SIMD + Vanilla Tree are validated, Vanilla Light Tree is NOT working ATM

src/post_treatments/Makefile.am

@@ -42,7 +42,8 @@ aevol_misc_lineage \
 aevol_misc_mutagenesis \
 aevol_misc_create_csv \
 aevol_misc_lucas \
-aevol_misc_ancestor_stats
+aevol_misc_ancestor_stats \
+aevol_misc_soft_lineage
 # aevol_misc_fixed_mutations
 # aevol_misc_gene_families
 # aevol_misc_mutational_robustness
@@ -77,3 +78,4 @@ aevol_misc_view_generation_SOURCES = view_generation.cpp
 aevol_misc_evaluate_regulation_SOURCES = evaluate_regulation.cpp
 aevol_misc_lucas_SOURCES = lucas.cpp
 aevol_misc_ancestor_stats_SOURCES = ancestor_stats.cpp
+aevol_misc_soft_lineage_SOURCES = soft_lineage.cpp
\ No newline at end of file

src/post_treatments/soft_lineage.cpp

+// ============================================================================
+//                                   Includes
+// ============================================================================
+#include <cerrno>
+#include <cinttypes>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <fstream>
+
+#include <zlib.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <assert.h>
+
+#include "aevol.h"
+
+using namespace aevol;
+
+int main(int argc, char** argv) {
+  int64_t luca_time;
+  int64_t last_gen;
+  int64_t t0 = 0;
+
+  printf("\n\n");
+  printf("====================================\n");
+  printf(" Loading the info of last save ... \n");
+
+  std::ifstream light_tree_file;
+  light_tree_file.open(LIGHTTREE_FILE_NAME);
+  if(light_tree_file and light_tree_file.peek() != EOF) {
+    light_tree_file >> luca_time;
+  }
+  else {
+    exit(EXIT_FAILURE);
+  }
+
+  last_gen = OutputManager::last_gener();
+
+  printf("OK\n");
+  printf("====================================\n");
+
+  ExpManager* exp_manager = new ExpManager();
+  exp_manager->load(t0, true, false);
+
+  // Check that the tree was recorded
+  if (not exp_manager->record_light_tree()) {
+    Utils::ExitWithUsrMsg("The phylogenetic tree wasn't recorded during "
+                          "evolution, could not reconstruct the lineage");
+  }
+  int64_t backup_step = exp_manager->backup_step();
+
+  //the table will be one index bigger for sementic. the index 0 will never be used
+  ReplicationReport** reports = new ReplicationReport*[last_gen+1];
+  reports[0] = nullptr;
+
+  printf("\n\n");
+  printf("====================================\n");
+  printf(" Loading the branch tree file ... ");
+  char input_file_name[255];
+
+  std::map<int64_t, std::map<int32_t, ReplicationReport*>> replics;
+
+  sprintf(input_file_name, "lightTree/tree_branches.ae");
+  gzFile branches_file = gzopen( input_file_name, "r" );
+  if (branches_file == Z_NULL) {
+    printf("ERROR : Could not read tree file %s\n", input_file_name);
+    exit(EXIT_FAILURE);
+  }
+
+  int c = gzgetc(branches_file);
+  while(c > -1) {
+    gzungetc(c, branches_file);
+    ReplicationReport* rep = new ReplicationReport(branches_file, nullptr);
+    int64_t generation;
+    gzread(branches_file, &generation, sizeof(generation));
+    //std::cout << "Load report from id : " << rep->id() << " generation : " << generation << '\n';
+    replics[generation][rep->id()] = rep;
+    c = gzgetc(branches_file);
+  }
+  gzclose(branches_file);
+  printf("OK\n");
+  printf("====================================\n");
+
+  //Find the best indiv
+  int32_t best_id = 0;
