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Provenance traces of Nipype example
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‎examples/nipype/code/merge_prov.py‎

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#!/usr/bin/python
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# coding: utf-8
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""" Merge available prov JSON files into one JSON-LD graph """
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import json
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from pathlib import Path
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# List of available prov files
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prov_soft_files = [
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'prov/prov-normalize_soft.prov.json'
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]
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prov_env_files = [
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'prov/prov-normalize_env.prov.json'
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]
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prov_act_files = [
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'derivatives/normalize/sub-001/anat/sub-001_prov-normalize_act.prov.json'
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]
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prov_ent_files = [
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'prov/prov-normalize_ent.prov.json'
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]
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sidecar_files = [
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'derivatives/normalize/sub-001/anat/sub-001_T1w_brain.json',
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'derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.json'
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]
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# Base jsonld
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base_provenance = {
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"Records": {
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"Software": [],
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"Activities": [],
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"Entities": []
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}
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}
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# Add context and version
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with open('prov/prov-normalize_base.prov.json', encoding = 'utf-8') as file:
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base_provenance.update(json.load(file))
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# Parse Software
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for prov_file in prov_soft_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Software'].append(value)
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# Parse Environments
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for prov_file in prov_env_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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# /!\ Workaround: environments are added in the Entities list because
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# the Environments term is not defined in the BIDS Prov context yet
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base_provenance['Records']['Entities'].append(value)
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# Parse Activities
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for prov_file in prov_act_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Activities'].append(value)
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# Parse Entities
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for prov_file in prov_ent_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Entities'].append(value)
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# Parse Sidecar files
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for sidecar_file in sidecar_files:
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# Identify data file(s) associated with the sidecar
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sidecar_filename = Path(sidecar_file)
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data_files = Path('').glob(f'{sidecar_filename.with_suffix("")}.*')
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data_files = [str(f) for f in list(data_files) if str(sidecar_filename) not in str(f)]
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# Write provenance
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with open(sidecar_file, encoding = 'utf-8') as file:
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data = json.load(file)
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if 'GeneratedBy' in data:
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activity_id = data['GeneratedBy']
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for data_file in data_files:
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base_provenance['Records']['Entities'].append({
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"Id": f"bids::{data_file}",
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"GeneratedBy": activity_id
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})
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# Write jsonld
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with open('prov/merged/prov-normalize.prov.jsonld', 'w', encoding = 'utf-8') as file:
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file.write(json.dumps(base_provenance, indent = 2))

‎examples/nipype/code/workflow.py‎

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#!/usr/bin/python
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# coding: utf-8
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"""
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A simple Nipype workflow performing brain extraction and normalisation
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of an anatomical file.
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"""
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from os.path import abspath
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from nipype.pipeline.engine import Workflow, Node
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from nipype.interfaces.fsl import BET, FLIRT, Info
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from nipype.interfaces.io import ExportFile
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# Create workflow
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workflow = Workflow(name='bids_prov_workflow')
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workflow.base_dir = abspath('derivatives/')
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# Create nodes
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brain_extraction = Node(BET(), name = 'brain_extraction')
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brain_extraction.inputs.in_file = abspath('sub-001/anat/sub-001_T1w.nii.gz')
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normalization = Node(FLIRT(), name = 'normalization')
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normalization.inputs.reference = Info.standard_image('MNI152_T1_1mm_brain.nii.gz')
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workflow.connect(brain_extraction, 'out_file', normalization, 'in_file')
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export_brain = Node(ExportFile(), name = 'export_brain')
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export_brain.inputs.clobber = True
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export_brain.inputs.out_file = abspath(
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'derivatives/normalize/sub-001/anat/sub-001_T1w_brain.nii.gz')
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workflow.connect(brain_extraction, 'out_file', export_brain, 'in_file')
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export_normalized_brain = Node(ExportFile(), name = 'export_normalized_brain')
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export_normalized_brain.inputs.clobber = True
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export_normalized_brain.inputs.out_file = abspath(
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'derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz')
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workflow.connect(brain_extraction, 'out_file', export_normalized_brain, 'in_file')
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# Run workflow
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workflow.run()

‎examples/nipype/derivatives/normalize/sub-001/anat/sub-001_T1w_brain.json‎

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{
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"GeneratedBy": "bids::prov/#export_file-i1cblvll"
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}

‎examples/nipype/derivatives/normalize/sub-001/anat/sub-001_T1w_brain.nii.gz‎

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‎examples/nipype/derivatives/normalize/sub-001/anat/sub-001_prov-normalize_act.prov.json‎

