Merge pull request #1236 from KrisThielemans/Array

update Array hierarchy and allocate nD arrays in a contiguous block by default
UCL · May 23, 2024 · f3719b4 · f3719b4
2 parents 41c74f5 + ae82826
commit f3719b4
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Showing 25 changed files with 968 additions and 176 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -14,7 +14,6 @@ version: '{build}'
 os:
   - Visual Studio 2022
   - Visual Studio 2019
-  - Visual Studio 2015
 
 platform:
   - x64

diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -79,7 +79,7 @@ jobs:
           compiler: gcc
           compiler_version: 12
           cuda_version: "12.1.0"
-          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
+          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
           ROOT: "OFF"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -33,7 +33,7 @@ include(src/cmake/SetC++Version.cmake)
 
 # minimum C++ version required (you can still ask for a more recent one
 # by setting CMAKE_CXX_STANDARD)
-UseCXX(14)
+UseCXX(17)
 
 # set default build-type to Release
 if(NOT CMAKE_BUILD_TYPE)
@@ -118,18 +118,12 @@ if(NOT DISABLE_LLN_MATRIX)
 endif()
 
 if(NOT DISABLE_CERN_ROOT)
-  find_package(CERN_ROOT)
+  find_package(CERN_ROOT 6.28.00) # required for C++17
   if (CERN_ROOT_FOUND)
     message(STATUS "ROOT Version: ${CERN_ROOT_VERSION}")
     if (${CERN_ROOT_VERSION} VERSION_GREATER 6.29.99)
         message(STATUS "ROOT Version is >= 6.30. Setting the minimum CXX version to 20.")
         UseCXX(20)
-    elseif (${CERN_ROOT_VERSION} VERSION_GREATER 6.27.99)
-        message(STATUS "ROOT Version is >= 6.28. Setting the minimum CXX version to 17.")
-        UseCXX(17)
-    elseif (${CERN_ROOT_VERSION} VERSION_GREATER 6.23.99)
-        message(STATUS "ROOT Version is >= 6.24. Setting the minimum CXX version to 14.")
-        UseCXX(14)
     endif()
   endif()
 endif()

diff --git a/documentation/release_6.2.htm b/documentation/release_6.2.htm
@@ -0,0 +1,125 @@
+<!DOCTYPE HTML>
+<html lang="en">
+  <head>
+    <title>Summary of changes in STIR release 6.2</title>
+  </head>
+
+  <body>
+    <h1>Summary of changes in STIR release 6.2</h1>
+
+    <p>
+      This version is 100% backwards compatible with STIR 6.1. However, C++-17 is now required.
+    </p>
+
+<h2>Overall summary</h2>
+    <p>
+
+    </p>
+
+    <p>
+      Of course, there is also the usual code-cleanup and improvements to the documentation.
+    </p>
+
+    <p>
+      This release contains mainly code written by Nicole Jurjew (UCL) and Kris Thielemans (UCL).
+    </p>
+
+<h2>Patch release info</h2>
+<ul>
+  <li>
+    6.2.0 released ??/2024<br>
+    <a href="https://github.com/UCL/STIR/milestone/11">GitHub Milestone 6.2</a>
+  </li>
+  <!--
+      <li> 4.0.1 released 28/04/2020
+        <ul>
+          <li><a href=https://github.com/UCL/STIR/pull/513>PR 513</a>  (suppress warnings with clang)</li>
+        </ul>
+        -->
+</ul>
+
+<h2> Summary for end users (also to be read by developers)</h2>
+
+
+<h3>New functionality</h3>
+<ul>
+</ul>
+
+
+<h3>Changed functionality</h3>
+<ul>
+</ul>
+
+
+<h3>Bug fixes</h3>
+<ul>
+</ul>
+
+<h3>Build system</h3>
+<ul
+  <li>
+    C++-17 is now required.
+  </li>
+</ul>
+
+<h3>Known problems</h3>
+    <p>See <a href=https://github.com/UCL/STIR/labels/bug>our issue tracker</a>.</p>
+
+
+<H2>What's new for developers (aside from what should be obvious
+from the above):</H2>
+
+<h3>Changed functionality</h3>
+<ul>
+    <li>
+      <code>Array</code> classes by default use contiguous memory allocation (as opposed to a sequence of 1D vectors).
+      This could speed up memory allocation and destruction of arrays with a high number of underlying 1D vectors. It also allows reading/writing
+      data in one call to the C++ library, as opposed to many small calls. Also added move constructors to the <code>Array</code>,
+      <code>VectorWithOffset</code> classes.
+      <br>
+      <a href=https://github.com/UCL/STIR/pull/1236>issue #1236</a>.
+    </li>
+</ul>
+
+<h3>Bug fixes</h3>
+<ul>
+  <li>
+    <code>PoissonLogLikelihoodWithLinearModelForMeanAndProjData</code> had a (minor?) problem with TOF data
+    that when computing the gradient, the normalisation object was not set-up with the TOF data,
+    but non-TOF instead. This did not happen in our normal reconstruction code, and would have thrown an error
+    if it occured.
+    <br>
+    Fixed in <a href=https://github.com/UCL/STIR/pull/1427>issue #1427</a>.
+  </li>
+</ul>
+
+
+<h3>Other code changes</h3>
+<ul>
+  <li>
+    Fixes an incompatibility with C++20.
+  </li>
+</ul>
+
+<h3>Build system</h3>
+<ul>
+  <li>
+    Force C++ version according to CERN ROOT versions: ROOT 6.28.10 needs C++17 and 6.30.2 needs C++20.
+    Also some fixes when relying on <code>root-config</code>.
+  </li>
+</ul>
+
+<h3>Test changes</h3>
+
+<h4>C++ tests</h4>
+<ul>
+  <li>
+    Objective functions (both projection-data and list-mode) and priors now have a numerical test for <code>accumulate_Hessian_times_input</code>
+    <br>
+    <a href=https://github.com/UCL/STIR/pull/1418> PR #1418</a>
+  </li>
+</ul>
+
+</body>
+
+</html>
diff --git a/src/buildblock/ProjDataInfoCylindrical.cxx b/src/buildblock/ProjDataInfoCylindrical.cxx
@@ -43,7 +43,6 @@ using std::min_element;
 using std::max_element;
 using std::min;
 using std::max;
-using std::swap;
 using std::endl;
 using std::string;
 using std::pair;
@@ -113,7 +112,7 @@ ProjDataInfoCylindrical::ProjDataInfoCylindrical(const shared_ptr<Scanner>& scan
                   min_ring_diff[segment_num],
                   max_ring_diff[segment_num],
                   segment_num);
-          swap(min_ring_diff[segment_num], max_ring_diff[segment_num]);
+          std::swap(min_ring_diff[segment_num], max_ring_diff[segment_num]);
         }
   }
 

diff --git a/src/cmake/FindCERN_ROOT.cmake b/src/cmake/FindCERN_ROOT.cmake
@@ -168,4 +168,6 @@ if (CERN_ROOT_DEBUG)
 endif()
 
 INCLUDE(FindPackageHandleStandardArgs)
-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)
+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"
+  VERSION_VAR CERN_ROOT_VERSION
+  REQUIRED_VARS CERN_ROOT_LIBRARIES CERN_ROOT_INCLUDE_DIRS)