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update github repos to synerbi (SyneRBI#372)
* update github repos to synerbi * CCPPETMR => SynerBI * ccppetmr.ac.uk => ccpsynerbi.ac.uk * mostly docker ccppetmr => synerbi * minor revert touching CHANGES * update hdf5 URL - see SyneRBI/SIRF#614 (comment) * docker: correct org name * update headers * further updates of string SynerBI to SyneRBI * Update version_config.cmake * formely => formerly * SynerBI => SyneRBI * added to CHANGES.md and fix typos in comments * fixed project name Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org> Co-authored-by: Casper da Costa-Luis <imaging@caspersci.uk.to>
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‎.travis.yml

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@@ -62,9 +62,9 @@ addons:
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# + or - refer to the value of the parameter affecting the specific package is passed to cmake:
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# i.e. -boost => -DUSE_SYSTEM_Boost=OFF, which means that Boost will be built.
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# Note: On trusty, we need to build Armadillo and boost ourselves (the system versions are too old)
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# Note: On trusty, g++-7 causes errors with the system ACE, so cannot use g++-7 or later https://github.com/CCPPETMR/SIRF-SuperBuild/issues/169
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# Note: On osx, we can't test SYSTEM_Boost=OFF due to excessive log size (https://github.com/CCPPETMR/SIRF-SuperBuild/issues/167)
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# Note: currently ACE is not building correctly, so ACE is not built on any configuration https://github.com/CCPPETMR/SIRF-SuperBuild/issues/#174
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# Note: On trusty, g++-7 causes errors with the system ACE, so cannot use g++-7 or later https://github.com/SyneRBI/SIRF-SuperBuild/issues/169
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# Note: On osx, we can't test SYSTEM_Boost=OFF due to excessive log size (https://github.com/SyneRBI/SIRF-SuperBuild/issues/167)
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# Note: currently ACE is not building correctly, so ACE is not built on any configuration https://github.com/SyneRBI/SIRF-SuperBuild/issues/#174
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env:
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global:
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- BUILD_FLAGS="-DCMAKE_BUILD_TYPE=Release"
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dpush() {
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# create and push alias $1 -> $2
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if [[ "$1" != "$2" ]]; then
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docker tag ccppetmr/sirf:$1 ccppetmr/sirf:$2
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docker tag synerbi/sirf:$1 synerbi/sirf:$2
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fi
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docker push ccppetmr/sirf:$2
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docker push synerbi/sirf:$2
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}
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if [[ -n "$TRAVIS_TAG" ]]; then ( set -ev
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# tag & push

‎CHANGES.md

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## x.x.x
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- make ${proj}_SOURCE_DIR a cached variables such that the user can point to an existing directory
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- Added support for passing CMAKE args to projects from the SuperBuild call.
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- Updated to reflect change from CCPPETMR to CCPSyneRBI
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## v2.1.0
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- Switch NiftyReg remote from `rijobro` to `KCL-BMEIS` (following the acceptance of one of our PRs to their code).

‎CMake/FindSPM.cmake

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# Copyright 2019 University College London
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# This file is part of SIRF.
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#========================================================================
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# Author: Richard Brown
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# Copyright 2019, 2020 University College London
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#
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# This file is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License as published by
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# the Free Software Foundation; either version 2.1 of the License, or
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# (at your option) any later version.
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# http://www.apache.org/licenses/LICENSE-2.0.txt
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#
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# This file is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Lesser General Public License for more details.
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# See STIR/LICENSE.txt for details
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#=========================================================================
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if (NOT SPM_DIR)
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set(SPM_DIR "" CACHE PATH "Path to SPM")

‎CMake/RenameVariable.cmake

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#========================================================================
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# Author: Kris Thielemans
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# Copyright 2019 University College London
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# Copyright 2019, 2020 University College London
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#
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# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.

‎CMake/SetCanonicalDirectoryNames.cmake

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# Author: Kris Thielemans
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# Copyright 2020 University College London
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#
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# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.

‎CMake/SetExternalProjectFlags.cmake

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# Author: Ander Biguri
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# Copyright 2020 University College London
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#
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# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.

‎CMake/SetGitTagAndRepo.cmake

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#========================================================================
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# Author: Richard Brown
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# Copyright 2019 University College London
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# Copyright 2019, 2020 University College London
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#
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# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.

