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Update h5ls help and rework dump_mem routines for attrs

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This commit is contained in:
Allen Byrne 2019-12-04 16:36:32 -06:00
parent cc2407257a
commit d552e97eae
14 changed files with 248 additions and 303 deletions
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4
tools/lib/h5tools.c
View File

@ -1521,7 +1521,7 @@ int
render_bin_output_region_data_blocks(hid_t region_id, FILE *stream,
hid_t container, unsigned ndims, hid_t type_id, hsize_t nblocks, hsize_t *ptdata)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
@ -1687,7 +1687,7 @@ render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container,
unsigned ndims, hid_t type_id, hsize_t npoints)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
hsize_t *dims1 = NULL;
size_t type_size;
hid_t mem_space = -1;

308
tools/lib/h5tools_dump.c
View File

@ -257,7 +257,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
h5tools_context_t *ctx, /* in,out */
unsigned flags, hsize_t nelmts, hid_t type, void *_mem)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
unsigned char *mem = (unsigned char*) _mem;
hsize_t i; /* element counter */
size_t size; /* size of each datum */
@ -493,7 +493,7 @@ h5tools_print_region_data_blocks(hid_t region_id,
h5tools_str_t *buffer, /* string into which to render */
size_t ncols, unsigned ndims, hid_t type_id, hsize_t nblocks, hsize_t *ptdata)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
hbool_t dimension_break = TRUE;
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
@ -888,7 +888,7 @@ h5tools_print_region_data_points(hid_t region_space, hid_t region_id,
h5tools_str_t *buffer, size_t ncols,
unsigned ndims, hid_t type_id, hsize_t npoints, hsize_t *ptdata)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
hbool_t dimension_break = TRUE;
hsize_t *dims1 = NULL;
hsize_t elmtno; /* elemnt index */
@ -1709,7 +1709,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont
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 */
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];
@ -1788,7 +1788,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont
}
}
else
H5TOOLS_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed");
ctx->continuation++;
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "stripmine read loop:%d complete", i);
@ -1817,17 +1817,27 @@ CATCH
*-------------------------------------------------------------------------
*/
static int
h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t obj_id,
hid_t type, hid_t space, void *mem)
h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx,
hid_t attr_id, hid_t p_type)
{
H5TOOLS_ERR_INIT(herr_t, SUCCEED)
int sndims; /* rank of dataspace */
unsigned i; /*counters */
hsize_t nelmts; /*total selected elmts */
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 */
unsigned char *buf = NULL; /* buffer for raw data */
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
H5TOOLS_PUSH_STACK();
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter");
sndims = H5Sget_simple_extent_ndims(space);
if (FAIL == (f_space = H5Aget_space(attr_id)))
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
sndims = H5Sget_simple_extent_ndims(f_space);
if(sndims < 0)
H5TOOLS_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed");
ctx->ndims = (unsigned)sndims;
@ -1837,30 +1847,54 @@ h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_conte
H5TOOLS_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(ctx->p_min_idx) failed");
/* Assume entire data space to be printed */
for (i = 0; i < ctx->ndims; i++)
ctx->p_min_idx[i] = 0;
if (ctx->ndims > 0)
for (i = 0; i < (size_t)ctx->ndims; i++)
ctx->p_min_idx[i] = 0;
H5Sget_simple_extent_dims(space, ctx->p_max_idx, NULL);
H5Sget_simple_extent_dims(f_space, total_size, NULL);
for (i = 0, nelmts = 1; ctx->ndims != 0 && i < ctx->ndims; i++)
nelmts *= ctx->p_max_idx[i] - ctx->p_min_idx[i];
/* calculate the number of elements we're going to print */
p_nelmts = 1;
if (nelmts == 0)
H5_LEAVE(SUCCEED); /* nothing to print */
if (ctx->ndims > 0) {
HDassert(ctx->p_max_idx[ctx->ndims - 1] == (hsize_t) ((int) ctx->p_max_idx[ctx->ndims - 1]));
ctx->size_last_dim = ctx->p_max_idx[ctx->ndims - 1];
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 (ctx->ndims > 0)
init_acc_pos(ctx, ctx->p_max_idx);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->ndims:%d", ctx->ndims);
if (p_nelmts == 0)
H5_LEAVE(SUCCEED); /* nothing to print */
if(h5tools_dump_simple_data(stream, info, obj_id, ctx, START_OF_DATA | END_OF_DATA, nelmts, type, mem) < 0)
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "h5tools_dump_simple_data failed");
/* 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);
HDassert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
if (NULL != (buf = (unsigned char *)HDmalloc((size_t)alloc_size))) {
if (ctx->ndims > 0)
init_acc_pos(ctx, total_size);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ctx->ndims:%d", ctx->ndims);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Read the data");
/* Read the data */
if (H5Aread(attr_id, p_type, buf) >= 0) {
if(h5tools_dump_simple_data(stream, info, attr_id, ctx, START_OF_DATA | END_OF_DATA, p_nelmts, p_type, buf) < 0)
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "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(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
HDfree(buf);
} /* if (NULL != (buf...)) */
done:
if(f_space >= 0 && H5Sclose(f_space) < 0)
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
CATCH
H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit");
H5TOOLS_POP_STACK();
@ -1888,11 +1922,11 @@ CATCH
int
h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset)
