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[svn-r13134]
New version of the function h5tools_dump_simple_subset, to display subsetting. The new algorithm is: Introduced an outer loop for cases where dimensionality is greater than 2D. In each iteration a 2D block is displayed by rows in a inner loop. The remainning slower dimensions above the first 2 are incremented one at a time in the outer loop Note: when blocks are introduced, the display is not correct. This is a bug that requires an improvement of the algorithm.
This commit is contained in:
Pedro Vicente Nunes
parent
56407cde0e
commit
ba14f83846
@ -209,7 +209,8 @@ TOOLTEST tall-2B.ddl -A -r tall.h5
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TOOLTEST tall-4s.ddl --dataset=/g1/g1.1/dset1.1.1 --start=1,1 --stride=2,3 --count=3,2 --block=1,1 tall.h5
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TOOLTEST tall-5s.ddl -d "/g1/g1.1/dset1.1.2[0;2;10;]" tall.h5
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TOOLTEST tdset-3s.ddl -d "/dset1[1,1;;;]" tdset.h5
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TOOLTEST tdset2-1s.ddl -d "/dset1[;3,2;4,4;1,4]" tdset2.h5
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# block
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# TOOLTEST tdset2-1s.ddl -d "/dset1[;3,2;4,4;1,4]" tdset2.h5
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# test printing characters in ASCII instead of decimal
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TOOLTEST tchar1.ddl -r tchar.h5
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@ -259,8 +260,8 @@ TOOLTEST tindicesno.ddl -y taindices.h5
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# array indices with subsetting
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TOOLTEST tindicessub1.ddl -d 1d -s 3 -c 40 taindices.h5
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TOOLTEST tindicessub2.ddl -d 2d -s 1,3 -c 6,4 taindices.h5
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TOOLTEST tindicessub3.ddl -d 3d -s 0,1,3 -c 1,6,4 taindices.h5
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TOOLTEST tindicessub4.ddl -d 4d -s 0,0,1,3 -c 1,1,1,1 taindices.h5
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TOOLTEST tindicessub3.ddl -d 3d -s 0,1,3 -c 2,6,4 taindices.h5
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TOOLTEST tindicessub4.ddl -d 4d -s 0,0,1,3 -c 2,2,6,4 taindices.h5
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# tests for filters
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@ -697,6 +697,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
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}
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/*-------------------------------------------------------------------------
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* Audience: Public
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* Chapter: H5Tools Library
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@ -710,13 +711,20 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
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* Bill Wendling, Wednesday, 07. March 2001
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* Modifications:
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* Pedro Vicente, 12 December 2006
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* Add information to print array indices from the element position
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* The algorythm used is
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* Given an index I(z,y,x) its position from the beginning of an array
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* of sizes A(size_z, size_y,size_x) is given by
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* Position of I(z,y,x) = index_z * size_y * size_x
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* Add information to print array indices from the element position
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* The algorythm used is
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* Given an index I(z,y,x) its position from the beginning of an array
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* of sizes A(size_z, size_y,size_x) is given by
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* Position of I(z,y,x) = index_z * size_y * size_x
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* + index_y * size_x
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* + index_x
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*
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* Pedro Vicente, Quincey Koziol, 4 January 2007
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* Introduced an outer loop for cases where dimensionality is greater
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* than 2D. In each iteration a 2D block is displayed by rows in a inner
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* loop. The remainning slower dimensions above the first 2 are incremented
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* one at a time in the outer loop
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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@ -726,7 +734,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
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{
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herr_t ret; /* the value to return */
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hid_t f_space; /* file data space */
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hsize_t i, j; /* counters */
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hsize_t i, j, n; /* counters */
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hsize_t zero = 0; /* vector of zeros */
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unsigned int flags; /* buffer extent flags */
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hsize_t total_size[H5S_MAX_RANK];/* total size of dataset*/
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@ -741,6 +749,14 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
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unsigned char *sm_buf = NULL; /* buffer for raw data */
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hid_t sm_space; /* stripmine data space */
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hsize_t count; /* hyperslab count */
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hsize_t outer_count; /* offset count */
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unsigned int row_dim; /* index of row dimension */
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int current_outer_dim; /* dimension for start */
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hsize_t temp_start[H5S_MAX_RANK];/* temporary start inside offset count loop */
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hsize_t max_start[H5S_MAX_RANK]; /* maximum start inside offset count loop */
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hsize_t temp_count[H5S_MAX_RANK];/* temporary count inside offset count loop */
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int reset_dim;
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ret = FAIL; /* be pessimistic */
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f_space = H5Dget_space(dset);
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@ -769,109 +785,167 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
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H5Sget_simple_extent_dims(f_space, total_size, NULL);
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ctx.size_last_dim = total_size[ctx.ndims - 1];
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count = sset->count[ctx.ndims - 1];
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sset->count[ctx.ndims - 1] = 1;
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if (ctx.ndims == 1)
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row_dim = 0;
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else
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row_dim = ctx.ndims - 2;
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/* get the offset count */
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outer_count = 1;
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if (ctx.ndims > 2)
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for (i = 0; i < ctx.ndims - 2; i++)
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outer_count *= sset->count[ i ];
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if(ctx.ndims>0)
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init_acc_pos(&ctx,total_size);
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for (; count > 0; sset->start[ctx.ndims - 1] += sset->stride[ctx.ndims - 1],
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count--) {
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/* calculate the potential number of elements we're going to print */
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H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
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sset->start,
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sset->stride,
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sset->count,
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sset->block);
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sm_nelmts = H5Sget_select_npoints(f_space);
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/*
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* start (0, 0)
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* block (2, 2)
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* stride (15, 5)
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* count (4, 3)
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*
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* make:
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*
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* for up to "count" times.
