mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-03-31 17:10:47 +08:00
[svn-r17450] Bring h5dump single subsetting selection and region reference changes from NPOESS
Tested: local linux smirom
This commit is contained in:
Allen Byrne
parent
4978a681f9
commit
c7590ca38e
3
MANIFEST
3
MANIFEST
@ -1151,6 +1151,9 @@
|
||||
./tools/testfiles/tattr-2.ddl
|
||||
./tools/testfiles/tattr-3.ddl
|
||||
./tools/testfiles/tattr.h5
|
||||
./tools/testfiles/tattrreg.h5
|
||||
./tools/testfiles/tattrreg.ddl
|
||||
./tools/testfiles/tattrregR.ddl
|
||||
./tools/testfiles/tbitfields.h5
|
||||
./tools/testfiles/tchar.h5
|
||||
./tools/testfiles/tchar1.ddl
|
||||
|
||||
@ -81,7 +81,6 @@ static const char *fp_format = NULL;
|
||||
const char *outfname=NULL;
|
||||
|
||||
|
||||
|
||||
/* things to display or which are set via command line parameters */
|
||||
static int display_all = TRUE;
|
||||
static int display_oid = FALSE;
|
||||
@ -94,6 +93,7 @@ static int display_dcpl = FALSE; /*dcpl */
|
||||
static int display_fi = FALSE; /*file index */
|
||||
static int display_ai = TRUE; /*array index */
|
||||
static int display_escape = FALSE; /*escape non printable characters */
|
||||
static int display_region = FALSE; /*print region reference data */
|
||||
|
||||
/* sort parameters */
|
||||
static H5_index_t sort_by = H5_INDEX_NAME; /*sort_by [creation_order | name] */
|
||||
@ -388,7 +388,7 @@ struct handler_t {
|
||||
* parameters. The long-named ones can be partially spelled. When
|
||||
* adding more, make sure that they don't clash with each other.
|
||||
*/
|
||||
static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b*F:s:S:Aq:z:m:";
|
||||
static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b*F:s:S:Aq:z:m:R";
|
||||
static struct long_options l_opts[] = {
|
||||
{ "help", no_arg, 'h' },
|
||||
{ "hel", no_arg, 'h' },
|
||||
@ -500,6 +500,7 @@ static struct long_options l_opts[] = {
|
||||
{ "sort_by", require_arg, 'q' },
|
||||
{ "sort_order", require_arg, 'z' },
|
||||
{ "format", require_arg, 'm' },
|
||||
{ "region", no_arg, 'R' },
|
||||
{ NULL, 0, '\0' }
|
||||
};
|
||||
|
||||
@ -655,6 +656,7 @@ usage(const char *prog)
|
||||
fprintf(stdout, " -m T, --format=T Set the floating point output format\n");
|
||||
fprintf(stdout, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n");
|
||||
fprintf(stdout, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
|
||||
fprintf(stdout, " -R, --region Print dataset pointed by region references\n");
|
||||
fprintf(stdout, " -x, --xml Output in XML using Schema\n");
|
||||
fprintf(stdout, " -u, --use-dtd Output in XML using DTD\n");
|
||||
fprintf(stdout, " -D U, --xml-dtd=U Use the DTD or schema at U\n");
|
||||
@ -665,14 +667,16 @@ usage(const char *prog)
|
||||
fprintf(stdout, " Subsetting is available by using the following options with a dataset\n");
|
||||
fprintf(stdout, " attribute. Subsetting is done by selecting a hyperslab from the data.\n");
|
||||
fprintf(stdout, " Thus, the options mirror those for performing a hyperslab selection.\n");
|
||||
fprintf(stdout, " The START and COUNT parameters are mandatory if you do subsetting.\n");
|
||||
fprintf(stdout, " The STRIDE and BLOCK parameters are optional and will default to 1 in\n");
|
||||
fprintf(stdout, " each dimension.\n");
|
||||
fprintf(stdout, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n");
|
||||
fprintf(stdout, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n");
|
||||
fprintf(stdout, " each dimension. START is optional and will default to 0 in each dimension.\n");
|
||||
fprintf(stdout, "\n");
|
||||
fprintf(stdout, " -s L, --start=L Offset of start of subsetting selection\n");
|
||||
fprintf(stdout, " -S L, --stride=L Hyperslab stride\n");
|
||||
fprintf(stdout, " -c L, --count=L Number of blocks to include in selection\n");
|
||||
fprintf(stdout, " -k L, --block=L Size of block in hyperslab\n");
|
||||
fprintf(stdout, " -s START, --start=START Offset of start of subsetting selection\n");
