Merge branch 'develop' into master

Version 6.0
JPETTomography · Oct 21, 2020 · a2a7ee2 · a2a7ee2
2 parents 9f5cb75 + 71193ba
commit a2a7ee2
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diff --git a/.github/workflows/ci-workflow.yml b/.github/workflows/ci-workflow.yml
@@ -0,0 +1,88 @@
+name: j-pet-continuous-integration-tests
+on: [push, pull_request]
+
+jobs:
+  build_and_run_all_tests_on_ubuntu:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-16.04, ubuntu-18.04]
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+    - name: system update
+      run: |
+       sudo apt-get -qq update
+       sudo apt-get install -y git libboost-all-dev libtbb-dev cmake libfftw3-3 libfftw3-dev sshpass
+      
+    - name: download  ROOT (for ubuntu 16.04)
+      run: |
+        wget https://root.cern/download/root_v6.12.06.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
+        tar xzf root_v6.12.06.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
+      if: matrix.os == 'ubuntu-16.04'
+
+    - name: download  ROOT (for ubuntu-18.04)
+      run: |
+        wget http://sphinx.if.uj.edu.pl/framework/root-6-20-06-ubuntu18-jpet.tar.gz 
+        tar xzf root-6-20-06-ubuntu18-jpet.tar.gz
+      if: matrix.os == 'ubuntu-18.04'
+
+    - name: build unpacker 
+      run: |
+        source root/bin/thisroot.sh
+        git clone https://github.com/JPETTomography/Unpacker2.git --single-branch --branch develop unpacker
+        mkdir -p unpacker/build
+        cd unpacker/build
+        cmake ..
+        cmake --build .
+        sudo make install
+        cd ../..
+
+    - name: build j-pet framework
+      run: |
+        source root/bin/thisroot.sh
+        source unpacker/build/bin/thisunpacker.sh
+        rm -rf j-pet-framework || true
+        git clone --single-branch --branch develop https://github.com/JPETTomography/j-pet-framework.git
+        mkdir -p j-pet-framework/build
+        cd j-pet-framework/build
+        cmake ..
+        cmake --build .
+        cd ../..
+
+    - name: build framework examples 
+      run: |
+        source root/bin/thisroot.sh
+        source unpacker/build/bin/thisunpacker.sh
+        source j-pet-framework/build/bin/thisframework.sh
+        mkdir build
+        cd build
+        cmake ..
+        make
+        make tests_largebarrel
+        make tests_imagereconstruction
+
+    - name: run image reconstruction test       
+      run: |
+        source root/bin/thisroot.sh
+        source unpacker/build/bin/thisunpacker.sh
+        cd build/ImageReconstruction
+        ctest -j6 -C Debug -T test --output-on-failure
+
+    - name: run large barrel test       
+      run: |
+        source root/bin/thisroot.sh
+        cd build/LargeBarrelAnalysis
+        ctest -j6 -C Debug -T test --output-on-failure
+        wget http://sphinx.if.uj.edu.pl/~alek/framework_integration_tests/dabc_17025151847.hld
+        wget http://sphinx.if.uj.edu.pl/~alek/framework_integration_tests/setupRun3.json
+        ./LargeBarrelAnalysis.x -t hld -f dabc_17025151847.hld -l setupRun3.json -i 3 -r 0 100
+        mkdir outdir
+        ./LargeBarrelAnalysis.x -t hld -f dabc_17025151847.hld -l setupRun3.json -i 3 -r 0 100 -o outdir
+        ./LargeBarrelAnalysis.x -t root -f dabc_17025151847.hld.root -l setupRun3.json -i 3 -r 0 100
+        sed -i 's/manager.useTask("TimeWindowCreator", "hld", "tslot.calib");//' ../../LargeBarrelAnalysis/main.cpp
+        make LargeBarrelAnalysis.x
+        ./LargeBarrelAnalysis.x -t root -f dabc_17025151847.tslot.calib.root   -r 0 100
diff --git a/.travis.yml b/.travis.yml
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -22,7 +22,7 @@ message(STATUS "")
 message(STATUS "    == ${PROJECT_NAME} Project configuration ==")
 message(STATUS "")
 
