/********************************************************************** * minicbf2nexus.c by J. Sloan of Diamond Light Source * * * * CBFlib Version 0.9.3 30 May 2013 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2013 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 * **********************************************************************/ #include #include #include #include #include #include #include #ifdef CBF_USE_ULP #include #endif #include "cbf.h" #include "cbf_simple.h" #include "img.h" #include "cbf_string.h" #include "cbf_copy.h" #include "cbf_hdf5.h" #include "cbf_getopt.h" #ifndef UINT64_MAX #define NO_UINT64_TYPE #endif #define C2CBUFSIZ 8192 #ifdef __MINGW32__ #define NOMKSTEMP #define NOTMPDIR #endif int local_exit (int status); int outerror(int err); int outerror(int err) { if ((err&CBF_FORMAT)==CBF_FORMAT) fprintf(stderr, " cif2cbf: The file format is invalid.\n"); if ((err&CBF_ALLOC)==CBF_ALLOC) fprintf(stderr, " cif2cbf Memory allocation failed.\n"); if ((err&CBF_ARGUMENT)==CBF_ARGUMENT) fprintf(stderr, " cif2cbf: Invalid function argument.\n"); if ((err&CBF_ASCII)==CBF_ASCII) fprintf(stderr, " cif2cbf: The value is ASCII (not binary).\n"); if ((err&CBF_BINARY)==CBF_BINARY) fprintf(stderr, " cif2cbf: The value is binary (not ASCII).\n"); if ((err&CBF_BITCOUNT)==CBF_BITCOUNT) fprintf(stderr, " cif2cbf: The expected number of bits does" " not match the actual number written.\n"); if ((err&CBF_ENDOFDATA)==CBF_ENDOFDATA) fprintf(stderr, " cif2cbf: The end of the data was reached" " before the end of the array.\n"); if ((err&CBF_FILECLOSE)==CBF_FILECLOSE) fprintf(stderr, " cif2cbf: File close error.\n"); if ((err&CBF_FILEOPEN)==CBF_FILEOPEN) fprintf(stderr, " cif2cbf: File open error.\n"); if ((err&CBF_FILEREAD)==CBF_FILEREAD) fprintf(stderr, " cif2cbf: File read error.\n"); if ((err&CBF_FILESEEK)==CBF_FILESEEK) fprintf(stderr, " cif2cbf: File seek error.\n"); if ((err&CBF_FILETELL)==CBF_FILETELL) fprintf(stderr, " cif2cbf: File tell error.\n"); if ((err&CBF_FILEWRITE)==CBF_FILEWRITE) fprintf(stderr, " cif2cbf: File write error.\n"); if ((err&CBF_IDENTICAL)==CBF_IDENTICAL) fprintf(stderr, " cif2cbf: A data block with the new name already exists.\n"); if ((err&CBF_NOTFOUND)==CBF_NOTFOUND) fprintf(stderr, " cif2cbf: The data block, category, column or" " row does not exist.\n"); if ((err&CBF_OVERFLOW)==CBF_OVERFLOW) fprintf(stderr, " cif2cbf: The number read cannot fit into the " "destination argument.\n The destination has been set to the nearest value.\n"); if ((err& CBF_UNDEFINED)==CBF_UNDEFINED) fprintf(stderr, " cif2cbf: The requested number is not defined (e.g. 0/0).\n"); if ((err&CBF_NOTIMPLEMENTED)==CBF_NOTIMPLEMENTED) fprintf(stderr, " cif2cbf: The requested functionality is not yet implemented.\n"); if ((err&CBF_H5ERROR)==CBF_H5ERROR) fprintf(stderr, " cif2cbf: HDF5 API error.\n"); return 0; } #undef cbf_failnez #undef cbf_onfailnez #ifndef __FILE__ #define cbf_failnez(x) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d \n", err); outerror(err); local_exit (-1); }} #define cbf_onfailnez(x,c) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d \n", err); \ { c; } outerror(err); local_exit (-1); }} #else #ifndef __func__ #define cbf_failnez(x) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d at %s:%d\n", err,__FILE__,__LINE__); outerror(err); local_exit (-1); }} #define cbf_onfailnez(x,c) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d at %s:%d\n", err,__FILE__,__LINE__); \ { c; } outerror(err); local_exit (-1); }} #else #define cbf_failnez(x) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d at %s:%d(%s)\n", err,__FILE__,__LINE__,__func__); outerror(err); local_exit (-1); }} #define cbf_onfailnez(x,c) {int err; err = (x); if (err) { fprintf (stderr, \ "\nCBFlib error %d at %s:%d(%s)\n", err,__FILE__,__LINE__,__func__); \ { c; } outerror(err); local_exit (-1); }} #endif #endif int main (int argc, char *argv []) { int error = CBF_SUCCESS; cbf_getopt_handle opts; size_t cifid = 0; unsigned long int h5_write_flags = 0L; const char ** const cifin = memset(malloc(argc*sizeof(char*)),0,argc*sizeof(char*)); const char *hdf5out = NULL; const char *config = NULL; const char *group = NULL; cbf_config_t * const vec = cbf_config_create(); /* Attempt to read the arguments */ if (CBF_SUCCESS != (error |= cbf_make_getopt_handle(&opts))) { fprintf(stderr,"Could not create a 'cbf_getopt' handle.