Merge branch 'UCL:master' into LMduration

.github/workflows/build-test.yml

@@ -86,7 +86,7 @@ jobs:
           ITK: "ON"
         - os: macOS-latest
           compiler: gcc
-          compiler_version: 11
+          # compiler_version: 11
           cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=OFF"
           parallelproj: "OFF"

.mailmap

@@ -68,3 +68,5 @@ Sam D Porter <[email protected]>
 Sam D Porter <[email protected]>  <[email protected]>
 Matthew Strugari <[email protected]>
 Matthew Strugari <[email protected]> <[email protected]>
+Imraj Singh <[email protected]>
+Imraj Singh <[email protected]> <[email protected]>

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
--   repo: https://github.com/doublify/pre-commit-clang-format
-    rev: '62302476'
-    hooks:
-    -   id: clang-format
-        files: \.(c|cc|cxx|cpp|h|hpp|hxx|inl|txx)$
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v14.0.6
+  hooks:
+  - id: clang-format
+    files: \.(c|cc|cxx|cpp|cu|h|hpp|hxx|inl|txx)$

CITATION.cff

@@ -81,23 +81,21 @@ authors:
     - family-names: Brusaferri
       given-names:  Ludovica
       affiliation:  University College London
-    - family-names: Pasca
-      given-names:  Edoardo
-      affiliation:  UK Research & Innovation
-      orcid:        'https://orcid.org/0000-0001-6957-2160'
     - family-names: Thomas
       given-names:  Benjamin
       orcid:        'https://orcid.org/0000-0002-9784-1177'
       affiliation:  University College London
+    - family-names: Pasca
+      given-names:  Edoardo
+      affiliation:  UK Research & Innovation
+      orcid:        'https://orcid.org/0000-0001-6957-2160'
     - family-names: Aguiar
       given-names:  Pablo
     - family-names: Niknejad
       given-names:  Tahereh
     - family-names: Sadki
       given-names:  Mustapha
       affiliation:  Brunel University (UK)
-    - family-names: Schmidtlein
-      given-names:  C Ross
     - family-names: Kerrouche
       given-names:  Nacer
       affiliation:  Hammersmith Imanet Ltd
@@ -110,16 +108,22 @@ authors:
     - family-names: Ehrhardt
       given-names:  Matthias J.
       orcid:        'https://orcid.org/0000-0001-8523-353X'
+    - family-names: Singh
+      given-names:  Imraj
+      orcid:        'https://orcid.org/0000-0003-2186-0977'
+      affiliation:  University College London (UK)
+    - family-names: Schmidtlein
+      given-names:  C Ross
+    - family-names: Ovtchinnikov
+      given-names:  Evgueni
+      orcid:        'https://orcid.org/0000-0002-9359-6514'
+      affiliation:  UK Research & Innovation
     - 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'
-      affiliation:  UK Research & Innovation
     - family-names: Schramm
       given-names:  Georg
       affiliation:  Katholieke Universiteit Leuven (Belgium)

CMakeLists.txt

@@ -186,6 +186,38 @@ else()
   message(STATUS "NiftyPET projector support disabled.")
 endif()
 
+if(NOT DISABLE_STIR_CUDA)
+  include(CheckLanguage)
+  check_language(CUDA)
+  if (CMAKE_CUDA_COMPILER)
+    enable_language(CUDA)
+    find_package(CUDAToolkit QUIET)
+    if (NOT CUDAToolkit_FOUND)
+      message(WARNING "CUDAToolkit not detected. Setting DISABLE_STIR_CUDA to ON.")
+      set(DISABLE_STIR_CUDA ON)
+      set(STIR_WITH_CUDA OFF)
+    else()
+      if("${CMAKE_VERSION}" VERSION_LESS "3.23")
+        message(FATAL_ERROR "CMake 3.23 or newer is required to use CMAKE_CUDA_ARCHITECTURES set to 'all'. Upgrade your CMake or set DISABLE_STIR_CUDA to ON.")
+      else()
+        set(CMAKE_CUDA_ARCHITECTURES "all")
+      endif()
+      message(STATUS "STIR CUDA support enabled. Using CUDA version ${CUDAToolkit_VERSION}.")
+      set(STIR_WITH_CUDA ON)
+    endif()
+    # check if run-time is available for ctests
+    find_program(NVIDIA_SMI nvidia-smi)
+    if (NOT NVIDIA_SMI)
+      message(WARNING "nvidia-smi not found. Disabling the ctests using CUDA")
+      set(SKIP_CUDA_TESTS ON)
+    endif()
+  else()
+    message(WARNING "No CUDA compiler found. Setting DISABLE_STIR_CUDA to ON.")
+    set(DISABLE_STIR_CUDA ON)
+    set(STIR_WITH_CUDA OFF)
+  endif()
+endif()
+
 # Parallelproj
 if(NOT DISABLE_Parallelproj_PROJECTOR)
     find_package(parallelproj 1.3.4 CONFIG)

