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-rw-r--r--tools/h5tools.c273
1 files changed, 119 insertions, 154 deletions
diff --git a/tools/h5tools.c b/tools/h5tools.c
index 78a8258..0a62934 100644
--- a/tools/h5tools.c
+++ b/tools/h5tools.c
@@ -26,7 +26,7 @@ int compound_data;
int nCols = 80;
FILE *rawdatastream; /* should initialize to stdout but gcc moans about it */
-static int h5tools_init_g = 0; /* if h5tools lib has been initialized */
+static int h5tools_init_g = 0; /* if h5tools lib has been initialized */
int print_data(hid_t oid, hid_t _p_type, int obj_data);
@@ -126,9 +126,10 @@ static int h5dump_vlen_dset(FILE *, const h5dump_t *, hid_t, hid_t, int);
void
h5tools_init(void)
{
- if (!h5tools_init_g){
+ if (!h5tools_init_g) {
if (!rawdatastream)
rawdatastream = stdout;
+
h5tools_init_g++;
}
}
@@ -152,13 +153,14 @@ h5tools_init(void)
void
h5tools_close(void)
{
- if (h5tools_init_g){
- if (rawdatastream && rawdatastream != stdout){
+ if (h5tools_init_g) {
+ if (rawdatastream && rawdatastream != stdout) {
if (fclose(rawdatastream))
perror("closing rawdatastream");
else
rawdatastream = NULL;
}
+
h5tools_init_g = 0;
}
}
@@ -584,12 +586,14 @@ h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info)
/* Print block information */
if (nblocks > 0) {
- int i, j;
+ int i;
ptdata = malloc(nblocks * ndims * 2 * sizeof(ptdata[0]));
H5Sget_select_hyper_blocklist(region, 0, nblocks, ptdata);
for (i = 0; i < nblocks; i++) {
+ int j;
+
h5dump_str_append(str, info->dset_blockformat_pre,
i ? "," OPTIONAL_LINE_BREAK " " : "",
(unsigned long)i);
@@ -610,12 +614,14 @@ h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info)
/* Print point information */
if (npoints > 0) {
- int i, j;
+ int i;
ptdata = malloc(npoints * ndims * sizeof(ptdata[0]));
H5Sget_select_elem_pointlist(region, 0, npoints, ptdata);
for (i = 0; i < npoints; i++) {
+ int j;
+
h5dump_str_append(str, info->dset_ptformat_pre ,
i ? "," OPTIONAL_LINE_BREAK " " : "",
(unsigned long)i);
@@ -934,13 +940,12 @@ h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info,
* indentation. Be warned that column number calculations will be
* incorrect and that object indices at the beginning of the line
* will be missing (h5dump doesn't display them anyway). */
- if (ctx->indent_level >= 0 &&
- str->len && '\n'==str->s[str->len-1]) {
+ if (ctx->indent_level >= 0 && str->len &&
+ str->s[str->len - 1] == '\n') {
h5dump_str_append(str, OPT(info->line_pre, ""), "");
- for (x=0; x<ctx->indent_level+1; x++) {
+ for (x = 0; x < ctx->indent_level + 1; x++)
h5dump_str_append(str, "%s", OPT(info->line_indent, ""));
- }
}
/* The name */
@@ -997,13 +1002,12 @@ h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info,
* (h5dump doesn't display them anyway). */
h5dump_str_append(str, "%s", OPT(info->cmpd_end, ""));
- if (ctx->indent_level >= 0 &&
- str->len && '\n'==str->s[str->len-1]) {
+ if (ctx->indent_level >= 0 && str->len &&
+ str->s[str->len - 1] == '\n') {
h5dump_str_append(str, OPT(info->line_pre, ""), "");
- for (x = 0; x < ctx->indent_level; x++) {
+ for (x = 0; x < ctx->indent_level; x++)
h5dump_str_append(str, "%s", OPT(info->line_indent, ""));
- }
}
h5dump_str_append(str, "%s", OPT(info->cmpd_suf, "}"));
@@ -1273,7 +1277,7 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++){
/* Render the element */
h5dump_str_reset(&buffer);
- h5dump_sprint(&buffer, info, container, type, mem+i*size, ctx);
+ h5dump_sprint(&buffer, info, container, type, mem + i * size, ctx);
if (i + 1 < nelmts || 0 == (flags & END_OF_DATA))
h5dump_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
@@ -1306,9 +1310,11 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
}
}
- /* we need to break after each row of a dimension---> we should
+ /*
+ * We need to break after each row of a dimension---> we should
* break at the end of the each last dimension well that is the
- * way the dumper did it before */
+ * way the dumper did it before
+ */
if (info->arr_linebreak && ctx->cur_elmt){
if ((ctx->cur_elmt % ctx->size_last_dim) == 0)
ctx->need_prefix = TRUE;
@@ -1351,8 +1357,10 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
* start a new line.
