print_partial_datasets

Command-line tool to scan a dataset organised in structured directories and print a table to highlight gaps. This is useful for spotting missing data or broken analyses. It relies on the wonderful fsl.utils.filetree tool from fslpy. For example:

Complete datasets
    participant    session    raw_T1    raw_bold    raw_fmap_mag    raw_fmap_ph
───────────────────────────────────────────────────────────────────────────────
            01         01         x           x               x              x
───────────────────────────────────────────────────────────────────────────────
            01         02         x           x               x              x
───────────────────────────────────────────────────────────────────────────────
Partial datasets
    participant    session    raw_T1    raw_bold    raw_fmap_mag    raw_fmap_ph
───────────────────────────────────────────────────────────────────────────────
            04         02                     x               x              x
───────────────────────────────────────────────────────────────────────────────
            07         02         x                           x              x
───────────────────────────────────────────────────────────────────────────────
            10         02         x                           x              x
───────────────────────────────────────────────────────────────────────────────

Installation

pip install print-partial-datasets

Usage

Specify your own file tree in a text file as shown in the fsl.utils.filetree documentation. This can be as simple as the example below. If your dataset is already organised in a structure such as BIDS, you may be able to use one of the preset trees:

sub-{participant}
  ses-{session}
    anat (anat_dir)
      sub-{participant}_ses-{session}_T1w.nii.gz (anat_image)
      sub-{participant}_ses-{session}_T1w_brain.nii.gz (brain_extracted)
    dwi (dwi_dir)
      sub-{participant}_ses-{session}_dwi.nii.gz (dwi_image)

You can either call the script from the command line, or programmatically from a python console or script.

Command line

print_partial_datasets -d  /data/directory -f /path/to/file.tree -s anat_image brain_extracted dwi_image -v participant session

Python

Example python usage:

from print_partial_datasets import print_partial_datasets

datadir = "/data/directory"
filetree = "/path/to/file.tree"
short_name = ["anat_image", "brain_extracted", "dwi_image"]
variables = ["participant", "session"]

print_partial_datasets(datadir, filetree, short_name, variables)

This should produce a nice printed summary of your data, with complete datasets followed by partial ones.

• Free software: Apache Software License 2.0

• Documentation: https://print-partial-datasets.readthedocs.io.

Credits

This is little more than a user-friendly wrapper around code written by Michiel Cottaar and Paul McCarthy.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.