Merge branch 'master' into ML_estimate_component_based_normalisation_…

…redesign
robbietuk · Dec 22, 2024 · fd194fc · fd194fc
2 parents cbe81ec + 7508bab
commit fd194fc
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diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -38,16 +38,16 @@ jobs:
     strategy:
       matrix:
         include:
-        - os: ubuntu-latest
+        - os: ubuntu-24.04
           compiler: gcc
-          compiler_version: 9
+          # compiler_version: 9
           cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
           ROOT: "ON"
           ITK: "OFF"
-        - os: ubuntu-latest
+        - os: ubuntu-24.04
           compiler: clang
           #compiler_version:
           cuda_version: "0"
@@ -57,7 +57,7 @@ jobs:
           ROOT: "OFF"
           # currently using ITK 5.2 which doesn't like clang 14
           ITK: "OFF"
-        - os: ubuntu-latest
+        - os: ubuntu-24.04
           compiler: gcc
           compiler_version: 10
           cuda_version: "0"
@@ -66,19 +66,20 @@ jobs:
           parallelproj: "OFF"
           ROOT: "OFF"
           ITK: "ON"
-        - os: ubuntu-latest
+        - os: ubuntu-24.04
           compiler: gcc
-          compiler_version: 12
+          compiler_version: 14
           cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=20"
           BUILD_TYPE: "RelWithDebInfo"
           parallelproj: "ON"
           ROOT: "OFF"
           ITK: "ON"
-        - os: ubuntu-latest
+        - os: ubuntu-24.04
           compiler: gcc
-          compiler_version: 12
-          cuda_version: "12.1.0"
+          # currently CUDA doesn't support gcc 14 yet
+          compiler_version: 13
+          cuda_version: "12.6.1"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
@@ -180,7 +181,7 @@ jobs:
           echo CXX="$CXX" >> $GITHUB_ENV
 
     - if: matrix.cuda_version != '0'
-      uses: Jimver/cuda-toolkit@v0.2.11
+      uses: Jimver/cuda-toolkit@v0.2.19
       id: cuda-toolkit
       with:
           cuda: ${{ matrix.cuda_version }}
@@ -234,13 +235,12 @@ jobs:
               # brew install openblas
               # export OPENBLAS=$(brew --prefix openblas)
               #python -m pip install --no-cache-dir --no-binary  numpy numpy # avoid the cached .whl!
-              python -m pip install numpy
+              python -m pip install numpy pytest
               ;;
             (*)
-              python -m pip install numpy
+              python -m pip install numpy pytest
               ;;
           esac
-          python -m pip install pytest
 
           if test "${{matrix.parallelproj}}XX" == "ONXX"; then
              git clone --depth 1 --branch v1.7.3 https://github.com/gschramm/parallelproj
@@ -255,13 +255,23 @@ jobs:
              rm -rf parallelproj
           fi
 
-          # Install ROOT (warning: currently only valid on Ubuntu)
+          # Install ROOT (warning: brittle due to OS versions etc)
           if test "${{matrix.ROOT}}XX" == "ONXX"; then
-             ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz
+             case ${{matrix.os}} in
+               (ubuntu*)
+               sudo apt install libtbb-dev libvdt-dev libgif-dev
+               ROOT_file=root_v6.34.00.Linux-ubuntu24.04-x86_64-gcc13.2.tar.gz
+               #root_v6.34.00.Linux-ubuntu24.10-x86_64-gcc14.2.tar.gz
+               ;;
+               (macOS*)
+               ROOT_file=https://root.cern/download/root_v6.34.00.macos-15.1-arm64-clang160.tar.gz
+               ;;
+             esac
              wget https://root.cern/download/"$ROOT_file"
              tar -xzvf "$ROOT_file"
              rm "$ROOT_file"
              source root/bin/thisroot.sh
+             echo ROOTSYS="$ROOTSYS" >> $GITHUB_ENV
           fi
 
           # we'll install some dependencies with shared libraries, so need to let the OS know
@@ -303,7 +313,11 @@ jobs:
           CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install
           # make available to jobs below
           echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV
-          EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`"
+          if [ -n "$ROOTSYS" ]; then
+            # make sure we find ROOT (and vdt, which is installed in the same place)
+            EXTRA_BUILD_FLAGS=-DCMAKE_PREFIX_PATH:PATH="$ROOTSYS"
+          fi
+          EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DBUILD_SWIG_PYTHON=ON -DPython_EXECUTABLE=`which python`"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL"
@@ -321,6 +335,13 @@ jobs:
               ;;
            esac
 
