niprov¶
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.
To get started, install niprov using pip:
pip install niprov
Keep in mind that to open image files you may need other libraries, such as mne-python, nibabel or pydicom.
The next step is to look through your directories for image files:
provenance discover /my/data/dir
After which you can start looking at what you’ve collected:
provenance report
You can do the same in python code:
import niprov
niprov.discover('.')
print(niprov.report()) #this will return a list of dictionaries
Read on to see other features and options.
Get in touch if you have questions or suggestions, by submitting an issue on http://github.com/ilogue/niprov or via email to jasperb@uw.edu, or at tweet to @niprovenance
Contents:
- Commandline Usage
- Code Examples
- Configuration
- Provenance Fields
- path
- hostname
- user
- location
- added
- version-added
- size
- hash
- created
- transient
- modality
- acquired
- duration
- subject
- dimensions
- project
- protocol
- subject-position
- water-fat-shift
- transformation
- parent
- code
- logtext
- script
- args
- kwargs
- sampling-frequency
- fif-type
- lowpass
- highpass
- bad-channels
- projection-description
- seriesuid
- filesInSeries
- technique
- repetition-time
- field-of-view
- epi-factor
- magnetization-transfer-contrast
- diffusion
- slice-thickness
- slice-orientation
- echo-time
- flip-angle
- inversion-time
- MongoDB setup
- niprov package
- Submodules
- niprov.adding module
- niprov.approval module
- niprov.basefile module
- niprov.camera module
- niprov.capturing module
- niprov.clock module
- niprov.cnt module
- niprov.commandline module
- niprov.comparing module
- niprov.config module
- niprov.context module
- niprov.dcm module
- niprov.dependencies module
- niprov.diff module
- niprov.discovery module
- niprov.exceptions module
- niprov.exporting module
- niprov.externals module
- niprov.fif module
- niprov.filefilter module
- niprov.files module
- niprov.filesystem module
- niprov.format module
- niprov.formatdict module
- niprov.formatfactory module
- niprov.formatjson module
- niprov.formatnarrated module
- niprov.formatobject module
- niprov.formatsimple module
- niprov.formatxml module
- niprov.hashing module
- niprov.importing module
- niprov.inheriting module
- niprov.inspection module
- niprov.jsonfile module
- niprov.libraries module
- niprov.location module
- niprov.locationfactory module
- niprov.mediumdirect module
- niprov.mediumfactory module
- niprov.mediumfile module
- niprov.mediumstdout module
- niprov.mediumviewer module
- niprov.mnefun module
- niprov.mongo module
- niprov.nifti module
- niprov.parrec module
- niprov.pictures module
- niprov.pipeline module
- niprov.pipelinefactory module
- niprov.plogging module
- niprov.querying module
- niprov.recording module
- niprov.renaming module
- niprov.reporting module
- niprov.repository module
- niprov.searching module
- niprov.users module
- niprov.views module
- niprov.webapp module
- Module contents
- Submodules