Removing sidecar jsonlds

Author: bclenet

examples/dcm2niix/README.md

@@ -54,37 +54,21 @@ tree sub-02/
 
 ## Associated provenance
 
-See the `dcm2niix.prov.jsonld` file that contains all provenance traces relative to the conversion steps.
-
-Two file level provenance files (`.prov.jsonld` sidecars) are also available, representing the provenance of the associated files:
-* `sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld`
-* `sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld`
-
-Note that these files are independant and self-sufficient, although they describe the same provenance traces. To be more specific: `dcm2niix.prov.jsonld` contains all information described by the two sidecar files.
+The `prov/dcm2niix.prov.jsonld` file contains all provenance traces relative to the conversion steps.
 
 We are able to visualize these provenance files using the following commands (current directory is `examples/dcm2niix/`):
 
 ```shell
+pip install -r ../../requirements.txt
 python ../../bids_prov/visualize.py --input_file prov/dcm2niix.prov.jsonld --output_file prov/dcm2niix.prov.png
 ```
 ![](/examples/dcm2niix/prov/dcm2niix.prov.png)
 
-```shell
-python ../../bids_prov/visualize.py --input_file sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.jsonld --output_file sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.png
-```
-![](/examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.prov.png)
-
-```shell
-python ../../bids_prov/visualize.py --input_file sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.jsonld --output_file sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.png
-```
-![](/examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.prov.png)
-
 ## Limitations
 
 ### Using the JSON-LD playground
 
-These example files can be tested inside the [JSON-LD playground](https://json-ld.org/playground/), although the context IRI must be changed to:
-`https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json`
+The `prov/dcm2niix.prov.jsonld` file can be tested inside the [JSON-LD playground](https://json-ld.org/playground/), although the context IRI must be changed to: `https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json`
 
 ### `Used` key for activities
 
@@ -94,9 +78,20 @@ Although the BIDS-Prov spec mentions:
 
 We represented used entities in a list to link all the dicom files of a directory to the corresponding conversion activity.
 
+### `Environments` not defined in the context
+
+We cannot use an `Environments` list because the current context (commit ce0eb77) does not define the `Environments` term. Therefore, we defined the `urn:fedora-b7hmkmqd` environments as an `Entity`.
+
 ### High number of dicom files
 
-As there is a high number of dicom files (384 in `acq1/` and 5460 in `acq2/`), we did not create an entity for each of these. Only the first three files of each directory were represented.
+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`.
 
 ### `TaskName` not generated
 

examples/dcm2niix/prov/dcm2niix.prov.jsonld

@@ -2,16 +2,9 @@
   "@context": "https://purl.org/nidash/bidsprov/context.json",
   "BIDSProvVersion": "0.0.1",
   "Records": {
-    "prov:Entity": [
-      {
-        "Id": "urn:fedora",
-        "Label": "Fedora release 36 (Thirty Six)",
-        "OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
-      }
-    ],
     "Software": [
       {
-        "Id": "urn:dcm2niix",
+        "Id": "urn:dcm2niix-xce5m9z3",
         "Label": "dcm2niix",
         "Version": "v1.0.20220720"
       }
@@ -21,51 +14,31 @@
         "Id": "urn:conversion-00f3a18f",
         "Label": "Conversion",
         "Command": "dcm2niix -o . -f sub-%i/ses-%t/anat/sub-%i_ses-%t_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/",
-        "AssociatedWith": "urn:dcm2niix",
+        "AssociatedWith": "urn:dcm2niix-xce5m9z3",
         "Used": [
-          "urn:fedora",
-          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm",
-          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm",
-          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm"
+          "urn:fedora-b7hmkmqd",
+          "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
         ]
       },
       {
         "Id": "urn:conversion-5a66f5be",
         "Label": "Conversion",
         "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/",
-        "AssociatedWith": "urn:dcm2niix",
+        "AssociatedWith": "urn:dcm2niix-xce5m9z3",
         "Used": [
-          "urn:fedora",
-          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586",
-          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588",
-          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590"
+          "urn:fedora-b7hmkmqd",
+          "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms"
         ]
       }
     ],
     "Entities": [
       {
-        "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0001.dcm",
-        "Label": "N2D_0001.dcm"
-      },
-      {
-        "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0002.dcm",
-        "Label": "N2D_0002.dcm"
-      },
-      {
-        "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/N2D_0003.dcm",
-        "Label": "N2D_0003.dcm"
+        "Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
+        "Label": "dicoms"
       },
       {
-        "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586",
-        "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042547586"
-      },
-      {
-        "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588",
-        "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042548588"
-      },
-      {
-        "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590",
-        "Label": "MR.1.3.46.670589.11.38317.5.0.4476.2014042516042551590"
+        "Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
+        "Label": "dicoms"
       },
       {
         "Id": "bids::sub-02/ses-20130717141500/anat/sub-02_ses-20130717141500_T1w.nii",
@@ -86,6 +59,11 @@
         "Id": "bids::sub-02/ses-20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
         "Label": "sub-02_ses-20140425155335_task-oneback_run-1_bold.json",
         "GeneratedBy": "urn:conversion-5a66f5be"
+      },
+      {
+        "Id": "urn:fedora-b7hmkmqd",
+        "Label": "Fedora release 36 (Thirty Six)",
+        "OperatingSystem": " GNU/Linux 6.2.15-100.fc36.x86_64"
       }
     ]
   }

