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authorAllen Byrne <byrn@hdfgroup.org>2013-09-09 18:30:25 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2013-09-09 18:30:25 (GMT)
commitf79eac6049aaf951cbd109214b8c45f6174fd4e7 (patch)
treedf87f689dab0f2bc8cee13b8d1161434d01f6956 /tools/h5repack
parent6b54dac504ccaad3ec512b57ba8b92609a74490b (diff)
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[svn-r24116] Correct indentation and create single exit point.
Tested : local linux
Diffstat (limited to 'tools/h5repack')
-rw-r--r--tools/h5repack/h5repack.c1818
-rw-r--r--tools/h5repack/h5repack_copy.c3243
-rw-r--r--tools/h5repack/h5repack_main.c1105
-rw-r--r--tools/h5repack/h5repack_opttable.c530
4 files changed, 3270 insertions, 3426 deletions
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 5c44e1a..742bb06 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -1,17 +1,17 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* Copyright by The HDF Group. *
-* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
-* access to either file, you may request a copy from help@hdfgroup.org. *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * Copyright by The HDF Group. *
+ * 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
@@ -23,223 +23,198 @@
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
-* File: h5repack.c
-* Purpose: Public API functions
-*-------------------------------------------------------------------------
-*/
+ * File: h5repack.c
+ * Purpose: Public API functions
+ *-------------------------------------------------------------------------
+ */
static int check_options(pack_opt_t *options);
static int check_objects(const char* fname, pack_opt_t *options);
-static const char* get_sfilter (H5Z_filter_t filtn);
+static const char* get_sfilter(H5Z_filter_t filtn);
static int have_request(pack_opt_t *options);
+/*-------------------------------------------------------------------------
+ * Function: h5repack
+ *
+ * Purpose: locate all high-level HDF5 objects in the file
+ * and compress/chunk them using options
+ *
+ * Algorithm: 2 traversals are made to the file; the 1st builds a list of
+ * the objects, the 2nd makes a copy of them, using the options;
+ * the reason for the 1st traversal is to check for invalid
+ * object name requests
+ *
+ * Return: 0, ok, -1, fail
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+ /* check input */
+ if (check_options(options) < 0)
+ return -1;
+ /* check for objects in input that are in the file */
+ if (check_objects(infile, options) < 0)
+ return -1;
-/*-------------------------------------------------------------------------
-* Function: h5repack
-*
-* Purpose: locate all high-level HDF5 objects in the file
-* and compress/chunk them using options
-*
-* Algorithm: 2 traversals are made to the file; the 1st builds a list of
-* the objects, the 2nd makes a copy of them, using the options;
-* the reason for the 1st traversal is to check for invalid
-* object name requests
-*
-* Return: 0, ok, -1, fail
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack(const char* infile,
- const char* outfile,
- pack_opt_t *options)
-{
- /* check input */
- if (check_options(options)<0)
- return -1;
-
- /* check for objects in input that are in the file */
- if (check_objects(infile,options) < 0)
- return -1;
-
- /* copy the objects */
- if (copy_objects(infile,outfile,options) < 0)
- return -1;
-
-
- return 0;
+ /* copy the objects */
+ if (copy_objects(infile, outfile, options) < 0)
+ return -1;
+
+ return 0;
}
+/*-------------------------------------------------------------------------
+ * Function: h5repack_init
+ *
+ * Purpose: initialize options
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_init(pack_opt_t *options, int verbose,
+ H5F_file_space_type_t strategy, hsize_t threshold) {
+ int k, n;
-/*-------------------------------------------------------------------------
-* Function: h5repack_init
-*
-* Purpose: initialize options
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-int
-h5repack_init(pack_opt_t *options, int verbose, H5F_file_space_type_t strategy,
- hsize_t threshold)
-{
- int k, n;
-
- HDmemset(options, 0, sizeof(pack_opt_t));
- options->min_comp = 0;
- options->verbose = verbose;
- options->layout_g = H5D_LAYOUT_ERROR;
-
- for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
- {
- options->filter_g[n].filtn = -1;
- options->filter_g[n].cd_nelmts = 0;
- for ( k = 0; k < CD_VALUES; k++)
- options->filter_g[n].cd_values[k] = 0;
- }
-
- options->fs_strategy = strategy;
- options->fs_threshold = threshold;
-
- return (options_table_init(&(options->op_tbl)));
-}
+ HDmemset(options, 0, sizeof(pack_opt_t));
+ options->min_comp = 0;
+ options->verbose = verbose;
+ options->layout_g = H5D_LAYOUT_ERROR;
+ for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
+ options->filter_g[n].filtn = -1;
+ options->filter_g[n].cd_nelmts = 0;
+ for (k = 0; k < CD_VALUES; k++)
+ options->filter_g[n].cd_values[k] = 0;
+ }
-/*-------------------------------------------------------------------------
-* Function: h5repack_end
-*
-* Purpose: free options table
-*
-*-------------------------------------------------------------------------
-*/
-
-int h5repack_end (pack_opt_t *options)
-{
- return options_table_free(options->op_tbl);
-}
+ options->fs_strategy = strategy;
+ options->fs_threshold = threshold;
+ return (options_table_init(&(options->op_tbl)));
+}
/*-------------------------------------------------------------------------
-* Function: h5repack_addfilter
-*
-* Purpose: add a compression -f option to table
-* Example: -f dset:GZIP=6
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack_addfilter(const char* str,
- pack_opt_t *options)
-{
- obj_list_t *obj_list=NULL; /* one object list for the -f and -l option entry */
- filter_info_t filter; /* filter info for the current -f option entry */
- int n_objs; /* number of objects in the current -f or -l option entry */
- int is_glb; /* is the filter global */
-
-
-
- /* parse the -f option */
- if(NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
- return -1;
-
- /* if it applies to all objects */
- if(is_glb)
- {
- int n;
-
- n = options->n_filter_g++; /* increase # of global filters */
-
- if(options->n_filter_g > H5_REPACK_MAX_NFILTERS)
- {
- error_msg("maximum number of filters exceeded for <%s>\n", str);
- HDfree(obj_list);
- return -1;
- }
-
- options->filter_g[n] = filter;
- }
- else
- options_add_filter(obj_list, n_objs, filter, options->op_tbl);
-
- HDfree(obj_list);
- return 0;
+ * Function: h5repack_end
+ *
+ * Purpose: free options table
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_end(pack_opt_t *options) {
+ return options_table_free(options->op_tbl);
}
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addfilter
+ *
+ * Purpose: add a compression -f option to table
+ * Example: -f dset:GZIP=6
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_addfilter(const char* str, pack_opt_t *options) {
+ obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
+ filter_info_t filter; /* filter info for the current -f option entry */
+ int n_objs; /* number of objects in the current -f or -l option entry */
+ int is_glb; /* is the filter global */
+
+ /* parse the -f option */
+ if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
+ return -1;
+
+ /* if it applies to all objects */
+ if (is_glb) {
+ int n;
+
+ n = options->n_filter_g++; /* increase # of global filters */
+
+ if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
+ error_msg("maximum number of filters exceeded for <%s>\n", str);
+ HDfree(obj_list);
+ return -1;
+ }
+
+ options->filter_g[n] = filter;
+ }
+ else
+ options_add_filter(obj_list, n_objs, filter, options->op_tbl);
+
+ HDfree(obj_list);
+ return 0;
+}
/*-------------------------------------------------------------------------
-* Function: h5repack_addlayout
-*
-* Purpose: add a layout option
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-
-int h5repack_addlayout(const char* str,
- pack_opt_t *options)
-{
-
- obj_list_t *obj_list=NULL; /*one object list for the -t and -c option entry */
- int n_objs; /*number of objects in the current -t or -c option entry */
- pack_info_t pack; /*info about layout to extract from parse */
- int j;
-
- init_packobject(&pack);
-
- if (options->all_layout==1){
- error_msg("invalid layout input: 'all' option \
- is present with other objects <%s>\n",str);
- return -1;
- }
-
- /* parse the layout option */
- obj_list=parse_layout(str,&n_objs,&pack,options);
- if (obj_list==NULL)
- return -1;
-
- /* set layout option */
- options->layout_g = pack.layout;
-
- /* no individual dataset specified */
- if (options->all_layout==1 )
- {
- if (pack.layout==H5D_CHUNKED)
- {
- /* -2 means the NONE option, remove chunking
- and set the global layout to contiguous */
- if (pack.chunk.rank==-2)
- {
- options->layout_g = H5D_CONTIGUOUS;
- }
- /* otherwise set the global chunking type */
- else
- {
- options->chunk_g.rank=pack.chunk.rank;
- for (j = 0; j < pack.chunk.rank; j++)
- options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
- }
- }
- }
-
- /* individual dataset specified */
- if (options->all_layout==0)
- options_add_layout(obj_list,
- n_objs,
- &pack,
- options->op_tbl);
-
- HDfree(obj_list);
- return 0;
+ * Function: h5repack_addlayout
+ *
+ * Purpose: add a layout option
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_addlayout(const char* str, pack_opt_t *options) {
+
+ obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
+ int n_objs; /*number of objects in the current -t or -c option entry */
+ pack_info_t pack; /*info about layout to extract from parse */
+ int j;
+ int ret_value = -1;
+
+ init_packobject(&pack);
+
+ if (options->all_layout == 1) {
+ error_msg(
+ "invalid layout input: 'all' option \
+ is present with other objects <%s>\n",
+ str);
+ return ret_value;
+ }
+
+ /* parse the layout option */
+ obj_list = parse_layout(str, &n_objs, &pack, options);
+ if (obj_list) {
+
+ /* set layout option */
+ options->layout_g = pack.layout;
+
+ /* no individual dataset specified */
+ if (options->all_layout == 1) {
+ if (pack.layout == H5D_CHUNKED) {
+ /* -2 means the NONE option, remove chunking
+ and set the global layout to contiguous */
+ if (pack.chunk.rank == -2) {
+ options->layout_g = H5D_CONTIGUOUS;
+ }
+ /* otherwise set the global chunking type */
+ else {
+ options->chunk_g.rank = pack.chunk.rank;
+ for (j = 0; j < pack.chunk.rank; j++)
+ options->chunk_g.chunk_lengths[j] =
+ pack.chunk.chunk_lengths[j];
+ }
+ }
+ }
+
+ /* individual dataset specified */
+ if (options->all_layout == 0)
+ ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
+
+ HDfree(obj_list);
+ ret_value = 0;
+ }
+
+ return ret_value;
}
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
@@ -249,765 +224,720 @@ int h5repack_addlayout(const char* str,
* others to static in h5repack_copy.c.
*/
/*-------------------------------------------------------------------------
-* Function: copy_named_datatype
-*
-* Purpose: Copies the specified datatype anonymously, and returns an open
-* id for that datatype in the output file. The first time this
-* is called it scans every named datatype in travt into a
-* private stack, afterwards it simply scans that stack. The id
-* returned must be closed after it is no longer needed.
-* named_datatype_free must be called before the program exits
-* to free the stack.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
-{
- named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
- named_dt_t *dt_ret = NULL; /* Datatype to return */
- H5O_info_t oinfo; /* Object info of input dtype */
- hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
-
- if(H5Oget_info(type_in, &oinfo) < 0)
- goto error;
-
- if(*named_dt_head_p)
- {
- /* Stack already exists, search for the datatype */
- while(dt && dt->addr_in != oinfo.addr)
- dt = dt->next;
-
- dt_ret = dt;
- }
- else
- {
- /* Create the stack */
- size_t i;
-
- for(i=0; i<travt->nobjs; i++)
- if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
- {
- /* Push onto the stack */
- if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
- goto error;
- dt->next = *named_dt_head_p;
- *named_dt_head_p = dt;
-
- /* Update the address and id */
- dt->addr_in = travt->objs[i].objno;
- dt->id_out = -1;
-
- /* Check if this type is the one requested */
- if(oinfo.addr == dt->addr_in)
- {
- HDassert(!dt_ret);
- dt_ret = dt;
- } /* end if */
- } /* end if */
- } /* end else */
-
- /* Handle the case that the requested datatype was not found. This is
- * possible if the datatype was committed anonymously in the input file. */
- if(!dt_ret)
- {
- /* Push the new datatype onto the stack */
- if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
- goto error;
- dt_ret->next = *named_dt_head_p;
- *named_dt_head_p = dt_ret;
-
- /* Update the address and id */
- dt_ret->addr_in = oinfo.addr;
- dt_ret->id_out = -1;
- } /* end if */
-
- /* If the requested datatype does not yet exist in the output file, copy it
- * anonymously */
- if(dt_ret->id_out < 0)
- {
- if (options->use_native==1)
- dt_ret->id_out = h5tools_get_native_type(type_in);
- else
- dt_ret->id_out = H5Tcopy(type_in);
- if(dt_ret->id_out < 0)
- goto error;
- if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
- } /* end if */
-
- /* Set return value */
- ret_value = dt_ret->id_out;
-
- /* Increment the ref count on id_out, because the calling function will try
- * to close it */
- if(H5Iinc_ref(ret_value) < 0)
- goto error;
-
- return(ret_value);
-
-error:
- return(-1);
+ * Function: copy_named_datatype
+ *
+ * Purpose: Copies the specified datatype anonymously, and returns an open
+ * id for that datatype in the output file. The first time this
+ * is called it scans every named datatype in travt into a
+ * private stack, afterwards it simply scans that stack. The id
+ * returned must be closed after it is no longer needed.
+ * named_datatype_free must be called before the program exits
+ * to free the stack.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
+ named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+ named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+ named_dt_t *dt_ret = NULL; /* Datatype to return */
+ H5O_info_t oinfo; /* Object info of input dtype */
+ hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
+
+ if (H5Oget_info(type_in, &oinfo) < 0)
+ goto done;
+
+ if (*named_dt_head_p) {
+ /* Stack already exists, search for the datatype */
+ while (dt && dt->addr_in != oinfo.addr)
+ dt = dt->next;
+
+ dt_ret = dt;
+ }
+ else {
+ /* Create the stack */
+ size_t i;
+
+ for (i = 0; i < travt->nobjs; i++) {
+ if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+ /* Push onto the stack */
+ if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+ goto done;
+ }
+ dt->next = *named_dt_head_p;
+ *named_dt_head_p = dt;
+
+ /* Update the address and id */
+ dt->addr_in = travt->objs[i].objno;
+ dt->id_out = -1;
+
+ /* Check if this type is the one requested */
+ if (oinfo.addr == dt->addr_in) {
+ HDassert(!dt_ret);
+ dt_ret = dt;
+ } /* end if */
+ } /* end if */
+ } /* end for */
+ } /* end else */
+
+ /* Handle the case that the requested datatype was not found. This is
+ * possible if the datatype was committed anonymously in the input file. */
+ if (!dt_ret) {
+ /* Push the new datatype onto the stack */
+ if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+ goto done;
+ }
+ dt_ret->next = *named_dt_head_p;
+ *named_dt_head_p = dt_ret;
+
+ /* Update the address and id */
+ dt_ret->addr_in = oinfo.addr;
+ dt_ret->id_out = -1;
+ } /* end if */
+
+ /* If the requested datatype does not yet exist in the output file, copy it
+ * anonymously */
+ if (dt_ret->id_out < 0) {
+ if (options->use_native == 1)
+ dt_ret->id_out = h5tools_get_native_type(type_in);
+ else
+ dt_ret->id_out = H5Tcopy(type_in);
+ if (dt_ret->id_out < 0)
+ goto done;
+ if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto done;
+ } /* end if */
+
+ /* Set return value */
+ ret_value = dt_ret->id_out;
+
+ /* Increment the ref count on id_out, because the calling function will try
+ * to close it */
+ if(H5Iinc_ref(ret_value) < 0) {
+ ret_value = -1;
+ }
+
+done:
+ return (ret_value);
} /* end copy_named_datatype */
-
/*-------------------------------------------------------------------------
-* Function: named_datatype_free
-*
-* Purpose: Frees the stack of named datatypes.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
-{
- named_dt_t *dt = *named_dt_head_p;
-
- while(dt)
- {
- /* Pop the datatype off the stack and free it */
- if(H5Tclose(dt->id_out) < 0 && !ignore_err)
- goto error;
- dt = dt->next;
- HDfree(*named_dt_head_p);
- *named_dt_head_p = dt;
- } /* end while */
-
- return 0;
-
-error:
- return -1;
+ * Function: named_datatype_free
+ *
+ * Purpose: Frees the stack of named datatypes.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+ named_dt_t *dt = *named_dt_head_p;
+ hid_t ret_value = -1;
+
+ while (dt) {
+ /* Pop the datatype off the stack and free it */
+ if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+ goto done;
+ dt = dt->next;
+ HDfree(*named_dt_head_p);
+ *named_dt_head_p = dt;
+ } /* end while */
+
+ ret_value = 0;
+
+done:
+ return (ret_value);
} /* end named_datatype_free */
/*-------------------------------------------------------------------------
-* Function: copy_attr
-*
-* Purpose: copy attributes located in LOC_IN, which is obtained either from
-* loc_id = H5Gopen2( fid, name);
-* loc_id = H5Dopen2( fid, name);
-* loc_id = H5Topen2( fid, name);
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 28, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int copy_attr(hid_t loc_in,
- hid_t loc_out,
- named_dt_t **named_dt_head_p,
- trav_table_t *travt,
- pack_opt_t *options)
-{
- hid_t attr_id=-1; /* attr ID */
- hid_t attr_out=-1; /* attr ID */
- hid_t space_id=-1; /* space ID */
- hid_t ftype_id=-1; /* file type ID */
- hid_t wtype_id=-1; /* read/write type ID */
- size_t msize; /* size of type */
- void *buf = NULL; /* data buffer */
- hsize_t nelmts; /* number of elements in dataset */
- int rank; /* rank of dataset */
- htri_t is_named; /* Whether the datatype is named */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- char name[255];
- H5O_info_t oinfo; /* object info */
- int j;
- unsigned u;
- hbool_t is_ref=0;
- H5T_class_t type_class = -1;
-
- if(H5Oget_info(loc_in, &oinfo) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy all attributes
- *-------------------------------------------------------------------------
- */
- for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
- /* open attribute */
- if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- goto error;
-
- /* get name */
- if(H5Aget_name(attr_id, (size_t)255, name) < 0)
- goto error;
-
- /* get the file datatype */
- if((ftype_id = H5Aget_type(attr_id)) < 0 )
- goto error;
-
- /* Check if the datatype is committed */
- if((is_named = H5Tcommitted(ftype_id)) < 0)
- goto error;
- if(is_named && travt) {
- hid_t fidout;
-
- /* Create out file id */
- if((fidout = H5Iget_file_id(loc_out)) < 0)
- goto error;
-
- /* Copy named dt */
- if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
- travt, options)) < 0)
- {
- H5Fclose(fidout);
- goto error;
- } /* end if */
-
- if(H5Fclose(fidout) < 0)
- goto error;
- } /* end if */
- else {
- if(options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
- } /* end else */
-
-
- /* get the dataspace handle */
- if((space_id = H5Aget_space(attr_id)) < 0)
- goto error;
-
- /* get dimensions */
- if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
- goto error;
-
- nelmts = 1;
- for(j = 0; j < rank; j++)
- nelmts *= dims[j];
-
- if((msize = H5Tget_size(wtype_id)) == 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * object references are a special case. We cannot just copy the buffers,
- * but instead we recreate the reference.
