copyRootTree.cxx

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/*
Copyright (C) 2002-2025 CERN for the benefit of the ATLAS collaboration
*/
 
#include "copyRootTree.h"
 
// Root tree copy function
//
// NOTE: I don't recommend trying to understand the variable buffer
// classes until you see the general workflow.
//
// The main work is done in copy_root_tree below, skip down to that to
// understand what is going on.
//
 
#include "HDF5Utils/HdfTuple.h"
 
#include "TFile.h"
#include "TTree.h"
#include "TLeaf.h"
 
#include <memory>
#include <regex>
#include <iostream>
#include <set>
#include <cmath>
 
// ______________________________________________________________________
// Variable buffer classes
//
// These classes act as glue between HDF and ROOT: they hold pointers
// to the buffers that ROOT will read into, and as such are
// "ROOT-side" buffers.
//
// The constructors are given a reference to a `VariableFillers`
// container, which contains the "HDF5-side" logic. Each of the
// VariableFiller objects contains a "filler" function that the HDF5
// writer will call to read from the ROOT buffer.
//
// Some of the filler functions close over an index vector. This
// vector is incremented by the HDF5 Writer to read out successive
// entires in a std::vector stored in the root file.
//
// If this all seems complicated, it's because it's the deep internals
// of the code. Try to understand the copy_root_tree function first.
 
// Base class, just to hold a virtual destructor
namespace H5Utils {
  namespace {
    class IBuffer
    {
    public:
      virtual ~IBuffer() {}
    };
 
// Simple variables types are stored in the `Buffer` class.
    template <typename T>
    class Buffer: public IBuffer
    {
    public:
      Buffer(VariableFillers& vars, TTree& tt, const std::string& name);
    private:
      T m_buffer;
    };
 
// Buffer for vector types
    template <typename T>
    class VBuf: public IBuffer
    {
    public:
      // These require an index for the vector (`idx`)
      VBuf(VariableFillers& vars, std::vector<size_t>& idx, TTree& tt,
           const std::string& name, T default_value = T());
      ~VBuf();
    private:
      std::vector<T>* m_buffer;
    };
 
// Buffer for vectors of vectors
    template <typename T>
    class VVBuf: public IBuffer
    {
    public:
      VVBuf(VariableFillers& vars, std::vector<size_t>& idx, TTree& tt,
            const std::string& name, T default_value = T());
      ~VVBuf();
    private:
      std::vector<std::vector<T> >* m_buffer;
    };
 
 
    // Selection function 
    //
    // Define a bool function that returns false if event doesn't
    // pass TTreeFormula cut.
    bool passTTreeCut(TTreeFormula* selection) {
      // GetNdim looks to see how many valid arguements there are.
      // Returns false for none.
      if ( !selection || !selection->GetNdim()) return true;
      Int_t ndata = selection->GetNdata();
      for(Int_t current = 0; current < ndata; current++) {
        if (selection->EvalInstance(current) == 0) return false;
      }
      return true;
    }
 
 
  } // close anonymous namespace
 
// _____________________________________________________________________
// main copy root tree function
//
// The basic workflow is as follows:
//
//  - Define the ROOT-side buffers that we'll read the information
//    into. At the same time, define HDF-side objects that read out of
//    these buffers and copy the information into the HDF5 buffer.
//
//  - Build the output HDF5 files
//
//  - Loop over the input tree and fill the output files
//
// Note that this means the event loop happens last: most of the work
// is just setting up the read and write buffers.
 
  void copyRootTree(TTree& tt, H5::Group& fg, const TreeCopyOpts& opts) {
 
    // define the buffers for root to read into
    std::vector<std::unique_ptr<IBuffer> > buffers;
 
    // this keeps track of the things we couldn't read
    std::set<std::string> skipped;
 
 
    // Each `VariableFiller` must be constructed with a "filler"
    // function (or callable object), which takes no arguments and
    // returns the variable we want to write out. In this case they are
    // implemented as closures over the buffers that ROOT is reading
    // into.
 
    // This is the 1d variables
    VariableFillers vars;
    std::vector<size_t> idx_dummy;
 
    // These are 2d variables (i.e. vector<T> in the root file)
    //
    // We also need an index which the HDF5 writer increments as it
    // fills. This is shared with the ROOT buffers to index entries in
    // std::vectors
    VariableFillers vars2d;
    std::vector<size_t> idx(1,0);
 
    // 3d variables (index is now 2d)
    VariableFillers vars3d;
    std::vector<size_t> idx2(2,0);
 
    // Iterate over all the leaf names. There are some duplicates in the
    // list of keys, so we have to build the set ourselves.
    std::regex branch_filter(opts.branch_regex);
    TIter next(tt.GetListOfLeaves());
    TLeaf* leaf;
    std::set<std::string> leaf_names;
    while ((leaf = dynamic_cast<TLeaf*>(next()))) {
      leaf_names.insert(leaf->GetName());
    }
    if (leaf_names.size() == 0) throw std::logic_error("no branches found");
 