-set(CMAKE_CXX_STANDARD 11) # maybe not best solution to set it globally? upgrate minimal cmake version to 3.8 or find another way to set it only for target with interface
+set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_PLATFORM_INDEPENDENT_CODE ON)
@@ -64,7 +64,7 @@ find_package(Threads REQUIRED)
 set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
-find_package(Boost 1.50 REQUIRED 
+find_package(Boost 1.50 REQUIRED
              COMPONENTS filesystem
                         program_options
                         regex
@@ -92,19 +92,24 @@ if(ROOT_FOUND)
   message(STATUS "ROOT (version ${ROOT_VERSION}) was found using ROOTConfig")
 endif()
 
-if(EXISTS "${ROOT_DIR}/modules/RootNewMacros.cmake")
-  include("${ROOT_DIR}/modules/RootNewMacros.cmake")
-  message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/modules!")
-elseif(EXISTS "${ROOT_DIR}/cmake/modules/RootNewMacros.cmake")
-  include("${ROOT_DIR}/cmake/modules/RootNewMacros.cmake")
-  message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/cmake/modules!")
-elseif(EXISTS "${ROOT_DIR}/../cmake/modules/RootNewMacros.cmake")
-  include("${ROOT_DIR}/../cmake/modules/RootNewMacros.cmake")
-  message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/../cmake/modules!")
-else()
-  message("ERROR! Could not find RootNewMacros.cmake file! Aborting..")
-  return(1)
+# the RootNewMacros.cmake file has to be found and included manually
+# only for ROOT versions prior to 6.20
+if(ROOT_VERSION VERSION_LESS "6.20")
+  if(EXISTS "${ROOT_DIR}/modules/RootNewMacros.cmake")
+    include("${ROOT_DIR}/modules/RootNewMacros.cmake")
+    message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/modules!")
+  elseif(EXISTS "${ROOT_DIR}/cmake/modules/RootNewMacros.cmake")
+    include("${ROOT_DIR}/cmake/modules/RootNewMacros.cmake")
+    message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/cmake/modules!")
+  elseif(EXISTS "${ROOT_DIR}/../cmake/modules/RootNewMacros.cmake")
+    include("${ROOT_DIR}/../cmake/modules/RootNewMacros.cmake")
+    message(STATUS "Found RootNewMacros.cmake in: ${ROOT_DIR}/../cmake/modules!")
+  else()
+    message("ERROR! Could not find RootNewMacros.cmake file! Aborting..")
+    return(1)
+  endif()
 endif()
+
 # fix missing include directories property in versions < ROOT 6.12
 set_target_properties(ROOT::Core PROPERTIES
     INTERFACE_INCLUDE_DIRECTORIES "${ROOT_INCLUDE_DIRS}")
@@ -145,7 +150,7 @@ endif(JPetFramework_FOUND)
 ## The script shouldn't do anything if the data is present and correct.
 option(DOWNLOAD_DATA "Download data" ON)
 if(DOWNLOAD_DATA)
-  set(DOWNLOAD_BASE_PATH ${PROJECT_SOURCE_DIR})  
+  set(DOWNLOAD_BASE_PATH ${PROJECT_SOURCE_DIR})
 
   file(DOWNLOAD "http://sphinx.if.uj.edu.pl/framework/examples_reformed.sha" ${DOWNLOAD_BASE_PATH}/examples_reformed.sha)
   file(READ ${DOWNLOAD_BASE_PATH}/examples_reformed.sha SHA_HASHES)
@@ -167,10 +172,6 @@ if(DOWNLOAD_DATA)
   file(REMOVE ${DOWNLOAD_BASE_PATH}/examples_reformed.sha)
 endif()
 