|
||||
fprintf(stdout, " -S STRIDE, --stride=STRIDE Hyperslab stride\n");
|
||||
fprintf(stdout, " -c COUNT, --count=COUNT Number of blocks to include in selection\n");
|
||||
fprintf(stdout, " -k BLOCK, --block=BLOCK Size of block in hyperslab\n");
|
||||
fprintf(stdout, " START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n");
|
||||
fprintf(stdout, " number of dimensions in the dataspace being queried\n");
|
||||
fprintf(stdout, "\n");
|
||||
fprintf(stdout, " D - is the file driver to use in opening the file. Acceptable values\n");
|
||||
fprintf(stdout, " are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n");
|
||||
@ -683,8 +687,6 @@ usage(const char *prog)
|
||||
fprintf(stdout, " P - is the full path from the root group to the object.\n");
|
||||
fprintf(stdout, " N - is an integer greater than 1.\n");
|
||||
fprintf(stdout, " T - is a string containing the floating point format, e.g '%%.3f'\n");
|
||||
fprintf(stdout, " L - is a list of integers the number of which are equal to the\n");
|
||||
fprintf(stdout, " number of dimensions in the dataspace being queried\n");
|
||||
fprintf(stdout, " U - is a URI reference (as defined in [IETF RFC 2396],\n");
|
||||
fprintf(stdout, " updated by [IETF RFC 2732])\n");
|
||||
fprintf(stdout, " B - is the form of binary output: NATIVE for a memory type, FILE for the\n");
|
||||
@ -1189,6 +1191,18 @@ print_datatype(hid_t type,unsigned in_group)
|
||||
|
||||
case H5T_REFERENCE:
|
||||
printf("H5T_REFERENCE");
|
||||
/* The BNF document states that the type of reference should be
|
||||
* displayed after "H5T_REFERENCE". Therefore add the missing
|
||||
* reference type if the region command line option is used. This
|
||||
* reference type will not be displayed if the region option is not used. */
|
||||
if(display_region) {
|
||||
if (H5Tequal(type, H5T_STD_REF_DSETREG)==TRUE) {
|
||||
printf(" { H5T_STD_REF_DSETREG }");
|
||||
}
|
||||
else {
|
||||
printf(" { H5T_STD_REF_OBJECT }");
|
||||
}
|
||||
}
|
||||
break;
|
||||
|
||||
case H5T_ENUM:
|
||||
@ -2391,13 +2405,29 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
|
||||
outputformat->pindex=display_index;
|
||||
|
||||
/* do not print indices for regions */
|
||||
if(obj_data == DATASET_DATA)
|
||||
{
|
||||
if(obj_data == DATASET_DATA) {
|
||||
hid_t f_type = H5Dget_type(obj_id);
|
||||
|
||||
if (H5Tequal(f_type, H5T_STD_REF_DSETREG))
|
||||
{
|
||||
outputformat->pindex = 0;
|
||||
if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
|
||||
/* For the region option, correct the display of indices */
|
||||
if (display_region) {
|
||||
if (display_index) {
|
||||
outputformat->pindex = 1;
|
||||
outputformat->idx_fmt = "(%s): ";
|
||||
outputformat->idx_n_fmt = HSIZE_T_FORMAT;
|
||||
outputformat->idx_sep = ",";
|
||||
outputformat->line_pre = "%s";
|
||||
}
|
||||
else {
|
||||
outputformat->pindex = 0;
|
||||
outputformat->idx_fmt = "";
|
||||
outputformat->idx_n_fmt = "";
|
||||
outputformat->idx_sep = "";
|
||||
outputformat->line_pre = "";
|
||||
}
|
||||
}
|
||||
else
|
||||
outputformat->pindex = 0;
|
||||
}
|
||||
H5Tclose(f_type);
|
||||
}
|
||||
@ -2470,13 +2500,15 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
|
||||
status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, sset, depth);
|
||||
|
||||
H5Tclose(f_type);
|
||||
} else {
|
||||
}
|
||||
else {
|
||||
/* need to call h5tools_dump_mem for the attribute data */
|
||||
space = H5Aget_space(obj_id);
|
||||
space_type = H5Sget_simple_extent_type(space);
|
||||
if(space_type == H5S_NULL || space_type == H5S_NO_CLASS) {
|
||||
status = SUCCEED;
|
||||
} else {
|
||||
}
|
||||
else {
|
||||
char string_prefix[64];
|
||||
h5tool_format_t string_dataformat;
|
||||
|
||||
@ -3516,21 +3548,13 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis
|
||||
}
|
||||
|
||||
if (!sset->count) {
|
||||
hsize_t dims[H5S_MAX_RANK];
|
||||
