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DOC: Added license files. Part of both issue #96 (Mention third party... 

DOC: Added license files. Part of both issue #96 (Mention third party licenses) and #155 (Release 1.0).
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SuperElastix Copyright Notice:
Copyright 2018 Leiden University Medical Center, Erasmus University Medical Center
and contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0.txt
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-------------------------------------------------------------------------------
See LICENSE file for details.
-------------------------------------------------------------------------------
SuperElastix contains code from third parties that have different copyrights.
They are:
* elastix
Please read ThirdPartyLicenses/elastix/NOTICE
* Insight Toolkit
Please read ThirdPartyLicenses/ITK/NOTICE
* GoogleTest
Please read ThirdPartyLicenses/GoogleTest/LICENSE
* Niftyreg
Please read ThirdPartyLicenses/Niftyreg/LICENSE.txt and ThirdPartyLicenses/Niftyreg/README.txt
* ATen
Please read ThirdPartyLicenses/ATen/LICENSE
SuperBuild/ExternalGoogleTest.cmake
View file @ 501ebe7f
......@@ -20,7 +20,7 @@
set( proj GoogleTest )
set( GTEST_TARGET_VERSION 1.7.0 )
set( GTEST_DOWNLOAD_SOURCE_HASH "2d6ec8ccdf5c46b05ba54a9fd1d130d7" )
set( GTEST_DOWNLOAD_SOURCE_HASH "b3a2048beb0f8d6cbb2d5c95e7f639780eff5805" )
set( GTEST_binary_dir ${CMAKE_CURRENT_BINARY_DIR}/${proj}-prefix/src/${proj}-build )
set( GTEST_source_dir ${CMAKE_CURRENT_BINARY_DIR}/${proj}-prefix/src/${proj} )
......
ThirdPartyLicenses/ATen/LICENSE 0 → 100644
View file @ 501ebe7f
Copyright (c) 2016- Facebook, Inc (Adam Paszke)
Copyright (c) 2014- Facebook, Inc (Soumith Chintala)
Copyright (c) 2011-2014 Idiap Research Institute (Ronan Collobert)
Copyright (c) 2012-2014 Deepmind Technologies (Koray Kavukcuoglu)
Copyright (c) 2011-2012 NEC Laboratories America (Koray Kavukcuoglu)
Copyright (c) 2011-2013 NYU (Clement Farabet)
Copyright (c) 2006-2010 NEC Laboratories America (Ronan Collobert, Leon Bottou, Iain Melvin, Jason Weston)
Copyright (c) 2006 Idiap Research Institute (Samy Bengio)
Copyright (c) 2001-2004 Idiap Research Institute (Ronan Collobert, Samy Bengio, Johnny Mariethoz)
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
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documentation and/or other materials provided with the distribution.
3. Neither the names of Facebook, Deepmind Technologies, NYU, NEC Laboratories America
and IDIAP Research Institute nor the names of its contributors may be
used to endorse or promote products derived from this software without
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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ThirdPartyLicenses/GoogleTest/LICENSE 0 → 100644
View file @ 501ebe7f
Copyright 2008, Google Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
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* Redistributions of source code must retain the above copyright
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
ThirdPartyLicenses/ITK/LICENSE 0 → 100644
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Apache License
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Notwithstanding the above, nothing herein shall supersede or modify
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ThirdPartyLicenses/Niftyreg/LICENSE.txt 0 → 100644
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Copyright (c) 2009, University College London, United-Kingdom
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
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.
Neither the name of the University College London nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
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
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.
ThirdPartyLicenses/Niftyreg/README.txt 0 → 100644
View file @ 501ebe7f
#####################
# NIFTY_REG PACKAGE #
#####################
##############################################################################
--------------------------------
1 WHAT DOES THE PACKAGE CONTAIN?
--------------------------------
The code contains programs to perform rigid, affine and non-linear registration
of 2D and 3D images stored as Nifti or Analyze (nii or hdr/img).
The rigid and affine registration are performed using an algorithm initially
presented by Ourselin et al.[1]. The symmetric versions of the rigid and
affine registration have been presented in Modat et al.[2].
The non-linear registration is based on the work is based on the work initially
presented by Rueckert et al.[3]. The current implementation has been presented
in Modat et al.[4].