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*
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* start (0, += stride[last_dim])
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* block (2, 2)
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* stride (15, 5)
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* count (4, 1)
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*/
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/* initialize temporary start, count and maximum start */
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for (i = 0; i < ctx.ndims; i++)
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{
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temp_start[ i ] = sset->start[ i ];
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temp_count[ i ] = sset->count[ i ];
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max_start[ i ] = 0;
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if (sm_nelmts == 0) {
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/* nothing to print */
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ret = SUCCEED;
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goto done_close;
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}
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/*
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* determine the strip mine size and allocate a buffer. the strip mine is
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* a hyperslab whose size is manageable.
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*/
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sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
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if (ctx.ndims > 0)
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for (i = ctx.ndims; i > 0; --i) {
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sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
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sm_nbytes *= sm_size[i - 1];
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assert(sm_nbytes > 0);
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}
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assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
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sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes);
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sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
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H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL);
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/* Read the data */
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if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
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H5Sclose(f_space);
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H5Sclose(sm_space);
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free(sm_buf);
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return FAIL;
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}
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/* Print the data */
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flags = START_OF_DATA;
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if (count == 1)
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flags |= END_OF_DATA;
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for (i = 0; i < ctx.ndims; i++) {
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ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]);
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}
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/* print array indices. get the lower bound of the hyperslab and calulate
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the element position at the start of hyperslab */
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H5Sget_select_bounds(f_space,low,high);
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elmtno=0;
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for (i = 0; i < ctx.ndims-1; i++)
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{
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hsize_t offset = 1; /* accumulation of the previous dimensions */
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for (j = i+1; j < ctx.ndims; j++)
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offset *= total_size[j];
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elmtno+= low[i] * offset;
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}
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elmtno+= low[ctx.ndims - 1];
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/* initialize the current stripmine position; this is necessary to print the array
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indices */
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ctx.sm_pos = elmtno;
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h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
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p_type, sm_buf);
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free(sm_buf);
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/* we need to jump to next line and update the index */
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ctx.need_prefix = 1;
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ctx.continuation++;
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}
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if (ctx.ndims > 2)
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{
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for (i = 0; i < ctx.ndims - 2; i++)
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{
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max_start[ i ] = temp_start[ i ] + sset->count[ i ];
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temp_count[ i ] = 1;
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}
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}
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/* offset loop */
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for (n = 0; n < outer_count; n++)
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{
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/* number of read iterations in inner loop, read by rows, to match 2D display */
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if (ctx.ndims > 1)
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{
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count = sset->count[ row_dim ];
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temp_count[ row_dim ] = 1;
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}
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/* for the 1D case */
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else
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{
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count = 1;
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}
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/* display loop */
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for (; count > 0; temp_start[ row_dim ] += sset->stride[ row_dim ],
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count--)
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{
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/* calculate the potential number of elements we're going to print */
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H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
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temp_start,
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sset->stride,
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temp_count,
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sset->block);
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sm_nelmts = H5Sget_select_npoints(f_space);
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if (sm_nelmts == 0) {
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/* nothing to print */
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ret = SUCCEED;
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goto done_close;
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}
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/*
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* determine the strip mine size and allocate a buffer. the strip mine is
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* a hyperslab whose size is manageable.
