Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update license to 3-clause BSD #272

Merged
merged 2 commits into from Jul 17, 2017
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
5 changes: 4 additions & 1 deletion CHANGES.rst
Expand Up @@ -11,6 +11,7 @@ New Features

- Add a row by row customization of the extraction label in the batch processing command line script, as well as both
batchprocessing examples.
(`#262 <https://github.com/Radiomics/pyradiomics/pull/262>`_)

Bug fixes
#########
Expand All @@ -19,6 +20,7 @@ Bug fixes
and not a copy of the array, causing erroneous results when adding it to the original array. use
``numpy.ndarray.copy`` to prevent this bug. **N.B. This affects the feature values calculated by GLCM when symmetrical
matrix is enabled (as is the default setting).**
(`#261 <https://github.com/Radiomics/pyradiomics/pull/261>`_)
- Use a python implementation to compute eigenvalues for ``shape.py`` instead of SimpleITK. The implementation in
SimpleITK assumes segmented voxels to be consecutive on the x-axis lines. Furthermore, it also assumes that all voxels
on a given line of x have the same values for y and z (which is not necessarily the case).
Expand All @@ -38,7 +40,8 @@ Documentation

- Update reference. (`#271 <https://github.com/Radiomics/pyradiomics/pull/271>`_)
- Move section "Customizing the Extraction" to the top level, to make it more visible.
(`#265 <https://github.com/Radiomics/pyradiomics/pull/271>`_)
(`#271 <https://github.com/Radiomics/pyradiomics/pull/271>`_)
- Change License to 3-clause BSD (`#272 <https://github.com/Radiomics/pyradiomics/pull/272>`_

Internal API
############
Expand Down
210 changes: 16 additions & 194 deletions LICENSE.txt
@@ -1,199 +1,21 @@
Copyright 2017 Harvard Medical School
Copy link
Collaborator

@fedorov fedorov Jul 14, 2017

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@JoostJM @hugoaerts @pieper thinking about this for dcmqi, I decided to list BWH as the copyright holder, see https://github.com/QIICR/dcmqi/blob/master/LICENSE.txt. The reason is that, in case of dcmqi, BWH is the recepient of the award from NIH. It might make sense to list DFCI here, since in the case of pyradiomics, DFCI is the recipient of the main award funding pyradiomics development.


For more information, please see:
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
following conditions are met:

http://www.slicer.org
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
disclaimer.

The 3D Slicer license below is a BSD style license, with extensions
to cover contributions and other issues specific to 3D Slicer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.

3D Slicer Contribution and Software License Agreement ("Agreement")
Version 1.0 (December 20, 2005)

This Agreement covers contributions to and downloads from the 3D
Slicer project ("Slicer") maintained by The Brigham and Women's
Hospital, Inc. ("Brigham"). Part A of this Agreement applies to
contributions of software and/or data to Slicer (including making
revisions of or additions to code and/or data already in Slicer). Part
B of this Agreement applies to downloads of software and/or data from
Slicer. Part C of this Agreement applies to all transactions with
Slicer. If you distribute Software (as defined below) downloaded from
Slicer, all of the paragraphs of Part B of this Agreement must be
included with and apply to such Software.

Your contribution of software and/or data to Slicer (including prior
to the date of the first publication of this Agreement, each a
"Contribution") and/or downloading, copying, modifying, displaying,
distributing or use of any software and/or data from Slicer
(collectively, the "Software") constitutes acceptance of all of the
terms and conditions of this Agreement. If you do not agree to such
terms and conditions, you have no right to contribute your
Contribution, or to download, copy, modify, display, distribute or use
the Software.

PART A. CONTRIBUTION AGREEMENT - License to Brigham with Right to
Sublicense ("Contribution Agreement").

1. As used in this Contribution Agreement, "you" means the individual
contributing the Contribution to Slicer and the institution or
entity which employs or is otherwise affiliated with such
individual in connection with such Contribution.

2. This Contribution Agreement applies to all Contributions made to
Slicer, including without limitation Contributions made prior to
the date of first publication of this Agreement. If at any time you
make a Contribution to Slicer, you represent that (i) you are
legally authorized and entitled to make such Contribution and to
grant all licenses granted in this Contribution Agreement with
respect to such Contribution; (ii) if your Contribution includes
any patient data, all such data is de-identified in accordance with
U.S. confidentiality and security laws and requirements, including
but not limited to the Health Insurance Portability and
Accountability Act (HIPAA) and its regulations, and your disclosure
of such data for the purposes contemplated by this Agreement is
properly authorized and in compliance with all applicable laws and
regulations; and (iii) you have preserved in the Contribution all
applicable attributions, copyright notices and licenses for any
third party software or data included in the Contribution.

