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-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * 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 */
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