Merge pull request #192 from JeffersonLab/nbrei_podio

WIP: PODIO integration

.gitignore

@@ -57,3 +57,8 @@ docs/latex/*
 *.swp
 cmake-build*/
 .idea/*
+
+# PODIO generated artifacts
+src/examples/PodioExample/datamodel/*
+src/examples/PodioExample/src/*
+src/examples/PodioExample/podio_generated_files.cmake

CMakeLists.txt

@@ -57,6 +57,7 @@ option(USE_PYTHON "Include Python dependency. This requires python-devel and pyt
 option(USE_ASAN "Compile with address sanitizer" OFF)
 option(USE_TSAN "Compile with thread sanitizer" OFF)
 option(USE_CUDA "Compile CUDA-involved examples (Needed for examples/SubeventCUDAExample)." OFF)
+option(USE_PODIO "Compile with PODIO support" OFF)
 option(BUILD_SHARED_LIBS "Build into both shared and static libs." ON)
 
 
@@ -110,6 +111,11 @@ if (${USE_CUDA})
     find_package(CUDA REQUIRED)
 endif()
 
+if (${USE_PODIO})
+    find_package(podio REQUIRED)
+    add_compile_definitions(HAVE_PODIO)
+endif()
+
 #---------
 # Report back to the user what we've discovered
 #---------
@@ -152,6 +158,11 @@ if (${USE_CUDA})
 else()
     message(STATUS "USE_CUDA    Off")
 endif()
+if (${USE_PODIO})
+    message(STATUS "USE_PODIO   On  --> " ${podio_DIR})
+else()
+    message(STATUS "USE_PODIO   Off")
+endif()
 if (${BUILD_SHARED_LIBS})
     message(STATUS "BUILD_SHARED_LIBS    On")
 else()

containers/Docker/podio.Dockerfile

@@ -0,0 +1,39 @@
+
+# Docker image for testing JANA/PODIO integration
+
+FROM rootproject/root:latest
+#root:6.26.10-ubuntu22.04
+
+USER root
+RUN mkdir /app
+WORKDIR /app
+
+RUN apt update -y \
+ && apt install -y build-essential gdb valgrind cmake wget unzip vim libasan6 less exa bat git zlib1g-dev pip
+
+#ENV JANA_HOME /app/JANA2/install
+
+#RUN git clone -b nbrei_podio https://github.com/JeffersonLab/JANA2 /app/JANA2
+#RUN git clone -b v00-16-02 https://github.com/AIDASoft/podio /app/podio
+RUN git clone -b nbrei_jana_integration https://github.com/nathanwbrei/podio /app/podio
+
+# RUN cd /app/JANA2 \
+#    && mkdir build install \
+#    && cmake -S . -B build \
+#    && cmake --build build -j 10 --target install
+
+RUN apt install -y libyaml-dev \
+    && pip install jinja2 pyyaml
+
+    # Suddenly incompatible with Catch somehow, in between v00-16-02 and tip of master: nlohmann-json3-dev \
+
+RUN cd /app/podio \
+    && mkdir build install \
+    && cd build \
+    && cmake -DCMAKE_INSTALL_PREFIX=../install -DUSE_EXTERNAL_CATCH2=OFF .. \
+    && make -j4 install
+
+
+
+CMD bash
+

src/examples/CMakeLists.txt

@@ -8,3 +8,4 @@ add_subdirectory(BlockExample)
 add_subdirectory(SubeventExample)
 add_subdirectory(SubeventCUDAExample)
 add_subdirectory(UnitTestingExample)
+add_subdirectory(PodioExample)

