merge fixing issue HEP-FCC/heppy#39

examples/PythiaConnector.cpp

@@ -78,9 +78,7 @@ papas::ListParticles PythiaConnector::makePapasParticlesFromGeneratedParticles(c
     if (ptc.core().status == 1) {  // only stable ones
 
       if (tlv.Pt() > 1e-5 && (abs(pdgid) != 12) && (abs(pdgid) != 14) && (abs(pdgid) != 16)) {
-
-        auto particle =
-            papas::Particle(pdgid, (double)ptc.core().charge, tlv, ptc.core().status, startVertex, endVertex);
+        papas::Particle particle(pdgid, (double)ptc.core().charge, tlv, ptc.core().status, startVertex, endVertex);
         particles.push_back(std::move(particle));
         // papas::PDebug::write("Selected Papas{}", particle);
       }
@@ -213,7 +211,7 @@ papas::Clusters PythiaConnector::ConvertClustersToPapas(const fcc::CaloClusterCo
   for (const auto& c : fccClusters) {
     const auto position = c.core().position;
     const auto energy = c.core().energy;
-    auto cluster = papas::Cluster(energy, TVector3(position.x, position.y, position.z), size,  clusters.size(), itemtype, subtype);
+    papas::Cluster cluster(energy, TVector3(position.x, position.y, position.z), size,  clusters.size(), itemtype, subtype);
     clusters.emplace(cluster.id(), std::move(cluster));
   }
   return clusters;

examples/example_dag_pair.cpp

@@ -42,18 +42,18 @@ int main() {
   // BFSVisitor uses an iterative method to traverse
   // output the Datatype of all children
   std::cout << std::endl << "TRAVERSE CHILDREN (start Node 0)  1 level" << std::endl;
-  for (auto n : bfs.traverseChildren(n0, 1)) {
+  for (const auto& n : bfs.traverseChildren(n0, 1)) {
     std::cout << n->value().itype << ":" << n->value().ivalue << std::endl;
   }
 
   std::cout << std::endl << "TRAVERSE UNDIRECTED (start Node 5) 2 levels " << std::endl;
-  for (auto n : bfs.traverseUndirected(n5, 2)) {
+  for (const auto& n : bfs.traverseUndirected(n5, 2)) {
     std::cout << n->value().itype << ":" << n->value().ivalue << std::endl;
   }
 
   std::cout << std::endl << "TRAVERSE CHILDREN (start Node 0)  all levels" << std::endl;
 
-  for (auto n : bfs.traverseChildren(n0)) {
+  for (const auto& n : bfs.traverseChildren(n0)) {
     std::cout << n->value().itype << ":" << n->value().ivalue << std::endl;
   }
 

examples/example_loop.cpp

@@ -30,15 +30,15 @@ int main(int argc, char* argv[]) {
   const char* fname = argv[1];
   // open the Pythia file fname
   try {
-    auto pythiaConnector = PythiaConnector(fname);
+    PythiaConnector pythiaConnector(fname);
 #if WITHSORT
     std::cout << "doing sorting";
 #else
     std::cout << "no sort";
 #endif
     // Create CMS detector and PapasManager
     papas::CMS CMSDetector;
-    auto papasManager = papas::PapasManager(CMSDetector);
+    papas::PapasManager papasManager(CMSDetector);
 
     unsigned int eventNo = 0;
     unsigned int nEvents = 100;

examples/example_pdebug_python_comparer.cpp

@@ -24,7 +24,7 @@ int main(int argc, char* argv[]) {
     return 1;
   }
   const char* fname = argv[1];
-  auto pythiaConnector = PythiaConnector(fname);
+  PythiaConnector pythiaConnector(fname);
 
   if (argc == 3) {
     const char* lname = argv[2];
@@ -37,7 +37,7 @@ int main(int argc, char* argv[]) {
   CMS CMSDetector;
   papas::PapasManager papasManager{CMSDetector};
   unsigned int eventNo = 0;
-  unsigned int nEvents = 5;
+  unsigned int nEvents = 10;
 
   auto start = std::chrono::steady_clock::now();
 

examples/example_plot.cpp

@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {
     return 1;
   }
   const char* fname = argv[1];
-  auto pythiaConnector = PythiaConnector(fname);
+  PythiaConnector pythiaConnector(fname);
 
