File: imcopy.c

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#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include "fitsio.h"

int main(int argc, char *argv[])
{
    fitsfile *infptr, *outfptr;   /* FITS file pointers defined in fitsio.h */
    int status = 0, tstatus, ii = 1, iteration = 0, single = 0, hdupos;
    int hdutype, bitpix, bytepix, naxis = 0, nkeys, datatype = 0, anynul;
    long naxes[9] = {1, 1, 1, 1, 1, 1, 1, 1, 1};
    long first, totpix = 0, npix;
    double *array, bscale = 1.0, bzero = 0.0, nulval = 0.;
    char card[81];

    if (argc != 3)
    {
 printf("\n");
 printf("Usage:  imcopy inputImage outputImage[compress]\n");
 printf("\n");
 printf("Copy an input image to an output image, optionally compressing\n");
 printf("or uncompressing the image in the process.  If the [compress]\n");
 printf("qualifier is appended to the output file name then the input image\n");
 printf("will be compressed using the tile-compressed format.  In this format,\n");
 printf("the image is divided into rectangular tiles and each tile of pixels\n");
 printf("is compressed and stored in a variable-length row of a binary table.\n");
 printf("If the [compress] qualifier is omitted, and the input image is\n");
 printf("in tile-compressed format, then the output image will be uncompressed.\n");
 printf("\n");
 printf("If an extension name or number is appended to the input file name, \n");
 printf("enclosed in square brackets, then only that single extension will be\n");
 printf("copied to the output file.  Otherwise, every extension in the input file\n");
 printf("will be processed in turn and copied to the output file.\n");
 printf("\n");
 printf("Examples:\n");
 printf("\n");
 printf("1)  imcopy image.fit 'cimage.fit[compress]'\n");
 printf("\n");
 printf("    This compresses the input image using the default parameters, i.e.,\n");
 printf("    using the Rice compression algorithm and using row by row tiles.\n");
 printf("\n");
 printf("2)  imcopy cimage.fit image2.fit\n");
 printf("\n");
 printf("    This uncompresses the image created in the first example.\n");
 printf("    image2.fit should be identical to image.fit if the image\n");
 printf("    has an integer datatype.  There will be small differences\n");
 printf("    in the pixel values if it is a floating point image.\n");
 printf("\n");
 printf("3)  imcopy image.fit 'cimage.fit[compress GZIP 100,100;q 16]'\n");
 printf("\n");
 printf("    This compresses the input image using the following parameters:\n");
 printf("         GZIP compression algorithm;\n");
 printf("         100 X 100 pixel compression tiles;\n");
 printf("         quantization level = 16 (only used with floating point images)\n");
 printf("\n");
 printf("The full syntax of the compression qualifier is:\n");
 printf("    [compress ALGORITHM TDIM1,TDIM2,...; q QLEVEL s SCALE]\n");
 printf("where the allowed ALGORITHM values are:\n");
 printf("      Rice, HCOMPRESS, HSCOMPRESS, GZIP, or PLIO. \n");
 printf("       (HSCOMPRESS is a variant of HCOMPRESS in which a small\n");
 printf("        amount of smoothing is applied to the uncompressed image\n");
 printf("        to help suppress blocky compression artifacts in the image\n");
 printf("        when using large values for the 'scale' parameter).\n");
 printf("TDIMn is the size of the compression tile in each dimension,\n");
 printf("\n");
 printf("QLEVEL specifies the quantization level when converting a floating\n");
 printf("point image into integers, prior to compressing the image.  The\n");
 printf("default value = 16, which means the image will be quantized into\n");
 printf("integer levels that are spaced at intervals of sigma/16., where \n");
 printf("sigma is the estimated noise level in background areas of the image.\n");
 printf("If QLEVEL is negative, this means use the absolute value for the\n");
 printf("quantization spacing (e.g. 'q -0.005' means quantize the floating\n");
 printf("point image such that the scaled integers represent steps of 0.005\n");
 printf("in the original image).\n");
 printf("\n");
 printf("SCALE is the integer scale factor that only applies to the HCOMPRESS\n");
 printf("algorithm.  The default value SCALE = 0 forces the image to be\n");
 printf("losslessly compressed; Greater amounts of lossy compression (resulting\n");
 printf("in smaller compressed files) can be specified with larger SCALE values.\n");
 printf("\n");
 printf("\n");
 printf("Note that it may be necessary to enclose the file names\n");
 printf("in single quote characters on the Unix command line.\n");
      return(0);
    }

