Merge pull request #158 from SuperElastix/SELX-155-Release-1.0

Selx 155 release 1.0

CMakeLists.txt

@@ -22,8 +22,8 @@ cmake_minimum_required( VERSION 3.5.1 )
 # ---------------------------------------------------------------------
 project( SuperElastix )
 
-set( SUPERELASTIX_MAJOR_VERSION 0)
-set( SUPERELASTIX_MINOR_VERSION 1)
+set( SUPERELASTIX_MAJOR_VERSION 1)
+set( SUPERELASTIX_MINOR_VERSION 0)
 set( SUPERELASTIX_PATCH_VERSION 0)
 set( SUPERELASTIX_VERSION ${SUPERELASTIX_MAJOR_VERSION}.${SUPERELASTIX_MINOR_VERSION}.${SUPERELASTIX_PATCH_VERSION})
 

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
+

README.md

@@ -19,6 +19,11 @@ modularity.
 - [Contributing](CONTRIBUTING.md)
 - ["The design of SuperElastix - a unifying framework for a wide range of image registration methodologies"](http://www.cv-foundation.org/openaccess/content_cvpr_2016_workshops/w15/papers/Berendsen_The_Design_of_CVPR_2016_paper.pdf), F. F. Berendsen, K. Marstal, S. Klein and M. Staring, [WBIR2016](http://wbir2016.doc.ic.ac.uk/), [[paper latex source](https://github.com/SuperElastix/Publications/tree/master/paperWBIR16)] [[poster](https://github.com/SuperElastix/Publications/blob/master/posterWBIR16/Poster_SuperElastix_WBIR.svg)]
 
+## Development ##
+- `SuperElastix v1.0` has been released! Please see our `master` branch
+- We encourage users that build SuperElastix from sources to use our `develop` branch
+- All branches and pull requests are build and unit tested by Continuous Integration: see our [CDash](https://my.cdash.org/index.php?project=SuperElastix) for the latest status
+
 ## Authors ##
 - [Floris Berendsen](https://www.lumc.nl/org/radiologie/medewerkers/BerendsenF)
 - [Kasper Marstal](http://www.bigr.nl/website/index.php?page=people&subpage=person&id=KasperMarstal)

SuperBuild/CMakeLists.txt

@@ -43,8 +43,8 @@ if(CMAKE_CONFIGURATION_TYPES)
   message(STATUS "Selected configuration type (CMAKE_CONFIGURATION_TYPES): " ${CMAKE_CONFIGURATION_TYPES})
 endif()
 
-set( SUPERELASTIXSUPERBUILD_MAJOR_VERSION 0)
-set( SUPERELASTIXSUPERBUILD_MINOR_VERSION 1)
+set( SUPERELASTIXSUPERBUILD_MAJOR_VERSION 1)
+set( SUPERELASTIXSUPERBUILD_MINOR_VERSION 0)
 set( SUPERELASTIXSUPERBUILD_PATCH_VERSION 0)
 set( SUPERELASTIXSUPERBUILD_VERSION ${SUPERELASTIXSUPERBUILD_MAJOR_VERSION}.${SUPERELASTIXSUPERBUILD_MINOR_VERSION}.${SUPERELASTIXSUPERBUILD_PATCH_VERSION})
 

SuperBuild/ExternalGoogleTest.cmake

@@ -32,7 +32,7 @@ if( MSVC )
 endif()
 
 set( MSVS_ARGS )
-if(MSVC_VERSION EQUAL 1700)
+if(NOT (MSVC_VERSION LESS 1700))
   set(MSVS_ARGS ${MSVS_ARGS} -D CMAKE_CXX_FLAGS=-DGTEST_HAS_TR1_TUPLE=0 ${CMAKE_CXX_FLAGS})
 endif()
 

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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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
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      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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+      including but not limited to software source code, documentation
+      source, and configuration files.
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+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
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+      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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+      form, that is based on (or derived from) the Work and for which the
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