reading of PETSIRD list-mode function

CMakeLists.txt

@@ -109,6 +109,7 @@ option(STIR_ENABLE_EXPERIMENTAL "disable use of STIR experimental code" OFF) # d
 option(DISABLE_NiftyPET_PROJECTOR "disable use of NiftyPET projector" OFF)
 option(DISABLE_Parallelproj_PROJECTOR "disable use of Parallelproj projector" OFF)
 OPTION(DOWNLOAD_ZENODO_TEST_DATA "download zenodo data for tests" OFF)
+option(DISABLE_PETSIRD "disable use of PETSIRD filetypes" OFF)
 option(DISABLE_UPENN "disable use of UPENN filetypes" OFF)
 
 find_package(Git QUIET)
@@ -278,6 +279,41 @@ else()
   message(STATUS "Parallelproj projector support disabled or not available.")
 endif()
 
+if(NOT DISABLE_PETSIRD)
+  find_package(PETSIRD CONFIG)
+
+  if(PETSIRD_FOUND)
+    message(STATUS "PETSIRD support enabled (found PETSIRD).")
+    set(HAVE_PETSIRD ON)
+
+    # Inspect PETSIRD transitive dependencies
+    if(TARGET PETSIRD::petsird)
+      get_target_property(_petsird_libs PETSIRD::petsird INTERFACE_LINK_LIBRARIES)
+
+      get_target_property(_petsird_features PETSIRD::petsird INTERFACE_COMPILE_FEATURES)
+      get_target_property(_petsird_libs PETSIRD::petsird INTERFACE_LINK_LIBRARIES)
+      message(STATUS "PETSIRD::petsird dependencies: ${_petsird_libs}")
+      message(STATUS "PETSIRD::petsird compile features: ${_petsird_features}")
+
+      # I have to give credit to AI for the following line. 
+      # Probably this will not be needed, but I will keep it here for future reference. 
+      # string(REGEX MATCH "cxx_std_([0-9]+)" _petsird_std_match "${_petsird_features}")
+      # if(CMAKE_MATCH_1)
+          # UseCXX(${CMAKE_MATCH_1})
+      # endif()
+
+    else()
+      message(FATAL_ERROR "PETSIRD::petsird target not found after find_package(PETSIRD)")
+    endif()
+
+  else()
+    message(STATUS "PETSIRD not found: PETSIRD support will be disabled.")
+    set(HAVE_PETSIRD OFF)
+  endif()
+else()
+  set(HAVE_PETSIRD OFF)
+endif()
+
 #### enable support for ctest
 ENABLE_TESTING()
 

documentation/devel/README.md

@@ -5,4 +5,6 @@ Please check files here for information/code practices for developers.
 - Do read our [contribution guidelines](../../CONTRIBUTING.md)
 - Set your editor settings appropriately: [instructions](editor-settings.md)
 - Install git hooks for serious development: [instructions](git-hooks.md)
-- Read the documentation, including the STIR developers guide
+- Read the documentation, including the STIR developers guide
+
+- To run the CI workflow locally with `act`: [instructions](local-CI.md)

documentation/devel/local-CI.md

@@ -0,0 +1,37 @@
+# Running the GitHub Actions workflow locally with `act`
+
+The GitHub Actions CI workflow can be tested locally using [`act`](https://github.com/nektos/act).
+This is useful for debugging workflow changes before pushing to GitHub.
+
+## Prerequisities
+
+Install `act` and make sure Docker or Podman is available and running.
+
+On Linux, the workflow can be run with an Ubuntu 24.04
+ container image compatible with GitHub Actions:
+
+```bash
+act -W .github/workflows/build-test.yml \
+  -P ubuntu-24.04=ghcr.io/catthehacker/ubuntu:act-24.04 \
+  --env ACT=true
+```
+
+* The ```-W``` option selects the workflow file to run
+* The ```-P``` option maps the GitHub Actions
+runner label ```ubuntu-24.04``` to a local container image.
+The image in the command above is suggested online.
+* The `--env ACT=true` option sets an environment variable
+ used by the workflow to detect that it is running under `act`.
+ Some GitHub steps are skipped.
+
+## NOTES
+
+* It is highly recommended to run only one job at the time.
+STIR has an array of different OSes and options.
+Don't try to spin them up all together in your local workstation.
+* Runnning the workflow locally with ```act``` is not always identical to GitHub.
+* If Docker runs out of disk space, remove old images and containers before running
+
+```bash
+docker system prune
+```

src/CMakeLists.txt

@@ -1,3 +1,4 @@
+# Copyright 2025, 2026, University Medical Center Groningen
 # Copyright 2011-01-01 - 2011-06-30 Hammersmith Imanet Ltd
 # Copyright 2011-07-01 - 2012 Kris Thielemans
 # Copyright 2016 ETH Zurich
@@ -278,6 +279,10 @@ else()
   target_link_libraries(stir_registries PUBLIC CUDA::cudart)
 endif()
 
+if (HAVE_PETSIRD)
+  target_link_libraries(stir_registries PUBLIC PETSIRD::petsird)
+endif()
+
 # go and look for CMakeLists.txt files in all those directories
 foreach(STIR_DIR ${STIR_DIRS} ${STIR_TEST_DIRS})
 	ADD_SUBDIRECTORY(${STIR_DIR})

src/IO/CMakeLists.txt

@@ -80,6 +80,12 @@ if (HAVE_HDF5)
  )
 endif()
 
