Merge branch 'master' into modifications_for_psmr2024

UCL · May 16, 2024 · e7a2656 · e7a2656
2 parents e67faec + 6b88234
commit e7a2656
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,8 @@
+# change to Apache 2.0 license
+47d1aa5f302c5b6b579de176535e01aa97d1ff27
+# run clang-tidy --modernize-use-override
+8af125617a113724f52d26e991bfc6c36abb952f
+# manual fixes in stir_experimental and clang-tidy modernize-use-override
+c5a1c6bc29d3f24d8fdb5c198946ec9580947257
+# stir_maintenance run pre-commit
+88f4ce70929a41c745fc39030e90c87bfaf046b7
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -162,9 +162,6 @@ jobs:
             CXX=${CXX}-${{ matrix.compiler_version }}            
           fi
           if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then
-            # need to force XCode version for the moment due to a linker bug
-            # see https://github.com/UCL/STIR/issues/1103
-            echo DEVELOPER_DIR="/Applications/Xcode_14.1.app/Contents/Developer" >> $GITHUB_ENV
             if test 'XX${{ matrix.compiler }}' = 'XXclang'; then
               brew install llvm@${{ matrix.compiler_version }}
               if test XX${HOMEBREW_PREFIX} = XX; then
@@ -353,7 +350,10 @@ jobs:
           fi
           # don't run all of them in Debug mode as it takes too long
           if test ${BUILD_TYPE} = Debug; then
-              EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection"
+              # Also excluding test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
+              # as it is a bit slow. Moreover it fails on MacOS (Debug)
+              # https://github.com/UCL/STIR/pull/1418#issuecomment-2109518132
+              EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection|test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin"
               EXCLUDE="${EXCLUDE_Debug}${EXCLUDE:+"|"}${EXCLUDE}"
           fi
           # prepend -E
@@ -363,6 +363,19 @@ jobs:
           # execute tests
           ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE}
 
+    - name: Upload ctest log files for debugging
+      uses: actions/upload-artifact@v4
+      if: failure()
+      with:
+        name: ctest_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
+        path: |
+          ${{ github.workspace }}/build/**/*.log
+          ${{ github.workspace }}/build/**/*.hv
+          ${{ github.workspace }}/build/**/*.v
+          ${{ github.workspace }}/build/**/*.hs
+          ${{ github.workspace }}/build/**/*.s
+        retention-days: 7
+
     - name: C++ examples with STIR_LOCAL
       shell: bash
       run: |
@@ -435,11 +448,12 @@ jobs:
           fi
 
     - name: Upload recon_test_pack log files for debugging
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
-        path: ${{ github.workspace }}/recon_test_pack/**/*.log
+        path: |
+          ${{ github.workspace }}/recon_test_pack/**/*.log
           ${{ github.workspace }}/recon_test_pack/**/my_*v
           ${{ github.workspace }}/recon_test_pack/**/my_*s
         retention-days: 7

diff --git a/.gitignore b/.gitignore
@@ -57,6 +57,7 @@ install_manifest.txt
 ~$*
 *~
 *.bak
+\#*#
 
 # Ignore Visual Studio User-specific files
 *.suo

diff --git a/.mailmap b/.mailmap
@@ -37,6 +37,7 @@ Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.ehrhardt@bath.ac.uk>
 Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.j.ehrhardt@damtp.cam.ac.uk>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <nikos.efthimiou@gmail.com>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <NikEfth@users.noreply.github.com>
+Nikos Efthimiou <nikos.efthimiou@gmail.com> <n.efthymiou@hull.ac.uk>
 Ottavia Bertolli <ottavia.bertolli.13@ucl.ac.uk>
 Palak Wadhwa <pwadhwa351@gmail.com> <38861704+pwadhwa351@users.noreply.github.com>
 Palak Wadhwa <pwadhwa351@gmail.com> <medpwad@leeds.ac.uk>

