/********************************************************************** * cbf_minicbf_header.c -- handle minicbf header in a cbf * * * * based in part on adsccbf2img by Chris Nielsen of ADSC in 2007 * * * * Version 0.9.5 19 September 2015 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2006 -- 2015 Herbert J. Bernstein * * * **********************************************************************/ /********************************************************************** * * * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL * * * * ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS * * OF 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 * * * **********************************************************************/ /************************* LGPL NOTICES ******************************* * * * This library is free software; you can redistribute it and/or * * modify it under the terms of the GNU Lesser General Public * * License as published by the Free Software Foundation; either * * version 2.1 of the License, or (at your option) any later version. * * * * This library 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 * * Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public * * License along with this library; if not, write to the Free * * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, * * MA 02110-1301 USA * * * **********************************************************************/ /********************************************************************** * * * Stanford University Notices * * for the CBFlib software package that incorporates SLAC software * * on which copyright is disclaimed * * * * This software * * ------------- * * The term "this software", as used in these Notices, refers to * * those portions of the software package CBFlib that were created by * * employees of the Stanford Linear Accelerator Center, Stanford * * University. * * * * Stanford disclaimer of copyright * * -------------------------------- * * Stanford University, owner of the copyright, hereby disclaims its * * copyright and all other rights in this software. Hence, anyone * * may freely use it for any purpose without restriction. * * * * Acknowledgement of sponsorship * * ------------------------------ * * This software was produced by the Stanford Linear Accelerator * * Center, Stanford University, under Contract DE-AC03-76SFO0515 with * * the Department of Energy. * * * * Government disclaimer of liability * * ---------------------------------- * * Neither the United States nor the United States Department of * * Energy, nor any of their employees, makes any warranty, express or * * implied, or assumes any legal liability or responsibility for the * * accuracy, completeness, or usefulness of any data, apparatus, * * product, or process disclosed, or represents that its use would * * not infringe privately owned rights. * * * * Stanford disclaimer of liability * * -------------------------------- * * Stanford University makes no representations or warranties, * * express or implied, nor assumes any liability for the use of this * * software. * * * * Maintenance of notices * * ---------------------- * * In the interest of clarity regarding the origin and status of this * * software, this and all the preceding Stanford University notices * * are to remain affixed to any copy or derivative of this software * * made or distributed by the recipient and are to be affixed to any * * copy of software made or distributed by the recipient that * * contains a copy or derivative of this software. * * * * Based on SLAC Software Notices, Set 4 * * OTT.002a, 2004 FEB 03 * **********************************************************************/ /********************************************************************** * 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 * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include "cbf_minicbf_header.h" #include /* cbf_set_minicbf_header -- format a minicbf header conforming both to DECTRIS "PILATUS CBF Header Specification" version 1.4 and to the requirements of Winter, Graeme, and Alun Ashton. "fast_dp." Methods 55 (2014): 81-93, https://zenodo.org/record/13039, */ #define MAX_SRCLEN 132 #define CBF_GET_COLUMN_VALUE(cbf, colname, scratch_value, result_value) \ /**/ result_value = NULL; \ /**/ if (!cbf_find_column((cbf),(colname)) \ /**/ &&!cbf_rewind_row((cbf)) \ /**/ &&!cbf_get_value((cbf),&(scratch_value)) \ /**/ &&(scratch_value) \ /**/ &&strlen((scratch_value))> 0) { \ /**/ \ /**/ result_value = (scratch_value); \ /**/ \ /**/ } static const char * cbf_trim_left(const char * src) { const char * trimmed = src; while (*trimmed && isspace(*trimmed)) trimmed++; return trimmed; } static int cbf_append_string(char * * dst, size_t * dstcapacity, size_t * dstsize, const char * src) { size_t srclen; if (!dst || !dstcapacity || !dstsize || ! src) return CBF_ARGUMENT; srclen = strlen(src); if (*dst) { if (*dstsize + srclen + 1 > *dstcapacity) { cbf_failnez(cbf_realloc((void **)dst,dstcapacity, sizeof(char), *dstsize + srclen + 1 + *dstcapacity )); } strncat(*dst,src,srclen); *dstsize += srclen; return CBF_SUCCESS; } cbf_failnez(cbf_alloc((void **)dst,NULL,sizeof(char),1+srclen)); *dstcapacity = 1+srclen; strncpy(*dst,src,srclen); (*dst)[srclen] = '\0'; *dstsize = srclen; return CBF_SUCCESS; } /* Populate or rewrite a minicbf header in _array_data.header_contents */ int cbf_set_minicbf_header(cbf_handle cbf, cbf_handle datacbf, char ** log) { char * header; size_t header_capacity, header_size, log_capacity, log_size; const char * array_id; char buffer[MAX_SRCLEN+1]; int dimension[2], precedence[2]; const char * array_intensities_details; double thickness; double wavelength; double beam_center[4]; double twotheta; const char * detector_type; const char * detector_details; const char * detector_serial_number; cbf_detector detector_handle; cbf_goniometer goniometer_handle; double goniometer_start, goniometer_increment; double sample_detector_distance; int reserved=0, year, month, day, hour, minute, timezone; double second; size_t rank; const char * integration_time; const char * integration_period; double dtime; const char * overload; const char * threshold; const char * gain; const char * energy_range_low; const char * energy_range_high; double sample_detector_voffset; const char * flux; const char * filter_transmission; const char * polarizn_source_ratio; const char * oscillations; int result; CBF_UNUSED( precedence ); /* check the arguments */ if (!cbf || !datacbf) return CBF_ARGUMENT; if (log) { *log = NULL; log_capacity = log_size = 0; } header = NULL; header_capacity = header_size = 0; cbf_failnez(cbf_rewind_datablock(cbf)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); /* fprintf(stderr,"header:\n%s\n",header); */ /* Get the image dimensions */ if (cbf_find_category(cbf, "array_structure_list") || cbf_find_column(cbf,"array_id") || cbf_rewind_row(cbf) || cbf_get_value(cbf,&array_id) || !(array_id) ) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: " "unable to locate 'array_structure_list.array_id' \n")); } return CBF_FORMAT; } if (cbf_get_array_section_rank(cbf,array_id,&rank) || rank!=2) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: " "unable to locate image array rank \n")); } return CBF_FORMAT; } cbf_failnez(cbf_find_category(cbf, "array_structure_list")); cbf_failnez(cbf_find_column(cbf,"array_id")); cbf_failnez( cbf_rewind_row(cbf) ); dimension[0] = 0; dimension[1] = 0; while (cbf_find_nextrow (cbf, array_id) == 0) { int i, index; const char * direction[rank]; cbf_failnez (cbf_find_column (cbf, "index")) cbf_failnez (cbf_get_integervalue (cbf, &index)) i = index; cbf_failnez (cbf_find_column (cbf, "precedence")) cbf_failnez (cbf_get_integervalue (cbf, &index)) if (index >= 1 && index <= 2) precedence[i-1] = index; cbf_failnez (cbf_find_column (cbf, "dimension")) cbf_failnez (cbf_get_integervalue (cbf, &dimension[i-1])) cbf_failnez (cbf_find_column (cbf, "direction")) cbf_failnez (cbf_get_value (cbf, &direction[i-1])) cbf_failnez (cbf_find_column (cbf, "array_id")) } if (dimension [0] == 0 || dimension [1] == 0) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to locate image array dimensions' \n")); } return CBF_FORMAT; } /* Get the wavelength and distance */ if (cbf_get_wavelength (cbf, &wavelength) || wavelength <= 0.) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to locate wavelength' \n")); } return CBF_FORMAT; } goniometer_handle = NULL; if (cbf_construct_goniometer (cbf, &goniometer_handle)) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to locate goniomete axes \n")); } return CBF_FORMAT; } /* Pick up goniometer start and increment */ result = cbf_get_rotation_range(goniometer_handle, reserved, &goniometer_start, &goniometer_increment); if (result) { goniometer_start = 0.0; goniometer_increment = 0.0; if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "unable to get goniometer start and increment \n")); } } cbf_failnez(cbf_free_goniometer(goniometer_handle)); detector_handle = NULL; if (cbf_construct_detector (cbf, &detector_handle, 0 ) || cbf_get_beam_center (detector_handle, &beam_center[0], &beam_center[1], &beam_center[2], &beam_center[3])) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to locate beam center \n")); } return CBF_FORMAT; } if (!detector_handle || cbf_get_detector_distance(detector_handle, &sample_detector_distance)) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to locate sample_detector_distancer \n")); } return CBF_FORMAT; } /* Pick up 2 theta */ { double normal[3]; cbf_failnez(cbf_get_detector_normal(detector_handle,&(normal[0]), &(normal[1]), &(normal[2]))); twotheta = atan2(sqrt(normal[0]*normal[0]+normal[1]*normal[1]),-normal[2])*45./atan2(1.,1.); } cbf_failnez(cbf_free_detector(detector_handle)); /* Gather gain and overload */ if (cbf_find_category (cbf, "array_intensities") || cbf_find_column (cbf, "gain") || cbf_rewind_row (cbf) || cbf_get_value (cbf, &gain)) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "unable to locate gain' \n")); } gain = NULL; } if (cbf_find_category (cbf, "array_intensities") || cbf_find_column (cbf, "overload") || cbf_rewind_row (cbf) || cbf_get_value (cbf, &overload)) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "unable to locate overload' \n")); } overload = NULL; } /* Construct the Detector: PILATUS 6M S/N01 line */ if (cbf_find_category(cbf,"diffrn_detector")) { detector_type = NULL; detector_details = NULL; detector_serial_number = NULL; } else { const char * value; CBF_GET_COLUMN_VALUE(cbf,"type",value,detector_type); CBF_GET_COLUMN_VALUE(cbf,"details",value,detector_details); CBF_GET_COLUMN_VALUE(cbf,"serial_number",value,detector_serial_number); } if (!detector_type) { if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to find diffrn_detector.type\n")); } return CBF_FORMAT; } { const char * idp; size_t idpcount; idpcount = 0; idp = detector_type; while (*idp && idpcount < MAX_SRCLEN) { buffer[idpcount++] = toupper(*idp++); } buffer[idpcount] = '\0'; } cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Detector: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); if (detector_serial_number) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_serial_number,"SN",2))) { snp += 2; } else if ((snp=cbf_cistrnstr(detector_serial_number,"S/N",3))) { snp += 3; } else { snp = detector_serial_number; } while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } strcpy(buffer,"SN: "); snpdst = (char *)buffer; snpdst += 4; isnp = 4; while (*snp && isnp <= MAX_SRCLEN) { if (*snp != ' ' && *snp != '=' && *snp != ':' && *snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, " ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } else if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"SN",2))) { snp += 2; } else if ((snp=cbf_cistrnstr(detector_details,"S/N",3))) { snp += 3; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } strcpy(buffer,"SN: "); snpdst = (char *)buffer; snpdst += 4; isnp = 4; while (*snp && isnp <= MAX_SRCLEN) { if (*snp != ' ' && *snp != '=' && *snp != ':' && *snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, " ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); /* Get the date and time */ if (!cbf_get_datestamp(cbf,reserved, &year,&month,&day,&hour,&minute,&second,&timezone)) { sprintf(buffer,"# %04d-%02d-%02dT%02d:%02d:%06.3f\n", year, month, day, hour, minute, second); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } else { time_t time_t_time; struct tm * tm_time; size_t strftlen; tm_time = localtime (&time_t_time); strftlen = strftime(buffer,MAX_SRCLEN,"# %Y-%m-%dT%H:%M:%S",tm_time); buffer[MAX_SRCLEN] = '\0'; if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "unable to find date and time\n")); } cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); if (!strftlen) return CBF_FORMAT; } /* Get the pixel sizes Pixel_size 172e-6 m x 172e-6 m */ { double psizes[rank]; if (!cbf_get_array_section_pixel_sizes(cbf,array_id,rank,psizes)) { int psizex, psizey; psizex = (int)(psizes[0]*1.e3+.05); psizey = (int)(psizes[1]*1.e3 +.05); sprintf(buffer,"# Pixel_size %de-6 m x %de-6 m\n", psizex, psizey); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } else { if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: error: " "unable to find pixel size\n")); } return CBF_FORMAT; } } /* Set the Silicon sensor, thickness 0.000320 m line*/ if (!cbf_find_category(cbf,"diffrn_detector") &&!cbf_find_column(cbf,"layer_thickness") &&!cbf_get_doublevalue(cbf,&thickness) &&thickness > 0.) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Silicon sensor, thickness ")); sprintf(buffer,"%12.7f m\n", thickness*1.e-3); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } else if (detector_details) { const char * snp; char * snpdst; size_t isnp; /* fprintf(stderr,detector_details); */ if ((snp=cbf_cistrnstr(detector_details,"thickness",9))) { snp += 9; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') { *snpdst = *snp; snpdst++; snp++; } else break; isnp++; } *snpdst = '\n'; snpdst++; *snpdst = '\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Silicon sensor, thickness ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } else if (log) { cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "layer_thickness not provided\n")); } /* Set N_excluded_pixels = 293 line*/ if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"N_excluded_pixels",17))) { snp += 15; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# N_excluded_pixels = ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } /* Set Excluded_pixels: badpix_mask.tif line */ if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"Excluded_pixels:",16))) { snp += 16; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Excluded_pixels: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } /* Set Flat_field: FF_p2m0109_E15000_T7500_vrf_m0p30.tif line*/ if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"Flat_field",10))) { snp += 10; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Flat_field: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } /* Trim_file: