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[svn-r6099]

Browse Source 
Purpose:
    bug fix.
Description:
    h5dump cannot dump data and datatype for VL string.
Platforms tested:
    eirene, arabica
Misc. update:
    MANIFEST, RELEASE.txt
This commit is contained in:
Raymond Lu 2002-11-18 11:38:11 -05:00
parent 02fe47462b
commit 0105a3b97c
11 changed files with 277 additions and 41 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
MANIFEST
View File

@ -1158,6 +1158,8 @@
./tools/testfiles/tvldtypes3.h5
./tools/testfiles/tvldtypes4.ddl
./tools/testfiles/tvldtypes4.h5
./tools/testfiles/tvlstr.h5
./tools/testfiles/tvlstr.ddl
# Expected output from h5ls tests
./tools/testfiles/help-1.ls
@ -1231,6 +1233,7 @@
./tools/testfiles/tvldtypes1.h5.xml
./tools/testfiles/tvldtypes2.h5.xml
./tools/testfiles/tvldtypes3.h5.xml
./tools/testfiles/tvlstr.h5.xml
./windows/all.zip
./windows/all_withf90.zip

2
release_docs/RELEASE.txt
View File

@ -198,6 +198,8 @@ Configuration
Tools
-----
* The VL string bug(data and datatype cannot be shown) in h5dump is fixed.
-SLU - 2002/11/18
* Fixed segfault if h5dump was invoked with some options but no file (e.g.,
h5dump -H). -AKC, 2002/10/15
* Fixed limitation in h5dumper with object names which reached over 1024

32
test/tvlstr.c
View File

@ -239,13 +239,17 @@ static void test_vlstring_type(void)
H5T_cset_t cset;
H5T_str_t pad;
herr_t ret;
size_t size;
/* Output message about test being performed */
MESSAGE(5, ("Testing VL String type\n"));
/* Create file */
fid = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fcreate");
/*fid = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fcreate");*/
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Create a datatype to refer to */
tid_vlstr = H5Tcopy(H5T_C_S1);
@ -280,8 +284,20 @@ static void test_vlstring_type(void)
/* Close datatype */
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
tid_vlstr = H5Topen(fid, VLSTR_TYPE);
CHECK(tid_vlstr, FAIL, "H5Topen");
ret = H5Tclose(tid_vlstr);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
fid = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(fid, FAIL, "H5Fopen");
/* Open the variable-length string datatype just created */
tid_vlstr = H5Topen(fid, VLSTR_TYPE);
CHECK(tid_vlstr, FAIL, "H5Topen");
@ -313,8 +329,8 @@ static void test_write_vl_string_attribute(void)
herr_t ret;
char *string_att_check;
file = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fcreate");
file = H5Fopen(DATAFILE, H5F_ACC_RDWR, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fopen");
/* Create a datatype to refer to. */
type = H5Tcopy (H5T_C_S1);
@ -375,6 +391,9 @@ static void test_read_vl_string_attribute(void)
hid_t type;
herr_t ret;
char *string_att_check;
hsize_t size[64];
hid_t space;
int ndims;
file = H5Fopen(DATAFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fopen");
@ -391,6 +410,9 @@ static void test_read_vl_string_attribute(void)
att = H5Aopen_name(root, "test_scalar");
CHECK(att, FAIL, "H5Aopen_name");
space = H5Aget_space(att);
ndims = H5Sget_simple_extent_dims(space, size, NULL);
ret = H5Aread(att, type, &string_att_check);
CHECK(ret, FAIL, "H5Aread");
@ -433,7 +455,7 @@ test_vlstrings(void)
test_vlstrings_basic();
test_vlstring_type();
/* Test using VL strings in attributes */
/*Test using VL strings in attributes */
test_write_vl_string_attribute();
test_read_vl_string_attribute();
} /* test_vlstrings() */

