#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <errno.h>

#include <iostream>
#include <string>
#include <algorithm>
#include <iterator>
#include <fstream>
using namespace std;

#define MAX_ROOTPATH_LEN 100
#define MAX_FULLPATH_LEN 150
#define MAX_OBJECTS 64000 //max objects per frame
#define MAX_NUM_SETS 100 //maximum number of image sets to process
#define MAX_FILESIZE 2252800  // maximum size (in bytes) of image files allowed; 2200kB
#define PATH_BEADS "PROC/BEAD/"
#define PATH_DATASET "PROC/DATASETS/"
#define DEBUG 1

int main(int argc, char *argv[]){

  char raw_fn[MAX_FULLPATH_LEN], 
    dataset_fn[MAX_FULLPATH_LEN],
    obj_count_fn[MAX_FULLPATH_LEN], 
    align_fn[MAX_FULLPATH_LEN], 
    bead_fn[MAX_FULLPATH_LEN],
    object_dir[MAX_FULLPATH_LEN],
    ROOT_PATH[MAX_ROOTPATH_LEN],
    curr_fn_index[5],
    curr_set_index[4],
    curr_obj_count[20],
    text[500],
    dataset_name[MAX_FULLPATH_LEN],
    error_string[200],
    even_odd=0;



  int num_frames,
    num_sets,
    set_index[MAX_NUM_SETS],
    curr_set,
    field_size,
    success,
    curr_frame,
    output_thresh,
    output_flag=0;
  
  FILE *infile[MAX_NUM_SETS],
    *outfile,
    *outfile2,
    *current_file;

  //short unsigned int input_frame=0,
  short unsigned int input_frame=0,
    input_set=0,
    input_size=0,
    input_centroid_x=0,
    input_centroid_y=0,
    input_border=0,
    input_value=0,
    input_border_temp=0;


  //  short unsigned int input_frame[10];
  
  field_size = sizeof(unsigned short int);
  

  //****************** Parse command-line arguments **********************
  //
  strcpy(ROOT_PATH, argv[1]);
  strcpy(dataset_name, argv[2]);
  num_sets = argc - 4;
  output_thresh = atoi(argv[3]);
  //
  //**********************************************************************


  //********** Open input bead files and output dataset files ************
  //
#ifdef DEBUG
  fprintf(stderr, "Opening input bead files and output dataset file (%d sets).\n",num_sets);
#endif
  
  // Generate filename for current output (dataset) file
  strcpy(dataset_fn, "");
  strcat(dataset_fn, ROOT_PATH);
  strcat(dataset_fn, PATH_DATASET);
  strcat(dataset_fn, dataset_name);
  strcat(dataset_fn, ".dataset");
  
#ifdef DEBUG
  fprintf(stderr, "Opening file %s for output: ", dataset_fn);
#endif
  if((outfile = fopen(dataset_fn, "w")) == NULL){
    fprintf(stderr, "ERROR OPENING OUTFILE.\n");
    exit(42);
  }
#ifdef DEBUG
  fprintf(stderr, "%s\n", strerror(errno));
#endif

  strcat(dataset_fn, "2");

#ifdef DEBUG
  fprintf(stderr, "Opening file %s for output: ", dataset_fn);
#endif
  if((outfile2 = fopen(dataset_fn, "w")) == NULL){
    fprintf(stderr, "ERROR OPENING OUTFILE2.\n");
    exit(42);
  }
#ifdef DEBUG
  fprintf(stderr, "%s\n", strerror(errno));
#endif

  for(curr_set = 0; curr_set < num_sets; curr_set++){
    set_index[curr_set] = atoi(argv[curr_set+4]); //set indices come from cmd-line args
    sprintf(curr_set_index, "%03d", *(set_index + curr_set)); //convert to 0-padded 4-digit
    // Generate filename for current input (bead) file
    strcpy(bead_fn, "");
    strcat(bead_fn, ROOT_PATH);
    strcat(bead_fn, PATH_BEADS);
    strcat(bead_fn, curr_set_index);
    strcat(bead_fn, ".beads");
    // Open files
#ifdef DEBUG
    fprintf(stderr, "Opening file %s for input: ", bead_fn);
#endif
    if((*(infile + curr_set) = fopen(bead_fn, "r")) == NULL){
      fprintf(stderr, "ERROR OPENING INFILE.\n");
      exit(42);
    }
#ifdef DEBUG
    fprintf(stderr, "%s\n", strerror(errno));
#endif
  }
  //
  //**********************************************************************

  curr_frame = 0;

  while(!feof(*infile)){

    /*    if((success=fread(&input_frame, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading output_frame from bead file %4.0d", curr_set); 
      exit(42);
      }*/
    if((success=fread(&input_frame, field_size, 1, *infile)) < 1){
      break;
    }


#ifdef DEBUG
    if(curr_frame + 1 < input_frame){
      fprintf(stderr, "Current frame %d\n", curr_frame + 2);
      curr_frame ++;
    }
#endif
    
    if((success=fread(&input_set, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_set from bead file %4.0d", curr_set); 
      exit(42);
    }
    if((success=fread(&input_size, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_size from bead file %4.0d", curr_set); 
      exit(42);
    }
    if((success=fread(&input_centroid_x, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_centroid_x from bead file %4.0d", curr_set); 
      exit(42);
    }
    if((success=fread(&input_centroid_y, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_centroid_y from bead file %4.0d", curr_set); 
      exit(42);
    }
    if((success=fread(&input_border, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_border from bead file %4.0d", curr_set); 
      exit(42);
    }
    if((success=fread(&input_value, field_size, 1, *infile)) < 1){
      fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
      exit(42);
    }

    if(input_value >= output_thresh){
      output_flag = 1;
    }
    else{
      output_flag = 0;
    }
    

    if(output_flag == 1){

      if(even_odd){
	current_file = outfile;
	even_odd=0;
      }
      else{
	current_file = outfile2;
	even_odd=1;
      }

      if((success=fwrite(&input_frame, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_frame to bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fwrite(&input_set, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_set to bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fwrite(&input_size, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_size to bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fwrite(&input_centroid_x, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_centroid_x to bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fwrite(&input_centroid_y, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_centroid_y to bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fwrite(&input_value, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_value to bead file %4.0d", curr_set); 
	exit(42);
      }
    }
    
    
    for(curr_set = 1; curr_set < num_sets; curr_set++){
      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }
      if((success=fread(&input_border_temp, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_border from bead file %4.0d", curr_set); 
	exit(42);
      }

      input_border = input_border + input_border_temp;

      if((success=fread(&input_value, field_size, 1, *(infile + curr_set))) < 1){
	fprintf(stderr, "ERROR reading input_value from bead file %4.0d", curr_set); 
	exit(42);
      }

      if(output_flag == 1){
	if((success=fwrite(&input_value, field_size, 1, current_file)) < 1){
	  fprintf(stderr, "ERROR writing input_value to bead file %4.0d", curr_set); 
	  exit(42);
	}
      }
    }//end for(curr_set)
    if(output_flag == 1){
      if((success=fwrite(&input_border, field_size, 1, current_file)) < 1){
	fprintf(stderr, "ERROR writing input_value to bead file %4.0d", curr_set); 
	exit(42);
      }
    }
    
  }//end while(!eof)
    
  for(curr_set = 0; curr_set < num_sets; curr_set++){
    fclose(*(infile + curr_set));    
  }
  fclose(outfile);
  fclose(outfile2);
  //
  //**********************************************************************
    
}