‎CMake/install_niftypet.cmake

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#========================================================================
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# Author: Richard Brown
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# Copyright 2019 University College London
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# Copyright 2019, 2020 University College London
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#
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# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.

‎CMakeLists.txt

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#========================================================================
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# Author: Benjamin A Thomas
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# Author: Kris Thielemans
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# Copyright 2017, 2020 University College London
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#
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# This file is part of the CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0.txt
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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#=========================================================================
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if (WIN32)
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cmake_minimum_required( VERSION 3.10.0 FATAL_ERROR)
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else()
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include(ExternalProject)
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include(ExternalProjectDependency)
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set(PRIMARY_PROJECT_NAME CCPPETMR)
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set(PRIMARY_PROJECT_NAME SyneRBI)
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option(${PRIMARY_PROJECT_NAME}_SUPERBUILD "Build ${PRIMARY_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ON)
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if(${PRIMARY_PROJECT_NAME}_SUPERBUILD)

‎CONTRIBUTING.md

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Please help us by finding problems, discussing on the mailing lists, contributing documentation,
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bug fixes or even features. Below are some brief guidelines. They are essentially a copy of
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the [SIRF Contribution guidelines](https://github.com/CCPPETMR/SIRF/blob/master/CONTRIBUTING.md).
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the [SIRF Contribution guidelines](https://github.com/SyneRBI/SIRF/blob/master/CONTRIBUTING.md).
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you might want to check those as well, in case they are more recent.
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## Reporting a problem
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3. Create a branch in your fork with a descriptive name and put your fixes there. If your fix is
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simple you could do it on github by editing a file, otherwise clone your project (or add a remote
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to your current git clone) and work as usual.
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4. If your change is important, add it to [CHANGES.md](https://github.com/CCPPETMR/SIRF-SuperBuild/blob/master/CHANGES.md)
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and even [README.md](https://github.com/CCPPETMR/SIRF-SuperBuild/blob/master/README.md) or other documentation files.
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4. If your change is important, add it to [CHANGES.md](https://github.com/SyneRBI/SIRF-SuperBuild/blob/master/CHANGES.md)
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and even [README.md](https://github.com/SyneRBI/SIRF-SuperBuild/blob/master/README.md) or other documentation files.
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5. Use [well-formed commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
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for each change (in particular with a single "subject" line
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followed by an empty line and then more details).
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you need to make sure its license is compatible with the SIRF license, and indicate clearly what the license
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of the copied code is (and follow its terms of course).
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In addition, you might need to add yourself to [NOTICE.txt](https://github.com/CCPPETMR/SIRF-SuperBuild/blob/master/NOTICE.txt).
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In addition, you might need to add yourself to [NOTICE.txt](https://github.com/SyneRBI/SIRF-SuperBuild/blob/master/NOTICE.txt).
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## Project rules
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* Easy cross-referencing of related issues, PRs, and commits
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+ The mailing list gets notified within 24 hours.
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[issue-tracker]: https://github.com/CCPPETMR/SIRF-SuperBuild/issues
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[pull-requests]: https://github.com/CCPPETMR/SIRF-SuperBuild/pulls
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[issue-tracker]: https://github.com/SyneRBI/SIRF-SuperBuild/issues
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[pull-requests]: https://github.com/SyneRBI/SIRF-SuperBuild/pulls
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[googlegroup]: https://groups.google.com/forum/#!forum/ccp-petmr-codebot

‎NOTICE.txt

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CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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Copyright 2017-2019 University College London (UCL)
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Copyright 2017-2019 Rutherford Appleton Laboratory STFC
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Copyright 2017-2019 King's College London (KCL)
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CCP SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
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Copyright 2017-2020 University College London (UCL)
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Copyright 2017-2020 Rutherford Appleton Laboratory STFC
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Copyright 2017-2020 King's College London (KCL)
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This software product is developed for the Collaborative Computational
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Project in Positron Emission Tomography and Magnetic Resonance imaging
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(http://www.ccppetmr.ac.uk/) at RAL STFC (http://www.stfc.ac.uk), UCL (http://www.ucl.ac.uk/)
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Project Synergistic Reconstruction for Biomedical Imaging
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(formerly in Positron Emission Tomography and Magnetic Resonance imaging)
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(http://www.ccpsynerbi.ac.uk/) at RAL STFC (http://www.stfc.ac.uk), UCL (http://www.ucl.ac.uk/)
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and other contributing institutions.
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Main contributors (see each file for authors):

