Merge remote-tracking branch 'origin/master' into GERDF8

KrisThielemans · Feb 8, 2024 · fe748ff · fe748ff
2 parents a628bc7 + ee307c7
commit fe748ff
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diff --git a/.clang-format b/.clang-format
@@ -25,12 +25,15 @@ BraceWrapping:
   SplitEmptyFunction: false
   SplitEmptyRecord: true
   SplitEmptyNamespace: true
+BinPackParameters: false
+BinPackArguments: false
 ColumnLimit:     130
 IndentPPDirectives: AfterHash
 PointerAlignment: Left
 SortIncludes:    false
 SortUsingDeclarations: false
 SpaceBeforeParens: ControlStatements
 PackConstructorInitializers: Never
+AllowShortFunctionsOnASingleLine: InlineOnly
 Standard:        Cpp11
 ...
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -130,7 +130,7 @@ jobs:
               # no idea how to do this
               ;;
            esac
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
 

diff --git a/.github/workflows/check.yml → .github/workflows/pre-commit-check.yml b/.github/workflows/check.yml → .github/workflows/pre-commit-check.yml
@@ -1,4 +1,4 @@
-name: Check
+name: Run pre-commit check
 on:
 - push
 - pull_request
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     name: pre-commit
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
     - run: sudo apt-get install -yqq clang-format
-    - uses: pre-commit/action@v2.0.0
+    - uses: pre-commit/action@v3.0.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 repos:
--   repo: git://github.com/doublify/pre-commit-clang-format
+-   repo: https://github.com/doublify/pre-commit-clang-format
     rev: '62302476'
     hooks:
     -   id: clang-format

