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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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" | ||
|
|
@@ -66,27 +66,28 @@ 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" | ||
| ROOT: "OFF" | ||
| ITK: "ON" | ||
| - os: macOS-latest | ||
| compiler: gcc | ||
| compiler_version: 11 | ||
| # compiler_version: 11 | ||
| cuda_version: "0" | ||
| BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | ||
| parallelproj: "OFF" | ||
|
|
@@ -180,7 +181,7 @@ jobs: | |
| echo CXX="$CXX" >> $GITHUB_ENV | ||
| - if: matrix.cuda_version != '0' | ||
| uses: Jimver/[email protected].11 | ||
| uses: Jimver/[email protected].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: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }} | ||
|
|
||
| - name: ctest | ||
| shell: bash | ||
| env: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -62,6 +62,7 @@ Georg Schramm <[email protected]> <[email protected] | |
| Georg Schramm <[email protected]> <[email protected]> | ||
| Georg Schramm <[email protected]> <[email protected]> | ||
| Nicole Jurjew <[email protected]> | ||
| Nicole Jurjew <[email protected]> <[email protected]> | ||
| Tahereh Niknejad <[email protected]> | ||
| Tahereh Niknejad <[email protected]> <[email protected]> | ||
| Sam D Porter <[email protected]> | ||
|
|
@@ -70,3 +71,4 @@ Matthew Strugari <[email protected]> | |
| Matthew Strugari <[email protected]> <[email protected]> | ||
| Imraj Singh <[email protected]> | ||
| Imraj Singh <[email protected]> <[email protected]> | ||
| Dimitra Kyriakopoulou <[email protected]> | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| repos: | ||
| - repo: https://github.com/doublify/pre-commit-clang-format | ||
| rev: '62302476' | ||
| hooks: | ||
| - id: clang-format | ||
| files: \.(c|cc|cxx|cpp|cu|h|hpp|hxx|inl|txx)$ | ||
| - 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)$ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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). |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| <!DOCTYPE HTML> | ||
| <html lang="en"> | ||
| <head> | ||
| <title>Summary of changes in STIR release 6.3</title> | ||
| </head> | ||
|
|
||
| <body> | ||
| <h1>Summary of changes in STIR release 6.3</h1> | ||
|
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||
|
|
||
| <h2>Overall summary</h2> | ||
|
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||
|
|
||
| <h2>Patch release info</h2> | ||
|
|
||
|
|
||
| <h2> Summary for end users (also to be read by developers)</h2> | ||
|
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|
|
||
| <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 | ||
| is disabled for backwards compatibility.<br> | ||
| <a href=https://github.com/UCL/STIR/pull/1291>PR #1291</a> | ||
| </li> | ||
| <li> | ||
| Data from GE Discovery MI systems in RDF9 should now be readable. TOF information on these scanners has also been added. | ||
| 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> | ||
|
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||
|
|
||
| <h3>Changed functionality</h3> | ||
| <ul> | ||
| <li> | ||
| Default ECAT scanner configurations updated to use a negative intrinsic tilt. | ||
| </li> | ||
| </ul> | ||
|
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||
| <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> | ||
|
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||
|
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||
| <H2>What is new for developers (aside from what should be obvious from the above):</H2> | ||
|
|
||
| <h3>New functionality</h3> | ||
|
|
||
| <li> | ||
| <code>ProjDataInMemory</code> <code>read_from_file</code> method now returns a <code>ProjDataInMemory</code> object. | ||
| </li> | ||
|
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| <h3>Changed functionality</h3> | ||
|
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|
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| <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> | ||
|
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||
| <h3>Other code changes</h3> | ||
|
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||
|
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| <h3>Test changes</h3> | ||
|
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| <h4>C++ tests</h4> | ||
|
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|
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| <h4>recon_test_pack</h4> | ||
|
|
||
| </body> | ||
|
|
||
| </html> |
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