3. Except for the licenses granted in this Agreement, you reserve all
right, title and interest in your Contribution.

4. You hereby grant to Brigham, with the right to sublicense, a
perpetual, worldwide, non-exclusive, no charge, royalty-free,
irrevocable license to use, reproduce, make derivative works of,
display and distribute the Contribution. If your Contribution is
protected by patent, you hereby grant to Brigham, with the right to
sublicense, a perpetual, worldwide, non-exclusive, no-charge,
royalty-free, irrevocable license under your interest in patent
rights covering the Contribution, to make, have made, use, sell and
otherwise transfer your Contribution, alone or in combination with
any other code.

5. You acknowledge and agree that Brigham may incorporate your
Contribution into Slicer and may make Slicer available to members
of the public on an open source basis under terms substantially in
accordance with the Software License set forth in Part B of this
Agreement. You further acknowledge and agree that Brigham shall
have no liability arising in connection with claims resulting from
your breach of any of the terms of this Agreement.

6. YOU WARRANT THAT TO THE BEST OF YOUR KNOWLEDGE YOUR CONTRIBUTION
DOES NOT CONTAIN ANY CODE THAT REQURES OR PRESCRIBES AN "OPEN
SOURCE LICENSE" FOR DERIVATIVE WORKS (by way of non-limiting
example, the GNU General Public License or other so-called
"reciprocal" license that requires any derived work to be licensed
under the GNU General Public License or other "open source
license").

PART B. DOWNLOADING AGREEMENT - License from Brigham with Right to
Sublicense ("Software License").

1. As used in this Software License, "you" means the individual
downloading and/or using, reproducing, modifying, displaying and/or
distributing the Software and the institution or entity which
employs or is otherwise affiliated with such individual in
connection therewith. The Brigham and Women?s Hospital,
Inc. ("Brigham") hereby grants you, with right to sublicense, with
respect to Brigham's rights in the software, and data, if any,
which is the subject of this Software License (collectively, the
"Software"), a royalty-free, non-exclusive license to use,
reproduce, make derivative works of, display and distribute the
Software, provided that:

(a) you accept and adhere to all of the terms and conditions of this
Software License;

(b) in connection with any copy of or sublicense of all or any portion
of the Software, all of the terms and conditions in this Software
License shall appear in and shall apply to such copy and such
sublicense, including without limitation all source and executable
forms and on any user documentation, prefaced with the following
words: "All or portions of this licensed product (such portions are
the "Software") have been obtained under license from The Brigham and
Women's Hospital, Inc. and are subject to the following terms and
conditions:"

(c) you preserve and maintain all applicable attributions, copyright
notices and licenses included in or applicable to the Software;

(d) modified versions of the Software must be clearly identified and
marked as such, and must not be misrepresented as being the original
Software; and

(e) you consider making, but are under no obligation to make, the
source code of any of your modifications to the Software freely
available to others on an open source basis.

2. The license granted in this Software License includes without
limitation the right to (i) incorporate the Software into
proprietary programs (subject to any restrictions applicable to
such programs), (ii) add your own copyright statement to your
modifications of the Software, and (iii) provide additional or
different license terms and conditions in your sublicenses of
modifications of the Software; provided that in each case your use,
reproduction or distribution of such modifications otherwise
complies with the conditions stated in this Software License.

3. This Software License does not grant any rights with respect to
third party software, except those rights that Brigham has been
authorized by a third party to grant to you, and accordingly you
are solely responsible for (i) obtaining any permissions from third
parties that you need to use, reproduce, make derivative works of,
display and distribute the Software, and (ii) informing your
sublicensees, including without limitation your end-users, of their
obligations to secure any such required permissions.

4. The Software has been designed for research purposes only and has
not been reviewed or approved by the Food and Drug Administration
or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL
APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Any
commercialization of the Software is at the sole risk of the party
or parties engaged in such commercialization. You further agree to
use, reproduce, make derivative works of, display and distribute
the Software in compliance with all applicable governmental laws,
regulations and orders, including without limitation those relating
to export and import control.