- * This is done on a second sweep of the file that just copies the referenced
- * objects at copy_refs_attr()
- *-------------------------------------------------------------------------
- */
- type_class = H5Tget_class(wtype_id);
- is_ref = (type_class == H5T_REFERENCE);
- if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
- hid_t base_type = -1;
- base_type = H5Tget_super(ftype_id);
- is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
- H5Tclose(base_type);
- }
-
- if (type_class == H5T_COMPOUND) {
- int nmembers = H5Tget_nmembers(wtype_id) ;
- for (j=0; j<nmembers; j++) {
- hid_t mtid = H5Tget_member_type( wtype_id, (unsigned) j );
- H5T_class_t mtclass = H5Tget_class(mtid);
- H5Tclose(mtid);
-
- if (mtclass==H5T_REFERENCE) {
- is_ref = 1;
- break;
- }
- } /* for (j=0; i<nmembers; j++) */
- } /* if (type_class == H5T_COMPOUND) */
-
- if(is_ref) {
- ; /* handled by copy_refs_attr() */
- }
- else {
- /*-------------------------------------------------------------------------
- * read to memory
- *-------------------------------------------------------------------------
- */
-
- buf = (void *)HDmalloc((size_t)(nelmts * msize));
- if(buf == NULL) {
- error_msg("h5repack", "cannot read into memory\n" );
- goto error;
- } /* end if */
- if(H5Aread(attr_id, wtype_id, buf) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- goto error;
- if(H5Awrite(attr_out, wtype_id, buf) < 0)
- goto error;
-
- /*close*/
- if(H5Aclose(attr_out) < 0)
- goto error;
-
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
- if (TRUE == h5tools_detect_vlen(wtype_id))
- H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
- HDfree(buf);
- buf = NULL;
- } /*H5T_REFERENCE*/
-
-
- if(options->verbose)
- printf(FORMAT_OBJ_ATTR, "attr", name);
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if(H5Tclose(ftype_id) < 0)
- goto error;
- if(H5Tclose(wtype_id) < 0)
- goto error;
- if(H5Sclose(space_id) < 0)
- goto error;
- if(H5Aclose(attr_id) < 0)
- goto error;
- } /* u */
-
- return 0;
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
+ trav_table_t *travt, pack_opt_t *options) {
+ hid_t attr_id = -1; /* attr ID */
+ hid_t attr_out = -1; /* attr ID */
+ hid_t space_id = -1; /* space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ size_t msize; /* size of type */
+ void *buf = NULL; /* data buffer */
+ hsize_t nelmts; /* number of elements in dataset */
+ int rank; /* rank of dataset */
+ htri_t is_named; /* Whether the datatype is named */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ char name[255];
+ H5O_info_t oinfo; /* object info */
+ int j;
+ unsigned u;
+ hbool_t is_ref = 0;
+ H5T_class_t type_class = -1;
+
+ if (H5Oget_info(loc_in, &oinfo) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy all attributes
+ *-------------------------------------------------------------------------
+ */
+ for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
+ /* open attribute */
+ if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER,
+ H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+
+ /* get name */
+ if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+ goto error;
+
+ /* get the file datatype */
+ if ((ftype_id = H5Aget_type(attr_id)) < 0)
+ goto error;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if (is_named && travt) {
+ hid_t fidout;
+
+ /* Create out file id */
+ if ((fidout = H5Iget_file_id(loc_out)) < 0)
+ goto error;
+
+ /* Copy named dt */
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+ named_dt_head_p, travt, options)) < 0) {
+ H5Fclose(fidout);
+ goto error;
+ } /* end if */
+
+ if (H5Fclose(fidout) < 0)
+ goto error;
+ } /* end if */
+ else {
+ if (options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end else */
+
+ /* get the dataspace handle */
+ if ((space_id = H5Aget_space(attr_id)) < 0)
+ goto error;
+
+ /* get dimensions */
+ if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+ goto error;
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * object references are a special case. We cannot just copy the buffers,
+ * but instead we recreate the reference.
+ * This is done on a second sweep of the file that just copies the referenced
+ * objects at copy_refs_attr()
+ *-------------------------------------------------------------------------
+ */
+ type_class = H5Tget_class(wtype_id);
+ is_ref = (type_class == H5T_REFERENCE);
+ if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
+ hid_t base_type = -1;
+ base_type = H5Tget_super(ftype_id);
+ is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
+ H5Tclose(base_type);
+ }
+
+ if (type_class == H5T_COMPOUND) {
+ int nmembers = H5Tget_nmembers(wtype_id);
+ for (j = 0; j < nmembers; j++) {
+ hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+ H5T_class_t mtclass = H5Tget_class(mtid);
+ H5Tclose(mtid);
+
+ if (mtclass == H5T_REFERENCE) {
+ is_ref = 1;
+ break;
+ }
+ } /* for (j=0; i<nmembers; j++) */
+ } /* if (type_class == H5T_COMPOUND) */
+
+ if (is_ref) {
+ ; /* handled by copy_refs_attr() */
+ }
+ else {
+ /*-------------------------------------------------------------------------
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
+
+ buf = (void *) HDmalloc((size_t)(nelmts * msize));
+ if (buf == NULL) {
+ error_msg("h5repack", "cannot read into memory\n");
+ goto error;
+ } /* end if */
+ if (H5Aread(attr_id, wtype_id, buf) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy
+ *-------------------------------------------------------------------------
+ */
+
+ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id,
+ H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+ if (H5Awrite(attr_out, wtype_id, buf) < 0)
+ goto error;
+
+ /*close*/
+ if (H5Aclose(attr_out) < 0)
+ goto error;
+
+ /* Check if we have VL data and string in the attribute's datatype that must
+ * be reclaimed */
+ if (TRUE == h5tools_detect_vlen(wtype_id))
+ H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+ HDfree(buf);
+ buf = NULL;
+ } /*H5T_REFERENCE*/
+
+ if (options->verbose)
+ printf(FORMAT_OBJ_ATTR, "attr", name);
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Tclose(wtype_id) < 0)
+ goto error;
+ if (H5Sclose(space_id) < 0)
+ goto error;
+ if (H5Aclose(attr_id) < 0)
+ goto error;
+ } /* u */
+
+ return 0;
error:
- H5E_BEGIN_TRY {
- if(buf) {
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
- if (TRUE == h5tools_detect_vlen(wtype_id))
- H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
- /* Free buf */
- HDfree(buf);
- } /* end if */
-
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Sclose(space_id);
- H5Aclose(attr_id);
- H5Aclose(attr_out);
- } H5E_END_TRY;
-
- return -1;
+ H5E_BEGIN_TRY
+ {
+ if (buf) {
+ /* Check if we have VL data and string in the attribute's datatype that must
+ * be reclaimed */
+ if (TRUE == h5tools_detect_vlen(wtype_id))
+ H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+ /* Free buf */
+ HDfree(buf);
+ } /* end if */
+
+ H5Tclose(ftype_id);
+ H5Tclose(wtype_id);
+ H5Sclose(space_id);
+ H5Aclose(attr_id);
+ H5Aclose(attr_out);
+ } H5E_END_TRY;
+
+ return -1;
} /* end copy_attr() */
/*-------------------------------------------------------------------------
-* Function: check_options
-*
-* Purpose: print options, checks for invalid options
-*
-* Return: void, return -1 on error
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-* Modification:
-* Peter Cao, July 9, 2007
-* Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*-------------------------------------------------------------------------
-*/
-static int check_options(pack_opt_t *options)
-{
- unsigned int i;
- int k, j, has_cp=0, has_ck=0;
- char slayout[30];
-
- /*-------------------------------------------------------------------------
- * objects to layout
- *-------------------------------------------------------------------------
- */
- if (options->verbose && have_request(options) /* only print if requested */)
- {
- printf("Objects to modify layout are...\n");
- if (options->all_layout==1)
- {
- switch (options->layout_g)
- {
- case H5D_COMPACT:
- strcpy(slayout,"compact");
- break;
- case H5D_CONTIGUOUS:
- strcpy(slayout,"contiguous");
- break;
- case H5D_CHUNKED:
- strcpy(slayout,"chunked");
- break;
- case H5D_LAYOUT_ERROR:
- case H5D_NLAYOUTS:
- error_msg("invalid layout\n");
- return -1;
- default:
- strcpy(slayout,"invalid layout\n");
- return -1;
- }
- printf(" Apply %s layout to all\n", slayout);
- if (H5D_CHUNKED==options->layout_g)
- {
- printf("with dimension [");
- for ( j = 0; j < options->chunk_g.rank; j++)
- printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
- printf("]\n");
- }
- }
- }/* verbose */
-
- for ( i = 0; i < options->op_tbl->nelems; i++)
- {
- char* name=options->op_tbl->objs[i].path;
-
- if (options->op_tbl->objs[i].chunk.rank>0)
- {
- if (options->verbose){
- printf(" <%s> with chunk size ",name);
- for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
- printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
- printf("\n");
- }
- has_ck=1;
- }
- else if (options->op_tbl->objs[i].chunk.rank==-2)
- {
- if (options->verbose)
- printf(" <%s> %s\n",name,"NONE (contigous)");
- has_ck=1;
- }
- }
-
- if (options->all_layout==1 && has_ck)
- {
- error_msg("invalid chunking input: 'all' option\
+ * Function: check_options
+ *
+ * Purpose: print options, checks for invalid options
+ *
+ * Return: void, return -1 on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ * Modification:
+ * Peter Cao, July 9, 2007
+ * Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_options(pack_opt_t *options) {
+ unsigned int i;
+ int k, j, has_cp = 0, has_ck = 0;
+ char slayout[30];
+
+ /*-------------------------------------------------------------------------
+ * objects to layout
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose && have_request(options) /* only print if requested */) {
+ printf("Objects to modify layout are...\n");
+ if (options->all_layout == 1) {
+ switch (options->layout_g) {
+ case H5D_COMPACT:
+ strcpy(slayout, "compact");
+ break;
+ case H5D_CONTIGUOUS:
+ strcpy(slayout, "contiguous");
+ break;
+ case H5D_CHUNKED:
+ strcpy(slayout, "chunked");
+ break;
+ case H5D_LAYOUT_ERROR:
+ case H5D_NLAYOUTS:
+ error_msg("invalid layout\n");
+ return -1;
+ default:
+ strcpy(slayout, "invalid layout\n");
+ return -1;
+ }
+ printf(" Apply %s layout to all\n", slayout);
+ if (H5D_CHUNKED == options->layout_g) {
+ printf("with dimension [");
+ for (j = 0; j < options->chunk_g.rank; j++)
+ printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+ printf("]\n");
+ }
+ }
+ }/* verbose */
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ char* name = options->op_tbl->objs[i].path;
+
+ if (options->op_tbl->objs[i].chunk.rank > 0) {
+ if (options->verbose) {
+ printf(" <%s> with chunk size ", name);
+ for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+ printf("%d ",
+ (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+ printf("\n");
+ }
+ has_ck = 1;
+ }
+ else if (options->op_tbl->objs[i].chunk.rank == -2) {
+ if (options->verbose)
+ printf(" <%s> %s\n", name, "NONE (contigous)");
+ has_ck = 1;
+ }
+ }
+
+ if (options->all_layout == 1 && has_ck) {
+ error_msg(
+ "invalid chunking input: 'all' option\
is present with other objects\n");
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * objects to filter
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose && have_request(options) /* only print if requested */)
- {
- printf("Objects to apply filter are...\n");
- if (options->all_filter==1)
- {
-
- for (k = 0; k < options->n_filter_g; k++ )
- {
- H5Z_filter_t filtn=options->filter_g[k].filtn;
- switch (filtn)
- {
- case H5Z_FILTER_NONE:
- printf(" Uncompress all\n");
- break;
- case H5Z_FILTER_SHUFFLE:
- case H5Z_FILTER_FLETCHER32:
- printf(" All with %s\n",get_sfilter(filtn));
- break;
- case H5Z_FILTER_SZIP:
- case H5Z_FILTER_DEFLATE:
- printf(" All with %s, parameter %d\n",
- get_sfilter(filtn),
- options->filter_g[k].cd_values[0]);
- break;
- default:
- printf(" User Defined %d\n", filtn);
- break;
- } /* k */
- };
- }
- } /* verbose */
-
- for ( i = 0; i < options->op_tbl->nelems; i++)
- {
- pack_info_t pack = options->op_tbl->objs[i];
- char* name = pack.path;
-
- for ( j=0; j<pack.nfilters; j++)
- {
- if (options->verbose)
- {
- printf(" <%s> with %s filter\n",
- name,
- get_sfilter(pack.filter[j].filtn));
- }
-
- has_cp=1;
-
- } /* j */
- } /* i */
-
- if (options->all_filter==1 && has_cp)
- {
- error_msg("invalid compression input: 'all' option\
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * objects to filter
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose && have_request(options) /* only print if requested */) {
+ printf("Objects to apply filter are...\n");
+ if (options->all_filter == 1) {
+ for (k = 0; k < options->n_filter_g; k++) {
+ H5Z_filter_t filtn = options->filter_g[k].filtn;
+ switch (filtn) {
+ case H5Z_FILTER_NONE:
+ printf(" Uncompress all\n");
+ break;
+ case H5Z_FILTER_SHUFFLE:
+ case H5Z_FILTER_FLETCHER32:
+ printf(" All with %s\n", get_sfilter(filtn));
+ break;
+ case H5Z_FILTER_SZIP:
+ case H5Z_FILTER_DEFLATE:
+ printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+ options->filter_g[k].cd_values[0]);
+ break;
+ default:
+ printf(" User Defined %d\n", filtn);
+ break;
+ } /* k */
+ };
+ }
+ } /* verbose */
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ pack_info_t pack = options->op_tbl->objs[i];
+ char* name = pack.path;
+
+ for (j = 0; j < pack.nfilters; j++) {
+ if (options->verbose) {
+ printf(" <%s> with %s filter\n", name,
+ get_sfilter(pack.filter[j].filtn));
+ }
+
+ has_cp = 1;
+
+ } /* j */
+ } /* i */
+
+ if (options->all_filter == 1 && has_cp) {
+ error_msg(
+ "invalid compression input: 'all' option\
is present with other objects\n");
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * check options for the latest format
- *-------------------------------------------------------------------------
- */
-
- if (options->grp_compact < 0)
- {
- error_msg("invalid maximum number of links to store as header messages\n");
- return -1;
- }
- if (options->grp_indexed < 0)
- {
- error_msg("invalid minimum number of links to store in the indexed format\n");
- return -1;
- }
- if (options->grp_indexed > options->grp_compact)
- {
- error_msg("minimum indexed size is greater than the maximum compact size\n");
- return -1;
- }
- for (i=0; i<8; i++)
- {
- if (options->msg_size[i]<0)
- {
- error_msg("invalid shared message size\n");
- return -1;
- }
- }
-
-
- /*--------------------------------------------------------------------------------
- * verify new user userblock options; file name must be present
- *---------------------------------------------------------------------------------
- */
- if ( options->ublock_filename != NULL && options->ublock_size == 0 )
- {
- if ( options->verbose )
- {
- printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
- options->ublock_filename);
- options->ublock_size = 1024;
- }
- }
-
- if ( options->ublock_filename == NULL && options->ublock_size != 0 )
- {
- error_msg("file name missing for user block\n",
- options->ublock_filename);
- return -1;
- }
-
-
- /*--------------------------------------------------------------------------------
- * verify alignment options; threshold is zero default but alignment not
- *---------------------------------------------------------------------------------
- */
-
- if ( options->alignment == 0 && options->threshold != 0 )
- {
- error_msg("alignment for H5Pset_alignment missing\n");
- return -1;
- }
-
- return 0;
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * check options for the latest format
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->grp_compact < 0) {
+ error_msg(
+ "invalid maximum number of links to store as header messages\n");
+ return -1;
+ }
+ if (options->grp_indexed < 0) {
+ error_msg(
+ "invalid minimum number of links to store in the indexed format\n");
+ return -1;
+ }
+ if (options->grp_indexed > options->grp_compact) {
+ error_msg(
+ "minimum indexed size is greater than the maximum compact size\n");
+ return -1;
+ }
+ for (i = 0; i < 8; i++) {
+ if (options->msg_size[i] < 0) {
+ error_msg("invalid shared message size\n");
+ return -1;
+ }
+ }
+
+ /*--------------------------------------------------------------------------------
+ * verify new user userblock options; file name must be present
+ *---------------------------------------------------------------------------------
+ */
+ if (options->ublock_filename != NULL && options->ublock_size == 0) {
+ if (options->verbose) {
+ printf(
+ "Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+ options->ublock_filename);
+ options->ublock_size = 1024;
+ }
+ }
+
+ if (options->ublock_filename == NULL && options->ublock_size != 0) {
+ error_msg("file name missing for user block\n",
+ options->ublock_filename);
+ return -1;
+ }
+
+ /*--------------------------------------------------------------------------------
+ * verify alignment options; threshold is zero default but alignment not
+ *---------------------------------------------------------------------------------
+ */
+
+ if (options->alignment == 0 && options->threshold != 0) {
+ error_msg("alignment for H5Pset_alignment missing\n");
+ return -1;
+ }
+
+ return 0;
}
-
/*-------------------------------------------------------------------------
-* Function: check_objects
-*
-* Purpose: locate all HDF5 objects in the file and compare with user
-* supplied list
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: September, 23, 2003
-*
-*-------------------------------------------------------------------------
-*/
-static int check_objects(const char* fname,
- pack_opt_t *options)
-{
- hid_t fid;
- unsigned int i;
- trav_table_t *travt = NULL;
-
- /* nothing to do */
- if(options->op_tbl->nelems == 0)
- return 0;
-
- /*-------------------------------------------------------------------------
- * open the file
- *-------------------------------------------------------------------------
- */
- if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
- {
- printf("<%s>: %s\n", fname, H5FOPENERROR );
- return -1;
- }
-
- /*-------------------------------------------------------------------------
- * get the list of objects in the file
- *-------------------------------------------------------------------------
- */
-
- /* init table */
- trav_table_init(&travt);
-
- /* get the list of objects in the file */
- if(h5trav_gettable(fid, travt) < 0)
- goto out;
-
- /*-------------------------------------------------------------------------
- * compare with user supplied list
- *-------------------------------------------------------------------------
- */
-
- if(options->verbose)
- printf("Opening file <%s>. Searching for objects to modify...\n", fname);
-
- for(i = 0; i < options->op_tbl->nelems; i++)
- {
- char* name=options->op_tbl->objs[i].path;
- if(options->verbose)
- printf(" <%s>",name);
-
- /* the input object names are present in the file and are valid */
- if(h5trav_getindext(name, travt) < 0)
- {
- error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
- (options->verbose?"\n":""),name,fname);
- goto out;
- }
- if(options->verbose)
- printf("...Found\n");
-
- /* check for extra filter conditions */
- switch(options->op_tbl->objs[i].filter->filtn)
- {
- /* chunk size must be smaller than pixels per block */
- case H5Z_FILTER_SZIP:
- {
- int j;
- hsize_t csize = 1;
- unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
- hsize_t dims[H5S_MAX_RANK];
- int rank;
- hid_t did;
- hid_t sid;
-
- if(options->op_tbl->objs[i].chunk.rank > 0) {
- rank = options->op_tbl->objs[i].chunk.rank;
- for(j = 0; j < rank; j++)
- csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
- }
- else {
- if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
- goto out;
- if((sid = H5Dget_space(did)) < 0)
- goto out;
- if((rank = H5Sget_simple_extent_ndims(sid)) < 0)
- goto out;
- HDmemset(dims, 0, sizeof dims);
- if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
- goto out;
- for(j = 0; j < rank; j++)
- csize *= dims[j];
- if(H5Sclose(sid) < 0)
- goto out;
- if(H5Dclose(did) < 0)
- goto out;
- }
-
- if (csize < ppb ) {
- printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
- goto out;
- }
- }
- break;
- default:
- break;
- }
- } /* i */
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
- H5Fclose(fid);
- trav_table_free(travt);
- return 0;
+ * Function: check_objects
+ *
+ * Purpose: locate all HDF5 objects in the file and compare with user
+ * supplied list
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_objects(const char* fname, pack_opt_t *options) {
+ hid_t fid;
+ unsigned int i;
+ trav_table_t *travt = NULL;
+
+ /* nothing to do */
+ if (options->op_tbl->nelems == 0)
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * open the file
+ *-------------------------------------------------------------------------
+ */
+ if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+ < 0) {
+ printf("<%s>: %s\n", fname, H5FOPENERROR);
+ return -1;
+ }
+
+ /*-------------------------------------------------------------------------
+ * get the list of objects in the file
+ *-------------------------------------------------------------------------
+ */
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fid, travt) < 0)
+ goto out;
+
+ /*-------------------------------------------------------------------------
+ * compare with user supplied list
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose)
+ printf("Opening file <%s>. Searching for objects to modify...\n",
+ fname);
+
+ for (i = 0; i < options->op_tbl->nelems; i++) {
+ char* name = options->op_tbl->objs[i].path;
+ if (options->verbose)
+ printf(" <%s>", name);
+
+ /* the input object names are present in the file and are valid */
+ if (h5trav_getindext(name, travt) < 0) {
+ error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+ (options->verbose ? "\n" : ""), name, fname);
+ goto out;
+ }
+ if (options->verbose)
+ printf("...Found\n");
+
+ /* check for extra filter conditions */
+ switch (options->op_tbl->objs[i].filter->filtn) {
+ /* chunk size must be smaller than pixels per block */
+ case H5Z_FILTER_SZIP:
+ {
+ int j;
+ hsize_t csize = 1;
+ unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+ hsize_t dims[H5S_MAX_RANK];
+ int rank;
+ hid_t did;
+ hid_t sid;
+
+ if (options->op_tbl->objs[i].chunk.rank > 0) {
+ rank = options->op_tbl->objs[i].chunk.rank;
+ for (j = 0; j < rank; j++)
+ csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+ }
+ else {
+ if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+ goto out;
+ if ((sid = H5Dget_space(did)) < 0)
+ goto out;
+ if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+ goto out;
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+ goto out;
+ for (j = 0; j < rank; j++)
+ csize *= dims[j];
+ if (H5Sclose(sid) < 0)
+ goto out;
+ if (H5Dclose(did) < 0)
+ goto out;
+ }
+
+ if (csize < ppb) {
+ printf(
+ " <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+ goto out;
+ }
+ }
+ break;
+ default:
+ break;
+ }
+ } /* i */
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ H5Fclose(fid);
+ trav_table_free(travt);
+ return 0;
out:
- H5Fclose(fid);
- trav_table_free(travt);
- return -1;
+ H5Fclose(fid);
+ trav_table_free(travt);