\n"); } else if (CBF_SUCCESS != (error |= cbf_getopt_parse(opts, argc, argv, "c(compression):C(config):g(group):o(output):Z(register):"))) { fprintf(stderr,"Could not parse arguments.\n"); } else { int errflg = 0; if (!cbf_rewind_getopt_option(opts)) { int c = 0; const char * optarg = NULL; for(; !cbf_get_getopt_data(opts,&c,NULL,NULL,&optarg); cbf_next_getopt_option(opts)) { switch (c) { case 'c': { /* compression */ if (!cbf_cistrcmp("zlib",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_ZLIB; } else if (!cbf_cistrcmp("cbf",optarg?optarg:"") ||!cbf_cistrcmp("cbf_nibble_offset",optarg?optarg:"") ||!cbf_cistrcmp("cbf-nibble-offset",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_CBF|CBF_NIBBLE_OFFSET; } else if (!cbf_cistrcmp("cbf_byte_offset",optarg?optarg:"") ||!cbf_cistrcmp("cbf-byte-offset",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_CBF|CBF_BYTE_OFFSET; } else if (!cbf_cistrcmp("lz4",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_LZ4; } else if (!cbf_cistrcmp("lz4**2",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_LZ4_2; } else if (!cbf_cistrcmp("bslz4",optarg?optarg:"")) { h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); h5_write_flags |= CBF_H5COMPRESSION_BSLZ4; } else if (!cbf_cistrcmp("none",optarg?optarg:"")) { /* remove any previously set (system default?) compressions */ h5_write_flags &= ~(CBF_COMPRESSION_MASK|CBF_FLAG_MASK); } else ++errflg; break; } case 'C': { /* config file */ if (config) errflg++; else config = optarg; break; } case 'g': { /* group within output file where data should be stored */ if (group) errflg++; else group = optarg; break; } case 'o': { /* output file */ if (hdf5out) errflg++; else hdf5out = optarg; break; } case 'Z': { /* automatic or manual filter registration? */ if (cbf_cistrcmp(optarg?optarg:"","manual") == 0) { h5_write_flags |= CBF_H5_REGISTER_COMPRESSIONS; } else if (cbf_cistrcmp(optarg?optarg:"","plugin") == 0) { h5_write_flags &= ~CBF_H5_REGISTER_COMPRESSIONS; } else { errflg++; } break; } case 0: { /* input file */ if (NULL != optarg) cifin[cifid++] = optarg; break; } default: { errflg++; break; } } } } if (!hdf5out) { fprintf(stderr,"No output file given.\n"); ++errflg; } if (!cifid) { fprintf(stderr,"No input files given.\n"); ++errflg; } if (!config) { fprintf(stderr,"No config file given.\n"); ++errflg; } if (errflg) { fprintf(stderr, "Usage:\n\t%s [options] -C|--config config_file -o|--output output_nexus input_minicbf_files...\n" "Options:\n" "\t-c|--compression cbf|cbf-byte-offset|lz4|lz4**2|bslz4|zlib|none (default: none)\n" "\t-g|--group output_group (default: 'entry')\n" "\t-Z|--register manual|plugin (default: plugin)\n" "These options are NOT case-sensitive.\n", argv[0]); error |= CBF_ARGUMENT; } } /* parse the config file */ if (CBF_SUCCESS == error) { int configError = cbf_configError_success; FILE * const configFile = fopen(config, "r"); configError = cbf_config_parse(configFile, stderr, vec); fclose(configFile); if (cbf_configError_success != configError) { fprintf(stderr, "config parsing error: %s\n", cbf_config_strerror(configError)); error |= CBF_UNDEFINED; } } if (CBF_SUCCESS == error) { size_t f = 0; /* prepare the output file */ cbf_h5handle h5out = NULL; if(CBF_SUCCESS != (error |= cbf_create_h5handle2(&h5out,hdf5out))) { fprintf(stderr,"Couldn't open the HDF5 file '%s'.