{
hid_t f_space = -1;
hid_t p_type = -1;
hid_t f_type = -1;
H5TOOLS_ERR_INIT(int, SUCCEED)
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;
int status = FAIL;
h5tool_format_t info_dflt;
/* Use default values */
if (!stream)
@ -1929,13 +1963,13 @@ h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *
/* Print the data */
if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) {
if(!ctx->sset)
status = h5tools_dump_simple_dset(rawdatastream, info, ctx, dset, p_type);
ret_value = h5tools_dump_simple_dset(rawdatastream, info, ctx, dset, p_type);
else
status = h5tools_dump_simple_subset(rawdatastream, info, ctx, dset, p_type);
ret_value = h5tools_dump_simple_subset(rawdatastream, info, ctx, dset, p_type);
}
else {
/* space is H5S_NULL */
status = SUCCEED;
ret_value = SUCCEED;
}
done:
if (f_type > 0)
@ -1945,7 +1979,7 @@ done:
if (f_space > 0)
H5Sclose(f_space);
return status;
return ret_value;
}
/*-------------------------------------------------------------------------
@ -1960,10 +1994,12 @@ done:
*-------------------------------------------------------------------------
*/
int
h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx,
hid_t obj_id, hid_t type, hid_t space, void *mem)
h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t attr_id)
{
H5TOOLS_ERR_INIT(int, SUCCEED)
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;
/* Use default values */
@ -1975,13 +2011,42 @@ h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, h5tools_context_t *c
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 */
if (H5Sis_simple(space) <= 0)
H5TOOLS_THROW(FAIL, H5E_tools_min_id_g, "H5Sis_simple failed")
f_space = H5Aget_space(attr_id);
if (f_space < 0)
goto done;
H5_LEAVE(h5tools_dump_simple_mem(rawattrstream, info, ctx, obj_id, type, space, mem))
/* Check the data space */
if (H5Sis_simple(f_space) <= 0) {
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "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);
CATCH
return ret_value;
}
@ -3901,22 +3966,17 @@ h5tools_dump_subsetting_header(FILE *stream, const h5tool_format_t *info, h5tool
void
h5tools_dump_data(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t obj_id, int obj_data)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
H5S_class_t space_type;
int ndims;
size_t i;
hid_t space = H5I_INVALID_HID;
hid_t p_type = H5I_INVALID_HID;
hid_t f_type = H5I_INVALID_HID;
hid_t new_obj_id = H5I_INVALID_HID;
hid_t new_obj_sid = H5I_INVALID_HID;
hsize_t total_size[H5S_MAX_RANK];
hsize_t size[64];
hsize_t alloc_size;
hsize_t nelmts = 1;
hsize_t elmt_counter = 0; /*counts the # elements printed. */
int status = -1;
void *buf = NULL;
hbool_t dimension_break;
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos = 0; /* total data element position */
@ -4205,140 +4265,62 @@ h5tools_dump_data(FILE *stream, const h5tool_format_t *info, h5tools_context_t *
}
}
else {
h5tools_context_t datactx = *ctx; /* print context */
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Print all the values");
string_dataformat = *info;
if((datactx.display_char && H5Tget_size(f_type) == 1) && (H5Tget_class(f_type) == H5T_INTEGER)) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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_context_t datactx = *ctx; /* print context */
string_dataformat = *info;
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Print all the dataset values file=%p", (void*)stream);
if((datactx.display_char && H5Tget_size(f_type) == 1) && (H5Tget_class(f_type) == H5T_INTEGER)) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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;
}
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "h5tools_dump_dset");
status = h5tools_dump_dset(stream, &string_dataformat, &datactx, obj_id);
if((datactx.display_char && H5Tget_size(f_type) == 1) && (H5Tget_class(f_type) == H5T_INTEGER)) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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);
}
}
else {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Print all the attribute values");
h5tools_context_t datactx = *ctx; /* print context */
/* 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 {
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
p_type = H5Tget_native_type(f_type, H5T_DIR_DEFAULT);
ndims = H5Sget_simple_extent_dims(space, size, NULL);
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == TRUE)
vl_data = TRUE;
for (i = 0; i < ndims; i++)
nelmts *= size[i];
alloc_size = nelmts * MAX(H5Tget_size(f_type), H5Tget_size(p_type));
HDassert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
if (alloc_size) {
buf = HDmalloc((size_t)alloc_size);
HDassert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0) {
string_dataformat = *info;
if (datactx.display_char && H5Tget_size(f_type) == 1 && H5Tget_class(f_type) == H5T_INTEGER) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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;
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "call h5tools_dump_mem");
status = h5tools_dump_mem(stream, &string_dataformat, &datactx, obj_id, p_type, space, buf);
if (datactx.display_char && H5Tget_size(f_type) == 1 && H5Tget_class(f_type) == H5T_INTEGER) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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);
}
}
else
H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
}
else {
status = SUCCEED;
} /* end if (alloc_size) */
H5Tclose(p_type);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "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(H5E_tools_min_dbg_id_g, "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(H5E_tools_min_dbg_id_g, "Print all the values Complete");
if (status == FAIL) {

