/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Purpose: A library for displaying the values of a dataset in a human
* readable format.
*/
#include "h5tools.h"
#include "h5tools_dump.h"
#include "h5tools_ref.h"
#include "h5tools_utils.h"
#include "H5private.h"
h5tool_format_t h5tools_dataformat = {
0, /*raw */
"", /*fmt_raw */
"%d", /*fmt_int */
"%u", /*fmt_uint */
"%hhd", /*fmt_schar */
"%u", /*fmt_uchar */
"%d", /*fmt_short */
"%u", /*fmt_ushort */
"%ld", /*fmt_long */
"%lu", /*fmt_ulong */
NULL, /*fmt_llong */
NULL, /*fmt_ullong */
"%g", /*fmt_double */
"%g", /*fmt_float */
0, /*ascii */
0, /*str_locale */
0, /*str_repeat */
"[ ", /*arr_pre */
",", /*arr_sep */
" ]", /*arr_suf */
1, /*arr_linebreak */
"", /*cmpd_name */
",\n", /*cmpd_sep */
"{", /*cmpd_pre */
"}", /*cmpd_suf */
"\n", /*cmpd_end */
NULL, /* cmpd_listv */
", ", /*vlen_sep */
"(", /*vlen_pre */
")", /*vlen_suf */
"", /*vlen_end */
"%s", /*elmt_fmt */
",", /*elmt_suf1 */
" ", /*elmt_suf2 */
"", /*idx_n_fmt */
"", /*idx_sep */
"", /*idx_fmt */
80,
/*line_ncols */ /*standard default columns */
0, /*line_per_line */
"", /*line_pre */
"%s", /*line_1st */
"%s", /*line_cont */
"", /*line_suf */
"", /*line_sep */
1, /*line_multi_new */
" ", /*line_indent */
1, /*skip_first */
1, /*obj_hidefileno */
" %" PRIuHADDR, /*obj_format */
1, /*dset_hidefileno */
"DATASET %s ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
1, /*array indices */
1 /*escape non printable characters */
};
const h5tools_dump_header_t h5tools_standardformat = {
"standardformat", /*name */
"HDF5", /*filebegin */
"", /*fileend */
SUPER_BLOCK, /*bootblockbegin */
"", /*bootblockend */
H5_TOOLS_GROUP, /*groupbegin */
"", /*groupend */
H5_TOOLS_DATASET, /*datasetbegin */
"", /*datasetend */
ATTRIBUTE, /*attributebegin */
"", /*attributeend */
H5_TOOLS_DATATYPE, /*datatypebegin */
"", /*datatypeend */
DATASPACE, /*dataspacebegin */
"", /*dataspaceend */
DATA, /*databegin */
"", /*dataend */
SOFTLINK, /*softlinkbegin */
"", /*softlinkend */
EXTLINK, /*extlinkbegin */
"", /*extlinkend */
UDLINK, /*udlinkbegin */
"", /*udlinkend */
SUBSET, /*subsettingbegin */
"", /*subsettingend */
START, /*startbegin */
"", /*startend */
STRIDE, /*stridebegin */
"", /*strideend */
COUNT, /*countbegin */
"", /*countend */
BLOCK, /*blockbegin */
"", /*blockend */
"{", /*fileblockbegin */
"}", /*fileblockend */
"{", /*bootblockblockbegin */
"}", /*bootblockblockend */
"{", /*groupblockbegin */
"}", /*groupblockend */
"{", /*datasetblockbegin */
"}", /*datasetblockend */
"{", /*attributeblockbegin */
"}", /*attributeblockend */
"", /*datatypeblockbegin */
"", /*datatypeblockend */
"", /*dataspaceblockbegin */
"", /*dataspaceblockend */
"{", /*datablockbegin */
"}", /*datablockend */
"{", /*softlinkblockbegin */
"}", /*softlinkblockend */
"{", /*extlinkblockbegin */
"}", /*extlinkblockend */
"{", /*udlinkblockbegin */
"}", /*udlinkblockend */
"H5T_ARRAY { ", /*arrblockbegin */
" }", /*arrblockend */
"H5T_COMPOUND {", /*cmpdblockbegin */
"}", /*cmpdblockend */
"H5T_ENUM {", /*enumblockbegin */
"}", /*enumblockend */
"H5T_OPAQUE {", /*opaqblockbegin */
"}", /*opaqblockend */
"H5T_REFERENCE { ", /*refblockbegin */
" }", /*refblockend */
"H5T_STRING {", /*strblockbegin */
"}", /*strblockend */
"H5T_VLEN { ", /*vlenblockbegin */
" }", /*vlenblockend */
"{", /*structblockbegin */
"}", /*structblockend */
"{", /*subsettingblockbegin */
"}", /*subsettingblockend */
"(", /*startblockbegin */
");", /*startblockend */
"(", /*strideblockbegin */
");", /*strideblockend */
"(", /*countblockbegin */
");", /*countblockend */
"(", /*blockblockbegin */
");", /*blockblockend */
"", /*dataspacedescriptionbegin */
"", /*dataspacedescriptionend */
"(", /*dataspacedimbegin */
")", /*dataspacedimend */
"", /*virtualselectionbegin */
"", /*virtualselectionend */
"{", /*virtualselectionblockbegin */
"}", /*virtualselectionblockend */
"\"", /*virtualfilenamebeginbegin */
"\"", /*virtualfilenamebeginend */
"\"", /*virtualdatasetnamebegin */
"\"", /*virtualdtatasetnameend */
};
const h5tools_dump_header_t *h5tools_dump_header_format;
table_t *h5dump_type_table = NULL; /* type table reference for datatype dump */
/* local prototypes */
static int h5tools_print_region_data_blocks(hid_t region_id, FILE *stream, const h5tool_format_t *info,
h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, /* string into which to render */
size_t ncols, unsigned ndims, hid_t type_id, hsize_t nblocks,
hsize_t *ptdata);
static int h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream,
const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, size_t ncols, unsigned ndims,
hid_t type_id, hsize_t npoints, hsize_t *ptdata);
void h5tools_print_dims(h5tools_str_t *buffer, hsize_t *s, int dims);
void h5tools_dump_subsetting_header(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx,
int dims);
static void h5tools_print_virtual_selection(hid_t vspace, FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, /* in,out */
h5tools_str_t *buffer, /* string into which to render */
hsize_t *curr_pos, /* total data element position */
size_t ncols);
void
h5tools_dump_init(void)
{
h5tools_dump_header_format = &h5tools_standardformat;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Prints NELMTS data elements to output STREAM.
* Description:
* Prints some (NELMTS) data elements to output STREAM. The elements are
* stored in _MEM as type TYPE and are printed according to the format
* described in INFO. The CTX struct contains context information shared
* between calls to this function. The FLAGS is a bit field that
* indicates whether the data supplied in this call falls at the
* beginning or end of the total data to be printed (START_OF_DATA and
* END_OF_DATA).
* Return: Success: SUCCEED
* Failure: FAIL
*
*-------------------------------------------------------------------------
*/
int
h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, /* in,out */
hid_t container, unsigned flags, hsize_t nelmts, hid_t type, void *_mem)
{
unsigned char *mem = (unsigned char *)_mem;
hsize_t i; /* element counter */
size_t size; /* size of each datum */
bool dimension_break = true;
size_t ncols = 80; /* available output width */
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos = 0; /* total data element position */
hsize_t elmt_counter = 0; /* counts the # elements printed.
* I (ptl?) needed something that
* isn't going to get reset when a new
* line is formed. I'm going to use
* this var to count elements and
* break after we see a number equal
* to the ctx->size_last_dim. */
int ret_value = 0;
H5TOOLS_START_DEBUG(" file=%p", (void *)stream);
H5TOOLS_DEBUG("rawdata file=%p", (void *)rawdatastream);
/* binary dump */
if (bin_output && (rawdatastream != NULL)) {
H5TOOLS_DEBUG("render_bin_output");
if (render_bin_output(rawdatastream, container, type, _mem, nelmts) < 0) {
PRINTVALSTREAM(rawoutstream, "\nError in writing binary stream\n");
}
} /* end if */
else {
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
size = H5Tget_size(type);
H5TOOLS_DEBUG("type size is %ld", size);
if (info->line_ncols > 0)
ncols = info->line_ncols;
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
curr_pos = ctx->sm_pos;
H5TOOLS_DEBUG("data render start:%ld", nelmts);
for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
void *memref = mem + i * size;
/* Render the data element begin*/
h5tools_str_reset(&buffer);
h5tools_str_sprint(&buffer, info, container, type, memref, ctx);
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, &curr_pos, ncols, i, elmt_counter);
/* Render the data element end*/
if (false == dimension_break)
elmt_counter = 0;
} /* end for (i = 0; i < nelmts... */
H5TOOLS_DEBUG("data render finish");
h5tools_str_close(&buffer);
} /* else bin */
H5TOOLS_ENDDEBUG("exit");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from an attribute referenced by object reference.
*
* Description:
* This is a special case subfunction to dump an attribute reference.
*
* Return:
* The function returns False if the last dimension has been reached, otherwise True
*
* In/Out:
* h5tools_context_t *ctx
* hsize_t *curr_pos
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* hsize_t curr_pos is the total data element position
* size_t ncols
* hsize_t region_elmt_counter is the region element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
bool
h5tools_dump_region_attribute(hid_t region_id, FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, /* in,out */
h5tools_str_t *buffer, /* string into which to render */
hsize_t *curr_pos, /* total data element position */
size_t ncols, hsize_t region_elmt_counter, /* element counter */
hsize_t elmt_counter)
{
bool dimension_break = true;
hid_t atype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
hid_t region_space = H5I_INVALID_HID;
h5tool_format_t outputformat; /* Use to disable prefix for DATA attribute display */
bool past_catch = false;
bool ret_value = true;
assert(info);
assert(ctx);
assert(buffer);
outputformat = *info;
outputformat.idx_fmt = "";
outputformat.idx_n_fmt = "";
outputformat.idx_sep = "";
outputformat.line_pre = "";
H5TOOLS_DEBUG("enter file=%p", (void *)stream);
H5TOOLS_DEBUG("rawdata file=%p", (void *)rawdatastream);
/* Render the region { element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, " {");
dimension_break = h5tools_render_element(stream, &outputformat, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the region { element end */
if ((region_space = H5Aget_space(region_id)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Aget_space failed");
if ((atype = H5Aget_type(region_id)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Aget_type failed");
if ((type_id = H5Tget_native_type(atype, H5T_DIR_DEFAULT)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Tget_native_type failed");
ctx->indent_level++;
ctx->need_prefix = true;
/* Render the datatype element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
ctx->need_prefix = true;
ctx->indent_level++;
h5tools_print_datatype(stream, buffer, info, ctx, atype, true);
ctx->indent_level--;
if (strlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the datatype element end */
ctx->need_prefix = true;
/* Render the dataspace element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(buffer, region_space);
if (strlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the dataspace element end */
if (region_output) {
ctx->need_prefix = true;
h5tools_dump_data(stream, &outputformat, ctx, region_id, false);
}
done:
if (H5Tclose(type_id) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (H5Tclose(atype) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (H5Sclose(region_space) < 0)
H5TOOLS_ERROR(dimension_break, "H5Sclose failed");
ctx->indent_level--;
ctx->need_prefix = true;
/* Render the region } element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "}");
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region } element end */
H5_LEAVE(dimension_break);
CATCH
H5TOOLS_ENDDEBUG(" ");
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 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 nblocks is the number of blocks in the region
*-------------------------------------------------------------------------
*/
static int
h5tools_print_region_data_blocks(hid_t region_id, FILE *stream, const h5tool_format_t *info,
h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, /* string into which to render */
size_t ncols, unsigned ndims, hid_t type_id, hsize_t nblocks,
hsize_t *ptdata)
{
bool dimension_break = true;
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
hsize_t blkndx;
hsize_t total_size[H5S_MAX_RANK];
hsize_t elmtno; /* element index */
hsize_t curr_pos = 0;
unsigned int region_flags; /* buffer extent flags */
hsize_t numelem;
hsize_t numindex;
unsigned indx;
unsigned jndx;
bool past_catch = false;
size_t type_size;
hid_t mem_space = H5I_INVALID_HID;
hid_t sid1 = H5I_INVALID_HID;
h5tools_context_t ctx;
void *region_buf = NULL;
int ret_value = 0;
assert(info);
assert(cur_ctx);
assert(buffer);
assert(ptdata);
memset(&ctx, 0, sizeof(ctx));
H5TOOLS_START_DEBUG(" ");
if ((type_size = H5Tget_size(type_id)) == 0)
H5TOOLS_THROW(FAIL, "H5Tget_size failed");
/* Get the dataspace of the dataset */
if ((sid1 = H5Dget_space(region_id)) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "H5Dget_space failed");
/* Allocate space for the dimension array */
if ((dims1 = (hsize_t *)malloc((size_t)(sizeof(hsize_t) * ndims))) == NULL)
H5TOOLS_GOTO_ERROR(FAIL, "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((int)ndims, dims1, NULL)) < 0)
H5TOOLS_GOTO_ERROR(FAIL, "H5Screate_simple failed");
if ((region_buf = malloc(type_size * (size_t)numelem)) == NULL)
H5TOOLS_GOTO_ERROR(FAIL, "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 *)malloc(sizeof(hsize_t) * ndims)) == NULL)
H5TOOLS_GOTO_ERROR(FAIL, "Could not allocate buffer for start");
if ((count = (hsize_t *)malloc(sizeof(hsize_t) * ndims)) == NULL)
H5TOOLS_GOTO_ERROR(FAIL, "Could not allocate buffer for count");
curr_pos = 0;
ctx.indent_level = cur_ctx->indent_level;
ctx.cur_column = cur_ctx->cur_column;
ctx.prev_multiline = cur_ctx->prev_multiline;
ctx.ndims = ndims;
for (blkndx = 0; blkndx < nblocks; blkndx++) {
ctx.need_prefix = true;
ctx.cur_elmt = 0;
for (indx = 0; indx < ndims; indx++) {
start[indx] = ptdata[indx + blkndx * ndims * 2];
count[indx] = dims1[indx];
}
if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) >= 0) {
if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) >= 0) {
ctx.indent_level++;
if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
/* assume entire data space to be printed */
init_acc_pos(ctx.ndims, total_size, ctx.acc, ctx.pos, ctx.p_min_idx);
/* reset data space to be printed */
for (indx = 0; indx < (unsigned)ctx.ndims; indx++)
ctx.p_min_idx[indx] = start[indx];
/* print the data */
region_flags = START_OF_DATA;
if (blkndx == nblocks - 1)
region_flags |= END_OF_DATA;
for (indx = 0; indx < (unsigned)ctx.ndims; indx++)
ctx.p_max_idx[indx] = dims1[indx];
curr_pos = 0;
ctx.sm_pos = blkndx * 2 * ndims;
ctx.size_last_dim = dims1[ndims - 1];
h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0);
H5TOOLS_DEBUG("data render start:%ld", numelem);
elmtno = 0;
for (numindex = 0; numindex < numelem; numindex++, elmtno++, ctx.cur_elmt++) {
/* Render the region data element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", numindex ? OPTIONAL_LINE_BREAK "" : "");
