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rest_vol_dataset: (fix) Memory-side hyperslab
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- The function RV_dataspace_is_contiguous() will return
  a non-regular hyperslab as non-contiguous in memory.
- Generalized the function RV_convert_start_to_offset() such
  it works for both regular and non-regular hyperslab.
- For completeness handle the other selection types explicitly
  in the function RV_dataspace_is_contiguous() and
  RV_convert_start_to_offset().
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@jwsblokland
jwsblokland committed Sep 14, 2023
1 parent 3267575 commit 7e8274d
Showing 1 changed file with 112 additions and 76 deletions.
188 changes: 112 additions & 76 deletions src/rest_vol_dataset.c
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Original file line number Diff line number Diff line change
Expand Up @@ -996,8 +996,7 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for the 'write_body' values");
if (H5Dgather(transfer_info[i].mem_space_id, buf[i], transfer_info[i].mem_type_id,
write_body_len, transfer_info[i].u.write_info.write_body, NULL,
transfer_info[i].u.write_info.write_body) < 0)
write_body_len, transfer_info[i].u.write_info.write_body, NULL, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't gather data to write buffer");
buf[i] = transfer_info[i].u.write_info.write_body;
}
Expand Down Expand Up @@ -1085,8 +1084,10 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
transfer_info[i].u.write_info.base64_encoded_values);
#endif

if (transfer_info[i].u.write_info.write_body)
if (transfer_info[i].u.write_info.write_body) {
RV_free(transfer_info[i].u.write_info.write_body);
transfer_info[i].u.write_info.write_body = NULL;
}
write_body_len = (strlen(fmt_string) - 4) + selection_body_len + value_body_len;
if (NULL == (transfer_info[i].u.write_info.write_body = RV_malloc(write_body_len + 1)))
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate space for write buffer");
Expand Down Expand Up @@ -4182,6 +4183,7 @@ RV_dataspace_selection_is_contiguous(hid_t space_id)
{
htri_t ret_value = TRUE;
hbool_t whole = TRUE;
htri_t regular = TRUE;
hsize_t *dims = NULL;
hsize_t *start = NULL;
hsize_t *stride = NULL;
Expand All @@ -4192,70 +4194,86 @@ RV_dataspace_selection_is_contiguous(hid_t space_id)
hssize_t npoints, nblocks;

if ((npoints = H5Sget_select_npoints(space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve number of selected points");
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get number of selected points");
if (npoints < 2)
FUNC_GOTO_DONE(TRUE);

if ((ndims = H5Sget_simple_extent_ndims(space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace dimensionality");
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get dataspace dimensionality");
if (!ndims)
FUNC_GOTO_DONE(TRUE);

if (H5S_SEL_HYPERSLABS == H5Sget_select_type(space_id)) {
if (NULL == (dims = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*dims))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for dimension 'dims' values");

if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get dataspace dimension size");

if (NULL == (start = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*start))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'start' values");
if (NULL == (stride = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*stride))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'stride' values");
if (NULL == (count = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*count))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'count' values");
if (NULL == (block = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*block))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'block' values");

if (nblocks = H5Sget_select_hyper_nblocks(space_id) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get number of hyperslab blocks");

if (H5Sget_regular_hyperslab(space_id, start, stride, count, block) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get regular hyperslab selection");

/* For contiguous, the stride should be 1. */
for (i = 0; i < ndims; i++) {
if (stride[i] > 1)
switch (H5Sget_select_type(space_id)) {
case H5S_SEL_HYPERSLABS: {
if ((regular = H5Sis_regular_hyperslab(space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't determine if the hyperslab is regular");
if (!regular)
FUNC_GOTO_DONE(FALSE);
}

if (nblocks > 1) {
/* Multiple blocks: count should be 1 except for the last dimension (fastest) */
for (i = 0; i < ndims - 1; i++) {
if (count[i] > 1)
if (NULL == (dims = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*dims))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for dimension 'dims' values");

if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get dataspace dimension size");

if (NULL == (start = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*start))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'start' values");
if (NULL == (stride = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*stride))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'stride' values");
if (NULL == (count = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*count))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'count' values");
if (NULL == (block = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*block))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL,
"can't allocate space for hyperslab selection 'block' values");

if (nblocks = H5Sget_select_hyper_nblocks(space_id) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get number of hyperslab blocks");

if (H5Sget_regular_hyperslab(space_id, start, stride, count, block) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get regular hyperslab selection");

/* For contiguous, the stride should be 1. */
for (i = 0; i < ndims; i++) {
if (stride[i] > 1)
FUNC_GOTO_DONE(FALSE);
}
}

