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).

NOTICE

+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

@@ -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

+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:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+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 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
+   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 OWNER 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.

ThirdPartyLicenses/GoogleTest/LICENSE

+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
+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 Google Inc. 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
+OWNER 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.

ThirdPartyLicenses/ITK/LICENSE

+
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+      "Contributor" shall mean Licensor and any individual or Legal Entity
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ThirdPartyLicenses/Niftyreg/LICENSE.txt

+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
+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.
+

ThirdPartyLicenses/Niftyreg/README.txt

+#####################
+# 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

+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
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+
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+
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+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
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+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
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+      "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
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+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
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+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
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+
+   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
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+
+      (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
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