   // Create CMS detector and PapasManager
   CMS CMSDetector;

examples/example_simple.cpp

@@ -33,7 +33,7 @@ int main(int argc, char* argv[]) {
     return 1;
   }
   const char* fname = argv[1];
-  auto pythiaConnector = PythiaConnector(fname);
+  PythiaConnector pythiaConnector(fname);
 
   if (argc == 3) {
     const char* lname = argv[2];

papas/datatypes/Cluster.h

@@ -28,6 +28,7 @@ class Cluster {
 
   /** Constructor: makes new cluster with a new id based on a copy of an existing cluster. The new id must be provided.
    @param[in]  cluster the cluster that is to be "copied"
+   @param[in]  index of the collection into which the cluster is to be stored 
    @param[in]  type eg IdCoder::kHcalCluster the identifier type
    @param[in]  subtype subtype of cluster eg 'm' for merged, 's' for smeared. Defaults to 'u' for unset.
    @param[in]  val the value that will be used when creating the Cluster identifier and which is used for sorting.

papas/datatypes/Event.h

@@ -173,7 +173,7 @@ class Event {
    *   @param[in]  collection the collection
    */
   template <class T>
-  Ids collectionIds(const T& collection) const;
+  Ids collectionIds(const T& collection, bool sort = false) const;
   /**
    *   @brief  takes all the history collection and merged them into one single history
    */
@@ -237,11 +237,13 @@ void Event::addCollectionInternal(
 }
 
 template <class T>
-Ids Event::collectionIds(const T& collection) const {
+Ids Event::collectionIds(const T& collection, bool sort) const {
   Ids ids;
   for (const auto& item : collection) {
     ids.push_back(item.first);
   }
+  if (sort)
+    ids.sort(std::greater<Identifier>());
   return ids;
 }
 }

papas/datatypes/HistoryHelper.h

@@ -17,7 +17,7 @@ namespace papas {
  
  @code
  Usage example:
- auto hhelper = HistoryHelper(event);
+ HistoryHelper hhelper(event);
  //find what is connected to (say) a reconstructed particle
  auto ids =hhelper.linkedIds(id);
  //filter the connected ids selecting only the ecals of subtype 'm'

papas/datatypes/src/Cluster.cpp

@@ -49,7 +49,7 @@ Cluster::Cluster(Cluster&& c)
   if (c.subClusters().size() == 1 && c.id() == (*c.subClusters().begin())->id())
     m_subClusters.push_back(this);  // non merged cluster point to itself
   else
-    for (auto s : c.subClusters())  // merged clusters
+    for (const auto& s : c.subClusters())  // merged clusters
       m_subClusters.push_back(s);
 }
 
@@ -100,7 +100,7 @@ std::ostream& operator<<(std::ostream& os, const Cluster& cluster) {
   os << "Cluster: " << std::setw(6) << std::left << IdCoder::pretty(cluster.id()) << ":" << cluster.id() << ": "
      << cluster.info();
   os << " sub(";
-  for (auto c : cluster.subClusters()) {
+  for (const auto& c : cluster.subClusters()) {
     os << IdCoder::pretty(c->id()) << ", ";
   }
   os << ")";

papas/datatypes/src/Event.cpp

@@ -69,7 +69,7 @@ const Blocks& Event::blocks(const IdCoder::SubType subtype) const {
 }
 bool Event::hasCollection(IdCoder::ItemType type, const IdCoder::SubType subtype) const {
   // Check if this collection is present
-  auto found = false;
+  bool found = false;
   switch (type) {
   case IdCoder::kEcalCluster:
     found = (m_ecalClustersCollection.find(subtype) != m_ecalClustersCollection.end());
@@ -125,7 +125,7 @@ bool Event::hasObject(Identifier id) const {
 void Event::extendHistory(const Nodes& history) {
   // A separate history is created at each stage.
   // the following adds this history into the papasevent history
-    for (const auto node : history) {
+    for (const auto& node : history) {
       for (const auto& c : node.second.children()) {
         makeHistoryLink(node.first, c->value(), *m_history);
       }

