/********************************************************************** * convert_image -- convert an image file to a cbf file * * * * Version 0.7.2.3 2 October 2002 * * * * Paul Ellis (ellis@ssrl.slac.stanford.edu) * **********************************************************************/ /********************************************************************** * 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 "cbf_simple.h" #include "img.h" #include #include #include #include #include int main (int argc, char *argv []) { FILE *in, *out; img_handle img; cbf_handle cbf; char detector_type [64], template_name [256], *c; const char *detector_name, *axis; double wavelength, distance, osc_start, osc_range, time; const char *date; static const char *monthname [] = { "Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec" }; /* Usage */ if (argc < 3) { fprintf (stderr, "\n Usage: %s imagefile cbffile\n", argv [0]); exit (2); } /* Read the image */ img = img_make_handle (); cbf_failnez (img_read (img, argv [1])) /* Identify the detector */ detector_name = img_get_field (img, "DETECTOR"); if (!detector_name) exit (3); for (c = detector_type; *detector_name; detector_name++) if (!isspace (*detector_name)) *c++ = tolower (*detector_name); *c = '\0'; /* Construct the template name */ sprintf (template_name, "template_%s_%dx%d.cbf", detector_type, img_columns (img), img_rows (img)); /* Read and modify the template */ cbf_failnez (cbf_make_handle (&cbf)) in = fopen (template_name, "rb"); if (!in) exit (4); cbf_failnez (cbf_read_template (cbf, in)) /* Wavelength */ wavelength = img_get_number (img, "WAVELENGTH"); if (wavelength) cbf_failnez (cbf_set_wavelength (cbf, wavelength)) /* Distance */ distance = img_get_number (img, "DISTANCE"); cbf_failnez (cbf_set_axis_setting (cbf, 0, "DETECTOR_Z", distance, 0)) /* Oscillation start and range */ axis = img_get_field (img, "OSCILLATION AXIS"); if (!axis) axis = "PHI"; osc_start = img_get_number (img, axis); osc_range = img_get_number (img, "OSCILLATION RANGE"); cbf_failnez (cbf_set_axis_setting (cbf, 0, "GONIOMETER_PHI", osc_start, osc_range)) /* Exposure time */ time = img_get_number (img, "EXPOSURE TIME"); if (time) cbf_failnez (cbf_set_integration_time (cbf, 0, time)) /* Date stamp */ date = img_get_field (img, "DATE"); if (date) { char monthstring [16]; int month, day, hour, minute, second, year; year = 0; sscanf (date, "%*s %s %d %d:%d:%d %d", monthstring, &day, &hour, &minute, &second, &year); if (year != 0) { for (month = 0; month < 12; month++) if (strcmp (monthname [month], monthstring) == 0) break; month++; if (month <= 12) cbf_failnez (cbf_set_datestamp (cbf, 0, year, month, day, hour, minute, second, CBF_NOTIMEZONE, 0)) } } /* diffrn.id */ cbf_failnez (cbf_set_diffrn_id (cbf, "DS1")) /* Image */ cbf_failnez (cbf_set_image (cbf, 0, 0, CBF_PACKED, &img_pixel (img, 0, 0), sizeof (int), 1, img_columns (img), img_rows (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)) /*****************************************************************************/ { const char *id; double d [4]; int i [4]; unsigned int u [4]; size_t s [4]; cbf_goniometer goniometer; cbf_detector detector; /* Change the diffrn.id entry in all the categories */ cbf_set_diffrn_id (cbf, "TEST"); /* Get the diffrn.id entry */ cbf_get_diffrn_id (cbf, &id); /* Change the diffrn.crystal_id entry */ cbf_set_crystal_id (cbf, "CTEST"); /* Get the diffrn.crystal_id entry */ cbf_get_crystal_id (cbf, &id); /* Set the wavelength */ cbf_set_wavelength (cbf, 2.14); /* Get the wavelength */ cbf_get_wavelength (cbf, &wavelength); /* Set the polarization */ cbf_set_polarization (cbf, 0.5, 0.75); /* Get the polarization */ cbf_get_polarization (cbf, &d [0], &d [1]); /* Set the divergence */ cbf_set_divergence (cbf, 0.3, 0.4, 0.5); /* Get the divergence */ cbf_get_divergence (cbf, &d [0], &d [1], &d [2]); /* Get the number of elements */ cbf_count_elements (cbf, &u [0]); /* Get the element id */ cbf_get_element_id (cbf, 0, &id); /* Set the gain of a detector element */ cbf_set_gain (cbf, 0, 0.24, 0.04); /* Get the gain of a detector element */ cbf_get_gain (cbf, 0, &d [0], &d [1]); /* Set the overload value of a detector element */ cbf_set_overload (cbf, 0, 100000); /* Get the overload value of a detector element */ cbf_get_overload (cbf, 0, &d [0]); /* Set the integration time */ cbf_set_integration_time (cbf, 0, 10.1); /* Get the integration time */ cbf_get_integration_time (cbf, 0, &d [0]); /* Set the collection date and time (1) as seconds since January 1 1970 */ cbf_set_timestamp (cbf, 0, 1000.0, CBF_NOTIMEZONE, 0.1); /* Get the collection date and time (1) as seconds since January 1 1970 */ cbf_get_timestamp (cbf, 0, &d [0], &i [0]); /* Get the image size */ cbf_get_image_size (cbf, 0, 0, &s [0], &s [1]); /* Change the setting of an axis */ cbf_set_axis_setting (cbf, 0, "GONIOMETER_PHI", 27.0, 0.5); /* Get the setting of an axis */ cbf_get_axis_setting (cbf, 0, "GONIOMETER_PHI", &d [0], &d [1]); /* Construct a goniometer */ cbf_construct_goniometer (cbf, &goniometer); /* Get the rotation axis */ cbf_get_rotation_axis (goniometer, 0, &d [0], &d [1], &d [2]); /* Get the rotation range */ cbf_get_rotation_range (goniometer, 0, &d [0], &d [1]); /* Reorient a vector */ cbf_rotate_vector (goniometer, 0, 0.5, 0.3, 0, 1, &d [0], &d [1], &d [2]); /* Convert a vector to reciprocal space */ cbf_get_reciprocal (goniometer, 0, 0.3, 0.98, 1, 2, -3, &d [0], &d [1], &d [2]); /* Construct a detector positioner */ cbf_construct_detector (cbf, &detector, 0); /* Get the beam center */ cbf_get_beam_center (detector, &d [0], &d [1], &d [2], &d [3]); /* Get the detector distance */ cbf_get_detector_distance (detector, &d [0]); /* Get the detector normal */ cbf_get_detector_normal (detector, &d [0], &d [1], &d [2]); /* Calcluate the coordinates of a pixel */ cbf_get_pixel_coordinates (detector, 1, 3, &d [0], &d [1], &d [2]); /* Calcluate the area of a pixel */ cbf_get_pixel_area (detector, 1, 3, &d [0], &d [1]); /* Free a detector */ cbf_free_detector (detector); /* Free a goniometer */ cbf_free_goniometer (goniometer); } /*****************************************************************************/ /* Free the cbf */ cbf_failnez (cbf_free_handle (cbf)) /* Free the image */ img_free_handle (img); /* Success */ return 0; }