src/examples/PodioExample/CMakeLists.txt

@@ -0,0 +1,34 @@
+
+set(PodioExample_SOURCES
+        PodioExample.cc
+        PodioExampleProcessor.cc
+        PodioExampleSource.cc
+        ExampleClusterFactory.cc
+        )
+
+if (USE_PODIO)
+
+    foreach( _conf ${CMAKE_CONFIGURATION_TYPES} )
+        string(TOUPPER ${_conf} _conf )
+        set( CMAKE_RUNTIME_OUTPUT_DIRECTORY_${_conf} ${CMAKE_CURRENT_BINARY_DIR} )
+        set( CMAKE_LIBRARY_OUTPUT_DIRECTORY_${_conf} ${CMAKE_CURRENT_BINARY_DIR} )
+        set( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${_conf} ${CMAKE_CURRENT_BINARY_DIR} )
+    endforeach()
+    PODIO_GENERATE_DATAMODEL(datamodel layout.yaml DATAMODEL_HEADERS DATAMODEL_SOURCES IO_BACKEND_HANDLERS ROOT)
+    PODIO_ADD_DATAMODEL_CORE_LIB(DataModelLib "${DATAMODEL_HEADERS}" "${DATAMODEL_SOURCES}")
+    PODIO_ADD_ROOT_IO_DICT(DataModelDict DataModelLib "${DATAMODEL_HEADERS}" src/selection.xml)
+
+    find_package(podio REQUIRED)
+    add_executable(PodioExample ${PodioExample_SOURCES})
+    target_include_directories(PodioExample PUBLIC .)
+    target_link_libraries(PodioExample jana2 podio::podio DataModelLib DataModelDict podio::podioRootIO)
+    set_target_properties(PodioExample PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+    install(TARGETS PodioExample DESTINATION bin)
+else()
+    message(STATUS "Skipping examples/PodioExample because USE_PODIO=Off")
+
+endif()
+
+
+

src/examples/PodioExample/DatamodelGlue.h

@@ -0,0 +1,109 @@
+
+// Copyright 2023, Jefferson Science Associates, LLC.
+// Subject to the terms in the LICENSE file found in the top-level directory.
+
+
+#ifndef JANA2_DATAMODELGLUE_H
+#define JANA2_DATAMODELGLUE_H
+
+#include <datamodel/ExampleHit.h>
+#include <datamodel/ExampleHitCollection.h>
+#include <datamodel/ExampleCluster.h>
+#include <datamodel/ExampleClusterCollection.h>
+#include <datamodel/EventInfo.h>
+#include <datamodel/EventInfoCollection.h>
+
+template <typename T>
+struct PodioCollectionMap {
+};
+
+template <>
+struct PodioCollectionMap<ExampleHitCollection> {
+    using contents_t = ExampleHit;
+};
+template <>
+struct PodioCollectionMap<ExampleClusterCollection> {
+    using contents_t = ExampleCluster;
+};
+template <>
+struct PodioCollectionMap<EventInfoCollection> {
+    using contents_t = EventInfo;
+};
+
+template <typename T>
+struct PodioTypeMap {
+};
+
+template <>
+struct PodioTypeMap<ExampleHit> {
+    using mutable_t = MutableExampleHit;
+    using collection_t = ExampleHitCollection;
+};
+
+template <>
+struct PodioTypeMap<ExampleCluster> {
+    using mutable_t = MutableExampleCluster;
+    using collection_t = ExampleClusterCollection;
+};
+
+template <>
+struct PodioTypeMap<EventInfo> {
+    using mutable_t = MutableEventInfo;
+    using collection_t = EventInfoCollection;
+};
+
+
+template<typename ... Ts>
+struct Overload : Ts ... {
+    using Ts::operator() ...;
+};
+template<class... Ts> Overload(Ts...) -> Overload<Ts...>;
+
+
+template <typename F, typename... ArgsT>
+void visitPodioType(const std::string& podio_typename, F& helper, ArgsT... args) {
+    if (podio_typename == "EventInfo") {
+        return helper.template operator()<EventInfo>(std::forward<ArgsT>(args)...);
+    }
+    else if (podio_typename == "ExampleHit") {
+        return helper.template operator()<ExampleHit>(std::forward<ArgsT>(args)...);
+    }
+    else if (podio_typename == "ExampleCluster") {
+        return helper.template operator()<ExampleCluster>(std::forward<ArgsT>(args)...);
+    }
+    throw std::runtime_error("Not a podio typename!");
+}
+
+// If you are using C++20, you can use templated lambdas to write your visitor completely inline like so:
+/*
+           visitPodioType(coll->getValueTypeName(),
+               [&]<typename T>(const podio::CollectionBase* coll, std::string name) {
+                   using CollT = const typename PodioTypeMap<T>::collection_t;
+                   CollT* typed_col = static_cast<CollT*>(coll);
+
+                   std::cout << name << std::endl;
+                   for (const T& object : *typed_col) {
+                       std::cout << coll->getValueTypeName() << std::endl;
+                       std::cout << object << std::endl;
+                   }
+            }, coll, coll_name);
+ */
+
+template <typename Visitor>
+struct DatamodelCollectionVisit {
+    void operator()(const podio::CollectionBase &collection, Visitor& visitor) {
+        std::string podio_typename = collection.getTypeName();
+        if (podio_typename == "EventInfoCollection") {
+            return visitor(static_cast<const EventInfoCollection &>(collection));
+        } else if (podio_typename == "ExampleHitCollection") {
+            return visitor(static_cast<const ExampleHitCollection &>(collection));
+        } else if (podio_typename == "ExampleClusterCollection") {
+            return visitor(static_cast<const ExampleClusterCollection &>(collection));
+        }
+        throw std::runtime_error("Unrecognized podio typename!");
+    }
+};
+
+// TODO: Change argument to collection pointer instead of reference because that is what we do everywhere else?
+
+#endif //JANA2_DATAMODELGLUE_H