+  int32_t best_rank = 0;
+  for(auto rep : replics[last_gen]) {
+    if(rep.second->rank() > best_rank) {
+      best_rank = rep.second->rank();
+      best_id = rep.first;
+    }
+  }
+  //His rank have to be the number of indivs
+  std::cout << "Best indiv is : " << best_id << " with rank : " << best_rank << '\n';
+  int32_t anc_id = best_id;
+
+  //Fill the end of all the replic with the lineage of the best
+  for(int64_t gen = last_gen ; gen >= luca_time and gen > 0 ; gen--) {
+    reports[gen] = replics[gen][anc_id];
+    anc_id = reports[gen]->parent_id();
+  }
+
+  printf("\n\n");
+  printf("====================================\n");
+  printf(" Loading the trunc tree files ... \n");
+
+  //Fill the rest of the lineage
+  int64_t current_gen = backup_step;
+
+  sprintf(input_file_name, "lightTree/tree_trunc" TIMESTEP_FORMAT ".ae", current_gen);
+  gzFile trunc_file = gzopen( input_file_name, "r" );
+  if (trunc_file == Z_NULL) {
+    printf("ERROR : Could not read tree file %s\n", input_file_name);
+    exit(EXIT_FAILURE);
+  }
+
+  for(int64_t gen = 1 ; gen < luca_time ; ) {
+    c = gzgetc(trunc_file);
+    if(c < 0) {
+      gzclose(trunc_file);
+      current_gen += backup_step;
+      if(current_gen > last_gen) {
+        break;
+      }
+      sprintf(input_file_name, "lightTree/tree_trunc" TIMESTEP_FORMAT ".ae", current_gen);
+      trunc_file = gzopen( input_file_name, "r" );
+      if (trunc_file == Z_NULL) {
+        printf("ERROR : Could not read tree file %s\n", input_file_name);
+        exit(EXIT_FAILURE);
+      }
+      continue;
+    }
+    gzungetc(c, trunc_file);
+    ReplicationReport* rep = new ReplicationReport(trunc_file, nullptr);
+    //printf("Getting the replication report for the ancestor at generation %" PRId64 "\n", gen);
+    reports[gen] = rep;
+    gen++;
+  }
+  printf("OK\n");
+  printf("====================================\n");
+
+  printf("\n\n\n");
+  printf("============================================================ \n");
+  printf(" Write the replication reports in the output file... \n");
+
+  // =======================
+  //  Open the output file
+  // =======================
+  char output_file_name[255];
+
+  sprintf(output_file_name, "soft_lineage" TIMESTEP_FORMAT ".ae", last_gen);
+
+  gzFile soft_lineage_file = gzopen(output_file_name, "w");
+  if (soft_lineage_file == nullptr) {
+    fprintf(stderr, "File %s could not be created.\n", output_file_name);
+    fprintf(stderr, "Please check your permissions in this directory.\n");
+    exit(EXIT_FAILURE);
+  }
+
+  const Individual& initial_ancestor = *(exp_manager->indiv_by_id(reports[1]->parent_id()));
+
+  // Write file "header"
+  gzwrite(soft_lineage_file, &t0, sizeof(t0));
+  gzwrite(soft_lineage_file, &last_gen, sizeof(last_gen));
+  gzwrite(soft_lineage_file, &best_id, sizeof(best_id));
+  gzwrite(soft_lineage_file, &best_rank, sizeof(best_rank));
+
+  initial_ancestor.grid_cell()->save(soft_lineage_file);
+
+  std::ofstream of;
+  of.open("lignée.txt");
+
+  for(int64_t i=1 ; i <= last_gen ; i++) {
+    of << i << " : " << reports[i]->parent_id() << "  " << reports[i]->id() << std::endl;
+    reports[i]->write_to_tree_file(soft_lineage_file);
+  }
+  of.close();
+  gzclose(soft_lineage_file);
+  printf("OK\n");
+  printf("====================================\n");
+
+  delete [] reports;
+  delete exp_manager;
+
+}