‎README.md

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```
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### Install CMake
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If you do not have CMake >= 3.10, install it first. You can probably use a package manager on your OS. Alternatively, you can do that either by following the official instructions ([download link](https://cmake.org/download/)) or running your own shell sript to do so (see an example [here](https://github.com/CCPPETMR/CCPPETMR_VM/blob/master/scripts/INSTALL_CMake.sh)).
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If you do not have CMake >= 3.10, install it first. You can probably use a package manager on your OS. Alternatively, you can do that either by following the official instructions ([download link](https://cmake.org/download/)) or running your own shell sript to do so (see an example [here](https://github.com/SyneRBI/SyneRBI_VM/blob/master/scripts/INSTALL_CMake.sh)).
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If you use a CMake installer, you will be asked to read and accept CMake's license. If you answered the last question during the CMake installation with yes, then you should use
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```bash
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cd ~
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git clone https://github.com/CCPPETMR/SIRF-SuperBuild.git
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git clone https://github.com/SyneRBI/SIRF-SuperBuild.git
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```
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### Build and Install
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Create a build directory and configure the software.
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Note that if you want to use MATLAB, you need to use (and specify) a compiler supported by MATLAB
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and might have to tell CMake where MATLAB is located. Please
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check our [SIRF and MATLAB page](https://github.com/CCPPETMR/SIRF/wiki/SIRF-and-MATLAB).
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check our [SIRF and MATLAB page](https://github.com/SyneRBI/SIRF/wiki/SIRF-and-MATLAB).
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```bash
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cd examples
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ls
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```
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See [our related Wiki page](https://github.com/CCPPETMR/SIRF/wiki/Examples) for more information.
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See [our related Wiki page](https://github.com/SyneRBI/SIRF/wiki/Examples) for more information.
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## OS specific information
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### Installation instructions for Ubuntu <a name="Ubuntu-install"></a>
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They can be found [here](https://github.com/CCPPETMR/SIRF/wiki/SIRF-SuperBuild-Ubuntu-16.04)
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They can be found [here](https://github.com/SyneRBI/SIRF/wiki/SIRF-SuperBuild-Ubuntu-16.04)
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### Installation instructions for Mac OS <a name="OSX-install"></a>
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They can be found [here](https://github.com/CCPPETMR/SIRF/wiki/SIRF-SuperBuild-on-MacOS)