+ return -1;
}
+/*-------------------------------------------------------------------------
+ * Function: have_request
+ *
+ * Purpose: check if a filter or layout was requested
+ *
+ * Return: 1 yes, 0 no
+ *
+ * Date: May, 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int have_request(pack_opt_t *options) {
+ if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+ return 1;
-
-
-/*-------------------------------------------------------------------------
-* Function: have_request
-*
-* Purpose: check if a filter or layout was requested
-*
-* Return: 1 yes, 0 no
-*
-* Date: May, 24, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int have_request(pack_opt_t *options)
-{
-
- if (options->all_filter || options->all_layout || options->op_tbl->nelems)
- return 1;
-
- return 0;
+ return 0;
}
-
/*-------------------------------------------------------------------------
-* Function: get_sfilter
-*
-* Purpose: return the filter as a string name
-*
-* Return: name of filter, exit on error
-*
-*-------------------------------------------------------------------------
-*/
-
-static const char* get_sfilter(H5Z_filter_t filtn)
-{
- if (filtn==H5Z_FILTER_NONE)
- return "NONE";
- else if (filtn==H5Z_FILTER_DEFLATE)
- return "GZIP";
- else if (filtn==H5Z_FILTER_SZIP)
- return "SZIP";
- else if (filtn==H5Z_FILTER_SHUFFLE)
- return "SHUFFLE";
- else if (filtn==H5Z_FILTER_FLETCHER32)
- return "FLETCHER32";
- else if (filtn==H5Z_FILTER_NBIT)
- return "NBIT";
- else if (filtn==H5Z_FILTER_SCALEOFFSET)
- return "SOFF";
- else
- return "UD";
+ * Function: get_sfilter
+ *
+ * Purpose: return the filter as a string name
+ *
+ * Return: name of filter, exit on error
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static const char* get_sfilter(H5Z_filter_t filtn) {
+ if (filtn == H5Z_FILTER_NONE)
+ return "NONE";
+ else if (filtn == H5Z_FILTER_DEFLATE)
+ return "GZIP";
+ else if (filtn == H5Z_FILTER_SZIP)
+ return "SZIP";
+ else if (filtn == H5Z_FILTER_SHUFFLE)
+ return "SHUFFLE";
+ else if (filtn == H5Z_FILTER_FLETCHER32)
+ return "FLETCHER32";
+ else if (filtn == H5Z_FILTER_NBIT)
+ return "NBIT";
+ else if (filtn == H5Z_FILTER_SCALEOFFSET)
+ return "SOFF";
+ else
+ return "UD";
}
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 2133b48..521b9bd 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -1,36 +1,36 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* Copyright by The HDF Group. *
-* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
-* access to either file, you may request a copy from help@hdfgroup.org. *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * Copyright by The HDF Group. *
+ * 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------
-* typedefs
-*-------------------------------------------------------------------------
-*/
+ * typedefs
+ *-------------------------------------------------------------------------
+ */
/*-------------------------------------------------------------------------
-* globals
-*-------------------------------------------------------------------------
-*/
+ * globals
+ *-------------------------------------------------------------------------
+ */
/*-------------------------------------------------------------------------
-* macros
-*-------------------------------------------------------------------------
-*/
+ * macros
+ *-------------------------------------------------------------------------
+ */
/* size of buffer/# of bytes to xfer at a time when copying userblock */
#define USERBLOCK_XFER_SIZE 512
@@ -48,1705 +48,1630 @@
} \
} H5E_END_TRY; \
}
-
+
/*-------------------------------------------------------------------------
-* local functions
-*-------------------------------------------------------------------------
-*/
-static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
-static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
-static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
-static int copy_user_block(const char *infile, const char *outfile, hsize_t size);
+ * local functions
+ *-------------------------------------------------------------------------
+ */
+static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+ size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
+static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
+static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+ pack_opt_t *options);
+static int copy_user_block(const char *infile, const char *outfile,
+ hsize_t size);
#if defined (H5REPACK_DEBUG_USER_BLOCK)
-static void print_user_block(const char *filename, hid_t fid);
+static void print_user_block(const char *filename, hid_t fid);
#endif
static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
/* get the major number from the error stack. */
-static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata)
-{
- if (err_desc)
- *((int *)udata) = err_desc->maj_num;
-
- return 0;
+static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
+ if (err_desc)
+ *((int *) udata) = err_desc->maj_num;
+
+ return 0;
}
/*-------------------------------------------------------------------------
-* Function: copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modification:
-* Peter Cao, June 13, 2007
-* Add "-L, --latest" and other options to pack a file with the latest file format
-*
-* Peter Cao, September 25, 2007
-* Copy user block when repacking a file
-*
-* Pedro Vicente, August 20, 2008
-* Add a user block to file if requested
-*
-*-------------------------------------------------------------------------
-*/
-
-int copy_objects(const char* fnamein,
- const char* fnameout,
- pack_opt_t *options)
-{
- hid_t fidin;
- hid_t fidout = -1;
- trav_table_t *travt = NULL;
- hsize_t ub_size = 0; /* size of user block */
- hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
- hid_t fapl = H5P_DEFAULT; /* file access property list ID */
-
- /*-------------------------------------------------------------------------
- * open input file
- *-------------------------------------------------------------------------
- */
- if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0)
- {
- error_msg("<%s>: %s\n", fnamein, H5FOPENERROR );
- goto out;
- }
-
- /* get user block size and file space strategy/threshold */
- {
- hid_t fcpl_in; /* file creation property list ID for input file */
-
- if((fcpl_in = H5Fget_create_plist(fidin)) < 0)
- {
- error_msg("failed to retrieve file creation property list\n");
- goto out;
- }
-
- if(H5Pget_userblock(fcpl_in, &ub_size) < 0)
- {
- error_msg("failed to retrieve userblock size\n");
- goto out;
- }
-
- if(!options->fs_strategy)
- {
- if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0)
- {
- error_msg("failed to retrieve file space strategy\n");
- goto out;
- }
- }
-
- if(!options->fs_threshold)
- {
- if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0)
- {
- error_msg("failed to retrieve file space threshold\n");
- goto out;
- }
- }
-
- if(H5Pclose(fcpl_in) < 0)
- {
- error_msg("failed to close property list\n");
- goto out;
- }
- }
-
- /* Check if we need to create a non-default file creation property list */
- if(options->latest || ub_size > 0)
- {
- /* Create file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
-
- if(ub_size > 0)
- {
- if(H5Pset_userblock(fcpl, ub_size) < 0)
- {
- error_msg("failed to set non-default userblock size\n");
- goto out;
- }
- }
-
- if(options->latest)
- {
- unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
-
- /* Adjust group creation parameters for root group */
- /* (So that it is created in "dense storage" form) */
- if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
- {
- error_msg("fail to adjust group creation parameters for root group\n");
- goto out;
- }
-
- for(i = 0; i < 5; i++)
- {
- if(options->msg_size[i] > 0)
- {
- switch(i)
- {
- case 0:
- mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
- break;
-
- case 1:
- mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
- break;
-
- case 2:
- mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
- break;
-
- case 3:
- mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
- break;
-
- case 4:
- mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
- break;
- default:
- break;
- } /* end switch */
- min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];
-
- nindex++;
- } /* end if */
- } /* end for */
-
- if(nindex > 0)
- {
- if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
- {
- error_msg("fail to set the number of shared object header message indexes\n");
- goto out;
- }
-
- /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
- for(i = 0; i < (nindex - 1); i++)
- {
- if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
- error_msg("fail to configure the specified shared object header message index\n");
- goto out;
- } /* end if */
- } /* end for */
- } /* if (nindex>0) */
-
- /* Create file access property list */
- if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- } /* end if */
-
- if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
- {
- error_msg("Could not set property for using latest version of the format\n");
- goto out;
- } /* end if */
- } /* end if */
- } /* end if */
+ * Function: copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modification:
+ * Peter Cao, June 13, 2007
+ * Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ * Peter Cao, September 25, 2007
+ * Copy user block when repacking a file
+ *
+ * Pedro Vicente, August 20, 2008
+ * Add a user block to file if requested
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
+ hid_t fidin;
+ hid_t fidout = -1;
+ trav_table_t *travt = NULL;
+ hsize_t ub_size = 0; /* size of user block */
+ hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+ hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+
+ /*-------------------------------------------------------------------------
+ * open input file
+ *-------------------------------------------------------------------------
+ */
+ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL,
+ (size_t) 0)) < 0) {
+ error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
+ goto out;
+ }
+
+ /* get user block size and file space strategy/threshold */
+ {
+ hid_t fcpl_in; /* file creation property list ID for input file */
+
+ if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ goto out;
+ }
+
+ if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ goto out;
+ }
+
+ if (!options->fs_strategy) {
+ if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
+ error_msg("failed to retrieve file space strategy\n");
+ goto out;
+ }
+ }
+
+ if (!options->fs_threshold) {
+ if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
+ error_msg("failed to retrieve file space threshold\n");
+ goto out;
+ }
+ }
+
+ if (H5Pclose(fcpl_in) < 0) {
+ error_msg("failed to close property list\n");
+ goto out;
+ }
+ }
+
+ /* Check if we need to create a non-default file creation property list */
+ if (options->latest || ub_size > 0) {
+ /* Create file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+
+ if (ub_size > 0) {
+ if (H5Pset_userblock(fcpl, ub_size) < 0) {
+ error_msg("failed to set non-default userblock size\n");
+ goto out;
+ }
+ }
+
+ if (options->latest) {
+ unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
+
+ /* Adjust group creation parameters for root group */
+ /* (So that it is created in "dense storage" form) */
+ if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed) < 0) {
+ error_msg(
+ "fail to adjust group creation parameters for root group\n");
+ goto out;
+ }
+
+ for (i = 0; i < 5; i++) {
+ if (options->msg_size[i] > 0) {
+ switch (i) {
+ case 0:
+ mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+ break;
+
+ case 1:
+ mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+ break;
+
+ case 2:
+ mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+ break;
+
+ case 3:
+ mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+ break;
+
+ case 4:
+ mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+ break;
+ default:
+ break;
+ } /* end switch */
+ min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
+
+ nindex++;
+ } /* end if */
+ } /* end for */
+
+ if (nindex > 0) {
+ if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
+ error_msg(
+ "fail to set the number of shared object header message indexes\n");
+ goto out;
+ }
+
+ /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
+ for (i = 0; i < (nindex - 1); i++) {
+ if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i],
+ min_mesg_sizes[i]) < 0) {
+ error_msg(
+ "fail to configure the specified shared object header message index\n");
+ goto out;
+ } /* end if */
+ } /* end for */
+ } /* if (nindex>0) */
+
+ /* Create file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ } /* end if */
+
+ if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+ error_msg(
+ "Could not set property for using latest version of the format\n");
+ goto out;
+ } /* end if */
+ } /* end if */
+ } /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
- print_user_block(fnamein, fidin);
+ print_user_block(fnamein, fidin);
#endif
- /*-------------------------------------------------------------------------
- * set the new user userblock options in the FCPL (before H5Fcreate )
- *-------------------------------------------------------------------------
- */
- if ( options->ublock_size > 0 )
- {
- /* either use the FCPL already created or create a new one */
- if(fcpl == H5P_DEFAULT)
- {
- /* create a file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
- }
-
- /* set user block size */
- if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
- {
- error_msg("failed to set userblock size\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set alignment options
- *-------------------------------------------------------------------------
- */
- if ( options->alignment > 0 )
- {
- /* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT)
- {
- /* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- }
- }
-
- if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
- {
- error_msg("failed to set alignment\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set metadata block size option
- *-------------------------------------------------------------------------
- */
- if ( options->meta_block_size > 0 )
- {
- /* either use the FAPL already created or create a new one */
- if (fapl == H5P_DEFAULT)
- {
- /* create a file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
- {
- error_msg("Could not create file access property list\n");
- goto out;
- }
- }
-
- if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
- {
- error_msg("failed to set metadata block size\n");
- goto out;
- }
- }
-
- /*-------------------------------------------------------------------------
- * set free-space strategy options
- *-------------------------------------------------------------------------
- */
-
- /* either use the FCPL already created or create a new one */
- if(fcpl == H5P_DEFAULT)
- {
- /* create a file creation property list */
- if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
- {
- error_msg("fail to create a file creation property list\n");
- goto out;
- }
- }
-
- /* set file space strategy and free space threshold */
- if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
- {
- error_msg("failed to set file space strategy & threshold \n");
- goto out;
- }
-
- /*-------------------------------------------------------------------------
- * create the output file
- *-------------------------------------------------------------------------
- */
- if(options->verbose)
- printf("Making file <%s>...\n",fnameout);
-
- if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
- {
- error_msg("<%s>: Could not create file\n", fnameout );
- goto out;
- }
-
-
- /*-------------------------------------------------------------------------
- * write a new user block if requested
- *-------------------------------------------------------------------------
- */
- if ( options->ublock_size > 0 )
- {
- if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 )
- {
- error_msg("Could not copy user block. Exiting...\n");
- goto out;
-
- }
- }
-
- /*-------------------------------------------------------------------------
- * get list of objects
- *-------------------------------------------------------------------------
- */
-
- /* init table */
- trav_table_init(&travt);
-
- /* get the list of objects in the file */
- if(h5trav_gettable(fidin, travt) < 0)
- goto out;
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
- if(do_copy_objects(fidin, fidout, travt, options) < 0)
- {
- error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
- goto out;
- } /* end if */
-
- /*-------------------------------------------------------------------------
- * do the copy of referenced objects
- * and create hard links
- *-------------------------------------------------------------------------
- */
- if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 )
- {
- printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
- goto out;
- }
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if(fapl > 0)
- H5Pclose(fapl);
-
- if(fcpl > 0)
- H5Pclose(fcpl);
-
- H5Fclose(fidin);
- H5Fclose(fidout);
-
- /* free table */
- trav_table_free(travt);
- travt = NULL;
-
- /*-------------------------------------------------------------------------
- * write only the input file user block if there is no user block file input
- *-------------------------------------------------------------------------
- */
-
- if( ub_size > 0 && options->ublock_size == 0 )
- {
- if ( copy_user_block(fnamein, fnameout, ub_size) < 0 )
- {
- error_msg("Could not copy user block. Exiting...\n");
- goto out;
-
- }
- }
-
- return 0;
-
- /*-------------------------------------------------------------------------
- * out
- *-------------------------------------------------------------------------
- */
+ /*-------------------------------------------------------------------------
+ * set the new user userblock options in the FCPL (before H5Fcreate )
+ *-------------------------------------------------------------------------
+ */
+ if (options->ublock_size > 0) {
+ /* either use the FCPL already created or create a new one */
+ if (fcpl == H5P_DEFAULT) {
+ /* create a file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+ }
+
+ /* set user block size */
+ if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
+ error_msg("failed to set userblock size\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set alignment options
+ *-------------------------------------------------------------------------
+ */
+ if (options->alignment > 0) {
+ /* either use the FAPL already created or create a new one */
+ if (fapl == H5P_DEFAULT) {
+ /* create a file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ }
+ }
+
+ if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
+ error_msg("failed to set alignment\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set metadata block size option
+ *-------------------------------------------------------------------------
+ */
+ if (options->meta_block_size > 0) {
+ /* either use the FAPL already created or create a new one */
+ if (fapl == H5P_DEFAULT) {
+ /* create a file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ goto out;
+ }
+ }
+
+ if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
+ error_msg("failed to set metadata block size\n");
+ goto out;
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * set free-space strategy options
+ *-------------------------------------------------------------------------
+ */
+
+ /* either use the FCPL already created or create a new one */
+ if (fcpl == H5P_DEFAULT) {
+ /* create a file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ goto out;
+ }
+ }
+
+ /* set file space strategy and free space threshold */
+ if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
+ error_msg("failed to set file space strategy & threshold \n");
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * create the output file
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose)
+ printf("Making file <%s>...\n", fnameout);
+
+ if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
+ error_msg("<%s>: Could not create file\n", fnameout);
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * write a new user block if requested
+ *-------------------------------------------------------------------------
+ */
+ if (options->ublock_size > 0) {
+ if (copy_user_block(options->ublock_filename, fnameout,
+ options->ublock_size) < 0) {
+ error_msg("Could not copy user block. Exiting...\n");
+ goto out;
+
+ }
+ }
+
+ /*-------------------------------------------------------------------------
+ * get list of objects
+ *-------------------------------------------------------------------------
+ */
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin, travt) < 0)
+ goto out;
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+ error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ goto out;
+ } /* end if */
+
+ /*-------------------------------------------------------------------------
+ * do the copy of referenced objects
+ * and create hard links
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
+ printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein,
+ fnameout);
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (fapl > 0)
+ H5Pclose(fapl);
+
+ if (fcpl > 0)
+ H5Pclose(fcpl);
+
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+
+ /* free table */
+ trav_table_free(travt);
+ travt = NULL;
+
+ /*-------------------------------------------------------------------------
+ * write only the input file user block if there is no user block file input
+ *-------------------------------------------------------------------------
+ */
+
+ if (ub_size > 0 && options->ublock_size == 0) {
+ if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
+ error_msg("Could not copy user block. Exiting...\n");
+ goto out;
+
+ }
+ }
+
+ return 0;
+
+ /*-------------------------------------------------------------------------
+ * out
+ *-------------------------------------------------------------------------
+ */
out:
- H5E_BEGIN_TRY
- {
- H5Pclose(fapl);
- H5Pclose(fcpl);
- H5Fclose(fidin);
- H5Fclose(fidout);
- } H5E_END_TRY;
- if(travt)
- trav_table_free(travt);
-
- return -1;
+ H5E_BEGIN_TRY
+ {
+ H5Pclose(fapl);
+ H5Pclose(fcpl);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ }H5E_END_TRY;
+ if (travt)
+ trav_table_free(travt);
+
+ return -1;
}
/*-------------------------------------------------------------------------
-* Function: Get_hyperslab
-*
-* Purpose: Calulate a hyperslab from a dataset for higher performance.
-* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
-* Return the hyperslab dimentions and size in byte.
-*
-* Return: 0 - SUCCEED, -1 FAILED
-*
-* Parameters:
-* dcpl_id : [IN] dataset creation property.
-* rank_dset : [IN] dataset rank
-* dims_dset[] : [IN] dataset dimentions
-* size_datum : [IN] size of a data element in byte
-* dims_hslab[] : [OUT] calculated hyperslab dimentions
-* * hslab_nbytes_p : [OUT] total byte of the hyperslab
-*
-* Programmer: Jonathan Kim
-* Date: Feburary, 2012
-* Update:
-* The hyperslab calucation would be depend on if the dataset is chunked
-* or not.