92
tools/h5dump/h5dump.c
View File

@ -677,12 +677,14 @@ print_datatype(hid_t type)
char *fname;
hid_t nmembers, mtype, str_type;
int i, j, ndims, perm[H5DUMP_MAX_RANK];
size_t size;
size_t size=0;
hsize_t dims[H5DUMP_MAX_RANK];
H5T_str_t str_pad;
H5T_cset_t cset;
H5G_stat_t statbuf;
hid_t super;
hid_t tmp_type;
htri_t is_vlstr=FALSE;
switch (H5Tget_class(type)) {
case H5T_INTEGER:
@ -770,15 +772,23 @@ print_datatype(hid_t type)
break;
case H5T_STRING:
size = H5Tget_size(type);
str_pad = H5Tget_strpad(type);
cset = H5Tget_cset(type);
/* Make a copy of type in memory in case when TYPE is on disk, the size
* will be bigger than in memory. This makes it easier to compare
* types in memory. */
tmp_type = H5Tcopy(type);
size = H5Tget_size(tmp_type);
str_pad = H5Tget_strpad(tmp_type);
cset = H5Tget_cset(tmp_type);
is_vlstr = H5Tis_variable_str(tmp_type);
printf("H5T_STRING %s\n", dump_header_format->strblockbegin);
indent += COL;
indentation(indent + COL);
printf("%s %d;\n", STRSIZE, (int) size);
if(is_vlstr)
printf("%s H5T_VARIABLE;\n", STRSIZE);
else
printf("%s %d;\n", STRSIZE, (int) size);
indentation(indent + COL);
printf("%s ", STRPAD);
@ -800,14 +810,17 @@ print_datatype(hid_t type)
printf("unknown_cset;\n");
str_type = H5Tcopy(H5T_C_S1);
if(is_vlstr)
H5Tset_size(str_type, H5T_VARIABLE);
else
H5Tset_size(str_type, size);
H5Tset_cset(str_type, cset);
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
indentation(indent + COL);
printf("%s ", CTYPE);
if (H5Tequal(type, str_type)) {
if (H5Tequal(tmp_type, str_type)) {
printf("H5T_C_S1;\n");
H5Tclose(str_type);
} else {
@ -817,7 +830,7 @@ print_datatype(hid_t type)
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
if (H5Tequal(type, str_type)) {
if (H5Tequal(tmp_type, str_type)) {
printf("H5T_FORTRAN_S1;\n");
} else {
printf("unknown_one_character_type;\n ");
@ -827,6 +840,8 @@ print_datatype(hid_t type)
H5Tclose(str_type);
}
H5Tclose(tmp_type);
indent -= COL;
indentation(indent + COL);
printf("%s", dump_header_format->strblockend);
@ -1887,13 +1902,14 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset)
alloc_size = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
buf = malloc((size_t)alloc_size);
assert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0)
status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type,
space, buf, depth);
space, buf, depth);
free(buf);
H5Tclose(p_type);
H5Sclose(space);
@ -2857,10 +2873,25 @@ done:
d_status = EXIT_FAILURE;
free_handler(hand, argc);
for(i=0; i<info.group_table->nobjs; i++) {
if(info.group_table->objs[i].objname)
free(info.group_table->objs[i].objname);
}
free(group_table->objs);
for(i=0; i<info.dset_table->nobjs; i++) {
if(info.dset_table->objs[i].objname)
free(info.dset_table->objs[i].objname);
}
free(dset_table->objs);
for(i=0; i<info.type_table->nobjs; i++) {
if(info.type_table->objs[i].objname)
free(info.type_table->objs[i].objname);
}
free(type_table->objs);
free(prefix);
free(info.prefix);
@ -4557,12 +4588,14 @@ xml_print_strs(hid_t did, int source)
{
herr_t e;
hid_t type, space;
char *buf;
void *buf;
char *bp;
char *onestring;
hsize_t ssiz;
size_t tsiz;
size_t tsiz, str_size;
size_t i;
htri_t is_vlstr;
if (source == DATASET_DATA) {
type = H5Dget_type(did);
} else if (source == ATTRIBUTE_DATA) {
@ -4575,12 +4608,14 @@ xml_print_strs(hid_t did, int source)
/* return an error */
return FAIL;
}
is_vlstr = H5Tis_variable_str(type);
if (source == DATASET_DATA) {
space = H5Dget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = calloc((size_t)ssiz, sizeof(char));
buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
@ -4596,11 +4631,12 @@ xml_print_strs(hid_t did, int source)
space = H5Aget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = calloc((size_t)ssiz, sizeof(char));
buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
}
e = H5Aread(did, type, buf);
if (e < 0) {
free(buf);
@ -4611,28 +4647,36 @@ xml_print_strs(hid_t did, int source)
return FAIL;
}
/* pull out each string... */
/* pull out each string... */
ssiz = H5Sget_simple_extent_npoints(space);
tsiz = H5Tget_size(type);
onestring = (char *) calloc((size_t)tsiz, sizeof(char));
bp = buf;
bp = (char*)buf;
if(!is_vlstr)
onestring = (char *) calloc(tsiz, sizeof(char));
for (i = 0; i < ssiz; i++) {
strncpy(onestring, bp, tsiz);
if(is_vlstr) {
onestring = *(char **)bp;
str_size = (size_t)strlen(onestring);
} else {
strncpy(onestring, bp, tsiz);
str_size = tsiz;
}
indentation(indent + COL);
if (!onestring) {
printf("\"%s\"\n", "NULL");
} else {
char *t_onestring = xml_escape_the_string(onestring, (int)tsiz);
char *t_onestring = xml_escape_the_string(onestring, (int)str_size);
printf("\"%s\"\n", xml_escape_the_string(onestring, (int)tsiz));
printf("\"%s\"\n", t_onestring);
free(t_onestring);
}
bp += tsiz;
bp += tsiz;
}
return SUCCEED;
}