h5tools_str_sprint(buffer, info, region_id, type_id,
((char *)region_buf + numindex * type_size), &ctx);
if (numindex + 1 < numelem || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos,
ncols, ptdata, numindex, elmtno);
/* Render the region data element end */
if (false == dimension_break)
elmtno = 0;
} /* end for (numindex = 0; numindex < numelem; numindex++, elmtno++, ctx.cur_elmt++) */
}
else {
H5TOOLS_ERROR(FAIL, "H5Sget_simple_extent_dims failed");
}
ctx.indent_level--;
}
else {
H5TOOLS_ERROR(FAIL, "H5Dread failed");
}
}
else {
H5TOOLS_ERROR(FAIL, "H5Sselect_hyperslab failed");
}
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
done:
free(start);
free(count);
free(region_buf);
free(dims1);
if (H5Sclose(mem_space) < 0)
H5TOOLS_ERROR(FAIL, "H5Sclose failed");
if (H5Sclose(sid1) < 0)
H5TOOLS_ERROR(FAIL, "H5Sclose failed");
CATCH
H5TOOLS_ENDDEBUG(" ");
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 the last dimension has been reached, otherwise True
*
* In/Out:
* h5tools_context_t *ctx
* hsize_t *curr_pos
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* hsize_t curr_pos is the total data element position
* size_t ncols
* hsize_t region_elmt_counter is the region element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
bool
h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, FILE *stream,
const h5tool_format_t *info, h5tools_context_t *ctx, /* in,out */
h5tools_str_t *buffer, /* string into which to render */
hsize_t *curr_pos, /* total data element position */
size_t ncols, hsize_t region_elmt_counter, /* element counter */
hsize_t elmt_counter)
{
bool dimension_break = true;
hssize_t snblocks;
hsize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata = NULL;
int sndims;
unsigned ndims;
hsize_t indx;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
h5tool_format_t outputformat; /* Use to disable prefix for DATA attribute display */
bool past_catch = false;
bool ret_value = true;
assert(info);
assert(ctx);
assert(buffer);
H5TOOLS_START_DEBUG(" ");
outputformat = *info;
outputformat.idx_fmt = "";
outputformat.idx_n_fmt = "";
outputformat.idx_sep = "";
outputformat.line_pre = "";
if ((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5TOOLS_THROW(dimension_break, "H5Sget_select_hyper_nblocks failed");
nblocks = (hsize_t)snblocks;
/* Print block information */
if ((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5TOOLS_THROW(dimension_break, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
H5TOOLS_DEBUG("enter ndims=%d", ndims);
/* Render the region { element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, " {");
dimension_break = h5tools_render_element(stream, &outputformat, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the region { element end */
ctx->indent_level++;
ctx->need_prefix = true;
/* Render the region datatype info and indices element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "REGION_TYPE BLOCK ");
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)
H5TOOLS_GOTO_ERROR(dimension_break, "Could not allocate buffer for ptdata");
if (H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, nblocks, ptdata) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Rget_select_hyper_blocklist failed");
for (indx = 0; indx < nblocks; indx++) {
unsigned loop_indx;
H5_GCC_CLANG_DIAG_OFF("format-nonliteral")
h5tools_str_append(buffer, outputformat.dset_blockformat_pre, indx ? "," OPTIONAL_LINE_BREAK " " : "",
(unsigned long)indx);
H5_GCC_CLANG_DIAG_ON("format-nonliteral")
/* Start coordinates and opposite corner */
for (loop_indx = 0; loop_indx < ndims; loop_indx++)
h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : "(",
ptdata[indx * 2 * ndims + loop_indx]);
for (loop_indx = 0; loop_indx < ndims; loop_indx++)
h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : ")-(",
ptdata[indx * 2 * ndims + loop_indx + ndims]);
h5tools_str_append(buffer, ")");
} /* end for (indx = 0; indx < nblocks; indx++) */
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region datatype info and indices element end */
ctx->need_prefix = true;
if ((dtype = H5Dget_type(region_id)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Dget_type failed");
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Tget_native_type failed");
/* Render the datatype element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
ctx->indent_level++;
h5tools_print_datatype(stream, buffer, info, ctx, dtype, true);
ctx->indent_level--;
if (strlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the datatype element end */
ctx->need_prefix = true;
/* Render the dataspace element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(buffer, region_space);
if (strlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the dataspace element end */
if (region_output) {
ctx->need_prefix = true;
/* Render the databegin element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->databegin,
h5tools_dump_header_format->datablockbegin);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the databegin element end */
ctx->need_prefix = true;
h5tools_print_region_data_blocks(region_id, rawdatastream, info, ctx, buffer, ncols, ndims, type_id,
nblocks, ptdata);
}
done:
free(ptdata);
if (type_id > 0 && H5Tclose(type_id) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (dtype > 0 && H5Tclose(dtype) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (region_output) {
ctx->need_prefix = true;
/* Render the dataend element begin */
h5tools_str_reset(buffer);
if (strlen(h5tools_dump_header_format->datablockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datablockend);
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataend);
dimension_break = h5tools_render_element(stream, &outputformat, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the dataend element end */
}
ctx->indent_level--;
ctx->need_prefix = true;
/* Render the region } element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "}");
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region } element end */
H5_LEAVE(dimension_break);
CATCH
H5TOOLS_ENDDEBUG(" ");
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
*-------------------------------------------------------------------------
*/
static int
h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream,
const h5tool_format_t *info, h5tools_context_t *cur_ctx,
h5tools_str_t *buffer, size_t ncols, unsigned ndims, hid_t type_id,
hsize_t npoints, hsize_t *ptdata)
{
bool dimension_break = true;
hsize_t *dims1 = NULL;
hsize_t elmtno; /* element index */
hsize_t curr_pos = 0;
hsize_t total_size[H5S_MAX_RANK];
hsize_t jndx;
unsigned indx;
size_t type_size;
unsigned int region_flags; /* buffer extent flags */
hid_t mem_space = H5I_INVALID_HID;
void *region_buf = NULL;
h5tools_context_t ctx;
bool past_catch = false;
int ret_value = 0;
assert(info);
assert(cur_ctx);
assert(buffer);
assert(ptdata);
assert(ndims > 0);
H5TOOLS_START_DEBUG(" ");
memset(&ctx, 0, sizeof(ctx));
/* Allocate space for the dimension array */
if ((dims1 = (hsize_t *)malloc(sizeof(hsize_t) * ndims)) == NULL)
H5TOOLS_THROW((-1), "Could not allocate buffer for dims");
dims1[0] = npoints;
/* Create dataspace for reading buffer */
if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0)
H5TOOLS_THROW((-1), "H5Screate_simple failed");
if ((type_size = H5Tget_size(type_id)) == 0)
H5TOOLS_THROW((-1), "H5Tget_size failed");
if ((region_buf = malloc(type_size * (size_t)npoints)) == NULL)
H5TOOLS_THROW((-1), "Could not allocate buffer for region");
curr_pos = 0;
ctx.indent_level = cur_ctx->indent_level;
ctx.cur_column = cur_ctx->cur_column;
ctx.prev_multiline = cur_ctx->prev_multiline;
ctx.ndims = ndims;
if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
H5TOOLS_DEBUG("data render start:%ld", npoints);
elmtno = 0;
for (jndx = 0; jndx < npoints; jndx++, elmtno++) {
ctx.need_prefix = true;
ctx.cur_elmt = 0; /* points are always 0 */
ctx.indent_level++;
if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) >= 0) {
/* assume entire data space to be printed */
init_acc_pos(ctx.ndims, total_size, ctx.acc, ctx.pos, ctx.p_min_idx);
/* print the data */
region_flags = START_OF_DATA;
if (jndx == npoints - 1)
region_flags |= END_OF_DATA;
for (indx = 0; indx < ctx.ndims; indx++)
ctx.p_max_idx[indx] = cur_ctx->p_max_idx[indx];
ctx.sm_pos = jndx * ndims;
if (ctx.ndims > 0)
ctx.size_last_dim = ctx.p_max_idx[ctx.ndims - 1];
else
ctx.size_last_dim = 0;
curr_pos = 0; /* points requires constant 0 */
h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0);
/* Render the point element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", jndx ? OPTIONAL_LINE_BREAK "" : "");
h5tools_str_sprint(buffer, info, region_id, type_id, ((char *)region_buf + jndx * type_size),
&ctx);
if (jndx + 1 < npoints || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos, ncols,
ptdata, (hsize_t)0, elmtno);
/* Render the point element end */
if (false == dimension_break)
elmtno = 0;
}
else {
H5TOOLS_ERROR((-1), "H5Sget_simple_extent_dims failed");
}
ctx.indent_level--;
} /* end for (jndx = 0; jndx < npoints; jndx++, elmtno++) */
done:
free(region_buf);
CATCH
free(dims1);
if (H5Sclose(mem_space) < 0)
H5TOOLS_ERROR((-1), "H5Sclose failed");
H5TOOLS_ENDDEBUG(" ");
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
*
* In/Out:
* h5tools_context_t *ctx
* hsize_t *curr_pos
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* hsize_t curr_pos is the total data element position
* size_t ncols
* hsize_t region_elmt_counter is the region element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
bool
h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, FILE *stream,
const h5tool_format_t *info, h5tools_context_t *ctx, h5tools_str_t *buffer,
hsize_t *curr_pos, size_t ncols, hsize_t region_elmt_counter,
hsize_t elmt_counter)
{
bool dimension_break = true;
hssize_t snpoints;
hsize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
int sndims;
unsigned ndims;
hsize_t indx;
hid_t dtype = H5I_INVALID_HID;
hid_t type_id = H5I_INVALID_HID;
h5tool_format_t outputformat; /* Use to disable prefix for DATA attribute display */
bool past_catch = false;
bool ret_value = true;
assert(info);
assert(ctx);
assert(buffer);
H5TOOLS_START_DEBUG(" ");
outputformat = *info;
outputformat.idx_fmt = "";
outputformat.idx_n_fmt = "";
outputformat.idx_sep = "";
outputformat.line_pre = "";
if ((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5TOOLS_THROW(dimension_break, "H5Sget_select_elem_npoints failed");
npoints = (hsize_t)snpoints;
/* Allocate space for the dimension array */
if ((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5TOOLS_THROW(dimension_break, "H5Sget_simple_extent_ndims failed");
ndims = (unsigned)sndims;
H5TOOLS_DEBUG("enter ndims=%d", ndims);
/* Render the region { element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "{");
dimension_break = h5tools_render_element(stream, &outputformat, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the region { element end */
ctx->indent_level++;
ctx->need_prefix = true;
/* Render the region datatype info and indices element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "REGION_TYPE POINT ");
alloc_size = npoints * ndims * sizeof(ptdata[0]);
assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
if (NULL == (ptdata = (hsize_t *)malloc((size_t)alloc_size)))
H5TOOLS_GOTO_ERROR(dimension_break, "Could not allocate buffer for ptdata");
if (H5Sget_select_elem_pointlist(region_space, (hsize_t)0, npoints, ptdata) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Sget_select_elem_pointlist failed");
for (indx = 0; indx < npoints; indx++) {
unsigned loop_indx;
H5_GCC_CLANG_DIAG_OFF("format-nonliteral")
h5tools_str_append(buffer, outputformat.dset_ptformat_pre, indx ? "," OPTIONAL_LINE_BREAK " " : "",
(unsigned long)indx);
H5_GCC_CLANG_DIAG_ON("format-nonliteral")
for (loop_indx = 0; loop_indx < ndims; loop_indx++)
h5tools_str_append(buffer, "%s%" PRIuHSIZE, loop_indx ? "," : "(",
ptdata[indx * ndims + loop_indx]);
h5tools_str_append(buffer, ")");
} /* end for (indx = 0; indx < npoints; indx++) */
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region datatype info and indices element end */
ctx->need_prefix = true;
if ((dtype = H5Dget_type(region_id)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Dget_type failed");
if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
H5TOOLS_GOTO_ERROR(dimension_break, "H5Tget_native_type failed");
/* Render the datatype element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
ctx->indent_level++;
h5tools_print_datatype(stream, buffer, info, ctx, dtype, true);
ctx->indent_level--;
if (strlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the datatype element end */
ctx->need_prefix = true;
/* Render the dataspace element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(buffer, region_space);
if (strlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the dataspace element end */
if (region_output) {
ctx->need_prefix = true;
/* Render the databegin element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->databegin,
h5tools_dump_header_format->datablockbegin);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
ctx->need_prefix = true;
h5tools_print_region_data_points(region_space, region_id, rawdatastream, info, ctx, buffer, ncols,
ndims, type_id, npoints, ptdata);
}
done:
free(ptdata);
if (type_id > 0 && H5Tclose(type_id) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (dtype > 0 && H5Tclose(dtype) < 0)
H5TOOLS_ERROR(dimension_break, "H5Tclose failed");
if (region_output) {
ctx->need_prefix = true;
/* Render the dataend element begin */
h5tools_str_reset(buffer);
if (strlen(h5tools_dump_header_format->datablockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datablockend);
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataend);
dimension_break = h5tools_render_element(stream, &outputformat, ctx, buffer, curr_pos, ncols,
region_elmt_counter, elmt_counter);
/* Render the dataend element end*/
}
ctx->indent_level--;
ctx->need_prefix = true;
/* Render the region } element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "}");
dimension_break =
h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region } element end */
H5_LEAVE(dimension_break);
CATCH
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: print out the data for a subset of a dataset.
