xcp_d.interfaces.bids.DerivativesDataSink

class xcp_d.interfaces.bids.DerivativesDataSink(allowed_entities=None, out_path_base=None, **inputs)[source]

Store derivative files.

A child class of the niworkflows DerivativesDataSink, using xcp_d’s configuration files.

Mandatory Inputs:

  • in_file (a list of items which are a pathlike object or string representing an existing file) – The object to be saved.

  • source_file (a list of items which are a pathlike object or string representing a file) – The source file(s) to extract entities from.

Optional Inputs:

  • base_directory (a string or os.PathLike object) – Path to the base directory for storing data.

  • check_hdr (a boolean) – Fix headers of NIfTI outputs. (Nipype default value: True)

  • compress (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None, default). (Nipype default value: [])

  • data_dtype (a string) – NumPy datatype to coerce NIfTI data to, or source tomatch the input file dtype.

  • dismiss_entities (a list of items which are a string or None) – A list entities that will not be propagated from the source file. (Nipype default value: [])

  • meta_dict (a dictionary with keys which are a value of class ‘str’ and with values which are any value) – An input dictionary containing metadata.

Outputs:

  • compression (a list of items which are a boolean or None) – Whether in_file should be compressed (True), uncompressed (False) or left unmodified (None).

  • fixed_hdr (a list of items which are a boolean) – Whether derivative header was fixed.

  • out_file (a list of items which are a pathlike object or string representing an existing file)

  • out_meta (a list of items which are a pathlike object or string representing an existing file)

__init__(allowed_entities=None, out_path_base=None, **inputs)[source]

Initialize the SimpleInterface and extend inputs with custom entities.

Methods

__init__([allowed_entities, out_path_base])

Initialize the SimpleInterface and extend inputs with custom entities.

aggregate_outputs([runtime, needed_outputs])

Collate expected outputs and apply output traits validation.

help([returnhelp])

Prints class help

load_inputs_from_json(json_file[, overwrite])

A convenient way to load pre-set inputs from a JSON file.

run([cwd, ignore_exception])

Execute this interface.

save_inputs_to_json(json_file)

A convenient way to save current inputs to a JSON file.

Attributes

always_run

Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.

can_resume

Defines if the interface can reuse partial results after interruption.

out_path_base

resource_monitor

version

interfaces should implement a version property