/********************************************************************** * cbf2nexus.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 * * * ********************************************************************** * * * 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 * * * ********************************************************************** * * * 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 #include #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 /* The 'strdup' function isn't available when compiling with -ansi on GCC, so provide an alternative. */ static char * _cbf_strdup(const char *s) { return s ? strcpy(malloc(sizeof(char)*(1+strlen(s))),s) : 0; } int main (int argc, char *argv []) { int error = CBF_SUCCESS; cbf_getopt_handle opts = NULL; size_t cifid = 0; int h5_write_flags = 0; int list = 0; int noCBFnames = 0; int update = 0; const char ** const cifin = memset(malloc(argc*sizeof(char*)),0,argc*sizeof(char*)); const char * scan_id = NULL; const char * sample_id = NULL; const char *hdf5out = NULL; const char *group = NULL; const char * datablock = NULL; const char * scan = NULL; /* 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):g(group):o(output):u(update):Z(register):\x03(experiment_id):\x04(sample_id):\x05(datablock):\x06(scan):\x01(list)\x02(no-list)\x07(CBFnames)\0x08(noCBFnames)" ))) { fprintf(stderr,"Could not parse arguments.\n"); } else { int errflg = 0; if (0) { /* debug the option processing code */ const cbf_getopt_optstruct * optstruct = 0; for (optstruct = opts->optstructs; optstruct != opts->optstructs+opts->optstructs_size; ++optstruct) { printf("(%c, %s, %s),\n", optstruct->optopt, optstruct->optstr, optstruct->optval); } } /* successful so far, try to make sense of the options */ if (!cbf_rewind_getopt_option(opts)) { int c = 0; const char * optarg = NULL; const char * optstr = NULL; for(; !cbf_get_getopt_data(opts,&c,NULL,&optstr,&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:"")) { 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:"")) { 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 'g': { /* group within output file where data should be stored */ if (group) ++errflg; else group = optarg; break; } case 'u': { /*update mode output*/ update = 1; } 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 '\x01': { if (list) errflg++; list = 1; break; } case '\x02': { if (list) errflg++; list = -1; break; } case '\x03': { if (scan_id) errflg++; scan_id = optarg; break; } case '\x04': { if (sample_id) errflg++; sample_id = optarg; break; } case '\x05': { if (datablock) errflg++; datablock = optarg; break; } case '\x06': { if (scan) errflg++; scan = optarg; break; } case '\x07': { if (noCBFnames) ++errflg; noCBFnames = -1; break; } case '\x08': { if (noCBFnames) ++errflg; noCBFnames = 1; break; } case 0: { /* input file */ cifin[cifid++] = optarg; break; } default: { ++errflg; break; } } } } /* check for missing data */ if (!hdf5out) { fprintf(stderr,"No output file given.\n"); ++errflg; } if (!cifid) { fprintf(stderr,"No input files given.\n"); ++errflg; } if (errflg) { fprintf(stderr, "Usage:\n\t%s [options] " "[-o|--output]|[-u|--update] output_nexus input_cbf_files...\n" "Options:\n" "\t-c|--compression cbf|none|zlib (default: none)\n" "\t-g|--group output_group (default: 'entry')\n" "\t-Z|--register manual|plugin (default: plugin)\n" "\t--datablock datablock_name\n" "\t--scan scan_name\n" "\t--experiment_id unique_experiment_id\n" "\t--sample_id unique_sample_id\n" "\t--[no-]list\n" "'datablock' should be the name of the datablock to use, or omitted to use all.\n" "'scan' should be the name of the scan to convert, or may be omitted if there is only one scan.\n" "'experiment_id' should be a unique identifier for the scan.\n" "'sample_id' should be a unique identifier for the sample.\n" "'list' and 'no-list' will determine whether the list of items that have been recognised during conversion is printed or not.\n", argv[0]); error |= CBF_ARGUMENT; } } /* If I could read the arguments then attempt to use them */ if (CBF_SUCCESS == error) { cbf_h5handle h5out = NULL; size_t f = 0; /* prepare the output file */ if( (update && CBF_SUCCESS != (error |= cbf_create_h5handle2u(&h5out,hdf5out))) ||((!update) && 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 { if (list > 0) { h5out->logfile = stdout; } else { h5out->logfile = NULL; } h5out->flags = h5_write_flags; if (noCBFnames >= 0) { h5out->flags |= CBF_H5_CBFNONAMES; } else { h5out->flags &= ~CBF_H5_CBFNONAMES; } h5out->scan_id = _cbf_strdup(scan_id); h5out->sample_id = _cbf_strdup(sample_id); #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((size_t)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_FILEOPEN; } /* 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_cbf2nx(cif, h5out, datablock, scan, list); /* 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); } { /* 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); error |= cbf_free_getopt_handle(opts); return CBF_SUCCESS==error ? 0 : 1; }