Terminal-based GUI for fsl-pipe. It allows interactively choosing which subset of potential output files you want an fsl-pipe pipeline to produce.

Installation

pip install fsl-pipe-gui

Any bug reports and feature requests are very welcome (see issue tracker).

Usage

For any pipelines using the standard command line interface, the GUI will be available using the -g/--gui flag. Some pipelines might have customised this flag. Please check their documentation.

When starting the GUI from your own custom python code, you will need:

• a file_tree describing the paths of the input and output files (see file-tree).
• a pipeline containing the recipes to produce the output from the input files (see fsl-pipe). The GUI can then be started using

pipeline.gui(file_tree)

This GUI consists of 3 parts, which will be presented to the user in sequence:

1. An interactive table, where the default values for placeholders (e.g., subject or session id) can be overwritten.
2. A visualisation of the file_tree on the left. For the template selected on the left, the matching filenames are shown on the right. If you want the pipeline to produce a specific file, simply click on the row to mark the checkbox. Files without a checkbox cannot be produced by this pipeline. If the checkbox has been replaced by an "M" then the file cannot be produced due to a missing input file. Filenames in blue already exist (but can be produced by the pipeline anyway if it has a checkbox).
3. A summary of which files are requested and which jobs will actually be run. If the user confirms this summary then the pipeline will actually run.