*/
- /* added the info->skip_first because the dumper does not want
- * this check to happen for the first line */
+ /*
+ * Added the info->skip_first because the dumper does not want
+ * this check to happen for the first line
+ */
if ((!info->skip_first || i) &&
(ctx->cur_column + strlen(section) +
strlen(OPT(info->elmt_suf2, " ")) +
@@ -1438,13 +1446,12 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
#endif
/*
- * Check that everything looks okay. The dimensionality must not be too
+ * Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof ctx);
ctx.indent_level = indentlevel;
- ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
f_space = H5Dget_space(dset);
ctx.ndims = H5Sget_simple_extent_ndims(f_space);
@@ -1467,13 +1474,13 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
ctx.size_last_dim = total_size[ctx.ndims - 1];
/*
- * Determine the strip mine size and allocate a buffer. The strip mine is
+ * Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
p_type_nbytes = H5Tget_size(p_type);
for (i = ctx.ndims, sm_nbytes = p_type_nbytes; i > 0; --i) {
- sm_size[i - 1] = MIN (total_size[i - 1], H5DUMP_BUFSIZE / sm_nbytes);
+ sm_size[i - 1] = MIN(total_size[i - 1], H5DUMP_BUFSIZE / sm_nbytes);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
@@ -1490,7 +1497,7 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
/* Calculate the hyperslab size */
if (ctx.ndims > 0) {
for (i = 0, hs_nelmts = 1; i < (hsize_t)ctx.ndims; i++) {
- hs_size[i] = MIN(total_size[i]-hs_offset[i], sm_size[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];
}
@@ -1504,7 +1511,7 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
H5Sselect_all(sm_space);
hs_nelmts = 1;
}
-
+
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
return -1;
@@ -1573,13 +1580,14 @@ h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type,
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof(ctx));
- ctx.indent_level = indentlevel;
- ctx.need_prefix = 1;
ctx.ndims = H5Sget_simple_extent_ndims(space);
if ((size_t)ctx.ndims > NELMTS(ctx.p_min_idx))
return -1;
+ ctx.indent_level = indentlevel;
+ ctx.need_prefix = 1;
+
/* Assume entire data space to be printed */
for (i = 0; i < (hsize_t)ctx.ndims; i++)
ctx.p_min_idx[i] = 0;
@@ -1593,7 +1601,6 @@ h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type,
return 0; /*nothing to print*/
ctx.size_last_dim = ctx.p_max_idx[ctx.ndims - 1];
- ctx.indent_level = indentlevel;
/* Print it */
h5dump_simple_data(stream, info, -1/*no dataset*/, &ctx,
@@ -1702,7 +1709,7 @@ h5dump_fixtype(hid_t f_type)
memb = calloc(nmembs, sizeof(hid_t));
name = calloc(nmembs, sizeof(char *));
ndims = calloc(nmembs, sizeof(int));
- dims = calloc(nmembs*4, sizeof(size_t));
+ dims = calloc(nmembs * 4, sizeof(size_t));
for (i = 0, size = 0; i < nmembs; i++) {
int j;
@@ -1890,94 +1897,64 @@ done:
return status;
}
-static
-void *vlcustom_alloc(size_t size, void *info)
-{
- void *ret_value = NULL;
- int *mem_used = (int *)info;
- size_t extra = MAX(sizeof(void *), sizeof(size_t));
-
- if ((ret_value = HDmalloc(extra + size)) != NULL) {
- *(size_t *)ret_value = size;
- *mem_used += size;
- }
-
- ret_value = ((unsigned char *)ret_value) + extra;
- return ret_value;
-}
-
-static
-void vlcustom_free(void *_mem, void *info)
-{
- if (_mem) {
- int *mem_used = (int *)info;
- size_t extra = MAX(sizeof(void *), sizeof(size_t));
- unsigned char *mem = ((unsigned char *)_mem) - extra;
-
- *mem_used -= *(size_t *)mem;
- HDfree(mem);
- }
-}
-
+/*-------------------------------------------------------------------------
+ * Function: h5dump_vlen_dset
+ *
+ * Purpose: Dump variable length datatypes to the STREAM. We can only
+ * support atomic, 1-dimensional variable length data since other
+ * types would be way too complicated to dump.
