Logo Search packages:      
Sourcecode: cbflib version File versions  Download package

makecbf.c

/**********************************************************************
 * makecbf -- convert an image file to a cbf file                     *
 *                                                                    *
 * Version 0.7.6 28 June 2006                                         *
 *                                                                    *
 *                          Paul Ellis and                            *
 *         Herbert J. Bernstein (yaya@bernstein-plus-sons.com)        *
 *                                                                    *
 * (C) Copyright 2006 Herbert J. Bernstein                            *
 *                                                                    *
 **********************************************************************/

/**********************************************************************
 *                                                                    *
 * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL *
 * WHILE YOU MAY ALTERNATIVE DISTRIBUTE THE API UNDER THE LGPL        *
 * YOU MAY ***NOT*** DISTRBUTE THIS PROGRAM UNDER THE LGPL            *
 *                                                                    *                                                                    *
 **********************************************************************/
 
/*************************** GPL NOTICES ******************************
 *                                                                    *
 * This program is free software; you can redistribute it and/or      *
 * modify it under the terms of the GNU General Public License as     *
 * published by the Free Software Foundation; either version 2 of     *
 * (the License, or (at your option) any later version.               *
 *                                                                    *
 * This program is distributed in the hope that it will be useful,    *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of     *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the      *
 * GNU General Public License for more details.                       *
 *                                                                    *
 * You should have received a copy of the GNU General Public License  *
 * along with this program; if not, write to the Free Software        *
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA           *
 * 02111-1307  USA                                                    *
 *                                                                    *
 **********************************************************************/
  
/**********************************************************************
 *                                 NOTICE                             *
 * Creative endeavors depend on the lively exchange of ideas. There   *
 * are laws and customs which establish rights and responsibilities   *
 * for authors and the users of what authors create.  This notice     *
 * is not intended to prevent you from using the software and         *
 * documents in this package, but to ensure that there are no         *
 * misunderstandings about terms and conditions of such use.          *
 *                                                                    *
 * Please read the following notice carefully.  If you do not         *
 * understand any portion of this notice, please seek appropriate     *
 * professional legal advice before making use of the software and    *
 * documents included in this software package.  In addition to       *
 * whatever other steps you may be obliged to take to respect the     *
 * intellectual property rights of the various parties involved, if   *
 * you do make use of the software and documents in this package,     *
 * please give credit where credit is due by citing this package,     *
 * its authors and the URL or other source from which you obtained    *
 * it, or equivalent primary references in the literature with the    *
 * same authors.                                                      *
 *                                                                    *
 * Some of the software and documents included within this software   *
 * package are the intellectual property of various parties, and      *
 * placement in this package does not in any way imply that any       *
 * such rights have in any way been waived or diminished.             *
 *                                                                    *
 * With respect to any software or documents for which a copyright    *
 * exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.   *
 *                                                                    *
 * Even though the authors of the various documents and software      *
 * found here have made a good faith effort to ensure that the        *
 * documents are correct and that the software performs according     *
 * to its documentation, and we would greatly appreciate hearing of   *
 * any problems you may encounter, the programs and documents any     *
 * files created by the programs are provided **AS IS** without any   *
 * warranty as to correctness, merchantability or fitness for any     *
 * particular or general use.                                         *
 *                                                                    *
 * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF    *
 * PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE   *
 * PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS   *
 * OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE          *
 * PROGRAMS OR DOCUMENTS.                                             *
 **********************************************************************/
 
