Merge pull request #283 from JPETTomography/develop

Develop

.github/workflows/ci-workflow.yml

@@ -7,20 +7,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-16.04, ubuntu-18.04]
+        os: [ubuntu-22.04, ubuntu-20.04, ubuntu-18.04]
 
     steps:
     - uses: actions/checkout@v2
     - name: system update
       run: |
        sudo apt-get -qq update
        sudo apt-get install -y git libboost-all-dev libtbb-dev cmake
-      
-    - name: download  ROOT (for ubuntu 16.04)
+
+    - name: download  ROOT (for ubuntu 22.04)
+      run: |
+        wget https://root.cern/download/root_v6.26.02.Linux-ubuntu22-x86_64-gcc11.2.tar.gz
+        tar xzf root_v6.26.02.Linux-ubuntu22-x86_64-gcc11.2.tar.gz
+      if: matrix.os == 'ubuntu-22.04'
+    - name: download  ROOT (for ubuntu 20.04)
       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'
+        wget https://root.cern/download/root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
+        tar xzf root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
+      if: matrix.os == 'ubuntu-20.04'
     - name: download  ROOT (for ubuntu-18.04)
       run: |
         wget http://sphinx.if.uj.edu.pl/framework/root-6-20-06-ubuntu18-jpet.tar.gz 

CMakeLists.txt

@@ -18,7 +18,7 @@ endif()
 # MAJOR version when you make incompatible API changes,
 # MINOR version when you add functionality in a backwards-compatible manner, and
 # PATCH version when you make backwards-compatible bug fixes.
-project(JPetFramework VERSION 9.0.0
+project(JPetFramework VERSION 10.0.0
                   LANGUAGES CXX)
 set(PROJECT_DESCRIPTION "JPetFramework module")
 

NOTICE

@@ -1,5 +1,5 @@
 J-PET Framework
-Copyright 2010-2020 The J-PET Framework Authors. All rights reserved.
+Copyright 2010-2021 The J-PET Framework Authors. All rights reserved.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

doc/doxygen/Doxyfile.in

@@ -11,14 +11,14 @@ QUIET                  = YES
 # Basic settings:
 PROJECT_NAME           = "@CMAKE_PROJECT_NAME@"
 PROJECT_NUMBER         = @PROJECT_VERSION_MAJOR@.@PROJECT_VERSION_MINOR@.@PROJECT_VERSION_PATCH@@VERSION_TYPE@
-STRIP_FROM_PATH        = @CMAKE_CURRENT_SOURCE_DIR@ \ 
+STRIP_FROM_PATH        = @CMAKE_CURRENT_SOURCE_DIR@ \
                          @PROJECT_SOURCE_DIR@
 INPUT                  = @PROJECT_SOURCE_DIR@/README.md \
                          @PROJECT_SOURCE_DIR@/INSTALL.md \
-                         @CMAKE_CURRENT_SOURCE_DIR@ \ 
+                         @CMAKE_CURRENT_SOURCE_DIR@ \
                          @PROJECT_SOURCE_DIR@/src \
                          @PROJECT_SOURCE_DIR@/include
-                         
+
 FILE_PATTERNS          = *.h \
                          *.hpp \
                          *.hh \
@@ -123,3 +123,7 @@ STRIP_CODE_COMMENTS    = NO
 # Side panel
 # If you enable this, change .container max-width: 960px; to 1240px
 GENERATE_TREEVIEW      = YES
+
+# Draw class inheritance graphs
+CLASS_DIAGRAMS = YES
+CLASS_GRAPH = YES

include/Core/JPetTaskFactory/JPetTaskFactory.h

@@ -79,7 +79,7 @@ class JPetTaskFactory
    * @return chain of task generators
    */
   TaskGeneratorChain createTaskGeneratorChain(const std::map<std::string, boost::any>& options) const;
-
+  
   /**
    * @brief Method to register the task generator. TDerived corresponds to the task type.
    * The name string is also passed as string parameter to the class constructor.
@@ -145,6 +145,8 @@ TaskGeneratorChain generateTaskGeneratorChain(const std::vector<TaskInfo>& taskI
   const std::map<std::string, boost::any>& options
 );
 
+  TaskGeneratorChain generateDirectTaskGeneratorChain(const std::vector<TaskInfo>& taskInfoVect, const std::map<std::string, TaskGenerator>& generatorsMap, const std::map<std::string, boost::any>& options);
+
 /**
  * @brief Function adds the set of predefined task generators
  *  to the beginning of outChain based on the provided options.

include/Core/JPetTaskIO/JPetTaskIO.h

@@ -16,14 +16,14 @@
 #ifndef JPETTASKIO_H
 #define JPETTASKIO_H
 
-#include "./JPetProgressBarManager/JPetProgressBarManager.h"
-#include "./JPetTaskInterface/JPetTaskInterface.h"
 #include "./JPetParamManager/JPetParamManager.h"
-#include "./JPetStatistics/JPetStatistics.h"
-#include "./JPetTaskIO/JPetOutputHandler.h"
-#include "./JPetTaskIO/JPetInputHandler.h"
 #include "./JPetParams/JPetParams.h"
+#include "./JPetProgressBarManager/JPetProgressBarManager.h"
+#include "./JPetStatistics/JPetStatistics.h"
 #include "./JPetTask/JPetTask.h"
+#include "./JPetTaskIO/JPetInputHandler.h"
+#include "./JPetTaskIO/JPetOutputHandler.h"
+#include "./JPetTaskInterface/JPetTaskInterface.h"
 #include <memory>
 #include <string>
 
