WORC v3.1.0
Workflow for Optimal Radiomics Classification
WORC is an open-source python package for the easy execution of full radiomics pipelines.
We aim to establish a general radiomics platform supporting easy integration of other tools. With our modular build and support of different software languages (python, MATLAB, ruby, java etc.), we want to facilitate and stimulate collaboration, standardisation and comparison of different radiomics approaches. By combining this in a single framework, we hope to find a universal radiomics strategy that can address various problems.
Disclaimer
This package is still under development. We try to thoroughly test and evaluate every new build and function, but bugs can off course still occur. Please contact us through the channels below if you find any and we will try to fix them as soon as possible, or create an issue on this Github.
Tutorial and Documentation
The WORC tutorial is hosted in a separate repository.
The official documentation can be found at https://worc.readthedocs.io.
Installation
WORC currently only supports Unix with Python 3.6+ (tested on 3.7.2 and 3.7.3) systems and has been tested on Ubuntu 16.04 and 18.04 and Windows 10.
The package can be installed through pip:
pip install WORC
Alternatively, you can directly install WORC from this repository:
python setup.py install
Make sure you install the requirements first:
pip install -r requirements.txt
Fastr Configuration
The installation will create a FASTR configuration file in the $HOME/.fastr/config.d folder called WORC_config.py. This file is used for configuring fastr, the pipeline execution toolbox we use. More information can be found at the FASTR website. In this file, so called mounts are defined, which are used to locate the WORC tools and your inputs and outputs. Please inspect the mounts and change them if neccesary.
echo "machine images.xnat.org > login admin > password admin" > ~/.netrc chmod 600 ~/.netrc
3rd-party packages used in WORC:
xnat (Collecting data from XNAT)
SimpleITK (Image loading and preprocessing)
See for other requirements the requirements file.
Start
We suggest you start with the WORC Tutorial. Besides a Jupyter notebook with instructions, we provide there also an example script for you to get started with. Make sure you input your own data as the sources. Also, check out the unit tests of several tools in the WORC/resources/fastr_tests directory. The example is explained in more detail in the documentation.
WIP
We are working on improving the documentation.
We are working on organizing clinically relevant datasets for examples and unit tests.
We are writing the paper on WORC.
License
This package is covered by the open source APACHE 2.0 License.
When using WORC, please cite this repository.
Contact
We are happy to help you with any questions. Please sent us a mail or place an issue on the Github.
We welcome contributions to WORC. For the moment, converting your toolbox into a FASTR tool is satisfactory.
Optional
Besides the default installation, there are several optional packages you could install to support WORC.
Graphviz
WORC can draw the network and save it as a SVG image using graphviz. In order to do so, please make sure you install graphviz. On Ubuntu, simply run
apt install graphiv
Elastix
Image registration is included in WORC through elastix and transformix. In order to use elastix, please download the binaries and place them in your fastr.config.mounts[‘apps’] path. Check the elastix tool description for the correct subdirectory structure. For example, on Linux, the binaries and libraries should be in “../apps/elastix/4.8/install/” and “../apps/elastix/4.8/install/lib” respectively.
Note: optionally, you can tell WORC to copy the metadata from the image file to the segmentation file before applying the deformation field. This requires ITK and ITKTools: see the ITKTools github for installation instructions.
XNAT
We use the XNATpy package to connect the toolbox to the XNAT online database platforms. You will only need this when you want to download or upload data from or to XNAT. We advise you to specify your account settings in a .netrc file when using this feature, such that you do not need to input them on every request:
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