-################################################################################
-## Add general modules files
-add_subdirectory(modules)
-
 ################################################################################
 ## Directories with examples
 add_subdirectory(InterThresholdCalibration)

diff --git a/CosmicAnalysis/CMakeLists.txt b/CosmicAnalysis/CMakeLists.txt
@@ -43,6 +43,8 @@ set(HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/EventCategorizerCosmic.h
             ${use_modules_from}/SignalFinder.h
             ${use_modules_from}/SignalFinderTools.h
             ${use_modules_from}/SignalTransformer.h
+            ${use_modules_from}/ToTEnergyConverter.h
+            ${use_modules_from}/ToTEnergyConverterFactory.h
             ${use_modules_from}/HitFinder.h
             ${use_modules_from}/HitFinderTools.h
             ${use_modules_from}/EventFinder.h
@@ -56,6 +58,8 @@ set(SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/EventCategorizerCosmic.cpp
             ${use_modules_from}/SignalFinder.cpp
             ${use_modules_from}/SignalFinderTools.cpp
             ${use_modules_from}/SignalTransformer.cpp
+            ${use_modules_from}/ToTEnergyConverter.cpp
+            ${use_modules_from}/ToTEnergyConverterFactory.cpp
             ${use_modules_from}/HitFinder.cpp
             ${use_modules_from}/HitFinderTools.cpp
             ${use_modules_from}/EventFinder.cpp

diff --git a/CosmicAnalysis/EventCategorizerCosmic.cpp b/CosmicAnalysis/EventCategorizerCosmic.cpp
@@ -14,6 +14,7 @@
  */
 
 #include "../LargeBarrelAnalysis/EventCategorizerTools.h"
+#include "../LargeBarrelAnalysis/HitFinderTools.h"
 #include <JPetOptionsTools/JPetOptionsTools.h>
 #include "EventCategorizerCosmic.h"
 #include <JPetWriter/JPetWriter.h>
@@ -36,19 +37,13 @@ bool EventCategorizerCosmic::init()
   } else {
     WARNING(Form("No value of the %s parameter provided by the user. Using default value of %lf.", kMinCosmicTOTParamKey.c_str(), fMinCosmicTOT));
   }
-  if (fSaveControlHistos) {
-    getStatistics().createHistogram(
-      new TH1F("Cosmic_TOT", "TOT of Cosmic Hits", 200, fMinCosmicTOT/1000.0, 100.0)
-    );
-    getStatistics().getHisto1D("Cosmic_TOT")->SetXTitle("TOT [ns]");
-    getStatistics().getHisto1D("Cosmic_TOT")->SetYTitle("Counts");
-
-    getStatistics().createHistogram(
-      new TH1F("CosmicHitsPerEvent", "Number of Cosmic Hits in Event", 50, -0.5, 49.5)
-    );
-    getStatistics().getHisto1D("CosmicHitsPerEvent")->SetXTitle("Number of Cosmic Hits in Event");
-    getStatistics().getHisto1D("CosmicHitsPerEvent")->SetYTitle("Counts");
+  if (isOptionSet(fParams.getOptions(), kTOTCalculationType)) {
+    fTOTCalculationType = getOptionAsString(fParams.getOptions(), kTOTCalculationType);
+  } else {
+    WARNING("No TOT calculation option given by the user. Using standard sum.");
   }
+
+  if(fSaveControlHistos) initialiseHistograms();
   return true;
 }
 
@@ -88,7 +83,7 @@ JPetEvent EventCategorizerCosmic::cosmicAnalysis(vector<JPetHit> hits)
 {
   JPetEvent cosmicEvent;
   for (unsigned i = 0; i < hits.size(); i++) {
-    double TOTofHit = EventCategorizerTools::calculateTOT(hits[i]);
+    double TOTofHit = HitFinderTools::calculateTOT(hits[i], HitFinderTools::getTOTCalculationType(fTOTCalculationType));
     if (TOTofHit >= fMinCosmicTOT) {
       cosmicEvent.addHit(hits[i]);
       //Uncomment if kCosmic type will be avalible
@@ -104,3 +99,18 @@ JPetEvent EventCategorizerCosmic::cosmicAnalysis(vector<JPetHit> hits)
   }
   return cosmicEvent;
 }
+
+void EventCategorizerCosmic::initialiseHistograms(){
+
+  getStatistics().createHistogram(
+      new TH1F("Cosmic_TOT", "TOT of Cosmic Hits", 200, fMinCosmicTOT/1000.0, 100.0)
+  );
+  getStatistics().getHisto1D("Cosmic_TOT")->SetXTitle("TOT [ns]");
+  getStatistics().getHisto1D("Cosmic_TOT")->SetYTitle("Counts");
+
+  getStatistics().createHistogram(
+      new TH1F("CosmicHitsPerEvent", "Number of Cosmic Hits in Event", 50, -0.5, 49.5)
+  );
+  getStatistics().getHisto1D("CosmicHitsPerEvent")->SetXTitle("Number of Cosmic Hits in Event");
+  getStatistics().getHisto1D("CosmicHitsPerEvent")->SetYTitle("Counts");
+}
diff --git a/CosmicAnalysis/EventCategorizerCosmic.h b/CosmicAnalysis/EventCategorizerCosmic.h
@@ -41,9 +41,12 @@ class EventCategorizerCosmic : public JPetUserTask
 
