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[svn-r19198] [BZ1953]implementation for the proposed changes suggested by the "h5dump_output_option" RFC. This required that the region reference code be duplicated and reduced to allow the do_bin_output() function to understand region references. The container type-id also needed to be propagated into the do_bin_output() function and functions referenced (render_bin_output*).

Browse Source 
Existing tests tested the binary function, so only one test was added to test the region reference generated file.
Tested: local linux
This commit is contained in:
Allen Byrne
2010-08-09 12:15:06 -05:00
parent a586c760ee
commit 02b5824f57
5 changed files with 400 additions and 15 deletions
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16
tools/h5dump/CMakeLists.txt
View File

@@ -312,6 +312,13 @@ IF (BUILD_TESTING)
ARGS -E copy_if_different ${HDF5_TOOLS_SOURCE_DIR}/testfiles/tbin1.ddl ${PROJECT_BINARY_DIR}/tbin1LE.ddl
)
ADD_CUSTOM_COMMAND (
TARGET h5dump
POST_BUILD
COMMAND ${CMAKE_COMMAND}
ARGS -E copy_if_different ${HDF5_TOOLS_SOURCE_DIR}/testfiles/tbinregR.exp ${PROJECT_BINARY_DIR}/tbinregR.exp
)
MACRO (ADD_SKIP_H5_TEST skipresultfile skipresultcode testtype)
IF (${testtype} STREQUAL "SKIP")
MESSAGE (STATUS "SKIP ${skipresultfile} ${ARGN}")
@@ -629,6 +636,15 @@ IF (BUILD_TESTING)
ADD_H5_TEST (tattrreg 0 tattrreg.h5)
ADD_H5_TEST (tattrregR 0 -R tattrreg.h5)
ADD_TEST (
NAME H5DUMP-output-tdatreg
COMMAND $<TARGET_FILE:h5dump> -d /Dataset1 -s 0 -R -y -o ${PROJECT_BINARY_DIR}/tbinregR.txt ${PROJECT_BINARY_DIR}/tdatareg.h5)
ADD_TEST (
NAME H5DUMP-output-cmp-tdatreg
COMMAND ${CMAKE_COMMAND}
-E compare_files ${PROJECT_BINARY_DIR}/tbinregR.txt ${PROJECT_BINARY_DIR}/tbinregR.exp)
# tests for group creation order
# "1" tracked, "2" name, root tracked
ADD_H5_TEST (tordergr1 0 --group=1 --sort_by=creation_order --sort_order=ascending tordergr.h5)

40
tools/h5dump/testh5dump.sh.in
View File

@@ -147,6 +147,44 @@ TOOLTEST1() {
}
# same as TOOLTEST1 but compares generated file to Expected output
# used for the binary tests that expect a full path in -o without -b
TOOLTEST2() {
expect="$srcdir/../testfiles/`basename $1 .exp`.txt"
actual="../testfiles/`basename $1 .exp`.out"
actual_err="../testfiles/`basename $1 .exp`.err"
shift
# Run test.
TESTING $DUMPER $@
(
cd $srcdir/../testfiles
$RUNSERIAL $DUMPER_BIN $@
) >$actual 2>$actual_err
cat $actual_err >> $actual
if [ ! -f $expect ]; then
# Create the expect file if it doesn't yet exist.
echo " CREATED"
cp $actual $expect
elif $CMP $expect $actual; then
echo " PASSED"
else
echo "*FAILED*"
echo " Expected result (*.ddl) differs from actual result (*.txt)"
nerrors="`expr $nerrors + 1`"
test yes = "$verbose" && $DIFF $expect $actual |sed 's/^/ /'
fi
# Clean up output file
if test -z "$HDF5_NOCLEANUP"; then
rm -f $actual $actual_err
fi
}
# Print a "SKIP" message
SKIP() {
@@ -494,6 +532,8 @@ TOOLTEST tdataregR.ddl -R tdatareg.h5
TOOLTEST tattrreg.ddl tattrreg.h5
TOOLTEST tattrregR.ddl -R tattrreg.h5
TOOLTEST2 tbinregR.exp -d /Dataset1 -s 0 -y -o $TESTDIR/tbinregR.txt tdatareg.h5
# tests for group creation order
# "1" tracked, "2" name, root tracked
TOOLTEST tordergr1.ddl --group=1 --sort_by=creation_order --sort_order=ascending tordergr.h5

