/***************************************************************************************
 * convert_raw.c                                                                       *
 *                                                                                     *
 *                                                                                     *
 * WRITTEN BY: Greg Porreca (Church Lab) 10-16-2005                                    *
 *                                                                                     *
 *                                                                                     *
 ***************************************************************************************/

#include <stdio.h>
#include <tiffio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <dirent.h>
#include <iostream>
#include <fstream>
#include <fnmatch.h>

using namespace std;

//function prototypes
int scandir_sel(struct dirent * ent);

//global variables
int STRIPSIZE = 8000;
int STRIPMAX = 250;  


int main(int argc, char *argv[]){
  FILE *infile;
  TIFF *outfile;
  struct dirent **namelist;
  char *tiff_img_pointer;
  
  char dirname[500];
  char curr_raw_filename[500];
  char curr_tif_filename[500];
  int num_imgs, i, j;
  int imageOffset, result;
  short unsigned int curr_img[1000000];

  if(argc != 2){
    fprintf(stdout, "\n");
    fprintf(stdout, "To use find_objects, execute as follows:\n");
    fprintf(stdout, " ./convert_raw dirname/\n");
    fprintf(stdout, "\n");
    exit(0);
  }

  strcpy(dirname, "");
  strcat(dirname, argv[1]);

  //turn annoying TIFF warnings off
  TIFFSetWarningHandler(0);
  
  num_imgs= scandir(dirname, &namelist, (int (*)(const struct dirent *))(scandir_sel), alphasort);

  for(i=0; i<num_imgs; i++){

    //build input and output filenames from directory listing
    strcpy(curr_raw_filename, "");
    strcat(curr_raw_filename, dirname);
    strcat(curr_raw_filename, namelist[i]->d_name);
    strcpy(curr_tif_filename, "");
    strncat(curr_tif_filename, curr_raw_filename, strlen(curr_raw_filename)-4);
    strcat(curr_tif_filename, ".tif");
    fprintf(stdout, "%s -> %s\n", curr_raw_filename, curr_tif_filename);

    //open input and output files
    if((infile = fopen(curr_raw_filename, "r")) == NULL){
      fprintf(stdout, "Could not open incoming raw file %s\n", curr_raw_filename);
      exit(42);
    }
    if((outfile = TIFFOpen(curr_tif_filename, "w")) == NULL){
      fprintf(stdout, "Could not open outgoing image %s\n", curr_tif_filename);
      exit(42);
    }

    //load raw image data into memory
    for(j=0; j<1000000; j++){
      if( (fread(&curr_img[j], sizeof(short unsigned int), 1, infile)) < 1){
	fprintf(stdout, "ERROR reading from raw file %s; failed at pixel %d\n", curr_raw_filename, j);
	exit(42);
      }
    }    
    fclose(infile);

    //set tiff image parameters
    TIFFSetField(outfile, TIFFTAG_IMAGEWIDTH, 1000);
    TIFFSetField(outfile, TIFFTAG_IMAGELENGTH, 1000);
    TIFFSetField(outfile, TIFFTAG_BITSPERSAMPLE, 16);
    TIFFSetField(outfile, TIFFTAG_ROWSPERSTRIP, 4);
    TIFFSetField(outfile, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
    TIFFSetField(outfile, TIFFTAG_PLANARCONFIG, PLANARCONFIG_CONTIG);
    TIFFSetField(outfile, TIFFTAG_XRESOLUTION, 72.0);
    TIFFSetField(outfile, TIFFTAG_YRESOLUTION, 72.0);
    TIFFSetField(outfile, TIFFTAG_RESOLUTIONUNIT, RESUNIT_INCH);


    // Write the data
    imageOffset = 0;
    tiff_img_pointer = (char*)curr_img; //TIFFWriteEncodedStrip takes a char*, not a short unsigned int*
    for (j = 0; j < STRIPMAX; j++){//iterate over the number of strips
      if((result = TIFFWriteEncodedStrip (outfile, j, tiff_img_pointer + imageOffset, STRIPSIZE)) == -1){
	fprintf(stdout, "Write error on input strip number %d\n", j);
	exit(42);
      }
      imageOffset += result;
    }
    TIFFClose(outfile);
  }
  free(namelist);
}  


//only returns files matching FILEMASK
int scandir_sel(struct dirent * ent){
  char* FILEMASK = "*.raw";
  if(1)
    return(!fnmatch(FILEMASK, ent->d_name, 0));
  return(0);
}