herr_t status = H5Sget_simple_extent_dims(sid, dims, NULL);
|
||||
unsigned int i;
|
||||
|
||||
if (status == FAIL) {
|
||||
error_msg(progname, "unable to get dataset dimensions\n");
|
||||
d_status = EXIT_FAILURE;
|
||||
H5Sclose(sid);
|
||||
return;
|
||||
}
|
||||
|
||||
sset->count = calloc(ndims, sizeof(hsize_t));
|
||||
|
||||
for (i = 0; i < ndims; i++)
|
||||
sset->count[i] = dims[i] - sset->start[i];
|
||||
sset->count[i] = 1;
|
||||
}
|
||||
|
||||
if (!sset->block) {
|
||||
@ -3872,6 +3896,10 @@ parse_command_line(int argc, const char *argv[])
|
||||
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
|
||||
parse_start:
|
||||
switch ((char)opt) {
|
||||
case 'R':
|
||||
display_region = TRUE;
|
||||
region_output = TRUE;
|
||||
break;
|
||||
case 'B':
|
||||
display_bb = TRUE;
|
||||
last_was_dset = FALSE;
|
||||
@ -3981,74 +4009,61 @@ parse_start:
|
||||
break;
|
||||
|
||||
case 'o':
|
||||
if ( bin_output ) {
|
||||
if (set_output_file(opt_arg, 1) < 0) {
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
else {
|
||||
if (set_output_file(opt_arg, 0) < 0) {
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
|
||||
if ( bin_output )
|
||||
{
|
||||
if (set_output_file(opt_arg, 1) < 0){
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
if (set_output_file(opt_arg, 0) < 0){
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
usingdasho = TRUE;
|
||||
last_was_dset = FALSE;
|
||||
outfname = opt_arg;
|
||||
break;
|
||||
|
||||
usingdasho = TRUE;
|
||||
last_was_dset = FALSE;
|
||||
outfname = opt_arg;
|
||||
break;
|
||||
case 'b':
|
||||
if ( opt_arg != NULL) {
|
||||
if ( ( bin_form = set_binary_form(opt_arg)) < 0) {
|
||||
/* failed to set binary form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
bin_output = TRUE;
|
||||
if (outfname!=NULL) {
|
||||
if (set_output_file(outfname, 1) < 0) {
|
||||
/* failed to set output file */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
case 'b':
|
||||
last_was_dset = FALSE;
|
||||
}
|
||||
break;
|
||||
|
||||
if ( opt_arg != NULL)
|
||||
{
|
||||
if ( ( bin_form = set_binary_form(opt_arg)) < 0)
|
||||
{
|
||||
/* failed to set binary form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
bin_output = TRUE;
|
||||
if (outfname!=NULL)
|
||||
{
|
||||
if (set_output_file(outfname, 1) < 0)
|
||||
{
|
||||
/* failed to set output file */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
last_was_dset = FALSE;
|
||||
}
|
||||
|
||||
break;
|
||||
case 'q':
|
||||
if ( ( sort_by = set_sort_by(opt_arg)) < 0) {
|
||||
/* failed to set "sort by" form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
break;
|
||||
|
||||
case 'q':
|
||||
case 'z':
|
||||
if ( ( sort_order = set_sort_order(opt_arg)) < 0) {
|
||||
/* failed to set "sort order" form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
break;
|
||||
|
||||
if ( ( sort_by = set_sort_by(opt_arg)) < 0)
|
||||
{
|
||||
/* failed to set "sort by" form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
break;
|
||||
|
||||
case 'z':
|
||||
|
||||
if ( ( sort_order = set_sort_order(opt_arg)) < 0)
|
||||
{
|
||||
/* failed to set "sort order" form */
|
||||
usage(progname);
|
||||
leave(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
break;
|
||||
break;
|
||||
|
||||
/** begin XML parameters **/
|
||||
case 'x':
|
||||
|
||||
@ -92,6 +92,7 @@
|
||||
#define FILE62 "textlinktar.h5"
|
||||
#define FILE63 "textlinkfar.h5"
|
||||
#define FILE64 "tarray8.h5"
|
||||
#define FILE65 "tattrreg.h5"
|
||||
|
||||
|
||||
|
||||
@ -1852,6 +1853,126 @@ static void gent_datareg(void)
|
||||
free(drbuf);
|
||||
}
|
||||
|
||||
static void gent_attrreg(void)
|
||||
{
|
||||
/*some code is taken from enum.c in the test dir */
|
||||
|
||||
hid_t fid1; /* HDF5 File IDs */
|
||||
hid_t dset1; /* Dataset ID */
|
||||
hid_t dset2; /* Dereferenced dataset ID */
|
||||
hid_t sid1; /* Dataspace ID #1 */
|
||||
hid_t sid2; /* Dataspace ID #2 */
|
||||
hid_t sid3; /* Dataspace ID #3 */
|