 protected:
 	const std::string kMinCosmicTOTParamKey = "EventCategorizer_MinCosmicTOT_float";
+    const std::string kTOTCalculationType = "HitFinder_TOTCalculationType_std::string";
 	void saveEvents(const std::vector<JPetEvent>& event);
 	double fMinCosmicTOT = 55000.0;
 	bool fSaveControlHistos = true;
+    std::string fTOTCalculationType = "";
+    void initialiseHistograms();
 };
 
 #endif /* !EVENTCATEGORIZERCOSMIC_H */
diff --git a/CosmicAnalysis/PARAMETERS.md b/CosmicAnalysis/PARAMETERS.md
@@ -34,6 +34,9 @@ time window for matching Signals on the same scintillator and different sides. D
 - `HitFinder_RefDetScinID_int`  
 `ID` of Reference Detector Scintillator, needed for creating reference hits
 
+- `HitFinder_TOTCalculationType_std::string`  
+Type of the calculations of the TOT - it can be standard sum (option "standard"), a extended sum taking into account thresholds differences and calculated as rectangulars (option "rectangular"), additional extension that add also differences between the TOTs on different thresholds and calculates sum as sum of the trapezes (option "trapeze"). Default value: 'standard'
+
 - `EventFinder_EventTime_float`  
 time window for grouping hits in one event. Default value `5 000 ps`
 

diff --git a/ImageReconstruction/CMakeLists.txt b/ImageReconstruction/CMakeLists.txt
@@ -35,26 +35,28 @@ set(HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/FilterEvents.h
             ${CMAKE_CURRENT_SOURCE_DIR}/ImageReco.h
             ${CMAKE_CURRENT_SOURCE_DIR}/MLEMRunner.h
             ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreator.h
-            ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreatorMC.h
+            ${CMAKE_CURRENT_SOURCE_DIR}/ReconstructionTask.h
             ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreatorTools.h
             ${CMAKE_CURRENT_SOURCE_DIR}/../j-pet-mlem/src/util/png_writer.h)
 
 set(SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/FilterEvents.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/ImageReco.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/MLEMRunner.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreator.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreatorMC.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/ReconstructionTask.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/SinogramCreatorTools.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/../j-pet-mlem/src/util/png_writer.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/main.cpp)
 
+add_subdirectory(Reconstruction)
+
 ################################################################################
 ## Add options from j-pet-mlem as compile flags removing PET_ prefix
 ## j-pet-mlem sets some parameters of the CMake build by using definitions,
 ## that are limited to project, it is necessary to copy them here
 # configuration time options
 set(PET_MAX_DETECTORS 512
-    CACHE INTEGER
+    CACHE STRING
     "maximum number of detectors allowed in the scanner (impacts performance)"  )
 set(PET_GRANULARITY_TYPE "WARP"
     CACHE STRING
@@ -75,13 +77,13 @@ set(PET_THROW_ON_ZERO_DENOMINATOR OFF
     CACHE BOOL
     "throw on zero denominator (event outside FOV)"  )
 set(PET_MAX_PIXELS_PER_THREAD 12
-    CACHE INTEGER
+    CACHE STRING
     "chosen arbitrarily, no more than 11 pixels per thread in current config"  )
 set(PET_WARP_SIZE 32
-    CACHE INTEGER
+    CACHE STRING
     "normally it should not be changed to anything else than 32"  )
 set(PET_MAX_THREADS_PER_BLOCK 512
-    CACHE INTEGER
+    CACHE STRING
     "not used in current implementation"  )
 set(PET_USE_FAST_TEXT_PARSER ON
     CACHE BOOL