351
tools/lib/h5tools.c
View File

@@ -202,8 +202,12 @@ BLOCK, /*blockbegin */
static const h5tools_dump_header_t * h5tools_dump_header_format;
/* local prototypes */
static int do_bin_output(FILE *stream, hsize_t nelmts, hid_t tid, void *_mem);
static int render_bin_output(FILE *stream, hid_t tid, void *_mem);
static int do_bin_output(FILE *stream, hid_t container, hsize_t nelmts, hid_t tid, void *_mem);
static int render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem);
static hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container, hid_t tid, void *_mem);
static hbool_t render_bin_output_region_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container, hid_t tid, void *_mem);
static hbool_t h5tools_is_zero(const void *_mem, size_t size);
hbool_t h5tools_render_element(FILE *stream, const h5tool_format_t *info,
@@ -871,7 +875,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
/* binary dump */
if (bin_output) {
do_bin_output(stream, nelmts, type, _mem);
do_bin_output(rawdatastream, container, nelmts, type, _mem);
} /* end if */
else {
/* setup */
@@ -952,7 +956,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
if (i + 1 < nelmts || (flags & END_OF_DATA) == 0)
h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
dimension_break = h5tools_render_element(stream, info, ctx, &buffer,
dimension_break = h5tools_render_element(rawdatastream, info, ctx, &buffer,
&curr_pos, ncols, i, elmt_counter);
/* Render the data element end*/
@@ -1581,7 +1585,7 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
ctx->need_prefix = TRUE;
h5tools_print_region_data_blocks(region_space, region_id,
stream, info, *ctx, buffer, ncols, ndims, type_id, nblocks, ptdata);
rawdatastream, info, *ctx, buffer, ncols, ndims, type_id, nblocks, ptdata);
done:
free(ptdata);
@@ -1883,7 +1887,7 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
ctx->need_prefix = TRUE;
h5tools_print_region_data_points(region_space, region_id,
stream, info, *ctx, buffer, ncols, ndims, type_id, npoints, ptdata);
rawdatastream, info, *ctx, buffer, ncols, ndims, type_id, npoints, ptdata);
done:
free(ptdata);
@@ -2663,10 +2667,10 @@ h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, hid_t dset,
/* Print the data */
if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) {
if (!sset) {
status = h5tools_dump_simple_dset(rawdatastream, info, dset, p_type, indentlevel);
status = h5tools_dump_simple_dset(stream, info, dset, p_type, indentlevel);
}
else {
status = h5tools_dump_simple_subset(rawdatastream, info, dset, p_type, sset, indentlevel);
status = h5tools_dump_simple_subset(stream, info, dset, p_type, sset, indentlevel);
}
}
else
@@ -3501,7 +3505,7 @@ init_acc_pos(h5tools_context_t *ctx, hsize_t *dims)
*-------------------------------------------------------------------------
*/
static
int do_bin_output(FILE *stream, hsize_t nelmts, hid_t tid, void *_mem)
int do_bin_output(FILE *stream, hid_t container, hsize_t nelmts, hid_t tid, void *_mem)
{
HERR_INIT(int, SUCCEED)
unsigned char *mem = (unsigned char*)_mem;
@@ -3512,7 +3516,7 @@ int do_bin_output(FILE *stream, hsize_t nelmts, hid_t tid, void *_mem)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
for (i = 0; i < nelmts; i++) {
if (render_bin_output(stream, tid, mem + i * size) < 0) {
if (render_bin_output(stream, container, tid, mem + i * size) < 0) {
printf("\nError in writing binary stream\n");
return FAIL;
}
@@ -3532,7 +3536,7 @@ CATCH
*-------------------------------------------------------------------------
*/
static int
render_bin_output(FILE *stream, hid_t tid, void *_mem)
render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem)
{
HERR_INIT(int, SUCCEED)
unsigned char *mem = (unsigned char*)_mem;
@@ -3779,7 +3783,7 @@ render_bin_output(FILE *stream, hid_t tid, void *_mem)
offset = H5Tget_member_offset(tid, j);
memb = H5Tget_member_type(tid, j);
if (render_bin_output(stream, memb, mem + offset) < 0)
if (render_bin_output(stream, container, memb, mem + offset) < 0)
return FAIL;
H5Tclose(memb);
@@ -3827,7 +3831,7 @@ render_bin_output(FILE *stream, hid_t tid, void *_mem)
/* dump the array element */
for (i = 0; i < nelmts; i++) {
if (render_bin_output(stream, memb, mem + i * size) < 0)
if (render_bin_output(stream, container, memb, mem + i * size) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
@@ -3847,11 +3851,34 @@ render_bin_output(FILE *stream, hid_t tid, void *_mem)
for (i = 0; i < nelmts; i++) {
/* dump the array element */
if (render_bin_output(stream, memb, ((char *) (((hvl_t *) mem)->p)) + i * size) < 0)
if (render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)) + i * size) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
H5Tclose(memb);
}
else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) {
if (region_output) {
/* region data */
hid_t region_id, region_space;
H5S_sel_type region_type;
region_id = H5Rdereference(container, H5R_DATASET_REGION, mem);
if (region_id >= 0) {
region_space = H5Rget_region(container, H5R_DATASET_REGION, mem);
if (region_space >= 0) {
region_type = H5Sget_select_type(region_space);
if(region_type==H5S_SEL_POINTS)
render_bin_output_region_points(region_space, region_id, stream, container, tid, mem);
else
render_bin_output_region_blocks(region_space, region_id, stream, container, tid, mem);
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
} /* end if (region_id >= 0) */
} /* end if (region_output... */
}
else if (H5Tequal(tid, H5T_STD_REF_OBJ)) {
}
else {
size_t i;
if (1 == size) {
@@ -3878,6 +3905,302 @@ CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print the data values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
* The function returns FAIL if there was an error, otherwise SUCEED
*
*-------------------------------------------------------------------------
*/
int
render_bin_output_region_data_blocks(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container,
int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) {
HERR_INIT(int, SUCCEED)
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
size_t numelem;
hsize_t total_size[H5S_MAX_RANK];
unsigned int region_flags; /* buffer extent flags */
int jndx;
int type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