54
tools/h5dump/h5dumpgentest.c
View File

@ -63,6 +63,7 @@
#define FILE35 "tfamily%05d.h5"
#define FILE36 "tmulti"
#define FILE37 "tlarge_objname.h5"
#define FILE38 "tvlstr.h5"
#define LENSTR 50
#define LENSTR2 11
@ -108,6 +109,9 @@ typedef struct s1_t {
#define ARRAY3_DIM1 6
#define ARRAY3_DIM2 3
/* VL string datatype name */
#define VLSTR_TYPE "vl_string_type"
static void gent_group(void)
{
hid_t fid, group;
@ -2838,6 +2842,55 @@ static void gent_large_objname(void)
H5Fclose(fid);
}
static void gent_vlstr(void)
{
const char *wdata[SPACE1_DIM1]= {
"Four score and seven years ago our forefathers brought forth on this continent a new nation,",
"conceived in liberty and dedicated to the proposition that all men are created equal.",
"Now we are engaged in a great civil war,",
"testing whether that nation or any nation so conceived and so dedicated can long endure."
}; /* Information to write */
char *string_att= "This is the string for the attribute";
hid_t fid1; /* HDF5 File IDs */
hid_t dataset, root; /* Dataset ID */
hid_t sid1, dataspace;/* Dataspace ID */
hid_t tid1, att; /* Datatype ID */
hsize_t dims1[] = {SPACE1_DIM1};
/* Create file */
fid1 = H5Fcreate(FILE38, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
/* Create a VL string datatype to refer to */
tid1 = H5Tcopy (H5T_C_S1);
H5Tset_size (tid1,H5T_VARIABLE);
/* Create a dataset and write VL string to it. */
dataset=H5Dcreate(fid1,"Dataset1",tid1,sid1,H5P_DEFAULT);
H5Dwrite(dataset,tid1,H5S_ALL,H5S_ALL,H5P_DEFAULT,wdata);
H5Dclose(dataset);
/* Create a named VL string type. Change padding of datatype */
H5Tset_strpad(tid1, H5T_STR_NULLPAD);
H5Tcommit(fid1, "vl_string_type", tid1);
/* Create an group attribute of VL string type */
root = H5Gopen(fid1, "/");
dataspace = H5Screate(H5S_SCALAR);
att = H5Acreate(root, "test_scalar", tid1, dataspace, H5P_DEFAULT);
H5Awrite(att, tid1, &string_att);
/* Close */
H5Tclose(tid1);
H5Sclose(sid1);
H5Sclose(dataspace);
H5Aclose(att);
H5Gclose(root);
H5Fclose(fid1);
}
int main(void)
{
gent_group();
@ -2888,6 +2941,7 @@ int main(void)
gent_multi();
gent_large_objname();
gent_vlstr();
return 0;
}

