Third example for dcm2niix

Author: bclenet

examples/dcm2niix_2/README.md

@@ -42,7 +42,7 @@ We are then able to visualize these provenance files using the following command
 
 ```shell
 pip install bids-prov==0.1.0
-    bids_prov_visualizer --input_file prov/merged/dcm2niix.prov.jsonld --output_file prov/merged/dcm2niix.prov.png
+bids_prov_visualizer --input_file prov/merged/dcm2niix.prov.jsonld --output_file prov/merged/dcm2niix.prov.png
 ```
 
 ![](/examples/dcm2niix_2/prov/merged/dcm2niix.prov.png)
@@ -51,13 +51,13 @@ pip install bids-prov==0.1.0
 
 Dataset is the same as the one for [example dcm2niix_1](/BEP028_BIDSprov/examples/dcm2niix_1/README.md#source-dataset).
 
-### Notes
+## Notes
 
 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:
 * `bids::prov/#dcm2niix-xce5m9z3`
 * `bids::prov/#fedora-b7hmkmqd`
 
-### Limitations
+## Limitations
 
 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.
 

examples/dcm2niix_3/README.md

@@ -1,44 +1,59 @@
 # BIDS Prov example for `dcm2niix`
 
-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.
+This example aims at showing provenance traces from a DICOM to Nifti conversion, performed by `dcm2niix` on a Linux-based (Fedora) operating system.
 
-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:
+## Overview
 
-```shell
-mkdir sourcedata
-cd sourcedata
-datalad install --recursive https://github.com/psychoinformatics-de/hirni-demo.git
-```
+This time, we describe the provenance records using BIDS Prov, but inside several *JSON* files.
+
+After conversion, and adding provenance traces, the resulting directory tree looks like this:
 
-> [!NOTE] Note that the dataset must be added inside the `sourcedata/` directory.
+```
+prov/
+├── prov-dcm2niix_act.prov.json
+├── prov-dcm2niix_base.prov.json
+├── prov-dcm2niix_env.prov.json
+└── prov-dcm2niix_soft.prov.json
+sourcedata/
+sub-02/
+└── anat
+    ├── sub-02_T1w.json
+    └── sub-02_T1w.nii
+```
 
-## Purpose
+Note that the `sourcedata/` directory contains the source dataset described in the [section hereafter](#source-dataset).
 
-The aim of the example is to describe the provenance records using BIDS Prov, but inside several *JSON* files.
 We use:
 
-* the `GeneratedBy` field of JSON sidecars, already existing in the BIDS specification
+* the `GeneratedBy` field of JSON sidecar, already existing in the BIDS specification
 * modality agnostic files inside the `prov/` directory
 
-as follows:
+## Provenance merge
 
+The python script `code/merge_prov.py` aims at merging all provenance records into one JSON-LD graph.
+
+```shell
+pip install bids-prov==0.1.0
+mkdir prov/merged/
+python code/merge_prov.py
 ```
-.
-├── prov
-│   ├── prov-dcm2niix_act.prov.json
-│   ├── prov-dcm2niix_base.prov.json
-│   ├── prov-dcm2niix_env.prov.json
-│   └── prov-dcm2niix_soft.prov.json
-└── sub-02
-    ├── ses-20130717141500
-    │   └── anat
-    │       └── sub-02_ses-20130717141500_T1w.json
-    └── ses-20140425155335
-        └── func
-            └── sub-02_ses-20140425155335_task-oneback_run-1_bold.json
+
+## Provenance visualization
+
+We are then able to visualize these provenance files using the following commands (current directory is `examples/dcm2niix_3/`):
+
+```shell
+pip install bids-prov==0.1.0
+bids_prov_visualizer --input_file prov/merged/prov-dcm2niix.prov.jsonld --output_file prov/merged/prov-dcm2niix.prov.png
 ```
 
-## New features for BIDS / BIDS Prov
+![](/examples/dcm2niix_3/prov/merged/prov-dcm2niix.prov.png)
+
+## Source dataset
+
+Dataset is the same as the one for [example dcm2niix_1](/BEP028_BIDSprov/examples/dcm2niix_1/README.md#source-dataset).
+
+## Notes
 
 We introduce the following BIDS entity that is currently not existing:
 * `prov`
@@ -54,26 +69,6 @@ We introduce the following BIDS suffixes that are currently not existing:
 
 We use the `GeneratedBy` field of JSON sidecars to link to `Activities` that created the file the sidecars refers to.
 
-## Merging JSON in a JSON-LD file and plotting graph
-
-The python script `code/merge_prov.py` aims at merging all these provenance records into one JSON-LD graph.
-
-```shell
-mkdir prov/merged/
-python code/merge_prov.py
-```
-
-From that, we generate the JSON-LD graph `prov/merge/prov-dcm2niix.prov.jsonld`. Then we were able to plot the graph as a png file. We used this command:
-
-```shell
-pip install bids-prov==0.1.0
-bids_prov_visualizer --input_file prov/merged/prov-dcm2niix.prov.jsonld --output_file prov/merged/prov-dcm2niix.prov.png
-```
-
-![](/examples/dcm2niix/prov/merged/prov-dcm2niix.prov.png)
-
-### Notes
-
 In this example, we rely on the fact that nodes defined in the `prov/*.prov.jsonld` files have `bids::prov/` as base IRIs.
 
 The `code/merge_prov.py` code is responsible for:
@@ -86,7 +81,6 @@ The `code/merge_prov.py` code is responsible for:
 
 2. 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`:
 * `bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms`
-* `bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms`
 
 although it is not allowed by the current version of the BIDS Prov specification to have directories as `Entities`.
 

examples/dcm2niix_3/prov/merged/prov-dcm2niix.prov.jsonld

@@ -0,0 +1,40 @@
+{
+  "Records": {
+    "Software": [
+      {
+        "Label": "dcm2niix",
+        "Version": "v1.0.20220720",
+        "Id": "bids::prov/#dcm2niix-khhkm7u1"
+      }
+    ],
+    "Activities": [
+      {
+        "Label": "Conversion",
+        "Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+        "AssociatedWith": "bids::prov/#dcm2niix-khhkm7u1",
+        "Used": [
+          "bids::prov/#fedora-uldfv058",
+          {
+            "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+            "Type": "Entity",
+            "Label": "dicoms"
+          }
+        ],
+        "Id": "bids::prov/#conversion-00f3a18f"
+      }
+    ],
+    "Entities": [
+      {
+        "Label": "Fedora release 36 (Thirty Six)",
+        "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64",
+        "Id": "bids::prov/#fedora-uldfv058"
+      },
+      {
+        "Id": "bids::sub-02/anat/sub-02_T1w.nii",
+        "GeneratedBy": "bids::prov/#conversion-00f3a18f"
+      }
+    ]
+  },
+  "@context": "https://purl.org/nidash/bidsprov/context.json",
+  "BIDSProvVersion": "0.0.1"
+}