diff --git a/CITATION.cff b/CITATION.cff
@@ -32,31 +32,31 @@ authors:
     - family-names: Jehl
       given-names:  Markus
       affiliation:  Positrigo
+    - family-names: Borgeaud
+      given-names:  Tim
+      affiliation:  Hammersmith Imanet Ltd
     - family-names: Strugari
       given-names:  Matthew
       affiliation:  Dalhousie University (Canada)
     - family-names: Khateri
       given-names:  Parisa
       affiliation:  ETH Zuerich
-    - family-names: Beisel
-      given-names:  Tobias
     - family-names: Wadhwa
       given-names:  Palak
       affiliation:  University of Leeds (UK)
-    - family-names: Borgeaud
-      given-names:  Tim
-      affiliation:  Hammersmith Imanet Ltd
+    - family-names: Beisel
+      given-names:  Tobias
     - family-names: Emond
       given-names:  Elise
       affiliation:  University College London
-    - family-names: Jacobson
-      given-names:  Matthew
     - family-names: Gillman
       given-names:  Ashley
       orcid:        'https://orcid.org/0000-0001-9130-1092'
       affiliation:  >-
         Commonwealth Scientific and Industrial Research
         Organisation, and University of Queensland
+    - family-names: Jacobson
+      given-names:  Matthew
     - family-names: Zverovich
       given-names:  Alexey
       affiliation:  Brunel University (UK)
@@ -113,6 +113,9 @@ authors:
     - family-names: Valente
       given-names:  Patrick
       affiliation:  Brunel University (UK)
+    - family-names: Jurjew
+      given-names:  Nicole
+      affiliation:  University College London
     - family-names: Ovtchinnikov
       given-names:  Evgueni
       orcid:        'https://orcid.org/0000-0002-9359-6514'
@@ -127,9 +130,6 @@ authors:
     - family-names: Belluzzo
       given-names:  Damiano
       affiliation:  Hospedale San Raffaele Milano (Italy)
-    - family-names: Jurjew
-      given-names:  Nicole
-      affiliation:  University College London
     - family-names: Ching
       given-names:  Daniel
     - family-names: Hague
@@ -178,10 +178,14 @@ authors:
 identifiers:
     - type: doi
       value: 10.1088/0031-9155/57/4/867
+    - type: doi
+      value: 10.3389/fnume.2023.1134774
     - type: doi
       value: 10.1186/s40658-019-0248-9
     - type: doi
       value: 10.3390/jimaging8060172
+    - type: doi
+      value: 10.1088/1361-6560/aaf9b9
     - type: doi
       value: 10.1109/NSSMIC.2018.8824341
     - type: doi

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -54,9 +54,9 @@ endif()
 
 ####### Set Version number etc
 set(VERSION_MAJOR   6)
-set(VERSION_MINOR   0)
+set(VERSION_MINOR   1)
 set(VERSION_PATCH   0)
-set(VERSION   060000) # only used in STIRConfig.h.in and swig/CMakeLists.txt
+set(VERSION   060100) # only used in STIRConfig.h.in and swig/CMakeLists.txt
 
 set(STIR_VERSION
   ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
@@ -121,7 +121,13 @@ if(NOT DISABLE_CERN_ROOT)
   find_package(CERN_ROOT)
   if (CERN_ROOT_FOUND)
     message(STATUS "ROOT Version: ${CERN_ROOT_VERSION}")
-    if (${CERN_ROOT_VERSION} VERSION_GREATER 6.23.99)
+    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()

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-6.0.0
+6.1.0
diff --git a/documentation/STIR-UsersGuide.tex b/documentation/STIR-UsersGuide.tex
@@ -44,7 +44,7 @@
 \\[3cm]
 
 \textbf{{\huge User's Guide\\
- Version 6.0}}
+ Version 6.1}}
 \end{center}
 
 \end{spacing}
@@ -444,7 +444,8 @@ \subsubsection{
 
 { \subsubsubsection{Cygwin on Windows}
 }
-\textit{Cygwin support has not been tested since about 2018 but likely still works. Instructions below might be out-of-date though.}
+\textit{Cygwin support has not been tested since about 2018 but likely still works. Instructions below are likely out-of-date though.
+We highly recommend to use WSL instead.}
 
 If you are using Windows but would like 
 to have nearly everything that Linux/Unix has to offer, Cygwin could help. Check out http://cygwin.com.

diff --git a/documentation/STIR-developers-overview.tex b/documentation/STIR-developers-overview.tex
@@ -60,8 +60,8 @@ \section{
 doxygen on the source files that come in the STIR distribution). 
 
 \subsection{Language support}
-STIR is written in C++ and currently requires C++-11, but it is compatible with newer versions of the C++ standard.
-We will enforce C++-14 from STIR 6.0.
+STIR is written in C++ and currently requires C++-14, but it is compatible with newer versions of the C++ standard.
+We will enforce C++-16 from STIR 6.2.
 
