diff options
Diffstat (limited to 'tools/misc')
| -rw-r--r-- | tools/misc/h5import.c | 152 | ||||
| -rw-r--r-- | tools/misc/pdb2hdf.c | 527 |
2 files changed, 0 insertions, 679 deletions
diff --git a/tools/misc/h5import.c b/tools/misc/h5import.c deleted file mode 100644 index 4192821..0000000 --- a/tools/misc/h5import.c +++ /dev/null @@ -1,152 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Robb Matzke <matzke@llnl.gov> - * Thursday, June 11, 1998 - * - * Purpose: Create an hdf5 file with a 1d dataset of uint8. - */ - -/* See H5private.h for how to include system headers */ -#include <hdf5.h> -#ifdef H5_STDC_HEADERS -# include <fcntl.h> -# include <string.h> -# include <stdlib.h> -# include <stdio.h> -#endif - -#ifdef H5_HAVE_UNISTD_H -# include <sys/types.h> -# include <unistd.h> -#endif - -#ifdef H5_HAVE_SYS_STAT_H -# include <sys/stat.h> -#endif - -#ifdef WIN32 -# include <io.h> -#endif - - -/*------------------------------------------------------------------------- - * Function: usage - * - * Purpose: Print a usage message and exit with non-zero status - * - * Return: never returns - * - * Programmer: Robb Matzke - * Thursday, June 11, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static void -usage (const char *argv0) -{ - fprintf (stderr, "Usage: %s -f HDF5-FILE FILES...\n", argv0); - exit (1); -} - - -/*------------------------------------------------------------------------- - * Function: main - * - * Purpose: - * - * Return: Success: 0 - * - * Failure: 1 - * - * Programmer: Robb Matzke - * Thursday, June 11, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -int -main (int argc, char *argv[]) -{ - hid_t file, space=-1, dset=-1; - const char *output_name, *dset_name; - int argno, fd=-1; - hsize_t size[1]; - struct stat sb; - - /* Parse arguments */ - if (argc<4) usage (argv[0]); - if (strcmp (argv[1], "-f")) usage (argv[0]); - output_name = argv[2]; - - /* create the file */ - H5E_BEGIN_TRY { - if ((file = H5Fcreate (output_name, H5F_ACC_EXCL, - H5P_DEFAULT, H5P_DEFAULT))<0 && - (file = H5Fopen (output_name, H5F_ACC_RDWR, H5P_DEFAULT)<0)) { - fprintf (stderr, "%s: unable to create or open hdf5 file\n", - output_name); - exit (1); - } - } H5E_END_TRY; - - /* process files from command-line */ - for (argno=3; argno<argc; argno++) { - - /* Open the file */ - if ((dset_name=strrchr (argv[argno], '/'))) dset_name++; - else dset_name = argv[argno]; - fprintf (stderr, "%s\n", dset_name); - if ((fd=open (argv[argno], O_RDONLY))<0) { - perror (argv[argno]); - goto next; - } - if (fstat (fd, &sb)<0) { - perror (argv[argno]); - goto next; - } - - /* Data space */ - size[0] = sb.st_size; - if ((space = H5Screate_simple (1, size, size))<0) goto next; - - /* Dataset */ - if ((dset=H5Dcreate (file, dset_name, H5T_NATIVE_SCHAR, - space, H5P_DEFAULT))<0) goto next; - - - - next: - if (fd>=0) close (fd); - fd = -1; - H5E_BEGIN_TRY { - if (space>=0) { - H5Sclose (space); - space = -1; - } - if (dset>=0) { - H5Dclose (dset); - dset = -1; - } - } H5E_END_TRY; - } - - /* Close the file */ - H5Fclose (file); - return 0; -} diff --git a/tools/misc/pdb2hdf.c b/tools/misc/pdb2hdf.c deleted file mode 100644 index c3e93aa..0000000 --- a/tools/misc/pdb2hdf.c +++ /dev/null @@ -1,527 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Robb Matzke <matzke@llnl.gov> - * Tuesday, October 12, 1999 - * - * Purpose: Creates an HDF5 file from a PDB file. The raw data can be - * left in the PDB file, creating an HDF5 file that contains - * meta data that points into the PDB file. - */ -#include <assert.h> -#include <stdio.h> -#include <string.h> - -#include "hdf5.h" - -/* Strictly speaking, the "ifdef H5_HAVE_PDB_H" is unnecessary, since this - * file won't be compiled unless PDB is available (see the Makefile.in for - * this directory, as well as the PDB detection in the main configure.in). - * However, the Intel C