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-rw-r--r--tools/lib/h5tools.c138
1 files changed, 83 insertions, 55 deletions
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index fc2d034..ca3c8a6 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -18,6 +18,9 @@
#include "hdf5.h"
#include "H5private.h"
+
+
+
/*
* The output functions need a temporary buffer to hold a piece of the
* dataset while it's being printed. This constant sets the limit on the
@@ -90,8 +93,8 @@ h5tools_close(void)
{
if (h5tools_init_g) {
if (rawdatastream && rawdatastream != stdout) {
- if (HDfclose(rawdatastream))
- HDperror("closing rawdatastream");
+ if (fclose(rawdatastream))
+ perror("closing rawdatastream");
else
rawdatastream = NULL;
}
@@ -204,7 +207,7 @@ h5tools_fopen(const char *fname, char *drivername, size_t drivername_size)
/* Save the driver name */
if (drivername && drivername_size) {
if (fid >= 0) {
- HDstrncpy(drivername, driver[drivernum].name, drivername_size);
+ strncpy(drivername, driver[drivernum].name, drivername_size);
drivername[drivername_size - 1] = '\0';
} else {
/*no file opened*/
@@ -271,13 +274,13 @@ h5tools_simple_prefix(FILE *stream, const h5dump_t *info,
if (!ctx->need_prefix)
return;
- HDmemset(&prefix, 0, sizeof(h5tools_str_t));
+ memset(&prefix, 0, sizeof(h5tools_str_t));
/* Terminate previous line, if any */
if (ctx->cur_column) {
- HDfputs(OPT(info->line_suf, ""), stream);
- HDputc('\n', stream);
- HDfputs(OPT(info->line_sep, ""), stream);
+ fputs(OPT(info->line_suf, ""), stream);
+ putc('\n', stream);
+ fputs(OPT(info->line_sep, ""), stream);
}
/* Calculate new prefix */
@@ -298,16 +301,16 @@ h5tools_simple_prefix(FILE *stream, const h5dump_t *info,
}
if (elmtno == 0 && secnum == 0 && info->line_1st)
- HDfputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
+ fputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
else if (secnum && info->line_cont)
- HDfputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
+ fputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
else
- HDfputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
+ fputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
templength = h5tools_str_len(&prefix);
for (i = 0; i < indentlevel; i++){
- HDfputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
+ fputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
templength += h5tools_str_len(&prefix);
}
@@ -366,7 +369,7 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*to the ctx->size_last_dim. */
/* Setup */
- HDmemset(&buffer, 0, sizeof(h5tools_str_t));
+ memset(&buffer, 0, sizeof(h5tools_str_t));
size = H5Tget_size(type);
if (info->line_ncols > 0)
@@ -390,8 +393,8 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*/
if (info->line_multi_new == 1 &&
(ctx->cur_column + h5tools_ncols(s) +
- HDstrlen(OPT(info->elmt_suf2, " ")) +
- HDstrlen(OPT(info->line_suf, ""))) > ncols) {
+ strlen(OPT(info->elmt_suf2, " ")) +
+ strlen(OPT(info->line_suf, ""))) > ncols) {
if (ctx->prev_multiline) {
/*
* ... and the previous element also occupied more than one
@@ -399,8 +402,8 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*/
ctx->need_prefix = TRUE;
} else if ((ctx->prev_prefix_len + h5tools_ncols(s) +
- HDstrlen(OPT(info->elmt_suf2, " ")) +
- HDstrlen(OPT(info->line_suf, ""))) <= ncols) {
+ strlen(OPT(info->elmt_suf2, " ")) +
+ strlen(OPT(info->line_suf, ""))) <= ncols) {
/*
* ...but *could* fit on one line otherwise, then we
* should end the current line and start this element on its
@@ -432,8 +435,8 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*/
if (info->line_multi_new == 1 && ctx->prev_multiline &&