4
tools/h5dump/testh5dump.sh
View File

@ -144,6 +144,9 @@ TOOLTEST tvldtypes2.ddl tvldtypes2.h5
TOOLTEST tvldtypes3.ddl tvldtypes3.h5
TOOLTEST tvldtypes4.ddl tvldtypes4.h5
#test for file with variable length string data
TOOLTEST tvlstr.ddl tvlstr.h5
# test for files with array data
TOOLTEST tarray1.ddl tarray1.h5
TOOLTEST tarray2.ddl tarray2.h5
@ -218,6 +221,7 @@ TOOLTEST tarray7.h5.xml --xml tarray7.h5
TOOLTEST tvldtypes1.h5.xml --xml tvldtypes1.h5
TOOLTEST tvldtypes2.h5.xml --xml tvldtypes2.h5
TOOLTEST tvldtypes3.h5.xml --xml tvldtypes3.h5
TOOLTEST tvlstr.h5.xml --xml tvlstr.h5
TOOLTEST tsaf.h5.xml --xml tsaf.h5
TOOLTEST tempty.h5.xml --xml tempty.h5

33
tools/lib/h5tools.c
View File

@ -457,6 +457,7 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*this var to count elements and
*break after we see a number equal
*to the ctx->size_last_dim. */
unsigned char *tmp=NULL;
/* Setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
@ -470,7 +471,12 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx);
if(H5Tis_variable_str(type)) {
tmp = ((unsigned char**)mem)[i];
h5tools_str_sprint(&buffer, info, container, type, tmp, ctx);
} else
h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx);
if (i + 1 < nelmts || (flags & END_OF_DATA) == 0)
h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
@ -785,7 +791,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
hsize_t sm_nelmts; /*elements per stripmine*/
unsigned char *sm_buf = NULL; /*buffer for raw data */
hid_t sm_space; /*stripmine data space */
/* Hyperslab info */
hssize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
@ -820,9 +826,6 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(f_space, total_size, NULL);
/* printf("total_size[ctx.ndims-1]%d\n",total_size[ctx.ndims-1]);
printf("total_size cast %d\n",(int)(total_size[ctx.ndims-1])); */
/*assert(total_size[ctx.ndims - 1]==(hsize_t)((int)(total_size[ctx.ndims - 1])));*/
ctx.size_last_dim = (total_size[ctx.ndims - 1]);
/* calculate the number of elements we're going to print */
@ -858,6 +861,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
sm_buf = malloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
@ -896,10 +900,10 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
flags = (elmtno == 0) ? START_OF_DATA : 0;
flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0;
h5tools_dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts,
p_type, sm_buf);
p_type, sm_buf);
/* Reclaim any VL memory, if necessary */
if (vl_data)
if(vl_data)
H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
/* Calculate the next hyperslab offset */
@ -925,7 +929,9 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
H5Sclose(sm_space);
H5Sclose(f_space);
free(sm_buf);
return SUCCEED;
}
@ -967,7 +973,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id,
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
/* Assume entire data space to be printed */
for (i = 0; i < (hsize_t)ctx.ndims; i++)
ctx.p_min_idx[i] = 0;
@ -976,7 +982,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id,
for (i = 0, nelmts = 1; ctx.ndims != 0 && i < (hsize_t)ctx.ndims; i++)
nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i];
if (nelmts == 0)
return SUCCEED; /*nothing to print*/
assert(ctx.p_max_idx[ctx.ndims - 1]==(hsize_t)((int)ctx.p_max_idx[ctx.ndims - 1]));
@ -1075,8 +1081,13 @@ h5tools_fixtype(hid_t f_type)
* strDUAction == TRUE. if it is false we will do the original action
* here.
*/
m_type = H5Tcopy(f_type);
H5Tset_cset(m_type, H5T_CSET_ASCII);
if(H5Tis_variable_str(f_type)) {
m_type = H5Tcopy(H5T_C_S1);
H5Tset_size(m_type, H5T_VARIABLE);
} else {
m_type = H5Tcopy(f_type);
H5Tset_cset(m_type, H5T_CSET_ASCII);
}
break;
case H5T_COMPOUND:

6
tools/lib/h5tools_str.c
View File

@ -545,7 +545,11 @@ h5tools_str_sprint(h5tools_str_t *str, const h5dump_t *info, hid_t container,
unsigned int i;
quote = '\0';
size = H5Tget_size(type);
if(H5Tis_variable_str(type)) {
size = HDstrlen(cp_vp);
} else {
size = H5Tget_size(type);
}
pad = H5Tget_strpad(type);
for (i = 0; i < size && (cp_vp[i] != '\0' || pad != H5T_STR_NULLTERM); i++) {

41
tools/testfiles/tvlstr.ddl Normal file
View File

@ -0,0 +1,41 @@
#############################
Expected output for 'h5dump tvlstr.h5'
#############################
HDF5 "tvlstr.h5" {
GROUP "/" {
ATTRIBUTE "test_scalar" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
"This is the string for the attribute"
}
}
DATASET "Dataset1" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
"Four score and seven years ago our forefathers brought forth on this continent a new nation,",
"conceived in liberty and dedicated to the proposition that all men are created equal.",
"Now we are engaged in a great civil war,",
"testing whether that nation or any nation so conceived and so dedicated can long endure."
}
}
DATATYPE "vl_string_type" H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
};
}
}

BIN
tools/testfiles/tvlstr.h5 Normal file
View File

Binary file not shown.

51
tools/testfiles/tvlstr.h5.xml Normal file
View File

@ -0,0 +1,51 @@
#############################
Expected output for 'h5dump --xml tvlstr.h5'
#############################
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE HDF5-File PUBLIC "HDF5-File.dtd" "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd">
<HDF5-File>
<RootGroup OBJ-XID="root">
<Attribute Name="test_scalar">
<Dataspace>
<ScalarDataspace />
</Dataspace>
<DataType>
<AtomicType>
<StringType Cset="H5T_CSET_ASCII" StrSize="4" StrPad="H5T_STR_NULLPAD"/>
</AtomicType>
</DataType>
<Data>
<DataFromFile>
"This is the string for the attribute"
</DataFromFile>
</Data>
</Attribute>
<NamedDataType Name="vl_string_type" OBJ-XID="/vl_string_type" Parents="root">
<DataType>
<AtomicType>
<StringType Cset="H5T_CSET_ASCII" StrSize="16" StrPad="H5T_STR_NULLPAD"/>
</AtomicType>
</DataType>
</NamedDataType>
<Dataset Name="Dataset1" OBJ-XID="/Dataset1" Parents="root">
<Dataspace>
<SimpleDataspace Ndims="1">
<Dimension DimSize="4" MaxDimSize="4"/>
</SimpleDataspace>
</Dataspace>
<DataType>
<AtomicType>
<StringType Cset="H5T_CSET_ASCII" StrSize="4" StrPad="H5T_STR_NULLTERM"/>
</AtomicType>
</DataType>
<Data>
<DataFromFile>
"Four score and seven years ago our forefathers brought forth on this continent a new nation,"
"conceived in liberty and dedicated to the proposition that all men are created equal."
"Now we are engaged in a great civil war,"
"testing whether that nation or any nation so conceived and so dedicated can long endure."
</DataFromFile>
</Data>
</Dataset>
</RootGroup>
</HDF5-File>