niprov
provenance for neuroimaging data
Ever encountered a file of which you weren’t sure what analysis steps it had gone through? Ever wanted to know what types of data you have available for a subject in one overview? Automatically document an analysis pipeline?
Provenance is meta-data that tracks the ‘history’ of a file, and niprov is a python program to create, store and publish provenance for brain imaging files.
A list with all provenance attributes collected can be found here. Read more in the full online documentation (or pdf). For additional detailed information on image files, install nibabel,mne and/or pydicom.
Commandline Usage
Install niprov:
pip install niprovLook for existing image files in your data directory:
provenance discover /my/data/directoryRun a transformation command and log it as provenance for the new file:
provenance record mcflirt -in t1flip_all_orig -out t1all_reg -refvol 0Store provenance of known MEG files as an xml file:
provenance export --modality "MEG" --xmlPython API
import niprov
provenance = niprov.ProvenanceContext()
# Log an analysis step:
someAnalysisPackage.correctmotion(input='JD-fmri.nii', output='JD-fmri-3dmc.nii')
provenance.log('JD-fmri.nii', 'motion correction', ['JD-fmri-3dmc.nii'])
# Loop over images of John Smith and display a preview:
for image in provenance.get().bySubject('John Smith'):
image.viewSnapshot()
# Make sure two files were acquired with the same parameters:
img1.compare(img2).assertEqualProtocol()Web browser
By running the command provenance serve you can start a mini webserver in the background, and browse images in your webbrowser:
1 maintainer
Metadata
1 maintainer
Release files for niprov 0.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| niprov-0.5.tar.gz | 239.6 kB | Without provenance | Details for niprov-0.5.tar.gz |
Release files / niprov-0.5.tar.gz
| Download URL | niprov-0.5.tar.gz |
|---|---|
| Size | 239.6 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
a0daa672b6564929865fedf2cb621dc34904446a7e5271d8b3736d4abf09d3ea
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BLAKE2b-256 checksum How to use checksums |
50c44ac2c6daea9ce96b9bc9a6d50e227277831b33afebc65c6eb94dc5f65779
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Security for niprov 0.5
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
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