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session if triggered
+      #if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3
+      timeout-minutes: 30
+      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
+
     - name: build
       shell: bash
       env:
@@ -330,12 +351,6 @@ jobs:
           source ${GITHUB_WORKSPACE}/my-env/bin/activate
           cmake --build . -j 2 --config ${BUILD_TYPE}} --target install
 
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session if triggered
-      uses: mxschmitt/action-tmate@v3
-      timeout-minutes: 15
-      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
-
     - name: ctest
       shell: bash
       env:

diff --git a/.mailmap b/.mailmap
@@ -62,6 +62,7 @@ Georg Schramm <georg.schramm@kuleuven.be> <40211162+gschramm@users.noreply.githu
 Georg Schramm <georg.schramm@kuleuven.be> <georg.schramm@posteo.net>
 Georg Schramm <georg.schramm@kuleuven.be> <georg.schramm@kuleuven.be>
 Nicole Jurjew <nicole.jurjew.20@ucl.ac.uk>
+Nicole Jurjew <nicole.jurjew.20@ucl.ac.uk> <86268422+NicoleJurjew@users.noreply.github.com>
 Tahereh Niknejad <tahereh.niknejad@tecnico.ulisboa.pt>
 Tahereh Niknejad <tahereh.niknejad@tecnico.ulisboa.pt> <tahereh@Taherehs-MacBook-Pro.local>
 Sam D Porter <92305641+samdporter@users.noreply.github.com>
@@ -70,3 +71,4 @@ Matthew Strugari <matthew.strugari@dal.ca>
 Matthew Strugari <matthew.strugari@dal.ca> <56315593+mastergari@users.noreply.github.com>
 Imraj Singh <imraj.singh.20@ucl.ac.uk>
 Imraj Singh <imraj.singh.20@ucl.ac.uk> <72553490+Imraj-Singh@users.noreply.github.com>
+Dimitra Kyriakopoulou <dimitra.kyriakopoulou.13@ucl.ac.uk>
diff --git a/.pre-commit-config.yaml b/.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|cu|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)$
diff --git a/documentation/devel/editor-settings.md b/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).
diff --git a/documentation/devel/git-hooks.md b/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.
diff --git a/documentation/release_6.3.htm b/documentation/release_6.3.htm
@@ -19,6 +19,21 @@ <h2> Summary for end users (also to be read by developers)</h2>
 
 <h3>New functionality</h3>
 <ul>
+  <li>
+    The analytic Spline Reconstruction Technique (SRT) algorithm has been added in 2 different versions: for PET
+    (inverting the 2D Radon transform) and for SPECT (inverting the 2D attenuated Radon transform). The latter
+    allows quantitatively correct analytic reconstruction of SPECT data (after scatter correction).
+
+    The reference for the implemented algorithms is:<br>
+    Fokas, A. S., A. Iserles, and V. Marinakis.
+    <cite>Reconstruction algorithm for single photon emission computed tomography and its numerical implementation.</cite>
+    Journal of the Royal Society Interface* 3.6 (2006): 45-54.
+    <br>
+    The reference for the implementation is:<br>
+    Dimitra Kyriakopoulou, <cite>Analytical and Numerical Aspects of Tomography</cite>, UCL PhD thesis, (not yet publically accessible)
+    <br>
+    <a href=https://github.com/UCL/STIR/pull/1420>PR #1420</a>
+  </li>
   <li>
     <code>ScatterSimulation</code> can now downsample the scanner transaxially (crystals per ring) for <code>BlocksOnCylindrical</code>,
     scanners, which speeds up <code>ScatterEstimation</code> considerably. By default, downsampling the detectors per reading
@@ -30,22 +45,50 @@ <h3>New functionality</h3>
     However, projection data is currently still always returned as non-TOF (but list-mode data is read as TOF).<br>
     <a href=https://github.com/UCL/STIR/pull/1503>PR #1503</a>
   </li>
+  <li>
+    <tt>stir_timings</tt> has now an extra option to parse a par-file for a projector-pair.
+  </li>
+  <li>
+    Added the ability to set a forward projector for mask projection in the <code>ScatterEstimation</code> class.<br>
+    <a href=https://github.com/UCL/STIR/pull/1530>PR #1530</a>
+  </li>
+  <li>
+    Duration in sinogram interfile/exam_info obtained from <tt>lm_to_projdata</tt> has the correct value if we unlist all the events. This is not true for ROOT files<br>
+    <a href=https://github.com/UCL/STIR/pull/1519>PR #1519</a>
+  </li>
 </ul>
 