3
tools/lib/h5tools_dump.h
View File

@ -39,8 +39,7 @@ H5TOOLS_DLL void h5tools_dump_init(void);
H5TOOLS_DLL int h5tools_dump_dset(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/, hid_t dset);
H5TOOLS_DLL int h5tools_dump_mem(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/, hid_t obj_id,
hid_t type, hid_t space, void *mem);
h5tools_context_t *ctx/*in,out*/, hid_t obj_id);
H5TOOLS_DLL int h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t container,
h5tools_context_t *ctx/*in,out*/, unsigned flags,
hsize_t nelmts, hid_t type, void *_mem);

4
tools/lib/h5tools_str.c
View File

@ -684,7 +684,7 @@ char *
h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t container,
hid_t type, void *vp, h5tools_context_t *ctx)
{
H5TOOLS_ERR_INIT(char*, NULL);
H5TOOLS_ERR_INIT(char*, NULL)
size_t nsize, offset, size=0, nelmts, start;
H5T_sign_t nsign;
char *name = NULL;
@ -1357,7 +1357,7 @@ void
h5tools_str_sprint_reference(h5tools_str_t *str, const h5tool_format_t *info,
hid_t container, H5R_ref_t *ref_vp)
{
H5TOOLS_ERR_INIT(int, SUCCEED);
H5TOOLS_ERR_INIT(int, SUCCEED)
ssize_t buf_size, status;
H5TOOLS_PUSH_STACK();