-*
-* There care 3 conditions to cover:
-* 1. If chunked and a chunk fits in buffer, each chunk would be a unit of
-* collection and the boundary would be dataset's dims.
-* 2. If chunked but a chunk doesn't fit in buffer, each data element would
-* be a unit of collection and the boundary would be the chunk itself.
-* 3. If not chunked, each data element would be a unit of collection and
-* the boundary would be dataset's dims.
-*
-* The calulation starts from the last dimention (h5dump dims output).
-*
-* Note:
-* Added for JIRA HDFFV-7862.
-*-----------------------------------------*/
-
-int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
- size_t size_datum,
- hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
-{
- int status = 0;
- int k;
- H5D_layout_t dset_layout;
- int rank_chunk;
- hsize_t dims_chunk[H5S_MAX_RANK];
- hsize_t size_chunk=1;
- hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
- hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
- hsize_t hslab_nbytes; /* size of hyperslab in byte */
-
- /* init to set as size of a data element */
- hslab_nbytes = size_datum;
-
- /* get layout of dataset */
- dset_layout = H5Pget_layout(dcpl_id);
-
- /* if dataset is chunked */
- if ( dset_layout == H5D_CHUNKED )
- {
- /* get chunk dims */
- rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
- if (rank_chunk < 0)
- {
- status = -1;
- goto out;
- }
-
- for (k = rank_dset; k > 0; --k)
- size_chunk *= dims_chunk[k-1];
-
- /* figure out how many chunks can fit in the hyperslab buffer */
- nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-
-
- /* 1. if a chunk fit in hyperslab buffer */
- if (nchunk_fit >= 1)
- {
- /* Calulate a hyperslab that contains as many chunks that can fit
- * in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- * In the loop, used mapping from a datum to a chunk to figure out
- * chunk based hyperslab.
- */
- for (k = rank_dset; k > 0; --k)
- {
- /* map dataset dimentions with a chunk dims */
- chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1];
-
- /* if reminder exist, increse by 1 to cover partial edge chunks */
- if (dims_dset[k-1] % dims_chunk[k-1] > 0)
- chunk_dims_map[k-1]++;
-
- /* get mapped hyperslab dims */
- hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
- /* prepare next round */
- nchunk_fit = nchunk_fit / chunk_dims_map[k-1];
- /* if a chunk is bigger than the rest of buffer */
- if (nchunk_fit == 0)
- nchunk_fit=1;
-
- /* get hyperslab dimentions as unmapping to actual size */
- dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k-1];
- }
- }
- /* 2. if a chunk is bigger than hyperslab buffer */
- else
- {
- /* Calulate a hyperslab that contains as many data elements that
- * can fit in hyperslab buffer. Hyperslab will be increased
- * starting from the last dimention of the chunk (see h5dump's dims
- * output).
- * The calculation boundary is a chunk dims.
- */
- for (k = rank_dset; k > 0; --k)
- {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if ( ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within a chunk boundary */
- dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0)
- {
- status = -1;
- goto out;
- }
- }
- }
- }
- /* 3. if dataset is not chunked */
- else
- {
- /* Calulate a hyperslab that contains as many data elements that can
- * fit in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- */
- for (k = rank_dset; k > 0; --k)
- {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if ( ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within dataset boundary */
- dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0)
- {
- status = -1;
- goto out;
- }
- }
- }
-
- /* pass out the hyperslab size*/
- *hslab_nbytes_p = hslab_nbytes;
+ * Function: Get_hyperslab
+ *
+ * Purpose: Calulate a hyperslab from a dataset for higher performance.
+ * The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
+ * Return the hyperslab dimentions and size in byte.
+ *
+ * Return: 0 - SUCCEED, -1 FAILED
+ *
+ * Parameters:
+ * dcpl_id : [IN] dataset creation property.
+ * rank_dset : [IN] dataset rank
+ * dims_dset[] : [IN] dataset dimentions
+ * size_datum : [IN] size of a data element in byte
+ * dims_hslab[] : [OUT] calculated hyperslab dimentions
+ * * hslab_nbytes_p : [OUT] total byte of the hyperslab
+ *
+ * Programmer: Jonathan Kim
+ * Date: Feburary, 2012
+ * Update:
+ * The hyperslab calucation would be depend on if the dataset is chunked
+ * or not.
+ *
+ * There care 3 conditions to cover:
+ * 1. If chunked and a chunk fits in buffer, each chunk would be a unit of
+ * collection and the boundary would be dataset's dims.
+ * 2. If chunked but a chunk doesn't fit in buffer, each data element would
+ * be a unit of collection and the boundary would be the chunk itself.
+ * 3. If not chunked, each data element would be a unit of collection and
+ * the boundary would be dataset's dims.
+ *
+ * The calulation starts from the last dimention (h5dump dims output).
+ *
+ * Note:
+ * Added for JIRA HDFFV-7862.
+ *-----------------------------------------*/
+
+int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+ size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) {
+ int status = 0;
+ int k;
+ H5D_layout_t dset_layout;
+ int rank_chunk;
+ hsize_t dims_chunk[H5S_MAX_RANK];
+ hsize_t size_chunk = 1;
+ hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+ hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+ hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+ /* init to set as size of a data element */
+ hslab_nbytes = size_datum;
+
+ /* get layout of dataset */
+ dset_layout = H5Pget_layout(dcpl_id);
+
+ /* if dataset is chunked */
+ if (dset_layout == H5D_CHUNKED) {
+ /* get chunk dims */
+ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+ if (rank_chunk < 0) {
+ status = -1;
+ goto out;
+ }
+
+ for (k = rank_dset; k > 0; --k)
+ size_chunk *= dims_chunk[k - 1];
+
+ /* figure out how many chunks can fit in the hyperslab buffer */
+ nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+ /* 1. if a chunk fit in hyperslab buffer */
+ if (nchunk_fit >= 1) {
+ /* Calulate a hyperslab that contains as many chunks that can fit
+ * in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ * In the loop, used mapping from a datum to a chunk to figure out
+ * chunk based hyperslab.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ /* map dataset dimentions with a chunk dims */
+ chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
+
+ /* if reminder exist, increse by 1 to cover partial edge chunks */
+ if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
+ chunk_dims_map[k - 1]++;
+
+ /* get mapped hyperslab dims */
+ hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+ /* prepare next round */
+ nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
+ /* if a chunk is bigger than the rest of buffer */
+ if (nchunk_fit == 0)
+ nchunk_fit = 1;
+
+ /* get hyperslab dimentions as unmapping to actual size */
+ dims_hslab[k - 1] =
+ MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+ }
+ }
+ /* 2. if a chunk is bigger than hyperslab buffer */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that
+ * can fit in hyperslab buffer. Hyperslab will be increased
+ * starting from the last dimention of the chunk (see h5dump's dims
+ * output).
+ * The calculation boundary is a chunk dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within a chunk boundary */
+ dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0) {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+ }
+ /* 3. if dataset is not chunked */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that can
+ * fit in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within dataset boundary */
+ dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0) {
+ status = -1;
+ goto out;
+ }
+ }
+ }
+
+ /* pass out the hyperslab size*/
+ *hslab_nbytes_p = hslab_nbytes;
out:
- return status;
+ return status;
}
/*-------------------------------------------------------------------------
-* Function: do_copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modifications:
-*
-* July 2004: Introduced the extra EC or NN option for SZIP
-*
-* December 2004: Added a check for H5Dcreate; if the dataset cannot be created
-* with the requested filter, use the input one
-*
-* October 2006: Read/write using the file type by default.
-*
-* October 2006: Read by hyperslabs for big datasets.
-*
-* A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
-* i.e., if the memory needed to read a dataset is greater than this limit,
-* then hyperslab I/O is done instead of one operation I/O
-* For each dataset, the memory needed is calculated according to
-*
-* memory needed = number of elements * size of each element
-*
-* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-* are done
-*
-* H5Dread( input_dataset1 )
-* H5Dread( input_dataset2 )
-*
-* with all elements in the datasets selected. If the memory needed is greater than
-* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-* a strip mine is defined for each dimension k (a strip mine is defined as a
-* hyperslab whose size is memory manageable) according to the formula
-*
-* (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
-*
-* where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
-* that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
-* mine size k is simply defined as its dimension k, but for larger datasets the
-* hyperslab size is still memory manageable.
-* a cycle is done until the number of elements in the dataset is reached. In each
-* iteration, two parameters are defined for the function H5Sselect_hyperslab,
-* the start and size of each hyperslab, according to
-*
-* (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
-*
-* where hyperslab_offset [k] is initially set to zero, and later incremented in
-* hyperslab_size[k] offsets. The reason for the operation
-*
-* dimension[k] - hyperslab_offset[k]
-*
-* in (2) is that, when using the strip mine size, it assures that the "remaining" part
-* of the dataset that does not fill an entire strip mine is processed.
-*
-* November 2006: Use H5Ocopy in the copy of objects. The logic for using
-* H5Ocopy or not is if a change of filters or layout is requested by the user
-* then use read/write else use H5Ocopy.
-*
-* May, 1, 2008: Add a printing of the compression ratio of old size / new size
-*
-* Feburary 2012: improve Read/Write by hyperslabs for big datasets.
-* Programmer: Jonathan Kim
-*
-* A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
-* i.e., if the memory needed to read a dataset is greater than this limit,
-* then hyperslab I/O is done instead of one operation I/O
-* For each dataset, the memory needed is calculated according to
-*
-* memory needed = number of elements * size of each element
-*
-* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-* are done
-*
-* H5Dread( input_dataset )
-* H5Dwrite( output_dataset )
-*
-* with all elements in the datasets selected. If the memory needed is greater than
-* H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-* 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
-* 2. Calculate the hyperslab selections as the selection is moving forward.
-* Selection would be same as the hyperslab except for the remaining edge portion
-* of the dataset. The code take care of the remaining portion if exist.
-*
-*-------------------------------------------------------------------------
-*/
-
-int do_copy_objects(hid_t fidin,
- hid_t fidout,
- trav_table_t *travt,
- pack_opt_t *options) /* repack options */
+ * Function: do_copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modifications:
+ *
+ * July 2004: Introduced the extra EC or NN option for SZIP
+ *
+ * December 2004: Added a check for H5Dcreate; if the dataset cannot be created
+ * with the requested filter, use the input one
+ *
+ * October 2006: Read/write using the file type by default.
+ *
+ * October 2006: Read by hyperslabs for big datasets.
+ *
+ * A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
+ * i.e., if the memory needed to read a dataset is greater than this limit,
+ * then hyperslab I/O is done instead of one operation I/O
+ * For each dataset, the memory needed is calculated according to
+ *
+ * memory needed = number of elements * size of each element
+ *
+ * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ * are done
+ *
+ * H5Dread( input_dataset1 )
+ * H5Dread( input_dataset2 )
+ *
+ * with all elements in the datasets selected. If the memory needed is greater than
+ * H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ * a strip mine is defined for each dimension k (a strip mine is defined as a
+ * hyperslab whose size is memory manageable) according to the formula
+ *
+ * (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
+ *
+ * where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
+ * that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
+ * mine size k is simply defined as its dimension k, but for larger datasets the
+ * hyperslab size is still memory manageable.
+ * a cycle is done until the number of elements in the dataset is reached. In each
+ * iteration, two parameters are defined for the function H5Sselect_hyperslab,
+ * the start and size of each hyperslab, according to
+ *
+ * (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
+ *
+ * where hyperslab_offset [k] is initially set to zero, and later incremented in
+ * hyperslab_size[k] offsets. The reason for the operation
+ *
+ * dimension[k] - hyperslab_offset[k]
+ *
+ * in (2) is that, when using the strip mine size, it assures that the "remaining" part
+ * of the dataset that does not fill an entire strip mine is processed.
+ *
+ * November 2006: Use H5Ocopy in the copy of objects. The logic for using
+ * H5Ocopy or not is if a change of filters or layout is requested by the user
+ * then use read/write else use H5Ocopy.
+ *
+ * May, 1, 2008: Add a printing of the compression ratio of old size / new size
+ *
+ * Feburary 2012: improve Read/Write by hyperslabs for big datasets.
+ * Programmer: Jonathan Kim
+ *
+ * A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
+ * i.e., if the memory needed to read a dataset is greater than this limit,
+ * then hyperslab I/O is done instead of one operation I/O
+ * For each dataset, the memory needed is calculated according to
+ *
+ * memory needed = number of elements * size of each element
+ *
+ * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ * are done
+ *
+ * H5Dread( input_dataset )
+ * H5Dwrite( output_dataset )
+ *
+ * with all elements in the datasets selected. If the memory needed is greater than
+ * H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ * 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
+ * 2. Calculate the hyperslab selections as the selection is moving forward.
+ * Selection would be same as the hyperslab except for the remaining edge portion
+ * of the dataset. The code take care of the remaining portion if exist.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+ pack_opt_t *options) /* repack options */
{
- hid_t grp_in = -1; /* group ID */
- hid_t grp_out = -1; /* group ID */
- hid_t dset_in = -1; /* read dataset ID */
- hid_t dset_out = -1; /* write dataset ID */
- hid_t gcpl_in = -1; /* group creation property list */
- hid_t gcpl_out = -1; /* group creation property list */
- hid_t type_in = -1; /* named type ID */
- hid_t type_out = -1; /* named type ID */
- hid_t dcpl_in = -1; /* dataset creation property list ID */
- hid_t dcpl_out = -1; /* dataset creation property list ID */
- hid_t f_space_id = -1; /* file space ID */
- hid_t ftype_id = -1; /* file type ID */
- hid_t wtype_id = -1; /* read/write type ID */
- named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
- H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
- int rank; /* rank of dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- hsize_t dsize_in; /* input dataset size before filter */
- hsize_t dsize_out; /* output dataset size after filter */
- int apply_s; /* flag for apply filter to small dataset sizes */
- int apply_f; /* flag for apply filter to return error on H5Dcreate */
- void *buf=NULL; /* buffer for raw data */
- void *hslab_buf=NULL; /* hyperslab buffer for raw data */
- int has_filter; /* current object has a filter */
- int req_filter; /* there was a request for a filter */
- int req_obj_layout=0; /* request layout to current object */
- unsigned crt_order_flags; /* group creation order flag */
- unsigned i;
- unsigned u;
- int is_ref=0;
- htri_t is_named;
- hbool_t limit_maxdims;
- hsize_t size_dset;
-
-
- /*-------------------------------------------------------------------------
- * copy the suppplied object list
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose)
- {
- printf("-----------------------------------------\n");
- printf(" Type Filter (Compression) Name\n");
- printf("-----------------------------------------\n");
- }
-
- for ( i = 0; i < travt->nobjs; i++)
- {
- /* init variables per obj */
- buf = NULL;
- limit_maxdims = FALSE;
-
- switch ( travt->objs[i].type )
- {
-
- case H5TRAV_TYPE_UNKNOWN:
- HDassert(0);
- break;
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_GROUP
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_GROUP:
-
- if (options->verbose)
- {
- printf(FORMAT_OBJ,"group",travt->objs[i].name );
- }
-
- /* open input group */
- if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
-
- /* get input group creation property list */
- if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
- goto error;
-
- /* query and set the group creation properties */
- if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
- goto error;
-
- /* set up group creation property list */
- if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
- goto error;
-
- if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- *-------------------------------------------------------------------------
- */
- if(HDstrcmp(travt->objs[i].name, "/") == 0)
- {
- if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
- goto error;
- }
-
- else
- {
-
- if (options->grp_compact>0 || options->grp_indexed>0)
- {
- if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
- goto error;
- }
-
- if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
- goto error;
-
- }
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
- goto error;
-
-
- if(H5Pclose(gcpl_out) < 0)
- goto error;
- if(H5Pclose(gcpl_in) < 0)
- goto error;
- if(H5Gclose(grp_out) < 0)
- goto error;
- if(H5Gclose(grp_in) < 0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_DATASET
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_DATASET:
-
- has_filter = 0;
- req_filter = 0;
-
- /* check if global filters were requested */
- if ( options->n_filter_g )
- req_filter = 1;
-
- /* check if filters were requested for individual objects */
- for (u = 0; u < options->op_tbl->nelems; u++) {
-
- if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
- if (options->op_tbl->objs[u].filter->filtn > 0) {
- req_filter = 1;
- }
- }
- }
-
- /* check if layout change requested individual object */
- if (options->layout_g != H5D_LAYOUT_ERROR)
- {
- pack_info_t *pckinfo;
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0)
- {
- /* check if object exist */
- pckinfo = options_get_object (travt->objs[i].name, options->op_tbl);
- if (pckinfo)
- {
- req_obj_layout = 1;
- }
- }
- }
-
- /* early detection of references */
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((ftype_id = H5Dget_type(dset_in)) < 0)
- goto error;
- if(H5T_REFERENCE == H5Tget_class(ftype_id))
- is_ref = 1;
-
- /* Check if the datatype is committed */
- if((is_named = H5Tcommitted(ftype_id)) < 0)
- goto error;
- if(is_named)
- if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
- goto error;
-
- if(H5Tclose(ftype_id) < 0)
- goto error;
- if(H5Dclose(dset_in) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * check if we should use H5Ocopy or not
- * if there is a request for filters/layout, we read/write the object
- * otherwise we do a copy using H5Ocopy
- *-------------------------------------------------------------------------
- */
- if ( options->op_tbl->nelems ||
- options->all_filter == 1 ||
- options->all_layout == 1 ||
- is_ref ||
- is_named)
- {
-
- int j;
-
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((f_space_id = H5Dget_space(dset_in)) < 0)
- goto error;
- if((ftype_id = H5Dget_type(dset_in)) < 0)
- goto error;
- if((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
- goto error;
- if((dcpl_out = H5Pcopy(dcpl_in)) < 0)
- goto error;
- if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
- goto error;
- HDmemset(dims, 0, sizeof dims);
- if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
- goto error;
-
- if(H5Dget_space_status(dset_in, &space_status) < 0)
- goto error;
-
- nelmts = 1;
- for(j = 0; j < rank; j++)
- nelmts *= dims[j];
-
- /* wtype_id will have already been set if using a named dtype */
- if(!is_named) {
- if(options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
- } /* end if */
-
- if((msize = H5Tget_size(wtype_id)) == 0)
- goto error;
-
- /* size of current dset */
- size_dset = nelmts * msize;
-
- /*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
- if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1)
- {
- apply_s=1;
- apply_f=1;
-
- /*-------------------------------------------------------------------------
- * references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- * in a second traversal of the output file
- *-------------------------------------------------------------------------
- */
- if (H5T_REFERENCE!=H5Tget_class(wtype_id))
- {
- /* get the storage size of the input dataset */
- dsize_in=H5Dget_storage_size(dset_in);
-
- /* check for small size datasets (less than 1k) except
- * changing to COMPACT. For the reference, COMPACT is limited
- * by size 64K by library.
- */
- if (options->layout_g != H5D_COMPACT)
- {
- if ( size_dset < options->min_comp )
- apply_s=0;
- }
-
- /* apply the filter */
- if (apply_s)
- {
- if (apply_filters(travt->objs[i].name,
- rank,
- dims,
- msize,
- dcpl_out,
- options,
- &has_filter) < 0)
- goto error;
- }
-
- /* only if layout change requested for entire file or
- * individual obj */
- if (options->all_layout > 0 || req_obj_layout == 1)
- /*-------------------------------------------------
- * Unset the unlimited max dims if convert to other
- * than chunk layouts, because unlimited max dims
- * only can be applied to chunk layout.