examples/dcm2niix/prov/dcm2niix.prov.png

@@ -0,0 +1,23 @@
+{
+    "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"
+}

examples/dcm2niix/sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.json

@@ -0,0 +1,61 @@
+{
+    "Modality": "MR",
+    "MagneticFieldStrength": 3,
+    "ImagingFrequency": 127.753,
+    "Manufacturer": "Philips",
+    "ManufacturersModelName": "Achieva dStream",
+    "PatientPosition": "HFS",
+    "ProcedureStepDescription": "Transrep2",
+    "SoftwareVersions": "5.1.1\\5.1.1.0",
+    "MRAcquisitionType": "2D",
+    "SeriesDescription": "func_task-oneback_run-1",
+    "ProtocolName": "func_task-oneback_run-1",
+    "TaskName": "oneback",
+    "ScanningSequence": "GR",
+    "SequenceVariant": "SK",
+    "ScanOptions": "FS",
+    "PulseSequenceName": "FEEPI",
+    "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"],
+    "SeriesNumber": 401,
+    "AcquisitionTime": "16:04:22.680000",
+    "AcquisitionNumber": 4,
+    "PhilipsRWVSlope": 4.00757,
+    "PhilipsRWVIntercept": 0,
+    "PhilipsRescaleSlope": 4.00757,
+    "PhilipsRescaleIntercept": 0,
+    "PhilipsScaleSlope": 0.0132383,
+    "UsePhilipsFloatNotDisplayScaling": 1,
+    "SliceThickness": 3,
+    "SpacingBetweenSlices": 3.3,
+    "SAR": 0.994626,
+    "EchoTime": 0.03,
+    "RepetitionTime": 1.79355,
+    "RepetitionTimeExcitation": 2,
+    "MTState": false,
+    "FlipAngle": 90,
+    "CoilString": "MULTI COIL",
+    "PercentPhaseFOV": 100,
+    "PercentSampling": 100,
+    "EchoTrainLength": 43,
+    "PhaseEncodingSteps": 80,
+    "AcquisitionMatrixPE": 80,
+    "ReconMatrixPE": 80,
+    "ParallelReductionFactorInPlane": 2,
+    "ParallelAcquisitionTechnique": "SENSE",
+    "WaterFatShift": 12.4991,
+    "EstimatedEffectiveEchoSpacing": 0.000355975,
+    "EstimatedTotalReadoutTime": 0.028122,
+    "AcquisitionDuration": 325.918,
+    "PixelBandwidth": 1920,
+    "PhaseEncodingAxis": "j",
+    "ImageOrientationPatientDICOM": [
+        0.999805,
+        -0.0114282,
+        0.0161145,
+        0.0147905,
+        0.973763,
+        -0.227084   ],
+    "InPlanePhaseEncodingDirectionDICOM": "COL",
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20220720"
+}