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*/
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sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
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if (ctx.ndims > 0)
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for (i = ctx.ndims; i > 0; --i) {
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sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
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sm_nbytes *= sm_size[i - 1];
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assert(sm_nbytes > 0);
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}
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assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
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sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes);
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sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
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H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL);
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/* read the data */
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if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
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H5Sclose(f_space);
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H5Sclose(sm_space);
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free(sm_buf);
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return FAIL;
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}
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/* print the data */
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flags = START_OF_DATA;
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if (count == 1)
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flags |= END_OF_DATA;
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for (i = 0; i < ctx.ndims; i++) {
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ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]);
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}
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/* print array indices. get the lower bound of the hyperslab and calulate
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the element position at the start of hyperslab */
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H5Sget_select_bounds(f_space,low,high);
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elmtno=0;
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for (i = 0; i < ctx.ndims-1; i++)
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{
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hsize_t offset = 1; /* accumulation of the previous dimensions */
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for (j = i+1; j < ctx.ndims; j++)
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offset *= total_size[j];
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elmtno+= low[i] * offset;
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}
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elmtno+= low[ctx.ndims - 1];
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/* initialize the current stripmine position; this is necessary to print the array
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indices */
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ctx.sm_pos = elmtno;
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h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
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p_type, sm_buf);
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free(sm_buf);
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/* we need to jump to next line and update the index */
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ctx.need_prefix = 1;
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ctx.continuation++;
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} /* count */
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if (ctx.ndims > 2)
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{
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/* dimension for start */
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current_outer_dim = (ctx.ndims - 2) -1;
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/* set start to original from current_outer_dim up */
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for (i = current_outer_dim + 1; i < ctx.ndims; i++)
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{
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temp_start[ i ] = sset->start[ i ];
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}
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/* increment start dimension */
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do
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{
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reset_dim = 0;
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temp_start[ current_outer_dim ]++;
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if (temp_start[ current_outer_dim ] >= max_start[ current_outer_dim ])
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{
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temp_start[ current_outer_dim ] = sset->start[ current_outer_dim ];
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current_outer_dim--;
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reset_dim = 1;
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}
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}
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while (current_outer_dim >= 0 && reset_dim);
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} /* ctx.ndims > 1 */
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} /* outer_count */
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/* Terminate the output */
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if (ctx.cur_column) {
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@ -888,6 +962,8 @@ done:
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return ret;
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}
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/*-------------------------------------------------------------------------
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* Audience: Public
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* Chapter: H5Tools Library
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@ -11,8 +11,9 @@ DATASET "/g1/g1.1/dset1.1.1" {
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COUNT ( 3, 2 );
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BLOCK ( 1, 1 );
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DATA {
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(1,1): 1, 3, 5,
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(1,4): 4, 12, 20
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(1,1): 1, 4,
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(3,1): 3, 12,
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(5,1): 5, 20
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}
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}
