbose (bool)
dry_run (bool)
_skip_logfile (bool)
_validate_layout (bool)

generate_fpath_log(dnames_parent=None, fname_stem=None)¶

Generate a log file path.

Parameters:

dnames_parent (Optional[str | list[str]])
fname_stem (Optional[str])

Return type:

pathlib.Path

run_setup()¶: Run the setup part of the workflow.

property config: nipoppy.config.main.Config¶

Load the configuration.

Raise error if not found.

Return type:: nipoppy.config.main.Config

property curation_status_table: nipoppy.tabular.curation_status.CurationStatusTable¶

Load the curation status file if it exists.

Otherwise, generate a new one.

Return type:: nipoppy.tabular.curation_status.CurationStatusTable

property dicom_dir_map: nipoppy.tabular.dicom_dir_map.DicomDirMap¶

Get the DICOM directory mapping.

Return type:: nipoppy.tabular.dicom_dir_map.DicomDirMap

dpath_root¶

fpath_layout = None¶

layout¶

property manifest: nipoppy.tabular.manifest.Manifest¶

Load the manifest.

Raise error if not found.

Return type:: nipoppy.tabular.manifest.Manifest

property processing_status_table: nipoppy.tabular.processing_status.ProcessingStatusTable¶

Load the processing status file it it exists.

Otherwise, return an empty processing status table.

Return type:: nipoppy.tabular.processing_status.ProcessingStatusTable