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‎examples/dcm2niix/README.md‎

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This example aims at showing the capture of provenance for a [`dcm2niix`](https://github.com/rordenlab/dcm2niix) usecase: converting DICOM data to Nifti files within a BIDS dataset.
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Source data for this example can be found here: https://github.com/psychoinformatics-de/hirni-demo. This is a datalad dataset containing anatomical and functional MRI acquisitions. The contents of this dataset can be downloaded using:
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```shell
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mkdir sourcedata
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cd sourcedata
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> [!NOTE] Note that the dataset must be added inside the `sourcedata/` directory.
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## Experiment #1
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## Purpose
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The aim of the example is to describe the provenance records inside several files. Here we use sidecars and modality agnostic files inside the `prov/` directory, as follows:
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The aim of the experiment is to describe the provenance records inside several files. Here we use sidecars and modality agnostic files inside the `prov/` directory, as follows:
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```
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.
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├── prov
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└── sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld
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```
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* `sub-02_ses-20130717141500_T1w.prov.jsonld` and `sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld` are sidecars defining provenance for the corresponding `.nii` files.
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* `sub-02_ses-20130717141500_T1w.prov.jsonld` and `sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld` are "sidecars" defining provenance for the corresponding `.nii` files.
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* `environments.prov.jsonld` mutualises the declaration of software environments objects for lower level prov files
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* `software.prov.jsonld` mutualises the declaration of software pieces objects for lower level prov files
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The python script `code/exp1_merge_prov.py` aims at merging all these provenance records into one RFD graph.
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The python script `code/merge_prov.py` aims at merging all these provenance records into one JSON-LD graph.
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```shell
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pip install -r code/requirements.txt
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mkdir prov/experiment_1/
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python code/exp1_merge_prov.py
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pip install bids-prov==0.1.0
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mkdir prov/merged/
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python code/merge_prov.py
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```
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From that, we generate the RDF graph `prov/experiment_1/merged_provenance.ttl`. Then we were able to plot the graph as a png file. We used this command:
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From that, we generate the graph `prov/merged/dcm2niix.prov.jsonld`. Then we were able to plot the graph as a png file. We used this command:
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```shell
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python code/plot_graph.py -i prov/experiment_1/merged_provenance_2.ttl -o prov/experiment_1/merged_provenance_2.png
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bids_prov_visualizer --input_file prov/merged/dcm2niix.prov.jsonld --output_file prov/merged/dcm2niix.prov.png
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```
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![](/examples/dcm2niix/prov/experiment_1/merged_provenance.png)
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![](/examples/dcm2niix/prov/merged/dicom2niix.prov.png)
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### Notes
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In this example, we rely on the fact that nodes defined in the `prov/*.prov.jsonld` files have `bids::prov/` as base IRIs. Here are the involved nodes:
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* `bids::prov/dcm2niix`
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* `bids::prov/fedora`
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* `bids::prov/dcm2niix-xce5m9z3`
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* `bids::prov/fedora-b7hmkmqd`
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### Limitations
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The `bids::prov/fedora` node defined in `prov/environments.prov.jsonld` (see grey node in the above graph plot) is not recognized as a `prov:Entity` as the current context (commit [ce0eb77](https://github.com/bids-standard/BEP028_BIDSprov/commit/ce0eb774abd9527e594bd69212a87d5047864678)) does not define the `Environments` term.
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The `bids::prov/fedora-b7hmkmqd` node defined in `prov/environments.prov.jsonld` is defined as an `Entity` as the current context (commit [ce0eb77](https://github.com/bids-standard/BEP028_BIDSprov/commit/ce0eb774abd9527e594bd69212a87d5047864678)) does not define the `Environments` term.
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Listing all the DICOM files used by the dcm2niix conversion steps would lower readability of the JSON-LD provenance files. Therefore we only listed the following directories as `Entities`:
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* `bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/`
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* `bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/`
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* `bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms`
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* `bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms`
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although it is not allowed by the current version of the BIDS Prov specification to have directories as `Entities`.

‎examples/dcm2niix/code/exp1_merge_prov.py‎

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‎examples/dcm2niix/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-LD files into one JSON-LD graph """
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import json
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from bids_prov.visualize import join_jsonld
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# List of available prov files
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prov_files = [
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'prov/software.prov.jsonld',
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'prov/environments.prov.jsonld',
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'sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld',
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'sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld'
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]
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# Generate JSON-LD graph of each file using pyld
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graphs = list()
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for prov_file in prov_files:
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with open(prov_file, encoding = 'utf-8') as file:
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graphs.append(json.load(file))
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# Merge graphs & Write JSON-LD graph
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with open('prov/merged/dcm2niix.prov.jsonld', 'w' , encoding = 'utf-8') as file:
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file.write(json.dumps(join_jsonld(graphs, omit_details = False), indent = 2))

‎examples/dcm2niix/code/plot_graph.py‎

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‎examples/dcm2niix/code/requirements.txt‎

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‎examples/dcm2niix/prov/environments.prov.jsonld‎

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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1",
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"Records": {
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"Environments": [
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"Entities": [
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{
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"Id": "bids::prov/fedora",
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"Id": "bids::prov/fedora-b7hmkmqd",
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
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}

‎examples/dcm2niix/prov/experiment_1/merged_provenance.png‎

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‎examples/dcm2niix/prov/experiment_1/merged_provenance.ttl‎

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‎examples/dcm2niix/prov/merged/dcm2niix.prov.jsonld‎

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{
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"Records": {
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"Software": [
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{
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"Id": "bids::prov/dcm2niix-xce5m9z3",
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"Label": "dcm2niix",
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"Version": "v1.0.20220720"
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}
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],
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"Entities": [
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{
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"Id": "bids::prov/fedora-b7hmkmqd",
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
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},
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"Label": "dicoms"
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},
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{
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"Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii",
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"Label": "sub-02_ses-20130717141500_T1w.nii",
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"GeneratedBy": "urn:conversion-00f3a18f"
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},
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{
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"Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.json",
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"Label": "sub-02_ses-20130717141500_T1w.json",
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"GeneratedBy": "urn:conversion-00f3a18f"
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},
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{
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"Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
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"Label": "dicoms"
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},
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{
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"Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.nii",
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"Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.nii",
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"GeneratedBy": "urn:conversion-5a66f5be"
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},
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{
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"Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
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"GeneratedBy": "urn:conversion-5a66f5be"
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}
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],
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"Activities": [
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{
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"Id": "urn:conversion-00f3a18f",
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"Label": "Conversion",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"AssociatedWith": "bids::prov/dcm2niix-xce5m9z3",
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"Used": [
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"bids::prov/fedora-b7hmkmqd",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
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]
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},
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{
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"Id": "urn:conversion-5a66f5be",
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"Label": "Conversion",
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"Command": "dcm2niix -o . -f sub-%i/ses-%t/func/sub-%i_ses-%t_task-oneback_run-1_bold sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
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"AssociatedWith": "bids::prov/dcm2niix-xce5m9z3",
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"Used": [
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"bids::prov/fedora-b7hmkmqd",
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"bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms"
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]
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}
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]
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}
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}

‎examples/dcm2niix/prov/merged/dcm2niix.prov.png‎

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