@@ -34,12 +34,10 @@ class JPetStatistics;
 /**
  * @brief Helper structure to encapsulate some fields
  */
-struct TaskIOFileInfo {
-  TaskIOFileInfo(
-    const std::string& inType, const std::string& outType,
-    const std::string& outFullPath, bool resetOutPath):
-    fInFileType(inType), fOutFileType(outType),
-    fOutFileFullPath(outFullPath), fResetOutputPath(resetOutPath) {};
+struct TaskIOFileInfo
+{
+  TaskIOFileInfo(const std::string& inType, const std::string& outType, const std::string& outFullPath, bool resetOutPath)
+      : fInFileType(inType), fOutFileType(outType), fOutFileFullPath(outFullPath), fResetOutputPath(resetOutPath){};
   std::string fInFileType;
   std::string fOutFileType;
   std::string fOutFileFullPath;
@@ -48,31 +46,27 @@ struct TaskIOFileInfo {
 
 /**
  * @brief Class representing computing task with input/output operations.
- * In the current implementation the single entry that is read by the reader
- * corresponds to a JPetTimeWindow object.
+ * It is not meant to be used directly, rather used as specialized classes
+ * that must provide an implementation of the method run().
  */
-class JPetTaskIO: public JPetTask
+class JPetTaskIO : public JPetTask
 {
 public:
   JPetTaskIO(const char* name = "", const char* in_file_type = "", const char* out_file_type = "");
   virtual ~JPetTaskIO();
   virtual bool init(const JPetParams& inOptions) override;
-  virtual bool run(const JPetDataInterface& inData) override;
+  virtual bool run(const JPetDataInterface& inData) = 0;
   virtual bool terminate(JPetParams& outOptions) override;
   virtual void addSubTask(std::unique_ptr<JPetTaskInterface> subTask) override;
   void displayProgressBar(std::string taskName, int currentEventNumber, int numberOfEvents) const;
-  virtual JPetParams mergeWithExtraParams(
-    const JPetParams& originalParams, const JPetParams& extraParams
-  ) const ;
+  virtual JPetParams mergeWithExtraParams(const JPetParams& originalParams, const JPetParams& extraParams) const;
   void setParams(const JPetParams& opts);
   JPetParams getParams() const;
   bool isOutput() const;
   bool isInput() const;
 
 protected:
-  virtual std::tuple<bool, std::string, std::string, bool> setInputAndOutputFile(
-    const jpet_options_tools::OptsStrAny options
-  ) const;
+  virtual std::tuple<bool, std::string, std::string, bool> setInputAndOutputFile(const jpet_options_tools::OptsStrAny options) const;
   virtual bool createInputObjects(const char* inputFilename);
   virtual bool createOutputObjects(const char* outputFilename);
   const JPetParamBank& getParamBank();

include/Core/JPetTaskIOLoopPerSubTask/JPetTaskIOLoopPerSubTask.h

@@ -0,0 +1,38 @@
+/**
+ *  @copyright Copyright 2020 The J-PET Framework Authors. All rights reserved.
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may find a copy of the License in the LICENCE file.
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *  @file JPetTaskIOLoopPerSubTask.h
+ */
+
+#include "./JPetTaskIO/JPetTaskIO.h"
+
+#ifndef JPETTASKIOLOOPPERSUBTASK_H
+#define JPETTASKIOLOOPPERSUBTASK_H
+
+/**
+ * @brief Class representing a stream of computing tasks (subtasks),
+ * executed by subsequently processing all events task by task.
+ * E.g. all events are first processed by the first subtask, next
+ * the results are processed by the second subtask and so on.
+ * The intermediate results are saved in the output root files and
+ * the subtasks are reading the events from those files.
+ *
+ * This class only overrides the "run" method of its base JPetTaskIO.
+ */
+class JPetTaskIOLoopPerSubTask : public JPetTaskIO
+{
+public:
+  JPetTaskIOLoopPerSubTask(const char* name = "", const char* in_file_type = "", const char* out_file_type = "");
+  virtual bool run(const JPetDataInterface& inData) override;
+  virtual ~JPetTaskIOLoopPerSubTask();
+};
+#endif /*  !JPETTASKIOLOOPPERSUBTASK_H */