* Description:
*
* Select a hyperslab from the dataset DSET using the parameters
* specified in SSET. Dump this out to STREAM.
*
* Hyperslabs select "count" blocks of size "block", spaced "stride" elements
* from each other, starting at coordinate "start".
*
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
*
* Algorithm
*
* The parameters from SSET are translated into temporary
* variables so that 1 row is printed at a time (getting the coordinate indices
* at each row).
* We define the stride, count and block to be 1 in the row dimension to achieve
* this and advance until all points are printed.
*
* The element position is obtained from the matrix according to:
* Given an index I(z,y,x) its position from the beginning of an array
* of sizes A(size_z, size_y,size_x) is given by
* Position of I(z,y,x) = index_z * size_y * size_x
* + index_y * size_x
* + index_x
*
*-------------------------------------------------------------------------
*/
static herr_t
h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset,
hid_t p_type, hid_t f_space, hsize_t hyperslab_count,
hsize_t *temp_start, /* start inside offset count loop */
hsize_t *temp_count, /* count inside offset count loop */
hsize_t *temp_block, /* block size used in loop */
hsize_t *temp_stride, /* stride size used in loop */
const hsize_t *total_size, /* total size of dataset */
unsigned int row_dim) /* index of row_counter dimension */
{
size_t i; /* counters */
size_t j; /* counters */
hsize_t zero[1] = {0}; /* vector of zeros */
unsigned int flags; /* buffer extent flags */
hsize_t low[H5S_MAX_RANK]; /* low bound of hyperslab */
hsize_t high[H5S_MAX_RANK]; /* higher bound of hyperslab */
size_t p_type_nbytes; /* size of memory type */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hssize_t ssm_nelmts; /* elements per stripmine*/
hsize_t sm_nelmts; /* elements per stripmine*/
unsigned char *sm_buf = NULL; /* buffer for raw data */
hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */
hsize_t size_row_block; /* size for blocks along rows */
hsize_t row_counter = 0;
bool past_catch = false;
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
herr_t ret_value = SUCCEED;
H5TOOLS_START_DEBUG(" ");
if ((size_t)ctx->ndims > NELMTS(sm_size))
H5TOOLS_THROW(FAIL, "ndims and sm_size comparison failed");
size_row_block = ctx->sset->block.data[row_dim];
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == true)
vl_data = true;
/* display loop */
for (; hyperslab_count > 0; temp_start[row_dim] += temp_stride[row_dim], hyperslab_count--) {
/* jump rows if size of block exceeded
cases where block > 1 only and stride > block */
if (size_row_block > 1 && row_counter == size_row_block &&
ctx->sset->stride.data[row_dim] > ctx->sset->block.data[row_dim]) {
hsize_t increase_rows = ctx->sset->stride.data[row_dim] - ctx->sset->block.data[row_dim];
temp_start[row_dim] += increase_rows;
row_counter = 0;
}
row_counter++;
/* calculate the potential number of elements we're going to print */
if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, temp_start, temp_stride, temp_count, temp_block) < 0)
H5TOOLS_THROW(FAIL, "H5Sselect_hyperslab failed");
if ((ssm_nelmts = H5Sget_select_npoints(f_space)) < 0)
H5TOOLS_THROW(FAIL, "H5Sget_select_npoints failed");
sm_nelmts = (hsize_t)ssm_nelmts;
if (sm_nelmts > 0) {
/*
* determine the strip mine size and allocate a buffer. the strip mine is
* a hyperslab whose size is manageable.
*/
if ((sm_nbytes = p_type_nbytes = H5Tget_size(p_type)) == 0)
H5TOOLS_THROW(FAIL, "H5Tget_size failed");
if (ctx->ndims > 0)
for (i = ctx->ndims; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(total_size[i - 1], size);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
if (NULL == (sm_buf = (unsigned char *)malloc((size_t)sm_nelmts * p_type_nbytes)))
H5TOOLS_THROW(FAIL, "Could not allocate buffer for strip-mine");
if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
H5TOOLS_THROW(FAIL, "H5Screate_simple failed");
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &sm_nelmts, NULL) < 0)
H5TOOLS_THROW(FAIL, "H5Sselect_hyperslab failed");
/* read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
H5TOOLS_THROW(FAIL, "H5Dread failed");
/* print the data */
flags = START_OF_DATA;
if (hyperslab_count == 1)
flags |= END_OF_DATA;
for (i = 0; i < ctx->ndims; i++)
ctx->p_max_idx[i] = ctx->p_min_idx[i] + MIN(total_size[i], sm_size[i]);
/* print array indices. get the lower bound of the hyperslab and calculate
the element position at the start of hyperslab */
if (H5Sget_select_bounds(f_space, low, high) < 0)
H5TOOLS_THROW(FAIL, "H5Sget_select_bounds failed");
/* initialize the current stripmine position; this is necessary to print the array indices */
ctx->sm_pos = 0;
for (i = 0; i < (size_t)ctx->ndims - 1; i++) {
hsize_t offset = 1; /* accumulation of the previous dimensions */
for (j = i + 1; j < (size_t)ctx->ndims; j++)
offset *= total_size[j];
ctx->sm_pos += low[i] * offset;
}
ctx->sm_pos += low[ctx->ndims - 1];
ctx->need_prefix = true;
if (h5tools_dump_simple_data(stream, info, ctx, dset, flags, sm_nelmts, p_type, sm_buf) < 0)
H5TOOLS_THROW(FAIL, "h5tools_dump_simple_data failed");
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
if (H5Sclose(sm_space) < 0)
H5TOOLS_THROW(FAIL, "H5Sclose failed");
if (sm_buf)
free(sm_buf);
sm_buf = NULL;
}
else
H5TOOLS_THROW(SUCCEED, "nothing to print");
ctx->continuation++;
} /* hyperslab_count loop */
CATCH
if (sm_buf)
free(sm_buf);
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: print out the data for a subset of a dataset.
* Description:
*
* Select a hyperslab from the dataset DSET using the parameters
* specified in SSET. Dump this out to STREAM.
*
* Hyperslabs select "count" blocks of size "block", spaced "stride" elements
* from each other, starting at coordinate "start".
*
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
*
* Algorithm
*
* The parameters from SSET are translated into temporary
* variables so that 1 row is printed at a time (getting the coordinate indices
* at each row).
* We define the stride, count and block to be 1 in the row dimension to achieve
* this and advance until all points are printed.
*
* The element position is obtained from the matrix according to:
* Given an index I(z,y,x) its position from the beginning of an array
* of sizes A(size_z, size_y,size_x) is given by
* Position of I(z,y,x) = index_z * size_y * size_x
* + index_y * size_x
* + index_x
*
*-------------------------------------------------------------------------
*/
static herr_t
h5tools_display_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset,
hid_t p_type, hid_t f_space, hsize_t *total_size)
{
size_t i; /* counters */
hsize_t n; /* counters */
hsize_t count; /* hyperslab count */
hsize_t outer_count; /* offset count */
unsigned int row_dim; /* index of row_counter dimension */
int current_outer_dim; /* dimension for start */
hsize_t temp_start[H5S_MAX_RANK]; /* temporary start inside offset count loop */
hsize_t max_start[H5S_MAX_RANK]; /* maximum start inside offset count loop */
hsize_t temp_count[H5S_MAX_RANK]; /* temporary count inside offset count loop */
hsize_t temp_block[H5S_MAX_RANK]; /* temporary block size used in loop */
hsize_t temp_stride[H5S_MAX_RANK]; /* temporary stride size used in loop */
int reset_dim;
herr_t ret_value = SUCCEED;
if (ctx->ndims == 1)
row_dim = 0;
else
row_dim = ctx->ndims - 2;
/* get the offset count */
outer_count = 1;
if (ctx->ndims > 2)
for (i = 0; i < (size_t)ctx->ndims - 2; i++) {
/* block size is handled by containing h5tools_print_simple_subset call */
outer_count = outer_count * ctx->sset->count.data[i];
}
/* initialize temporary start, count and maximum start */
for (i = 0; i < ctx->ndims; i++) {
temp_start[i] = ctx->sset->start.data[i];
temp_count[i] = ctx->sset->count.data[i];
temp_block[i] = ctx->sset->block.data[i];
temp_stride[i] = ctx->sset->stride.data[i];
max_start[i] = 0;
}
if (ctx->ndims > 2) {
for (i = 0; i < (size_t)ctx->ndims - 2; i++) {
max_start[i] = temp_start[i] + ctx->sset->count.data[i] * ctx->sset->stride.data[i];
temp_count[i] = 1;
}
}
/* offset loop */
for (n = 0; n < outer_count; n++) {
/* number of read iterations in inner loop, read by rows, to match 2D display */
if (ctx->ndims > 1) {
/* count is the number of iterations to display all the rows,
the block size count times */
count = ctx->sset->count.data[row_dim] * ctx->sset->block.data[row_dim];
/* always 1 row_counter at a time, that is a block of size 1, 1 time */
temp_count[row_dim] = 1;
temp_block[row_dim] = 1;
/* advance 1 row_counter at a time */
if (ctx->sset->block.data[row_dim] > 1)
temp_stride[row_dim] = 1;
}
/* for the 1D case */
else {
count = 1;
}
h5tools_print_simple_subset(stream, info, ctx, dset, p_type, f_space, count, temp_start, temp_count,
temp_block, temp_stride, total_size, row_dim);
if (ctx->ndims > 2) {
/* dimension for start */
current_outer_dim = (int)(ctx->ndims - 2) - 1;
/* set start to original from current_outer_dim up */
for (i = (size_t)(current_outer_dim + 1); i < ctx->ndims; i++)
temp_start[i] = ctx->sset->start.data[i];
/* increment start dimension */
do {
reset_dim = 0;
temp_start[current_outer_dim] += ctx->sset->stride.data[current_outer_dim];
if (temp_start[current_outer_dim] >= max_start[current_outer_dim]) {
temp_start[current_outer_dim] = ctx->sset->start.data[current_outer_dim];
current_outer_dim--;
reset_dim = 1;
}
} while (current_outer_dim >= 0 && reset_dim);
} /* ctx.ndims > 1 */
} /* outer_count */
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Dump out a subset of a dataset.
* Description:
*
* Select a hyperslab from the dataset DSET using the parameters
* specified in SSET. Dump this out to STREAM.
*
* Hyperslabs select "count" blocks of size "block", spaced "stride" elements
* from each other, starting at coordinate "start".
*
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
*
* Algorithm
*
* In a inner loop, the parameters from SSET are translated into temporary
* variables so that 1 row is printed at a time (getting the coordinate indices
* at each row).
* We define the stride, count and block to be 1 in the row dimension to achieve
* this and advance until all points are printed.
* An outer loop for cases where dimensionality is greater than 2D is made.
* In each iteration, the 2D block is displayed in the inner loop. The remaining
* slower dimensions above the first 2 are incremented one at a time in the outer loop
*
* The element position is obtained from the matrix according to:
* Given an index I(z,y,x) its position from the beginning of an array
* of sizes A(size_z, size_y,size_x) is given by
* Position of I(z,y,x) = index_z * size_y * size_x
* + index_y * size_x
* + index_x
*
*-------------------------------------------------------------------------
*/
static herr_t
h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset,
hid_t p_type)
{
int sndims;
hid_t f_space = H5I_INVALID_HID; /* file data space */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
bool past_catch = false;
herr_t ret_value = SUCCEED;
H5TOOLS_START_DEBUG(" ");
if ((f_space = H5Dget_space(dset)) < 0)
H5TOOLS_THROW(FAIL, "H5Dget_space failed");
if ((sndims = H5Sget_simple_extent_ndims(f_space)) < 0)
H5TOOLS_THROW(FAIL, "H5Sget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
/* assume entire data space to be printed */
if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
H5TOOLS_THROW(FAIL, "H5Sget_simple_extent_dims failed");
init_acc_pos(ctx->ndims, total_size, ctx->acc, ctx->pos, ctx->p_min_idx);
ctx->size_last_dim = total_size[ctx->ndims - 1];
/* Set the compound datatype field list for display */
ctx->cmpd_listv = info->cmpd_listv;
h5tools_display_simple_subset(stream, info, ctx, dset, p_type, f_space, total_size);
CATCH
if (f_space >= 0 && H5Sclose(f_space) < 0)
H5TOOLS_THROW(FAIL, "H5Sclose failed");
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset with a simple data space.
* Description:
* This is a special case of h5tools_dump_dset(). This function only
* intended for dumping datasets -- it does strip mining and some other
* things which are unnecessary for smaller objects such as attributes
* (to print small objects like attributes simply read the attribute and
* call h5tools_dump_simple_mem()).
* Return:
* On success, the function returns SUCCEED. Otherwise, the function
* returns FAIL.