||||
hid_t attr1; /* Attribute ID */
|
||||
hsize_t dims1[] = {SPACE1_DIM1};
|
||||
hsize_t dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
|
||||
hsize_t start[SPACE2_RANK]; /* Starting location of hyperslab */
|
||||
hsize_t stride[SPACE2_RANK]; /* Stride of hyperslab */
|
||||
hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */
|
||||
hsize_t block[SPACE2_RANK]; /* Block size of hyperslab */
|
||||
hsize_t coord1[POINT1_NPOINTS][SPACE2_RANK]; /* Coordinates for point selection */
|
||||
hdset_reg_ref_t *wbuf; /* buffer to write to disk */
|
||||
hdset_reg_ref_t *rbuf; /* buffer read from disk */
|
||||
uint8_t *dwbuf; /* Buffer for writing numeric data to disk */
|
||||
uint8_t *drbuf; /* Buffer for reading numeric data from disk */
|
||||
uint8_t *tu8; /* Temporary pointer to uint8 data */
|
||||
int i; /* counting variables */
|
||||
|
||||
/* Allocate write & read buffers */
|
||||
wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
|
||||
rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
|
||||
dwbuf=malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2);
|
||||
drbuf=calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2);
|
||||
|
||||
/* Create file */
|
||||
fid1 = H5Fcreate(FILE65, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
/* Create dataspace for datasets */
|
||||
sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);
|
||||
|
||||
/* Create a dataset */
|
||||
dset2 = H5Dcreate2(fid1, "Dataset2", H5T_STD_U8BE, sid2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
||||
|
||||
for(tu8 = dwbuf, i = 0; i < SPACE2_DIM1 * SPACE2_DIM2; i++)
|
||||
*tu8++=i*3;
|
||||
|
||||
/* Write selection to disk */
|
||||
H5Dwrite(dset2, H5T_NATIVE_UCHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, dwbuf);
|
||||
|
||||
/* Close Dataset */
|
||||
H5Dclose(dset2);
|
||||
|
||||
/*
|
||||
* Create dataset with a null dataspace to serve as the parent for
|
||||
* the attribute.
|
||||
*/
|
||||
sid1 = H5Screate (H5S_NULL);
|
||||
dset1 = H5Dcreate (fid1, "Dataset1", H5T_STD_I32LE, sid1, H5P_DEFAULT,
|
||||
H5P_DEFAULT, H5P_DEFAULT);
|
||||
H5Sclose (sid1);
|
||||
|
||||
/* Create references */
|
||||
|
||||
/* Select 6x6 hyperslab for first reference */
|
||||
start[0] = 2; start[1] = 2;
|
||||
stride[0] = 1; stride[1] = 1;
|
||||
count[0] = 6; count[1] = 6;
|
||||
block[0] = 1; block[1] = 1;
|
||||
H5Sselect_hyperslab(sid2, H5S_SELECT_SET, start, stride, count, block);
|
||||
|
||||
H5Sget_select_npoints(sid2);
|
||||
|
||||
/* Store first dataset region */
|
||||
H5Rcreate(&wbuf[0], fid1, "/Dataset2", H5R_DATASET_REGION, sid2);
|
||||
|
||||
/* Select sequence of ten points for second reference */
|
||||
coord1[0][0]=6; coord1[0][1]=9;
|
||||
coord1[1][0]=2; coord1[1][1]=2;
|
||||
coord1[2][0]=8; coord1[2][1]=4;
|
||||
coord1[3][0]=1; coord1[3][1]=6;
|
||||
coord1[4][0]=2; coord1[4][1]=8;
|
||||
coord1[5][0]=3; coord1[5][1]=2;
|
||||
coord1[6][0]=0; coord1[6][1]=4;
|
||||
coord1[7][0]=9; coord1[7][1]=0;
|
||||
coord1[8][0]=7; coord1[8][1]=1;
|
||||
coord1[9][0]=3; coord1[9][1]=3;
|
||||
H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(hsize_t *)coord1);
|
||||
|
||||
H5Sget_select_npoints(sid2);
|
||||
|
||||
/* Store second dataset region */
|
||||
H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
|
||||
|
||||
/* Create dataspace for the attribute */
|
||||
sid3 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
|
||||
|
||||
/* Create the attribute and write the region references to it. */
|
||||
attr1 = H5Acreate (dset1, "Attribute1", H5T_STD_REF_DSETREG, sid3, H5P_DEFAULT,
|
||||
H5P_DEFAULT);
|
||||
H5Awrite (attr1, H5T_STD_REF_DSETREG, wbuf);
|
||||
|
||||
/* Close attribute dataspace */
|
||||
H5Sclose(sid3);
|
||||
|
||||
/* Close attribute */
|
||||
H5Aclose (attr1);
|
||||
|
||||
/* Close Dataset */
|
||||
H5Dclose(dset1);
|
||||
|
||||
/* Close uint8 dataset dataspace */
|
||||
H5Sclose(sid2);
|
||||
|
||||
/* Close file */