 Python and MATLAB support is provided via \R2Lurl{http://www.swig.org/}{SWIG}. This means that Python/MATLAB interfaces follow
 the C++ classes closely, although some differences are required as these languages do not support templates for instance.
@@ -170,8 +170,8 @@ \subsection{
 view.
 \end{itemize} 
 
-Note that in STIR version 6.0, Time-of-Flight (TOF) will be supported. This introduces another
-index. However, \texttt{Sinogram} and \texttt{Viewgram} will remain 2D objects, and \texttt{Segment*} 3D.
+Note that since STIR version 6.0, Time-of-Flight (TOF) is supported. This introduces another
+index. However, \texttt{Sinogram} and \texttt{Viewgram} remain 2D objects, and \texttt{Segment*} 3D.
 This will also be the case once we have layers and energy windows.
 In STIR 5.2, we have therefore introduced new classes
 \texttt{SinogramIndices}, \texttt{ViewgramIndices}\footnote{Replacing \texttt{ViewSegmentNumbers} in previous versions of STIR.}
@@ -897,7 +897,7 @@ \subsubsection{
 \end{itemize}
 
 
-At the moment, we have three derived classes:
+At the moment, we have the following derived classes:
 \begin{itemize}
 \item 
 \texttt{ProjMatrixByBinUsingRayTracing} uses essentially the same 
@@ -916,6 +916,10 @@ \subsubsection{
 part of the projection matrix needs to be stored. Our current 
 implementation does not yet provide a very compact format for 
 storing the elements (although they are of course stored sparsely).
+\item
+\texttt{ProjMatrixByBinSPECTUB} is for parallel hole SPECT
+\item
+\texttt{ProjMatrixByBinPinholeSPECTUB} is for multi-pinhole SPECT
 \end{itemize}
 
 \begin{figure}[htbp]
@@ -956,8 +960,10 @@ \subsection{Objective functions}
 that is computed is generally not the gradient of the
 log-likelihood that corresponds to the forward projector.
 However, one hopes that it still points towards the optimum.
-The corresponding objective function is implemented in the class\\
-\texttt{PoissonLogLikelihoodWithLinearModelForMeanAndProjData}.
+The corresponding objective function is implemented in the classes\\
+\texttt{PoissonLogLikelihoodWithLinearModelForMeanAndProjData} for
+projection data and \texttt{PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin}
+for list-mode data. There are classes for dynamic and gated data as well.
 
 There can be different objective function that use common operations.
 For instance, the objective function could implement a least squares

diff --git a/documentation/credits.htm b/documentation/credits.htm
@@ -116,9 +116,9 @@ <h2>contributions since the PARAPET EU project (April 2000)</h2>
     Roethlisberger, Michael
 
 16. Positrigo, Switserland
-    SWIG improvements and "blocks on cylindrical" testing
-    Mikhaylova, Ekaterina
+    SWIG improvements, "blocks on cylindrical" testing and fixes
     Jehl, Markus
+    Mikhaylova, Ekaterina
     Fisher, Jannis
 
 17. National Physical Laboratory, UK
@@ -132,7 +132,8 @@ <h2>contributions since the PARAPET EU project (April 2000)</h2>
 
 19. University College London, UK
     (2013-2024)
-    scatter updates, dynamic data updates, OPENMP, PLS, RDP etc priors, reconstruction hierarchy, Siemens ECAT8 support etc
+    scatter updates, dynamic data updates, OPENMP, PLS, RDP etc priors, reconstruction hierarchy, Siemens ECAT8 support,
+    TOF support, parallelproj integration etc
     pinhole SPECT modelling
     help with integration and general maintenance
     Brown, Richard

diff --git a/documentation/history.htm b/documentation/history.htm
@@ -11,6 +11,7 @@ <h1>History of public releases of the STIR software</h1>
 The following links give you a summary what has changed. However,
 the ChangeLog is the definite (but tedious) information.
 <ul >
+<li><a href="release_6.1.htm">version 6.1.0 (dated 16 May 2024)</a></li>
 <li><a href="release_6.0.htm">version 6.0.0 (dated 07 February 2024)</a></li>
 <li><a href="release_5.2.htm">version 5.2.0 (dated 30 October 2023)</a></li>
 <li><a href="release_5.1.htm">version 5.1.2 (dated 10 September 2023)</a></li>
@@ -49,7 +50,7 @@ <h1>History of public releases of the PARAPET software</h1>
 
 <!-- Created: Wed Jul 19 16:03:02 BST 2000 -->
 <!-- hhmts start -->
-Last modified: 7 February 2024
+Last modified: 16 May 2024
 <!-- hhmts end -->
   </body>
 </html>