LICENSE.txt

@@ -1,4 +1,4 @@
-Licensing information for STIR 6.0.0
+Licensing information for STIR 6.2.0
 ----------------------------------
 
 See for more info http://stir.sourceforge.net, section Registration.
@@ -209,6 +209,7 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/recon_buildblock/BackProjectorByBinUsingInterpolation.h
 ./src/include/stir/recon_buildblock/SymmetryOperations_PET_CartesianGrid.h
 ./src/include/stir/recon_buildblock/ProjMatrixElemsForOneBin.h
+./src/include/stir/recon_buildblock/distributable.txx
 ./src/include/stir/recon_buildblock/RelatedBins.h
 ./src/include/stir/recon_buildblock/RelatedDensels.inl
 ./src/include/stir/recon_buildblock/ProjMatrixByBin.h
@@ -219,6 +220,7 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/CPUTimer.h
 ./src/include/stir/VoxelsOnCartesianGrid.inl
 ./src/include/stir/stream.h
+./src/include/stir/HigherPrecision.h
 ./src/include/stir_experimental/phantoms/Utah.h
 ./src/test/test_ByteOrder.cxx
 ./src/test/test_VectorWithOffset.cxx

VERSION.txt

@@ -1 +1 @@
-6.1.0
+6.2.0

documentation/STIR-UsersGuide.tex

@@ -44,7 +44,7 @@
 \\[3cm]
 
 \textbf{{\huge User's Guide\\
- Version 6.1}}
+ Version 6.2}}
 \end{center}
 
 \end{spacing}
@@ -1092,17 +1092,18 @@ \subsubsection{
 the same idea while still allowing preserving some of the obliqueness. 
 For instance, for a dataset with 9 segments, \textbf{SSRB} can produce 
 a new dataset with only 3 segments. This essentially increases 
-the axial compression (or \textit{span} in CTI terminology), see the 
+the axial compression (or \textit{span} in CTI/Siemens terminology), see the 
 \textit{STIR} Glossary on axial compression. In addition, \textbf{SSRB} can 
 introduce extra \textit{mashing} (see the \textit{STIR} Glossary) of the data, 
-i.e. add views together.
+i.e. add views and/or TOF bins together.
 
 
 \textit{Usage:}
 
 \cmdline{SSRB output\_filename input\_projdata\_name {\textbackslash} \\
 num\_segments\_to\_combine [num\_views\_to\_combine {\textbackslash}\\
-{[}do\_normalisation [max\_in\_segment\_num\_to\_process ]]]}
+{[}do\_normalisation [max\_in\_segment\_num\_to\_process {\textbackslash}\\
+{[}num\_tof\_bins\_to\_combine ]]]]}
 or
 \cmdline{SSRB --template template\_filename output\_filename input\_projdata\_name [do\_normalisation]}
 
@@ -1116,8 +1117,8 @@ \subsubsection{
 the result is normalised, i.e. divided by \textit{num\_segments\_to\_combine*num\_views\_to\_combine}. 
 This is appropriate for rebinning data where normalisation has 
 already been applied, but inappropriate otherwise.
-
-\item[template\_filename] inicated by the \textit{--template} flag, 
+\item[num\_tof\_bins\_to\_combine] defaults to 1, so TOF bins are not combined.
+\item[template\_filename] indicated by the \textit{--template} flag, 
 is the sinogram type that the \textit{input\_projdata\_name} will 
 be mapped to. This allows for the effective use of 
 \textit{num\_segments\_to\_combine} to be an even number, 
@@ -4446,6 +4447,12 @@ \subsubsection{
   END Relative Difference Prior Parameters:=
   \end{verbatim}
 
+  Note that if you have the \em{CUDA} drivers (and toolkit when building), setting
+  \begin{verbatim}
+  prior type := Cuda Relative Difference Prior
+  \end{verbatim}
+  will enable a \em{CUDA} implementation (with some restrictions). Other parameter
+  settings are identical.
 
 { \subsubsubsection{Logcosh} \label{sec:priors:Logcosh}
 }

documentation/STIR-developers-overview.tex

@@ -16,7 +16,7 @@
 \textbf{{\huge STIR \\
 Overview for developers}}\\
 \textbf{Kris Thielemans}\\
-\textbf{\textit{version 6.0}}
+\textbf{\textit{version 6.2}}
 
 \end{center}
 
@@ -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++-14, but it is compatible with newer versions of the C++ standard.
-We will enforce C++-16 from STIR 6.2.
+STIR is written in C++ and currently requires C++-17, but it is compatible with newer versions of the C++ standard.
+We will enforce C++-20 from STIR 7.0 (possibly earlier).
 