include/Core/JPetTaskStreamIO/JPetTaskStreamIO.h

@@ -0,0 +1,40 @@
+/**
+ *  @copyright Copyright 2020 The J-PET Framework Authors. All rights reserved.
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may find a copy of the License in the LICENCE file.
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *  @file JPetTaskStreamIO.h
+ */
+
+#ifndef JPETTASKSTREAMIO_H
+#define JPETTASKSTREAMIO_H
+
+#include "./JPetTaskIO/JPetTaskIO.h"
+
+/**
+ * @brief Class representing a stream of computing tasks (subtasks),
+ * executed on event by event basis (JPetTimeWindow object). E.g.
+ * first event is processed by all subtasks, then the next one and so on.
+ * The input and output is used only for the first and last task
+ * in the stream.
+ *
+ * This class only overrides the "run" method of its base JPetTaskIO.
+ */
+class JPetTaskStreamIO : public JPetTaskIO
+{
+public:
+  JPetTaskStreamIO(const char* name = "", const char* in_file_type = "", const char* out_file_type = "");
+  virtual bool run(const JPetDataInterface& inData) override;
+  virtual ~JPetTaskStreamIO();
+
+protected:
+private:
+};
+#endif /* !JPETTASKSTREAMIO_H */

include/Core/JPetWriter/JPetWriter.h

@@ -1,5 +1,5 @@
 /**
- *  @copyright Copyright 2018 The J-PET Framework Authors. All rights reserved.
+ *  @copyright Copyright 2021 The J-PET Framework Authors. All rights reserved.
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
  *  You may find a copy of the License in the LICENCE file.
@@ -23,23 +23,29 @@ namespace boost;
 class boost::noncopyable;
 #endif /* __CINT __ */
 
-#include "./JPetBarrelSlot/JPetBarrelSlot.h"
-#include "./JPetPhysSignal/JPetPhysSignal.h"
-#include "./JPetTimeWindow/JPetTimeWindow.h"
-#include "./JPetSigCh/JPetSigCh.h"
-#include "./JPetEvent/JPetEvent.h"
-#include "./JPetLoggerInclude.h"
-#include "./JPetScin/JPetScin.h"
-#include "./JPetHit/JPetHit.h"
-#include "./JPetLOR/JPetLOR.h"
-#include "./JPetFEB/JPetFEB.h"
-#include "./JPetTRB/JPetTRB.h"
-#include "./JPetPM/JPetPM.h"
+#include "JPetBarrelSlot/JPetBarrelSlot.h"
+#include "JPetBaseHit/JPetBaseHit.h"
+#include "JPetRawMCHit/JPetRawMCHit.h"
+#include "JPetEvent/JPetEvent.h"
+#include "JPetFEB/JPetFEB.h"
+#include "JPetHit/JPetHit.h"
+#include "JPetLOR/JPetLOR.h"
+#include "JPetLoggerInclude.h"
+#include "JPetMCRecoHit/JPetMCRecoHit.h"
+#include "JPetPM/JPetPM.h"
+#include "JPetPhysRecoHit/JPetPhysRecoHit.h"
+#include "JPetPhysSignal/JPetPhysSignal.h"
+#include "JPetRecoHit/JPetRecoHit.h"
+#include "JPetScin/JPetScin.h"
+#include "JPetSigCh/JPetSigCh.h"
+#include "JPetTRB/JPetTRB.h"
+#include "JPetTimeWindow/JPetTimeWindow.h"
+
 #include <TFile.h>
 #include <TList.h>
 #include <TTree.h>
-#include <vector>
 #include <string>
+#include <vector>
 
 /**
  * @brief A class responsible for writing any data to ROOT trees.
@@ -64,18 +70,17 @@ class JPetWriter : private boost::noncopyable
   JPetWriter(const char* p_fileName);
   virtual ~JPetWriter(void);
   void closeFile();
-  template <class T> bool write(const T& obj);
+  template <class T>
+  bool write(const T& obj);
   void writeHeader(TObject* header);
-  void writeCollection(const TCollection* hash, const char* dirname,
-    const char* subdirname = "");
-  int writeObject(const TObject* obj, const char* name)
-  {
-    return fFile->WriteTObject(obj, name);
-  }
+  void writeCollection(const TCollection* hash, const char* dirname, const char* subdirname = "");
+  int writeObject(const TObject* obj, const char* name) { return fFile->WriteTObject(obj, name); }
   virtual bool isOpen() const
   {
-    if (fFile) return (fFile->IsOpen() && !fFile->IsZombie());
-    else return false;
+    if (fFile)
+      return (fFile->IsOpen() && !fFile->IsZombie());
+    else
+      return false;
   }
 
 protected:
@@ -90,7 +95,8 @@ template <class T>
 bool JPetWriter::write(const T& obj)
 {
   DEBUG("JPetWriter");
-  if ( !fFile->IsOpen() ) {
+  if (!fFile->IsOpen())
+  {
     ERROR("Could not write to file. Have you closed it already?");
     return false;
   }
@@ -101,7 +107,8 @@ bool JPetWriter::write(const T& obj)
   DEBUG("filler");
   T* filler = const_cast<T*>(&obj);
   assert(filler);
-  if (!fIsBranchCreated) {
+  if (!fIsBranchCreated)
+  {
     DEBUG("Branch name:" + std::string(filler->GetName()));
     assert(fTree);
     fTree->Branch(filler->GetName(), filler->GetName(), &filler);