/**********************************************************************
 *                                                                    *
 *                           The IUCr Policy                          *
 *      for the Protection and the Promotion of the STAR File and     *
 *     CIF Standards for Exchanging and Archiving Electronic Data     *
 *                                                                    *
 * Overview                                                           *
 *                                                                    *
 * The Crystallographic Information File (CIF)[1] is a standard for   *
 * information interchange promulgated by the International Union of  *
 * Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the     *
 * recommended method for submitting publications to Acta             *
 * Crystallographica Section C and reports of crystal structure       *
 * determinations to other sections of Acta Crystallographica         *
 * and many other journals. The syntax of a CIF is a subset of the    *
 * more general STAR File[2] format. The CIF and STAR File approaches *
 * are used increasingly in the structural sciences for data exchange *
 * and archiving, and are having a significant influence on these     *
 * activities in other fields.                                        *
 *                                                                    *
 * Statement of intent                                                *
 *                                                                    *
 * The IUCr's interest in the STAR File is as a general data          *
 * interchange standard for science, and its interest in the CIF,     *
 * a conformant derivative of the STAR File, is as a concise data     *
 * exchange and archival standard for crystallography and structural  *
 * science.                                                           *
 *                                                                    *
 * Protection of the standards                                        *
 *                                                                    *
 * To protect the STAR File and the CIF as standards for              * 
 * interchanging and archiving electronic data, the IUCr, on behalf   *
 * of the scientific community,                                       *
 *                                                                    *
 * * holds the copyrights on the standards themselves,                *
 *                                                                    *
 * * owns the associated trademarks and service marks, and            *
 *                                                                    *
 * * holds a patent on the STAR File.                                 *
 *                                                                    *
 * These intellectual property rights relate solely to the            *
 * interchange formats, not to the data contained therein, nor to     *
 * the software used in the generation, access or manipulation of     *
 * the data.                                                          *
 *                                                                    *
 * Promotion of the standards                                         *
 *                                                                    *
 * The sole requirement that the IUCr, in its protective role,        *
 * imposes on software purporting to process STAR File or CIF data    *
 * is that the following conditions be met prior to sale or           *
 * distribution.                                                      *
 *                                                                    *
 * * Software claiming to read files written to either the STAR       *
 * File or the CIF standard must be able to extract the pertinent     *
 * data from a file conformant to the STAR File syntax, or the CIF    *
 * syntax, respectively.                                              *
 *                                                                    *
 * * Software claiming to write files in either the STAR File, or     *
 * the CIF, standard must produce files that are conformant to the    *
 * STAR File syntax, or the CIF syntax, respectively.                 *
 *                                                                    *
 * * Software claiming to read definitions from a specific data       *
 * dictionary approved by the IUCr must be able to extract any        *
 * pertinent definition which is conformant to the dictionary         *
 * definition language (DDL)[3] associated with that dictionary.      *
 *                                                                    *
 * The IUCr, through its Committee on CIF Standards, will assist      *
 * any developer to verify that software meets these conformance      *
 * conditions.                                                        *
 *                                                                    *
 * Glossary of terms                                                  *
 *                                                                    *
 * [1] CIF:  is a data file conformant to the file syntax defined     *
 * at http://www.iucr.org/iucr-top/cif/spec/index.html                *
 *                                                                    *
 * [2] STAR File:  is a data file conformant to the file syntax       *
 * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html   *
 *                                                                    *
 * [3] DDL:  is a language used in a data dictionary to define data   *
 * items in terms of "attributes". Dictionaries currently approved    *
 * by the IUCr, and the DDL versions used to construct these          *
 * dictionaries, are listed at                                        *
 * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html               *
 *                                                                    *
 * Last modified: 30 September 2000                                   *
 *                                                                    *
 * IUCr Policy Copyright (C) 2000 International Union of              *
 * Crystallography                                                    *
 **********************************************************************/

#include "cbf.h"
#include "img.h"

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

int local_exit(int status) {
  exit(status);
  return status;    /* to avoid warning messages */
}

#undef cbf_failnez
#define cbf_failnez(x) \
 {int err; \
  err = (x); \
  if (err) { \
    fprintf(stderr,"\nCBFlib fatal error %x \n",err); \
    local_exit(-1); \
  } \
 }


int main (int argc, char *argv [])
{
  FILE *in, *out;

  clock_t a,b;

  img_handle img, cbf_img;

  cbf_handle cbf;

  int id, index;

  unsigned int column, row;

  size_t nelem_read;

  double pixel_size, gain, wavelength, distance;

  int overload, dimension [2], precedence [2];

  const char *detector;

  char *detector_char;

  char detector_id [64];

  const char *direction [2], *array_id;


     /* Usage */ 

  if (argc < 3)
  {
    fprintf (stderr, "\n Usage: %s imagefile cbffile\n", argv [0]);

    exit (2);
  }


    /* Read the image */

  img = img_make_handle ();

  a = clock ();

  cbf_failnez (img_read (img, argv [1]))

  b = clock ();

  fprintf (stderr, " Time to read the image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC);


    /* Get some detector parameters */

    /* Detector identifier */

  detector = img_get_field (img, "DETECTOR");

  if (!detector)

    detector = "unknown";

  strncpy (detector_id, detector, 63);

  detector_id [63] = 0;

  detector_char = detector_id;

  while (*detector_char)

    if (isspace (*detector_char))

      memmove (detector_char, detector_char + 1, strlen (detector_char));

    else
    {
      *detector_char = tolower (*detector_char);

      detector_char++;
    }


    /* Pixel size */
    
  pixel_size = img_get_number (img, "PIXEL SIZE") * 0.001;