+if (HAVE_PETSIRD)
+list(APPEND ${dir_LIB_SOURCES}
+  PETSIRDCListmodeInputFileFormat.cxx
+)
+endif()
+
 endif() # MINI_STIR
 
 target_sources(${STIR_BUILDBLOCK_LIB} PRIVATE ${${dir_LIB_SOURCES}})
@@ -137,3 +143,7 @@ if (HAVE_JSON)
   get_target_property(TMP nlohmann_json::nlohmann_json INTERFACE_INCLUDE_DIRECTORIES)
   target_include_directories(${TARGET} PRIVATE "${TMP}")
 endif()
+
+if(HAVE_PETSIRD)
+  target_link_libraries(${TARGET} PUBLIC PETSIRD::petsird)
+endif()

src/IO/IO_registries.cxx

@@ -1,4 +1,5 @@
 /*
+    Copyright 2025, 2026, University Medical Center Groningen
     Copyright (C) 2002-2011, Hammersmith Imanet Ltd
     Copyright (C) 2012, Kris Thielemans
     Copyright (C) 2013, Institute for Bioengineering of Catalonia
@@ -66,6 +67,10 @@
 #    include "stir/IO/InputStreamFromROOTFileForECATPET.h"
 #  endif
 
+#  ifdef HAVE_PETSIRD
+#    include "stir/IO/PETSIRDCListmodeInputFileFormat.h"
+#  endif
+
 #  ifdef HAVE_UPENN
 #    include "stir/IO/PENNListmodeInputFileFormat.h"
 #    include "stir/IO/InputStreamWithRecordsFromUPENNbin.h"
@@ -156,5 +161,9 @@ static InputStreamWithRecordsFromUPENNtxt::RegisterIt dummy686062;
 // static RegisterInputFileFormat<PENNImageInputFileFormat> idummy1(2);
 #  endif
 
+#  ifdef HAVE_PETSIRD
+static RegisterInputFileFormat<PETSIRDCListmodeInputFileFormat> LMdummyPETSIRD(10);
+#  endif
+
 #endif // MINI_STIR
 END_NAMESPACE_STIR

src/IO/PETSIRDCListmodeInputFileFormat.cxx

@@ -0,0 +1,86 @@
+/* PETSIRDCListmodeInputFileFormat.h
+
+ Class defining input file format for coincidence listmode data for PETSIRD.
+
+  Copyright 2025, 2026, University Medical Center Groningen
+  Copyright 2025 National Physical Laboratory
+
+    SPDX-License-Identifier: Apache-2.0
+    See STIR/LICENSE.txt for details
+  */
+#include "stir/IO/PETSIRDCListmodeInputFileFormat.h"
+#include "petsird/binary/protocols.h"
+#include "petsird/hdf5/protocols.h"
+#include "stir/error.h"
+#include "stir/format.h"
+#include <array>
+// #include "../../PETSIRD/cpp/generated/types.h"
+// #include "../../PETSIRD/cpp/helpers/include/petsird_helpers.h"
+
+START_NAMESPACE_STIR
+
+/*!
+
+  \file
+  \ingroup listmode
+  \brief Implementation of class stir::PETSIRDCListmodeInputFileFormat
+
+  \author Nikos Efthimiou
+  \author Daniel Deidda
+
+*/
+
+bool
+PETSIRDCListmodeInputFileFormat::can_read(const FileSignature& signature, const std::string& filename) const
+{
+
+  std::array<char, 4> hdf5_signature = { 'H', 'D', 'F', '5' };
+  std::array<char, 4> binary_signature = { 'y', 'a', 'r', 'd' };
+
+  std::ifstream file(filename, std::ios::binary);
+  if (!file.is_open())
+    {
+      error(format("Cannot open file: {}", filename));
+      return false;
+    }
+  std::array<char, 4> signature_{};
+  auto it = std::istreambuf_iterator<char>(file);
+  auto end = std::istreambuf_iterator<char>();
+
+  for (size_t i = 0; i < signature_.size() && it != end; ++i, ++it)
+    {
+      signature_[i] = *it;
+    }
+
+  if (!file)
+    error("Stream error while reading file signature");
+
+  if (signature_ == hdf5_signature)
+    {
+      use_hdf5 = true;
+      return use_hdf5;
+    }
+
+  if (signature_ == binary_signature)
+    {
+      use_hdf5 = false;
+      return true;
+    }
+
+  // petsird::hdf5::PETSIRDReader* petsird_reader = new petsird::hdf5::PETSIRDReader(filename);
+
+  // if (is_null_ptr(petsird_reader))
+  //   {
+
+  //     petsird::binary::PETSIRDReader* petsird_reader = new petsird::binary::PETSIRDReader(filename);
+  //     if (is_null_ptr(petsird_reader))
+  //       {
+  //         return false;
+  //       }
+  //     return true;
+  //   }
+
+  return false;
+}
+
+END_NAMESPACE_STIR

src/buildblock/CMakeLists.txt

@@ -107,7 +107,12 @@ if (NOT MINI_STIR)
     list(APPEND ${dir_LIB_SOURCES}
       ProjDataGEHDF5.cxx
       )
-endif()
+  endif()
+  if (HAVE_PETSIRD)
+    list(APPEND ${dir_LIB_SOURCES}
+      PETSIRDInfo.cxx
+    )
+  endif()
 
 endif() # MINI_STIR
 
@@ -154,3 +159,7 @@ endif()
 if (STIR_OPENMP)
   target_link_libraries(${TARGET} PUBLIC ${OpenMP_EXE_LINKER_FLAGS})
 endif()
+
+if(HAVE_PETSIRD)
+  target_link_libraries(${TARGET} PUBLIC PETSIRD::petsird)
+endif()