Ourselin et al.[1] presented an algorithm called Aladin, which is based on
a block-matching approach and a Trimmed Least Square (TLS) scheme. Firstly,
the block matching provides a set of corresponding points between a reference
and a warped floating image. Secondly, using this set of corresponding points,
the best rigid or affine transformation is evaluated. This two-step loop is
repeated until convergence to the best transformation.
In our implementation, we used the normalised cross-correlation between the
reference and warped floating blocks to extract the best correspondence. The
block width is constant and has been set to 4 pixels or voxels. A coarse-to-
fine approach is used, where the registration is first performed on down-sampled
images (using a Gaussian pyramid) and finally performed on full resolution
images. The symmetric approach optimises concurrently forward and backward
transformations.
reg aladin is the name of the command to perform rigid or affine registration.
The non-rigid algorithm implementation is based on the Free-From Deformation
presented by Rueckert et al.[3]. However, the algorithm has been re-factored
in order to speed-up registration. The deformation of the floating image is
performed using cubic B-splines to generate the deformation field. Concretely,
a lattice of equally spaced control points is defined over the reference image
and moving each point allows to locally modify the mapping to the floating
image. In order to assess the quality of the warping between both input images,
an objective function composed from the Normalised Mutual Information (NMI) and
the Bending-Energy (BE) is used. The objective function value is optimised
using the analytical derivative of both, the NMI and the BE within a conjugate
gradient scheme. The symmetric version of the algorithm takes advantage of
stationary velocity field parametrisation.
reg f3d is the command to perform non-linear registration.
A third program, called reg resample, is been embedded in the package. It
uses the output of reg aladin and reg f3d to apply transformation, generate
deformation fields or Jacobian map images for example.
The code has been implemented for CPU and GPU architecture. The former
code is based on the C/C++ language, whereas the later is based on CUDA
(http://www.nvidia.com).
The nifti library (http://nifti.nimh.nih.gov/) is used to read and write
images. The code is thus dealing with nifti and analyse formats.
If you are planning to use any of our research, we would be grateful if you
would be kind enough to cite reference(s) 2 (rigid or affine) and/or
4 (non-rigid).
##############################################################################
---------
2 LICENSE
---------
Copyright (c) 2009, University College London, United-Kingdom
All rights reserved.
Redistribution and use in floating and binary forms, with or without
modification,
are permitted provided that the following conditions are met:
Redistributions of floating code must retain the above copyright notice,
this list of conditions and the following disclaimer.
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.
Neither the name of the University College London nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
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.
##############################################################################
---------
3 CONTACT
---------
For any comment, please, feel free to contact Marc Modat (m.modat@ucl.ac.uk).
##############################################################################
------------
4 REFERENCES
------------
[1] Ourselin, et al. (2001). Reconstructing a 3D structure from serial
histological sections. Image and Vision Computing, 19(1-2), 25–31.
[2] Modat, et al. (2014). Global image registration using a symmetric block-
matching approach. Journal of Medical Imaging, 1(2), 024003–024003.
doi:10.1117/1.JMI.1.2.024003
[3] Rueckert, et al.. (1999). Nonrigid registration using free-form
deformations: Application to breast MR images. IEEE Transactions on Medical
Imaging, 18(8), 712–721. doi:10.1109/42.796284
[4] Modat, et al. (2010). Fast free-form deformation using graphics processing
units. Computer Methods And Programs In Biomedicine,98(3), 278–284.
doi:10.1016/j.cmpb.2009.09.002
##############################################################################
##############################################################################
##############################################################################
##############################################################################
ThirdPartyLicenses/elastix/LICENSE 0 → 100644
View file @ 501ebe7f
Apache License
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http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
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outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
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including but not limited to software source code, documentation
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"Object" form shall mean any form resulting from mechanical
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not limited to compiled object code, generated documentation,
and conversions to other media types.
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copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
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"Contribution" shall mean any work of authorship, including
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to that Work or Derivative Works thereof, that is intentionally
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or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
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Licensor for the purpose of discussing and improving the Work, but
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copyright license to reproduce, prepare Derivative Works of,
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use, offer to sell, sell, import, and otherwise transfer the Work,
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by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be