papas/datatypes/src/HistoryHelper.cpp

@@ -8,12 +8,12 @@ namespace papas {
 HistoryHelper::HistoryHelper(const Event& event) : m_event(event) {}
 
 Ids HistoryHelper::linkedIds(Identifier id, DAG::enumVisitType direction) const {
-  const auto history = m_event.history();
-  auto& startnode = history->at(id);
-  auto bfs = DAG::BFSRecurseVisitor<PFNode>();
-  auto nodes = bfs.traverseNodes(startnode, direction);
+  const auto& history = m_event.history();
+  const auto& startnode = history->at(id);
+  DAG::BFSRecurseVisitor<PFNode> bfs;
+  const auto& nodes = bfs.traverseNodes(startnode, direction);
   Ids ids;
-  for (auto node : nodes) {
+  for (const auto& node : nodes) {
     ids.push_back(node->value());
   }
   return ids;

papas/display/src/Display.cpp

@@ -14,7 +14,7 @@ Display::Display(std::list<ViewPane::Projection> views) {
     views = {ViewPane::Projection::xy, ViewPane::Projection::yz, ViewPane::Projection::xz};
   }
   /// Creates viewpanes
-  for (auto view : views) {
+  for (auto& view : views) {
     if ((view == ViewPane::Projection::xy) | (view == ViewPane::Projection::yz) | (view == ViewPane::Projection::xz)) {
       m_views[ViewPane::ProjectionStrings[view]] =
           std::unique_ptr<ViewPane>{new ViewPane(view, 100, -4, 4, 100, -4, 4)};
@@ -27,7 +27,7 @@ Display::Display(std::list<ViewPane::Projection> views) {
 };
 
 void Display::addToRegister(std::shared_ptr<Drawable> obj, int layer, bool clearable) {
-  for (auto const& view : m_views) {
+  for (auto& view : m_views) {
     view.second->addToRegister(obj, layer, clearable);
   }
 };

papas/graphtools/DefinitionsNodes.h

@@ -20,9 +20,7 @@ typedef std::list<const Nodes*> ListNodes;  ///< collection of Nodes
 
 inline PFNode& findOrMakeNode(Identifier id, Nodes& history) {
   if (history.empty() || (history.find(id) == history.end()) ) {
-
-      auto newnode = PFNode(id);
-
+      PFNode newnode(id);
       history.emplace(id, newnode);
   }
   return history.at(id);
@@ -41,8 +39,8 @@ inline void makeHistoryLinks(const Ids& parentids, const Ids& childids, Nodes& h
 }
 
 inline void printHistory(const Nodes& history) {
-  for (auto node : history)
-    for (auto cnode : node.second.children())
+  for (const auto& node : history)
+    for (const auto& cnode : node.second.children())
       std::cout << IdCoder::pretty(node.first) << ":" << IdCoder::pretty(cnode->value()) << "   ";
 }
 

papas/graphtools/DirectedAcyclicGraph.h

@@ -222,7 +222,7 @@ void BFSVisitor<N>::traverse(const Nodeset<N>& nodes, typename DAG::enumVisitTyp
   std::queue<int> nodeDepth;  // keeps track of the node depths so we can limit how deep we go if we wish
 