src/examples/PodioExample/ExampleClusterFactory.cc

@@ -0,0 +1,57 @@
+
+// Copyright 2023, Jefferson Science Associates, LLC.
+// Subject to the terms in the LICENSE file found in the top-level directory.
+
+
+#include "ExampleClusterFactory.h"
+#include "datamodel/ExampleHit.h"
+#include <JANA/JEvent.h>
+
+ExampleClusterFactory::ExampleClusterFactory() {
+    SetTag("clusters");
+    // TODO: Need to throw an exception if you try to register a PODIO factory with an empty or non-unique tag
+}
+
+void ExampleClusterFactory::Process(const std::shared_ptr<const JEvent> &event) {
+
+    // This example groups hits according to the quadrant in which they lie on the x-y plane.
+
+    MutableExampleCluster quadrant1, quadrant2, quadrant3, quadrant4;
+
+    auto hits = event->GetCollection<ExampleHit>("hits");
+    for (auto hit : *hits) {
+        if (hit.x() > 0) {
+            if (hit.y() > 0) {
+                quadrant1.addHits(hit);
+                quadrant1.energy(quadrant1.energy() + hit.energy());
+            }
+            else {
+                quadrant4.addHits(hit);
+                quadrant4.energy(quadrant4.energy() + hit.energy());
+            }
+        }
+        else {
+            if (hit.y() > 0) {
+                quadrant2.addHits(hit);
+                quadrant2.energy(quadrant2.energy() + hit.energy());
+
+            }
+            else {
+                quadrant3.addHits(hit);
+                quadrant3.energy(quadrant3.energy() + hit.energy());
+            }
+
+        }
+    }
+    auto* clusters = new ExampleClusterCollection();
+    if (quadrant1.Hits_size() > 0) clusters->push_back(quadrant1);
+    if (quadrant2.Hits_size() > 0) clusters->push_back(quadrant2);
+    if (quadrant3.Hits_size() > 0) clusters->push_back(quadrant3);
+    if (quadrant4.Hits_size() > 0) clusters->push_back(quadrant4);
+
+    // If no hits were assigned to a cluster, it will self-destruct when it goes out of scope
+    SetCollection(clusters);
+}
+
+
+// TODO: Expose collections as refs, not ptrs?