/* For contiguous, all faster running dimensions than the current dimension should be selected
* completely */
whole = (start[ndims - 1] == 0) && (count[ndims - 1] * block[ndims - 1] == dims[ndims - 1]);
for (i = ndims - 2; i >= 0; i--) {
if ((dims[i] > 1) && (count[i] * block[i] > 1) && !whole)
FUNC_GOTO_DONE(FALSE);
if (nblocks > 1) {
/* Multiple blocks: count should be 1 except for the last dimension (fastest) */
for (i = 0; i < ndims - 1; i++) {
if (count[i] > 1)
FUNC_GOTO_DONE(FALSE);
}
}

whole = whole && (start[i] == 0) && (count[i] * block[i] == dims[i]);
}
} /* end if*/
else if (H5S_SEL_POINTS == H5Sget_select_type(space_id)) {
/* Assumption: any point selection is non-contiguous in memory */
FUNC_GOTO_DONE(FALSE);
} /* end else if */
/* For contiguous, all faster running dimensions than the current dimension should be selected
* completely */
whole = (start[ndims - 1] == 0) && (count[ndims - 1] * block[ndims - 1] == dims[ndims - 1]);
for (i = ndims - 2; i >= 0; i--) {
if ((dims[i] > 1) && (count[i] * block[i] > 1) && !whole)
FUNC_GOTO_DONE(FALSE);

whole = whole && (start[i] == 0) && (count[i] * block[i] == dims[i]);
}
break;
} /* H5S_SEL_HYPERSLABS */

case H5S_SEL_POINTS:
/* Assumption: any point selection is non-contiguous in memory */
FUNC_GOTO_DONE(FALSE);
break;

case H5S_SEL_ALL:
case H5S_SEL_ERROR:
case H5S_SEL_N:
case H5S_SEL_NONE:
default:
FUNC_GOTO_DONE(TRUE);
} /* end switch */

done:
if (block)
Expand Down Expand Up @@ -4287,40 +4305,58 @@ RV_convert_start_to_offset(hid_t space_id)
{
hsize_t *dims = NULL;
hsize_t *start = NULL;
hsize_t *end = NULL;
hssize_t ret_value = 0;
int ndims, i;

if (H5S_SEL_HYPERSLABS == H5Sget_select_type(space_id)) {
if ((ndims = H5Sget_simple_extent_ndims(space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1, "can't retrieve dataspace dimensionality");
switch (H5Sget_select_type(space_id)) {
case H5S_SEL_HYPERSLABS: {
if ((ndims = H5Sget_simple_extent_ndims(space_id)) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1, "can't retrieve dataspace dimensionality");

if (NULL == (dims = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*dims))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, -1,
"can't allocate space for dimension 'dims' values");
if (NULL == (dims = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*dims))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, -1,
"can't allocate space for dimension 'dims' values");

if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1, "can't get dataspace dimension size");
if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1, "can't get dataspace dimension size");

if (NULL == (start = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*start))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, -1,
"can't allocate space for hyperslab selection 'start' values");
if (NULL == (start = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*start))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, -1,
"can't allocate space for hyperslab selection 'start' values");
if (NULL == (end = (hsize_t *)RV_malloc((size_t)ndims * sizeof(*end))))
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, -1,
"can't allocate space for hyperslab selection 'end' values");

if (H5Sget_regular_hyperslab(space_id, start, NULL, NULL, NULL) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1, "can't get regular hyperslab selection");
if (H5Sget_select_bounds(space_id, start, end) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, -1,
"can't get bounding box of hyperslab selection");

ret_value = start[0];
for (i = 1; i < ndims; i++) {
ret_value = ret_value * dims[i] + start[i];
}
} /* end if */
else if (H5S_SEL_POINTS == H5Sget_select_type(space_id)) {
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, -1,
"for point selection, computing the offset is not supported");
} /* end else if */
ret_value = start[0];
for (i = 1; i < ndims; i++) {
ret_value = ret_value * dims[i] + start[i];
}
break;
} /* H5S_SEL_HYPERSLABS */

case H5S_SEL_POINTS:
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, -1,
"for point selection, computing the offset is not supported");
break;

case H5S_SEL_ALL:
case H5S_SEL_ERROR:
case H5S_SEL_N:
case H5S_SEL_NONE:
default:
ret_value = 0;
} /* end switch */

done:
if (dims)
RV_free(dims);
if (end)
RV_free(end);
if (start)
RV_free(start);

Expand Down

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