int blkndx;
hid_t sid1 = -1;
/* Get the dataspace of the dataset */
if((sid1 = H5Dget_space(region_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims");
/* find the dimensions of each data space from the block coordinates */
numelem = 1;
for (jndx = 0; jndx < ndims; jndx++) {
dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1;
numelem = dims1[jndx] * numelem;
}
/* Create dataspace for reading buffer */
if((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
if((type_size = H5Tget_size(type_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((region_buf = HDmalloc(type_size * numelem)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate region buffer");
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for start");
if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for count");
for (blkndx = 0; blkndx < nblocks; blkndx++) {
for (jndx = 0; jndx < ndims; jndx++) {
start[jndx] = ptdata[jndx + blkndx * ndims * 2];
count[jndx] = dims1[jndx];
}
if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed");
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
for (jndx = 0; jndx < numelem; jndx++) {
render_bin_output(stream, container, type_id,
((char*)region_buf + jndx * type_size));
/* Render the region data element end */
} /* end for (jndx = 0; jndx < numelem; jndx++) */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
done:
HDfree(start);
HDfree(count);
HDfree(region_buf);
HDfree(dims1);
if(H5Sclose(mem_space) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
if(H5Sclose(sid1) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to dump a region reference using blocks.
*
* Return:
* The function returns False if ERROR, otherwise True
*
*-------------------------------------------------------------------------
*/
hbool_t
render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container, hid_t tid, void *_mem) {
HERR_INIT(hbool_t, TRUE)
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
int ndims;
hid_t dtype;
hid_t type_id;
int i;
if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
/* Print block information */
if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
if((ptdata = (hsize_t*) malloc((size_t) alloc_size)) == NULL)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");
H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t);
if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed");
if((dtype = H5Dget_type(region_id)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
render_bin_output_region_data_blocks(region_space, region_id,
stream, container, ndims, type_id, nblocks, ptdata);
done:
free(ptdata);
if(H5Tclose(type_id) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(dtype) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
H5_LEAVE(TRUE)
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print the data values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type points.
*
* Return:
* The function returns FAIL on error, otherwise SUCCEED
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* size_t ncols
* int ndims is the number of dimensions of the region element
* hssize_t npoints is the number of points in the region
*-------------------------------------------------------------------------
*/
int
render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container,
int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) {
HERR_INIT(int, SUCCEED)
hsize_t alloc_size;
hsize_t *dims1 = NULL;
unsigned int region_flags; /* buffer extent flags */
int indx;
int jndx;
int type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
if((type_size = H5Tget_size(type_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((region_buf = HDmalloc(type_size * npoints)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region");
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims");
dims1[0] = npoints;
if((mem_space = H5Screate_simple(1, dims1, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
for (jndx = 0; jndx < npoints; jndx++) {
if(H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
render_bin_output(stream, container, type_id,
((char*)region_buf + jndx * type_size));
} /* end for (jndx = 0; jndx < npoints; jndx++) */
done:
HDfree(region_buf);
HDfree(dims1);
if(H5Sclose(mem_space) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to dump a region reference using points.
*
* Return:
* The function returns False if the last dimension has been reached, otherwise True
*
*-------------------------------------------------------------------------
*/
hbool_t
render_bin_output_region_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container, hid_t tid, void *_mem) {
HERR_INIT(hbool_t, TRUE)
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
int ndims;
int indx;
hid_t dtype;
hid_t type_id;
if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
/* Allocate space for the dimension array */
if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
alloc_size = npoints * ndims * sizeof(ptdata[0]);
assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
if((ptdata = malloc((size_t) alloc_size)) == NULL)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");
H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t);
if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed");
if((dtype = H5Dget_type(region_id)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
render_bin_output_region_data_points(region_space, region_id,
stream, container, ndims, type_id, npoints, ptdata);
done:
free(ptdata);
if(H5Tclose(type_id) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(dtype) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
H5_LEAVE(ret_value)
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: h5tools_is_zero
*

1
tools/lib/h5tools.h
View File

@@ -574,7 +574,6 @@ int h5tools_print_datatype(h5tools_str_t *buffer/*in,out*/,
const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/,
hid_t type);
int h5tools_print_enum(h5tools_str_t *buffer/*in,out*/, hid_t type);
#ifdef __cplusplus
}
#endif

7
tools/testfiles/tbinregR.exp Normal file
View File

@@ -0,0 +1,7 @@
66, 69, 72, 75, 78, 81,
96, 99, 102, 105, 108, 111,
126, 129, 132, 135, 138, 141,
156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201,
216, 219, 222, 225, 228, 231