    /* Wavelength */

  wavelength = img_get_number (img, "WAVELENGTH");
  

    /* Distance */

  distance = img_get_number (img, "DISTANCE") * 0.001;
  

    /* Image size and orientation & gain and overload */

  if (strcmp (detector_id, "mar180") == 0 ||
      strcmp (detector_id, "mar300") == 0)
  {
    gain = 1.08;

    overload = 120000;

    dimension [0] = img_rows (img);
    dimension [1] = img_columns (img);

    precedence [0] = 1;
    precedence [1] = 2;

    direction [0] = "decreasing";
    direction [1] = "increasing";
  }
  else

    if (strcmp (detector_id, "mar345") == 0)
    {
      gain = 1.55;

      overload = 240000;

      dimension [0] = img_columns (img);
      dimension [1] = img_rows (img);

      precedence [0] = 2;
      precedence [1] = 1;

      direction [0] = "increasing";
      direction [1] = "increasing";
    }
    else

      if (strncmp (detector_id, "adscquantum", 11) == 0)
      {
        gain = 0.20;

        overload = 65000;

        dimension [0] = img_columns (img);
        dimension [1] = img_rows (img);

        precedence [0] = 2;
        precedence [1] = 1;

        direction [0] = "increasing";
        direction [1] = "increasing";
      }
      else
      {
        gain = 0.0;

        overload = 0;

        dimension [0] = img_rows (img);
        dimension [1] = img_columns (img);

        precedence [0] = 1;
        precedence [1] = 2;

        direction [0] = NULL;
        direction [1] = NULL;
      }


    /* Make a cbf version of the image */

  a = clock ();
                                                

    /* Create the cbf */

  cbf_failnez (cbf_make_handle (&cbf))


    /* Make a new data block */

  cbf_failnez (cbf_new_datablock (cbf, "image_1"))


    /* Make the _diffrn category */

  cbf_failnez (cbf_new_category (cbf, "diffrn"))
  cbf_failnez (cbf_new_column   (cbf, "id"))
  cbf_failnez (cbf_set_value    (cbf, "DS1"))


    /* Make the _diffrn_source category */

  cbf_failnez (cbf_new_category (cbf, "diffrn_source"))
  cbf_failnez (cbf_new_column   (cbf, "diffrn_id"))
  cbf_failnez (cbf_set_value    (cbf, "DS1"))
  cbf_failnez (cbf_new_column   (cbf, "source"))
  cbf_failnez (cbf_set_value    (cbf, "synchrotron"))
  cbf_failnez (cbf_new_column   (cbf, "type"))
  cbf_failnez (cbf_set_value    (cbf, "ssrl crystallography"))


    /* Make the _diffrn_radiation category */  

  cbf_failnez (cbf_new_category (cbf, "diffrn_radiation"))
  cbf_failnez (cbf_new_column   (cbf, "diffrn_id"))
  cbf_failnez (cbf_set_value    (cbf, "DS1"))
  cbf_failnez (cbf_new_column   (cbf, "wavelength_id"))
  cbf_failnez (cbf_set_value    (cbf, "L1"))


    /* Make the _diffrn_radiation_wavelength category */

  cbf_failnez (cbf_new_category    (cbf, "diffrn_radiation_wavelength"))
  cbf_failnez (cbf_new_column      (cbf, "id"))
  cbf_failnez (cbf_set_value       (cbf, "L1"))
  cbf_failnez (cbf_new_column      (cbf, "wavelength"))

  if (wavelength)
  
    cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", wavelength))

  cbf_failnez (cbf_new_column      (cbf, "wt"))
  cbf_failnez (cbf_set_value       (cbf, "1.0"))


    /* Make the _diffrn_measurement category */  

  cbf_failnez (cbf_new_category (cbf, "diffrn_measurement"))
  cbf_failnez (cbf_new_column   (cbf, "diffrn_id"))
  cbf_failnez (cbf_set_value    (cbf, "DS1"))
  cbf_failnez (cbf_new_column   (cbf, "method"))
  cbf_failnez (cbf_set_value    (cbf, "oscillation"))
  cbf_failnez (cbf_new_column   (cbf, "sample_detector_distance"))

  if (distance)

    cbf_failnez (cbf_set_doublevalue (cbf, "%.4f", distance))