*-------------------------------------------------------------------------
*/
static int
h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset,
hid_t p_type)
{
hid_t f_space = H5I_INVALID_HID; /* file data space */
hsize_t elmtno; /* counter */
size_t i = 0; /* counter */
int sndims; /* rank of dataspace */
int carry; /* counter carry value */
hsize_t zero[8]; /* vector of zeros */
unsigned int flags; /* buffer extent flags */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
bool past_catch = false;
/* Print info */
size_t p_type_nbytes; /* size of memory type */
hsize_t p_nelmts; /* total selected elmts */
/* Stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
hsize_t sm_nbytes; /* bytes per stripmine */
hsize_t sm_nelmts; /* elements per stripmine*/
unsigned char *sm_buf = NULL; /* buffer for raw data */
hid_t sm_space = H5I_INVALID_HID; /* stripmine data space */
/* Hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /* size this pass */
hsize_t hs_nelmts; /* elements in request */
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
if (H5I_INVALID_HID == (f_space = H5Dget_space(dset)))
H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed");
sndims = H5Sget_simple_extent_ndims(f_space);
if (sndims < 0)
H5TOOLS_GOTO_ERROR((-1), "H5Dget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
H5TOOLS_DEBUG("sndims:%d", sndims);
if ((size_t)ctx->ndims > NELMTS(sm_size))
H5TOOLS_GOTO_ERROR((-1), "ctx->ndims > NELMTS(sm_size) failed");
/* Assume entire data space to be printed */
H5Sget_simple_extent_dims(f_space, total_size, NULL);
init_acc_pos(ctx->ndims, total_size, ctx->acc, ctx->pos, ctx->p_min_idx);
/* calculate the number of elements we're going to print */
p_nelmts = 1;
if (ctx->ndims > 0) {
for (i = 0; i < ctx->ndims; i++)
p_nelmts *= total_size[i];
ctx->size_last_dim = (total_size[ctx->ndims - 1]);
} /* end if */
else
ctx->size_last_dim = 0;
if (p_nelmts == 0) {
H5_LEAVE(SUCCEED); /* nothing to print */
}
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == true)
vl_data = true;
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
if (ctx->ndims > 0) {
for (i = ctx->ndims; i > 0; --i) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(total_size[i - 1], size);
sm_nbytes *= sm_size[i - 1];
}
}
if (!sm_nbytes)
goto done;
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
if (NULL != (sm_buf = (unsigned char *)malloc((size_t)sm_nbytes))) {
H5TOOLS_DEBUG("stripmine size:%ld", sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
H5TOOLS_DEBUG("sm_nelmts size:%ld", sm_nelmts);
H5TOOLS_DEBUG("ctx->ndims:%d", ctx->ndims);
/* The stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
H5TOOLS_DEBUG("stripmine read loop:%d", i);
/* Calculate the hyperslab size */
if (ctx->ndims > 0) {
for (i = 0, hs_nelmts = 1; i < ctx->ndims; i++) {
hs_size[i] = MIN(total_size[i] - hs_offset[i], sm_size[i]);
ctx->p_max_idx[i] = ctx->p_min_idx[i] + hs_size[i];
hs_nelmts *= hs_size[i];
}
if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
H5TOOLS_ERROR((-1), "H5Sselect_hyperslab hs_offset failed");
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
H5TOOLS_ERROR((-1), "H5Sselect_hyperslab zero failed");
}
else {
if (H5Sselect_all(f_space) < 0)
H5TOOLS_ERROR((-1), "H5Sselect_all f_space failed");
if (H5Sselect_all(sm_space) < 0)
H5TOOLS_ERROR((-1), "H5Sselect_all sm_space failed");
hs_nelmts = 1;
}
H5TOOLS_DEBUG("Read the data");
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) >= 0) {
/* Print the data */
flags = (elmtno == 0) ? START_OF_DATA : 0;
flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0;
/* initialize the current stripmine position; this is necessary to print the array
indices */
ctx->sm_pos = elmtno;
if (h5tools_dump_simple_data(stream, info, ctx, dset, flags, hs_nelmts, p_type, sm_buf) < 0)
H5TOOLS_ERROR((-1), "h5tools_dump_simple_data failed");
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
H5TOOLS_DEBUG("Calculate the next hyperslab offset");
/* Calculate the next hyperslab offset */
for (i = ctx->ndims, carry = 1; i > 0 && carry; --i) {
ctx->p_min_idx[i - 1] = ctx->p_max_idx[i - 1];
hs_offset[i - 1] += hs_size[i - 1];
if (hs_offset[i - 1] == total_size[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
}
}
else
H5TOOLS_ERROR((-1), "H5Dread failed");
ctx->continuation++;
H5TOOLS_DEBUG("stripmine read loop:%d complete", i);
}
free(sm_buf);
} /* if (NULL != (sm_buf...)) */
done:
if (sm_space >= 0 && H5Sclose(sm_space) < 0)
H5TOOLS_ERROR((-1), "H5Sclose failed");
if (f_space >= 0 && H5Sclose(f_space) < 0)
H5TOOLS_ERROR((-1), "H5Sclose failed");
CATCH
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_simple_mem
*
* Purpose: Print some values from memory with a simple data space.
* This is a special case of h5tools_dump_mem().
*
* Return: Success: SUCCEED
* Failure: FAIL
*-------------------------------------------------------------------------
*/
static int
h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t attr_id,
hid_t p_type)
{
hid_t f_space = H5I_INVALID_HID; /* file data space */
hsize_t alloc_size;
int sndims; /* rank of dataspace */
unsigned i; /* counters */
hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/
hsize_t p_nelmts; /* total selected elmts */
bool past_catch = false;
unsigned char *buf = NULL; /* buffer for raw data */
int ret_value = 0;
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
H5TOOLS_START_DEBUG(" ");
if (H5I_INVALID_HID == (f_space = H5Aget_space(attr_id)))
H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed");
sndims = H5Sget_simple_extent_ndims(f_space);
if (sndims < 0)
H5TOOLS_THROW((-1), "H5Dget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
H5TOOLS_DEBUG("sndims:%d", sndims);
if ((size_t)ctx->ndims > NELMTS(ctx->p_min_idx))
H5TOOLS_THROW((-1), "ctx->ndims > NELMTS(ctx->p_min_idx) failed");
/* Assume entire data space to be printed */
H5Sget_simple_extent_dims(f_space, total_size, NULL);
init_acc_pos(ctx->ndims, total_size, ctx->acc, ctx->pos, ctx->p_min_idx);
/* calculate the number of elements we're going to print */
p_nelmts = 1;
if (ctx->ndims > 0) {
for (i = 0; i < ctx->ndims; i++)
p_nelmts *= total_size[i];
ctx->size_last_dim = (total_size[ctx->ndims - 1]);
} /* end if */
else
ctx->size_last_dim = 0;
if (p_nelmts == 0)
H5_LEAVE(SUCCEED); /* nothing to print */
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == true)
vl_data = true;
alloc_size = p_nelmts * H5Tget_size(p_type);
assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
if (NULL != (buf = (unsigned char *)malloc((size_t)alloc_size))) {
H5TOOLS_DEBUG("ctx->ndims:%d", ctx->ndims);
H5TOOLS_DEBUG("Read the data");
/* Read the data */
if (H5Aread(attr_id, p_type, buf) >= 0) {
if (h5tools_dump_simple_data(stream, info, ctx, attr_id, START_OF_DATA | END_OF_DATA, p_nelmts,
p_type, buf) < 0)
H5TOOLS_ERROR((-1), "h5tools_dump_simple_data failed");
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, f_space, H5P_DEFAULT, buf);
}
else
H5TOOLS_ERROR((-1), "H5Aread failed");
free(buf);
} /* if (NULL != (buf...)) */
done:
if (f_space >= 0 && H5Sclose(f_space) < 0)
H5TOOLS_ERROR((-1), "H5Sclose failed");
CATCH
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_dset
*
* Purpose: Print some values from a dataset DSET to the file STREAM
* after converting all types to P_TYPE (which should be a
* native type). If P_TYPE is a negative value then it will be
* computed from the dataset type using only native types.
*
* Note: This function is intended only for datasets since it does
* some things like strip mining which are unnecessary for
* smaller objects such as attributes. The easiest way to print
* small objects is to read the object into memory and call
* h5tools_dump_mem().
*
* Return: Success: SUCCEED
* Failure: FAIL
*-------------------------------------------------------------------------
*/
int
h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset)
{
hid_t f_space = H5I_INVALID_HID;
hid_t p_type = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
H5S_class_t space_type;
h5tool_format_t info_dflt;
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
/* Use default values */
if (!stream)
stream = rawoutstream;
if (!info) {
memset(&info_dflt, 0, sizeof info_dflt);
info = &info_dflt;
}
f_type = H5Dget_type(dset);
if (f_type < 0)
goto done;
if (info->raw || bin_form == 1)
p_type = H5Tcopy(f_type);
else if (bin_form == 2)
p_type = h5tools_get_little_endian_type(f_type);
else if (bin_form == 3)
p_type = h5tools_get_big_endian_type(f_type);
else
p_type = H5Tget_native_type(f_type, H5T_DIR_DEFAULT);
if (p_type < 0)
goto done;
/* Check the data space */
f_space = H5Dget_space(dset);
if (f_space < 0)
goto done;
space_type = H5Sget_simple_extent_type(f_space);
/* Print the data */
if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) {
if (!ctx->sset)
ret_value = h5tools_dump_simple_dset(rawdatastream, info, ctx, dset, p_type);
else
ret_value = h5tools_dump_simple_subset(rawdatastream, info, ctx, dset, p_type);
}
else {
/* space is H5S_NULL */
ret_value = SUCCEED;
}
done:
if (f_type > 0)
H5Tclose(f_type);
if (p_type > 0)
H5Tclose(p_type);
if (f_space > 0)
H5Sclose(f_space);
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_mem
*
* Purpose: Displays the data contained in MEM. MEM must have the
* specified data TYPE and SPACE. Currently only simple data
* spaces are allowed and only the `all' selection.
*
* Return: Success: SUCCEED
* Failure: FAIL
*-------------------------------------------------------------------------
*/
int
h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t attr_id)
{
hid_t f_space = H5I_INVALID_HID;
hid_t p_type = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
h5tool_format_t info_dflt;
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
/* Use default values */
if (!stream)
stream = rawoutstream;
if (!info) {
memset(&info_dflt, 0, sizeof(info_dflt));
info = &info_dflt;
}
f_type = H5Aget_type(attr_id);
if (f_type < 0)
goto done;
if (info->raw || bin_form == 1)
p_type = H5Tcopy(f_type);
else if (bin_form == 2)
p_type = h5tools_get_little_endian_type(f_type);
else if (bin_form == 3)
p_type = h5tools_get_big_endian_type(f_type);
else
p_type = H5Tget_native_type(f_type, H5T_DIR_DEFAULT);
if (p_type < 0)
goto done;
/* Check the data space */
f_space = H5Aget_space(attr_id);
if (f_space < 0)
goto done;
/* Check the data space */
if (H5Sis_simple(f_space) <= 0) {
H5TOOLS_ERROR((-1), "H5Sis_simple failed");
}
else {
ret_value = h5tools_dump_simple_mem(rawattrstream, info, ctx, attr_id, p_type);
}
done:
if (f_type > 0)
H5Tclose(f_type);
if (p_type > 0)
H5Tclose(p_type);
if (f_space > 0)
H5Sclose(f_space);
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: print_datatype
*
* Purpose: print the datatype - do not prefix.
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
int
h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t type, int object_search)
{
char *mname;
hid_t mtype = H5I_INVALID_HID;
hid_t str_type = H5I_INVALID_HID;
hid_t super = H5I_INVALID_HID;
hid_t tmp_type = H5I_INVALID_HID;
int snmembers;
int sndims;
unsigned nmembers;
unsigned i;
size_t size = 0;
size_t ncols = 80; /*available output width */
hsize_t dims[H5TOOLS_DUMP_MAX_RANK];
hsize_t curr_pos = 0; /* total data element position */
H5T_str_t str_pad;
H5T_cset_t cset;
H5T_order_t order;
H5T_class_t type_class;
H5T_sign_t sign; /* sign scheme value */
htri_t is_vlstr = false;
bool past_catch = false;
const char *sign_s = NULL; /* sign scheme string */
const char *order_s = NULL; /* byte order string */
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
if ((type_class = H5Tget_class(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_class failed");
if (object_search && H5Tcommitted(type) > 0) {
H5O_info2_t oinfo;
obj_t *obj = NULL; /* Found object */
H5Oget_info3(type, &oinfo, H5O_INFO_BASIC);
obj = search_obj(h5dump_type_table, &oinfo.token);
if (obj) {
if (!obj->recorded) {
char *obj_tok_str = NULL;
H5Otoken_to_str(type, &oinfo.token, &obj_tok_str);
h5tools_str_append(buffer, "\"/#%s\"", obj_tok_str);
H5free_memory(obj_tok_str);
}
else
h5tools_str_append(buffer, "\"%s\"", obj->objname);
}
else {
error_msg("unknown committed type.\n");
h5tools_setstatus(EXIT_FAILURE);
}
return ret_value;
}
if (info->line_ncols > 0)
ncols = info->line_ncols;
switch (type_class) {
case H5T_INTEGER:
if (H5Tequal(type, H5T_STD_I8BE) == true)
h5tools_str_append(buffer, "H5T_STD_I8BE");
else if (H5Tequal(type, H5T_STD_I8LE) == true)
h5tools_str_append(buffer, "H5T_STD_I8LE");
else if (H5Tequal(type, H5T_STD_I16BE) == true)
h5tools_str_append(buffer, "H5T_STD_I16BE");
else if (H5Tequal(type, H5T_STD_I16LE) == true)
h5tools_str_append(buffer, "H5T_STD_I16LE");
else if (H5Tequal(type, H5T_STD_I32BE) == true)
h5tools_str_append(buffer, "H5T_STD_I32BE");
else if (H5Tequal(type, H5T_STD_I32LE) == true)