(ctx->cur_column + h5tools_ncols(s) +
- HDstrlen(OPT(info->elmt_suf2, " ")) +
- HDstrlen(OPT(info->line_suf, ""))) > ncols)
+ strlen(OPT(info->elmt_suf2, " ")) +
+ strlen(OPT(info->line_suf, ""))) > ncols)
ctx->need_prefix = TRUE;
/*
@@ -463,8 +466,8 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
*/
if ((!info->skip_first || i) &&
(ctx->cur_column + strlen(section) +
- HDstrlen(OPT(info->elmt_suf2, " ")) +
- HDstrlen(OPT(info->line_suf, ""))) > ncols)
+ strlen(OPT(info->elmt_suf2, " ")) +
+ strlen(OPT(info->line_suf, ""))) > ncols)
ctx->need_prefix = 1;
/*
@@ -477,13 +480,13 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
h5tools_simple_prefix(stream, info, ctx, i, secnum);
} else if ((i || ctx->continuation) && secnum == 0) {
- HDfputs(OPT(info->elmt_suf2, " "), stream);
- ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " "));
+ fputs(OPT(info->elmt_suf2, " "), stream);
+ ctx->cur_column += strlen(OPT(info->elmt_suf2, " "));
}
/* Print the section */
- HDfputs(section, stream);
- ctx->cur_column += HDstrlen(section);
+ fputs(section, stream);
+ ctx->cur_column += strlen(section);
}
ctx->prev_multiline = multiline;
@@ -513,7 +516,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
{
herr_t ret; /*the value to return */
hid_t f_space; /*file data space */
- hsize_t i; /*counters */
+ hsize_t elmtno, i; /*counters */
hssize_t zero = 0; /*vector of zeros */
unsigned int flags; /*buffer extent flags */
hsize_t total_size[H5S_MAX_RANK];/*total size of dataset*/
@@ -542,7 +545,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
- HDmemset(&ctx, 0, sizeof(ctx));
+ memset(&ctx, 0, sizeof(ctx));
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
ctx.ndims = H5Sget_simple_extent_ndims(f_space);
@@ -564,8 +567,11 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
for (; count > 0; sset->start[ctx.ndims - 1] += sset->stride[ctx.ndims - 1],
count--) {
/* calculate the potential number of elements we're going to print */
- H5Sselect_hyperslab(f_space, H5S_SELECT_SET, sset->start, sset->stride,
- sset->count, sset->block);
+ H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
+ (hssize_t*)sset->start,
+ (hsize_t*)sset->stride,
+ (hsize_t*)sset->count,
+ (hsize_t*)sset->block);
sm_nelmts = H5Sget_select_npoints(f_space);
/*
@@ -604,7 +610,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
}
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
- sm_buf = HDmalloc((size_t)sm_nelmts * p_type_nbytes);
+ sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes);
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL);
@@ -613,7 +619,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
H5Sclose(f_space);
H5Sclose(sm_space);
- HDfree(sm_buf);
+ free(sm_buf);
return FAIL;
}
@@ -629,15 +635,15 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset,
h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
p_type, sm_buf);
- HDfree(sm_buf);
+ free(sm_buf);
ctx.continuation++;
}
/* Terminate the output */
if (ctx.cur_column) {
- HDfputs(OPT(info->line_suf, ""), stream);
- HDputc('\n', stream);
- HDfputs(OPT(info->line_sep, ""), stream);
+ fputs(OPT(info->line_suf, ""), stream);
+ putc('\n', stream);
+ fputs(OPT(info->line_sep, ""), stream);
}
ret = SUCCEED;
@@ -707,7 +713,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
- HDmemset(&ctx, 0, sizeof(ctx));
+ memset(&ctx, 0, sizeof(ctx));
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
ctx.ndims = H5Sget_simple_extent_ndims(f_space);
@@ -757,13 +763,13 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
}
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
