Adding provenance files

Author: bclenet

examples/dcm2niix_5/README.md

@@ -12,9 +12,10 @@ After conversion, and adding provenance traces, the resulting directory tree loo
 
 ```
 prov/
-├── prov-dcm2niix_act.prov.json
-├── prov-dcm2niix_env.prov.json
-└── prov-dcm2niix_soft.prov.json
+├── prov-dcm2niix_act.json
+├── prov-dcm2niix_ent.json
+├── prov-dcm2niix_env.json
+└── prov-dcm2niix_soft.json
 sourcedata/
 sub-02/
 └── anat
@@ -71,7 +72,7 @@ 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.
 
-In this example, we rely on the fact that nodes defined in the `prov/*.prov.jsonld` files have `bids::prov/` as base IRIs.
+In this example, we rely on the fact that nodes defined in the `prov/*.jsonld` files have `bids::prov/` as base IRIs.
 
 The `code/merge_prov.py` code is responsible for:
 * merging the JSON provenance traces into the base JSON-LD graph;

examples/dcm2niix_5/prov/prov-dcm2niix_act.json

@@ -0,0 +1,14 @@
+{
+  "Activities": [
+    {
+      "Id": "bids::prov/#conversion-00f3a18f",
+      "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",
+        "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
+      ]
+    }
+  ]
+}

examples/dcm2niix_5/prov/prov-dcm2niix_ent.json

@@ -0,0 +1,9 @@
+{
+  "Entities": [
+    {
+      "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+      "Type": "Entity",
+      "Label": "dicoms"
+    }
+  ]
+}

examples/dcm2niix_5/prov/prov-dcm2niix_env.json

@@ -0,0 +1,9 @@
+{
+  "Environments": [
+    {
+      "Id": "bids::prov/#fedora-uldfv058",
+      "Label": "Fedora release 36 (Thirty Six)",
+      "OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64"
+    }
+  ]
+}

examples/dcm2niix_5/prov/prov-dcm2niix_soft.json

@@ -0,0 +1,9 @@
+{
+  "Software": [
+    {
+      "Id": "bids::prov/#dcm2niix-khhkm7u1",
+      "Label": "dcm2niix",
+      "Version": "v1.0.20220720"
+    }
+  ]
+}

examples/dcm2niix_5/sub-02/anat/sub-02_T1w.json

@@ -0,0 +1,25 @@
+{
+    "Modality": "MR",
+    "ManufacturersModelName": "nifti2dicom",
+    "SoftwareVersions": "0.4.11",
+    "SeriesDescription": "anat-T1w",
+    "ProtocolName": "anat-T1w",
+    "ImageType": ["DERIVED", "SECONDARY"],
+    "RawImage": false,
+    "SeriesNumber": 401,
+    "AcquisitionTime": "13:25:18.000000",
+    "AcquisitionNumber": 1,
+    "SliceThickness": 0.666667,
+    "SpacingBetweenSlices": 0.666667,
+    "ImageOrientationPatientDICOM": [
+        0.999032,
+        -0.0217884,
+        0.0382096,
+        0.0265195,
+        0.991414,
+        -0.128044   ],
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20220720",
+    "GeneratedBy": "bids::prov/#conversion-00f3a18f",
+    "SidecarGeneratedBy": "bids::prov/#conversion-00f3a18f"
+}