{ "info": { "author": "M. Starmans", "author_email": "m.starmans@erasmusmc.nl", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Education", "Intended Audience :: Healthcare Industry", "Intended Audience :: Information Technology", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: System :: Distributed Computing", "Topic :: System :: Logging", "Topic :: Utilities" ], "description": "|Build Status|\n\nWORC v3.0.0\n===========\n\nWorkflow for Optimal Radiomics Classification\n---------------------------------------------\n\nWORC is an open-source python package for the easy execution of full\nradiomics pipelines.\n\nWe aim to establish a general radiomics platform supporting easy\nintegration of other tools. With our modular build and support of\ndifferent software languages (python, MATLAB, ruby, java etc.), we want\nto facilitate and stimulate collaboration, standardisation and\ncomparison of different radiomics approaches. By combining this in a\nsingle framework, we hope to find a universal radiomics strategy that\ncan address various problems.\n\nDisclaimer\n----------\n\nThis package is still under development. We try to thoroughly test and\nevaluate every new build and function, but bugs can off course still\noccur. Please contact us through the channels below if you find any and\nwe will try to fix them as soon as possible, or create an issue on this\nGithub.\n\nTutorial and Documentation\n--------------------------\n\nThe WORC tutorial is hosted in a `separate\nrepository `__.\n\nThe official documentation can be found at https://worc.readthedocs.io.\n\nInstallation\n------------\n\nWORC currently only supports Unix with Python 3.6+ (tested on 3.7.2 and\n3.7.3) systems and has been tested on Ubuntu 16.04 and 18.04 and Windows\n10.\n\nThe package can be installed through pip:\n\n::\n\n pip install WORC\n\nAlternatively, you can directly install WORC from this repository:\n\n::\n\n python setup.py install\n\nMake sure you install the requirements first:\n\n::\n\n pip install -r requirements.txt\n\nFastr Configuration\n~~~~~~~~~~~~~~~~~~~\n\nThe installation will create a FASTR configuration file in the\n$HOME/.fastr/config.d folder called WORC\\_config.py. This file is used\nfor configuring fastr, the pipeline execution toolbox we use. More\ninformation can be found at `the FASTR\nwebsite `__.\nIn this file, so called mounts are defined, which are used to locate the\nWORC tools and your inputs and outputs. Please inspect the mounts and\nchange them if neccesary.\n\n::\n\n echo \"machine images.xnat.org\n > login admin\n > password admin\" > ~/.netrc\n chmod 600 ~/.netrc\n\n3rd-party packages used in WORC:\n--------------------------------\n\n- `FASTR (Workflow design and\n building) `__\n- xnat (Collecting data from XNAT)\n- SimpleITK (Image loading and preprocessing)\n- `Pyradiomics `__\n- `PREDICT `__\n\nSee for other requirements the `requirements file `__.\n\nStart\n-----\n\nWe suggest you start with the `WORC\nTutorial `__. Besides a\nJupyter notebook with instructions, we provide there also an example\nscript for you to get started with. Make sure you input your own data as\nthe sources. Also, check out the unit tests of several tools in the\nWORC/resources/fastr\\_tests directory. The example is explained in more\ndetail in the `documentation `__.\n\nWIP\n---\n\n- We are working on improving the documentation.\n- We are working on organizing clinically relevant datasets for\n examples and unit tests.\n- We are writing the paper on WORC.\n\nLicense\n-------\n\nThis package is covered by the open source `APACHE 2.0\nLicense `__.\n\nWhen using WORC, please cite this repository.\n\nContact\n-------\n\nWe are happy to help you with any questions. Please sent us a mail or\nplace an issue on the Github.\n\nWe welcome contributions to WORC. For the moment, converting your\ntoolbox into a FASTR tool is satisfactory.\n\nOptional\n--------\n\nBesides the default installation, there are several optional packages\nyou could install to support WORC.\n\nGraphviz\n~~~~~~~~\n\nWORC can draw the network and save it as a SVG image using\n`graphviz `__. In order to do so, please make\nsure you install graphviz. On Ubuntu, simply run\n\n::\n\n apt install graphiv\n\nElastix\n~~~~~~~\n\nImage registration is included in WORC through `elastix and\ntransformix `__. In order to use elastix,\nplease download the binaries and place them in your\nfastr.config.mounts['apps'] path. Check the elastix tool description for\nthe correct subdirectory structure. For example, on Linux, the binaries\nand libraries should be in \"../apps/elastix/4.8/install/\" and\n\"../apps/elastix/4.8/install/lib\" respectively.\n\nNote: optionally, you can tell WORC to copy the metadata from the image\nfile to the segmentation file before applying the deformation field.\nThis requires ITK and ITKTools: see `the ITKTools\ngithub `__ for installation\ninstructions.