src/examples/PodioExample/ExampleClusterFactory.h

@@ -0,0 +1,20 @@
+
+// Copyright 2023, Jefferson Science Associates, LLC.
+// Subject to the terms in the LICENSE file found in the top-level directory.
+
+
+#ifndef JANA2_EXAMPLECLUSTERFACTORY_H
+#define JANA2_EXAMPLECLUSTERFACTORY_H
+
+#include <JANA/Podio/JFactoryPodioT.h>
+#include "datamodel/ExampleCluster.h"
+#include "DatamodelGlue.h"
+
+class ExampleClusterFactory : public JFactoryPodioT<ExampleCluster> {
+public:
+    ExampleClusterFactory();
+    void Process(const std::shared_ptr<const JEvent> &event) override;
+};
+
+
+#endif //JANA2_EXAMPLECLUSTERFACTORY_H

src/examples/PodioExample/PodioExample.cc

@@ -0,0 +1,85 @@
+
+// Copyright 2023, Jefferson Science Associates, LLC.
+// Subject to the terms in the LICENSE file found in the top-level directory.
+#include <iostream>
+#include <podio/CollectionBase.h>
+#include <podio/Frame.h>
+#include "datamodel/MutableExampleHit.h"
+#include "datamodel/ExampleHitCollection.h"
+#include <podio/ROOTFrameWriter.h>
+#include <podio/ROOTFrameReader.h>
+
+#include <JANA/JApplication.h>
+#include <JANA/JFactoryGenerator.h>
+#include <JANA/Podio/JEventProcessorPodio.h>
+
+#include "PodioExampleSource.h"
+#include "PodioExampleProcessor.h"
+#include "ExampleClusterFactory.h"
+
+
+void create_hits_file() {
+
+    EventInfo eventinfo1(7, 22);
+    EventInfoCollection eventinfos1;
+    eventinfos1.push_back(eventinfo1);
+
+    ExampleHitCollection hits1;
+    hits1.push_back({22, -1, -1, 0, 100});
+    hits1.push_back({49, 1, 1, 0, 15.5});
+    hits1.push_back({47, 1, 2, 0, 0.5});
+    hits1.push_back({42, 2, 1, 0, 4.0});
+
+    podio::Frame event1;
+    event1.put(std::move(hits1), "hits");
+    event1.put(std::move(eventinfos1), "eventinfos");
+
+    podio::ROOTFrameWriter writer("hits.root");
+    writer.writeFrame(event1, "events");
+
+    EventInfo eventinfo2(8, 22);
+    EventInfoCollection eventinfos2;
+    eventinfos2.push_back(eventinfo2);
+
+    ExampleHitCollection hits2;
+    hits2.push_back({42, 5, -5, 5, 7.6});
+    hits2.push_back({618, -3, -5, 1, 99.9});
+    hits2.push_back({27, -10, 10, 10, 22.2});
+    hits2.push_back({28, -9, 11, 10, 7.8});
+
+    podio::Frame event2;
+    event2.put(std::move(hits2), "hits");
+    event2.put(std::move(eventinfos2), "eventinfos");
+
+    writer.writeFrame(event2, "events");
+    writer.finish();
+
+}
+
+void verify_clusters_file() {
+    podio::ROOTFrameReader reader;
+    reader.openFile("podio_output.root");
+    auto event0 = podio::Frame(reader.readEntry("events", 0));
+
+    std::cout << "Event 0: Expected 2 clusters, got " << event0.get("clusters")->size() << std::endl;
+
+    auto event1 = podio::Frame(reader.readEntry("events", 1));
+    std::cout << "Event 1: Expected 3 clusters, got " << event1.get("clusters")->size() << std::endl;
+}
+
+
+int main() {
+
+    create_hits_file();
+
+    JApplication app;
+    app.Add(new PodioExampleProcessor);
+    app.Add(new JEventProcessorPodio);
+    app.Add(new JFactoryGeneratorT<ExampleClusterFactory>());
+    app.Add(new PodioExampleSource("hits.root"));
+    app.Run();
+
+    verify_clusters_file();
+
+}
+