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KrisThielemansKrisThielemans
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Merge pull request #1236 from KrisThielemans/Array
update Array hierarchy and allocate nD arrays in a contiguous block by default
2 parents 41c74f5 + ae82826 commit f3719b4

25 files changed

+968
-176
lines changed

Diff for: ‎.appveyor.yml

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@@ -14,7 +14,6 @@ version: '{build}'
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os:
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- Visual Studio 2022
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- Visual Studio 2019
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- Visual Studio 2015
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platform:
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- x64

Diff for: ‎.github/workflows/build-test.yml

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compiler: gcc
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compiler_version: 12
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cuda_version: "12.1.0"
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BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
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BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
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BUILD_TYPE: "Release"
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parallelproj: "ON"
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ROOT: "OFF"

Diff for: ‎CMakeLists.txt

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@@ -33,7 +33,7 @@ include(src/cmake/SetC++Version.cmake)
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# minimum C++ version required (you can still ask for a more recent one
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# by setting CMAKE_CXX_STANDARD)
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UseCXX(14)
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UseCXX(17)
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# set default build-type to Release
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if(NOT CMAKE_BUILD_TYPE)
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endif()
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if(NOT DISABLE_CERN_ROOT)
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find_package(CERN_ROOT)
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find_package(CERN_ROOT 6.28.00) # required for C++17
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if (CERN_ROOT_FOUND)
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message(STATUS "ROOT Version: ${CERN_ROOT_VERSION}")
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if (${CERN_ROOT_VERSION} VERSION_GREATER 6.29.99)
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message(STATUS "ROOT Version is >= 6.30. Setting the minimum CXX version to 20.")
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UseCXX(20)
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elseif (${CERN_ROOT_VERSION} VERSION_GREATER 6.27.99)
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message(STATUS "ROOT Version is >= 6.28. Setting the minimum CXX version to 17.")
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UseCXX(17)
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elseif (${CERN_ROOT_VERSION} VERSION_GREATER 6.23.99)
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message(STATUS "ROOT Version is >= 6.24. Setting the minimum CXX version to 14.")
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UseCXX(14)
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endif()
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endif()
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endif()

Diff for: ‎documentation/release_6.2.htm

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<title>Summary of changes in STIR release 6.2</title>
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</head>
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<body>
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<h1>Summary of changes in STIR release 6.2</h1>
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<p>
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This version is 100% backwards compatible with STIR 6.1. However, C++-17 is now required.
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</p>
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<h2>Overall summary</h2>
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<p>
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</p>
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<p>
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Of course, there is also the usual code-cleanup and improvements to the documentation.
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</p>
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<p>
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This release contains mainly code written by Nicole Jurjew (UCL) and Kris Thielemans (UCL).
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</p>
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<h2>Patch release info</h2>
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<ul>
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<li>
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6.2.0 released ??/2024<br>
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<a href="https://github.com/UCL/STIR/milestone/11">GitHub Milestone 6.2</a>
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</li>
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<!--
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<li> 4.0.1 released 28/04/2020
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<ul>
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<li><a href=https://github.com/UCL/STIR/pull/513>PR 513</a> (suppress warnings with clang)</li>
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</ul>
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-->
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</ul>
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<h2> Summary for end users (also to be read by developers)</h2>
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<h3>New functionality</h3>
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<ul>
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</ul>
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<h3>Changed functionality</h3>
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<ul>
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</ul>
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<h3>Bug fixes</h3>
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<ul>
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</ul>
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<h3>Build system</h3>
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<ul
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<li>
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C++-17 is now required.
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</li>
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</ul>
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<h3>Known problems</h3>
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<p>See <a href=https://github.com/UCL/STIR/labels/bug>our issue tracker</a>.</p>
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<H2>What's new for developers (aside from what should be obvious
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from the above):</H2>
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<h3>Changed functionality</h3>
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<ul>
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<li>
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<code>Array</code> classes by default use contiguous memory allocation (as opposed to a sequence of 1D vectors).
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This could speed up memory allocation and destruction of arrays with a high number of underlying 1D vectors. It also allows reading/writing
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data in one call to the C++ library, as opposed to many small calls. Also added move constructors to the <code>Array</code>,
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<code>VectorWithOffset</code> classes.
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<br>
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<a href=https://github.com/UCL/STIR/pull/1236>issue #1236</a>.
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</li>
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</ul>
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<h3>Bug fixes</h3>
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<ul>
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<li>
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<code>PoissonLogLikelihoodWithLinearModelForMeanAndProjData</code> had a (minor?) problem with TOF data
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that when computing the gradient, the normalisation object was not set-up with the TOF data,
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but non-TOF instead. This did not happen in our normal reconstruction code, and would have thrown an error
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if it occured.
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<br>
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Fixed in <a href=https://github.com/UCL/STIR/pull/1427>issue #1427</a>.
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</li>
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</ul>
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<h3>Other code changes</h3>
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<ul>
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<li>
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Fixes an incompatibility with C++20.
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</li>
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</ul>
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<h3>Build system</h3>
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<ul>
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<li>
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Force C++ version according to CERN ROOT versions: ROOT 6.28.10 needs C++17 and 6.30.2 needs C++20.
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Also some fixes when relying on <code>root-config</code>.
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</li>
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</ul>
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<h3>Test changes</h3>
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<h4>C++ tests</h4>
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<ul>
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<li>
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Objective functions (both projection-data and list-mode) and priors now have a numerical test for <code>accumulate_Hessian_times_input</code>
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<br>
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<a href=https://github.com/UCL/STIR/pull/1418> PR #1418</a>
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</li>
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</ul>
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</body>
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</html>

Diff for: ‎src/buildblock/ProjDataInfoCylindrical.cxx

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@@ -43,7 +43,6 @@ using std::min_element;
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using std::max_element;
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using std::min;
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using std::max;
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using std::swap;
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using std::endl;
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using std::string;
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using std::pair;
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min_ring_diff[segment_num],
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max_ring_diff[segment_num],
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segment_num);
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swap(min_ring_diff[segment_num], max_ring_diff[segment_num]);
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std::swap(min_ring_diff[segment_num], max_ring_diff[segment_num]);
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}
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}
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Diff for: ‎src/cmake/FindCERN_ROOT.cmake

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endif()
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INCLUDE(FindPackageHandleStandardArgs)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(CERN_ROOT "CERN ROOT not found. If you do have it, set ROOT_DIR (preferred), ROOTSYS or add root-config to your path" CERN_ROOT_VERSION CERN_ROOT_LIBRARIES CERN_ROOT_INCLUDE_DIRS)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(CERN_ROOT FAIL_MESSAGE "CERN ROOT not found. If you do have it, set ROOT_DIR (preferred), ROOTSYS or add root-config to your path"
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VERSION_VAR CERN_ROOT_VERSION
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REQUIRED_VARS CERN_ROOT_LIBRARIES CERN_ROOT_INCLUDE_DIRS)

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