2
tools/src/h5dump/h5dump.c
View File

@ -1703,6 +1703,8 @@ main(int argc, const char *argv[])
/* To Do: clean up XML table */
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(h5tools_getstatus());
done:

42
tools/src/h5dump/h5dump_xml.c
View File

@ -1880,47 +1880,17 @@ xml_dump_data(hid_t obj_id, int obj_data, struct subset_t H5_ATTR_UNUSED *sset,
status = xml_print_strs(obj_id, ATTRIBUTE_DATA);
}
else { /* all other data */
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT);
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == TRUE)
vl_data = TRUE;
H5Tclose(type);
space = H5Aget_space(obj_id);
if(space == H5S_NULL || space == H5S_NO_CLASS) {
status = SUCCEED;
}
else {
ndims = H5Sget_simple_extent_dims(space, size, NULL);
for (i = 0; i < ndims; i++)
nelmts *= size[i];
if((buf = HDmalloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))))) == NULL) {
error_msg("unable to allocate buffer\n");
h5tools_setstatus(EXIT_FAILURE);
status = FAIL;
}
else {
if (H5Aread(obj_id, p_type, buf) >= 0) {
h5tools_context_t datactx;
HDmemset(&datactx, 0, sizeof(datactx));
datactx.need_prefix = TRUE;
datactx.indent_level = ctx.indent_level;
datactx.cur_column = ctx.cur_column;
status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id, p_type, space, buf);
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
}
h5tools_context_t datactx;
HDmemset(&datactx, 0, sizeof(datactx));
datactx.need_prefix = TRUE;
datactx.indent_level = ctx.indent_level;
datactx.cur_column = ctx.cur_column;
status = h5tools_dump_mem(rawoutstream, outputformat, &datactx, obj_id);
}
H5Tclose(p_type);
H5Sclose(space);