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They can be found [here](https://github.com/SyneRBI/SIRF/wiki/SIRF-SuperBuild-on-MacOS)
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### Installation instructions for Docker <a name="Docker-install"></a>
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They can be found [here](https://github.com/CCPPETMR/SIRF/wiki/SIRF-SuperBuild-on-Docker)
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They can be found [here](https://github.com/SyneRBI/SIRF/wiki/SIRF-SuperBuild-on-Docker)
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## Advanced installation
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### Building with Intel Math Kernel Library
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[Gadgetron](https://github.com/CCPPETMR/SIRF/wiki/SIRF,-Gadgetron-and-MKL) and Armadillo can make use of Intel's Math Kernel Library.
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[Gadgetron](https://github.com/SyneRBI/SIRF/wiki/SIRF,-Gadgetron-and-MKL) and Armadillo can make use of Intel's Math Kernel Library.
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1. Install Intel MKL following the instructions at [their](https://software.intel.com/en-us/mkl) website. For debian based linux follow [this link](https://software.intel.com/en-us/articles/installing-intel-free-libs-and-python-apt-repo). The latter will install MKL in `opt/intel`
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2. Gadgetron's [FindMKL.cmake](https://github.com/gadgetron/gadgetron/blob/master/cmake/FindMKL.cmake#L23) will try to look for MKL libraries in `/opt/intel` on Unix/Apple and in `C:/Program Files (x86)/Intel/Composer XE` in Windows. Make sure that this is the location of the library or pass the vatiable `MKLROOT_PATH` (Unix/Apple) or set the environment variable `MKLROOT_PATH` on Windows.
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* CMake does come with FindArmadillo.cmake but it currently (at least up to CMake 3.12) has no variable to specify its location at all. This implies that when using `USE_SYSTEM_ARMADILLO=On`, you have to install armadillo in a system location, unless some extra work is done. See [this post on stackoverflow](https://stackoverflow.com/questions/35304513/cmake-find-armadillo-library-installed-in-a-custom-location) for some suggestions, which we haven't tried.
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[CI-badge]: https://travis-ci.org/CCPPETMR/SIRF-SuperBuild.svg?branch=master
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[CI-link]: https://travis-ci.org/CCPPETMR/SIRF-SuperBuild
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[CI-badge]: https://travis-ci.org/SyneRBI/SIRF-SuperBuild.svg?branch=master
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[CI-link]: https://travis-ci.org/SyneRBI/SIRF-SuperBuild
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[style-badge]: https://api.codacy.com/project/badge/Grade/c1a4613d4bd247d19780881f8194eaf8
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[style-link]: https://www.codacy.com/app/CCP-PETMR/SIRF-SuperBuild
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[docker-badge]: https://img.shields.io/docker/pulls/ccppetmr/sirf.svg
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[docker-link]: https://hub.docker.com/r/ccppetmr/sirf
