trialbureautools

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Command line utility for the radboudumc trial bureau.

Features

  • Sort DICOM files into folders based on DICOM tag patterns

  • Set windows icacls folder permissions

Getting started

See Getting started

Credits

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

trialbureautools

https://img.shields.io/pypi/v/trialbureautools.svg https://img.shields.io/travis/sjoerdk/trialbureautools.svg Documentation Status Updates

Command line utility for the radboudumc trial bureau.

Features

  • Sort DICOM files into folders based on DICOM tag patterns

  • Set windows icacls folder permissions

Getting started

See Getting started

Credits

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

Installation

Stable release

To install trialbureautools, run this command in your terminal:

$ pip install trialbureautools

This is the preferred method to install trialbureautools, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for trialbureautools can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/sjoerdk/trialbureautools

Or download the tarball:

$ curl  -OL https://github.com/sjoerdk/trialbureautools/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Usage

Basics

The trial bureau tools are accessed from command line. On windows you can start a command line (also called ‘terminal’ or ‘shell’) in the following way:

  • Press windows-key + r

  • type ‘cmd’ and press enter

After that, typing 'tbt' + enter will show the different commands available trial bureau tools.

You can add ‘–help’ to any command to see more info on using it. For example tbt sort --help

DICOM sorter

To sort all DICOM files in directory job1 using the nucmed pattern:

$ tbt sorter sort job1 nucmed

To see what the ‘nucmed’ pattern is exactly:

$ tbt sorter pattern list

By default, sorting /folder1 will write sorted output to /folder1_sorted. You can also set the output folder manually:

$ tbt sorter sort job1 nucmed --output_folder C:/temp/myfolder

DICOM path patterns

Typing tbt sorter pattern list will by default show the following:

$ tbt sorter pattern list
> idis: (0010,0020)/(0008,1030)-(0008,0050)/(0008,103e)-(0008,0060)-(0020,0011)/(count:SOPInstanceUID)
> nucmed: (0010,0020)/(0008,1030)-(0008,0050)/(0008,0020)/(0008,103e)-(0008,0060)-(0020,0011)/(count:SOPInstanceUID)

These are the DICOM path patterns. These are text strings consisting of any combination of the following elements:

Element

Examples

Description

Text

Folder file- /tmp. .dcm

Just any free text, inc. slash and -

Dicom Tag Code

(0010,0020) (0008,103e)

A dicom tag with colons around it

Dicom Tag Name

(PatientID) (SopInstanceUID)

A dicom tag name

count: marker

(count:PatientID) (count:0008,103e)

Will number the given tag

To see a list of available Dicom tag codes and names, use tbt sorter pattern list_dicomtags

Dicom Pattern resolution

For each DICOM file a new path will be created by reading its values and filling in the pattern. For example, for a file with PatientID ‘1234’ and SopInstanceUID ‘1.1.1’:

Pattern

Result (1 file)

/folder1/(PatientID)/(SopInstanceUID).dcm

/folder1/1234/1.1.1.dcm
Counting

Counting can be useful to make paths shorter. By adding count: to an element, the sorter will number each unique value. For example, for three files with the same PatientID but separate SopInstanceUIDs:

Pattern without :count

Result (3 files)

/folder1/(PatientID)/(SopInstanceUID).dcm

/folder1/1234/1.3451.35356.4234.1.dcm

/folder1/1234/1.3451.35356.4234.2.dcm

/folder1/1234/1.3451.35356.4234.3.dcm

Pattern with :count

Result (3 files)

/folder1/(PatientID)/file(count:SopInstanceUID).dcm

/folder1/1234/file0.dcm

/folder1/1234/file1.dcm

/folder1/1234/file2.dcm
Adding custom patterns

To add a new pattern /folder1/(PatientID)/file(count:SopInstanceUID).dcm named test:

$ tbt sorter pattern add test /folder1/(PatientID)/file(count:SopInstanceUID).dcm

To remove this pattern again:

$ tbt sorter pattern remove test

Modules

dicomsort

Core
mappers
parser
folderprocessing

Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/sjoerdk/trialbureautools/issues.

If you are reporting a bug, please include:

  • Your operating system name and version.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

trialbureautools could always use more documentation, whether as part of the official trialbureautools docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/sjoerdk/trialbureautools/issues.

If you are proposing a feature:

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up trialbureautools for local development.

  1. Fork the trialbureautools repo on GitHub.

  2. Clone your fork locally:

    $ git clone git@github.com:your_name_here/trialbureautools.git

  3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

    $ mkvirtualenv trialbureautools
$ cd trialbureautools/
$ python setup.py develop

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:

    $ flake8 trialbureautools tests
$ python setup.py test or py.test
$ tox

    To get flake8 and tox, just pip install them into your virtualenv.

  6. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

  7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.

  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.

  3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check https://travis-ci.org/sjoerdk/trialbureautools/pull_requests and make sure that the tests pass for all supported Python versions.

Tips

To run a subset of tests:

$ py.test tests.test_trialbureautools

Deploying

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst). Then run:

$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags

Travis will then deploy to PyPI if tests pass.

Credits

Development Lead

Contributors

None yet. Why not be the first?

History

0.1.0 (2018-12-05)

  • Alpha