|
||||
H5Fclose(fid1);
|
||||
|
||||
/* Free memory buffers */
|
||||
free(wbuf);
|
||||
free(rbuf);
|
||||
free(dwbuf);
|
||||
free(drbuf);
|
||||
}
|
||||
|
||||
/*taken from Elena's compound test file*/
|
||||
static void gent_nestcomp(void)
|
||||
{
|
||||
@ -6351,6 +6472,7 @@ int main(void)
|
||||
gent_enum();
|
||||
gent_objref();
|
||||
gent_datareg();
|
||||
gent_attrreg();
|
||||
gent_nestcomp();
|
||||
gent_opaque();
|
||||
gent_bitfields();
|
||||
|
||||
3165
tools/lib/h5tools.c
3165
tools/lib/h5tools.c
File diff suppressed because it is too large
Load Diff
@ -50,6 +50,147 @@
|
||||
/* format for hsize_t */
|
||||
#define HSIZE_T_FORMAT "%"H5_PRINTF_LL_WIDTH"u"
|
||||
|
||||
#define H5TOOLS_DUMP_MAX_RANK H5S_MAX_RANK
|
||||
|
||||
/*
|
||||
* Strings for output - these were duplicated from the h5dump.h
|
||||
* file in order to support region reference data display
|
||||
*/
|
||||
#define ATTRIBUTE "ATTRIBUTE"
|
||||
#define BLOCK "BLOCK"
|
||||
#define SUPER_BLOCK "SUPER_BLOCK"
|
||||
#define COMPRESSION "COMPRESSION"
|
||||
#define CONCATENATOR "//"
|
||||
#define COMPLEX "COMPLEX"
|
||||
#define COUNT "COUNT"
|
||||
#define CSET "CSET"
|
||||
#define CTYPE "CTYPE"
|
||||
#define DATA "DATA"
|
||||
#define DATASPACE "DATASPACE"
|
||||
#define EXTERNAL "EXTERNAL"
|
||||
#define FILENO "FILENO"
|
||||
#define HARDLINK "HARDLINK"
|
||||
#define NLINK "NLINK"
|
||||
#define OBJID "OBJECTID"
|
||||
#define OBJNO "OBJNO"
|
||||
#define S_SCALAR "SCALAR"
|
||||
#define S_SIMPLE "SIMPLE"
|
||||
#define S_NULL "NULL"
|
||||
#define SOFTLINK "SOFTLINK"
|
||||
#define EXTLINK "EXTERNAL_LINK"
|
||||
#define UDLINK "USERDEFINED_LINK"
|
||||
#define START "START"
|
||||
#define STRIDE "STRIDE"
|
||||
#define STRSIZE "STRSIZE"
|
||||
#define STRPAD "STRPAD"
|
||||
#define SUBSET "SUBSET"
|
||||
#define FILTERS "FILTERS"
|
||||
#define DEFLATE "COMPRESSION DEFLATE"
|
||||
#define DEFLATE_LEVEL "LEVEL"
|
||||
#define SHUFFLE "PREPROCESSING SHUFFLE"
|
||||
#define FLETCHER32 "CHECKSUM FLETCHER32"
|
||||
#define SZIP "COMPRESSION SZIP"
|
||||
#define NBIT "COMPRESSION NBIT"
|
||||
#define SCALEOFFSET "COMPRESSION SCALEOFFSET"
|
||||
#define SCALEOFFSET_MINBIT "MIN BITS"
|
||||
#define STORAGE_LAYOUT "STORAGE_LAYOUT"
|
||||
#define CONTIGUOUS "CONTIGUOUS"
|
||||
#define COMPACT "COMPACT"
|
||||
#define CHUNKED "CHUNKED"
|
||||
#define EXTERNAL_FILE "EXTERNAL_FILE"
|
||||
#define FILLVALUE "FILLVALUE"
|
||||
#define FILE_CONTENTS "FILE_CONTENTS"
|
||||
|
||||
#define BEGIN "{"
|
||||
#define END "}"
|
||||
|
||||
/*
|
||||
* dump structure for output - this was duplicated from the h5dump.h
|
||||
* file in order to support region reference data display
|
||||
*/
|
||||
typedef struct h5tools_dump_header_t {
|
||||
const char *name;
|
||||
const char *filebegin;
|
||||
const char *fileend;
|
||||
const char *bootblockbegin;
|
||||
const char *bootblockend;
|
||||
const char *groupbegin;
|
||||
const char *groupend;
|
||||
const char *datasetbegin;
|
||||
const char *datasetend;
|
||||
const char *attributebegin;
|
||||
const char *attributeend;
|
||||
const char *datatypebegin;
|
||||
const char *datatypeend;
|
||||
const char *dataspacebegin;
|
||||
const char *dataspaceend;
|
||||
const char *databegin;
|
||||
const char *dataend;
|
||||
const char *softlinkbegin;
|
||||
const char *softlinkend;
|
||||
const char *extlinkbegin;
|
||||
const char *extlinkend;
|
||||
const char *udlinkbegin;
|
||||
const char *udlinkend;
|
||||
const char *subsettingbegin;
|
||||
const char *subsettingend;
|
||||
const char *startbegin;
|
||||
const char *startend;
|
||||
const char *stridebegin;
|
||||
const char *strideend;
|
||||
const char *countbegin;
|
||||
const char *countend;
|
||||
const char *blockbegin;
|
||||
const char *blockend;
|
||||
|
||||
const char *fileblockbegin;
|
||||
const char *fileblockend;
|
||||
const char *bootblockblockbegin;
|
||||
const char *bootblockblockend;
|
||||