109
tools/src/h5ls/h5ls.c
View File

@ -132,7 +132,6 @@ static hbool_t no_dangling_link_g = FALSE; /* treat dangling link is error */
static hbool_t follow_elink_g = FALSE; /* follow external links */
static hbool_t grp_literal_g = FALSE; /* list group, not contents */
static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */
static hbool_t show_errors_g = FALSE; /* print HDF5 error messages */
static hbool_t simple_output_g = FALSE; /* make output more machine-readable */
static hbool_t show_file_name_g = FALSE; /* show file name for full names */
static hbool_t no_line_wrap_g = FALSE; /* show data content without line wrap */
@ -193,7 +192,7 @@ usage (void)
PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n");
PRINTVALSTREAM(rawoutstream, " Must be used with --follow-symlinks option;\n");
PRINTVALSTREAM(rawoutstream, " otherwise, h5ls shows error message and returns an exit\n");
PRINTVALSTREAM(rawoutstream, " code of 1. \n");
PRINTVALSTREAM(rawoutstream, " code of 1.\n");
PRINTVALSTREAM(rawoutstream, " Check for any symbolic links (soft links or external links)\n");
PRINTVALSTREAM(rawoutstream, " that do not resolve to an existing object (dataset, group,\n");
PRINTVALSTREAM(rawoutstream, " or named datatype).\n");
@ -228,11 +227,8 @@ usage (void)
PRINTVALSTREAM(rawoutstream, " \"%%05d\" to open a file family.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Deprecated Options\n");
PRINTVALSTREAM(rawoutstream, " The following options have been deprecated in HDF5. While they remain\n");
PRINTVALSTREAM(rawoutstream, " available, they have been superseded as indicated and may be removed\n");
PRINTVALSTREAM(rawoutstream, " from HDF5 in the future. Use the indicated replacement option in all\n");
PRINTVALSTREAM(rawoutstream, " new work; where possible, existing scripts, et cetera, should also be\n");
PRINTVALSTREAM(rawoutstream, " updated to use the replacement option.\n");
PRINTVALSTREAM(rawoutstream, " The following options have been removed in HDF5 1.12. Use the indicated\n");
PRINTVALSTREAM(rawoutstream, " replacement option in all work.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " -E or --external Follow external links.\n");
PRINTVALSTREAM(rawoutstream, " Replaced by --follow-symlinks.\n");
@ -1530,6 +1526,7 @@ dump_dataset_values(hid_t dset)
{
H5TOOLS_ERR_INIT(herr_t, SUCCEED)
hid_t f_type = H5I_INVALID_HID;
hid_t space = H5I_INVALID_HID;
hid_t new_obj_id = H5I_INVALID_HID;
hid_t new_obj_sid = H5I_INVALID_HID;
hsize_t total_size[H5S_MAX_RANK];
@ -1537,7 +1534,6 @@ dump_dataset_values(hid_t dset)
hsize_t elmt_counter = 0; /*counts the # elements printed. */
int ndims;
size_t i;
size_t size;
char string_prefix[64];
static char fmt_double[16];
static char fmt_float[16];
@ -1553,7 +1549,7 @@ dump_dataset_values(hid_t dset)
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter");
f_type = H5Dget_type(dset);
size = H5Tget_size(f_type);
space = H5Dget_space(dset);
HDmemset(&ctx, 0, sizeof(ctx));
HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@ -1623,7 +1619,7 @@ dump_dataset_values(hid_t dset)
* command line switch was given. */
outputformat.raw = TRUE;
}
else if (string_g && 1 == size && H5T_INTEGER == H5Tget_class(f_type)) {
else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) {
/* Print 1-byte integer data as an ASCI character string instead of
* integers if the `-s' or `--string' command-line option was given. */
outputformat.ascii = TRUE;
@ -1640,11 +1636,12 @@ dump_dataset_values(hid_t dset)
/* Print all the values. */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " Data:\n");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
ctx.need_prefix = TRUE;
ctx.cur_column = (size_t)curr_pos;
if (H5Tget_class(f_type) == H5T_REFERENCE) {
hid_t space = H5Dget_space(dset);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference class type");
if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && !H5Tequal(f_type, H5T_STD_REF_OBJ)) {
HGOTO_DONE(SUCCEED);
@ -1659,13 +1656,12 @@ dump_dataset_values(hid_t dset)
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(space, total_size, NULL);
H5Sclose(space);
if (ctx.ndims > 0)
init_acc_pos(&ctx, total_size);
ctx.need_prefix = TRUE;
if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) {
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread reference read");
H5TOOLS_DEBUG(H5E_tools_min_id_g, "H5Dread reference read");
if(H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf) < 0) {
HDfree(ref_buf);
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread reference failed");
@ -1682,6 +1678,7 @@ dump_dataset_values(hid_t dset)
}
}
done:
H5Sclose(space);
H5Tclose(f_type);
h5tools_str_close(&buffer);
@ -1843,10 +1840,11 @@ dump_attribute_values(hid_t attr, const char *attr_name)
H5Sget_simple_extent_dims(space, total_size, NULL);
if (ctx.ndims > 0)
init_acc_pos(&ctx, total_size);
ctx.need_prefix = TRUE;
if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute reference read");
if(H5Aread(attr, H5T_STD_REF, ref_buf) >= 0) {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "H5Aread reference read");
if(H5Aread(attr, H5T_STD_REF, ref_buf) < 0) {
HDfree(ref_buf);
H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread reference failed");