h5tools_str_append(buffer, "H5T_STD_I32LE");
else if (H5Tequal(type, H5T_STD_I64BE) == true)
h5tools_str_append(buffer, "H5T_STD_I64BE");
else if (H5Tequal(type, H5T_STD_I64LE) == true)
h5tools_str_append(buffer, "H5T_STD_I64LE");
else if (H5Tequal(type, H5T_STD_U8BE) == true)
h5tools_str_append(buffer, "H5T_STD_U8BE");
else if (H5Tequal(type, H5T_STD_U8LE) == true)
h5tools_str_append(buffer, "H5T_STD_U8LE");
else if (H5Tequal(type, H5T_STD_U16BE) == true)
h5tools_str_append(buffer, "H5T_STD_U16BE");
else if (H5Tequal(type, H5T_STD_U16LE) == true)
h5tools_str_append(buffer, "H5T_STD_U16LE");
else if (H5Tequal(type, H5T_STD_U32BE) == true)
h5tools_str_append(buffer, "H5T_STD_U32BE");
else if (H5Tequal(type, H5T_STD_U32LE) == true)
h5tools_str_append(buffer, "H5T_STD_U32LE");
else if (H5Tequal(type, H5T_STD_U64BE) == true)
h5tools_str_append(buffer, "H5T_STD_U64BE");
else if (H5Tequal(type, H5T_STD_U64LE) == true)
h5tools_str_append(buffer, "H5T_STD_U64LE");
else if (H5Tequal(type, H5T_NATIVE_SCHAR) == true)
h5tools_str_append(buffer, "H5T_NATIVE_SCHAR");
else if (H5Tequal(type, H5T_NATIVE_UCHAR) == true)
h5tools_str_append(buffer, "H5T_NATIVE_UCHAR");
else if (H5Tequal(type, H5T_NATIVE_SHORT) == true)
h5tools_str_append(buffer, "H5T_NATIVE_SHORT");
else if (H5Tequal(type, H5T_NATIVE_USHORT) == true)
h5tools_str_append(buffer, "H5T_NATIVE_USHORT");
else if (H5Tequal(type, H5T_NATIVE_INT) == true)
h5tools_str_append(buffer, "H5T_NATIVE_INT");
else if (H5Tequal(type, H5T_NATIVE_UINT) == true)
h5tools_str_append(buffer, "H5T_NATIVE_UINT");
else if (H5Tequal(type, H5T_NATIVE_LONG) == true)
h5tools_str_append(buffer, "H5T_NATIVE_LONG");
else if (H5Tequal(type, H5T_NATIVE_ULONG) == true)
h5tools_str_append(buffer, "H5T_NATIVE_ULONG");
else if (H5Tequal(type, H5T_NATIVE_LLONG) == true)
h5tools_str_append(buffer, "H5T_NATIVE_LLONG");
else if (H5Tequal(type, H5T_NATIVE_ULLONG) == true)
h5tools_str_append(buffer, "H5T_NATIVE_ULLONG");
else {
/* byte order */
if (H5Tget_size(type) > 1) {
order = H5Tget_order(type);
if (H5T_ORDER_LE == order)
order_s = " little-endian";
else if (H5T_ORDER_BE == order)
order_s = " big-endian";
else if (H5T_ORDER_VAX == order)
order_s = " mixed-endian";
else
order_s = " unknown-byte-order";
}
else
order_s = "";
/* sign */
if ((sign = H5Tget_sign(type)) >= 0) {
if (H5T_SGN_NONE == sign)
sign_s = " unsigned";
else if (H5T_SGN_2 == sign)
sign_s = "";
else
sign_s = " unknown-sign";
}
else
sign_s = " unknown-sign";
/* print size, order, sign, and precision */
h5tools_str_append(buffer, "%zu-bit%s%s integer %zu-bit precision", 8 * H5Tget_size(type),
order_s, sign_s, H5Tget_precision(type));
}
break;
case H5T_FLOAT:
if (H5Tequal(type, H5T_IEEE_F32BE) == true)
h5tools_str_append(buffer, "H5T_IEEE_F32BE");
else if (H5Tequal(type, H5T_IEEE_F32LE) == true)
h5tools_str_append(buffer, "H5T_IEEE_F32LE");
else if (H5Tequal(type, H5T_IEEE_F64BE) == true)
h5tools_str_append(buffer, "H5T_IEEE_F64BE");
else if (H5Tequal(type, H5T_IEEE_F64LE) == true)
h5tools_str_append(buffer, "H5T_IEEE_F64LE");
else if (H5Tequal(type, H5T_VAX_F32) == true)
h5tools_str_append(buffer, "H5T_VAX_F32");
else if (H5Tequal(type, H5T_VAX_F64) == true)
h5tools_str_append(buffer, "H5T_VAX_F64");
else if (H5Tequal(type, H5T_NATIVE_FLOAT) == true)
h5tools_str_append(buffer, "H5T_NATIVE_FLOAT");
else if (H5Tequal(type, H5T_NATIVE_DOUBLE) == true)
h5tools_str_append(buffer, "H5T_NATIVE_DOUBLE");
else {
/* print what the library knows */
/* byte order */
if (H5Tget_size(type) > 1) {
order = H5Tget_order(type);
if (H5T_ORDER_LE == order)
order_s = " little-endian";
else if (H5T_ORDER_BE == order)
order_s = " big-endian";
else if (H5T_ORDER_VAX == order)
order_s = " mixed-endian";
else
order_s = " unknown-byte-order";
}
else
order_s = "";
/* print size. byte order, and precision */
h5tools_str_append(buffer, "%zu-bit%s floating-point %zu-bit precision",
8 * H5Tget_size(type), order_s, H5Tget_precision(type));
}
break;
case H5T_TIME:
h5tools_str_append(buffer, "H5T_TIME: not yet implemented");
break;
case H5T_STRING:
/* 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);
curr_pos = ctx->cur_column;
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->strblockbegin);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
if (is_vlstr)
h5tools_str_append(buffer, "%s H5T_VARIABLE;", STRSIZE);
else
h5tools_str_append(buffer, "%s %d;", STRSIZE, (int)size);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s ", STRPAD);
switch (str_pad) {
case H5T_STR_NULLTERM:
h5tools_str_append(buffer, "H5T_STR_NULLTERM;");
break;
case H5T_STR_NULLPAD:
h5tools_str_append(buffer, "H5T_STR_NULLPAD;");
break;
case H5T_STR_SPACEPAD:
h5tools_str_append(buffer, "H5T_STR_SPACEPAD;");
break;
case H5T_STR_RESERVED_3:
case H5T_STR_RESERVED_4:
case H5T_STR_RESERVED_5:
case H5T_STR_RESERVED_6:
case H5T_STR_RESERVED_7:
case H5T_STR_RESERVED_8:
case H5T_STR_RESERVED_9:
case H5T_STR_RESERVED_10:
case H5T_STR_RESERVED_11:
case H5T_STR_RESERVED_12:
case H5T_STR_RESERVED_13:
case H5T_STR_RESERVED_14:
case H5T_STR_RESERVED_15:
h5tools_str_append(buffer, "H5T_STR_UNKNOWN;");
break;
case H5T_STR_ERROR:
h5tools_str_append(buffer, "H5T_STR_ERROR;");
break;
default:
h5tools_str_append(buffer, "ERROR;");
break;
}
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s ", CSET);
switch (cset) {
case H5T_CSET_ASCII:
h5tools_str_append(buffer, "H5T_CSET_ASCII;");
break;
case H5T_CSET_UTF8:
h5tools_str_append(buffer, "H5T_CSET_UTF8;");
break;
case H5T_CSET_RESERVED_2:
case H5T_CSET_RESERVED_3:
case H5T_CSET_RESERVED_4:
case H5T_CSET_RESERVED_5:
case H5T_CSET_RESERVED_6:
case H5T_CSET_RESERVED_7:
case H5T_CSET_RESERVED_8:
case H5T_CSET_RESERVED_9:
case H5T_CSET_RESERVED_10:
case H5T_CSET_RESERVED_11:
case H5T_CSET_RESERVED_12:
case H5T_CSET_RESERVED_13:
case H5T_CSET_RESERVED_14:
case H5T_CSET_RESERVED_15:
h5tools_str_append(buffer, "H5T_CSET_UNKNOWN;");
break;
case H5T_CSET_ERROR:
h5tools_str_append(buffer, "H5T_CSET_ERROR;");
break;
default:
h5tools_str_append(buffer, "ERROR;");
break;
}
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(buffer);
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_strpad(str_type, str_pad);
h5tools_str_append(buffer, "%s ", CTYPE);
/* Check C variable-length string first. Are the two types equal? */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_C_S1;");
goto found_string_type;
}
/* Change the endianness and see if they're equal. */
order = H5Tget_order(tmp_type);
if (order == H5T_ORDER_LE) {
if (H5Tset_order(str_type, H5T_ORDER_LE) < 0)
H5TOOLS_ERROR((-1), "H5Tset_order failed");
} /* end if */
else if (order == H5T_ORDER_BE) {
if (H5Tset_order(str_type, H5T_ORDER_BE) < 0)
H5TOOLS_ERROR((-1), "H5Tset_order failed");
} /* end if */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_C_S1;");
goto found_string_type;
}
/* If not equal to C variable-length string, check Fortran type. */
if (H5Tclose(str_type) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
str_type = H5Tcopy(H5T_FORTRAN_S1);
H5Tset_cset(str_type, cset);
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
/* Are the two types equal? */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_FORTRAN_S1;");
goto found_string_type;
}
/* Change the endianness and see if they're equal. */
order = H5Tget_order(tmp_type);
if (order == H5T_ORDER_LE) {
if (H5Tset_order(str_type, H5T_ORDER_LE) < 0)
H5TOOLS_ERROR((-1), "H5Tset_order failed");
} /* end if */
else if (order == H5T_ORDER_BE) {
if (H5Tset_order(str_type, H5T_ORDER_BE) < 0)
H5TOOLS_ERROR((-1), "H5Tset_order failed");
} /* end if */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_FORTRAN_S1;");
goto found_string_type;
}
/* Type doesn't match any of above. */
h5tools_str_append(buffer, "unknown_one_character_type;");
found_string_type:
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
if (H5Tclose(str_type) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
if (H5Tclose(tmp_type) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->strblockend);
break;
case H5T_BITFIELD:
if (H5Tequal(type, H5T_STD_B8BE) == true)
h5tools_str_append(buffer, "H5T_STD_B8BE");
else if (H5Tequal(type, H5T_STD_B8LE) == true)
h5tools_str_append(buffer, "H5T_STD_B8LE");
else if (H5Tequal(type, H5T_STD_B16BE) == true)
h5tools_str_append(buffer, "H5T_STD_B16BE");
else if (H5Tequal(type, H5T_STD_B16LE) == true)
h5tools_str_append(buffer, "H5T_STD_B16LE");
else if (H5Tequal(type, H5T_STD_B32BE) == true)
h5tools_str_append(buffer, "H5T_STD_B32BE");
else if (H5Tequal(type, H5T_STD_B32LE) == true)
h5tools_str_append(buffer, "H5T_STD_B32LE");
else if (H5Tequal(type, H5T_STD_B64BE) == true)
h5tools_str_append(buffer, "H5T_STD_B64BE");
else if (H5Tequal(type, H5T_STD_B64LE) == true)
h5tools_str_append(buffer, "H5T_STD_B64LE");
else
h5tools_str_append(buffer, "undefined bitfield");
break;
case H5T_OPAQUE:
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->opaqblockbegin);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
{
char *ttag;
if (NULL == (ttag = H5Tget_tag(type)))
H5TOOLS_THROW((-1), "H5Tget_tag failed");
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "OPAQUE_TAG \"%s\";", ttag);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
H5free_memory(ttag);
if ((size = H5Tget_size(type)) <= 0) {
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "OPAQUE_SIZE \"%zu\";", size);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->opaqblockend);
break;
case H5T_COMPOUND:
if ((snmembers = H5Tget_nmembers(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_nmembers failed");
nmembers = (unsigned)snmembers;
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->cmpdblockbegin);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
for (i = 0; i < nmembers; i++) {
mname = H5Tget_member_name(type, i);
if ((mtype = H5Tget_member_type(type, i)) >= 0) {
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_print_datatype(stream, buffer, info, ctx, mtype, true);
h5tools_str_append(buffer, " \"%s\";", mname);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
if (H5Tclose(mtype) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
}
else
H5TOOLS_ERROR((-1), "H5Tget_member_type failed");
H5free_memory(mname);
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->cmpdblockend);
break;
case H5T_REFERENCE:
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->refblockbegin);
if (H5Tequal(type, H5T_STD_REF_DSETREG) == true) {
h5tools_str_append(buffer, "H5T_STD_REF_DSETREG");
}
else if (H5Tequal(type, H5T_STD_REF_OBJ) == true) {
h5tools_str_append(buffer, "H5T_STD_REF_OBJECT");
}
else if (H5Tequal(type, H5T_STD_REF) == true) {
h5tools_str_append(buffer, "H5T_STD_REF");
}
else {
h5tools_str_append(buffer, "UNDEFINED");
}
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->refblockend);
break;
case H5T_ENUM:
if ((super = H5Tget_super(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_super failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->enumblockbegin);
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_print_datatype(stream, buffer, info, ctx, super, true);
if (H5Tclose(super) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
h5tools_str_append(buffer, ";");
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
h5tools_print_enum(stream, buffer, info, ctx, type);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->enumblockend);
break;
case H5T_VLEN:
if ((super = H5Tget_super(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_super failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->vlenblockbegin);
h5tools_print_datatype(stream, buffer, info, ctx, super, true);
if (H5Tclose(super) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->vlenblockend);
break;
case H5T_ARRAY:
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->arrblockbegin);
/* Get array information */
if ((sndims = H5Tget_array_ndims(type)) >= 0) {
unsigned ndims = (unsigned)sndims;
if (H5Tget_array_dims2(type, dims) >= 0) {
/* Print array dimensions */
for (i = 0; i < ndims; i++)
h5tools_str_append(buffer, "[%" PRIuHSIZE "]", dims[i]);
h5tools_str_append(buffer, " ");
}
else
H5TOOLS_ERROR((-1), "H5Tget_array_dims2 failed");
}
else
H5TOOLS_ERROR((-1), "H5Tget_array_ndims failed");
/* Get array base type */
if ((super = H5Tget_super(type)) >= 0) {
/* Print base type */
h5tools_print_datatype(stream, buffer, info, ctx, super, true);
/* Close array base type */
if (H5Tclose(super) < 0)
H5TOOLS_ERROR((-1), "H5Tclose failed");
}
else
H5TOOLS_ERROR((-1), "H5Tget_super failed");
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->arrblockend);
break;
case H5T_NO_CLASS:
case H5T_NCLASSES:
default:
h5tools_str_append(buffer, "unknown datatype");
break;
}
CATCH
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: print_dataspace
*
* Purpose: print the dataspace.