+ *
+ * Return: Success: 0
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Bill Wendling
+ * Wednesday, November 8, 2000
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
static int
h5dump_vlen_dset(FILE *stream, const h5dump_t *info, hid_t dset,
hid_t type, int indentlevel)
{
- hvl_t *rdata = NULL; /*information to read in */
+ h5dump_context_t ctx; /*print context */
hid_t base_type; /*the base type of the VL data */
hid_t xfer_pid; /*dataset transfer property list id */
hid_t f_space; /*file data space */
hsize_t dims[H5S_MAX_RANK]; /*size of the dimensions */
+ hid_t mem_space;
const char *bad_type;
- hsize_t mem_needed;
- size_t ncols = 80;
herr_t ret;
-
- /* Print info */
- size_t size; /*size of memory type */
- hsize_t p_nelmts; /*total selected elmts */
- int mem_used = 0;
+ hssize_t start = 0, count = 1;
unsigned int i;
- base_type = H5Tget_super(type);
- xfer_pid = H5Pcreate(H5P_DATA_XFER);
-
- if (xfer_pid == FAIL)
- return FAIL;
-
- ret = H5Pset_vlen_mem_manager(xfer_pid, vlcustom_alloc, &mem_used,
- vlcustom_free, &mem_used);
-
- if (ret == FAIL) {
- H5Pclose(xfer_pid);
- return FAIL;
- }
-
+ memset(&ctx, 0, sizeof(h5dump_context_t));
+ ctx.indent_level = indentlevel;
+ ctx.need_prefix = 1;
f_space = H5Dget_space(dset);
+ ctx.ndims = H5Sget_simple_extent_ndims(f_space);
- if ((size_t)H5Sget_simple_extent_ndims(f_space) > 1) {
- fprintf(stream,
- "Multidimensional variable length datatypes not supported\n");
+ if (ctx.ndims > 1) {
ret = FAIL;
- goto done;
+ goto free_space;
}
- H5Dvlen_get_buf_size(dset, type, f_space, &mem_needed);
-
- H5Sget_simple_extent_dims(f_space, dims, NULL);
- rdata = HDmalloc(dims[0] * sizeof(hvl_t));
+ base_type = H5Tget_super(type);
+ xfer_pid = H5Pcreate(H5P_DATA_XFER);
- if (!rdata) {
+ if (xfer_pid == FAIL) {
ret = FAIL;
- goto done;
+ goto free_xfer;
}
- ret = H5Dread(dset, type, H5S_ALL, H5S_ALL, xfer_pid, rdata);
-
- if (info->line_ncols > 0)
- ncols = info->line_ncols;
+ H5Sget_simple_extent_dims(f_space, dims, NULL);
+ ctx.size_last_dim = dims[ctx.ndims - 1];
- size = H5Tget_size(base_type);
+ /* Assume entire data space to be printed */
+ for (i = 0; i < (hsize_t)ctx.ndims; i++)
+ ctx.p_min_idx[i] = 0;
recheck:
switch (H5Tget_class(base_type)) {
@@ -2016,78 +1993,66 @@ recheck:
bad_type = "H5T_TIME";
default:
fprintf(stream,
- "Dumper doesn't support %s variable length datatype at this time\n",
- bad_type ? bad_type : "(null)");
- goto done;
+ "Dumper doesn't support %s variable length datatype at this time.\n",
+ OPT(bad_type, "(null)"));
+ goto free_xfer;
}
+ /* Create a simple memory space so that we can read in the hvl_t object */
