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Activities in prov/ dir
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‎examples/dcm2niix/README.md‎

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@@ -39,18 +39,19 @@ as follows:
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## New features for BIDS / BIDS Prov
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We introduce the following BIDS suffixes that are currently not existing:
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* `soft`: the file describes BIDS Prov `Software` for the provenance traces
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* `env`: the file describes BIDS Prov `Environments` for the provenance traces
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* `base`: the file describes common BIDS Prov parameters for the provenance traces (version and context for BIDS Prov)
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We introduce the following BIDS entity that is currently not existing:
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* `prov`
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* Full name: Provenance traces
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* Format: `prov-<label>`
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* Definition: A grouping of provenance traces. Defining multiple provenance traces groups is appropriate when several processings have been performed on data.
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We use the `GeneratedBy` field of JSON sidecars to describe `Activities` that created the file the sidecars refers to.
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We introduce the following BIDS suffixes that are currently not existing:
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* `act`: the file describes BIDS Prov `Activities` for the group of provenance traces
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* `soft`: the file describes BIDS Prov `Software` for the group of provenance traces
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* `env`: the file describes BIDS Prov `Environments` for the group of provenance traces
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* `base`: the file describes common BIDS Prov parameters for the group of provenance traces (version and context for BIDS Prov)
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We use the `GeneratedBy` field of JSON sidecars to link to `Activities` that created the file the sidecars refers to.
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## Merging JSON in a JSON-LD file and plotting graph
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‎examples/dcm2niix/code/merge_prov.py‎

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@@ -13,6 +13,9 @@
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prov_env_files = [
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'prov/prov-dcm2niix_env.prov.json'
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]
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prov_act_files = [
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'prov/prov-dcm2niix_act.prov.json'
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]
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sidecar_files = [
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'sub_02/ses_20130717141500/anat/sub-02_ses-20130717141500_T1w.json',
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'sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json'
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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 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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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 = data['GeneratedBy']
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base_provenance['Records']['Activities'].append(activity)
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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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"GeneratedBy": activity_id
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})
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# Write jsonld

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

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@@ -9,8 +9,6 @@
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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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"Type": "Activity",
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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-khhkm7u1",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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],
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"Id": "bids::prov/conversion-00f3a18f"
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},
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{
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"Id": "urn:conversion-5a66f5be",
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"Type": "Activity",
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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-khhkm7u1",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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],
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"Id": "bids::prov/conversion-5a66f5be"
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}
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],
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"Entities": [
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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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"GeneratedBy": "urn:conversion-00f3a18f"
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"GeneratedBy": "bids::prov/conversion-00f3a18f"
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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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"GeneratedBy": "urn:conversion-5a66f5be"
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"GeneratedBy": "bids::prov/conversion-5a66f5be"
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}
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]
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},

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

-18 Bytes
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‎examples/dcm2niix/prov/prov-dcm2niix_act.prov.json‎

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{
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"bids::prov/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-khhkm7u1",
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"Used": [
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"bids::prov/fedora-uldfv058",
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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},
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"bids::prov/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-khhkm7u1",
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"Used": [
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"bids::prov/fedora-uldfv058",
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{
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"Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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}
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}

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

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-0.128044 ],
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20220720",
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"GeneratedBy": {
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"Id": "urn:conversion-00f3a18f",
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"Type": "Activity",
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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-khhkm7u1",
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"Used": [
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"bids::prov/fedora-uldfv058",
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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}
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"GeneratedBy": "bids::prov/conversion-00f3a18f"
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}

‎examples/dcm2niix/sub_02/ses_20140425155335/func/sub-02_ses-20140425155335_task-oneback_run-1_bold.json‎

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"InPlanePhaseEncodingDirectionDICOM": "COL",
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20220720",
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"GeneratedBy": {
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"Id": "urn:conversion-5a66f5be",
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"Type": "Activity",
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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-khhkm7u1",
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"Used": [
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"bids::prov/fedora-uldfv058",
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{
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"Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
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"Type": "Entity",
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"Label": "dicoms"
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}
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]
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}
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"GeneratedBy": "bids::prov/conversion-5a66f5be"
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}

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