diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/Makefile.in | 7 | ||||
| -rw-r--r-- | tools/pdb2hdf.c | 500 |
2 files changed, 505 insertions, 2 deletions
diff --git a/tools/Makefile.in b/tools/Makefile.in index dfc6c9f..0740ece 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -25,7 +25,7 @@ TEST_SCRIPTS=$(srcdir)/testh5dump.sh @TESTH5TOH4@ LT_LINK_LIB=$(LT) --mode=link $(CC) -static -rpath $(libdir) LIB=libh5tools.la LIBHDF5=../src/libhdf5.la -PROGS=h5debug h5import h5ls h5repart h5dump h5dumptst @H5TOH4@ +PROGS=h5debug h5import h5ls h5repart h5dump h5dumptst @H5TOH4@ @PDB2HDF@ ## Source and object files for the library; do not install LIB_SRC=h5tools.c h5findshd.c @@ -34,7 +34,7 @@ PUB_LIB= ## Source and object files for programs... PROG_SRC=h5debug.c h5import.c h5ls.c h5repart.c h5dump.c h5dumputil.c \ - h5toh4.c h5dumptst.c + h5toh4.c h5dumptst.c pdb2hdf.c PROG_OBJ=$(PROG_SRC:.c=.lo) PRIVATE_HDR=h5tools.h @@ -70,4 +70,7 @@ h5toh4: h5toh4.lo h5dumptst: h5dumptst.lo @$(LT_LINK_EXE) $(CFLAGS) -o $@ h5dumptst.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) +pdb2hdf: pdb2hdf.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ pdb2hdf.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + @CONCLUDE@ diff --git a/tools/pdb2hdf.c b/tools/pdb2hdf.c new file mode 100644 index 0000000..10a4a86 --- /dev/null +++ b/tools/pdb2hdf.c @@ -0,0 +1,500 @@ +/* + * Copyright © 1999 Spizella Software + * All rights reserved. + * + * Programmer: Robb Matzke <robb@arborea.spizella.com> + * 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 <hdf5.h> +#include <pdb.h> +#include <score.h> +#include <stdio.h> +#include <string.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 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) +{ + char *progname; + + if ((progname=strrchr(arg0, '/')) && progname[1]) progname++; + else progname = arg0; + + printf("This is %s version %u.%u release %u\n", + progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE); +} + + +/*------------------------------------------------------------------------- + * 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; + } + + } 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); + } + + } + 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; +} |