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
int
h5tools_print_dataspace(h5tools_str_t *buffer, hid_t space)
{
hsize_t size[H5TOOLS_DUMP_MAX_RANK];
hsize_t maxsize[H5TOOLS_DUMP_MAX_RANK];
int ndims = -1;
H5S_class_t space_type = -1;
bool past_catch = false;
int i;
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
if ((ndims = H5Sget_simple_extent_dims(space, size, maxsize)) < 0)
H5TOOLS_THROW((-1), "H5Sget_simple_extent_dims failed");
if ((space_type = H5Sget_simple_extent_type(space)) < 0)
H5TOOLS_THROW((-1), "H5Sget_simple_extent_type failed");
switch (space_type) {
case H5S_SCALAR:
/* scalar dataspace */
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin,
S_SCALAR);
break;
case H5S_SIMPLE:
/* simple dataspace */
h5tools_str_append(buffer, "%s %s { %s %" PRIuHSIZE,
h5tools_dump_header_format->dataspacedescriptionbegin, S_SIMPLE,
h5tools_dump_header_format->dataspacedimbegin, size[0]);
for (i = 1; i < ndims; i++)
h5tools_str_append(buffer, ", %" PRIuHSIZE, size[i]);
h5tools_str_append(buffer, " %s / ", h5tools_dump_header_format->dataspacedimend);
if (maxsize[0] == H5S_UNLIMITED)
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedimbegin,
"H5S_UNLIMITED");
else
h5tools_str_append(buffer, "%s %" PRIuHSIZE, h5tools_dump_header_format->dataspacedimbegin,
maxsize[0]);
for (i = 1; i < ndims; i++)
if (maxsize[i] == H5S_UNLIMITED)
h5tools_str_append(buffer, ", %s", "H5S_UNLIMITED");
else
h5tools_str_append(buffer, ", %" PRIuHSIZE, maxsize[i]);
h5tools_str_append(buffer, " %s }", h5tools_dump_header_format->dataspacedimend);
break;
case H5S_NULL:
/* null dataspace */
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin,
S_NULL);
break;
case H5S_NO_CLASS:
default:
h5tools_str_append(buffer, "%s unknown dataspace %s\n", BEGIN, END);
break;
} /* end switch */
CATCH
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: print_enum
*
* Purpose: prints the enum data
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*
*-----------------------------------------------------------------------*/
int
h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *info, h5tools_context_t *ctx,
hid_t type)
{
char **name = NULL; /*member names */
unsigned char *value = NULL; /*value array */
unsigned i;
unsigned nmembs = 0; /*number of members */
int snmembs;
hid_t super = H5I_INVALID_HID; /*enum base integer type */
hid_t native = H5I_INVALID_HID; /*native integer datatype */
H5T_sign_t sign_type; /*sign of value type */
size_t type_size; /*value type size */
size_t dst_size; /*destination value type size */
size_t ncols = 80; /*available output width */
hsize_t curr_pos = 0; /* total data element position */
bool past_catch = false;
int ret_value = 0;
H5TOOLS_START_DEBUG(" ");
if (info->line_ncols > 0)
ncols = info->line_ncols;
if ((snmembs = H5Tget_nmembers(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_nmembers failed");
nmembs = (unsigned)snmembs;
assert(nmembs > 0);
if ((super = H5Tget_super(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_super failed");
if ((type_size = H5Tget_size(type)) <= 0)
H5TOOLS_THROW((-1), "H5Tget_size(type) failed");
/*
* Determine what datatype to use for the native values. To simplify
* things we entertain three possibilities:
* 1. long long -- the largest native signed integer
* 2. unsigned long long -- the largest native unsigned integer
* 3. raw format
*/
if (type_size <= sizeof(long long)) {
dst_size = sizeof(long long);
if ((sign_type = H5Tget_sign(type)) < 0)
H5TOOLS_THROW((-1), "H5Tget_sign failed");
if (H5T_SGN_NONE == sign_type)
native = H5T_NATIVE_ULLONG;
else
native = H5T_NATIVE_LLONG;
} /* end if */
else
dst_size = type_size;
/* Get the names and raw values of all members */
if (NULL == (name = (char **)calloc((size_t)nmembs, sizeof(char *))))
H5TOOLS_THROW((-1), "Could not allocate buffer for member name");
if (NULL == (value = (unsigned char *)calloc((size_t)nmembs, MAX(type_size, dst_size))))
H5TOOLS_THROW((-1), "Could not allocate buffer for member value");
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
if (H5Tget_member_value(type, i, value + i * type_size) < 0)
H5TOOLS_THROW((-1), "H5Tget_member_value failed");
}
/* Convert values to native datatype */
if (native > 0)
if (H5Tconvert(super, native, (size_t)nmembs, value, NULL, H5P_DEFAULT) < 0)
H5TOOLS_THROW((-1), "H5Tconvert failed");
/*
* Sort members by increasing value
* ***not implemented yet***
*/
/* Print members */
for (i = 0; i < nmembs; i++) {
int nchars; /*number of output characters */
ctx->need_prefix = true;
h5tools_simple_prefix(stream, info, ctx, (hsize_t)0, 0);
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "\"%s\"", name[i]);
nchars = (int)strlen(name[i]);
h5tools_str_append(buffer, "%*s ", MAX(0, 16 - nchars), "");
if (native < 0) {
size_t j;
h5tools_str_append(buffer, "0x");
for (j = 0; j < dst_size; j++)
h5tools_str_append(buffer, "%02x", value[i * dst_size + j]);
}
else if (H5T_SGN_NONE == H5Tget_sign(native)) {
unsigned long long copy;
memcpy(©, value + i * dst_size, sizeof(copy));
h5tools_str_append(buffer, "%llu", copy);
}
else {
long long copy;
memcpy(©, value + i * dst_size, sizeof(copy));
h5tools_str_append(buffer, "%lld", copy);
}
h5tools_str_append(buffer, ";");
h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
}
CATCH
if (name) {
/* Release resources */
for (i = 0; i < nmembs; i++)
if (name[i])
H5free_memory(name[i]);
free(name);
} /* end if */
if (value)
free(value);
if (super >= 0 && H5Tclose(super) < 0)
H5TOOLS_THROW((-1), "Could not close datatype's super class");
if (0 == nmembs)
h5tools_str_append(buffer, "\n<empty>");
H5TOOLS_ENDDEBUG(" ");
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: dump_datatype
*
* Purpose: Dump the datatype. Datatype can be HDF5 predefined
* atomic datatype or committed/transient datatype.
*
* Return: void
*
* In/Out: h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
void
h5tools_dump_datatype(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t type)
{
h5tools_str_t buffer; /* string into which to render */
size_t ncols = 80; /* available output width */
hsize_t curr_pos = ctx->sm_pos; /* total data element position */
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
h5tools_print_datatype(stream, &buffer, info, ctx, type, true);
if (strlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(&buffer, " ");
}
if (strlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: dump_dataspace
*
* Purpose: Dump the dataspace.
*
* Return: void
*
* In/Out: h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
void
h5tools_dump_dataspace(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t type)
{
h5tools_str_t buffer; /* string into which to render */
size_t ncols = 80; /* available output width */
hsize_t curr_pos = ctx->sm_pos; /* total data element position */
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(&buffer, type);
if (strlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(&buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->dataspaceend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: dump_oid
*
* Purpose: Dump the oid.
*
* Return: void
*
* In/Out: h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
void
h5tools_dump_oid(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t oid)
{
h5tools_str_t buffer; /* string into which to render */
size_t ncols = 80; /* available output width */
hsize_t curr_pos = ctx->sm_pos; /* total data element position */
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s %" PRId64 " %s", OBJID, BEGIN, oid, END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: print_virtual_selection
*
* Purpose: Print the virtual dataset selection.
*
* Return: void
*-------------------------------------------------------------------------
*/
static void
h5tools_print_virtual_selection(hid_t vspace, FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, /* in,out*/
h5tools_str_t *buffer, /* string into which to render */
hsize_t *curr_pos, /* total data element position */
size_t ncols)
{
switch (H5Sget_select_type(vspace)) {
case H5S_SEL_NONE: /* Nothing selected */
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", VDS_NONE);
break;
case H5S_SEL_POINTS: /* Sequence of points selected */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ", VDS_POINT,
h5tools_dump_header_format->virtualselectionblockbegin);
h5tools_str_dump_space_points(buffer, vspace, info);
h5tools_str_append(buffer, " %s", h5tools_dump_header_format->virtualselectionblockend);
break;
case H5S_SEL_HYPERSLABS: /* "New-style" hyperslab selection defined */
ctx->need_prefix = true;
h5tools_str_reset(buffer);
if (H5Sis_regular_hyperslab(vspace)) {
h5tools_str_append(buffer, "%s %s ", VDS_REG_HYPERSLAB,
h5tools_dump_header_format->virtualselectionblockbegin);
h5tools_render_element(stream, info, ctx, buffer, curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
h5tools_str_reset(buffer);
h5tools_str_dump_space_slabs(buffer, vspace, info, ctx);
}
else {
h5tools_str_append(buffer, "%s %s ", VDS_IRR_HYPERSLAB,
h5tools_dump_header_format->virtualselectionblockbegin);
h5tools_render_element(stream, info, ctx, buffer, curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_simple_prefix(stream, info, ctx, *curr_pos, 0);
h5tools_str_reset(buffer);
h5tools_str_dump_space_blocks(buffer, vspace, info);
ctx->indent_level--;
}
h5tools_render_element(stream, info, ctx, buffer, curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->virtualselectionblockend);
break;
case H5S_SEL_ALL: /* Entire extent selected */
ctx->need_prefix = true;
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", VDS_ALL);
break;
case H5S_SEL_ERROR:
case H5S_SEL_N:
default:
h5tools_str_append(buffer, "Unknown Selection");
}
h5tools_render_element(stream, info, ctx, buffer, curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
}
/*-------------------------------------------------------------------------
* Function: dump_fill_value
*
* Purpose: prints the fill value
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_print_fill_value(h5tools_str_t *buffer /*in,out*/, const h5tool_format_t *info,
h5tools_context_t *ctx /*in,out*/, hid_t dcpl, hid_t type_id, hid_t obj_id)
{
size_t size;
hid_t n_type = H5I_INVALID_HID;
void *buf = NULL;
bool vl_data = false;
n_type = H5Tget_native_type(type_id, H5T_DIR_DEFAULT);
if (h5tools_detect_vlen(type_id) == true)
vl_data = true;
size = H5Tget_size(n_type);
buf = malloc(size);
H5Pget_fill_value(dcpl, n_type, buf);
h5tools_str_sprint(buffer, info, obj_id, n_type, buf, ctx);
H5Tclose(n_type);
if (vl_data) {
hsize_t dims[1] = {1};
hid_t space_id = H5I_INVALID_HID;
space_id = H5Screate_simple(1, dims, NULL);
H5Treclaim(type_id, space_id, H5P_DEFAULT, buf);
H5Sclose(space_id);
}
if (buf)
free(buf);
}
/*-------------------------------------------------------------------------
* Function: dump_dcpl
*
* Purpose: prints several dataset create property list properties
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dcpl_id,
hid_t type_id, hid_t dset_id)
{
int nfilters = -1; /* number of filters */
int rank; /* rank */
int i;
unsigned j;
unsigned filt_flags; /* filter flags */
unsigned cd_values[20]; /* filter client data values */
unsigned szip_options_mask;
unsigned szip_pixels_per_block;
H5Z_filter_t filtn; /* filter identification number */
H5D_fill_value_t fvstatus = H5D_FILL_VALUE_ERROR;
H5D_alloc_time_t at = H5D_ALLOC_TIME_ERROR;
H5D_fill_time_t ft = H5D_FILL_TIME_ERROR;
H5D_layout_t stl = H5D_LAYOUT_ERROR;
size_t ncols = 80; /* available output width */
size_t cd_nelmts; /* filter client number of values */
off_t offset; /* offset of external file */
char f_name[256]; /* filter name */
char name[256]; /* external or virtual file name */
hsize_t chsize[64]; /* chunk size in elements */
hsize_t size; /* size of external file */
hsize_t storage_size;
hsize_t curr_pos = 0; /* total data element position */
h5tools_str_t buffer; /* string into which to render */
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
storage_size = H5Dget_storage_size(dset_id);
if (dcpl_id >= 0)
nfilters = H5Pget_nfilters(dcpl_id);
strcpy(f_name, "\0");
/*-------------------------------------------------------------------------
* STORAGE_LAYOUT
*-------------------------------------------------------------------------
*/
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", STORAGE_LAYOUT, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
if (dcpl_id >= 0)
stl = H5Pget_layout(dcpl_id);
switch (stl) {
case H5D_CHUNKED:
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s ", CHUNKED);
rank = H5Pget_chunk(dcpl_id, (int)NELMTS(chsize), chsize);
h5tools_str_append(&buffer, "%s %" PRIuHSIZE, h5tools_dump_header_format->dataspacedimbegin,
chsize[0]);
for (i = 1; i < rank; i++)
h5tools_str_append(&buffer, ", %" PRIuHSIZE, chsize[i]);
h5tools_str_append(&buffer, " %s", h5tools_dump_header_format->dataspacedimend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
/* if there are filters, print a compression ratio */
if (nfilters) {
hsize_t dims[H5S_MAX_RANK];
hsize_t nelmts = 1;
double ratio = 0;
int ok = 0;
hid_t tid = H5Dget_type(dset_id);
hid_t sid = H5Dget_space(dset_id);
size_t datum_size = H5Tget_size(tid);
int ndims = H5Sget_simple_extent_dims(sid, dims, NULL);
/* only print the compression ratio for these filters */
for (i = 0; i < nfilters && !ok; i++) {
cd_nelmts = NELMTS(cd_values);
filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, cd_values,
sizeof(f_name), f_name, NULL);
ok = (filtn >= 0);
}
if (ndims && ok) {
hsize_t uncomp_size;
for (i = 0; i < ndims; i++) {
nelmts *= dims[i];
}
uncomp_size = nelmts * datum_size;
/* compression ratio = uncompressed size / compressed size */
if (storage_size != 0)
ratio = (double)uncomp_size / (double)storage_size;
h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE " (%.3f:1 COMPRESSION)", storage_size,
ratio);
}
else
h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size);
H5Sclose(sid);
H5Tclose(tid);
}
else {
h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size);
}
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level--;
break;
case H5D_COMPACT:
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", COMPACT);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level--;
break;
case H5D_CONTIGUOUS: {
int n_external;
n_external = H5Pget_external_count(dcpl_id);
ctx->indent_level++;
if (n_external) {
/* EXTERNAL FILE */
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", CONTIGUOUS);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", EXTERNAL, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
for (j = 0; j < (unsigned)n_external; j++) {
H5Pget_external(dcpl_id, j, sizeof(name), name, &offset, &size);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "FILENAME %s SIZE %" PRIuHSIZE, name, size);
/* Using %lld with a cast to (long long) is probably the only portable
* way to print off_t values. There's no real standard for off_t other
* than it must be signed, according to POSIX.
*/
h5tools_str_append(&buffer, " OFFSET %lld", (long long)offset);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
else {
haddr_t ioffset;
uint64_t supported = 0;
/* NORMAL FILE */
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", CONTIGUOUS);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "SIZE %" PRIuHSIZE, storage_size);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
/* Only dump the offset if the VOL connector implements
* the functionality.