}
@ -1858,40 +1856,13 @@ dump_attribute_values(hid_t attr, const char *attr_name)
}
else {
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read");
if (hexdump_g)
p_type = H5Tcopy(f_type);
else
p_type = H5Tget_native_type(f_type, H5T_DIR_DEFAULT);
if (p_type >= 0) {
/* VL data special information */
unsigned int vl_data = 0; /* contains VL datatypes */
/* Check if we have VL data in the dataset's datatype */
if (h5tools_detect_vlen(p_type) == TRUE)
vl_data = TRUE;
temp_need = nelmts * MAX(H5Tget_size(f_type), H5Tget_size(p_type));
need = (size_t)temp_need;
if((buf = HDmalloc(need)) != NULL) {
if(H5Aread(attr, p_type, buf) >= 0) {
ctx.indent_level++;
if (h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf) < 0) {
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " Unable to print data.");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
}
ctx.indent_level--;
}
/* Reclaim any VL memory, if necessary */
if (vl_data)
H5Treclaim(p_type, space, H5P_DEFAULT, buf);
HDfree(buf);
}
H5Tclose(p_type);
} /* end if */
ctx.indent_level++;
if (h5tools_dump_mem(rawoutstream, info, &ctx, attr) < 0) {
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, " Unable to print data.");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
}
ctx.indent_level--;
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read complete");
}
done:
@ -1919,7 +1890,7 @@ static herr_t
list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo,
void H5_ATTR_UNUSED *op_data)
{
H5TOOLS_ERR_INIT(herr_t, SUCCEED);
H5TOOLS_ERR_INIT(herr_t, SUCCEED)
hid_t attr = H5I_INVALID_HID;
hid_t space = H5I_INVALID_HID;
hid_t type = H5I_INVALID_HID;
@ -1952,7 +1923,7 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain
print_string(&buffer, attr_name, TRUE);
H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute name:%s", attr_name);
if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) < 0) {
if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) >= 0) {
space = H5Aget_space(attr);
type = H5Aget_type(attr);
@ -2344,7 +2315,7 @@ datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name)
static herr_t
list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void *_iter)
{
H5TOOLS_ERR_INIT(herr_t, SUCCEED);
H5TOOLS_ERR_INIT(herr_t, SUCCEED)
H5O_type_t obj_type = oinfo->type; /* Type of the object */
iter_t *iter = (iter_t*)_iter;
hsize_t curr_pos = 0; /* total data element position */
@ -2892,6 +2863,10 @@ main(int argc, const char *argv[])
const char *preferred_driver = NULL;
int err_exit = 0;
hid_t fapl_id = H5P_DEFAULT;
H5E_auto2_t func;
H5E_auto2_t tools_func;
void *edata;
void *tools_edata;
#ifdef H5_HAVE_ROS3_VFD
/* default "anonymous" s3 configuration */
@ -2919,9 +2894,17 @@ main(int argc, const char *argv[])
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
/* Disable tools error reporting */
H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL);
/* Build object display table */
DISPATCH(H5O_TYPE_GROUP, "Group", NULL, NULL);
DISPATCH(H5O_TYPE_DATASET, "Dataset", dataset_list1, dataset_list2);
@ -2948,11 +2931,11 @@ main(int argc, const char *argv[])
data_g = TRUE;
}
else if (!HDstrcmp(argv[argno], "--enable-error-stack")) {
show_errors_g = TRUE;
enable_error_stack = 1;
/* deprecated --errors */
}
else if (!HDstrcmp(argv[argno], "--errors")) {
show_errors_g = TRUE;
enable_error_stack = 1;
}
else if (!HDstrcmp(argv[argno], "--follow-symlinks")) {
follow_symlink_g = TRUE;
@ -3201,7 +3184,7 @@ main(int argc, const char *argv[])
/* deprecated -e */
case 'e': /* --errors */
show_errors_g = TRUE;
enable_error_stack = 1;
break;
case 'E': /* --external */
@ -3309,10 +3292,10 @@ main(int argc, const char *argv[])
}
} /* preferred_driver defined */
/* Turn off HDF5's automatic error printing unless you're debugging h5ls */
if(!show_errors_g)
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
if (enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
}
/* Each remaining argument is an hdf5 file followed by an optional slash
* and object name.
@ -3376,6 +3359,7 @@ main(int argc, const char *argv[])
x = oname;
if (NULL == (oname = HDstrdup(oname))) {
HDfprintf(rawerrorstream, "memory allocation failed\n");
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
}
*x = '\0';
@ -3420,6 +3404,7 @@ main(int argc, const char *argv[])
h5tools_str_reset(&buffer);
print_obj_name(&buffer, &iter, oname, "**NOT FOUND**");
h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0);
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
} /* end if */
} /* end if */
@ -3428,8 +3413,10 @@ main(int argc, const char *argv[])
/* Open the object and display it's information */
if (li.type == H5L_TYPE_HARD) {
if (visit_obj(file, oname, &iter) < 0)
if (visit_obj(file, oname, &iter) < 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
}
} /* end if(li.type == H5L_TYPE_HARD) */
else {
/* Specified name is not for object -- list that link */
@ -3458,10 +3445,12 @@ main(int argc, const char *argv[])
if (fapl_id != H5P_DEFAULT) {
if (0 < H5Pclose(fapl_id)) {
HDfprintf(rawerrorstream, "Error: Unable to set close fapl entry\n\n");
H5Eset_auto2(H5E_DEFAULT, func, edata);
leave(EXIT_FAILURE);
}
}
H5Eset_auto2(H5E_DEFAULT, func, edata);
if (err_exit)
leave(EXIT_FAILURE);
else