    /* Make the _diffrn_detector category */  

  cbf_failnez (cbf_new_category (cbf, "diffrn_detector"))
  cbf_failnez (cbf_new_column   (cbf, "id"))
  cbf_failnez (cbf_set_value    (cbf, detector_id))
  cbf_failnez (cbf_new_column   (cbf, "diffrn_id"))
  cbf_failnez (cbf_set_value    (cbf, "DS1"))
  cbf_failnez (cbf_new_column   (cbf, "type"))
  cbf_failnez (cbf_set_value    (cbf, detector))


    /* Make the _diffrn_detector_element category */  

  cbf_failnez (cbf_new_category     (cbf, "diffrn_detector_element"))
  cbf_failnez (cbf_new_column       (cbf, "id"))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_new_column       (cbf, "detector_id"))
  cbf_failnez (cbf_set_value        (cbf, detector_id))


    /* Make the _diffrn_frame_data category */  

  cbf_failnez (cbf_new_category     (cbf, "diffrn_frame_data"))
  cbf_failnez (cbf_new_column       (cbf, "id"))
  cbf_failnez (cbf_set_value        (cbf, "frame_1"))
  cbf_failnez (cbf_new_column       (cbf, "detector_element_id"))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_new_column       (cbf, "detector_id"))
  cbf_failnez (cbf_set_value        (cbf, detector_id))
  cbf_failnez (cbf_new_column       (cbf, "array_id"))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_column       (cbf, "binary_id"))
  cbf_failnez (cbf_set_integervalue (cbf, 1))


    /* Make the _array_structure_list category */  

  cbf_failnez (cbf_new_category     (cbf, "array_structure_list"))
  cbf_failnez (cbf_new_column       (cbf, "array_id"))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_row          (cbf))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_column       (cbf, "index"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_next_row         (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, 2))
  cbf_failnez (cbf_new_column       (cbf, "dimension"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, dimension [0]))
  cbf_failnez (cbf_next_row         (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, dimension [1]))
  cbf_failnez (cbf_new_column       (cbf, "precedence"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, precedence [0]))
  cbf_failnez (cbf_next_row         (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, precedence [1]))
  cbf_failnez (cbf_new_column       (cbf, "direction"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_set_value        (cbf, direction [0]))
  cbf_failnez (cbf_next_row         (cbf))
  cbf_failnez (cbf_set_value        (cbf, direction [1]))


    /* Make the _array_element_size category */

  cbf_failnez (cbf_new_category     (cbf, "array_element_size"))
  cbf_failnez (cbf_new_column       (cbf, "array_id"))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_row          (cbf))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_column       (cbf, "index"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_next_row         (cbf))
  cbf_failnez (cbf_set_integervalue (cbf, 2))
  cbf_failnez (cbf_new_column       (cbf, "size"))

  if (pixel_size > 0)
  {
    cbf_failnez (cbf_rewind_row       (cbf))
    cbf_failnez (cbf_set_doublevalue  (cbf, "%.1fe-6", pixel_size * 1e6))
    cbf_failnez (cbf_next_row         (cbf))
    cbf_failnez (cbf_set_doublevalue  (cbf, "%.1fe-6", pixel_size * 1e6))
  }


    /* Make the _array_intensities category */

  cbf_failnez (cbf_new_category     (cbf, "array_intensities"))
  cbf_failnez (cbf_new_column       (cbf, "array_id"))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_column       (cbf, "binary_id"))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_new_column       (cbf, "linearity"))
  cbf_failnez (cbf_set_value        (cbf, "linear"))
  cbf_failnez (cbf_new_column       (cbf, "gain"))

  if (gain)
  
    cbf_failnez (cbf_set_doublevalue  (cbf, "%.3g", gain))
    
  cbf_failnez (cbf_new_column       (cbf, "overload"))

  if (overload)
    
    cbf_failnez (cbf_set_integervalue (cbf, overload))
    
  cbf_failnez (cbf_new_column       (cbf, "undefined"))
  cbf_failnez (cbf_set_integervalue (cbf, 0))


    /* Make the _array_data category */

  cbf_failnez (cbf_new_category     (cbf, "array_data"))
  cbf_failnez (cbf_new_column       (cbf, "array_id"))
  cbf_failnez (cbf_set_value        (cbf, "image_1"))
  cbf_failnez (cbf_new_column       (cbf, "binary_id"))
  cbf_failnez (cbf_set_integervalue (cbf, 1))
  cbf_failnez (cbf_new_column       (cbf, "data"))