 
 <h3>Changed functionality</h3>
-
     <li>
       Rework <code>MLEstimateComponentBasedNormalisation</code> into a class.
       This allows for more flexibility in the use of the class without calling CLI executables. <br>
       <a href=https://github.com/UCL/STIR/pull/1499>PR # 1499</a>
     </li>
 
+    <ul>
+      <li>
+        Default ECAT scanner configurations updated to use a negative intrinsic tilt.
+      </li>
+    </ul>
 <h3>Bug fixes</h3>
-
+    <ul>
+        <li>
+            Fixed a bug in the scatter estimation code (introduced in release 5.1.0) if input data is 3D and "cylindrical" (there was no bug for "blocksoncylindrical" data).
+            The scatter estimation runs on data constructed via SSRB. However, the attenuation correction factors were incorrectly obtained with adding of oblique segments (as opposed to averaging).
+            This resulted in intermediate images that had the wrong attenuation correction which were approximately num_segments times larger. This was compensated by the tail-fitting, but resulted in unexpected scale factors (scale factors were around 1/num_segments times what was expected).
+            This means that if you used the "min/max scale factor" feature in the scatter estimate, you will have to adjust your threshold values. Expected scatter tail-fitting scale factors should now be restored to ~1-1.5 (depending on the amount of multiple and out-of-FOV scatter).
+            See <a href="https://github.com/UCL/STIR/issues/1532">Issue #1532</a> for more detail. Fixed by using averaging functionality of SSRB instead of adding segments for attenuation correction factors.
+            <a href=https://github.com/UCL/STIR/pull/1531>PR #1531</a>
+        </li>
+    </ul>
 
 <h3>Build system</h3>
-
+<ul>
+  <li>Enable more diagnostics in CMake when finding CERN's ROOT (we used to silence them)<br>
+    <a href=https://github.com/UCL/STIR/pull/1552>PR #1552</a>
+  </li>
+</ul>
 
 <h3>Known problems</h3>
     <p>See <a href=https://github.com/UCL/STIR/labels/bug>our issue tracker</a>.</p>
@@ -63,7 +106,11 @@ <h3>Changed functionality</h3>
 
 
 <h3>Bug fixes</h3>
-
+<ul>
+  <li>Fixed minor incompatibility with gcc-14 and clang-18 buy adding an extra include file<br>
+    <a href=https://github.com/UCL/STIR/pull/1552>PR #1552</a>
+  </li>
+</ul>
 
 <h3>Other code changes</h3>
 

diff --git a/examples/samples/SRT2D.par b/examples/samples/SRT2D.par
@@ -0,0 +1,18 @@
+SRT2DParameters :=
+input file := sino_hof_no_noise.hs
+
+xy output image size (in pixels) := -1  
+z output image size (in pixels) := -1
+zoom := 1 
+
+;post-filter type := Wiener
+;Wiener Filter Parameters :=
+;End Wiener Filter Parameters :=
+
+;post-filter type := Gamma
+;Gamma Filter Parameters :=
+;End Gamma Filter Parameters :=
+
+output filename prefix := SRT2D
+
+END :=
diff --git a/examples/samples/SRT2DSPECT.par b/examples/samples/SRT2DSPECT.par
@@ -0,0 +1,20 @@
+SRT2DSPECTParameters :=
+
+;SRT2DSPECT receives as input the forward projection of the attenuation image (attensino.hs) and the measured emission sinogram (sino.hs).
+input file := sino.hs
+attenuation projection filename := attensino.hs
+
+xy output image size (in pixels) := -1
+
+;post-filter type := Wiener
+;Wiener Filter Parameters :=
+;End Wiener Filter Parameters :=
+
+;post-filter type := Gamma
+;Gamma Filter Parameters :=
+;End Gamma Filter Parameters :=
+
+output filename prefix := srt_recon
+
+
+end:=