9
tools/testfiles/help-1.ls
View File

@ -20,7 +20,7 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
--no-dangling-links
Must be used with --follow-symlinks option;
otherwise, h5ls shows error message and returns an exit
code of 1.
code of 1.
Check for any symbolic links (soft links or external links)
that do not resolve to an existing object (dataset, group,
or named datatype).
@ -55,11 +55,8 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
"%05d" to open a file family.
Deprecated Options
The following options have been deprecated in HDF5. While they remain
available, they have been superseded as indicated and may be removed
from HDF5 in the future. Use the indicated replacement option in all
new work; where possible, existing scripts, et cetera, should also be
updated to use the replacement option.
The following options have been removed in HDF5 1.12. Use the indicated
replacement option in all work.
-E or --external Follow external links.
Replaced by --follow-symlinks.

9
tools/testfiles/help-2.ls
View File

@ -20,7 +20,7 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
--no-dangling-links
Must be used with --follow-symlinks option;
otherwise, h5ls shows error message and returns an exit
code of 1.
code of 1.
Check for any symbolic links (soft links or external links)
that do not resolve to an existing object (dataset, group,
or named datatype).
@ -55,11 +55,8 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
"%05d" to open a file family.
Deprecated Options
The following options have been deprecated in HDF5. While they remain
available, they have been superseded as indicated and may be removed
from HDF5 in the future. Use the indicated replacement option in all
new work; where possible, existing scripts, et cetera, should also be
updated to use the replacement option.
The following options have been removed in HDF5 1.12. Use the indicated
replacement option in all work.
-E or --external Follow external links.
Replaced by --follow-symlinks.

9
tools/testfiles/help-3.ls
View File

@ -20,7 +20,7 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
--no-dangling-links
Must be used with --follow-symlinks option;
otherwise, h5ls shows error message and returns an exit
code of 1.
code of 1.
Check for any symbolic links (soft links or external links)
that do not resolve to an existing object (dataset, group,
or named datatype).
@ -55,11 +55,8 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
"%05d" to open a file family.
Deprecated Options
The following options have been deprecated in HDF5. While they remain
available, they have been superseded as indicated and may be removed
from HDF5 in the future. Use the indicated replacement option in all
new work; where possible, existing scripts, et cetera, should also be
updated to use the replacement option.
The following options have been removed in HDF5 1.12. Use the indicated
replacement option in all work.
-E or --external Follow external links.
Replaced by --follow-symlinks.