- * Also perform only for targeted dataset
- * Also check for size limit to convert to compact
- *-------------------------------------------------*/
- if (options->layout_g != H5D_CHUNKED)
- {
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0)
- {
- /* if current obj match specified obj */
- if (options_get_object (travt->objs[i].name, options->op_tbl))
- limit_maxdims = TRUE;
- }
- else /* no dataset is specified */
- {
- limit_maxdims = TRUE;
- }
-
- /* if convert to COMPACT */
- if (options->layout_g == H5D_COMPACT)
- {
- /* should be smaller than 64K */
- if ( size_dset > MAX_COMPACT_DSIZE )
- limit_maxdims = FALSE;
- }
-
- /* unset unlimited max dims */
- if (limit_maxdims)
- H5Sset_extent_simple( f_space_id, rank, dims, NULL );
- }
-
- /*-------------------------------------------------------------------------
- * create the output dataset;
- * disable error checking in case the dataset cannot be created with the
- * modified dcpl; in that case use the original instead
- *-------------------------------------------------------------------------
- */
- H5E_BEGIN_TRY {
- dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
- } H5E_END_TRY;
-
- if(dset_out == FAIL)
- {
- if(options->verbose)
- printf(" warning: could not create dataset <%s>. Applying original settings\n",
- travt->objs[i].name);
-
- if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
- goto error;
- apply_f = 0;
- }
-
- /*-------------------------------------------------------------------------
- * read/write
- *-------------------------------------------------------------------------
- */
- if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
- {
- size_t need = (size_t)(nelmts * msize); /* bytes needed */
-
- /* have to read the whole dataset if there is only one element in the dataset */
- if(need < H5TOOLS_MALLOCSIZE)
- buf = HDmalloc(need);
-
- if(buf != NULL) {
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-
- /* Check if we have VL data in the dataset's
- * datatype that must be reclaimed */
- if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
- if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
- goto error;
- }
- else /* possibly not enough memory, read/write by hyperslabs */
- {
- size_t p_type_nbytes = msize; /*size of memory type */
- hsize_t p_nelmts = nelmts; /*total elements */
- hsize_t elmtno; /*counter */
- int carry; /*counter carry value */
- unsigned int vl_data = 0; /*contains VL datatypes */
-
- /* hyperslab info */
- hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
- hsize_t hslab_nbytes; /*bytes per hyperslab */
- hsize_t hslab_nelmts; /*elements per hyperslab*/
- hid_t hslab_space; /*hyperslab data space */
-
- /* hyperslab selection info */
- hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
- hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
- hsize_t hs_select_nelmts; /* selected elements */
- hsize_t zero[8]; /*vector of zeros */
- int k;
- H5D_layout_t dset_layout;
- hid_t dcpl_tmp = -1; /* dataset creation property list ID */
-
- /* check if we have VL data in the dataset's datatype */
- if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
- vl_data = TRUE;
-
-
- /* check first if writing dataset is chunked,
- * if so use its chunk layout for better performance. */
- dset_layout = H5Pget_layout(dcpl_out);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_out; /* writing dataset */
- else /* if reading dataset is chunked */
- {
- dset_layout = H5Pget_layout(dcpl_in);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_in; /* reading dataset */
- }
-
- /* get hyperslab dims and size in byte */
- if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
- goto error;
-
- hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
- hslab_nelmts = hslab_nbytes / p_type_nbytes;
- hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
-
- /* the hyperslab selection loop */
- HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
- HDmemset(zero, 0, sizeof zero);
-
- for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts)
- {
- if (rank > 0)
- {
- /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
- */
- for (k = 0, hs_select_nelmts = 1; k < rank; k++)
- {
- /* MIN() is used to get the remaining edge portion if exist.
- * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
- hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
- hs_select_nelmts *= hs_sel_count[k];
- }
-
- if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
- goto error;
- if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
- goto error;
- }
- else
- {
- H5Sselect_all(f_space_id);
- H5Sselect_all(hslab_space);
- hs_select_nelmts = 1;
- } /* rank */
-
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-
- /* reclaim any VL memory, if necessary */
- if(vl_data)
- H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
-
- /* calculate the next hyperslab offset */
- for (k = rank, carry = 1; k > 0 && carry; --k)
- {
- hs_sel_offset[k - 1] += hs_sel_count[k - 1];
- /* if reached the end of a dim */
- if (hs_sel_offset[k - 1] == dims[k - 1])
- hs_sel_offset[k - 1] = 0;
- else
- carry = 0;
- } /* k */
- } /* elmtno */
-
- H5Sclose(hslab_space);
- /* free */
- if (hslab_buf!=NULL)
- {
- HDfree(hslab_buf);
- hslab_buf=NULL;
- }
- } /* hyperslab read */
- } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
- /*-------------------------------------------------------------------------
- * amount of compression used
- *-------------------------------------------------------------------------
- */
- if (options->verbose)
- {
- double ratio=0;
-
- /* only print the compression ration if there was a filter request */
- if (apply_s && apply_f && req_filter)
- {
- /* get the storage size of the output dataset */
- dsize_out=H5Dget_storage_size(dset_out);
-
- /* compression ratio = uncompressed size / compressed size */
- if (dsize_out!=0)
- ratio = (double) dsize_in / (double) dsize_out;
-
- print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
- }
- else
- print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0);
-
- /* print a message that the filter was not applied
- (in case there was a filter)
- */
- if ( has_filter && apply_s == 0 )
- printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
- travt->objs[i].name,
- (int)options->min_comp);
-
- if ( has_filter && apply_f == 0 )
- printf(" <warning: could not apply the filter to %s>\n",
- travt->objs[i].name);
-
- } /* verbose */
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- goto error;
- /*close */
- if (H5Dclose(dset_out) < 0)
- goto error;
-
- }/*!H5T_REFERENCE*/
- }/*h5tools_canreadf*/
-
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
- if (H5Tclose(ftype_id) < 0)
- goto error;
- if (H5Tclose(wtype_id) < 0)
- goto error;
- if (H5Pclose(dcpl_in) < 0)
- goto error;
- if (H5Pclose(dcpl_out) < 0)
- goto error;
- if (H5Sclose(f_space_id) < 0)
- goto error;
- if (H5Dclose(dset_in) < 0)
- goto error;
-
- }
- /*-------------------------------------------------------------------------
- * we do not have request for filter/chunking use H5Ocopy instead
- *-------------------------------------------------------------------------
- */
- else
- {
- hid_t pid;
-
- /* create property to pass copy options */
- if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
- goto error;
-
- /* set options for object copy */
- if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
-
- if(H5Ocopy(fidin, /* Source file or group identifier */
- travt->objs[i].name, /* Name of the source object to be copied */
- fidout, /* Destination file or group identifier */
- travt->objs[i].name, /* Name of the destination object */
- pid, /* Properties which apply to the copy */
- H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
- goto error;
-
- /* close property */
- if(H5Pclose(pid) < 0)
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * copy attrs manually
- *-------------------------------------------------------------------------
- */
- if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
- if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- goto error;
- if(H5Dclose(dset_in) < 0)
- goto error;
- if(H5Dclose(dset_out) < 0)
- goto error;
-
-
- if (options->verbose)
- printf(FORMAT_OBJ,"dset",travt->objs[i].name );
-
-
- } /* end do we have request for filter/chunking */
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_NAMED_DATATYPE
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_NAMED_DATATYPE:
-
- if(options->verbose)
- printf(FORMAT_OBJ, "type", travt->objs[i].name);
-
- if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- goto error;
-
- /* Copy the datatype anonymously */
- if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
- travt, options)) < 0)
- goto error;
-
- /* Link in to group structure */
- if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
- H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
- goto error;
-
- if(H5Tclose(type_in) < 0)
- goto error;
- if(H5Tclose(type_out) < 0)
- goto error;
-
-
-
- break;
-
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_LINK
- * H5TRAV_TYPE_UDLINK
- *
- * Only handles external links; H5Lcopy will fail for other UD link types
- * since we don't have creation or copy callbacks for them.
- *-------------------------------------------------------------------------
- */
-
- case H5TRAV_TYPE_LINK:
- case H5TRAV_TYPE_UDLINK:
- {
-
- if(options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
-
- if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
- goto error;
-
- if (options->verbose)
- printf(FORMAT_OBJ,"link",travt->objs[i].name );
-
- }
- break;
-
- default:
- goto error;
- } /* switch */
-
- /* free */
- if (buf!=NULL)
- {
- HDfree(buf);
- buf=NULL;
- }
-
- } /* i */
-
- /* Finalize (link) the stack of named datatypes (if any) */
- named_datatype_free(&named_dt_head, 0);
-
- return 0;
+ hid_t grp_in = -1; /* group ID */
+ hid_t grp_out = -1; /* group ID */
+ hid_t dset_in = -1; /* read dataset ID */
+ hid_t dset_out = -1; /* write dataset ID */
+ hid_t gcpl_in = -1; /* group creation property list */
+ hid_t gcpl_out = -1; /* group creation property list */
+ hid_t type_in = -1; /* named type ID */
+ hid_t type_out = -1; /* named type ID */
+ hid_t dcpl_in = -1; /* dataset creation property list ID */
+ hid_t dcpl_out = -1; /* dataset creation property list ID */
+ hid_t f_space_id = -1; /* file space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
+ size_t msize; /* size of type */
+ hsize_t nelmts; /* number of elements in dataset */
+ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ hsize_t dsize_in; /* input dataset size before filter */
+ hsize_t dsize_out; /* output dataset size after filter */
+ int apply_s; /* flag for apply filter to small dataset sizes */
+ int apply_f; /* flag for apply filter to return error on H5Dcreate */
+ void *buf = NULL; /* buffer for raw data */
+ void *hslab_buf = NULL; /* hyperslab buffer for raw data */
+ int has_filter; /* current object has a filter */
+ int req_filter; /* there was a request for a filter */
+ int req_obj_layout = 0; /* request layout to current object */
+ unsigned crt_order_flags; /* group creation order flag */
+ unsigned i;
+ unsigned u;
+ int is_ref = 0;
+ htri_t is_named;
+ hbool_t limit_maxdims;
+ hsize_t size_dset;
+
+ /*-------------------------------------------------------------------------
+ * copy the suppplied object list
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->verbose) {
+ printf("-----------------------------------------\n");
+ printf(" Type Filter (Compression) Name\n");
+ printf("-----------------------------------------\n");
+ }
+
+ for (i = 0; i < travt->nobjs; i++) {
+ /* init variables per obj */
+ buf = NULL;
+ limit_maxdims = FALSE;
+
+ switch (travt->objs[i].type) {
+
+ case H5TRAV_TYPE_UNKNOWN:
+ HDassert(0);
+ break;
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_GROUP:
+
+ if (options->verbose) {
+ printf(FORMAT_OBJ, "group", travt->objs[i].name);
+ }
+
+ /* open input group */
+ if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+
+ /* get input group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ goto error;
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ goto error;
+
+ /* set up group creation property list */
+ if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+ goto error;
+
+ if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * the root is a special case, we get an ID for the root group
+ * and copy its attributes using that ID
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(travt->objs[i].name, "/") == 0) {
+ if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+ goto error;
+ }
+ else {
+
+ if (options->grp_compact > 0 || options->grp_indexed > 0) {
+ if (H5Pset_link_phase_change(gcpl_out,
+ (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed) < 0)
+ goto error;
+ }
+
+ if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
+ H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+ goto error;
+
+ }
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+ goto error;
+
+ if (H5Pclose(gcpl_out) < 0)
+ goto error;
+ if (H5Pclose(gcpl_in) < 0)
+ goto error;
+ if (H5Gclose(grp_out) < 0)
+ goto error;
+ if (H5Gclose(grp_in) < 0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_DATASET:
+
+ has_filter = 0;
+ req_filter = 0;
+
+ /* check if global filters were requested */
+ if (options->n_filter_g)
+ req_filter = 1;
+
+ /* check if filters were requested for individual objects */
+ for (u = 0; u < options->op_tbl->nelems; u++) {
+
+ if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+ if (options->op_tbl->objs[u].filter->filtn > 0) {
+ req_filter = 1;
+ }
+ }
+ }
+
+ /* check if layout change requested individual object */
+ if (options->layout_g != H5D_LAYOUT_ERROR) {
+ pack_info_t *pckinfo;
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* check if object exist */
+ pckinfo = options_get_object(travt->objs[i].name,
+ options->op_tbl);
+ if (pckinfo) {
+ req_obj_layout = 1;
+ }
+ }
+ }
+
+ /* early detection of references */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ goto error;
+ if (H5T_REFERENCE == H5Tget_class(ftype_id))
+ is_ref = 1;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ goto error;
+ if (is_named)
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+ &named_dt_head, travt, options)) < 0)
+ goto error;
+
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * check if we should use H5Ocopy or not
+ * if there is a request for filters/layout, we read/write the object
+ * otherwise we do a copy using H5Ocopy
+ *-------------------------------------------------------------------------
+ */
+ if (options->op_tbl->nelems || options->all_filter == 1
+ || options->all_layout == 1 || is_ref || is_named) {
+
+ int j;
+
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ goto error;
+ if ((f_space_id = H5Dget_space(dset_in)) < 0)
+ goto error;
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ goto error;
+ if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+ goto error;
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+ goto error;
+ if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+ goto error;
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+ goto error;
+
+ if (H5Dget_space_status(dset_in, &space_status) < 0)
+ goto error;
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ /* wtype_id will have already been set if using a named dtype */
+ if (!is_named) {
+ if (options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end if */
+
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ goto error;
+
+ /* size of current dset */
+ size_dset = nelmts * msize;
+
+ /*-------------------------------------------------------------------------
+ * check if the dataset creation property list has filters that
+ * are not registered in the current configuration
+ * 1) the external filters GZIP and SZIP might not be available
+ * 2) the internal filters might be turned off
+ *-------------------------------------------------------------------------
+ */
+ if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
+ apply_s = 1;
+ apply_f = 1;
+
+ /*-------------------------------------------------------------------------
+ * references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ * in a second traversal of the output file
+ *-------------------------------------------------------------------------
+ */
+ if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
+ /* get the storage size of the input dataset */
+ dsize_in = H5Dget_storage_size(dset_in);
+
+ /* check for small size datasets (less than 1k) except
+ * changing to COMPACT. For the reference, COMPACT is limited
+ * by size 64K by library.
+ */
+ if (options->layout_g != H5D_COMPACT) {
+ if (size_dset < options->min_comp)
+ apply_s = 0;
+ }
+
+ /* apply the filter */
+ if (apply_s) {
+ if (apply_filters(travt->objs[i].name, rank, dims,
+ msize, dcpl_out, options, &has_filter) < 0)
+ goto error;
+ }
+
+ /* only if layout change requested for entire file or
+ * individual obj */
+ if (options->all_layout > 0 || req_obj_layout == 1)
+ /*-------------------------------------------------
+ * Unset the unlimited max dims if convert to other
+ * than chunk layouts, because unlimited max dims
+ * only can be applied to chunk layout.
+ * Also perform only for targeted dataset
+ * Also check for size limit to convert to compact
+ *-------------------------------------------------*/
+ if (options->layout_g != H5D_CHUNKED) {
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* if current obj match specified obj */
+ if (options_get_object(travt->objs[i].name,
+ options->op_tbl))
+ limit_maxdims = TRUE;
+ }
+ else { /* no dataset is specified */
+ limit_maxdims = TRUE;
+ }
+
+ /* if convert to COMPACT */
+ if (options->layout_g == H5D_COMPACT) {
+ /* should be smaller than 64K */
+ if (size_dset > MAX_COMPACT_DSIZE)
+ limit_maxdims = FALSE;
+ }
+
+ /* unset unlimited max dims */
+ if (limit_maxdims)
+ H5Sset_extent_simple(f_space_id, rank, dims,
+ NULL);
+ }
+
+ /*-------------------------------------------------------------------------
+ * create the output dataset;
+ * disable error checking in case the dataset cannot be created with the
+ * modified dcpl; in that case use the original instead
+ *-------------------------------------------------------------------------
+ */
+ H5E_BEGIN_TRY
+ {
+ dset_out = H5Dcreate2(fidout,
+ travt->objs[i].name, wtype_id,
+ f_space_id, H5P_DEFAULT, dcpl_out,
+ H5P_DEFAULT);
+ }H5E_END_TRY;
+
+ if (dset_out == FAIL) {
+ if (options->verbose)
+ printf(
+ " warning: could not create dataset <%s>. Applying original settings\n",
+ travt->objs[i].name);
+
+ if ((dset_out = H5Dcreate2(fidout,
+ travt->objs[i].name, wtype_id, f_space_id,
+ H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+ goto error;
+ apply_f = 0;
+ }
+
+ /*-------------------------------------------------------------------------
+ * read/write
+ *-------------------------------------------------------------------------
+ */
+ if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
+ size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+ /* have to read the whole dataset if there is only one element in the dataset */
+ if (need < H5TOOLS_MALLOCSIZE)
+ buf = HDmalloc(need);
+
+ if (buf != NULL) {
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id,
+ H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
+ H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+ /* Check if we have VL data in the dataset's
+ * datatype that must be reclaimed */
+ if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+ if (H5Dvlen_reclaim(wtype_id, f_space_id,
+ H5P_DEFAULT, buf) < 0)
+ goto error;
+ }
+ else { /* possibly not enough memory, read/write by hyperslabs */
+ size_t p_type_nbytes = msize; /*size of memory type */
+ hsize_t p_nelmts = nelmts; /*total elements */
+ hsize_t elmtno; /*counter */
+ int carry; /*counter carry value */
+ unsigned int vl_data = 0; /*contains VL datatypes */
+
+ /* hyperslab info */
+ hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+ hsize_t hslab_nbytes; /*bytes per hyperslab */
+ hsize_t hslab_nelmts; /*elements per hyperslab*/
+ hid_t hslab_space; /*hyperslab data space */
+
+ /* hyperslab selection info */
+ hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+ hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+ hsize_t hs_select_nelmts; /* selected elements */
+ hsize_t zero[8]; /*vector of zeros */
+ int k;
+ H5D_layout_t dset_layout;
+ hid_t dcpl_tmp = -1; /* dataset creation property list ID */
+
+ /* check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+ vl_data = TRUE;
+
+ /* check first if writing dataset is chunked,
+ * if so use its chunk layout for better performance. */
+ dset_layout = H5Pget_layout(dcpl_out);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_out; /* writing dataset */
+ else { /* if reading dataset is chunked */
+ dset_layout = H5Pget_layout(dcpl_in);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_in; /* reading dataset */
+ }
+
+ /* get hyperslab dims and size in byte */
+ if (Get_hyperslab(dcpl_tmp, rank, dims,
+ p_type_nbytes, hslab_dims,
+ &hslab_nbytes) < 0)
+ goto error;
+
+ hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+ hslab_nelmts = hslab_nbytes / p_type_nbytes;
+ hslab_space = H5Screate_simple(1, &hslab_nelmts,
+ NULL);
+
+ /* the hyperslab selection loop */
+ HDmemset(hs_sel_offset, 0,
+ sizeof hs_sel_offset);
+ HDmemset(zero, 0, sizeof zero);
+
+ for (elmtno = 0; elmtno < p_nelmts; elmtno +=
+ hs_select_nelmts) {
+ if (rank > 0) {
+ /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
+ */
+ for (k = 0, hs_select_nelmts = 1;
+ k < rank; k++) {
+ /* MIN() is used to get the remaining edge portion if exist.
+ * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+ hs_sel_count[k] =
+ MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+ hs_select_nelmts *= hs_sel_count[k];
+ }
+
+ if (H5Sselect_hyperslab(f_space_id,
+ H5S_SELECT_SET, hs_sel_offset,
+ NULL, hs_sel_count, NULL) < 0)
+ goto error;
+ if (H5Sselect_hyperslab(hslab_space,
+ H5S_SELECT_SET, zero, NULL,
+ &hs_select_nelmts, NULL) < 0)
+ goto error;
+ }
+ else {
+ H5Sselect_all(f_space_id);
+ H5Sselect_all(hslab_space);
+ hs_select_nelmts = 1;
+ } /* rank */
+
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, dset_in,
+ wtype_id, hslab_space, f_space_id,
+ H5P_DEFAULT, hslab_buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, dset_out,
+ wtype_id, hslab_space, f_space_id,
+ H5P_DEFAULT, hslab_buf);
+
+ /* reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(wtype_id, hslab_space,
+ H5P_DEFAULT, hslab_buf);
+
+ /* calculate the next hyperslab offset */
+ for (k = rank, carry = 1; k > 0 && carry;
+ --k) {
+ hs_sel_offset[k - 1] += hs_sel_count[k
+ - 1];
+ /* if reached the end of a dim */
+ if (hs_sel_offset[k - 1] == dims[k - 1])
+ hs_sel_offset[k - 1] = 0;
+ else
+ carry = 0;
+ } /* k */
+ } /* elmtno */
+
+ H5Sclose(hslab_space);
+ /* free */
+ if (hslab_buf != NULL) {
+ HDfree(hslab_buf);
+ hslab_buf = NULL;
+ }
+ } /* hyperslab read */
+ } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+
+ /*-------------------------------------------------------------------------
+ * amount of compression used
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose) {
+ double ratio = 0;
+
+ /* only print the compression ration if there was a filter request */
+ if (apply_s && apply_f && req_filter) {
+ /* get the storage size of the output dataset */
+ dsize_out = H5Dget_storage_size(dset_out);
+
+ /* compression ratio = uncompressed size / compressed size */
+ if (dsize_out != 0)
+ ratio = (double) dsize_in
+ / (double) dsize_out;
+
+ print_dataset_info(dcpl_out,
+ travt->objs[i].name, ratio, 1);
+ }
+ else
+ print_dataset_info(dcpl_in, travt->objs[i].name,
+ ratio, 0);
+
+ /* print a message that the filter was not applied
+ (in case there was a filter)
+ */
+ if (has_filter && apply_s == 0)
+ printf(
+ " <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+ travt->objs[i].name,
+ (int) options->min_comp);
+
+ if (has_filter && apply_f == 0)
+ printf(
+ " <warning: could not apply the filter to %s>\n",
+ travt->objs[i].name);
+
+ } /* verbose */
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
+ options) < 0)
+ goto error;
+ /*close */
+ if (H5Dclose(dset_out) < 0)
+ goto error;
+
+ }/*!H5T_REFERENCE*/
+ }/*h5tools_canreadf*/
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tclose(ftype_id) < 0)
+ goto error;
+ if (H5Tclose(wtype_id) < 0)
+ goto error;
+ if (H5Pclose(dcpl_in) < 0)
+ goto error;
+ if (H5Pclose(dcpl_out) < 0)
+ goto error;
+ if (H5Sclose(f_space_id) < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+
+ }
+ /*-------------------------------------------------------------------------
+ * we do not have request for filter/chunking use H5Ocopy instead
+ *-------------------------------------------------------------------------
+ */
+ else {
+ hid_t pid;
+
+ /* create property to pass copy options */
+ if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
+ goto error;
+
+ /* set options for object copy */
+ if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Ocopy(fidin, /* Source file or group identifier */
+ travt->objs[i].name, /* Name of the source object to be copied */
+ fidout, /* Destination file or group identifier */
+ travt->objs[i].name, /* Name of the destination object */
+ pid, /* Properties which apply to the copy */
+ H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
+ goto error;
+
+ /* close property */
+ if (H5Pclose(pid) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy attrs manually
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+ if ((dset_out = H5Dopen2(fidout, travt->objs[i].name,
+ H5P_DEFAULT)) < 0)
+ goto error;
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options)
+ < 0)
+ goto error;
+ if (H5Dclose(dset_in) < 0)
+ goto error;
+ if (H5Dclose(dset_out) < 0)
+ goto error;
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+
+ } /* end do we have request for filter/chunking */
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_NAMED_DATATYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_NAMED_DATATYPE:
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
+ if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+ < 0)
+ goto error;
+
+ /* Copy the datatype anonymously */
+ if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
+ travt, options)) < 0)
+ goto error;
+
+ /* Link in to group structure */
+ if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
+ H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(type_in, type_out, &named_dt_head, travt, options)
+ < 0)
+ goto error;
+
+ if (H5Tclose(type_in) < 0)
+ goto error;
+ if (H5Tclose(type_out) < 0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_LINK
+ * H5TRAV_TYPE_UDLINK
+ *
+ * Only handles external links; H5Lcopy will fail for other UD link types
+ * since we don't have creation or copy callbacks for them.
+ *-------------------------------------------------------------------------
+ */
+
+ case H5TRAV_TYPE_LINK:
+ case H5TRAV_TYPE_UDLINK: {
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+ if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
+ H5P_DEFAULT, H5P_DEFAULT) < 0)
+ goto error;
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+ }
+ break;
+
+ default:
+ goto error;
+ } /* switch */
+
+ /* free */
+ if (buf != NULL) {
+ HDfree(buf);
+ buf = NULL;
+ }
+
+ } /* i */
+
+ /* Finalize (link) the stack of named datatypes (if any) */
+ named_datatype_free(&named_dt_head, 0);
+
+ return 0;
error:
- H5E_BEGIN_TRY {
- H5Gclose(grp_in);
- H5Gclose(grp_out);
- H5Pclose(dcpl_in);
- H5Pclose(gcpl_in);
- H5Pclose(gcpl_out);
- H5Sclose(f_space_id);
- H5Dclose(dset_in);
- H5Dclose(dset_out);
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Tclose(type_in);
- H5Tclose(type_out);
- named_datatype_free(&named_dt_head, 1);
- } H5E_END_TRY;
- /* free */
- if (buf!=NULL)
- HDfree(buf);
- if (hslab_buf!=NULL)
- HDfree(hslab_buf);
- return -1;
+ H5E_BEGIN_TRY
+ {
+ H5Gclose(grp_in);
+ H5Gclose(grp_out);
+ H5Pclose(dcpl_in);
+ H5Pclose(gcpl_in);
+ H5Pclose(gcpl_out);
+ H5Sclose(f_space_id);
+ H5Dclose(dset_in);
+ H5Dclose(dset_out);
+ H5Tclose(ftype_id);
+ H5Tclose(wtype_id);
+ H5Tclose(type_in);
+ H5Tclose(type_out);
+ named_datatype_free(&named_dt_head, 1);
+ }H5E_END_TRY;
+ /* free */
+ if (buf != NULL)
+ HDfree(buf);
+ if (hslab_buf != NULL)
+ HDfree(hslab_buf);
+ return -1;
}
-
/*-------------------------------------------------------------------------
-* Function: print_dataset_info
-*
-* Purpose: print name, filters, percentage compression of a dataset
-*
-*-------------------------------------------------------------------------
-*/
-static void print_dataset_info(hid_t dcpl_id,
- char *objname,
- double ratio,
- int pr)
-{
- char strfilter[255];
+ * Function: print_dataset_info
+ *
+ * Purpose: print name, filters, percentage compression of a dataset
+ *
+ *-------------------------------------------------------------------------
+ */
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
+ int pr) {
+ char strfilter[255];
#if defined (PRINT_DEBUG )
- char temp[255];
+ char temp[255];
#endif
- int nfilters; /* number of filters */
- unsigned filt_flags; /* filter flags */
- H5Z_filter_t filtn; /* filter identification number */
- unsigned cd_values[20]; /* filter client data values */
- size_t cd_nelmts; /* filter client number of values */
- char f_objname[256]; /* filter objname */
- int i;
-
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ char f_objname[256]; /* filter objname */
+ int i;
- HDstrcpy(strfilter,"\0");
+ HDstrcpy(strfilter, "\0");
- /* get information about input filters */
- if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
- return;
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+ return;
- for(i = 0; i < nfilters; i++) {
- cd_nelmts = NELMTS(cd_values);
+ for (i = 0; i < nfilters; i++) {
+ cd_nelmts = NELMTS(cd_values);
- filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
- cd_values, sizeof(f_objname), f_objname, NULL);
+ filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+ cd_values, sizeof(f_objname), f_objname, NULL);
- switch(filtn) {
+ switch (filtn) {
- case H5Z_FILTER_NONE:
- HDstrcat(strfilter,"NONE ");
- break;
+ case H5Z_FILTER_NONE:
+ HDstrcat(strfilter, "NONE ");
+ break;
- case H5Z_FILTER_DEFLATE:
- HDstrcat(strfilter,"GZIP ");
+ case H5Z_FILTER_DEFLATE:
+ HDstrcat(strfilter, "GZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned level=cd_values[0];
- sprintf(temp,"(%d)",level);
- HDstrcat(strfilter,temp);
- }
+ {
+ unsigned level=cd_values[0];
+ sprintf(temp,"(%d)",level);
+ HDstrcat(strfilter,temp);
+ }
#endif
- break;
+ break;
- case H5Z_FILTER_SZIP:
- HDstrcat(strfilter,"SZIP ");
+ case H5Z_FILTER_SZIP:
+ HDstrcat(strfilter, "SZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
- unsigned ppb=cd_values[1];
- sprintf(temp,"(%d,",ppb);
- HDstrcat(strfilter,temp);
- if (options_mask & H5_SZIP_EC_OPTION_MASK)
- HDstrcpy(temp,"EC) ");
- else if (options_mask & H5_SZIP_NN_OPTION_MASK)
- HDstrcpy(temp,"NN) ");
- }
- HDstrcat(strfilter,temp);
+ {
+ unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
+ unsigned ppb=cd_values[1];
+ sprintf(temp,"(%d,",ppb);
+ HDstrcat(strfilter,temp);
+ if (options_mask & H5_SZIP_EC_OPTION_MASK)
+ HDstrcpy(temp,"EC) ");
+ else if (options_mask & H5_SZIP_NN_OPTION_MASK)
+ HDstrcpy(temp,"NN) ");
+ }
+ HDstrcat(strfilter,temp);
#endif
- break;
-
- case H5Z_FILTER_SHUFFLE:
- HDstrcat(strfilter,"SHUF ");
- break;
-
- case H5Z_FILTER_FLETCHER32:
- HDstrcat(strfilter,"FLET ");
- break;
-
- case H5Z_FILTER_NBIT:
- HDstrcat(strfilter,"NBIT ");
- break;
-
- case H5Z_FILTER_SCALEOFFSET:
- HDstrcat(strfilter,"SCALEOFFSET ");
- break;
-
- default:
- HDstrcat(strfilter,"UD ");
- break;
- } /* switch */
- }/*i*/
-
- if(!pr)
- printf(FORMAT_OBJ,"dset",objname );
- else
- {
- char str[255], temp[28];
- HDstrcpy(str,"dset ");
- HDstrcat(str,strfilter);
- sprintf(temp," (%.3f:1)",ratio);
- HDstrcat(str,temp);
- printf(FORMAT_OBJ,str,objname);
- }
+ break;
+
+ case H5Z_FILTER_SHUFFLE:
+ HDstrcat(strfilter, "SHUF ");
+ break;
+
+ case H5Z_FILTER_FLETCHER32:
+ HDstrcat(strfilter, "FLET ");
+ break;
+
+ case H5Z_FILTER_NBIT:
+ HDstrcat(strfilter, "NBIT ");
+ break;
+
+ case H5Z_FILTER_SCALEOFFSET:
+ HDstrcat(strfilter, "SCALEOFFSET ");
+ break;
+
+ default:
+ HDstrcat(strfilter, "UD ");
+ break;
+ } /* switch */
+ }/*i*/
+
+ if (!pr)
+ printf(FORMAT_OBJ, "dset", objname);
+ else {
+ char str[255], temp[28];
+ HDstrcpy(str, "dset ");
+ HDstrcat(str, strfilter);
+ sprintf(temp, " (%.3f:1)", ratio);
+ HDstrcat(str, temp);
+ printf(FORMAT_OBJ, str, objname);
+ }
}
-
/*-------------------------------------------------------------------------
-* Function: copy_user_block
-*
-* Purpose: copy user block from one file to another
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Peter Cao
-*
-* Date: October, 25, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int
-copy_user_block(const char *infile, const char *outfile, hsize_t size)
-{
- int infid = -1, outfid = -1; /* File descriptors */
- int status = 0; /* Return value */
-
- /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
- HDassert(size > 0);
-
- /* Open files */
- if((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
- status = -1;
- goto done;
- }
- if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
- status = -1;
- goto done;
- }
-
- /* Copy the userblock from the input file to the output file */
- while(size > 0) {
- ssize_t nread, nbytes; /* # of bytes transfered, etc. */
- char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
- const char *wbuf; /* Pointer into buffer, for writing */
-
- /* Read buffer from source file */
- if(size > USERBLOCK_XFER_SIZE)
- nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(infid, rbuf, (size_t)size);
- if(nread < 0) {
- status = -1;
- goto done;
- } /* end if */
-
- /* Write buffer to destination file */
- /* (compensating for interrupted writes & checking for errors, etc.) */
- nbytes = nread;
- wbuf = rbuf;
- while(nbytes > 0) {
- ssize_t nwritten; /* # of bytes written */
-
- do {
- nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
- } while(-1 == nwritten && EINTR == errno);
- if(-1 == nwritten) { /* error */
- status = -1;
- goto done;
- } /* end if */
- HDassert(nwritten > 0);
- HDassert(nwritten <= nbytes);
-
- /* Update # of bytes left & offset in buffer */
- nbytes -= nwritten;
- wbuf += nwritten;
- HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
- } /* end while */
-
- /* Update size of userblock left to transfer */
- size = size - (hsize_t)nread;
- } /* end while */
+ * Function: copy_user_block
+ *
+ * Purpose: copy user block from one file to another
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Peter Cao
+ *
+ * Date: October, 25, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int copy_user_block(const char *infile, const char *outfile,
+ hsize_t size) {
+ int infid = -1, outfid = -1; /* File descriptors */
+ int status = 0; /* Return value */
+
+ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
+ HDassert(size > 0);
+
+ /* Open files */
+ if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
+ status = -1;
+ goto done;
+ }
+ if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
+ status = -1;
+ goto done;
+ }
+
+ /* Copy the userblock from the input file to the output file */
+ while (size > 0) {
+ ssize_t nread, nbytes; /* # of bytes transfered, etc. */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
+ const char *wbuf; /* Pointer into buffer, for writing */
+
+ /* Read buffer from source file */
+ if (size > USERBLOCK_XFER_SIZE)
+ nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(infid, rbuf, (size_t)size);
+ if (nread < 0) {
+ status = -1;
+ goto done;
+ } /* end if */
+
+ /* Write buffer to destination file */
+ /* (compensating for interrupted writes & checking for errors, etc.) */
+ nbytes = nread;
+ wbuf = rbuf;
+ while (nbytes > 0) {
+ ssize_t nwritten; /* # of bytes written */
+
+ do {
+ nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
+ } while (-1 == nwritten && EINTR == errno);
+ if (-1 == nwritten) { /* error */
+ status = -1;
+ goto done;
+ } /* end if */
+ HDassert(nwritten > 0);
+ HDassert(nwritten <= nbytes);
+
+ /* Update # of bytes left & offset in buffer */
+ nbytes -= nwritten;
+ wbuf += nwritten;
+ HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+ } /* end while */
+
+ /* Update size of userblock left to transfer */
+ size = size - (hsize_t) nread;
+ } /* end while */
done:
- if(infid > 0)
- HDclose(infid);
- if(outfid > 0)
- HDclose(outfid);
+ if (infid > 0)
+ HDclose(infid);
+ if (outfid > 0)
+ HDclose(outfid);
- return status;
+ return status;
}
-
-
/*-------------------------------------------------------------------------
-* Function: print_user_block
-*
-* Purpose: print user block
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente
-*
-* Date: August, 20, 2008
-*
-*-------------------------------------------------------------------------
-*/
+ * Function: print_user_block
+ *
+ * Purpose: print user block
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente
+ *
+ * Date: August, 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static
void print_user_block(const char *filename, hid_t fid)
{
- int fh; /* file handle */
- hsize_t ub_size; /* user block size */
- hsize_t size; /* size read */
- hid_t fcpl; /* file creation property list ID for HDF5 file */
- int i;
-
- /* get user block size */
- if(( fcpl = H5Fget_create_plist(fid)) < 0)
- {
- error_msg("failed to retrieve file creation property list\n");
- goto done;
- }
-
- if(H5Pget_userblock(fcpl, &ub_size) < 0)
- {
- error_msg("failed to retrieve userblock size\n");
- goto done;
- }
-
- if(H5Pclose(fcpl) < 0)
- {
- error_msg("failed to close property list\n");
- goto done;
- }
-
- /* open file */
- if((fh = HDopen(filename, O_RDONLY, 0)) < 0)
- {
- goto done;
- }
-
- size = ub_size;
-
- /* read file */
- while(size > 0)
- {
- ssize_t nread; /* # of bytes read */
- char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
-
- /* read buffer */
- if(size > USERBLOCK_XFER_SIZE)
- nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(fh, rbuf, (size_t)size);
-
- for(i = 0; i < nread; i++)
- {
-
- printf("%c ", rbuf[i]);
-
- }
- printf("\n");
-
- if(nread < 0)
- {
- goto done;
- }
-
-
- /* update size of userblock left to transfer */
- size -= nread;
- }
+ int fh; /* file handle */
+ hsize_t ub_size; /* user block size */
+ hsize_t size; /* size read */
+ hid_t fcpl; /* file creation property list ID for HDF5 file */
+ int i;
-done:
- if(fh > 0)
- HDclose(fh);
+ /* get user block size */
+ if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ goto done;
+ }
+
+ if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ goto done;
+ }
+
+ if(H5Pclose(fcpl) < 0) {
+ error_msg("failed to close property list\n");
+ goto done;
+ }
+
+ /* open file */
+ if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+ goto done;
+ }
+ size = ub_size;
+
+ /* read file */
+ while(size > 0) {
+ ssize_t nread; /* # of bytes read */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+
+ /* read buffer */
+ if(size > USERBLOCK_XFER_SIZE)
+ nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(fh, rbuf, (size_t)size);
+
+ for(i = 0; i < nread; i++) {
+
+ printf("%c ", rbuf[i]);
+
+ }
+ printf("\n");
+
+ if(nread < 0) {
+ goto done;
+ }
+
+ /* update size of userblock left to transfer */
+ size -= nread;
+ }
+
+done:
+ if(fh > 0)
+ HDclose(fh);
- return;
+ return;
}
#endif
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index b5f9d31..7af776d 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -20,267 +20,345 @@
/* Name of tool */
#define PROGRAMNAME "h5repack"
-static void usage(const char *prog);
-static void parse_command_line(int argc, const char **argv, pack_opt_t* options);
-static void read_info(const char *filename,pack_opt_t *options);
-
+static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
/* module-scoped variables */
-static int has_i_o = 0;
-const char *infile = NULL;
-const char *outfile = NULL;
-
+static int has_i_o = 0;
+const char *infile = NULL;
+const char *outfile = NULL;
/*
* Command-line options: The user can specify short or long-named
* parameters.