    // Loop over all the leafs, assign buffers to each
    //
    // These `Buffer` classes are defined above. The buffers turn the
    // branchs on, so we can set them all off to start.
    tt.SetBranchStatus("*", false);
    for (const auto& lname: leaf_names) {
      bool keep = true;
      if (opts.branch_regex.size() > 0) {
        keep = std::regex_search(lname, branch_filter);
      }
      if (opts.verbose) {
        std::cout << (keep ? "found " : "rejecting ") << lname << std::endl;
      }
      if (!keep) continue;
 
      leaf = tt.GetLeaf(lname.c_str());
      std::string branchName = leaf->GetBranch()->GetName();
      std::string leaf_type = leaf->GetTypeName();
      if (leaf_type == "Int_t") {
        buffers.emplace_back(new Buffer<int>(vars, tt, branchName));
      } else if (leaf_type == "Float_t") {
        buffers.emplace_back(new Buffer<float>(vars, tt, branchName));
      } else if (leaf_type == "Double_t") {
        buffers.emplace_back(new Buffer<double>(vars, tt, branchName));
      } else if (leaf_type == "Bool_t") {
        buffers.emplace_back(new Buffer<bool>(vars, tt, branchName));
      } else if (leaf_type == "Long64_t") {
        buffers.emplace_back(new Buffer<long long>(vars, tt, branchName));
      } else if (leaf_type == "ULong64_t") {
        buffers.emplace_back(new Buffer<unsigned long long>(vars, tt, branchName));
      } else if (leaf_type == "UInt_t") {
        buffers.emplace_back(new Buffer<unsigned int>(vars, tt, branchName));
      } else if (leaf_type == "UChar_t") {
        buffers.emplace_back(new Buffer<unsigned char>(vars, tt, branchName));
      } else if (leaf_type == "vector<float>") {
        buffers.emplace_back(new VBuf<float>(vars2d, idx, tt, branchName, NAN));
      } else if (leaf_type == "vector<double>") {
        buffers.emplace_back(new VBuf<double>(vars2d, idx, tt, branchName, NAN));
      } else if (leaf_type == "vector<int>") {
        buffers.emplace_back(new VBuf<int>(vars2d, idx, tt, branchName, 0));
      } else if (leaf_type == "vector<unsigned int>") {
        buffers.emplace_back(new VBuf<unsigned int>(vars2d, idx, tt, branchName, 0));
      } else if (leaf_type == "vector<unsigned char>") {
        buffers.emplace_back(new VBuf<unsigned char>(vars2d, idx, tt, branchName, 0));
      } else if (leaf_type == "vector<bool>") {
        buffers.emplace_back(new VBuf<bool>(vars2d, idx, tt, branchName, 0));
      } else if (leaf_type == "vector<vector<int> >") {
        buffers.emplace_back(new VVBuf<int>(vars3d, idx2, tt, branchName, 0));
      } else if (leaf_type == "vector<vector<unsigned int> >") {
        buffers.emplace_back(new VVBuf<unsigned int>(vars3d, idx2, tt, branchName, 0));
      } else if (leaf_type == "vector<vector<unsigned char> >") {
        buffers.emplace_back(new VVBuf<unsigned char>(vars3d, idx2, tt, branchName, 0));
      } else if (leaf_type == "vector<vector<float> >") {
        buffers.emplace_back(new VVBuf<float>(vars3d, idx2, tt, branchName, NAN));
      } else if (leaf_type == "vector<vector<double> >") {
        buffers.emplace_back(new VVBuf<double>(vars3d, idx2, tt, branchName, NAN));
      } else if (leaf_type == "vector<vector<bool> >") {
        buffers.emplace_back(new VVBuf<bool>(vars3d, idx2, tt, branchName, 0));
      } else {
        skipped.insert(std::move(leaf_type));
      }
    }
 
    // Build HDF5 Outputs
    //
    // In the simple case where we're not reading vectors, we store one
    // dataset with the same name as the tree. If there are vectors, we
    // instead create a group with the same name as the tree, and name
    // the datasets 1d, 2d, etc.
    //
    const std::string tree_name = tt.GetName();
 
    std::unique_ptr<WriterXd> writer1d;
    std::unique_ptr<WriterXd> writer2d;
    std::unique_ptr<WriterXd> writer3d;
    std::unique_ptr<H5::Group> top_group;
    if (opts.vector_lengths.size() > 0) {
      if (opts.vector_lengths.size() > 2) throw std::logic_error(
        "we don't support outputs with rank > 3");
      size_t length = opts.vector_lengths.at(0);
      top_group.reset(new H5::Group(fg.createGroup(tree_name)));
      if (opts.vector_lengths.size() > 1) {
        size_t length2 = opts.vector_lengths.at(1);
        if (vars3d.size() > 0) {
          writer3d.reset(new WriterXd(*top_group, "3d", std::move(vars3d),
                                      {length, length2}, opts.chunk_size));
        }
      }
      if (vars2d.size() > 0) {
        writer2d.reset(new WriterXd(*top_group, "2d", std::move(vars2d),
                                    {length}, opts.chunk_size));
      }
      if (vars.size() > 0) {
        writer1d.reset(new WriterXd(*top_group, "1d",
                                    std::move(vars), {}, opts.chunk_size));
      }
    } else {
      if (vars.size() > 0) {
        writer1d.reset(new WriterXd(fg, tree_name, std::move(vars), {}, opts.chunk_size));
      }
    }
 
