labcas-svsedit 0.0.0

PHI/PII removal tool for SVS files

🔬 SVS edit

Editing SVS files (headers) using python module tifftools.

📀 Installation

Create a Python virtual environment (to isolate dependencies from other Python packages you may be using), activate it, and then install it. Typically:

$ python3.13 -m venv svs
$ cd svs
$ source bin/activate  # Or source bin/activate.csh for csh/tcsh users
(venv) $ pip install labcas-svsedit

This makes the svs-edit command-line tool available; run:

svs-edit --help

To see the options. For example, to replace the Filename field with the text deid in input.svs and write to output.svs, run:

svs-edit --edit-desc Filename=deid input.svs output.svs

You can run on batches of files by wrapping the svs-edit invocation in a loop. For example, to replace the Filename field with the basename (without extension) of the SVS's file's name:

$ for f in *.svs; do
> svs-edit --edit-desc Filename=$(basename $f .svs) $f subdir/$f
> done

Or in csh/tcsh:

% foreach f (*.svs)
foreach? svs-edit. --edit-desc Filename=$f:r $f subdir/$f
foreach? end

By default the above replaces only those components which have the corresponding tag.

Changes can be tested by dumping the header of the newly written file using: tifftools dump subdir/svsfile.svs

🛠️ Development

To develop and debug this software, clone this repository and install the source code into a Python virtual environment in editable mode:

$ git clone https://github.com/jpl-labcas/svs_edit.git
$ cs svs_edit
$ python3.13 -m venv .venv
$ source .venv/bin/activate  # Or source .venv/bin/activate.csh for csh/tcsh users
(venv) $ pip install --editable .

The svs-edit command now uses the source code under src/jpl/labacs/svs and changes made to Python files take effect when the command is next run.

🥧 Making Releases

To release the software to the Python Package Index use build and twine:

$ pip install build twine
$ .venv/bin/python3 -m build .
$ twine upload dist/*

👥 Contributing

Within the JPL Informatics Center, we value the health of our community as much as the code, and that includes participation in creating and refining this software. Towards that end, we ask that you read and practice what's described in these documents:

• Our contributor's guide delineates the kinds of contributions we accept.
• Our code of conduct outlines the standards of behavior we practice and expect by everyone who participates with our software.

🔢 Versioning

We use the SemVer philosophy for versioning this software.

📃 License

The project is licensed under the Apache version 2 license.