*/
H5VLquery_optional(dset_id, H5VL_SUBCLS_DATASET, H5VL_NATIVE_DATASET_GET_OFFSET, &supported);
if (supported & H5VL_OPT_QUERY_SUPPORTED) {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
ioffset = H5Dget_offset(dset_id);
if (HADDR_UNDEF == ioffset)
h5tools_str_append(&buffer, "OFFSET HADDR_UNDEF");
else
h5tools_str_append(&buffer, "OFFSET %" PRIuHADDR, ioffset);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
}
ctx->indent_level--;
} break;
case H5D_VIRTUAL: {
char dsetname[256]; /* virtual dataset name */
size_t n_vmaps;
H5Pget_virtual_count(dcpl_id, &n_vmaps);
if (n_vmaps) {
size_t curr_vmap;
ssize_t H5_ATTR_NDEBUG_UNUSED ssize_out;
ctx->indent_level++;
for (curr_vmap = 0; curr_vmap < n_vmaps; curr_vmap++) {
hid_t virtual_vspace = H5Pget_virtual_vspace(dcpl_id, curr_vmap);
hid_t virtual_srcspace = H5Pget_virtual_srcspace(dcpl_id, curr_vmap);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %zu %s ", VDS_MAPPING, curr_vmap, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", VDS_VIRTUAL, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
h5tools_print_virtual_selection(virtual_vspace, stream, info, ctx, &buffer, &curr_pos,
(size_t)ncols);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", VDS_SOURCE, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level++;
ssize_out = H5Pget_virtual_filename(dcpl_id, curr_vmap, NULL, 0);
assert(ssize_out > 0);
assert((size_t)ssize_out < sizeof(name));
H5Pget_virtual_filename(dcpl_id, curr_vmap, name, sizeof(name));
ssize_out = H5Pget_virtual_dsetname(dcpl_id, curr_vmap, NULL, 0);
assert(ssize_out > 0);
assert((size_t)ssize_out < sizeof(name));
H5Pget_virtual_dsetname(dcpl_id, curr_vmap, dsetname, sizeof(dsetname));
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", VDS_SRC_FILE,
h5tools_dump_header_format->virtualfilenamebegin);
h5tools_str_append(&buffer, "%s", name);
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->virtualfilenameend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", VDS_SRC_DATASET,
h5tools_dump_header_format->virtualdatasetnamebegin);
h5tools_str_append(&buffer, "%s", dsetname);
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->virtualdatasetnameend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
h5tools_print_virtual_selection(virtual_srcspace, stream, info, ctx, &buffer, &curr_pos,
(size_t)ncols);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
ctx->indent_level--;
}
} break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
default:
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", "Unknown layout");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
} /*switch*/
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
/*-------------------------------------------------------------------------
* FILTERS
*-------------------------------------------------------------------------
*/
if (H5D_VIRTUAL != stl) {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", FILTERS, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level++;
if (nfilters) {
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_name), f_name, NULL);
if (filtn < 0)
continue; /* nothing to print for invalid filter */
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
switch (filtn) {
case H5Z_FILTER_DEFLATE:
h5tools_str_append(&buffer, "%s %s %s %d %s", DEFLATE, BEGIN, DEFLATE_LEVEL,
cd_values[0], END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
case H5Z_FILTER_SHUFFLE:
h5tools_str_append(&buffer, "%s", SHUFFLE);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
case H5Z_FILTER_FLETCHER32:
h5tools_str_append(&buffer, "%s", FLETCHER32);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
case H5Z_FILTER_SZIP:
szip_options_mask = cd_values[0];
szip_pixels_per_block = cd_values[1];
h5tools_str_append(&buffer, "%s %s", SZIP, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "PIXELS_PER_BLOCK %d", szip_pixels_per_block);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
if (szip_options_mask & H5_SZIP_CHIP_OPTION_MASK)
h5tools_str_append(&buffer, "MODE %s", "HARDWARE");
else if (szip_options_mask & H5_SZIP_ALLOW_K13_OPTION_MASK)
h5tools_str_append(&buffer, "MODE %s", "K13");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
if (szip_options_mask & H5_SZIP_EC_OPTION_MASK)
h5tools_str_append(&buffer, "CODING %s", "ENTROPY");
else if (szip_options_mask & H5_SZIP_NN_OPTION_MASK)
h5tools_str_append(&buffer, "CODING %s", "NEAREST NEIGHBOUR");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
if (szip_options_mask & H5_SZIP_LSB_OPTION_MASK)
h5tools_str_append(&buffer, "BYTE_ORDER %s", "LSB");
else if (szip_options_mask & H5_SZIP_MSB_OPTION_MASK)
h5tools_str_append(&buffer, "BYTE_ORDER %s", "MSB");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
if (szip_options_mask & H5_SZIP_RAW_OPTION_MASK) {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "HEADER %s", "RAW");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
case H5Z_FILTER_NBIT:
h5tools_str_append(&buffer, "%s", NBIT);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
case H5Z_FILTER_SCALEOFFSET:
h5tools_str_append(&buffer, "%s %s %s %d %s", SCALEOFFSET, BEGIN, SCALEOFFSET_MINBIT,
cd_values[0], END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
default:
h5tools_str_append(&buffer, "%s %s", "USER_DEFINED_FILTER", BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "FILTER_ID %d", filtn);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
if (f_name[0] != '\0') {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "COMMENT %s", f_name);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
}
if (cd_nelmts) {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", "PARAMS", BEGIN);
for (j = 0; j < cd_nelmts; j++)
h5tools_str_append(&buffer, "%d ", cd_values[j]);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
break;
} /*switch*/
} /*i*/
} /*nfilters*/
else {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "NONE");
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
} /* end if (H5D_VIRTUAL != stl) */
/*-------------------------------------------------------------------------
* FILLVALUE
*-------------------------------------------------------------------------
*/
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", FILLVALUE, BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "FILL_TIME ");
if (dcpl_id >= 0)
H5Pget_fill_time(dcpl_id, &ft);
switch (ft) {
case H5D_FILL_TIME_ALLOC:
h5tools_str_append(&buffer, "%s", "H5D_FILL_TIME_ALLOC");
break;
case H5D_FILL_TIME_NEVER:
h5tools_str_append(&buffer, "%s", "H5D_FILL_TIME_NEVER");
break;
case H5D_FILL_TIME_IFSET:
h5tools_str_append(&buffer, "%s", "H5D_FILL_TIME_IFSET");
break;
case H5D_FILL_TIME_ERROR:
default:
h5tools_str_append(&buffer, "%s", "INVALID");
break;
}
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s ", "VALUE ");
if (dcpl_id >= 0)
H5Pfill_value_defined(dcpl_id, &fvstatus);
switch (fvstatus) {
case H5D_FILL_VALUE_UNDEFINED:
h5tools_str_append(&buffer, "%s", "H5D_FILL_VALUE_UNDEFINED");
break;
case H5D_FILL_VALUE_DEFAULT:
h5tools_str_append(&buffer, "%s", "H5D_FILL_VALUE_DEFAULT");
break;
case H5D_FILL_VALUE_USER_DEFINED:
ctx->indent_level--;
h5tools_print_fill_value(&buffer, info, ctx, dcpl_id, type_id, dset_id);
ctx->indent_level++;
break;
case H5D_FILL_VALUE_ERROR:
default:
h5tools_str_append(&buffer, "%s", "INVALID");
break;
}
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
/*-------------------------------------------------------------------------
* ALLOCATION_TIME
*-------------------------------------------------------------------------
*/
if (H5D_VIRTUAL != stl) {
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "ALLOCATION_TIME %s", BEGIN);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
if (dcpl_id >= 0)
H5Pget_alloc_time(dcpl_id, &at);
switch (at) {
case H5D_ALLOC_TIME_EARLY:
h5tools_str_append(&buffer, "%s", "H5D_ALLOC_TIME_EARLY");
break;
case H5D_ALLOC_TIME_INCR:
h5tools_str_append(&buffer, "%s", "H5D_ALLOC_TIME_INCR");
break;
case H5D_ALLOC_TIME_LATE:
h5tools_str_append(&buffer, "%s", "H5D_ALLOC_TIME_LATE");
break;
case H5D_ALLOC_TIME_ERROR:
case H5D_ALLOC_TIME_DEFAULT:
default:
h5tools_str_append(&buffer, "%s", "INVALID");
break;
}
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s", END);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
} /* end if (H5D_VIRTUAL != stl) */
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: dump_comment
*
* Purpose: prints the comment for the object name
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_dump_comment(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t obj_id)
{
char *comment = NULL;
ssize_t cmt_bufsize = -1;
size_t buf_size = 0;
size_t ncols = 80; /* available output width */
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos = ctx->sm_pos; /* total data element position */
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
uint64_t supported = 0;
/* Check if comments are supported and return if not */
H5VLquery_optional(obj_id, H5VL_SUBCLS_OBJECT, H5VL_NATIVE_OBJECT_GET_COMMENT, &supported);
if (!(supported & H5VL_OPT_QUERY_SUPPORTED))
return;
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
cmt_bufsize = H5Oget_comment(obj_id, comment, buf_size);
/* call H5Oget_comment again with the correct value */
if (cmt_bufsize > 0) {
comment = (char *)malloc((size_t)(cmt_bufsize + 1)); /* new_size including null terminator */
if (comment) {
cmt_bufsize = H5Oget_comment(obj_id, comment, (size_t)cmt_bufsize);
if (cmt_bufsize > 0) {
comment[cmt_bufsize] = '\0'; /* necessary because null char is not returned */
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "COMMENT \"%s\"", comment);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
h5tools_str_close(&buffer);
}
free(comment);
}
}
} /* end dump_comment() */
/*-------------------------------------------------------------------------
* Function: dump_attribute
*
* Purpose: Dump the attribute.
*
* Return: void
*
* In/Out: h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
void
h5tools_dump_attribute(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx,
const char *attr_name, hid_t attr_id)
{
h5tools_str_t buffer; /* string into which to render */
size_t ncols = 80; /* available output width */
hsize_t curr_pos = ctx->sm_pos; /* total data element position */
/* pass to the prefix in h5tools_simple_prefix the total position
* instead of the current stripmine position i; this is necessary
* to print the array indices
*/
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->attributebegin, attr_name,
h5tools_dump_header_format->attributeblockbegin);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
if (attr_id < 0) {
error_msg("unable to open attribute \"%s\"\n", attr_name);
}
else {
hid_t type = H5I_INVALID_HID;
hid_t space = H5I_INVALID_HID;
ctx->indent_level++;
type = H5Aget_type(attr_id);
h5tools_dump_datatype(stream, info, ctx, type);
space = H5Aget_space(attr_id);
h5tools_dump_dataspace(stream, info, ctx, space);
if (oid_output)
h5tools_dump_oid(stream, info, ctx, attr_id);
if (data_output || attr_data_output)
h5tools_dump_data(stream, info, ctx, attr_id, false);
ctx->indent_level--;
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
}
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
if (strlen(h5tools_dump_header_format->attributeblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeblockend);
if (strlen(h5tools_dump_header_format->attributeend))
h5tools_str_append(&buffer, " ");
}
if (strlen(h5tools_dump_header_format->attributeend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: dump_dims
*
* Purpose: Dump the dimensions handed to it in a comma separated list
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_print_dims(h5tools_str_t *buffer, hsize_t *s, int dims)
{
int i;
for (i = 0; i < dims; i++) {
h5tools_str_append(buffer, "%" PRIuHSIZE, s[i]);
if (i + 1 != dims)
h5tools_str_append(buffer, ", ");
}
}
/*-------------------------------------------------------------------------
* Function: print_packed_bits
*
* Purpose: Prints the packed bits offset and length
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_print_packed_bits(h5tools_str_t *buffer, hid_t type)
{
unsigned packed_bits_size = 0;
hid_t n_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
if (H5Tget_class(n_type) == H5T_INTEGER) {
if (H5Tequal(n_type, H5T_NATIVE_SCHAR) == true)
packed_bits_size = 8 * sizeof(char);
else if (H5Tequal(n_type, H5T_NATIVE_UCHAR) == true)
packed_bits_size = 8 * sizeof(unsigned char);
else if (H5Tequal(n_type, H5T_NATIVE_SHORT) == true)
packed_bits_size = 8 * sizeof(short);
else if (H5Tequal(n_type, H5T_NATIVE_USHORT) == true)
packed_bits_size = 8 * sizeof(unsigned short);
else if (H5Tequal(n_type, H5T_NATIVE_INT) == true)
packed_bits_size = 8 * sizeof(int);
else if (H5Tequal(n_type, H5T_NATIVE_UINT) == true)
packed_bits_size = 8 * sizeof(unsigned int);
else if (H5Tequal(n_type, H5T_NATIVE_LONG) == true)
packed_bits_size = 8 * sizeof(long);
else if (H5Tequal(n_type, H5T_NATIVE_ULONG) == true)
packed_bits_size = 8 * sizeof(unsigned long);
else if (H5Tequal(n_type, H5T_NATIVE_LLONG) == true)
packed_bits_size = 8 * sizeof(long long);
else if (H5Tequal(n_type, H5T_NATIVE_ULLONG) == true)
packed_bits_size = 8 * sizeof(unsigned long long);
else
error_msg("Packed Bit not valid for this datatype");
}
if ((packed_bits_size > 0) && (packed_data_offset + packed_data_length) > packed_bits_size) {
error_msg("Packed Bit offset+length value(%u) too large. Max is %d\n",
packed_data_offset + packed_data_length, packed_bits_size);
packed_data_mask = 0;
}
h5tools_str_append(buffer, "%s %s=%u %s=%u", PACKED_BITS, PACKED_OFFSET, packed_data_offset,
PACKED_LENGTH, packed_data_length);
}
/*-------------------------------------------------------------------------
* Function: dump_subsetting_header
*
* Purpose: Dump the subsetting header like specified in the DDL.