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,44 +8,47 @@ message: >-
   metadata from this file.
 type: software
 authors:
-    - family-names: Mustafovic
-      given-names:  Sanida
-      affiliation:  Imperial College London (UK)
     - family-names: Efthimiou
       given-names:  Nikos
       orcid:        'https://orcid.org/0000-0003-1947-5033'
+    - family-names: Mustafovic
+      given-names:  Sanida
+      affiliation:  Imperial College London (UK)
     - family-names: Brown
       given-names:  Richard
       orcid:        'https://orcid.org/0000-0001-6989-9200'
       affiliation:  University College London
     - family-names: Twyman Skelly
       given-names:  Robert
       affiliation:  University College London and Prescient Imaging
-    - family-names: Tsoumpas
-      given-names:  Charalampos
     - family-names: Deidda
       given-names:  Daniel
       orcid:        'https://orcid.org/0000-0002-2766-4339'
       affiliation:  National Physics Laboratory (UK)
+    - family-names: Tsoumpas
+      given-names:  Charalampos
     - family-names: Falcon
       given-names:  Carles
-    - family-names: Borgeaud
-      given-names:  Tim
-      affiliation:  Hammersmith Imanet Ltd
-    - family-names: Khateri
-      given-names:  Parisa
-      affiliation:  ETH Zuerich
     - family-names: Jehl
       given-names:  Markus
       affiliation:  Positrigo
-    - family-names: Wadhwa
-      given-names:  Palak
-      affiliation:  University of Leeds (UK)
     - 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: Emond
+      given-names:  Elise
+      affiliation:  University College London
     - family-names: Jacobson
       given-names:  Matthew
     - family-names: Gillman
@@ -57,26 +60,24 @@ authors:
     - family-names: Zverovich
       given-names:  Alexey
       affiliation:  Brunel University (UK)
-    - family-names: Emond
-      given-names:  Elise
-      affiliation:  University College London
-    - family-names: Biguri
-      given-names:  Ander
-      orcid:        'https://orcid.org/0000-0002-2636-3032'
-      affiliation:  University College London
     - family-names: Fuster Marti
       given-names:  Berta
       affiliation:  University of Barcelona (Spain)
     - family-names: Labbe
       given-names:  Claire
+    - family-names: Biguri
+      given-names:  Ander
+      orcid:        'https://orcid.org/0000-0002-2636-3032'
+      affiliation:  University College London
     - family-names: Fischer
       given-names:  Jannis
       orcid:        'https://orcid.org/0000-0002-8329-0220'
     - family-names: Roethlisberger
       given-names:  Michael
       affiliation:  ETH Zuerich
-    - family-names: Aguiar
-      given-names:  Pablo
+    - family-names: Bertolli
+      given-names:  Ottavia
+      affiliation:  University College London
     - family-names: Brusaferri
       given-names:  Ludovica
       affiliation:  University College London
@@ -88,35 +89,34 @@ authors:
       given-names:  Benjamin
       orcid:        'https://orcid.org/0000-0002-9784-1177'
       affiliation:  University College London
-    - family-names: Bertolli
-      given-names:  Ottavia
-      affiliation:  University College London
+    - family-names: Aguiar
+      given-names:  Pablo
     - family-names: Niknejad
       given-names:  Tahereh
-    - family-names: Dikaios
-      given-names:  Nikos
     - family-names: Sadki
       given-names:  Mustapha
       affiliation:  Brunel University (UK)
-    - family-names: Fardell
-      given-names:  Gemma
-      orcid:        'https://orcid.org/0000-0003-2388-5211'
-      affiliation:  UK Research & Innovation
+    - family-names: Schmidtlein
+      given-names:  C Ross
     - family-names: Kerrouche
       given-names:  Nacer
       affiliation:  Hammersmith Imanet Ltd
-    - family-names: Ovtchinnikov
-      given-names:  Evgueni
-      orcid:        'https://orcid.org/0000-0002-9359-6514'
+    - family-names: Dikaios
+      given-names:  Nikos
+    - family-names: Fardell
+      given-names:  Gemma
+      orcid:        'https://orcid.org/0000-0003-2388-5211'
       affiliation:  UK Research & Innovation
     - family-names: Ehrhardt
       given-names:  Matthias J.
       orcid:        'https://orcid.org/0000-0001-8523-353X'
-    - family-names: Schmidtlein
-      given-names:  C Ross
     - family-names: Valente
       given-names:  Patrick
       affiliation:  Brunel University (UK)
+    - 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)
@@ -127,6 +127,9 @@ 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
@@ -137,24 +140,24 @@ authors:
       affiliation:  University of Leeds (UK)
     - family-names: Chen
       given-names:  Gefei
-    - family-names: Dao
-      given-names:  Viet Anh
-      affiliation:  University of Leeds (UK)
-    - family-names: Mikhaylova
-      given-names:  Ekaterina
-      affiliation:  Positrigo
     - family-names: Porter
       given-names:  Sam David
       affiliation:  University College London, National Physics Laboratory (UK)
+    - family-names: Mikhaylova
+      given-names:  Ekaterina
+      affiliation:  Positrigo
+    - family-names: Dao
+      given-names:  Viet Anh
+      affiliation:  University of Leeds (UK)
     - family-names: da Costa-Luis
       given-names:  Casper O.
       orcid:        'https://orcid.org/0000-0002-7211-1557'
-    - family-names: Rashidnasab
-      given-names:  Alaleh
-      affiliation:  University College London
     - family-names: Whitehead
       given-names:  Alexander C.
       affiliation:  University College London
+    - family-names: Rashidnasab
+      given-names:  Alaleh
+      affiliation:  University College London
     - family-names: Gillen
       given-names:  Rebecca
       affiliation:  University College London