   // Mark the current node as visited and enqueue it
-  for (auto const& node : nodes) {
+  for (auto& node : nodes) {
     if (m_visited.find(node) == m_visited.end()) {  // if node is not listed as already being visited
       node->accept(*this);                          // mark as visited and add to results
       nodeQueue.push(node);                         // put into the queue
@@ -242,7 +242,7 @@ void BFSVisitor<N>::traverse(const Nodeset<N>& nodes, typename DAG::enumVisitTyp
 
     if ((depth < 0 || curdepth < depth) &&  // NB depth=-1 means we are visiting everything
         ((visittype == pt::CHILDREN) | (visittype == pt::UNDIRECTED))) {  // use the children
-      for (auto node : nodeQueue.front()->children()) {
+      for (auto& node : nodeQueue.front()->children()) {
         if (m_visited.find(node) == m_visited.end()) {  // check node is not already being visited
           node->accept(*this);
           nodeQueue.push(node);
@@ -252,7 +252,7 @@ void BFSVisitor<N>::traverse(const Nodeset<N>& nodes, typename DAG::enumVisitTyp
     }
     if ((depth < 0 || curdepth < depth) &&                               // NB depth=-1 means we are visiting everything
         ((visittype == pt::PARENTS) | (visittype == pt::UNDIRECTED))) {  // use the parents
-      for (auto node : nodeQueue.front()->parents()) {
+      for (auto& node : nodeQueue.front()->parents()) {
 
         if (m_visited.find(node) == m_visited.end()) {  // check node is not already being visited
           node->accept(*this);
@@ -283,7 +283,7 @@ void BFSRecurseVisitor<N>::traverse(const Nodeset<N>& nodes, typename DAG::enumV
     return;  // end of the recursion
   }
 
-  for (auto node : nodes) {
+  for (auto& node : nodes) {
 
     // Only process a node if not already visited
     if (BFSVisitor<N>::m_visited.find(node) == BFSVisitor<N>::m_visited.end()) {
@@ -294,11 +294,11 @@ void BFSRecurseVisitor<N>::traverse(const Nodeset<N>& nodes, typename DAG::enumV
       // and store these into visitnextnodes
       // NB depth=-1 means we are visiting everything
       if (depth != 0 && (visittype == pt::CHILDREN | visittype == pt::UNDIRECTED))
-        for (const auto child : node->children()) {
+        for (const auto& child : node->children()) {
           if (!this->alreadyVisited(child)) visitnextnodes.insert(child);
         }
       if (depth != 0 && (visittype == pt::PARENTS | visittype == pt::UNDIRECTED))
-        for (const auto parent : node->parents()) {
+        for (const auto& parent : node->parents()) {
           if (!this->alreadyVisited(parent)) visitnextnodes.insert(parent);
         }
     }

papas/graphtools/FloodFill.h

@@ -66,7 +66,7 @@ std::vector<typename FloodFill<T>::Nodevector> FloodFill<T>::traverse(FloodFill<
   m_visited.clear();
   BFSVisitor<TNode> bfs;
 
-  for (auto& elem : nodes) {
+  for (const auto& elem : nodes) {
 
     if (m_visited.find(&elem.second) != m_visited.end()) continue;  // already done this node so skip the rest
 

papas/graphtools/GraphBuilder.h

@@ -20,7 +20,7 @@ namespace papas {
 
  Usage example:
 @code
- auto builder  = GraphBuilder(ids, edges);
+ GraphBuilder builder(ids, edges);
  for (b in builder.blocks()) {
  ...
  }

papas/graphtools/src/GraphBuilder.cpp

@@ -20,21 +20,22 @@ GraphBuilder::GraphBuilder(const Ids& ids, Edges&& edges) : m_edges(edges), m_el
   }
   DAG::FloodFill<Identifier> FFill;
   // traverse does the work and returns a vector of connected node groups
-  for (auto& group : FFill.traverse(m_localNodes)) {
+  for (const auto& group : FFill.traverse(m_localNodes)) {
     // each of the nodevectors is about to become a separate block
     // we need the vector of ids and the map of edges in order to make the block
     Ids subgraph;
-    for (auto& node : group) {
+    for (const auto& node : group) {
       subgraph.push_back(node->value());
     }
+    #if WITHSORT
+    sortIds(subgraph); //sort in descending order
+    #endif
     m_subGraphs.push_back(subgraph);
   }
 }
 
 void GraphBuilder::sortIds(Ids& ids) {
-#if WITHSORT
   ids.sort(std::greater<uint64_t>()); //sort in descending order
-#endif
 }
 