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_dump_subsetting_header(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, int dims)
{
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos = 0; /* total data element position */
size_t ncols = 80; /* available output width */
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->subsettingbegin,
h5tools_dump_header_format->subsettingblockbegin);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level++;
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->startbegin,
h5tools_dump_header_format->startblockbegin);
h5tools_print_dims(&buffer, ctx->sset->start.data, dims);
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->startend,
h5tools_dump_header_format->startblockend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->stridebegin,
h5tools_dump_header_format->strideblockbegin);
h5tools_print_dims(&buffer, ctx->sset->stride.data, dims);
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->strideend,
h5tools_dump_header_format->strideblockend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->countbegin,
h5tools_dump_header_format->countblockbegin);
if (ctx->sset->count.data)
h5tools_print_dims(&buffer, ctx->sset->count.data, dims);
else
h5tools_str_append(&buffer, "DEFAULT");
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->countend,
h5tools_dump_header_format->countblockend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->blockbegin,
h5tools_dump_header_format->blockblockbegin);
if (ctx->sset->block.data)
h5tools_print_dims(&buffer, ctx->sset->block.data, dims);
else
h5tools_str_append(&buffer, "DEFAULT");
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->blockend,
h5tools_dump_header_format->blockblockend);
h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
ctx->indent_level--;
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: dump_reference
*
* Purpose: Dump reference data
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t container,
H5R_ref_t *ref_buf, int ndims)
{
hid_t new_obj_id = H5I_INVALID_HID;
hid_t new_obj_sid = H5I_INVALID_HID;
hsize_t elmt_counter = 0; /*counts the # elements printed. */
size_t ncols = 80; /* available output width */
int i;
hsize_t curr_pos = 0; /* total data element position */
h5tools_str_t buffer; /* string into which to render */
h5tools_context_t datactx; /* print context */
H5TOOLS_START_DEBUG(" ");
datactx = *ctx; /* print context */
/* Assume entire data space to be printed */
datactx.need_prefix = true;
memset(&buffer, 0, sizeof(h5tools_str_t));
for (i = 0; i < ndims; i++, datactx.cur_elmt++, elmt_counter++) {
H5O_type_t obj_type = -1; /* Object type */
H5R_type_t ref_type; /* Reference type */
H5TOOLS_DEBUG("reference loop:%d with curr_pos=%ld", i, curr_pos);
datactx.need_prefix = true;
h5tools_str_reset(&buffer);
H5TOOLS_DEBUG("reference loop - h5tools_str_sprint with H5T_STD_REF:%d", i);
h5tools_str_sprint(&buffer, info, container, H5T_STD_REF, &ref_buf[i], &datactx);
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)i,
(hsize_t)ndims);
ref_type = H5Rget_type((const H5R_ref_t *)&ref_buf[i]);
switch (ref_type) {
case H5R_OBJECT1:
H5TOOLS_DEBUG("ref_type is H5R_OBJECT1");
if (H5Rget_obj_type3(&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_DATASET:
if ((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_data(stream, info, &datactx, new_obj_id, true);
// h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
if (H5Dclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Dclose H5R_OBJECT1:H5O_TYPE_DATASET failed");
}
else
H5TOOLS_INFO("H5Ropen_object H5R_OBJECT1:H5O_TYPE_DATASET failed");
break;
case H5O_TYPE_GROUP:
case H5O_TYPE_NAMED_DATATYPE:
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
}
else
H5TOOLS_INFO("H5Rget_obj_type3 H5R_OBJECT1 failed");
break;
case H5R_DATASET_REGION1:
H5TOOLS_DEBUG("ref_type is H5R_DATASET_REGION1");
if ((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_data(stream, info, &datactx, new_obj_id, true);
// h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
if (H5Dclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Dclose H5R_DATASET_REGION1 failed");
}
else
H5TOOLS_INFO("H5Ropen_object H5R_DATASET_REGION1 failed");
break;
case H5R_OBJECT2:
H5TOOLS_DEBUG("ref_type is H5R_OBJECT2");
if (H5Rget_obj_type3(&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) {
switch (obj_type) {
case H5O_TYPE_GROUP:
break;
case H5O_TYPE_DATASET:
if ((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
datactx.indent_level++;
h5tools_dump_data(stream, info, &datactx, new_obj_id, true);
// h5tools_dump_dset(stream, info, &datactx, new_obj_id);
datactx.indent_level--;
if (H5Oclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Oclose H5R_OBJECT2 failed");
}
else
H5TOOLS_INFO("H5Ropen_object H5R_OBJECT2 failed");
break;
case H5O_TYPE_NAMED_DATATYPE:
break;
case H5O_TYPE_MAP:
case H5O_TYPE_UNKNOWN:
case H5O_TYPE_NTYPES:
default:
break;
} /* end switch */
}
else
H5TOOLS_INFO("H5Rget_obj_type3 H5R_OBJECT2 failed");
break;
case H5R_DATASET_REGION2:
H5TOOLS_DEBUG("ref_type is H5R_DATASET_REGION2");
if (info->line_ncols > 0)
ncols = info->line_ncols;
/* if (new_obj_id < 0) - could mean that no reference was written do not throw failure */
if ((new_obj_id = H5Ropen_object(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) < 0)
H5TOOLS_INFO("H5Ropen_object H5R_DATASET_REGION2 failed");
else {
if ((new_obj_sid = H5Ropen_region(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
if (h5tools_is_zero(&ref_buf[i], H5Tget_size(H5T_STD_REF))) {
H5TOOLS_DEBUG("NULL H5R_DATASET_REGION2");
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " {");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
datactx.need_prefix = true;
datactx.indent_level++;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "NULL");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
datactx.indent_level--;
datactx.need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "}");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
}
else {
H5S_sel_type region_type;
region_type = H5Sget_select_type(new_obj_sid);
if (region_type == H5S_SEL_POINTS) {
/* Print point information */
H5TOOLS_DEBUG("H5S_SEL_POINTS H5R_DATASET_REGION2");
h5tools_dump_region_data_points(new_obj_sid, new_obj_id, stream, info,
&datactx, &buffer, &curr_pos, ncols,
(hsize_t)i, elmt_counter);
}
else if (region_type == H5S_SEL_HYPERSLABS) {
/* Print block information */
H5TOOLS_DEBUG("H5S_SEL_HYPERSLABS H5R_DATASET_REGION2");
h5tools_dump_region_data_blocks(new_obj_sid, new_obj_id, stream, info,
&datactx, &buffer, &curr_pos, ncols,
(hsize_t)i, elmt_counter);
}
else
H5TOOLS_INFO("invalid region type");
} /* end else to if (h5tools_is_zero(... */
if (H5Sclose(new_obj_sid) < 0)
H5TOOLS_INFO("H5Sclose H5R_DATASET_REGION2 failed");
}
else
H5TOOLS_INFO("H5Ropen_region H5R_DATASET_REGION2 failed");
if (H5Dclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Dclose H5R_DATASET_REGION2 failed");
}
break;
case H5R_ATTR:
H5TOOLS_DEBUG("ref_type is H5R_ATTR");
if ((new_obj_id = H5Ropen_attr(&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) {
h5tools_dump_region_attribute(new_obj_id, stream, info, &datactx, &buffer, &curr_pos,
(size_t)ncols, (hsize_t)0, (hsize_t)0);
if (H5Aclose(new_obj_id) < 0)
H5TOOLS_INFO("H5Aclose H5R_ATTR failed");
}
else {
H5TOOLS_DEBUG("NULL H5R_ATTR");
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " {");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
datactx.need_prefix = true;
datactx.indent_level++;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "NULL");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
datactx.indent_level--;
datactx.need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "}");
h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
H5TOOLS_INFO("H5Ropen_attr H5R_ATTR failed");
}
break;
case H5R_BADTYPE:
case H5R_MAXTYPE:
default:
break;
} /* end switch */
if (H5Rdestroy(&ref_buf[i]) < 0)
H5TOOLS_INFO("H5Rdestroy failed");
H5TOOLS_DEBUG("finished reference loop:%d", i);
} /* end for(i = 0; i < ndims; i++, ctx->cur_elmt++, elmt_counter++) */
h5tools_str_close(&buffer);
H5TOOLS_ENDDEBUG(" ");
}
/*-------------------------------------------------------------------------
* Function: dump_data
*
* Purpose: Dump attribute, obj_data is false, or dataset data, obj_data is true
*
* Return: void
*-------------------------------------------------------------------------
*/
void
h5tools_dump_data(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t obj_id,
int obj_data)
{
H5S_class_t space_type;
int ndims;
hid_t space = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
hsize_t total_size[H5S_MAX_RANK];
int status = -1;
h5tools_context_t datactx; /* print context */
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos = 0; /* total data element position */
size_t ncols = 80; /* available output width */
h5tool_format_t string_dataformat;
h5tool_format_t outputformat;
H5R_ref_t *ref_buf = NULL;
H5TOOLS_START_DEBUG(" file=%p", (void *)stream);
H5TOOLS_DEBUG("rawdata file=%p", (void *)rawdatastream);
/* setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
if (info->line_ncols > 0)
ncols = info->line_ncols;
outputformat = *info;
string_dataformat = *info;
/* print the matrix indices */
string_dataformat.pindex = ctx->display_index;
if (obj_data) {
H5TOOLS_DEBUG("dataset");
f_type = H5Dget_type(obj_id);
space = H5Dget_space(obj_id);
}
else {
H5TOOLS_DEBUG("attribute");
f_type = H5Aget_type(obj_id);
space = H5Aget_space(obj_id);
}
if (string_dataformat.pindex) {
string_dataformat.idx_fmt = "(%s): ";
string_dataformat.idx_n_fmt = "%" PRIuHSIZE;
string_dataformat.idx_sep = ",";
string_dataformat.line_pre = "%s";
}
info = &string_dataformat;
if (ctx->sset && obj_data) {
h5tools_dump_subsetting_header(stream, &outputformat, ctx, H5Sget_simple_extent_ndims(space));
ctx->indent_level++;
}
ctx->need_prefix = true;
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "%s %s", h5tools_dump_header_format->databegin,
h5tools_dump_header_format->datablockbegin);
h5tools_render_element(stream, &outputformat, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
if (H5Tget_class(f_type) == H5T_REFERENCE) {
ctx->indent_level++;
datactx = *ctx;
H5TOOLS_DEBUG("reference class type");
if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) &&
!H5Tequal(f_type, H5T_STD_REF_OBJ)) {
H5TOOLS_GOTO_DONE_NO_RET();
}
ndims = (int)H5Sget_simple_extent_npoints(space);
H5TOOLS_DEBUG("ndims=%d - datactx.ndims=%d", ndims, datactx.ndims);
/* Assume entire data space to be printed */
H5Sget_simple_extent_dims(space, total_size, NULL);
init_acc_pos(datactx.ndims, total_size, datactx.acc, datactx.pos, datactx.p_min_idx);
datactx.need_prefix = true;
if (NULL !=
(ref_buf = (H5R_ref_t *)calloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)ndims))) {
if (obj_data) {
if (H5Dread(obj_id, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf) < 0) {
free(ref_buf);
H5TOOLS_INFO("H5Dread reference failed");
H5TOOLS_GOTO_DONE_NO_RET();
}
}
else {
if (H5Aread(obj_id, H5T_STD_REF, ref_buf) < 0) {
free(ref_buf);
H5TOOLS_INFO("H5Aread reference failed");
H5TOOLS_GOTO_DONE_NO_RET();
}
}
h5tools_dump_reference(stream, &outputformat, &datactx, obj_id, ref_buf, ndims);
free(ref_buf);
}
ctx->indent_level--;
}
else {
H5TOOLS_DEBUG("Print all the values");
datactx = *ctx;
string_dataformat = *info;
if ((datactx.display_char && H5Tget_size(f_type) == 1) && (H5Tget_class(f_type) == H5T_INTEGER)) {
H5TOOLS_DEBUG("Print 1-byte integer data as an ASCII character string");
/*
* Print 1-byte integer data as an ASCII character string
* instead of integers if the `-r' or `--string' command-line
* option was given.
*
* We don't want to modify the global dataformat, so make a
* copy of it instead.
*/
string_dataformat.idx_fmt = "\"";
datactx.indent_level++;
datactx.need_prefix = true;
h5tools_simple_prefix(stream, &string_dataformat, &datactx, (hsize_t)0, 0);
string_dataformat.line_multi_new = 1;
string_dataformat.str_repeat = 8;
string_dataformat.ascii = true;
string_dataformat.elmt_suf1 = "";
string_dataformat.elmt_suf2 = "";
string_dataformat.line_suf = "\"";
}
else {
datactx.need_prefix = true;
}
/* Print all the values. */
if (obj_data) {
H5TOOLS_DEBUG("h5tools_dump_dset");
status = h5tools_dump_dset(stream, &string_dataformat, &datactx, obj_id);
}
else {
/* need to call h5tools_dump_mem for the attribute data */
space_type = H5Sget_simple_extent_type(space);
if (space_type == H5S_NULL || space_type == H5S_NO_CLASS) {
status = SUCCEED;
}
else {
H5TOOLS_DEBUG("call h5tools_dump_mem");
status = h5tools_dump_mem(stream, &string_dataformat, &datactx, obj_id);
}
}
if (datactx.display_char && H5Tget_size(f_type) == 1 && H5Tget_class(f_type) == H5T_INTEGER) {
H5TOOLS_DEBUG("Print 1-byte integer data as an ASCII character string eol=%s",
string_dataformat.line_suf);
datactx.need_prefix = false;
string_dataformat.arr_linebreak = 0;
string_dataformat.idx_fmt = "";
string_dataformat.line_multi_new = 0;
string_dataformat.line_suf = "";
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, "\"");
h5tools_render_element(stream, &string_dataformat, &datactx, &buffer, &curr_pos, (size_t)ncols,
(hsize_t)0, (hsize_t)0);
}
H5TOOLS_DEBUG("Print all the values Complete");
if (status == FAIL) {
error_msg("unable to print data\n");
h5tools_setstatus(EXIT_FAILURE);
}
}
done:
H5Sclose(space);
H5Tclose(f_type);
ctx->need_prefix = true;
h5tools_simple_prefix(stream, &outputformat, ctx, (hsize_t)0, 0);
h5tools_str_reset(&buffer);
if (strlen(h5tools_dump_header_format->datablockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datablockend);
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(&buffer, " ");
}
if (strlen(h5tools_dump_header_format->dataend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->dataend);
h5tools_render_element(stream, &outputformat, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
if (ctx->sset && obj_data) {
ctx->indent_level--;
ctx->need_prefix = true;
h5tools_simple_prefix(stream, &outputformat, ctx, (hsize_t)0, 0);
h5tools_str_reset(&buffer);
if (strlen(h5tools_dump_header_format->subsettingblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->subsettingblockend);
if (strlen(h5tools_dump_header_format->subsettingend))
h5tools_str_append(&buffer, " ");
}
if (strlen(h5tools_dump_header_format->subsettingend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->subsettingend);
h5tools_render_element(stream, &outputformat, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0,
(hsize_t)0);
}
h5tools_str_close(&buffer);
H5TOOLS_ENDDEBUG(" ");
}