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -29,23 +29,25 @@ This is our recommended process. If it sounds too daunting, ask for help.
 3. Create a branch in your fork with a descriptive name and put your fixes there. If your fix is
 simple you could do it on github by editing a file, otherwise clone your project (or add a remote
 to your current git clone) and work as usual.
-4. If your change is important, add it to the release notesfor the upcoming version, [see](https://github.com/UCL/STIR/blob/master/documentation/)
+4. Configure your editor and potentially even [pre-commit](https://pre-commit.com/), see
+[documentation/devel/README.md](documentation/devel/README.md).
+5. If your change is important, add it to the release notes for the upcoming version in the [documentation folder](https://github.com/UCL/STIR/tree/master/documentation/)
 and even the [User's Guide](https://github.com/UCL/STIR/blob/master/documentation/STIR-UsersGuide.tex) or other documentation files.
-5. Use [well-formed commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
+6. Use [well-formed commit messages](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html)
 for each change (in particular with a single "subject" line
-followed by an empty line and then more details). If the change affects comments only, it is recommended to put `[ci skip]` in your subject line. This avoids unnecessary computation, and clogging our Travis/Appveyor queues.
-6. Push the commits to your fork and submit a [pull request (PR)](https://help.github.com/articles/creating-a-pull-request)
-(enable changes by project admins.) Give your pull request a descriptive name (i.e. don't call if *Fix #issuenumber*. Be prepared to add further commits to your branch after discussion.
-In the description of the PR, add a statement about which Issue this applies to
-using [a phrase such that github auto-closes the issue when merged to master](https://help.github.com/articles/closing-issues-using-keywords/).
-7. Be prepared to add further commits to your branch after discussion.
+followed by an empty line and then more details).
 Please by mindful about the resources used by our Continuous Integration (CI) workflows:
   - Group your commits and only push once your code compiles and tests succeed on your machine (ideally you have sensible commit messages at every stage)
   - Use specific keywords in the first line of the last commit that you push to prevent CI being run:
      - `[ci skip]` skips all CI runs (e.g. when you only change documentation, or when your update isn't ready yet)
      - `[actions skip]` does not run GitHub Actions, see [here](https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/). Note: this can be in the main commit message.
      - `[skip appveyor]` does not run Appveyor, see [here](https://www.appveyor.com/docs/how-to/filtering-commits/#skip-directive-in-commit-message)
-8. After acceptance of your PR, go home with a nice warm feeling.
+7. Push the commits to your fork and submit a [pull request (PR)](https://help.github.com/articles/creating-a-pull-request)
+(enable changes by project admins.) Give your pull request a descriptive name (i.e. don't call if *Fix #issuenumber*. Be prepared to add further commits to your branch after discussion.
+In the description of the PR, add a statement about which Issue this applies to
+using [a phrase such that github auto-closes the issue when merged to master](https://help.github.com/articles/closing-issues-using-keywords/).
+8. Be prepared to add further commits to your branch after discussion.
+9. After acceptance of your PR, go home with a nice warm feeling.
 
 Suggested reading: 
 https://help.github.com/articles/fork-a-repo/, https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project or https://guides.github.com/activities/forking/.

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Licensing information for STIR 5.1.0
+Licensing information for STIR 6.0.0
 ----------------------------------
 
 See for more info http://stir.sourceforge.net, section Registration.
@@ -27,7 +27,6 @@ Explicit list of files that carry the PARAPET license
 ./documentation/STIR-glossary.tex
 ./documentation/STIR-general-overview.tex
 ./documentation/STIR-developers-overview.tex
-./src/IO/InterfileHeaderSiemens.cxx
 ./src/IO/stir_ecat_common.cxx
 ./src/IO/ecat6_utils.cxx
 ./src/IO/interfile.cxx
@@ -69,7 +68,6 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/IO/interfile.h
 ./src/include/stir/IO/InputStreamWithRecordsFromUPENNbin.h
 ./src/include/stir/IO/InterfileHeader.h
-./src/include/stir/IO/InterfileHeaderSiemens.h
 ./src/include/stir/IO/ecat6_utils.h
 ./src/include/stir/IO/stir_ecat_common.h
 ./src/include/stir/IO/stir_ecat7.h
@@ -84,7 +82,6 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/interpolate.h
 ./src/include/stir/ProjDataInfoCylindrical.h
 ./src/include/stir/ByteOrder.inl
-./src/include/stir/ViewSegmentNumbers.h
 ./src/include/stir/evaluation/ROIValues.h
 ./src/include/stir/TimedBlock.h
 ./src/include/stir/CartesianCoordinate3D.inl
@@ -115,13 +112,13 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/ProjDataInfoCylindricalArcCorr.inl
 ./src/include/stir/Coordinate2D.inl
 ./src/include/stir/linear_regression.inl
-./src/include/stir/Array1d.h
 ./src/include/stir/Segment.inl
 ./src/include/stir/IndexRange.h
 ./src/include/stir/Viewgram.h
 ./src/include/stir/BasicCoordinate.h
 ./src/include/stir/BasicCoordinate.inl
 ./src/include/stir/VectorWithOffset.h
+./src/include/stir/SegmentIndices.inl
 ./src/include/stir/doxygen_doc_for_boost.h
 ./src/include/stir/utilities.h
 ./src/include/stir/NumericInfo.h
@@ -154,10 +151,11 @@ Explicit list of files that carry the PARAPET license
 ./src/include/stir/Scanner.inl
 ./src/include/stir/DiscretisedDensity.inl
 ./src/include/stir/SegmentByView.h
-./src/include/stir/ProjDataGEAdvance.h
+./src/include/stir/ViewgramIndices.inl
 ./src/include/stir/Coordinate4D.h
 ./src/include/stir/CartesianCoordinate2D.h
 ./src/include/stir/Sinogram.inl
+./src/include/stir/SinogramIndices.inl
 ./src/include/stir/error.h
 ./src/include/stir/line.h
 ./src/include/stir/Succeeded.h
@@ -242,7 +240,6 @@ Explicit list of files that carry the PARAPET license
 ./src/buildblock/ByteOrder.cxx
 ./src/buildblock/interfile_keyword_functions.cxx
 ./src/buildblock/RelatedViewgrams.cxx
-./src/buildblock/ProjDataGEAdvance.cxx
 ./src/buildblock/ProjDataInfo.cxx
 ./src/buildblock/linear_regression.cxx
 ./src/buildblock/ProjDataInfoGeneric.cxx