+ mem_space = H5Screate_simple(0, NULL, NULL);
+
for (i = 0; i < dims[0]; i++) {
- hsize_t j;
-
- p_nelmts = rdata[i].len;
-
-#define OUTPUT_ELEMENTS(type, fmt) { \
- unsigned char *_data = (unsigned char *)rdata[i].p; \
- \
- indentation(indent + COL); \
- for (j = 0; j < p_nelmts; j++, _data += size) { \
- fprintf(stream, "%" ## fmt ## "%s", *(type *)_data, \
- j == p_nelmts - 1 ? "\n" : ", "); \
- } \
-}
+ unsigned char *buffer;
+ hsize_t mem_needed;
+ herr_t ret;
+ hvl_t *vldata;
+ h5dump_context_t tmp;
- switch (H5Tget_class(base_type)) {
- case H5T_INTEGER:
- if (H5Tget_sign(base_type) == H5T_SGN_NONE) {
- if (size <= sizeof(unsigned char)) {
- OUTPUT_ELEMENTS(unsigned char, "c");
- } else if (size <= sizeof(unsigned short)) {
- OUTPUT_ELEMENTS(unsigned short, "dhu");
- } else if (size <= sizeof(unsigned int)) {
- OUTPUT_ELEMENTS(unsigned int, "u");
- } else if (size <= sizeof(unsigned long)) {
- OUTPUT_ELEMENTS(unsigned long, "lu");
- } else {
- OUTPUT_ELEMENTS(unsigned long_long, PRINTF_LL_WIDTH "u");
- }
- } else {
- if (size <= sizeof(char)) {
- OUTPUT_ELEMENTS(char, "c");
- } else if (size <= sizeof(short)) {
- OUTPUT_ELEMENTS(short, "dh");
- } else if (size <= sizeof(int)) {
- OUTPUT_ELEMENTS(int, "d");
- } else if (size <= sizeof(long)) {
- OUTPUT_ELEMENTS(long, "ld");
- } else {
- OUTPUT_ELEMENTS(long_long, PRINTF_LL_WIDTH "d");
- }
- }
+ start = i;
+ ret = H5Sselect_hyperslab(f_space, H5S_SELECT_SET, &start, NULL, &count, NULL);
- break;
+ if (ret == FAIL)
+ goto free_mem;
- case H5T_FLOAT:
- if (size <= sizeof(float)) {
- OUTPUT_ELEMENTS(float, "e");
- } else if (size <= sizeof(double)) {
- OUTPUT_ELEMENTS(double, "e");
- } else {
- OUTPUT_ELEMENTS(long double, "e");
- }
+ ret = H5Dvlen_get_buf_size(dset, type, f_space, &mem_needed);
- break;
+ if (ret == FAIL)
+ goto free_mem;
- default:
- break;
+ mem_needed += sizeof(hvl_t);
+ buffer = calloc(mem_needed, 1);
+
+ if (!buffer) {
+ indentation(indentlevel);
+ fprintf(stream,
+ "Unable to allocate %ld bytes for variable length data.\n",
+ (long)mem_needed);
+ continue;
}
- }
- ret = H5Dvlen_reclaim(type, f_space, xfer_pid, rdata);
+ ret = H5Dread(dset, type, mem_space, f_space, H5P_DEFAULT, buffer);
-done:
+ if (ret == FAIL)
+ goto free_mem;
+
+ vldata = (hvl_t *)buffer;
+
+ /* I cast, therefore, I think I know what I am doing */
+ tmp = ctx;
+ h5dump_simple_data(stream, info, dset, &ctx,
+ START_OF_DATA | END_OF_DATA,
+ vldata->len, base_type, (void *)vldata->p);
+ ctx = tmp;
+ fputs("\n", stream);
+ free(buffer);
+ }
+
+free_mem:
+ H5Sclose(mem_space);
+free_xfer:
H5Pclose(xfer_pid);
+free_space:
H5Sclose(f_space);
- free(rdata);
return ret;
}