compiler, v7.1, seems to have problems generating - * correct dependencies with the -MG flag when include files are not found - * and having this ifdef here removes the PDB headers from its consideration. - * QAK - 2004/02/07 - */ -#ifdef H5_HAVE_PDB_H - -#include "pdb.h" -#include "score.h" - -/* - * libsilo renames all the PDB functions. However, this source files uses - * their documented names, so we have #define's to translate them to Silo - * terminology. - */ -#ifdef H5_HAVE_LIBSILO -# define PD_open lite_PD_open -# define PD_close lite_PD_close -# define PD_ls lite_PD_ls -# define PD_cd lite_PD_cd -# define PD_inquire_entry lite_PD_inquire_entry -# define PD_read lite_PD_read -# define _PD_fixname _lite_PD_fixname -# define _PD_rl_defstr _lite_PD_rl_defstr -# define SC_free lite_SC_free -#endif - -static int verbose_g = 0; /*verbose output? */ -static int cached_g = 0; /*use core file driver? */ - - -/*------------------------------------------------------------------------- - * Function: usage - * - * Purpose: Print a usage message. - * - * Return: void - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static void -usage(const char *arg0) -{ - char *progname; - - if ((progname=strrchr(arg0, '/')) && progname[1]) progname++; - else progname = arg0; - - fprintf(stderr, "\ -usage: %s [OPTIONS] [PDBFILE ...]\n\ - OPTIONS\n\ - -h, -?, --help Print a usage message and exit\n\ - -c, --cached Cache all data in memory before writing the output\n\ - -v, --verbose Print the name of each object processed\n\ - -V, --version Show the version number of this program\n\ -\n\ - The options and PDB file names may be interspersed and are processed from\n\ - left to right.\n\ -\n\ - The name of the HDF5 file is generated by taking the basename of the PDB\n\ - file and replacing the last extension (or appending if no extension) with\n\ - the characters \".h5\". For example, \"/tmp/test/eos.data\" would result\n\ - in an HDF5 file called \"eos.h5\" in the current directory.\n", - progname); - -} - - -/*------------------------------------------------------------------------- - * Function: version - * - * Purpose: Print the version number. - * - * Return: void - * - * Programmer: Robb Matzke - * Friday, October 15, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static void -version(const char *arg0) -{ - const char *progname; - - if ((progname=strrchr(arg0, '/')) && progname[1]) progname++; - else progname = arg0; - print_version(progname); -} - - -/*------------------------------------------------------------------------- - * Function: fix_name - * - * Purpose: Given a PDB file name create the corresponding HDF5 file - * name. This is done by taking the base name of the PDB file - * and replacing (or appending) the last extension with ".h5". - * - * Return: Success: HDF_NAME - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static char * -fix_name(const char *pdb_name, char *hdf_name, size_t size) -{ - char *s; - const char *ext; - - if (!pdb_name || !hdf_name) return NULL; - if ((s=strrchr(pdb_name, '/'))) pdb_name = s; - if (NULL==(ext=strrchr(pdb_name, '.'))) ext = pdb_name + strlen(pdb_name); - if ((size_t)((ext-pdb_name)+4) > size) return NULL; /*overflow*/ - memcpy(hdf_name, pdb_name, ext-pdb_name); - strcpy(hdf_name+(ext-pdb_name), ".h5"); - return hdf_name; -} - - -/*------------------------------------------------------------------------- - * Function: fix_type - * - * Purpose: Given a PDB datatype return a corresponding hdf5 datatype. - * The hdf5 datatype should be closed when the caller is - * finished using it. - * - * Return: Success: HDF5 datatype - * - * Failure: negative - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hid_t -fix_type(PDBfile *pdb, const char *s) -{ - hid_t type = -1; - defstr *d = _lite_PD_lookup_type((char*)s, pdb->chart); - - /* PDB checking */ - assert(d); - assert(d->size>0); - if (d->onescmp) return -1; - - - if (!strcmp(s, "char")) { - /* - * Character datatypes. Use whatever sign the native system uses by - * default. - */ - type = H5Tcopy(H5T_NATIVE_CHAR); - - } else if (!strcmp(s, "integer")) { - /* - * Integer datatypes. PDB supports various sizes of signed or - * unsigned integers. - */ - type = H5Tcopy(d->unsgned?H5T_NATIVE_UINT:H5T_NATIVE_INT); - H5Tset_size(type, d->size); - H5Tset_precision(type, 8*d->size); - assert(NORMAL_ORDER==d->order_flag || REVERSE_ORDER==d->order_flag); - H5Tset_order(type, - NORMAL_ORDER==d->order_flag?H5T_ORDER_BE:H5T_ORDER_LE); - - } else if (!strcmp(s, "float") || !strcmp(s, "double")) { - /* - * Floating-point datatypes - */ - size_t nbits, spos, epos, esize, mpos, msize; - - type = H5Tcopy(H5T_NATIVE_FLOAT); - H5Tset_size(type, d->size); - H5Tset_precision(type, 8*d->size); - assert(d->order); - H5Tset_order(type, 1==d->order[0]?H5T_ORDER_BE:H5T_ORDER_LE); - - /* - * format[0] = # of bits per number - * format[1] = # of bits in exponent - * format[2] = # of bits in mantissa - * format[3] = start bit of sign - * format[4] = start bit of exponent - * format[5] = start bit of mantissa - * format[6] = high order mantissa bit (CRAY needs this) - * format[7] = bias of exponent - */ - assert(d->format && d->format[0] == 8*d->size); - nbits = d->format[0]; - spos = nbits - (d->format[3]+1); - esize = d->format[1]; - epos = nbits - (d->format[4]+esize); - msize = d->format[2]; - mpos = nbits - (d->format[5]+msize); - H5Tset_fields(type, spos, epos, esize, mpos, msize); - H5Tset_ebias(type, d->format[7]); - } - return type; -} - - -/*------------------------------------------------------------------------- - * Function: fix_space - * - * Purpose: Convert a PDB dimension list into an HDF5 data space. - * - * Return: Success: HDF5 data space - * - * Failure: negative - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static hid_t -fix_space(const dimdes *dim) -{ - hsize_t size[H5S_MAX_RANK]; - int rank; - - for (rank=0; rank<H5S_MAX_RANK && dim; rank++, dim=dim->next) { - size[rank] = dim->number; - } - if (rank>=H5S_MAX_RANK) return -1; - return H5Screate_simple(rank, size, NULL); -} - - -/*------------------------------------------------------------------------- - * Function: fix_external - * - * Purpose: Sets the external file information for a dataset creation - * property list based on information from PDB. - * - * Return: Success: non-negative - * - * Failure: negative - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static int -fix_external(hid_t dcpl, const char *pdb_file_name, long nelmts, - hsize_t elmt_size, symblock *block) -{ - int i; - - for (i=0; nelmts>0; i++) { - hsize_t nbytes = block[i].number * elmt_size; - H5Pset_external(dcpl, pdb_file_name, block[i].diskaddr, nbytes); - nelmts -= block[i].number; - } - return 0; -} - - -/*------------------------------------------------------------------------- - * Function: traverse - * - * Purpose: Traverse the current working directory of the PDB file. - * - * Return: Success: 0 - * - * Failure: -1 - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static int -traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf) -{ - int nitems, i, in_subdir=FALSE; - char **list=NULL; - hid_t group=-1, h_type=-1, h_space=-1, dset=-1, dcpl=-1; - hsize_t elmt_size; - const syment *ep=NULL; - - if (NULL==(list=PD_ls(pdb, ".", NULL, &nitems))) { - fprintf(stderr, "cannot obtain PDB directory contents\n"); - goto error; - } - - for (i=0; i<nitems; i++) { - ep = PD_inquire_entry(pdb, list[i], TRUE, NULL); - if (verbose_g) { - printf("%s %s\n", _PD_fixname(pdb, list[i]), ep->type); - fflush(stdout); - } - - - if ('/'==list[i][strlen(list[i])-1]) { - /* - * This is a PDB directory. Make a corresponding HDF5 group and - * traverse into that PDB directory and HDF5 group - */ - if ((group=H5Gcreate(hdf, list[i], 0))<0) { - fprintf(stderr, "cannot create HDF group %s\n", list[i]); - goto error; - } - if (!PD_cd(pdb, list[i])) { - fprintf(stderr, "cannot cd into PDB directory %s\n", list[i]); - goto error; - } else { - in_subdir = TRUE; - } - - traverse(pdb, pdb_file_name, group); - if (!PD_cd(pdb, "..")) { - fprintf(stderr, "cannot traverse out of PDB %s\n", list[i]); - goto error; - } - H5Gclose(group); - - } else { - /* This is some non-directory PDB object */ - - /* Create an HDF5 datatype from the PDB type */ - if ((h_type=fix_type(pdb, ep->type))<0) { - fprintf(stderr, "cannot create datatype for %s (%s)\n", - list[i], ep->type); - continue; - } - elmt_size = H5Tget_size(h_type); - - /* Create an HDF5 dataspace from the PDB dimensions */ - if ((h_space=fix_space(ep->dimensions))<0) { - fprintf(stderr, "cannot create datatype for %s\n", list[i]); - continue; - } - - /* Create pointers to the external PDB data */ - dcpl = H5Pcreate(H5P_DATASET_CREATE); - fix_external(dcpl, pdb_file_name, ep->number, elmt_size, - ep->blocks); - - /* Create the dataset */ - if ((dset=H5Dcreate(hdf, list[i], h_type, h_space, dcpl))<0) { - fprintf(stderr, "cannot create dataset for %s\n", list[i]); - } - - H5Pclose(dcpl); - H5Dclose(dset); - H5Sclose(h_space); - H5Tclose(h_type); - } - - } - - for (i=0; i<nitems; i++) { - SC_free(list[i]); - } - SC_free(list); - return 0; - - error: - if (group>=0) H5Gclose(group); - if (in_subdir) PD_cd(pdb, ".."); - if (list) { - for (i=0; i<nitems; i++) { - SC_free(list[i]); - } - SC_free(list); - } - return -1; -} - - -/*------------------------------------------------------------------------- - * Function: main - * - * Purpose: Create an HDF5 file from a PDB file. - * - * Return: Success: 0 - * - * Failure: non-zero - * - * Programmer: Robb Matzke - * Tuesday, October 12, 1999 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -int -main(int argc, char *argv[]) -{ - int argno; - char _hdf_name[512], *hdf_name, *pdb_name, *s; - PDBfile *pdb; - hid_t hdf, fapl; - - /* Print a help message if called with no arguments */ - if (1==argc) { - usage(argv[0]); - exit(1); - } - - /* Process arguments in order; switches interspersed with files */ - for (argno=1; argno<argc; argno++) { - if (!strcmp("--help", argv[argno])) { - usage(argv[0]); - exit(1); - } else if (!strcmp("--verbose", argv[argno])) { - verbose_g++; - } else if (!strcmp("--cached", argv[argno])) { - cached_g++; - } else if (!strcmp("--version", argv[argno])) { - version(argv[0]); - } else if ('-'==argv[argno][0] && '-'!=argv[argno][1]) { - for (s=argv[argno]+1; *s; s++) { - switch (*s) { - case '?': - case 'h': /*--help*/ - usage(argv[0]); - exit(0); - case 'c': /*--cached*/ - cached_g++; - break; - case 'v': /*--verbose*/ - verbose_g++; - break; - case 'V': /*--version*/ - version(argv[0]); - break; - default: - usage(argv[0]); - exit(1); - } - } - } else if ('-'==argv[argno][0]) { - usage(argv[0]); - exit(1); - } else { - /* This must be a file name. Process it. */ - fapl = H5Pcreate(H5P_FILE_ACCESS); - if (cached_g) H5Pset_fapl_core(fapl, 1024*1024, TRUE); - - pdb_name = argv[argno]; - hdf_name = fix_name(argv[argno], _hdf_name, sizeof _hdf_name); - if (NULL==(pdb=PD_open(pdb_name, "r"))) { - fprintf(stderr, "%s: unable to open PDB file\n", pdb_name); - exit(1); - } - if ((hdf=H5Fcreate(hdf_name, H5F_ACC_TRUNC, H5P_DEFAULT, - fapl))<0) { - fprintf(stderr, "%s: unable to open HDF file\n", hdf_name); - exit(1); - } - H5Pclose(fapl); - - /* - * Traverse the PDB file to create the HDF5 file. - */ - traverse(pdb, pdb_name, hdf); - - /* Close the files */ - if (!PD_close(pdb)) { - fprintf(stderr, "%s: problems closing PDB file\n", pdb_name); - exit(1); - } - if (H5Fclose(hdf)<0) { - fprintf(stderr, "%s: problems closing HDF file\n", hdf_name); - exit(1); - } - } - } - return 0; -} -#endif /* H5_HAVE_PDB_H */ |