5. The Software is provided "AS IS" and neither Brigham nor any
contributor to the software (each a "Contributor") shall have any
obligation to provide maintenance, support, updates, enhancements
or modifications thereto. BRIGHAM AND ALL CONTRIBUTORS SPECIFICALLY
DISCLAIM ALL EXPRESS AND IMPLIED WARRANTIES OF ANY KIND INCLUDING,
BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR
A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL
BRIGHAM OR ANY CONTRIBUTOR BE LIABLE TO ANY PARTY FOR DIRECT,
INDIRECT, SPECIAL, INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY ARISING IN ANY WAY
RELATED TO THE SOFTWARE, EVEN IF BRIGHAM OR ANY CONTRIBUTOR HAS
BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. TO THE MAXIMUM
EXTENT NOT PROHIBITED BY LAW OR REGULATION, YOU FURTHER ASSUME ALL
LIABILITY FOR YOUR USE, REPRODUCTION, MAKING OF DERIVATIVE WORKS,
DISPLAY, LICENSE OR DISTRIBUTION OF THE SOFTWARE AND AGREE TO
INDEMNIFY AND HOLD HARMLESS BRIGHAM AND ALL CONTRIBUTORS FROM AND
AGAINST ANY AND ALL CLAIMS, SUITS, ACTIONS, DEMANDS AND JUDGMENTS
ARISING THEREFROM.

6. None of the names, logos or trademarks of Brigham or any of
Brigham's affiliates or any of the Contributors, or any funding
agency, may be used to endorse or promote products produced in
whole or in part by operation of the Software or derived from or
based on the Software without specific prior written permission
from the applicable party.

7. Any use, reproduction or distribution of the Software which is not
in accordance with this Software License shall automatically revoke
all rights granted to you under this Software License and render
Paragraphs 1 and 2 of this Software License null and void.

8. This Software License does not grant any rights in or to any
intellectual property owned by Brigham or any Contributor except
those rights expressly granted hereunder.

PART C. MISCELLANEOUS

This Agreement shall be governed by and construed in accordance with
the laws of The Commonwealth of Massachusetts without regard to
principles of conflicts of law. This Agreement shall supercede and
replace any license terms that you may have agreed to previously with
respect to Slicer.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
6 changes: 3 additions & 3 deletions README.md
Expand Up @@ -15,9 +15,9 @@ With this package we aim to establish a reference standard for Radiomic Analysis
open-source platform for easy and reproducible Radiomic Feature extraction. By doing so, we hope to increase awareness
of radiomic capabilities and expand the community.

The platform supports both the feature extraction in 2D and 3D.
The platform supports both the feature extraction in 2D and 3D. **Not intended for clinical use.**

**If you publish any work which uses this package, please cite the following publication:**\
**If you publish any work which uses this package, please cite the following publication:**
*Joost JM van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina GH
Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, Hugo JWL Aerts, “Computational Radiomics System to Decode the
Radiographic Phenotype”; Accepted Cancer Research 2017*
Expand Down Expand Up @@ -107,7 +107,7 @@ See also the [requirements file](requirements.txt).
- Implementation of this package as an [extension](https://github.com/Radiomics/SlicerRadiomics) to [3D Slicer](slicer.org)

### License
This package is covered by the open source [3D Slicer License](LICENSE.txt).
This package is covered by the open source [3-clause BSD License](LICENSE.txt).

### Developers
- [Joost van Griethuysen](https://github.com/JoostJM)<sup>1,3,4</sup>
Expand Down
6 changes: 5 additions & 1 deletion docs/index.rst
Expand Up @@ -21,6 +21,10 @@ Radiographic Phenotype”; Accepted Cancer Research 2017*
This work was supported in part by the US National Cancer Institute grant
5U24CA194354, QUANTITATIVE RADIOMICS SYSTEM DECODING THE TUMOR PHENOTYPE.

.. warning::

Not intended for clinical use.

Table of Contents
-----------------

Expand Down Expand Up @@ -119,7 +123,7 @@ Pyradiomics Indices and Tables
License
-------

This package is covered by the open source `3D Slicer License <https://github.com/Radiomics/pyradiomics/blob/master/LICENSE.txt>`_.
This package is covered by the open source `3-clause BSD License <https://github.com/Radiomics/pyradiomics/blob/master/LICENSE.txt>`_.

Developers
----------
Expand Down