tools/clitkMergeRootFiles.cxx

   1 /**
   2    =================================================
   3    * @file   clitkMergeRootFiles.cxx
   4    * @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
   5    * @author Brent Huisman <brent.huisman@insa-lyon.fr>
   6    * @date   06 May 2014
   7    *
   8    * @brief
   9    *
  10    =================================================*/
  11
  12 #include "clitkMergeRootFiles_ggo.h"
  13 #include "clitkCommon.h"
  14 #include "GateMergeManager.hh"
  15 #include <string>
  16 #include <TROOT.h>
  17 #include <TPluginManager.h>
  18 #include <TFile.h>
  19 #include <TKey.h>
  20 #include <TFileMerger.h>
  21 #include <TTree.h>
  22 #include <TChain.h>
  23 #include <TH1.h>
  24 #include <TH2.h>
  25 #include <iostream>
  26 #include <TApplication.h>
  27
  28 using std::endl;
  29 using std::cout;
  30
  31 struct PetInputFile {
  32     string filename;
  33     double mean_time;
  34 };
  35
  36 bool sort_pet_input_file(const PetInputFile &a, const PetInputFile &b) {
  37     return a.mean_time < b.mean_time;
  38 };
  39
  40 typedef std::vector<PetInputFile> PetInputFiles;
  41
  42 //-----------------------------------------------------------------------------
  43 int main(int argc, char *argv[]) {
  44         //this fixes a bug in TFileMerger. See http://root.cern.ch/phpBB3/viewtopic.php?t=18016.
  45     TApplication app("app", 0, 0);
  46
  47     gROOT->GetPluginManager()->AddHandler("TVirtualStreamerInfo", "*",
  48                                           "TStreamerInfo", "RIO", "TStreamerInfo()");
  49
  50     // init command line
  51     GGO(clitkMergeRootFiles, args_info);
  52
  53     // Check parameters
  54     if (args_info.input_given < 2) {
  55         FATAL("Error, please provide at least two inputs files");
  56     }
  57
  58     /* The following block does some bookkeeping necesary for files originating from a pet simulation.
  59     Seems fixing some timing info, for coincidences between files perhaps.
  60     It seems the files are later on reopened and merged, if the conditions were met.
  61     It's not required for merging other .root files.
  62     GateMergeManager reportedly exists specifically for the purpose of merging pet simulations. */
  63     {
  64         // Detect Pet output
  65         bool all_pet_output = true;
  66         PetInputFiles pet_input_files;
  67         for (uint i = 0; i < args_info.input_given; i++) {
  68             const char *filename = args_info.input_arg[i];
  69             PetInputFile input_file;
  70             input_file.filename = filename;
  71             TFile *handle = TFile::Open(filename, "READ");
  72             assert(handle);
  73             TTree *hits = dynamic_cast<TTree *>(handle->Get("Hits"));
  74             TTree *singles = dynamic_cast<TTree *>(handle->Get("Singles"));
  75             const bool is_pet_output = (hits != NULL) && (singles != NULL);
  76             cout << "testing " << filename << " is_pet_output " << is_pet_output;
  77
  78                 //TTree *histos = dynamic_cast<TH1F *>(handle->Get("histo;1"));
  79                 //const bool is_hist_output = (histos != NULL);
  80
  81
  82             if (is_pet_output) {
  83                 double time;
  84                 double time_accum = 0;
  85                 singles->SetBranchAddress("time", &time);
  86                 size_t total = singles->GetEntries();
  87                 for (size_t kk = 0; kk < total; kk++) {
  88                     singles->GetEntry(kk);
  89                     time_accum += time;
  90                 }
  91
  92                 input_file.mean_time = time_accum / total;
  93                 pet_input_files.push_back(input_file);
  94                 cout << " mean_time " << input_file.mean_time;
  95             }
  96
  97             cout << endl;
  98
  99             handle->Close();
 100             delete handle;
 101             //bitwise on booleans?
 102             all_pet_output &= is_pet_output;
 103         }
 104         cout << "all_pet_output " << all_pet_output << endl;
 105
 106         if (all_pet_output) {
 107             GateMergeManager manager(args_info.fastmerge_given, args_info.verbose_arg, true, 0, "");
 108
 109             cout << "sorting input file using singles time" << endl;
 110             std::sort(pet_input_files.begin(), pet_input_files.end(), sort_pet_input_file);
 111
 112             Strings input_filenames;
 113             for (PetInputFiles::const_iterator iter = pet_input_files.begin(); iter != pet_input_files.end(); iter++)
 114                 input_filenames.push_back(iter->filename);
 115
 116             manager.StartMergingFromFilenames(input_filenames, args_info.output_arg);
 117             //if the file was PET, then we're done.
 118             return 0;
 119         }
 120     }
 121
 122     //if the file was not PET, but a generic Rootfile, use TFileMerger.
 123
 124     // Merge
 125     TFileMerger *merger = new TFileMerger;
 126     for (uint i = 0; i < args_info.input_given; i++) merger->AddFile(args_info.input_arg[i]);
 127     merger->OutputFile(args_info.output_arg);
 128     bool whatbool = merger->Merge();
 129
 130     cout << "whatbool: " << whatbool << " no more whatbool" << endl;
 131     // this is the end my friend
 132     return 0;
 133
 134 }
 135 //-----------------------------------------------------------------------------