- sm_buf = HDmalloc((size_t)sm_nbytes);
+ sm_buf = malloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* The stripmine loop */
- HDmemset(hs_offset, 0, sizeof hs_offset);
- HDmemset(zero, 0, sizeof zero);
+ memset(hs_offset, 0, sizeof hs_offset);
+ memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
@@ -788,7 +794,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
H5Sclose(f_space);
H5Sclose(sm_space);
- HDfree(sm_buf);
+ free(sm_buf);
return FAIL;
}
@@ -818,14 +824,14 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
/* Terminate the output */
if (ctx.cur_column) {
- HDfputs(OPT(info->line_suf, ""), stream);
- HDputc('\n', stream);
- HDfputs(OPT(info->line_sep, ""), stream);
+ fputs(OPT(info->line_suf, ""), stream);
+ putc('\n', stream);
+ fputs(OPT(info->line_sep, ""), stream);
}
H5Sclose(sm_space);
H5Sclose(f_space);
- HDfree(sm_buf);
+ free(sm_buf);
return SUCCEED;
}
@@ -859,7 +865,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id,
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
- HDmemset(&ctx, 0, sizeof(ctx));
+ memset(&ctx, 0, sizeof(ctx));
ctx.ndims = H5Sget_simple_extent_ndims(space);
if ((size_t)ctx.ndims > NELMTS(ctx.p_min_idx))
@@ -888,9 +894,9 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id,
/* Terminate the output */
if (ctx.cur_column) {
- HDfputs(OPT(info->line_suf, ""), stream);
- HDputc('\n', stream);
- HDfputs(OPT(info->line_sep, ""), stream);
+ fputs(OPT(info->line_suf, ""), stream);
+ putc('\n', stream);
+ fputs(OPT(info->line_sep, ""), stream);
}
return SUCCEED;
@@ -989,12 +995,34 @@ h5tools_fixtype(hid_t f_type)
*/
nmembs = H5Tget_nmembers(f_type);
assert(nmembs > 0);
- memb = HDcalloc((size_t)nmembs, sizeof(hid_t));
- name = HDcalloc((size_t)nmembs, sizeof(char *));
+ memb = calloc((size_t)nmembs, sizeof(hid_t));
+ name = calloc((size_t)nmembs, sizeof(char *));
for (i = 0, size = 0; i < nmembs; i++) {
/* Get the member type and fix it */
f_memb = H5Tget_member_type(f_type, i);
+#ifdef WANT_H5_V1_2_COMPAT
+ /* v1.2 returns the base type of an array field, work around this */
+ {
+ hid_t new_f_memb; /* datatype for array, if necessary */
+ int arrndims; /* Array rank for reading */
+ size_t dims[H5S_MAX_RANK]; /* Array dimensions for reading */
+ hsize_t arrdims[H5S_MAX_RANK]; /* Array dimensions for reading */
+ int j; /* Local index variable */
+
+ /* Get the array dimensions */
+ arrndims=H5Tget_member_dims(f_type,i,dims,NULL);
+
+ /* Patch up array information */
+ if(arrndims>0) {
+ for(j=0; j<arrndims; j++)
+ arrdims[j]=dims[j];
+ new_f_memb=H5Tarray_create(f_memb,arrndims,arrdims,NULL);
+ H5Tclose(f_memb);
+ f_memb=new_f_memb;
+ } /* end if */
+ }
+#endif /* WANT_H5_V1_2_COMPAT */
memb[i] = h5tools_fixtype(f_memb);
H5Tclose(f_memb);
@@ -1087,18 +1115,18 @@ h5tools_fixtype(hid_t f_type)
done:
/* Clean up temp buffers */
if (memb && name) {
- int j;
+ register int j;
for (j = 0; j < nmembs; j++) {
if (memb[j] >= 0)
H5Tclose(memb[j]);
if (name[j])
- HDfree(name[j]);
+ free(name[j]);
}
- HDfree(memb);
- HDfree(name);
+ free(memb);
+ free(name);
}
return m_type;
@@ -1151,7 +1179,7 @@ h5tools_dump_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type,
stream = stdout;
if (!info) {
- HDmemset(&info_dflt, 0, sizeof info_dflt);
+ memset(&info_dflt, 0, sizeof info_dflt);
info = &info_dflt;
}
@@ -1221,7 +1249,7 @@ h5tools_dump_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, hid_t type,
stream = stdout;
if (!info) {
- HDmemset(&info_dflt, 0, sizeof(info_dflt));
+ memset(&info_dflt, 0, sizeof(info_dflt));
info = &info_dflt;
}
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