p2m0109_E15000_T7500_vrf_m0p30.bin */ if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"Trim_file",9))) { snp += 9; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Trim_file: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } /* Image_path: /ramdisk/e13295/20120404/6D/BCW/1947_9_3/short/15kev/ */ if (detector_details) { const char * snp; char * snpdst; size_t isnp; if ((snp=cbf_cistrnstr(detector_details,"Image_path",10))) { snp += 10; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Image_path: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, buffer)); } } /* Set Exposure_time 0.095000 s line*/ if (!cbf_find_category(cbf,"diffrn_scan_frame") && !cbf_find_column(cbf,"integration_time") && !cbf_rewind_row(cbf) && !cbf_get_value(cbf,&integration_time) && (integration_time) && (*integration_time) ) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Exposure_time ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, integration_time)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "s \n")); } /* Set Exposure_period 0.100000 s line*/ if (!cbf_find_category(cbf,"diffrn_scan_frame") && !cbf_find_column(cbf,"integration_period") && !cbf_rewind_row(cbf) && !cbf_get_value(cbf,&integration_period) && (integration_period) && (*integration_period) ) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Exposure_period ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, integration_period)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, " s\n")); } /* Set Tau = 0 s line */ if (!cbf_find_category(cbf,"diffrn_detector") && !cbf_find_column(cbf,"dtime") && !cbf_rewind_row(cbf) && !cbf_get_doublevalue(cbf,&dtime) && dtime >=0.) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Tau = ")); sprintf(buffer,"%15.6g s\n",dtime/1.e6); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } else if (!cbf_find_category(cbf,"diffrn_radiation") && !cbf_find_column(cbf,"tau") && !cbf_rewind_row(cbf) && !cbf_get_doublevalue(cbf,&dtime) && dtime >=0.) { /* handle the older, misplaced tau */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Tau = ")); sprintf(buffer,"%15.6g s\n",dtime/1.e6); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } else { /* Dummy in a 0 */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Tau = 0 s\n")); if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "dummy Tau = 0 s used\n")); } } /* Set Count_cutoff 1048575 counts line */ if (!(overload)) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Count_cutoff ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, overload)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); } /* Set Threshold_setting 5000 eV line */ if (!cbf_find_category(cbf,"diffrn_detector") && !cbf_find_column(cbf,"threshold") && !cbf_rewind_row(cbf) && !cbf_get_value(cbf,&threshold) && (threshold) && (*threshold)) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Threshold_setting ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, threshold)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, " eV\n")); } /* Set Gain: 1.00 line */ if (!(gain)) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Gain: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, gain)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); } /* Set Gain_setting: low gain (vrf = -0.300) line */ if (!cbf_find_category(cbf,"array_intensities") &&!cbf_find_column(cbf,"details") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&array_intensities_details) &&(array_intensities_details) &&(*array_intensities_details)) { char * snp; char * snpdst; size_t isnp; if ((snp=(char *)cbf_cistrnstr(detector_details,"Gain_setting",12))) { snp += 12; } else { snp = NULL; } if (snp) { while (*snp) { if (*snp == ' ' || *snp == '=' || *snp == ':' || *snp == ',' || *snp == '(' || *snp == ')' || *snp == '#') snp++; else break; } snpdst = (char *)buffer; isnp = 0; while (*snp && isnp <= MAX_SRCLEN-1) { if (*snp != '\n' && *snp != '\r') *(snpdst++) = *(snp++); else break; isnp++; } snpdst[0]='\n'; snpdst++; snpdst[0]='\0'; snpdst++; cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Gain_setting: ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } } if (wavelength > 0.) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Wavelength ")); sprintf(buffer,"%9.4f A\n",wavelength); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } if (!cbf_find_category(cbf,"diffrn_detector") &&!cbf_find_column(cbf,"energy_range_low") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&energy_range_low) &&energy_range_low && (*energy_range_low) &&!cbf_find_column(cbf,"energy_range_high") &&!cbf_get_value(cbf,&energy_range_high) &&energy_range_high && (*energy_range_high) ) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Energy_range ( ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, energy_range_low)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, ", ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, energy_range_high)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, ") eV\n")); } else { /*Dummy in a Energy_range (0, 0) eV\n */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Energy_range (0, 0) eV\n")); if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "dummy Energy_range (0, 0) eV used\n")); } } /* Set Detector_distance 0.79988 m line */ if (sample_detector_distance > 0.) { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Detector_distance ")); sprintf(buffer,"%9.5f m\n",sample_detector_distance/1.e3); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } /* Set Detector_Voffset -0.00002 m line */ if (!cbf_find_category(cbf,"diffrn_measurement") &&!cbf_find_column(cbf,"sample_detector_voffset") &&!cbf_rewind_row(cbf) &&!cbf_get_doublevalue(cbf,&sample_detector_voffset)){ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Detector_Voffset ")); sprintf(buffer,"%14.5f m\n",sample_detector_voffset/1.e3); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } else { /*Dummy in a Voffset of 0 */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Detector_Voffset 0.00000 m\n")); if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "dummy Detector_Voffset 0 m used\n")); } } /* Set Beam_xy (1231.50, 1263.50) pixels line */ { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Beam_xy (")); sprintf(buffer,"%10.2f, ", beam_center[1]); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); sprintf(buffer,"%10.2f) pixels\n", beam_center[0]); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } /* Set Flux 0 ph/s line */ if (!cbf_find_category(cbf,"diffrn_radiation") &&!cbf_find_column(cbf,"flux") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&flux) && (flux) && (*flux)){ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Flux ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, flux)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, " ph/s\n")); } else { /*Dummy in a Flux of 0 */ if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "dummy Flux 0 ph/s used\n")); } } /* Set Filter_transmission 1.0000 line */ if (!cbf_find_category(cbf,"diffrn_radiation") &&!cbf_find_column(cbf,"filter_transmission") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&filter_transmission) && (filter_transmission) && (*filter_transmission)){ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Filter_transmission ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, filter_transmission)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); } /* Set Start_angle 0.0900 deg. */ { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Start_angle ")); sprintf(buffer,"%11.4f deg.\n", goniometer_start); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } /* Set Oscillation_axis X, CW line */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Oscillation_axis X, CW\n")); /* Set Angle_increment 0.0100 deg. line */ { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Angle_increment ")); sprintf(buffer,"%11.4f deg.\n", goniometer_increment); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } /* Set Detector_2theta 0.0000 deg. line */ { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Detector_2theta ")); sprintf(buffer,"%11.4f deg.\n", twotheta); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, cbf_trim_left(buffer))); } /* Set Polarization 0.950 line */ if (!cbf_find_category(cbf,"diffrn_radiation") &&!cbf_find_column(cbf,"polarizn_source_ratio") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&polarizn_source_ratio) && (polarizn_source_ratio) && (*polarizn_source_ratio)){ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Polarization ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, polarizn_source_ratio)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); } else { /* dummy in 0.000 */ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# Polarization 0.000\n")); if (log){ cbf_failnez(cbf_append_string(log,&log_capacity,&log_size, "cbf_set_minicbf_header: warning: " "dummy Polarization 0.000 used\n")); } } /* For each goniometer angle ANGLE set ANGLE 0.0000 deg. line set ANGLE_increment 0.0000 deg. line removing GONIOMETER_ prefixes */ /* Set N_oscillations 1 line */ if (!cbf_find_category(cbf,"diffrn_scan_frame") &&!cbf_find_column(cbf,"oscillations") &&!cbf_rewind_row(cbf) &&!cbf_get_value(cbf,&oscillations) && (oscillations) && (*oscillations)){ cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# N_oscillations ")); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, oscillations)); cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "\n")); } else { cbf_failnez(cbf_append_string(&header,&header_capacity,&header_size, "# N_oscillations 1\n")); } /* Write the header to the CBF */ if ((!cbf_require_category(datacbf, "array_data")) && !cbf_require_column(datacbf,"header_convention") && !cbf_rewind_row(datacbf)) { cbf_failnez(cbf_set_value(datacbf,"PILATUS_1.4")); } if ((!cbf_require_category(datacbf, "array_data")) && !cbf_require_column(datacbf,"header_contents") && !cbf_rewind_row(datacbf)) { cbf_failnez(cbf_set_value(datacbf,header)); } cbf_failnez(cbf_free_text((const char * *)&header,NULL)); return CBF_SUCCESS; } #ifdef __cplusplus } #endif