    /* Save the binary data */

  cbf_failnez (cbf_set_integerarray (cbf, CBF_PACKED, 1,
                                 img_pixelptr (img, 0, 0), sizeof (int), 1,
                                 img_rows (img) * img_columns (img)))
  

    /* Write the new file */

  out = fopen (argv [2], "w+b");

  if (!out)
  {
    fprintf (stderr, " Couldn't open the CBF file %s\n", argv [2]);

    exit (1);
  }

  cbf_failnez (cbf_write_file (cbf, out, 1, CBF, MSG_DIGEST | MIME_HEADERS, 0))
  

    /* Free the cbf */

  cbf_failnez (cbf_free_handle (cbf))

  b = clock ();

  fprintf (stderr, " Time to write the CBF image: %.3fs\n", 
                                      ((b - a) * 1.0) / CLOCKS_PER_SEC); 


    /* Read the CBF file and compare the image to the original */
    
  a = clock ();


    /* Create the cbf */

  cbf_failnez (cbf_make_handle (&cbf))


    /* Read the file */

  in = fopen (argv [2], "rb");

  if (!in)
  {
    fprintf (stderr, " Couldn't reopen the CBF file %s\n", argv [2]);

    exit (1);
  }

  cbf_failnez (cbf_read_file (cbf, in, MSG_DIGEST))


    /* Get the image identifier */

  cbf_failnez (cbf_rewind_datablock (cbf))
  cbf_failnez (cbf_find_category    (cbf, "diffrn_frame_data"))
  cbf_failnez (cbf_find_column      (cbf, "array_id"))
  cbf_failnez (cbf_get_value        (cbf, &array_id))
  

    /* Get the image dimensions (second dimension = fast, first = slow) */

  cbf_failnez (cbf_find_category    (cbf, "array_structure_list"))
  cbf_failnez (cbf_rewind_row       (cbf))
  cbf_failnez (cbf_find_column      (cbf, "array_id"))

  dimension [0] = dimension [1] = 0;

  while (cbf_find_nextrow (cbf, array_id) == 0)
  {
    cbf_failnez (cbf_find_column      (cbf, "precedence"))
    cbf_failnez (cbf_get_integervalue (cbf, &index))

    if (index >= 1 && index <= 2)
    {
      cbf_failnez (cbf_find_column (cbf, "dimension"))

      cbf_failnez (cbf_get_integervalue (cbf, &dimension [2 - index]))
    }
    else

      exit (1);

    cbf_failnez (cbf_find_column (cbf, "array_id"))
  }

  if (dimension [0] == 0 || dimension [1] == 0)

    exit (1);


    /* Create the new image */

  cbf_img = img_make_handle ();

  img_set_dimensions (cbf_img, dimension [0], dimension [1]);


    /* Find the binary data */
  
  cbf_failnez (cbf_find_category (cbf, "array_data"))
  cbf_failnez (cbf_find_column   (cbf, "array_id"))
  cbf_failnez (cbf_find_row      (cbf, array_id))
  cbf_failnez (cbf_find_column   (cbf, "data"))


    /* Read the binary data */
  
  cbf_failnez (cbf_get_integerarray (cbf,
                                 &id, img_pixelptr (cbf_img, 0, 0), sizeof (int), 1,
                                 img_rows (cbf_img) * img_columns (cbf_img), &nelem_read))


    /* Free the cbf */

  cbf_failnez (cbf_free_handle (cbf))

  b = clock ();

  fprintf (stderr, " Time to read the CBF image: %.3fs\n", 
                                     ((b - a) * 1.0) / CLOCKS_PER_SEC);


    /* Compare the images */

  if (img_rows (img) != img_rows (cbf_img) || img_columns (img) != img_columns (cbf_img))
  {
    fprintf (stderr, " The dimensions of the CBF image don't match the original\n");

    exit (1);
  }

  for (column = 0; column < (unsigned int) img_columns (cbf_img); column++)

    for (row = 0; row < (unsigned int) img_rows (cbf_img); row++)

      if (img_pixel (cbf_img, column, row) != img_pixel (img, column, row))
      {
        fprintf (stderr, " The CBF image differs from the original at (%d, %d)\n", column, row);

        exit (1);
      }

  fprintf (stderr, " The CBF image matches the original\n");


    /* Free the images */

  img_free_handle (img);

  img_free_handle (cbf_img);


    /* Success */

  return 0;
}

Generated by  Doxygen 1.6.0   Back to index