\n", hdf5out); } else if (CBF_SUCCESS != (error |= cbf_h5handle_require_entry_definition(h5out,0,group,"NXmx","1.2",0))) { fprintf(stderr,"Couldn't create an NXentry group in the HDF5 file '%s'.\n", hdf5out); } else { h5out->flags = h5_write_flags; } #ifdef CBF_USE_ULP /* set up some parameters for comparing floating point numbers */ h5out->cmp_double_as_float = 0; h5out->float_ulp = 4; #ifndef NO_UINT64_TYPE h5out->double_ulp = 4; #endif #endif for (f = 0; CBF_SUCCESS == error && f != cifid; ++f) { cbf_handle cif = NULL; #ifdef NOTMPDIR char ciftmp[] = "cif2cbfXXXXXX"; #else char ciftmp[] = "/tmp/cif2cbfXXXXXX"; int ciftmpfd; #endif /* Get suitable file - reading from stdin to a temporary file if needed */ if (!(cifin[f]) || strcmp(cifin[f]?cifin[f]:"","-") == 0) { FILE *file = NULL; int nbytes; char buf[C2CBUFSIZ]; #ifdef NOMKSTEMP if (mktemp(ciftmp) == NULL ) { fprintf(stderr,"%s: Can't create temporary file name %s.\n%s\n", argv[0], ciftmp,strerror(errno)); error |= CBF_FILEOPEN; } else if ((file = fopen(ciftmp,"wb+")) == NULL) { fprintf(stderr,"Can't open temporary file %s.\n%s\n", ciftmp,strerror(errno)); error |= CBF_FILEOPEN; } #else if ((ciftmpfd = mkstemp(ciftmp)) == -1 ) { fprintf(stderr,"%s: Can't create temporary file %s.\n%s\n", argv[0], ciftmp,strerror(errno)); error |= CBF_FILEOPEN; } else if ((file = fdopen(ciftmpfd, "w+")) == NULL) { fprintf(stderr,"Can't open temporary file %s.\n%s\n", ciftmp,strerror(errno)); error |= CBF_FILEOPEN; } #endif while ((nbytes = fread(buf, 1, C2CBUFSIZ, stdin))) { if(nbytes != fwrite(buf, 1, nbytes, file)) { fprintf(stderr,"Failed to write %s.\n", ciftmp); error |= CBF_FILEWRITE; break; } } fclose(file); cifin[f] = ciftmp; } /* Read the file */ if (CBF_SUCCESS == error) { /* start timing */ clock_t a = clock(), b; /* prepare the file */ FILE * in = NULL; if (NULL == (in = fopen(cifin[f], "rb"))) { fprintf (stderr,"Couldn't open the input CIF file '%s': %s\n", cifin[f], strerror(errno)); error |= CBF_FILEREAD; } /* ensure temporary file is removed when the program closes */ if (ciftmp == cifin[f]) { if (unlink(ciftmp)) { fprintf(stderr,"Can't unlink temporary file '%s': %s\n", ciftmp,strerror(errno)); error |= CBF_FILECLOSE; } } if (CBF_SUCCESS == error) { /* make the handle */ if (CBF_SUCCESS != (error |= cbf_make_handle(&cif))) { fprintf(stderr,"Failed to create handle for input_cif\n"); error |= CBF_ALLOC; } else if (CBF_SUCCESS != (error |= cbf_read_file(cif, in, MSG_DIGEST))) { fprintf(stderr,"Couldn't read the input CIF file '%s': %s\n", cifin[f], cbf_strerror(error)); error |= CBF_FILEREAD; } else { /* ensure the file can be cleaned up after any errors but is not accidentally closed */ in = NULL; } } /* clean up local variables */ if (in) fclose(in); /* stop timing */ b = clock (); printf("Time to read '%s': %.3fs\n", cifin[f], ((float)(b - a))/CLOCKS_PER_SEC); } /* Do the conversion */ if (CBF_SUCCESS == error) { /* start timing */ clock_t a = clock(), b; error |= cbf_write_minicbf_h5file(cif, h5out, vec); /* stop timing */ b = clock (); printf("Time to convert '%s': %.3fs\n", cifin[f], ((float)(b - a))/CLOCKS_PER_SEC); } /* Clean up */ if (cif) cbf_free_handle(cif); cbf_failnez(error); } { /* Write the file/close the handle */ /* start timing */ clock_t a = clock(), b; /* clean up cbf handles */ error |= cbf_free_h5handle(h5out); /* stop timing */ b = clock (); printf("Time to write '%s': %.3fs\n", hdf5out, ((float)(b - a))/CLOCKS_PER_SEC); } /******************************************************************************************************/ } /* Cleanup */ free(cifin); cbf_config_free(vec); error |= cbf_free_getopt_handle(opts); return CBF_SUCCESS==error ? 0 : 1; } int local_exit (int status) { exit(status); return 1; /* avoid warnings */ }