const char *groupblockbegin;
|
||||
const char *groupblockend;
|
||||
const char *datasetblockbegin;
|
||||
const char *datasetblockend;
|
||||
const char *attributeblockbegin;
|
||||
const char *attributeblockend;
|
||||
const char *datatypeblockbegin;
|
||||
const char *datatypeblockend;
|
||||
const char *dataspaceblockbegin;
|
||||
const char *dataspaceblockend;
|
||||
const char *datablockbegin;
|
||||
const char *datablockend;
|
||||
const char *softlinkblockbegin;
|
||||
const char *softlinkblockend;
|
||||
const char *extlinkblockbegin;
|
||||
const char *extlinkblockend;
|
||||
const char *udlinkblockbegin;
|
||||
const char *udlinkblockend;
|
||||
const char *strblockbegin;
|
||||
const char *strblockend;
|
||||
const char *enumblockbegin;
|
||||
const char *enumblockend;
|
||||
const char *structblockbegin;
|
||||
const char *structblockend;
|
||||
const char *vlenblockbegin;
|
||||
const char *vlenblockend;
|
||||
const char *subsettingblockbegin;
|
||||
const char *subsettingblockend;
|
||||
const char *startblockbegin;
|
||||
const char *startblockend;
|
||||
const char *strideblockbegin;
|
||||
const char *strideblockend;
|
||||
const char *countblockbegin;
|
||||
const char *countblockend;
|
||||
const char *blockblockbegin;
|
||||
const char *blockblockend;
|
||||
|
||||
const char *dataspacedescriptionbegin;
|
||||
const char *dataspacedescriptionend;
|
||||
const char *dataspacedimbegin;
|
||||
const char *dataspacedimend;
|
||||
|
||||
} h5tools_dump_header_t;
|
||||
|
||||
/*
|
||||
* Information about how to format output.
|
||||
*/
|
||||
@ -373,11 +514,16 @@ struct subset_t {
|
||||
hsize_t *block;
|
||||
};
|
||||
|
||||
/* The following include, h5tools_str.h, must be after the
|
||||
* above stucts are defined. There is a dependency in the following
|
||||
* include that hasn't been identified yet. */
|
||||
|
||||
#include "h5tools_str.h"
|
||||
|
||||
extern FILE *rawdatastream; /* output stream for raw data */
|
||||
extern int bin_output; /* binary output */
|
||||
extern int bin_form; /* binary form */
|
||||
|
||||
|
||||
extern int region_output; /* region output */
|
||||
|
||||
/* Strings for output */
|
||||
#define H5_TOOLS_GROUP "GROUP"
|
||||
@ -407,6 +553,19 @@ extern int h5tools_canreadf(const char* name,
|
||||
extern int h5tools_can_encode(H5Z_filter_t filtn);
|
||||
|
||||
void init_acc_pos(h5tools_context_t *ctx, hsize_t *dims);
|
||||
|
||||
/*
|
||||
* new functions needed to display region reference data
|
||||
*/
|
||||
void h5tools_dump_datatype(FILE *stream, const h5tool_format_t *info,
|
||||
h5tools_context_t *ctx/*in,out*/, hid_t type);
|
||||
void h5tools_print_dataspace(h5tools_str_t *buffer/*in,out*/,
|
||||
const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/,
|
||||
hid_t space);
|
||||
void h5tools_print_datatype(h5tools_str_t *buffer/*in,out*/,
|
||||
const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/,
|
||||
hid_t type);
|
||||
void h5tools_print_enum(h5tools_str_t *buffer/*in,out*/,
|
||||
const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/,
|
||||
hid_t type);
|
||||
#endif /* H5TOOLS_H__ */
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -35,7 +35,18 @@ extern char *h5tools_str_fmt(h5tools_str_t *str, size_t start, const char *fm
|
||||
extern char *h5tools_str_prefix(h5tools_str_t *str, const h5tool_format_t *info,
|
||||
hsize_t elmtno, unsigned ndims, hsize_t min_idx[],
|
||||
hsize_t max_idx[], h5tools_context_t *ctx);
|
||||
extern int h5tools_str_dump_region(h5tools_str_t *, hid_t, const h5tool_format_t *);
|
||||
/*
|
||||
* new functions needed to display region reference data
|
||||
*/
|
||||
extern char *h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info,
|
||||
hsize_t elmtno, hsize_t *ptdata, unsigned ndims, hsize_t min_idx[],
|
||||
hsize_t max_idx[], h5tools_context_t *ctx);
|
||||
extern void h5tools_str_dump_region_blocks(h5tools_str_t *, hid_t, const h5tool_format_t *,
|