*/
static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:T:";
-static struct long_options l_opts[] = {
- { "help", no_arg, 'h' },
- { "version", no_arg, 'V' },
- { "verbose", no_arg, 'v' },
- { "filter", require_arg, 'f' },
- { "layout", require_arg, 'l' },
- { "minimum", require_arg, 'm' },
- { "file", require_arg, 'e' },
- { "native", no_arg, 'n' },
- { "latest", no_arg, 'L' },
- { "compact", require_arg, 'c' },
- { "indexed", require_arg, 'd' },
- { "ssize", require_arg, 's' },
- { "ublock", require_arg, 'u' },
- { "block", require_arg, 'b' },
- { "metadata_block_size", require_arg, 'M' },
- { "threshold", require_arg, 't' },
- { "alignment", require_arg, 'a' },
- { "infile", require_arg, 'i' }, /* -i for backward compability */
- { "outfile", require_arg, 'o' }, /* -o for backward compability */
- { "fs_strategy", require_arg, 'S' },
- { "fs_threshold", require_arg, 'T' },
- { NULL, 0, '\0' }
-};
-
-
-
+static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "version",
+ no_arg, 'V' }, { "verbose", no_arg, 'v' },
+ { "filter", require_arg, 'f' }, { "layout", require_arg, 'l' }, {
+ "minimum", require_arg, 'm' }, { "file", require_arg, 'e' }, {
+ "native", no_arg, 'n' }, { "latest", no_arg, 'L' }, { "compact",
+ require_arg, 'c' }, { "indexed", require_arg, 'd' }, { "ssize",
+ require_arg, 's' }, { "ublock", require_arg, 'u' }, { "block",
+ require_arg, 'b' }, { "metadata_block_size", require_arg, 'M' },
+ { "threshold", require_arg, 't' }, { "alignment", require_arg, 'a' }, {
+ "infile", require_arg, 'i' }, /* -i for backward compability */
+ { "outfile", require_arg, 'o' }, /* -o for backward compability */
+ { "fs_strategy", require_arg, 'S' },
+ { "fs_threshold", require_arg, 'T' }, { NULL, 0, '\0' } };
/*-------------------------------------------------------------------------
- * Function: main
+ * Function: usage
*
- * Purpose: h5repack main program
+ * Purpose: print usage
*
- * Return: Success: EXIT_SUCCESS(0)
+ * Return: void
*
- * Failure: EXIT_FAILURE(1)
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) {
+ printf("usage: %s [OPTIONS] file1 file2\n", prog);
+ printf(" file1 Input HDF5 File\n");
+ printf(" file2 Output HDF5 File\n");
+ printf(" OPTIONS\n");
+ printf(" -h, --help Print a usage message and exit\n");
+ printf(
+ " -v, --verbose Verbose mode, print object information\n");
+ printf(" -V, --version Print version number and exit\n");
+ printf(
+ " -n, --native Use a native HDF5 type when repacking\n");
+ printf(" -L, --latest Use latest version of file format\n");
+ printf(
+ " -c L1, --compact=L1 Maximum number of links in header messages\n");
+ printf(
+ " -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
+ printf(
+ " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
+ printf(
+ " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n");
+ printf(
+ " -e E, --file=E Name of file E with the -f and -l options\n");
+ printf(
+ " -u U, --ublock=U Name of file U with user block data to be added\n");
+ printf(" -b B, --block=B Size of user block to be added\n");
+ printf(
+ " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
+ printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n");
+ printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n");
+ printf(" -f FILT, --filter=FILT Filter type\n");
+ printf(" -l LAYT, --layout=LAYT Layout type\n");
+ printf(
+ " -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n");
+ printf(
+ " -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n");
+
+ printf("\n");
+
+ printf(
+ " M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
+ printf(" E - is a filename.\n");
+ printf(" S - is an integer\n");
+ printf(" U - is a filename.\n");
+ printf(" T - is an integer\n");
+ printf(" A - is an integer greater than zero\n");
+ printf(
+ " B - is the user block size, any value that is 512 or greater and is\n");
+ printf(" a power of 2 (1024 default)\n");
+ printf(
+ " F - is the shared object header message type, any of <dspace|dtype|fill|\n");
+ printf(
+ " pline|attr>. If F is not specified, S applies to all messages\n");
+ printf("\n");
+ printf(
+ " FS_STRGY is the file space management strategy to use for the output file.\n");
+ printf(" It is a string as listed below:\n");
+ printf(
+ " ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
+ printf(" for file space allocation\n");
+ printf(
+ " ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
+ printf(" for file space allocation\n");
+ printf(
+ " AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
+ printf(" VFD - Use virtual file driver for file space allocation\n");
+ printf("\n");
+ printf(
+ " FS_THRD is the free-space section threshold to use for the output file.\n");
+ printf(
+ " It is the minimum size (in bytes) of free-space sections to be tracked\n");
+ printf(" by the the library's free-space managers.\n");
+ printf("\n");
+
+ printf(" FILT - is a string with the format:\n");
+ printf("\n");
+ printf(" <list of objects>:<name of filter>=<filter parameters>\n");
+ printf("\n");
+ printf(
+ " <list of objects> is a comma separated list of object names, meaning apply\n");
+ printf(
+ " compression only to those objects. If no names are specified, the filter\n");
+ printf(" is applied to all objects\n");
+ printf(" <name of filter> can be:\n");
+ printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+ printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+ printf(" SHUF, to apply the HDF5 shuffle filter\n");
+ printf(" FLET, to apply the HDF5 checksum filter\n");
+ printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+ printf(" SOFF, to apply the HDF5 Scale/Offset filter\n");
+ printf(" UD, to apply a user defined filter\n");
+ printf(" NONE, to remove all filters\n");
+ printf(
+ " <filter parameters> is optional filter parameter information\n");
+ printf(" GZIP=<deflation level> from 1-9\n");
+ printf(
+ " SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+ printf(" 2-32 and coding method is either EC or NN\n");
+ printf(" SHUF (no parameter)\n");
+ printf(" FLET (no parameter)\n");
+ printf(" NBIT (no parameter)\n");
+ printf(
+ " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+ printf(" is either IN or DS\n");
+ printf(
+ " UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
+ printf(
+ " required values for filter_number,cd_value_count,value_1\n");
+ printf(" optional values for value_2 to value_N\n");
+ printf(" NONE (no parameter)\n");
+ printf("\n");
+ printf(" LAYT - is a string with the format:\n");
+ printf("\n");
+ printf(" <list of objects>:<layout type>=<layout parameters>\n");
+ printf("\n");
+ printf(
+ " <list of objects> is a comma separated list of object names, meaning that\n");
+ printf(
+ " layout information is supplied for those objects. If no names are\n");
+ printf(" specified, the layout type is applied to all objects\n");
+ printf(" <layout type> can be:\n");
+ printf(" CHUNK, to apply chunking layout\n");
+ printf(" COMPA, to apply compact layout\n");
+ printf(" CONTI, to apply contiguous layout\n");
+ printf(" <layout parameters> is optional layout information\n");
+ printf(
+ " CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+ printf(" COMPA (no parameter)\n");
+ printf(" CONTI (no parameter)\n");
+ printf("\n");
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+ printf("\n");
+ printf(" GZIP compression with level 1 to all objects\n");
+ printf("\n");
+ printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
+ printf("\n");
+ printf(
+ " SZIP compression with 8 pixels per block and NN coding method to object A\n");
+ printf("\n");
+ printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
+ printf("\n");
+ printf(
+ " Chunked layout, with a layout size of 20x10, to objects A and B\n");
+ printf(" and remove filters to objects C, D, F\n");
+ printf("\n");
+ printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
+ printf("\n");
+ printf(
+ " Using latest file format with maximum compact group size of 10 and\n");
+ printf(" and minimum shared datatype size of 20\n");
+ printf("\n");
+ printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+ printf("\n");
+ printf(" Add both filters SHUF and GZIP in this order to all datasets\n");
+ printf("\n");
+ printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
+ printf("\n");
+ printf(" Add bzip2 filter to all datasets\n");
+ printf("\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function: leave
*
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Purpose: Shutdown MPI & HDF5 and call exit()
*
- * Date: May 9, 2003
+ * Return: Does not return
*
- * Comments:
+ * Programmer: Quincey Koziol
+ * Saturday, 31. January 2004
+ *
+ * Modifications:
*
*-------------------------------------------------------------------------
*/
-int main(int argc, const char **argv)
-{
-
- pack_opt_t options; /*the global options */
- int ret=-1;
-
- h5tools_setprogname(PROGRAMNAME);
- h5tools_setstatus(EXIT_SUCCESS);
-
- /* Initialize h5tools lib */
- h5tools_init();
-
- /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
- if ( h5tools_getenv_update_hyperslab_bufsize() < 0)
- HDexit(EXIT_FAILURE);
-
- /* initialize options */
- h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t)0);
-
- parse_command_line(argc, argv, &options);
-
- /* get file names if they were not yet got */
- if ( has_i_o == 0 )
- {
-
- if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL )
- {
- infile = argv[ opt_ind ];
- outfile = argv[ opt_ind + 1 ];
-
- if ( HDstrcmp( infile, outfile ) == 0 )
- {
- error_msg("file names cannot be the same\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
-
- }
- }
-
- else
- {
- error_msg("file names missing\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
- }
- }
-
-
- /* pack it */
- ret=h5repack(infile,outfile,&options);
+static void leave(int ret) {
+ h5tools_close();
- /* free tables */
- h5repack_end(&options);
-
- if (ret==-1)
- return 1;
- else
- return 0;
+ HDexit(ret);
}
-
-
/*-------------------------------------------------------------------------
- * Function: usage
+ * Function: read_info
*
- * Purpose: print usage
+ * Purpose: read comp and chunk options from a file
*
- * Return: void
+ * Return: void, exit on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
*
*-------------------------------------------------------------------------
*/
-static void usage(const char *prog)
-{
- printf("usage: %s [OPTIONS] file1 file2\n", prog);
- printf(" file1 Input HDF5 File\n");
- printf(" file2 Output HDF5 File\n");
- printf(" OPTIONS\n");
- printf(" -h, --help Print a usage message and exit\n");
- printf(" -v, --verbose Verbose mode, print object information\n");
- printf(" -V, --version Print version number and exit\n");
- printf(" -n, --native Use a native HDF5 type when repacking\n");
- printf(" -L, --latest Use latest version of file format\n");
- printf(" -c L1, --compact=L1 Maximum number of links in header messages\n");
- printf(" -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
- printf(" -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
- printf(" -m M, --minimum=M Do not apply the filter to datasets smaller than M\n");
- printf(" -e E, --file=E Name of file E with the -f and -l options\n");
- printf(" -u U, --ublock=U Name of file U with user block data to be added\n");
- printf(" -b B, --block=B Size of user block to be added\n");
- printf(" -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n");
- printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n");
- printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n");
- printf(" -f FILT, --filter=FILT Filter type\n");
- printf(" -l LAYT, --layout=LAYT Layout type\n");
- printf(" -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n");
- printf(" -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n");
-
- printf("\n");
-
- printf(" M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
- printf(" E - is a filename.\n");
- printf(" S - is an integer\n");
- printf(" U - is a filename.\n");
- printf(" T - is an integer\n");
- printf(" A - is an integer greater than zero\n");
- printf(" B - is the user block size, any value that is 512 or greater and is\n");
- printf(" a power of 2 (1024 default)\n");
- printf(" F - is the shared object header message type, any of <dspace|dtype|fill|\n");
- printf(" pline|attr>. If F is not specified, S applies to all messages\n");
- printf("\n");
- printf(" FS_STRGY is the file space management strategy to use for the output file.\n");
- printf(" It is a string as listed below:\n");
- printf(" ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
- printf(" for file space allocation\n");
- printf(" ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
- printf(" for file space allocation\n");
- printf(" AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
- printf(" VFD - Use virtual file driver for file space allocation\n");
- printf("\n");
- printf(" FS_THRD is the free-space section threshold to use for the output file.\n");
- printf(" It is the minimum size (in bytes) of free-space sections to be tracked\n");
- printf(" by the the library's free-space managers.\n");
- printf("\n");
-
- printf(" FILT - is a string with the format:\n");
- printf("\n");
- printf(" <list of objects>:<name of filter>=<filter parameters>\n");
- printf("\n");
- printf(" <list of objects> is a comma separated list of object names, meaning apply\n");
- printf(" compression only to those objects. If no names are specified, the filter\n");
- printf(" is applied to all objects\n");
- printf(" <name of filter> can be:\n");
- printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
- printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
- printf(" SHUF, to apply the HDF5 shuffle filter\n");
- printf(" FLET, to apply the HDF5 checksum filter\n");
- printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
- printf(" SOFF, to apply the HDF5 Scale/Offset filter\n");
- printf(" UD, to apply a user defined filter\n");
- printf(" NONE, to remove all filters\n");
- printf(" <filter parameters> is optional filter parameter information\n");
- printf(" GZIP=<deflation level> from 1-9\n");
- printf(" SZIP=<pixels per block,coding> pixels per block is a even number in\n");
- printf(" 2-32 and coding method is either EC or NN\n");
- printf(" SHUF (no parameter)\n");
- printf(" FLET (no parameter)\n");
- printf(" NBIT (no parameter)\n");
- printf(" SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
- printf(" is either IN or DS\n");
- printf(" UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
- printf(" required values for filter_number,cd_value_count,value_1\n");
- printf(" optional values for value_2 to value_N\n");
- printf(" NONE (no parameter)\n");
- printf("\n");
- printf(" LAYT - is a string with the format:\n");
- printf("\n");
- printf(" <list of objects>:<layout type>=<layout parameters>\n");
- printf("\n");
- printf(" <list of objects> is a comma separated list of object names, meaning that\n");
- printf(" layout information is supplied for those objects. If no names are\n");
- printf(" specified, the layout type is applied to all objects\n");
- printf(" <layout type> can be:\n");
- printf(" CHUNK, to apply chunking layout\n");
- printf(" COMPA, to apply compact layout\n");
- printf(" CONTI, to apply contiguous layout\n");
- printf(" <layout parameters> is optional layout information\n");
- printf(" CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
- printf(" COMPA (no parameter)\n");
- printf(" CONTI (no parameter)\n");
- printf("\n");
- printf("Examples of use:\n");
- printf("\n");
- printf("1) h5repack -v -f GZIP=1 file1 file2\n");
- printf("\n");
- printf(" GZIP compression with level 1 to all objects\n");
- printf("\n");
- printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
- printf("\n");
- printf(" SZIP compression with 8 pixels per block and NN coding method to object A\n");
- printf("\n");
- printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
- printf("\n");
- printf(" Chunked layout, with a layout size of 20x10, to objects A and B\n");
- printf(" and remove filters to objects C, D, F\n");
- printf("\n");
- printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
- printf("\n");
- printf(" Using latest file format with maximum compact group size of 10 and\n");
- printf(" and minimum shared datatype size of 20\n");
- printf("\n");
- printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
- printf("\n");
- printf(" Add both filters SHUF and GZIP in this order to all datasets\n");
- printf("\n");
- printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
- printf("\n");
- printf(" Add bzip2 filter to all datasets\n");
- printf("\n");
-}
+static
+int read_info(const char *filename, pack_opt_t *options) {
+
+ char stype[10];
+ char comp_info[1024];
+ FILE *fp = NULL;
+ char c;
+ int i, rc = 1;
+ int ret_value = EXIT_SUCCESS;
+
+ if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+ error_msg("cannot open options file %s\n", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+
+ /* cycle until end of file reached */
+ while (1) {
+ rc = fscanf(fp, "%s", stype);
+ if (rc == -1)
+ break;
+
+ /*-------------------------------------------------------------------------
+ * filter
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(stype,"-f") == 0) {
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ comp_info[i] = c;
+ i++;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+
+ if (h5repack_addfilter(comp_info, options) == -1) {
+ error_msg("could not add compression option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * layout
+ *-------------------------------------------------------------------------
+ */
+ else if (HDstrcmp(stype,"-l") == 0) {
+
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ if (HDfeof(fp))
+ break;
+ }
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ fscanf(fp, "%c", &c);
+ comp_info[i] = c;
+ i++;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+
+ if (h5repack_addlayout(comp_info, options) == -1) {
+ error_msg("could not add chunck option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+ /*-------------------------------------------------------------------------
+ * not valid
+ *-------------------------------------------------------------------------
+ */
+ else {
+ error_msg("bad file format for %s", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+ }
+
+done:
+ if (fp)
+ HDfclose(fp);
+
+ return ret_value;
+}
/*-------------------------------------------------------------------------
* Function: parse_command_line
@@ -291,316 +369,275 @@ static void usage(const char *prog)
*/
static
-void parse_command_line(int argc, const char **argv, pack_opt_t* options)
-{
-
- int opt;
-
- /* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
- {
- switch ((char)opt)
- {
-
- /* -i for backward compability */
- case 'i':
- infile = opt_arg;
- has_i_o = 1;
- break;
- /* -o for backward compability */
- case 'o':
- outfile = opt_arg;
- has_i_o = 1;
- break;
-
-
- case 'h':
- usage(h5tools_getprogname());
- HDexit(EXIT_SUCCESS);
- case 'V':
- print_version(h5tools_getprogname());
- HDexit(EXIT_SUCCESS);
- case 'v':
- options->verbose = 1;
- break;
- case 'f':
-
- /* parse the -f filter option */
- if (h5repack_addfilter( opt_arg, options)<0)
- {
- error_msg("in parsing filter\n");
- HDexit(EXIT_FAILURE);
- }
- break;
- case 'l':
-
- /* parse the -l layout option */
- if (h5repack_addlayout( opt_arg, options)<0)
- {
- error_msg("in parsing layout\n");
- HDexit(EXIT_FAILURE);
- }
- break;
-
-
- case 'm':
-
- options->min_comp = HDatoi( opt_arg );
- if ((int)options->min_comp<=0)
- {
- error_msg("invalid minimum compress size <%s>\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
-
- case 'e':
- read_info( opt_arg, options);
- break;
-
- case 'n':
- options->use_native = 1;
- break;
-
- case 'L':
- options->latest = 1;
- break;
-
- case 'c':
-
- options->grp_compact = HDatoi( opt_arg );
- if (options->grp_compact>0)
- options->latest = 1; /* must use latest format */
- break;
-
-
- case 'd':
-
- options->grp_indexed = HDatoi( opt_arg );
- if (options->grp_indexed>0)
- options->latest = 1; /* must use latest format */
- break;
-
- case 's':
-
- {
-
- int idx = 0;
- int ssize = 0;
- char *msgPtr = HDstrchr( opt_arg, ':');
- options->latest = 1; /* must use latest format */
- if (msgPtr == NULL)
- {
- ssize = HDatoi( opt_arg );
- for (idx=0; idx<5; idx++)
- options->msg_size[idx] = ssize;
- }
- else
- {
- char msgType[10];
- HDstrcpy(msgType, msgPtr+1);
- msgPtr[0] = '\0';
- ssize = HDatoi( opt_arg );
- if (HDstrncmp(msgType, "dspace",6) == 0) {
- options->msg_size[0] = ssize;
- }
- else if (HDstrncmp(msgType, "dtype", 5) == 0) {
- options->msg_size[1] = ssize;
- }
- else if (HDstrncmp(msgType, "fill", 4) == 0) {
- options->msg_size[2] = ssize;
- }
- else if (HDstrncmp(msgType, "pline", 5) == 0) {
- options->msg_size[3] = ssize;
- }
- else if (HDstrncmp(msgType, "attr", 4) == 0) {
- options->msg_size[4] = ssize;
- }
- }
- }
-
- break;
-
- case 'u':
-
- options->ublock_filename = opt_arg;
- break;
-
- case 'b':
-
- options->ublock_size = (hsize_t)HDatol( opt_arg );
- break;
-
- case 'M':
-
- options->meta_block_size = (hsize_t)HDatol( opt_arg );
- break;
-
- case 't':
-
- options->threshold = (hsize_t)HDatol( opt_arg );
- break;
-
- case 'a':
-
- options->alignment = HDatol( opt_arg );
- if ( options->alignment < 1 )
- {
- error_msg("invalid alignment size\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
-
- case 'S':
- {
- char strategy[MAX_NC_NAME];
-
- HDstrcpy(strategy, opt_arg);
- if(!HDstrcmp(strategy, "ALL_PERSIST"))
- options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
- else if(!HDstrcmp(strategy, "ALL"))
- options->fs_strategy = H5F_FILE_SPACE_ALL;