    /* Open the input file and create output file */
    fits_open_file(&infptr, argv[1], READONLY, &status);
    fits_create_file(&outfptr, argv[2], &status);

    if (status != 0) {    
        fits_report_error(stderr, status);
        return(status);
    }

    fits_get_hdu_num(infptr, &hdupos);  /* Get the current HDU position */

    /* Copy only a single HDU if a specific extension was given */ 
    if (hdupos != 1 || strchr(argv[1], '[')) single = 1;

    for (; !status; hdupos++)  /* Main loop through each extension */
    {

      fits_get_hdu_type(infptr, &hdutype, &status);

      if (hdutype == IMAGE_HDU) {

          /* get image dimensions and total number of pixels in image */
          for (ii = 0; ii < 9; ii++)
              naxes[ii] = 1;

          fits_get_img_param(infptr, 9, &bitpix, &naxis, naxes, &status);

          totpix = naxes[0] * naxes[1] * naxes[2] * naxes[3] * naxes[4]
             * naxes[5] * naxes[6] * naxes[7] * naxes[8];
      }

      if (hdutype != IMAGE_HDU || naxis == 0 || totpix == 0) { 

          /* just copy tables and null images */
          fits_copy_hdu(infptr, outfptr, 0, &status);

      } else {

          /* Explicitly create new image, to support compression */
          fits_create_img(outfptr, bitpix, naxis, naxes, &status);
          if (status) {
                 fits_report_error(stderr, status);
                 return(status);
          }

          if (fits_is_compressed_image(outfptr, &status)) {
              /* write default EXTNAME keyword if it doesn't already exist */
	      tstatus = 0;
              fits_read_card(infptr, "EXTNAME", card, &tstatus);
	      if (tstatus) {
	         strcpy(card, "EXTNAME = 'COMPRESSED_IMAGE'   / name of this binary table extension");
	         fits_write_record(outfptr, card, &status);
	      }
          }
	  	    
          /* copy all the user keywords (not the structural keywords) */
          fits_get_hdrspace(infptr, &nkeys, NULL, &status); 

          for (ii = 1; ii <= nkeys; ii++) {
              fits_read_record(infptr, ii, card, &status);
              if (fits_get_keyclass(card) > TYP_CMPRS_KEY)
                  fits_write_record(outfptr, card, &status);
          }

              /* delete default EXTNAME keyword if it exists */
/*
          if (!fits_is_compressed_image(outfptr, &status)) {
	      tstatus = 0;
              fits_read_key(outfptr, TSTRING, "EXTNAME", card, NULL, &tstatus);
	      if (!tstatus) {
	         if (strcmp(card, "COMPRESSED_IMAGE") == 0)
	            fits_delete_key(outfptr, "EXTNAME", &status);
	      }
          }
*/
	  
          switch(bitpix) {
              case BYTE_IMG:
                  datatype = TBYTE;
                  break;
              case SHORT_IMG:
                  datatype = TSHORT;
                  break;
              case LONG_IMG:
                  datatype = TINT;
                  break;
              case FLOAT_IMG:
                  datatype = TFLOAT;
                  break;
              case DOUBLE_IMG:
                  datatype = TDOUBLE;
                  break;
          }

          bytepix = abs(bitpix) / 8;

          npix = totpix;
          iteration = 0;

          /* try to allocate memory for the entire image */
          /* use double type to force memory alignment */
          array = (double *) calloc(npix, bytepix);

          /* if allocation failed, divide size by 2 and try again */
          while (!array && iteration < 10)  {
              iteration++;
              npix = npix / 2;
              array = (double *) calloc(npix, bytepix);
          }

          if (!array)  {
              printf("Memory allocation error\n");
              return(0);
          }

          /* turn off any scaling so that we copy the raw pixel values */
          fits_set_bscale(infptr,  bscale, bzero, &status);
          fits_set_bscale(outfptr, bscale, bzero, &status);

          first = 1;
          while (totpix > 0 && !status)
          {
             /* read all or part of image then write it back to the output file */
             fits_read_img(infptr, datatype, first, npix, 
                     &nulval, array, &anynul, &status);

             fits_write_img(outfptr, datatype, first, npix, array, &status);
             totpix = totpix - npix;
             first  = first  + npix;
          }
          free(array);
      }

      if (single) break;  /* quit if only copying a single HDU */
      fits_movrel_hdu(infptr, 1, NULL, &status);  /* try to move to next HDU */
    }

    if (status == END_OF_FILE)  status = 0; /* Reset after normal error */

    fits_close_file(outfptr,  &status);
    fits_close_file(infptr, &status);

    /* if error occurred, print out error message */
    if (status)
       fits_report_error(stderr, status);
    return(status);
}