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-6.0.0-pre
+6.0.0
diff --git a/documentation/STIR-UsersGuide.tex b/documentation/STIR-UsersGuide.tex
@@ -44,7 +44,7 @@
 \\[3cm]
 
 \textbf{{\huge User's Guide\\
- Version 5.2}}
+ Version 6.0}}
 \end{center}
 
 \end{spacing}
@@ -1466,6 +1466,10 @@ \subsubsection{
 \texttt{boost::format} is used, so the pattern can be more flexible.} to allow
 constructing different filenames for each subset.
 
+\item[use time-of-flight sensitivities]
+Defaults to 0, i.e. off. By default, the sensitivity calculation will be non-TOF. However,
+this fails when using a TOF proj-data, as used by Siemens for the Vision 600 etc. In this case,
+you will need to set this parameter to 1.
 
 \item[Projector pair type]
 Specifies the back/forward projector pair to be used in the reconstruction. 
@@ -5714,25 +5718,28 @@ \section{Using STIR in an external C++ project
 \label{sec:ExternalProjectC++}}
 STIR exports its CMake settings. Therefore, an external project can do
 \begin{verbatim}
-find_package(STIR 5.2 CONFIG)
+find_package(STIR 6.0 REQUIRED CONFIG)
 add_library(my_lib file1.cxx file2.cxx)
 # my_lib uses STIR functionality
 target_link_libraries(my_lib PUBLIC ${STIR_LIBRARIES})
 add_executable(my_exe my_exe.cxx ${STIR_REGISTRIES})
-target_link_libraries(my_exe PUBLIC my_lib)
+target_link_libraries(my_exe PUBLIC my_lib))
 \end{verbatim}
 In addition, if your CMake is older than 3.12, you need to add
 \begin{verbatim}
 include_directories("${STIR_INCLUDE_DIRS}")
 \end{verbatim}
-to your CMake file to get the source code files listed in \texttt{STIR\_REGISTRIES} to compile.
-For more recent CMake, this should not be necessary (as \texttt{STIR\_REGISTRIES} is set to
+to your CMakeLists.txt file to get the source code files listed in \texttt{STIR\_REGISTRIES} to compile.
+(For more recent CMake, this should not be necessary (as \texttt{STIR\_REGISTRIES} is set to
 a list of compiled files).
 
+A fully working example is provided in the \texttt{examples/C++} folder, see also the
+\url{https://github.com/UCL/STIR/tree/master/examples/C\%2B\%2B/using_installed_STIR}{using\_installed\_STIR folder on GitHub}.
+
 Note that if CMake did not find the STIR files, you can point it to where they are installed.
 For example, if you installed STIR with
 \texttt{CMAKE\_INSTALL\_PREFIX=\$HOME/install}, set
-\texttt{STIR\_DIR=\$HOME/install/lib/cmake}.
+\texttt{CMAKE\_PREFIX\_PATH=\$HOME/install} or \texttt{STIR\_DIR=\$HOME/install/lib/cmake/STIR-6.0}.
 \footnote{This uses CMake Config mode for \texttt{find\_package}. There is no need for a \texttt{FindSTIR.cmake}}
 
 \section{