- else if(!HDstrcmp(strategy, "AGGR_VFD"))
- options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
- else if(!HDstrcmp(strategy, "VFD"))
- options->fs_strategy = H5F_FILE_SPACE_VFD;
- else {
- error_msg("invalid file space management strategy\n", opt_arg );
- HDexit(EXIT_FAILURE);
- }
- break;
- }
-
- case 'T':
-
- options->fs_threshold = (hsize_t)HDatol( opt_arg );
- break;
- default:
- break;
- } /* switch */
-
-
- } /* while */
-
- if ( has_i_o == 0 )
- {
- /* check for file names to be processed */
- if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
- {
- error_msg("missing file names\n");
- usage(h5tools_getprogname());
- HDexit(EXIT_FAILURE);
- }
- }
-
+int parse_command_line(int argc, const char **argv, pack_opt_t* options) {
+
+ int opt;
+ int ret_value = 0;
+
+ /* parse command line options */
+ while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ switch ((char) opt) {
+
+ /* -i for backward compability */
+ case 'i':
+ infile = opt_arg;
+ has_i_o = 1;
+ break;
+
+ /* -o for backward compability */
+ case 'o':
+ outfile = opt_arg;
+ has_i_o = 1;
+ break;
+
+ case 'h':
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ ret_value = -1;
+ goto done;
+
+ case 'V':
+ print_version(h5tools_getprogname());
+ h5tools_setstatus(EXIT_SUCCESS);
+ ret_value = -1;
+ goto done;
+
+ case 'v':
+ options->verbose = 1;
+ break;
+
+ case 'f':
+ /* parse the -f filter option */
+ if (h5repack_addfilter(opt_arg, options) < 0) {
+ error_msg("in parsing filter\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'l':
+ /* parse the -l layout option */
+ if (h5repack_addlayout(opt_arg, options) < 0) {
+ error_msg("in parsing layout\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'm':
+ options->min_comp = HDatoi( opt_arg );
+ if ((int) options->min_comp <= 0) {
+ error_msg("invalid minimum compress size <%s>\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'e':
+ ret_value = read_info(opt_arg, options);
+ if (ret_value < 0)
+ goto done;
+ break;
+
+ case 'n':
+ options->use_native = 1;
+ break;
+
+ case 'L':
+ options->latest = 1;
+ break;
+
+ case 'c':
+ options->grp_compact = HDatoi( opt_arg );
+ if (options->grp_compact > 0)
+ options->latest = 1; /* must use latest format */
+ break;
+
+ case 'd':
+ options->grp_indexed = HDatoi( opt_arg );
+ if (options->grp_indexed > 0)
+ options->latest = 1; /* must use latest format */
+ break;
+
+ case 's':
+ {
+ int idx = 0;
+ int ssize = 0;
+ char *msgPtr = HDstrchr( opt_arg, ':');
+ options->latest = 1; /* must use latest format */
+ if (msgPtr == NULL) {
+ ssize = HDatoi( opt_arg );
+ for (idx = 0; idx < 5; idx++)
+ options->msg_size[idx] = ssize;
+ }
+ else {
+ char msgType[10];
+ HDstrcpy(msgType, msgPtr + 1);
+ msgPtr[0] = '\0';
+ ssize = HDatoi( opt_arg );
+ if (HDstrncmp(msgType, "dspace",6) == 0) {
+ options->msg_size[0] = ssize;
+ }
+ else if (HDstrncmp(msgType, "dtype", 5) == 0) {
+ options->msg_size[1] = ssize;
+ }
+ else if (HDstrncmp(msgType, "fill", 4) == 0) {
+ options->msg_size[2] = ssize;
+ }
+ else if (HDstrncmp(msgType, "pline", 5) == 0) {
+ options->msg_size[3] = ssize;
+ }
+ else if (HDstrncmp(msgType, "attr", 4) == 0) {
+ options->msg_size[4] = ssize;
+ }
+ }
+ }
+ break;
+
+ case 'u':
+ options->ublock_filename = opt_arg;
+ break;
+
+ case 'b':
+ options->ublock_size = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 'M':
+ options->meta_block_size = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 't':
+ options->threshold = (hsize_t) HDatol( opt_arg );
+ break;
+
+ case 'a':
+ options->alignment = HDatol( opt_arg );
+ if (options->alignment < 1) {
+ error_msg("invalid alignment size\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ break;
+
+ case 'S':
+ {
+ char strategy[MAX_NC_NAME];
+
+ HDstrcpy(strategy, opt_arg);
+ if (!HDstrcmp(strategy, "ALL_PERSIST"))
+ options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
+ else if (!HDstrcmp(strategy, "ALL"))
+ options->fs_strategy = H5F_FILE_SPACE_ALL;
+ else if (!HDstrcmp(strategy, "AGGR_VFD"))
+ options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
+ else if (!HDstrcmp(strategy, "VFD"))
+ options->fs_strategy = H5F_FILE_SPACE_VFD;
+ else {
+ error_msg("invalid file space management strategy\n", opt_arg);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ goto done;
+ }
+ }
+ break;
+
+ case 'T':
+ options->fs_threshold = (hsize_t) HDatol( opt_arg );
+ break;
+
+ default:
+ break;
+ } /* switch */
+
+ } /* while */
+
+ if (has_i_o == 0) {
+ /* check for file names to be processed */
+ if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+ error_msg("missing file names\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+
+done:
+ return ret_value;
}
/*-------------------------------------------------------------------------
- * Function: read_info
+ * Function: main
*
- * Purpose: read comp and chunk options from a file
+ * Purpose: h5repack main program
*
- * Return: void, exit on error
+ * Return: Success: EXIT_SUCCESS(0)
*
- * Programmer: pvn@ncsa.uiuc.edu
+ * Failure: EXIT_FAILURE(1)
*
- * Date: September, 22, 2003
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
*
*-------------------------------------------------------------------------
*/
-
-static
-void read_info(const char *filename,
- pack_opt_t *options)
-{
-
- char stype[10];
- char comp_info[1024];
- FILE *fp;
- char c;
- int i, rc=1;
-
- if ((fp = HDfopen(filename, "r")) == (FILE *)NULL) {
- error_msg("cannot open options file %s\n", filename);
- HDexit(EXIT_FAILURE);
- }
-
- /* cycle until end of file reached */
- while( 1 )
- {
- rc=fscanf(fp, "%s", stype);
- if (rc==-1)
- break;
-
- /*-------------------------------------------------------------------------
- * filter
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(stype,"-f") == 0) {
-
- /* find begining of info */
- i=0; c='0';
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- if (HDfeof(fp)) break;
- }
- c='0';
- /* go until end */
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- comp_info[i]=c;
- i++;
- if (HDfeof(fp)) break;
- if (c==10 /*eol*/) break;
- }
- comp_info[i-1]='\0'; /*cut the last " */
-
- if (h5repack_addfilter(comp_info,options)==-1){
- error_msg("could not add compression option\n");
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * layout
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(stype,"-l") == 0) {
-
- /* find begining of info */
- i=0; c='0';
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- if (HDfeof(fp)) break;
- }
- c='0';
- /* go until end */
- while( c!=' ' )
- {
- fscanf(fp, "%c", &c);
- comp_info[i]=c;
- i++;
- if (HDfeof(fp)) break;
- if (c==10 /*eol*/) break;
- }
- comp_info[i-1]='\0'; /*cut the last " */
-
- if (h5repack_addlayout(comp_info,options)==-1){
- error_msg("could not add chunck option\n");
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * not valid
- *-------------------------------------------------------------------------
- */
- else {
- error_msg("bad file format for %s", filename);
- HDexit(EXIT_FAILURE);
- }
- }
-
- HDfclose(fp);
- return;
+int main(int argc, const char **argv) {
+
+ pack_opt_t options; /*the global options */
+ int ret = -1;
+
+ h5tools_setprogname(PROGRAMNAME);
+ h5tools_setstatus(EXIT_SUCCESS);
+
+ /* Initialize h5tools lib */
+ h5tools_init();
+
+ /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
+ if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+
+ /* initialize options */
+ h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t) 0);
+
+ if (parse_command_line(argc, argv, &options) < 0)
+ goto done;
+
+ /* get file names if they were not yet got */
+ if (has_i_o == 0) {
+
+ if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+ infile = argv[opt_ind];
+ outfile = argv[opt_ind + 1];
+
+ if ( HDstrcmp( infile, outfile ) == 0) {
+ error_msg("file names cannot be the same\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+ }
+ else {
+ error_msg("file names missing\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+ }
+
+ /* pack it */
+ h5tools_setstatus(h5repack(infile, outfile, &options));
+
+done:
+ /* free tables */
+ h5repack_end(&options);
+
+ leave(h5tools_getstatus());
}
+
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index bcddbb9..b54e887 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -1,4 +1,4 @@
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
@@ -27,21 +27,19 @@
*-------------------------------------------------------------------------
*/
-void init_packobject(pack_info_t *obj)
-{
- int j, k;
-
- HDstrcpy(obj->path,"\0");
- for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
- {
- obj->filter[j].filtn = -1;
- for ( k=0; k<CD_VALUES; k++)
- obj->filter[j].cd_values[k] = 0;
- }
- obj->chunk.rank = -1;
- obj->refobj_id = -1;
- obj->layout = H5D_LAYOUT_ERROR;
- obj->nfilters = 0;
+void init_packobject(pack_info_t *obj) {
+ int j, k;
+
+ HDstrcpy(obj->path, "\0");
+ for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) {
+ obj->filter[j].filtn = -1;
+ for (k = 0; k < CD_VALUES; k++)
+ obj->filter[j].cd_values[k] = 0;
+ }
+ obj->chunk.rank = -1;
+ obj->refobj_id = -1;
+ obj->layout = H5D_LAYOUT_ERROR;
+ obj->nfilters = 0;
}
/*-------------------------------------------------------------------------
@@ -54,19 +52,16 @@ void init_packobject(pack_info_t *obj)
*-------------------------------------------------------------------------
*/
-static void aux_tblinsert_filter(pack_opttbl_t *table,
- unsigned int I,
- filter_info_t filt)
-{
- if (table->objs[ I ].nfilters<H5_REPACK_MAX_NFILTERS)
- {
- table->objs[ I ].filter[ table->objs[ I ].nfilters++ ] = filt;
- }
- else
- {
- error_msg("cannot insert the filter in this object.\
+static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I,
+ filter_info_t filt) {
+ if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) {
+ table->objs[I].filter[table->objs[I].nfilters++] = filt;
+ }
+ else {
+ error_msg(
+ "cannot insert the filter in this object.\
Maximum capacity exceeded\n");
- }
+ }
}
/*-------------------------------------------------------------------------
@@ -79,33 +74,28 @@ static void aux_tblinsert_filter(pack_opttbl_t *table,
*-------------------------------------------------------------------------
*/
-static void aux_tblinsert_layout(pack_opttbl_t *table,
- unsigned int I,
- pack_info_t *pack)
-{
- int k;
-
- table->objs[I].layout = pack->layout;
- if (H5D_CHUNKED==pack->layout)
- {
- /* -2 means the NONE option, remove chunking
- and set the layout to contiguous */
- if (pack->chunk.rank==-2)
- {
- table->objs[I].layout = H5D_CONTIGUOUS;
- table->objs[I].chunk.rank = -2;
- }
- /* otherwise set the chunking type */
- else
- {
- table->objs[I].chunk.rank = pack->chunk.rank;
- for (k = 0; k < pack->chunk.rank; k++)
- table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k];
- }
- }
+static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I,
+ pack_info_t *pack) {
+ int k;
+
+ table->objs[I].layout = pack->layout;
+ if (H5D_CHUNKED == pack->layout) {
+ /* -2 means the NONE option, remove chunking
+ and set the layout to contiguous */
+ if (pack->chunk.rank == -2) {
+ table->objs[I].layout = H5D_CONTIGUOUS;
+ table->objs[I].chunk.rank = -2;
+ }
+ /* otherwise set the chunking type */
+ else {
+ table->objs[I].chunk.rank = pack->chunk.rank;
+ for (k = 0; k < pack->chunk.rank; k++)
+ table->objs[I].chunk.chunk_lengths[k] =
+ pack->chunk.chunk_lengths[k];
+ }
+ }
}
-
/*-------------------------------------------------------------------------
* Function: aux_inctable
*
@@ -116,21 +106,20 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
*-------------------------------------------------------------------------
*/
-static int aux_inctable(pack_opttbl_t *table, int n_objs )
-{
- unsigned int i;
-
- table->size += n_objs;
- table->objs = (pack_info_t*)HDrealloc(table->objs, table->size * sizeof(pack_info_t));
- if (table->objs==NULL) {
- error_msg("not enough memory for options table\n");
- return -1;
- }
- for (i = table->nelems; i < table->size; i++)
- {
- init_packobject(&table->objs[i]);
- }
- return 0;
+static int aux_inctable(pack_opttbl_t *table, int n_objs) {
+ unsigned int i;
+
+ table->size += n_objs;
+ table->objs =
+ (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t));
+ if (table->objs == NULL) {
+ error_msg("not enough memory for options table\n");
+ return -1;
+ }
+ for (i = table->nelems; i < table->size; i++) {
+ init_packobject(&table->objs[i]);
+ }
+ return 0;
}
@@ -143,31 +132,29 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
*
*-------------------------------------------------------------------------
*/
-int options_table_init( pack_opttbl_t **tbl )
-{
- unsigned int i;
- pack_opttbl_t *table;
-
- if(NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t))))
- {
- error_msg("not enough memory for options table\n");
- return -1;
- }
-
- table->size = 30;
- table->nelems = 0;
- if(NULL == (table->objs = (pack_info_t*)HDmalloc(table->size * sizeof(pack_info_t))))
- {
- error_msg("not enough memory for options table\n");
- HDfree(table);
- return -1;
- }
-
- for(i = 0; i < table->size; i++)
- init_packobject(&table->objs[i]);
-
- *tbl = table;
- return 0;
+int options_table_init(pack_opttbl_t **tbl) {
+ unsigned int i;
+ pack_opttbl_t *table;
+
+ if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) {
+ error_msg("not enough memory for options table\n");
+ return -1;
+ }
+
+ table->size = 30;
+ table->nelems = 0;
+ if (NULL == (table->objs =
+ (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) {
+ error_msg("not enough memory for options table\n");
+ HDfree(table);
+ return -1;
+ }
+
+ for (i = 0; i < table->size; i++)
+ init_packobject(&table->objs[i]);
+
+ *tbl = table;
+ return 0;
}
@@ -181,11 +168,10 @@ int options_table_init( pack_opttbl_t **tbl )
*-------------------------------------------------------------------------
*/
-int options_table_free( pack_opttbl_t *table )
-{
- HDfree(table->objs);
- HDfree(table);
- return 0;
+int options_table_free(pack_opttbl_t *table) {
+ HDfree(table->objs);
+ HDfree(table);
+ return 0;
}
/*-------------------------------------------------------------------------
@@ -198,95 +184,81 @@ int options_table_free( pack_opttbl_t *table )
*-------------------------------------------------------------------------
*/
-
-int options_add_layout( obj_list_t *obj_list,
- int n_objs,
- pack_info_t *pack,
- pack_opttbl_t *table )
-{
- unsigned int i, I;
- int j, added=0, found=0;
-
- /* increase the size of the collection by N_OBJS if necessary */
- if (table->nelems+n_objs >= table->size)
- {
- if (aux_inctable(table,n_objs)<0)
- return -1;
- }
-
- /* search if this object is already in the table; "path" is the key */
- if (table->nelems>0)
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- /* linear table search */
- for (i = 0; i < table->nelems; i++)
- {
- /*already on the table */
- if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
- {
- /* already chunk info inserted for this one; exit */
- if (table->objs[i].chunk.rank>0)
- {
- error_msg("chunk information already inserted for <%s>\n",obj_list[j].obj);
- HDexit(EXIT_FAILURE);
- }
- /* insert the layout info */
- else
- {
- aux_tblinsert_layout(table,i,pack);
- found=1;
- break;
- }
- } /* if */
- } /* i */
-
- if (found==0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
- }
- /* cases where we have an already inserted name but there is a new name also
- example:
- -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
- dset1 is already inserted, but dset2 must also be
- */
- else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
- }
- } /* j */
- }
-
- /* first time insertion */
- else
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_layout(table,I,pack);
-
- }
- }
-
- table->nelems+= added;
-
- return 0;
+int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack,
+ pack_opttbl_t *table) {
+ unsigned int i, I;
+ int j, added = 0, found = 0;
+
+ /* increase the size of the collection by N_OBJS if necessary */
+ if (table->nelems + n_objs >= table->size) {
+ if (aux_inctable(table, n_objs) < 0)
+ return -1;
+ }
+
+ /* search if this object is already in the table; "path" is the key */
+ if (table->nelems > 0) {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ /* linear table search */
+ for (i = 0; i < table->nelems; i++) {
+ /*already on the table */
+ if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+ /* already chunk info inserted for this one; exit */
+ if (table->objs[i].chunk.rank > 0) {
+ error_msg(
+ "chunk information already inserted for <%s>\n",
+ obj_list[j].obj);
+ HDexit(EXIT_FAILURE);
+ }
+ /* insert the layout info */
+ else {
+ aux_tblinsert_layout(table, i, pack);
+ found = 1;
+ break;
+ }
+ } /* if */
+ } /* i */
+
+ if (found == 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+ }
+ /* cases where we have an already inserted name but there is a new name also
+ example:
+ -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
+ dset1 is already inserted, but dset2 must also be
+ */
+ else if (found == 1
+ && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+ }
+ } /* j */
+ }
+
+ /* first time insertion */
+ else {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_layout(table, I, pack);
+
+ }
+ }
+
+ table->nelems += added;
+
+ return 0;
}
-
-
/*-------------------------------------------------------------------------
* Function: options_add_filter
*
@@ -297,81 +269,70 @@ int options_add_layout( obj_list_t *obj_list,
*-------------------------------------------------------------------------
*/
-int options_add_filter(obj_list_t *obj_list,
- int n_objs,
- filter_info_t filt,
- pack_opttbl_t *table )
-{
-
- unsigned int i, I;
- int j, added=0, found=0;
-
- /* increase the size of the collection by N_OBJS if necessary */
- if (table->nelems+n_objs >= table->size)
- {
- if (aux_inctable(table,n_objs)<0)
- return -1;
- }
-
- /* search if this object is already in the table; "path" is the key */
- if (table->nelems>0)
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- /* linear table search */
- for (i = 0; i < table->nelems; i++)
- {
- /*already on the table */
- if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
- {
- /* insert */
- aux_tblinsert_filter(table,i,filt);
- found=1;
- break;
- } /* if */
- } /* i */
-
- if (found==0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- /* cases where we have an already inserted name but there is a new name also
- example:
- -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
- dset1 is already inserted, but dset2 must also be
- */
- else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
- {
- /* keep the grow in a temp var */
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- } /* j */
- }
-
- /* first time insertion */
- else
- {
- /* go tru the supplied list of names */
- for (j = 0; j < n_objs; j++)
- {
- I = table->nelems + added;
- added++;
- HDstrcpy(table->objs[I].path,obj_list[j].obj);
- aux_tblinsert_filter(table,I,filt);
- }
- }
-
- table->nelems+= added;
-
- return 0;
+int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt,
+ pack_opttbl_t *table) {
+
+ unsigned int i, I;
+ int j, added = 0, found = 0;
+
+ /* increase the size of the collection by N_OBJS if necessary */
+ if (table->nelems + n_objs >= table->size) {
+ if (aux_inctable(table, n_objs) < 0)
+ return -1;
+ }
+
+ /* search if this object is already in the table; "path" is the key */
+ if (table->nelems > 0) {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ /* linear table search */
+ for (i = 0; i < table->nelems; i++) {
+ /*already on the table */
+ if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+ /* insert */
+ aux_tblinsert_filter(table, i, filt);
+ found = 1;
+ break;
+ } /* if */
+ } /* i */
+
+ if (found == 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ /* cases where we have an already inserted name but there is a new name also
+ example:
+ -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
+ dset1 is already inserted, but dset2 must also be
+ */
+ else if (found == 1
+ && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+ /* keep the grow in a temp var */
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ } /* j */
+ }
+
+ /* first time insertion */
+ else {
+ /* go tru the supplied list of names */
+ for (j = 0; j < n_objs; j++) {
+ I = table->nelems + added;
+ added++;
+ HDstrcpy(table->objs[I].path, obj_list[j].obj);
+ aux_tblinsert_filter(table, I, filt);
+ }
+ }
+
+ table->nelems += added;
+
+ return 0;
}
/*-------------------------------------------------------------------------
@@ -384,34 +345,25 @@ int options_add_filter(obj_list_t *obj_list,
*-------------------------------------------------------------------------
*/
-pack_info_t* options_get_object( const char *path,
- pack_opttbl_t *table )
-{
- unsigned int i;
- char tbl_path[MAX_NC_NAME+1]; /* +1 for start with "/" case */
-
-
- for ( i = 0; i < table->nelems; i++)
- {
- /* make full path (start with "/") to compare correctly */
- if (HDstrncmp(table->objs[i].path, "/", 1))
- {
- HDstrcpy(tbl_path, "/");
- HDstrcat(tbl_path, table->objs[i].path);
- }
- else
- HDstrcpy(tbl_path, table->objs[i].path);
-
- /* found it */
- if (HDstrcmp(tbl_path, path)==0)
- {
- return (&table->objs[i]);
- }
- }
-
- return NULL;
+pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) {
+ unsigned int i;
+ char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */
+
+ for (i = 0; i < table->nelems; i++) {
+ /* make full path (start with "/") to compare correctly */
+ if (HDstrncmp(table->objs[i].path, "/", 1)) {
+ HDstrcpy(tbl_path, "/");
+ HDstrcat(tbl_path, table->objs[i].path);
+ }
+ else
+ HDstrcpy(tbl_path, table->objs[i].path);
+
+ /* found it */
+ if (HDstrcmp(tbl_path, path) == 0) {
+ return (&table->objs[i]);
+ }
+ }
+
+ return NULL;
}
-
-
-