||||
h5tools_context_t *ctx);
|
||||
extern void h5tools_str_dump_region_points(h5tools_str_t *, hid_t, const h5tool_format_t *,
|
||||
h5tools_context_t *ctx);
|
||||
extern void h5tools_str_sprint_region(h5tools_str_t *str, const h5tool_format_t *info, hid_t container,
|
||||
void *vp, h5tools_context_t *ctx);
|
||||
extern char *h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info,
|
||||
hid_t container, hid_t type, void *vp,
|
||||
h5tools_context_t *ctx);
|
||||
|
||||
38
tools/testfiles/tattrreg.ddl
Normal file
38
tools/testfiles/tattrreg.ddl
Normal file
@ -0,0 +1,38 @@
|
||||
#############################
|
||||
Expected output for 'h5dump tattrreg.h5'
|
||||
#############################
|
||||
HDF5 "tattrreg.h5" {
|
||||
GROUP "/" {
|
||||
DATASET "Dataset1" {
|
||||
DATATYPE H5T_STD_I32LE
|
||||
DATASPACE NULL
|
||||
DATA {
|
||||
}
|
||||
ATTRIBUTE "Attribute1" {
|
||||
DATATYPE H5T_REFERENCE
|
||||
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
|
||||
DATA {
|
||||
(0): DATASET /Dataset2 {(2,2)-(7,7)}, DATASET /Dataset2 {(6,9),
|
||||
(1): (2,2), (8,4), (1,6), (2,8), (3,2), (0,4), (9,0), (7,1),
|
||||
(1): (3,3)}, NULL, NULL
|
||||
}
|
||||
}
|
||||
}
|
||||
DATASET "Dataset2" {
|
||||
DATATYPE H5T_STD_U8BE
|
||||
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
|
||||
DATA {
|
||||
(0,0): 0, 3, 6, 9, 12, 15, 18, 21, 24, 27,
|
||||
(1,0): 30, 33, 36, 39, 42, 45, 48, 51, 54, 57,
|
||||
(2,0): 60, 63, 66, 69, 72, 75, 78, 81, 84, 87,
|
||||
(3,0): 90, 93, 96, 99, 102, 105, 108, 111, 114, 117,
|
||||
(4,0): 120, 123, 126, 129, 132, 135, 138, 141, 144, 147,
|
||||
(5,0): 150, 153, 156, 159, 162, 165, 168, 171, 174, 177,
|
||||
(6,0): 180, 183, 186, 189, 192, 195, 198, 201, 204, 207,
|
||||
(7,0): 210, 213, 216, 219, 222, 225, 228, 231, 234, 237,
|
||||
(8,0): 240, 243, 246, 249, 252, 255, 2, 5, 8, 11,
|
||||
(9,0): 14, 17, 20, 23, 26, 29, 32, 35, 38, 41
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
BIN
tools/testfiles/tattrreg.h5
Normal file
BIN
tools/testfiles/tattrreg.h5
Normal file
Binary file not shown.
66
tools/testfiles/tattrregR.ddl
Normal file
66
tools/testfiles/tattrregR.ddl
Normal file
@ -0,0 +1,66 @@
|
||||
#############################
|
||||
Expected output for 'h5dump -R tattrreg.h5'
|
||||
#############################
|
||||
HDF5 "tattrreg.h5" {
|
||||
GROUP "/" {
|
||||
DATASET "Dataset1" {
|
||||
DATATYPE H5T_STD_I32LE
|
||||
DATASPACE NULL
|
||||
DATA {
|
||||
}
|
||||
ATTRIBUTE "Attribute1" {
|
||||
DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
|
||||
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
|
||||
DATA {
|
||||
(0): DATASET /Dataset2 {
|
||||
(0): REGION_TYPE BLOCK (2,2)-(7,7)
|
||||
(0): DATATYPE H5T_STD_U8BE
|
||||
(0): DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
|
||||
(0): DATA {
|
||||
(2,2): 66, 69, 72, 75, 78, 81,
|
||||
(3,2): 96, 99, 102, 105, 108, 111,
|
||||
(4,2): 126, 129, 132, 135, 138, 141,
|
||||
(5,2): 156, 159, 162, 165, 168, 171,
|
||||
(6,2): 186, 189, 192, 195, 198, 201,
|
||||
(7,2): 216, 219, 222, 225, 228, 231
|
||||
(0): }
|
||||
(0): }
|
||||
(1): DATASET /Dataset2 {
|
||||
(1): REGION_TYPE POINT (6,9), (2,2), (8,4), (1,6), (2,8),
|
||||
(1): (3,2), (0,4), (9,0), (7,1), (3,3)
|
||||
(1): DATATYPE H5T_STD_U8BE
|
||||
(1): DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
|
||||
(1): DATA {
|
||||
(6,9): 207,
|
||||
(2,2): 66,
|
||||
(8,4): 252,
|
||||
(1,6): 48,
|
||||
(2,8): 84,
|
||||
(3,2): 96,
|
||||
(0,4): 12,
|
||||
(9,0): 14,
|
||||
(7,1): 213,
|
||||
(3,3): 99
|
||||
(1): }
|
||||
(1): }
|
||||
}
|
||||
}
|
||||
}
|
||||
DATASET "Dataset2" {
|
||||
DATATYPE H5T_STD_U8BE
|
||||
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
|
||||
DATA {
|
||||
(0,0): 0, 3, 6, 9, 12, 15, 18, 21, 24, 27,
|
||||
(1,0): 30, 33, 36, 39, 42, 45, 48, 51, 54, 57,
|
||||
(2,0): 60, 63, 66, 69, 72, 75, 78, 81, 84, 87,
|
||||
(3,0): 90, 93, 96, 99, 102, 105, 108, 111, 114, 117,
|
