Pipeline Development¶
Validation Schema¶
C-PAC uses voluptuous to validate pipeline configurations against defined types and value restrictions. Default values should be set in the default pipeline along with comments explaining each option.
Validation schema for C-PAC pipeline configurations.
- CPAC.pipeline.schema.name_motion_filter(mfilter, mfilters=None)[source]¶
Given a motion filter, create a short string for the filename.
Examples
>>> name_motion_filter({'filter_type': 'notch', 'filter_order': 2, ... 'center_frequency': 0.31, 'filter_bandwidth': 0.12}) 'notch2fc0p31bw0p12' >>> name_motion_filter({'filter_type': 'notch', 'filter_order': 4, ... 'breathing_rate_min': 0.19, 'breathing_rate_max': 0.43}) 'notch4fl0p19fu0p43' >>> name_motion_filter({'filter_type': 'lowpass', 'filter_order': 4, ... 'lowpass_cutoff': .0032}) 'lowpass4fc0p0032' >>> name_motion_filter({'filter_type': 'lowpass', 'filter_order': 2, ... 'breathing_rate_min': 0.19}) 'lowpass2fl0p19' >>> name_motion_filter({'filter_type': 'lowpass', 'filter_order': 2, ... 'breathing_rate_min': 0.19}, [{'Name': 'lowpass2fl0p19'}]) 'lowpass2fl0p19dup1' >>> name_motion_filter({'filter_type': 'lowpass', 'filter_order': 2, ... 'breathing_rate_min': 0.19}, [{'Name': 'lowpass2fl0p19'}, ... {'Name': 'lowpass2fl0p19dup1'}]) 'lowpass2fl0p19dup2'
- CPAC.pipeline.schema.permutation_message(key, options)[source]¶
Give a human-readable error message for keys that accept permutation values.
- CPAC.pipeline.schema.sanitize(filename)[source]¶
Sanitize a filename and replace whitespaces with underscores.
- CPAC.pipeline.schema.schema(config_dict)[source]¶
Validate a participant-analysis pipeline configuration.
Validate against the latest validation schema by first applying backwards- compatibility patches, then applying Voluptuous validation, then handling complex configuration interaction checks before returning validated config_dict.
- CPAC.pipeline.schema.str_to_bool1_1(x)[source]¶
Convert strings to Booleans for YAML1.1 syntax.
Ref https://yaml.org/type/bool.html
- Parameters:
x (
any
)- Return type:
Pipeline Utilities¶
C-PAC pipeline engine utilities.
- CPAC.pipeline.utils.name_fork(resource_idx, cfg, json_info, out_dct)[source]¶
Create and insert entities for forkpoints.
- CPAC.pipeline.utils.present_outputs(outputs: dict, keys: list) dict [source]¶
Return the subset of
outputs
including only that are present inkeys
.I.e.,
motion_correct_connections
will have different items in itsoutputs
dictionary at different times depending on themotion_correction
configuration;func_motion_estimates
can then wrap thatoutputs
in this function and provide a list of keys of the desired outputs to include, if they are present in the providedoutputs
dictionary, eliminating the need for multiple NodeBlocks that differ only by configuration options and relevant output keys.- Parameters:
- Returns:
outputs filtered down to keys
- Return type:
Examples
>>> present_outputs({'a': 1, 'b': 2, 'c': 3}, ['b']) {'b': 2} >>> present_outputs({'a': 1, 'b': 2, 'c': 3}, ['d']) {} >>> present_outputs({'a': 1, 'b': 2, 'c': 3}, ['a', 'c']) {'a': 1, 'c': 3}
- CPAC.pipeline.utils.source_set(sources: str | list | set) set [source]¶
Given a CpacProvenance, return a set of {resource}:{source} strings.
Examples
>>> source_set([[[['bold:func_ingress', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_truncate'], ... ['TR:func_metadata_ingress'], ... ['tpattern:func_metadata_ingress'], ... 'desc-preproc_bold:func_slice_time'], ... [['bold:func_ingress', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_truncate'], ... ['bold:func_ingress', 'desc-reorient_bold:func_reorient'], ... 'motion-basefile:get_motion_ref_fmriprep_reference'], ... 'desc-preproc_bold:motion_correction_only_mcflirt'], ... [[['bold:func_ingress', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_truncate'], ... ['bold:func_ingress', 'desc-reorient_bold:func_reorient'], ... 'motion-basefile:get_motion_ref_fmriprep_reference'], ... [[['bold:func_ingress', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_truncate'], ... ['TR:func_metadata_ingress'], ... ['tpattern:func_metadata_ingress'], ... 'desc-preproc_bold:func_slice_time'], ... [['bold:func_ingress', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_truncate'], ... ['bold:func_ingress', 'desc-reorient_bold:func_reorient'], ... 'motion-basefile:get_motion_ref_fmriprep_reference'], ... 'desc-preproc_bold:motion_correction_only_mcflirt'], ... ['FSL-AFNI-bold-ref:template_resample'], ... ['FSL-AFNI-brain-mask:template_resample'], ... ['FSL-AFNI-brain-probseg:template_resample'], ... 'space-bold_desc-brain_mask:bold_mask_fsl_afni'], ... 'desc-preproc_bold:bold_masking']) == set({ ... 'FSL-AFNI-bold-ref:template_resample', ... 'FSL-AFNI-brain-mask:template_resample', ... 'FSL-AFNI-brain-probseg:template_resample', ... 'TR:func_metadata_ingress', ... 'bold:func_ingress', ... 'desc-preproc_bold:bold_masking', ... 'desc-preproc_bold:func_reorient', ... 'desc-preproc_bold:func_slice_time', ... 'desc-preproc_bold:func_truncate', ... 'desc-preproc_bold:motion_correction_only_mcflirt', ... 'desc-reorient_bold:func_reorient', ... 'motion-basefile:get_motion_ref_fmriprep_reference', ... 'space-bold_desc-brain_mask:bold_mask_fsl_afni', ... 'tpattern:func_metadata_ingress'}) True