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{
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"bids::prov/#bet-ys913vx4": {
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"Label": "brain_extraction",
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"Command": "bet sub-001_T1w.nii.gz sub-001_T1w_brain.nii.gz",
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"AssociatedWith": "bids::prov/#fsl-e1oq534p",
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"Used": [
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{
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"Id": "bids::sub-001/anat/sub-001_T1w.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w.nii.gz"
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},
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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]
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},
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"bids::prov/#flirt-xzje9hjh": {
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"Label": "normalization",
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"Command": "flirt -in /work/derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out sub-001_T1w_brain_flirt.nii.gz -omat sub-001_T1w_brain_flirt.mat",
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"AssociatedWith": "bids::prov/#fsl-e1oq534p",
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"Used": [
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{
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"Id": "bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w_brain.nii.gz",
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"GeneratedBy": "bids::prov/#bet-ys913vx4"
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},
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"/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz",
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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]
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},
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"bids::prov/#export_file-i1cblvll": {
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"Label": "export_brain",
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"Command": "shutil.copy",
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"AssociatedWith": "bids::prov/#nipype-s9w94f9u",
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"Used": [
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"bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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]
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},
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"bids::prov/#export_file-fpw3jrwy": {
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"Label": "export_normalized_brain",
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"Command": "shutil.copy",
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"AssociatedWith": "bids::prov/#nipype-s9w94f9u",
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"Used": [
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{
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"Id": "bids::derivatives/bids_prov_workflow/normalization/sub-001_T1w_brain_flirt.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w_brain_flirt.nii.gz",
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"GeneratedBy": "bids::prov/#flirt-xzje9hjh"
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},
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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]
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}
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}

‎examples/nipype/derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.json‎

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{
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"GeneratedBy": "bids::prov/#export_file-fpw3jrwy"
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}

‎examples/nipype/derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz‎

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‎examples/nipype/prov/merged/prov-normalize.prov.jsonld‎

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{
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"Records": {
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"Software": [
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{
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"Label": "Nipype",
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"Version": "1.8.6.dev0",
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"AltIdentifier": "RRID:SCR_002502",
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"Id": "bids::prov/#nipype-s9w94f9u"
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},
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{
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"Label": "FSL",
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"Version": "5.0",
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"AltIdentifier": "RRID:SCR_002823",
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"prov:actedOnBehalfOf": "bids::prov/#nipype-s9w94f9u",
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"Id": "bids::prov/#fsl-e1oq534p"
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}
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],
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"Activities": [
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{
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"Label": "brain_extraction",
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"Command": "bet sub-001_T1w.nii.gz sub-001_T1w_brain.nii.gz",
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"AssociatedWith": "bids::prov/#fsl-e1oq534p",
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"Used": [
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{
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"Id": "bids::sub-001/anat/sub-001_T1w.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w.nii.gz"
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},
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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],
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"Id": "bids::prov/#bet-ys913vx4"
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},
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{
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"Label": "normalization",
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"Command": "flirt -in /work/derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out sub-001_T1w_brain_flirt.nii.gz -omat sub-001_T1w_brain_flirt.mat",
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"AssociatedWith": "bids::prov/#fsl-e1oq534p",
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"Used": [
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{
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"Id": "bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w_brain.nii.gz",
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"GeneratedBy": "bids::prov/#bet-ys913vx4"
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},
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"/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz",
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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],
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"Id": "bids::prov/#flirt-xzje9hjh"
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},
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{
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"Label": "export_brain",
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"Command": "shutil.copy",
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"AssociatedWith": "bids::prov/#nipype-s9w94f9u",
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"Used": [
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"bids::derivatives/bids_prov_workflow/brain_extraction/sub-001_T1w_brain.nii.gz",
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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],
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"Id": "bids::prov/#export_file-i1cblvll"
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},
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{
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"Label": "export_normalized_brain",
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"Command": "shutil.copy",
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"AssociatedWith": "bids::prov/#nipype-s9w94f9u",
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"Used": [
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{
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"Id": "bids::derivatives/bids_prov_workflow/normalization/sub-001_T1w_brain_flirt.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w_brain_flirt.nii.gz",
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"GeneratedBy": "bids::prov/#flirt-xzje9hjh"
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},
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"bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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],
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"Id": "bids::prov/#export_file-fpw3jrwy"
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}
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],
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"Entities": [
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{
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"Label": "nipype/nipype:py38 docker image",
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"OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64",
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"Id": "bids::prov/#docker.io/nipype/nipype:py38-vavfao8v"
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},
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{
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"Label": "MNI152_T1_1mm_brain.nii.gz",
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"Id": "/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz"
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},
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{
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"Id": "bids::derivatives/normalize/sub-001/anat/sub-001_T1w_brain.nii.gz",
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"GeneratedBy": "bids::prov/#export_file-i1cblvll"
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},
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{
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"Id": "bids::derivatives/normalize/sub-001/anat/sub-001_space-mni152nlin2009casym_T1w_brain.nii.gz",
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"GeneratedBy": "bids::prov/#export_file-fpw3jrwy"
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}
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]
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},
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1"
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}

‎examples/nipype/prov/merged/prov-normalize.prov.png‎

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‎examples/nipype/prov/prov-normalize_base.prov.json‎

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{
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1"
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}

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