17
tools/testfiles/tattrreg_be.ls
View File

@ -2,10 +2,19 @@ Opened "tattrreg.h5" with sec2 driver.
Dataset1 Dataset {NULL}
Attribute: Attribute1 {4}
Type: dataset region reference
Data: DSET-/Dataset2 {Blk0: (2,2)-(7,7)}
DSET-/Dataset2 {Pt0: (6,9), Pt1: (2,2), Pt2: (8,4), Pt3: (1,6),
Pt4: (2,8), Pt5: (3,2), Pt6: (0,4), Pt7: (9,0), Pt8: (7,1),
Pt9: (3,3)}
Data:
DATASET tattrreg.h5/Dataset2 {
REGION_TYPE BLOCK Blk0: (2,2)-(7,7)
DATATYPE H5T_STD_U8BE
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
}
DATASET tattrreg.h5/Dataset2 {
REGION_TYPE POINT Pt0: (6,9), Pt1: (2,2), Pt2: (8,4),
Pt3: (1,6), Pt4: (2,8), Pt5: (3,2), Pt6: (0,4),
Pt7: (9,0), Pt8: (7,1), Pt9: (3,3)
DATATYPE H5T_STD_U8BE
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
}
NULL
NULL
Location: 1:1400

17
tools/testfiles/tattrreg_le.ls
View File

@ -2,10 +2,19 @@ Opened "tattrreg.h5" with sec2 driver.
Dataset1 Dataset {NULL}
Attribute: Attribute1 {4}
Type: dataset region reference
Data: DSET-/Dataset2 {Blk0: (2,2)-(7,7)}
DSET-/Dataset2 {Pt0: (6,9), Pt1: (2,2), Pt2: (8,4), Pt3: (1,6),
Pt4: (2,8), Pt5: (3,2), Pt6: (0,4), Pt7: (9,0), Pt8: (7,1),
Pt9: (3,3)}
Data:
DATASET tattrreg.h5/Dataset2 {
REGION_TYPE BLOCK Blk0: (2,2)-(7,7)
DATATYPE H5T_STD_U8BE
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
}
DATASET tattrreg.h5/Dataset2 {
REGION_TYPE POINT Pt0: (6,9), Pt1: (2,2), Pt2: (8,4),
Pt3: (1,6), Pt4: (2,8), Pt5: (3,2), Pt6: (0,4),
Pt7: (9,0), Pt8: (7,1), Pt9: (3,3)
DATATYPE H5T_STD_U8BE
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
}
NULL
NULL
Location: 1:1400

9
tools/testfiles/textlinksrc-nodangle-1.ls
View File

@ -20,7 +20,7 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
--no-dangling-links
Must be used with --follow-symlinks option;
otherwise, h5ls shows error message and returns an exit
code of 1.
code of 1.
Check for any symbolic links (soft links or external links)
that do not resolve to an existing object (dataset, group,
or named datatype).
@ -55,11 +55,8 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
"%05d" to open a file family.
Deprecated Options
The following options have been deprecated in HDF5. While they remain
available, they have been superseded as indicated and may be removed
from HDF5 in the future. Use the indicated replacement option in all
new work; where possible, existing scripts, et cetera, should also be
updated to use the replacement option.
The following options have been removed in HDF5 1.12. Use the indicated
replacement option in all work.
-E or --external Follow external links.
Replaced by --follow-symlinks.

9
tools/testfiles/tgroup-1.ls
View File

@ -20,7 +20,7 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
--no-dangling-links
Must be used with --follow-symlinks option;
otherwise, h5ls shows error message and returns an exit
code of 1.
code of 1.
Check for any symbolic links (soft links or external links)
that do not resolve to an existing object (dataset, group,
or named datatype).
@ -55,11 +55,8 @@ usage: h5ls [OPTIONS] file[/OBJECT] [file[/[OBJECT]...]
"%05d" to open a file family.
Deprecated Options
The following options have been deprecated in HDF5. While they remain
available, they have been superseded as indicated and may be removed
from HDF5 in the future. Use the indicated replacement option in all
new work; where possible, existing scripts, et cetera, should also be
updated to use the replacement option.
The following options have been removed in HDF5 1.12. Use the indicated
replacement option in all work.
-E or --external Follow external links.
Replaced by --follow-symlinks.