 }  // end namespace papas

papas/graphtools/src/Ruler.cpp

@@ -19,8 +19,8 @@ Distance Ruler::clusterClusterDistance(const Cluster& cluster1, const Cluster& c
     std::list<double> allDistances;
     std::list<double> linkedDistances;
     bool isLinked = false;
-    for (const auto c1 : cluster1.subClusters()) {
-      for (const auto c2 : cluster2.subClusters()) {
+    for (const auto& c1 : cluster1.subClusters()) {
+      for (const auto& c2 : cluster2.subClusters()) {
         Distance d = clusterClusterDistance(*c1, *c2);  // recursive call
         allDistances.push_back(d.distance());
         if (d.isLinked()) {

papas/reconstruction/BlockBuilder.h

@@ -16,7 +16,7 @@ namespace papas {
 
  Usage example:
  @code
- auto builder = BlockBuilder (ids, edges, history, blocks, 'r');
+ BlockBuilder builder(ids, edges, history, blocks, 'r');
 
  }
  @endcode

papas/reconstruction/PFBlock.h

@@ -43,7 +43,7 @@ class PFBlock {
   PFBlock(const Ids& elementIds, Edges& edges, unsigned int index,
           char subtype = 'u');  // relevant parts of edges will be removed and become owned by PFBlock
   PFBlock(PFBlock&& pfblock) = default;  // allow move
-  const Ids& elementIds() const { return m_elementIds; }  ///< returns vector of all ids in the block
+  const Ids& elementIds(bool sort = false) const { return m_elementIds; }  ///< returns vector of all ids in the block
   const Edge& findEdge(Edge::EdgeKey key) const; ///< return Edge corresponding to Edge key
   /**
   Returns list of all edges of a given edge type that are connected to a given id.
@@ -60,7 +60,8 @@ class PFBlock {
    @param[in] edgetype : is an optional type of edge. If specified only links of the given edgetype will be returned
    @return vector of ids that are linked to the id
   */
-  Ids linkedIds(Identifier id, Edge::EdgeType edgetype = Edge::EdgeType::kUnknown) const;
+
+  Ids linkedIds(Identifier id, Edge::EdgeType edgetype = Edge::EdgeType::kUnknown, bool sort = false) const;
 
   std::string shortName() const;  ///< Short descriptor of block such as E3H1T2 (three Ecals, 1 Hcal, 2 tracks)
   int countEcal() const;          ///< Counts how many ecal cluster ids are in the block

papas/reconstruction/PFBlockSplitter.h

@@ -21,7 +21,7 @@ Usage example:
 @code
  auto& simplifiedblocks = createBlocks();
  auto& history = createHistory();
- auto blockBuilder = PFBlockSplitter(m_event, blockSubtype, simplifiedblocks, history);
+ PFBlockSplitter blockBuilder(m_event, blockSubtype, simplifiedblocks, history);
 
  //store a pointer to the ouputs into the event
  m_event.addCollection(simplifiedblocks);

papas/reconstruction/PFReconstructor.h

@@ -59,10 +59,10 @@ class PFReconstructor {
    Ids ids = m_pfEvent.mergedElementIds();
    
    // create the blocks of linked ids
-   auto bBuilder = PFBlockBuilder(m_pfEvent, ids);
+   PFBlockBuilder bBuilder(m_pfEvent, ids);
    
    // do the reconstruction of the blocks
-   auto pfReconstructor = PFReconstructor(m_pfEvent);
+   PFReconstructor pfReconstructor(m_pfEvent);
    pfReconstructor.reconstruct(bBuilder.blocks());
    m_pfEvent.setReconstructedParticles(std::move(pfReconstructor.particles()));
    @endcode