cuikbioatlastrrt.c

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#include "bioworld.h"
#include "parameters.h"

#include "defines.h"
#include "error.h"
#include "filename.h"
#include "atlasrrt.h"
#include "random.h"
#include "geom.h"
#include "chart.h"
#include "samples.h"
#include "averages.h"

#include <stdlib.h>
#include <string.h>
#include <time.h>

int main(int argc, char **arg)
{
  if (argc>1)
    {     
      #if (ATLAS_ON_CUIKSYSTEM)
        Error("cuikbioatlastrrt can ony operate on worlds");
      #else
      TBioWorld bioWorld;      /* The molecular information.  */
      Tparameters parameters;  /* Parameters used in the Cuik process. */

      Tfilename fparam;
  
      double *s1,*s2;          /* Origin/goal of the RRT. */
  
      unsigned int nvs;

      Tatlasrrt atlasrrt;

      boolean connected;
      double pl, pc;
      unsigned int ns;
      double **path;

      double planningTime;

      unsigned int it,nRepetitions;
      Taverages averages;

      unsigned int ri; /* random seed*/
      time_t t;        /* Used to timestamp the results */
      TAtlasBase ba;

      unsigned int db;
      
      TAtlasRRTStatistics *arst;

      #if (EXPLORATION_RRT)
        nRepetitions=1;
      #else
        if (argc>2)
          {
            nRepetitions=atoi(arg[2]);
            if (nRepetitions==0)
              Error("The repetition parameter for cuikbioatlastrrt is wrong");
          }
        else
          nRepetitions=1;
      #endif

      if ((nRepetitions>1)&&(GET_ATLASRRT_STATISTICS))
        Error("To get meaninful statistics results, please set GET_ATLASRRT_STATISTICS to 0");

      if ((nRepetitions>1)&&(ATLASRRT_VERBOSE))
        Error("To get meaninful statistics results, please set ATLASRRT_VERBOSE to 0");

      if ((GET_ATLASRRT_STATISTICS)&&(nRepetitions>1))
        {
          NEW(arst,1,TAtlasRRTStatistics);
          InitAtlasRRTStatistics(arst);
        }
      else
        arst=NULL;

      /*Init parameters*/
      CreateFileName(NULL,arg[1],NULL,PARAM_EXT,&fparam);
      fprintf(stderr,"Reading parameters from           : %s\n",GetFileFullName(&fparam));          
      InitParametersFromFile(GetFileFullName(&fparam),&parameters);

      db=(unsigned int)GetParameter(CT_DETECT_BIFURCATIONS,&parameters);
      if (db>0)
        Error("cuikatlastrrt does not deal with bifurcations (yet)");

      /*Read the bio-information from file*/
      InitBioWorld(&parameters,arg[1],NO_UINT,&s1,&bioWorld);
      free(s1);
      CS_WD_FROM_WORLD(BioWorldWorld(&bioWorld),&ba);

      /* Read the goal sample */
      #if (EXPLORATION_RRT)
        nvs=ReadOneSample(&parameters,arg[1],CS_WD_GET_NUM_SYSTEM_VARS(&ba),&s1);
        NEW(s2,nvs,double);
        memcpy(s2,s1,sizeof(double)*nvs);
      #else
        nvs=ReadTwoSamples(&parameters,arg[1],CS_WD_GET_NUM_SYSTEM_VARS(&ba),&s1,&s2);
      #endif

      /* Random seed initialization */     
      t=time(NULL);  /* Get the time at which input files have been read */
      ri=(unsigned int)t; 
      randomSet(ri);
      fprintf(stderr,"Random seed                       : %u\n",ri);

      /* Start the process to connect the two samples */
      InitAverages(nRepetitions,TRUE,TRUE,NO_UINT,&averages);

      for(it=0;it<nRepetitions;it++)
        {
          /* Initialize the atlas */
          fprintf(stderr,"************************************************\n");   
          InitAtlasRRT(&parameters,FALSE/*parallel*/,s1,ONE_TREE,FALSE,s2,&ba,&atlasrrt);
                
          /* Define the path using the atlas */   
          connected=AtlasTRRT(&parameters,s2,
                              &planningTime,
                              &pl,&pc,&ns,&path,BioWorldEnergy,
                              (void *)&bioWorld,arst,&atlasrrt);
      
          /* Save the results (only if one shot execution) */
          if (nRepetitions==1)
            {
              if (connected)
                SaveSamples(arg[1],FALSE,nvs,ns,path);

              SaveAtlasRRT(&parameters,arg[1],&atlasrrt);
            }

          /* Summarize and release allocated objects for this repetition*/

          if ((EXPLORATION_RRT)||(connected))
            {
              NewSuccesfulExperiment(planningTime,AtlasRRTMemSize(&atlasrrt),pl,pc,
                                     (double)GetAtlasRRTNumCharts(&atlasrrt),
                                     (double)GetAtlasRRTNumNodes(&atlasrrt),
                                     NULL,NULL,
                                     &averages);
              DeleteSamples(ns,path);
            }
          else
            fprintf(stderr,"  Execution failed (%f sec)\n",planningTime);

          DeleteAtlasRRT(&atlasrrt);

          fprintf(stderr,"Execution compleated %u/%u\n",it+1,nRepetitions);
        }
      
      /* Print statistics about the execution (only if many iterations) */
      if (nRepetitions>1)
        {         
          PrintAveragesHeader(stderr,argc,arg,&averages);

          fprintf(stderr,"%% **************************************************\n");
          fprintf(stderr,"Random seed : %u\n",ri);
          fprintf(stderr,"GlobalNN: %u  GlobalCurv: %u  Tree_ATLAS: %u\n",
                  ATLASRRT_GLOBAL_NN,GET_ATLASRRT_GLOBAL_CURV_CHECK,USE_ATLAS_TREE);
          PrintParameters(stderr,&parameters);

          #if (GET_ATLASRRT_STATISTICS)
            PrintAtlasRRTStatistics(NULL,arst);
            DeleteAtlasRRTStatistics(arst);
            free(arst);
          #endif

          PrintAverages(stderr,&averages);

          fprintf(stderr,"%% **************************************************\n");
        }

      /* Release memory */
      DeleteAverages(&averages);

      /* Release memory */
      free(s1);
      free(s2);

      DeleteParameters(&parameters);
      DeleteBioWorld(&bioWorld);

      DeleteFileName(&fparam);
      #endif
    }
 else
   {
     fprintf(stderr,"  Wrong number of parameters.\n");
     fprintf(stderr,"  Use:\n");   
     fprintf(stderr,"      cuikbioatlastrrt <problem filename>.world [num Repetitions]\n");
     fprintf(stderr,"  where <problem filename>.pdb the equations/world description\n");
     fprintf(stderr,"        <num Repetitions> experiment repetitions to gather statistics\n");
     fprintf(stderr,"                          This is optional.\n");
     fprintf(stderr,"  The '.pab' extension is required\n");
     fprintf(stderr,"  All the extensions managed by OpenBabel can be used\n");
   }
  return(EXIT_SUCCESS);
}