||||
(4,0): 120, 123, 126, 129, 132, 135, 138, 141, 144, 147,
|
||||
(5,0): 150, 153, 156, 159, 162, 165, 168, 171, 174, 177,
|
||||
(6,0): 180, 183, 186, 189, 192, 195, 198, 201, 204, 207,
|
||||
(7,0): 210, 213, 216, 219, 222, 225, 228, 231, 234, 237,
|
||||
(8,0): 240, 243, 246, 249, 252, 255, 2, 5, 8, 11,
|
||||
(9,0): 14, 17, 20, 23, 26, 29, 32, 35, 38, 41
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -8,27 +8,10 @@ DATASET "/dset1" {
|
||||
SUBSET {
|
||||
START ( 1, 1 );
|
||||
STRIDE ( 1, 1 );
|
||||
COUNT ( 9, 19 );
|
||||
COUNT ( 1, 1 );
|
||||
BLOCK ( 1, 1 );
|
||||
DATA {
|
||||
(1,1): 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
|
||||
(1,19): 20,
|
||||
(2,1): 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
|
||||
(2,18): 20, 21,
|
||||
(3,1): 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
|
||||
(3,18): 21, 22,
|
||||
(4,1): 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
|
||||
(4,18): 22, 23,
|
||||
(5,1): 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
|
||||
(5,18): 23, 24,
|
||||
(6,1): 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
|
||||
(6,17): 23, 24, 25,
|
||||
(7,1): 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
|
||||
(7,17): 24, 25, 26,
|
||||
(8,1): 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
|
||||
(8,17): 25, 26, 27,
|
||||
(9,1): 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
|
||||
(9,17): 26, 27, 28
|
||||
(1,1): 2
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -28,6 +28,7 @@ usage: h5dump [OPTIONS] file
|
||||
-m T, --format=T Set the floating point output format
|
||||
-q Q, --sort_by=Q Sort groups and attributes by index Q
|
||||
-z Z, --sort_order=Z Sort groups and attributes by order Z
|
||||
-R, --region Print dataset pointed by region references
|
||||
-x, --xml Output in XML using Schema
|
||||
-u, --use-dtd Output in XML using DTD
|
||||
-D U, --xml-dtd=U Use the DTD or schema at U
|
||||
@ -38,14 +39,16 @@ usage: h5dump [OPTIONS] file
|
||||
Subsetting is available by using the following options with a dataset
|
||||
attribute. Subsetting is done by selecting a hyperslab from the data.
|
||||
Thus, the options mirror those for performing a hyperslab selection.
|
||||
The START and COUNT parameters are mandatory if you do subsetting.
|
||||
The STRIDE and BLOCK parameters are optional and will default to 1 in
|
||||
each dimension.
|
||||
One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.
|
||||
The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
|
||||
each dimension. START is optional and will default to 0 in each dimension.
|
||||
|
||||
-s L, --start=L Offset of start of subsetting selection
|
||||
-S L, --stride=L Hyperslab stride
|
||||
-c L, --count=L Number of blocks to include in selection
|
||||
-k L, --block=L Size of block in hyperslab
|
||||
-s START, --start=START Offset of start of subsetting selection
|
||||
-S STRIDE, --stride=STRIDE Hyperslab stride
|
||||
-c COUNT, --count=COUNT Number of blocks to include in selection
|
||||
-k BLOCK, --block=BLOCK Size of block in hyperslab
|
||||
START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
|
||||
number of dimensions in the dataspace being queried
|
||||
|
||||
D - is the file driver to use in opening the file. Acceptable values
|
||||
are "sec2", "family", "split", "multi", "direct", and "stream". Without
|
||||
@ -56,8 +59,6 @@ usage: h5dump [OPTIONS] file
|
||||
P - is the full path from the root group to the object.
|
||||
N - is an integer greater than 1.
|
||||
T - is a string containing the floating point format, e.g '%.3f'
|
||||
L - is a list of integers the number of which are equal to the
|
||||
number of dimensions in the dataspace being queried
|
||||
U - is a URI reference (as defined in [IETF RFC 2396],
|
||||
updated by [IETF RFC 2732])
|
||||
B - is the form of binary output: NATIVE for a memory type, FILE for the
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user