 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.
@@ -392,7 +392,7 @@ \subsection{
 with info on the file and line number where the assertion failed.
 
 \subsection{C++ conventions}
-STIR uses C++-14 and is compatible with C++-20 to the best of our knowledge.
+STIR uses C++-17 and is compatible with C++-20 to the best of our knowledge.
 For legacy reasons, we have some preprocessor 
 macros (see \textit{stir/common.h}) to define the stir namespace (see below).
 These should disappear at a 
@@ -622,6 +622,12 @@ \subsubsection{typedefs}
 };
 \end{verbatim}
 
+\section{CUDA support}
+STIR 6.2 introduced first versions of some CUDA code. The include file
+\texttt{cuda\_utilities.h} contains some helpers classes to copy
+arrays to/from the device. This is still work-in-progress as objects
+cannot remain on the device.
+
 \section{
 Overview of classes}
 

documentation/STIR-glossary.tex

@@ -14,7 +14,7 @@
 \end{center}
 
 \begin{center}
-\textit{Version 6.0}\\
+\textit{Version 6.2}\\
 Originally based on PARAPET Deliverable 4.1,
 Extended for Quantitative Reconstruction and motion compensation
 
@@ -207,7 +207,7 @@ \section*{Different (lossy) data compressions used}
 by the scanner (in list-mode) over the actual number of TOF bins. Currently in STIR, this
 ratio has to be an integer. The size of a TOF bin is computed by multiplying the
 \textbf{TOF mashing factor} with the \textbf{size of unmashed TOF time bins}, with the latter
-defined as a scanner property.\\
+defined as a scanner property. \texttt{SSRB} can be used to increase the TOF mashing factor.\\
 Note that many PET scanners use a \textbf{TOF mashing factor} greater than 1
 for their standard histogrammed projection data.
 

documentation/credits.htm

@@ -142,6 +142,7 @@ <h2>contributions since the PARAPET EU project (April 2000)</h2>
     Emond, Elise
     Falc&oacute;n, Carl&eacute;s
     Twyman, Robert
+    Singh, Imraj
     Jurjew, Nicole
     Bertolli, Ottavia
     Tsai, Yu-jung
@@ -244,7 +245,7 @@ <h2>Web site</h2>
 <hr>
 <!-- Created: Fri Jan 04  2002 -->
 <!-- hhmts start -->
-Last modified: Wed Feb 07  2024
+Last modified: Tue Jul 23 2024
 <!-- hhmts end -->
   </body>
 </html>

documentation/devel/editor-settings.md

@@ -1,5 +1,9 @@
 # Developer documentation: editor settings
 
 White-spaces and indentation with multiple developers are a pain. Please adhere to
-our white-space policy, which we try to enforce via [clang-format](https://clang.llvm.org/docs/ClangFormat.html).
-Check that site for integration with your editor/IDE.
+our white-space policy, which we enforce via [pre-commit](https://pre-commit.com/), including
+running of [clang-format](https://clang.llvm.org/docs/ClangFormat.html).
+See [git-hooks.md](git-hooks.md) for more information.
+
+Developer experience will be best if you set your editor/IDE to use the same settings,
+including versions of the formatters (`clang-format` in particular).

documentation/devel/git-hooks.md

@@ -3,11 +3,27 @@
 We use [pre-commit](https://pre-commit.com) to check coding conventions, including
 white-space formatting rules.
 
-Unfortunately, exact formatting used depends on the `clang-format` version. Therefore,
-you do have to install the same version as what is currently used in our GitHub Action.
+Unfortunately, exact formatting used depends on the `clang-format` (and others?) version. Therefore,
+you might need to install the same version as what is currently used in our
+[.pre-commit-config.yaml](../../.pre-commit-config.yaml) for your editor to pick up
+the same version.
 
 ## Installation of software
 
+### TL;DR
+
+```sh
+pip/conda install pre-commit
+git add blabla
+pre-commit run
+# optionally check files
+# "add" changes made by the hooks
+git add blabla
+git commit
+```
+
+### More detail
+
 We highly recommend to use `conda`:
 ```sh
 cd /whereever/STIR
@@ -48,4 +64,4 @@ or one-off with
 
     git commit --no-verify
 
-You will then need to run `pre-commit run --all-files` when done before we will merge your pull request.
+You will then need to run `pre-commit run --all-files` when done before we will merge your pull request.

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_6.2.htm">version 6.2.0 (dated 23 July 2024)</a></li>
 <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>