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[install-badge]: https://img.shields.io/badge/dynamic/json.svg?label=users&uri=https%3A//raw.githubusercontent.com/ccp-petmr-codebot/github-stats/CCPPETMR/SIRF-SuperBuild/CCPPETMR_SIRF_SuperBuild.json&query=total&colorB=8000f0&logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAD0ElEQVR4nMSXS2ic5RfGf5lL/pPMZP7JjB0ba53axkvRegGhpFaxVkqjOxetoi6UUjG4ELdVFy50I6gLtfUCFilUiwheilZXIm1FiZSCpYmYRppoUpvRJONMOpmJnOT54DBtxk4CmQPDl/d85z3vc55zeb%2BEWJr0AE8uxcFSAWwE7mwkgE7gqkYCWAGkGwkgBVQaCSACFBsJwPaXgGijAJhMAonlAvAc0OHWlv8pB8BS8hLQtFhAtaRFdD%2BodQz4BngbuEm624BZ4MYFfFwUcD0MdAGjeqKojf4Jx8B1wAhwwwI%2BLuqYegBkgePAKq2Tot9AtEln744Bay7XaS0Are4wk6uBPmCl1gkByDsGMrLx%2B1L61Q3gBeBTt7axe9I5C1LgGcjIxo/nvcC%2BhQ6J1ACwWREmlWeLfNBVeELR5x0AA/czcKXzE6SjSQV6SQbiwLdAt9bNMu5zFZ5REXoAU6F5u4TTjcgfAvI78AuwVrprge%2BB1R7Aw0Leq7VV82mgX3%2BbXAGcd1G0J0Ik18foSoVply4MFFyA64ABpSUI5HEFNndW5NEo2c9LPNQT5fkS7IxBdqDCXRUY6wpxtgKZKGS/KNH6QJTV09D3P1hzqkznvRl2b2%2Bj8P4Qr8%2BGyB6ZoXlbhGwRfjA//RXuaIKJtSFOV6DD/BwuseX%2BKE8VYHcLZJuOZ3hr1zjbDqb5%2BAK0hGFm7xTd6yMM3hNj2HQxyO88zyMfpjkwDfEoFF6bZOPdGTZvbeOfE6McWgVju3Ls2J/ioyLEm6HwTp7udWGGt8YYsn3lWSq9OXr2p%2BbPCkHZWPgAeFr0GC1PAJ%2Bokls17ez5tWz2aRi9uCnOm70reKMzwgHR/6VsrPI3yHaD3h0FtgCvyGY7cMi64DfgXSnN6Bn1/IgrrE4Vk8lfug/ix/IcPFWkmCuzB/i/WhLZrtTwGmI%2B0gv6hjwqm6%2BA260I97g7/QRwq4omkBngGgfobytAa71ZOJcrz%2B1JCEBONsMKol0tbHIEeEyMomJ%2BuXoOmHIHMO50Z4FNYgod0uFG8bQuprTYCfZ0K/JAXgU%2Bc4Dm5FKTcEDtFki/qBvUekLRJsUGmg1Jl4JfgfuAM85PoYrZBQFUy0/69D7pGEi5uyCQtGPOANyifq8ptUZxIFbZz4pWXBGG3fVaUb6DFMyomA//l/PLYaCg/AUyrmj93mmNVl8777nOWRKAavlT94L/uLCauV7v6pLFABhXf09WgboZGFsOAEG%2BR53uDzEwuhwA0HQbdOszOrzuf1LCiwRg7fedi/icfj/W6%2BjfAAAA///cZAAN8LSlZAAAAABJRU5ErkJggg%3D%3D
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[docker-badge]: https://img.shields.io/docker/pulls/synerbi/sirf.svg
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[docker-link]: https://hub.docker.com/r/synerbi/sirf
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[install-badge]: https://img.shields.io/badge/dynamic/json.svg?label=users&uri=https%3A//raw.githubusercontent.com/ccp-petmr-codebot/github-stats/SyneRBI/SIRF-SuperBuild/SyneRBI_SIRF_SuperBuild.json&query=total&colorB=8000f0&logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAD0ElEQVR4nMSXS2ic5RfGf5lL/pPMZP7JjB0ba53axkvRegGhpFaxVkqjOxetoi6UUjG4ELdVFy50I6gLtfUCFilUiwheilZXIm1FiZSCpYmYRppoUpvRJONMOpmJnOT54DBtxk4CmQPDl/d85z3vc55zeb%2BEWJr0AE8uxcFSAWwE7mwkgE7gqkYCWAGkGwkgBVQaCSACFBsJwPaXgGijAJhMAonlAvAc0OHWlv8pB8BS8hLQtFhAtaRFdD%2BodQz4BngbuEm624BZ4MYFfFwUcD0MdAGjeqKojf4Jx8B1wAhwwwI%2BLuqYegBkgePAKq2Tot9AtEln744Bay7XaS0Are4wk6uBPmCl1gkByDsGMrLx%2B1L61Q3gBeBTt7axe9I5C1LgGcjIxo/nvcC%2BhQ6J1ACwWREmlWeLfNBVeELR5x0AA/czcKXzE6SjSQV6SQbiwLdAt9bNMu5zFZ5REXoAU6F5u4TTjcgfAvI78AuwVrprge%2BB1R7Aw0Leq7VV82mgX3%2BbXAGcd1G0J0Ik18foSoVply4MFFyA64ABpSUI5HEFNndW5NEo2c9LPNQT5fkS7IxBdqDCXRUY6wpxtgKZKGS/KNH6QJTV09D3P1hzqkznvRl2b2%2Bj8P4Qr8%2BGyB6ZoXlbhGwRfjA//RXuaIKJtSFOV6DD/BwuseX%2BKE8VYHcLZJuOZ3hr1zjbDqb5%2BAK0hGFm7xTd6yMM3hNj2HQxyO88zyMfpjkwDfEoFF6bZOPdGTZvbeOfE6McWgVju3Ls2J/ioyLEm6HwTp7udWGGt8YYsn3lWSq9OXr2p%2BbPCkHZWPgAeFr0GC1PAJ%2Bokls17ez5tWz2aRi9uCnOm70reKMzwgHR/6VsrPI3yHaD3h0FtgCvyGY7cMi64DfgXSnN6Bn1/IgrrE4Vk8lfug/ix/IcPFWkmCuzB/i/WhLZrtTwGmI%2B0gv6hjwqm6%2BA260I97g7/QRwq4omkBngGgfobytAa71ZOJcrz%2B1JCEBONsMKol0tbHIEeEyMomJ%2BuXoOmHIHMO50Z4FNYgod0uFG8bQuprTYCfZ0K/JAXgU%2Bc4Dm5FKTcEDtFki/qBvUekLRJsUGmg1Jl4JfgfuAM85PoYrZBQFUy0/69D7pGEi5uyCQtGPOANyifq8ptUZxIFbZz4pWXBGG3fVaUb6DFMyomA//l/PLYaCg/AUyrmj93mmNVl8777nOWRKAavlT94L/uLCauV7v6pLFABhXf09WgboZGFsOAEG%2BR53uDzEwuhwA0HQbdOszOrzuf1LCiwRg7fedi/icfj/W6%2BjfAAAA///cZAAN8LSlZAAAAABJRU5ErkJggg%3D%3D

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