\n\nXNAT\n~~~~\n\nWe use the XNATpy package to connect the toolbox to the XNAT online\ndatabase platforms. You will only need this when you want to download or\nupload data from or to XNAT. We advise you to specify your account\nsettings in a .netrc file when using this feature, such that you do not\nneed to input them on every request:\n\n.. |Build Status| image:: https://travis-ci.com/MStarmans91/WORC.svg?token=qyvaeq7Cpwu7hJGB98Gp&branch=master\n :target: https://travis-ci.com/MStarmans91/WORC\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/MStarmans91/WORC", "keywords": "bioinformatics radiomics features", "license": "Apache License, Version 2.0", "maintainer": "", "maintainer_email": "", "name": "WORC", "package_url": "https://pypi.org/project/WORC/", "platform": "", "project_url": "https://pypi.org/project/WORC/", "project_urls": { "Homepage": "https://github.com/MStarmans91/WORC" }, "release_url": "https://pypi.org/project/WORC/3.0.0/", "requires_dist": [ "fastr (>=3.1.1)", "xnat (>=0.2.2)", "configparser (>=3.5.0)", "natsort (>=5.0.1)", "drmaa (>=0.7.6)", "nose (>=1.3.7)", "nose-parameterized (>=0.5.0)", "numpy (>=1.16.3)", "tqdm (>=4.7.1)", "six (>=1.10.0)", "sphinx (>=1.4)", "pyOpenSSL (>=16.2.0)", "boto3 (>=1.7.74)", "pandas (>=0.24.2)", "xlrd (>=1.2.0)", "tables (>=3.5.1)", "pydicom (>=1.2.2)", "ghalton (>=0.6.1)", "imbalanced-learn (>=0.4.3)", "scikit-learn (>=0.20.3)", "scipy (>=1.2.1)", "SimpleITK (>=1.2.0)", "missingpy (>=0.2.0)", "matplotlib2tikz (>=0.7.4)", "lifelines (>=0.21.1)", "PREDICT (>=3.0.0)" ], "requires_python": ">=3.6", "summary": "Workflow for Optimal Radiomics Classification.", "version": "3.0.0" }, "last_serial": 5241685, "releases": { "2.1.0": [ { "comment_text": "", "digests": { "md5": "129825cfa02e3c7175a175775d062cb9", "sha256": "fbee02a1058d2e3e7fe62236a7cfc20260d66f14c4ca4e6b47fde15a9aa08bba" }, "downloads": -1, "filename": "WORC-2.1.0_2.tar.gz", "has_sig": false, "md5_digest": "129825cfa02e3c7175a175775d062cb9", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 551592, "upload_time": "2018-08-13T12:46:16", "url": "https://files.pythonhosted.org/packages/fb/c0/fb3ee89289dd4e46d7724fd3b9b4b373d3e148abda90c607d802004f3adc/WORC-2.1.0_2.tar.gz" } ], "2.1.1": [ { "comment_text": "", "digests": { "md5": "1bfa2e1afd813de6945389e91f42cab1", "sha256": "9b3ef96276859ac7aee27cb2ce42bd77d3019f894503beadb14686960ecd1944" }, "downloads": -1, "filename": "WORC-2.1.1.tar.gz", "has_sig": false, "md5_digest": "1bfa2e1afd813de6945389e91f42cab1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 720279, "upload_time": "2019-02-15T16:51:47", "url": "https://files.pythonhosted.org/packages/25/28/02c546b403b32e46bd607b56881c7cbefdd9d3c9dc135efa57b9e317a340/WORC-2.1.1.tar.gz" } ], "2.1.2": [ { "comment_text": "", "digests": { "md5": "8a180c56d63cfb35e46385ce2278170b", "sha256": "a10e452c347c33b26701a34d6293932cae244abc8fc8a48c3b20c2ad727f3535" }, "downloads": -1, "filename": "WORC-2.1.2.tar.gz", "has_sig": false, "md5_digest": "8a180c56d63cfb35e46385ce2278170b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 714938, "upload_time": "2019-04-02T16:06:33", "url": "https://files.pythonhosted.org/packages/a1/b3/c1cb8914d7f521606f435aadef03db9fcb4d2317e2359a3bcbf125e5f596/WORC-2.1.2.tar.gz" } ], "2.1.3": [ { "comment_text": "", "digests": { "md5": "74f84704265c119e078785e481ffae96", "sha256": "28255298491d37d6ffe4400f49dced3d72af2fd801b803ec591d53bc2f5911c5" }, "downloads": -1, "filename": "WORC-2.1.3.tar.gz", "has_sig": false, "md5_digest": "74f84704265c119e078785e481ffae96", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 720540, "upload_time": "2019-04-08T15:45:37", "url": "https://files.pythonhosted.org/packages/b0/67/cb70dfc0e9af71b698c8a12f2582630c9eff1b768d259f9227705d30834b/WORC-2.1.3.tar.gz" } ], "3.0.0": [ { "comment_text": "", "digests": { "md5": "c870c76bcba05cbe1b988e5ff0ce630b", "sha256": "54a58aecdf1f0848c77c4779ed4a4ea237f3396717899c534c6170c0cfa1a40b" }, "downloads": -1, "filename": "WORC-3.0.0-py3-none-any.whl", "has_sig": false, "md5_digest": "c870c76bcba05cbe1b988e5ff0ce630b", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 11220543, "upload_time": "2019-05-08T07:01:38", "url": "https://files.pythonhosted.org/packages/c1/f6/cfe7a9ec43d44b6b35a4629fe4971fba4a7340a9ad56975305963719f5c9/WORC-3.0.0-py3-none-any.whl" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "c870c76bcba05cbe1b988e5ff0ce630b", "sha256": "54a58aecdf1f0848c77c4779ed4a4ea237f3396717899c534c6170c0cfa1a40b" }, "downloads": -1, "filename": "WORC-3.0.0-py3-none-any.whl", "has_sig": false, "md5_digest": "c870c76bcba05cbe1b988e5ff0ce630b", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3.6", "size": 11220543, "upload_time": "2019-05-08T07:01:38", "url": "https://files.pythonhosted.org/packages/c1/f6/cfe7a9ec43d44b6b35a4629fe4971fba4a7340a9ad56975305963719f5c9/WORC-3.0.0-py3-none-any.whl" } ] }