    // Main event loop
    //
    // Very little actually happens here since the buffers are already
    // defined, as are the HDF5 reader functions.
    //
    
    // Get the selection string and build a new TTreeFormula
    std::string cut_string = opts.selection;
    const char * cut_char = cut_string.c_str();
    TTreeFormula *cut =0;
    if(!cut_string.empty()){
      // This is so a cut can be applied without requiring the 
      // branch to be output to the hdf5 file.
      tt.SetBranchStatus("*", true);
      cut = new TTreeFormula("selection", cut_char, &tt);
    }
 
    size_t n_entries = tt.GetEntries();
    if (opts.n_entries) n_entries = std::min(n_entries, opts.n_entries);
    int print_interval = opts.print_interval;
    if (print_interval == -1) {
      print_interval = std::max(1UL, n_entries / 100);
    }
 
    for (size_t iii = 0; iii < n_entries; iii++) {
      if (print_interval && (iii % print_interval == 0)) {
        std::cout << "events processed: " << iii
                  << " (" << std::round(iii*1e2 / n_entries) << "% of "
                  << n_entries << ")" << std::endl;
      }
      tt.GetEntry(iii);
      if(cut) cut->UpdateFormulaLeaves();
      if (!passTTreeCut(cut)) continue;
      if (writer1d) writer1d->fillWhileIncrementing(idx_dummy);
      if (writer2d) writer2d->fillWhileIncrementing(idx);
      if (writer3d) writer3d->fillWhileIncrementing(idx2);
    }
 
    // Flush the memory buffers on the HDF5 side. (This is done by the
    // destructor automatically, but we do it here to make any errors
    // more explicit.)
    if (writer1d) writer1d->flush();
    if (writer2d) writer2d->flush();
    if (writer3d) writer3d->flush();
 
    // Print the names of any classes that we were't able to read from
    // the root file.
    if (opts.verbose) {
      for (const auto& name: skipped) {
        std::cerr << "could not read branch of type " << name << std::endl;
      }
    }
  } // end copyRootTree
 
// ______________________________________________________________________
// Buffer implementation
 
  namespace {
// 1d buffer
 
    template <typename T>
    Buffer<T>::Buffer(VariableFillers& vars, TTree& tt,
                      const std::string& name)
    {
      tt.SetBranchStatus(name.c_str(), true);
      tt.SetBranchAddress(name.c_str(), &m_buffer);
      T& buf = m_buffer;
      vars.add<T>(name, [&buf](){return buf;});
    }
 
// 2d buffer
    template <typename T>
    VBuf<T>::VBuf(VariableFillers& vars, std::vector<size_t>& idx, TTree& tt,
                  const std::string& name, T default_value):
      m_buffer(new std::vector<T>)
    {
      tt.SetBranchStatus(name.c_str(), true);
      tt.SetBranchAddress(name.c_str(), &m_buffer);
      std::vector<T>& buf = *m_buffer;
      auto filler = [&buf, &idx, default_value]() -> T {
        if (idx.at(0) < buf.size()) {
          return buf.at(idx.at(0));
        } else {
          return default_value;
        }
      };
      vars.add<T>(name, filler);
    }
    template <typename T>
    VBuf<T>::~VBuf() {
      delete m_buffer;
    }
 
 
// 3d buffers
    template <typename T>
    VVBuf<T>::VVBuf(VariableFillers& vars, std::vector<size_t>& idx, TTree& tt,
                    const std::string& name, T default_value):
      m_buffer(new std::vector<std::vector<T> >)
    {
      tt.SetBranchStatus(name.c_str(), true);
      tt.SetBranchAddress(name.c_str(), &m_buffer);
      std::vector<std::vector<T> >& buf = *m_buffer;
      auto filler = [&buf, &idx, default_value]() -> T {
        size_t idx1 = idx.at(0);
        size_t idx2 = idx.at(1);
        if (idx1 < buf.size()) {
          if (idx2 < buf.at(idx1).size()) {
            return buf.at(idx1).at(idx2);
          }
        }
        return default_value;
      };
      vars.add<T>(name, filler);
    }
    template <typename T>
    VVBuf<T>::~VVBuf() {
      delete m_buffer;
    }
 
  } // close anonymous namespace
}   // close H5 namespace