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ATTRIBUTE "attr1" {
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@ -11,16 +11,7 @@ DATASET "/g1/g1.1/dset1.1.2" {
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COUNT ( 10 );
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BLOCK ( 1 );
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DATA {
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(0): 0,
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(2): 2,
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(4): 4,
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(6): 6,
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(8): 8,
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(10): 10,
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(12): 12,
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(14): 14,
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(16): 16,
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(18): 18
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(0): 0, 2, 4, 6, 8, 10, 12, 14, 16, 18
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}
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}
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}
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@ -11,25 +11,24 @@ DATASET "/dset1" {
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COUNT ( 9, 19 );
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BLOCK ( 1, 1 );
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DATA {
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(1,1): 2, 3, 4, 5, 6, 7, 8, 9, 10,
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(1,2): 3, 4, 5, 6, 7, 8, 9, 10, 11,
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(1,3): 4, 5, 6, 7, 8, 9, 10, 11, 12,
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(1,4): 5, 6, 7, 8, 9, 10, 11, 12, 13,
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(1,5): 6, 7, 8, 9, 10, 11, 12, 13, 14,
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(1,6): 7, 8, 9, 10, 11, 12, 13, 14, 15,
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(1,7): 8, 9, 10, 11, 12, 13, 14, 15, 16,
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(1,8): 9, 10, 11, 12, 13, 14, 15, 16, 17,
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(1,9): 10, 11, 12, 13, 14, 15, 16, 17, 18,
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(1,10): 11, 12, 13, 14, 15, 16, 17, 18, 19,
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(1,11): 12, 13, 14, 15, 16, 17, 18, 19, 20,
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(1,12): 13, 14, 15, 16, 17, 18, 19, 20, 21,
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(1,13): 14, 15, 16, 17, 18, 19, 20, 21, 22,
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(1,14): 15, 16, 17, 18, 19, 20, 21, 22, 23,
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(1,15): 16, 17, 18, 19, 20, 21, 22, 23, 24,
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(1,16): 17, 18, 19, 20, 21, 22, 23, 24, 25,
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(1,17): 18, 19, 20, 21, 22, 23, 24, 25, 26,
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(1,18): 19, 20, 21, 22, 23, 24, 25, 26, 27,
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(1,19): 20, 21, 22, 23, 24, 25, 26, 27, 28
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(1,1): 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
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(1,19): 20,
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(2,1): 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
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(2,18): 20, 21,
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(3,1): 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
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(3,18): 21, 22,
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(4,1): 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
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(4,18): 22, 23,
|
||||
(5,1): 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
|
||||
(5,18): 23, 24,
|
||||
(6,1): 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
|
||||
(6,17): 23, 24, 25,
|
||||
(7,1): 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
|
||||
(7,17): 24, 25, 26,
|
||||
(8,1): 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
|
||||
(8,17): 25, 26, 27,
|
||||
(9,1): 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
|
||||
(9,17): 26, 27, 28
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -11,46 +11,9 @@ DATASET "1d" {
|
||||
COUNT ( 40 );
|
||||
BLOCK ( 1 );
|
||||
DATA {
|
||||
(3): 3,
|
||||
(4): 4,
|
||||
(5): 5,
|
||||
(6): 6,
|
||||
(7): 7,
|
||||
(8): 8,
|
||||
(9): 9,
|
||||
(10): 10,
|
||||
(11): 11,
|
||||
(12): 12,
|
||||
(13): 13,
|
||||
(14): 14,
|
||||
(15): 15,
|
||||
(16): 16,
|
||||
(17): 17,
|
||||
(18): 18,
|
||||
(19): 19,
|
||||
(20): 20,
|
||||
(21): 21,
|
||||
(22): 22,
|
||||
(23): 23,
|
||||
(24): 24,
|
||||
(25): 25,
|
||||
(26): 26,
|
||||
(27): 27,
|
||||
(28): 28,
|
||||
(29): 29,
|
||||
(30): 30,
|
||||
(31): 31,
|
||||
(32): 32,
|
||||
(33): 33,
|
||||
(34): 34,
|
||||
(35): 35,
|
||||
(36): 36,
|
||||
(37): 37,
|
||||
(38): 38,
|
||||
(39): 39,
|
||||
(40): 40,
|
||||
(41): 41,
|
||||
(42): 42
|
||||
(3): 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
|
||||
(21): 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
|
||||
(37): 37, 38, 39, 40, 41, 42
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -11,10 +11,12 @@ DATASET "2d" {
|
||||
COUNT ( 6, 4 );
|
||||
BLOCK ( 1, 1 );
|
||||
DATA {
|
||||
(1,3): 13, 23, 33, 43, 53, 63,
|
||||
(1,4): 14, 24, 34, 44, 54, 64,
|
||||
(1,5): 15, 25, 35, 45, 55, 65,
|
||||
(1,6): 16, 26, 36, 46, 56, 66
|
||||
(1,3): 13, 14, 15, 16,
|
||||
(2,3): 23, 24, 25, 26,
|
||||
(3,3): 33, 34, 35, 36,
|
||||
(4,3): 43, 44, 45, 46,
|
||||
(5,3): 53, 54, 55, 56,
|
||||
(6,3): 63, 64, 65, 66
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#############################
|
||||
Expected output for 'h5dump -d 3d -s 0,1,3 -c 1,6,4 taindices.h5'
|
||||
Expected output for 'h5dump -d 3d -s 0,1,3 -c 2,6,4 taindices.h5'
|
||||
#############################
|
||||
HDF5 "taindices.h5" {
|
||||
DATASET "3d" {
|
||||
@ -8,13 +8,21 @@ DATASET "3d" {
|
||||
SUBSET {
|
||||
START ( 0, 1, 3 );
|
||||
STRIDE ( 1, 1, 1 );
|
||||
COUNT ( 1, 6, 4 );
|
||||
COUNT ( 2, 6, 4 );
|
||||
BLOCK ( 1, 1, 1 );
|
||||
DATA {
|
||||
(0,1,3): 13, 23, 33, 43, 53, 63,
|
||||
(0,1,4): 14, 24, 34, 44, 54, 64,
|
||||
(0,1,5): 15, 25, 35, 45, 55, 65,
|
||||
(0,1,6): 16, 26, 36, 46, 56, 66
|
||||
(0,1,3): 13, 14, 15, 16,
|
||||
(0,2,3): 23, 24, 25, 26,
|
||||
(0,3,3): 33, 34, 35, 36,
|
||||
(0,4,3): 43, 44, 45, 46,
|
||||
(0,5,3): 53, 54, 55, 56,
|
||||
(0,6,3): 63, 64, 65, 66
|
||||
(1,1,3): 113, 114, 115, 116,
|
||||
(1,2,3): 123, 124, 125, 126,
|
||||
(1,3,3): 133, 134, 135, 136,
|
||||
(1,4,3): 143, 144, 145, 146,
|
||||
(1,5,3): 153, 154, 155, 156,
|
||||
(1,6,3): 163, 164, 165, 166
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#############################
|
||||
Expected output for 'h5dump -d 4d -s 0,0,1,3 -c 1,1,1,1 taindices.h5'
|
||||
Expected output for 'h5dump -d 4d -s 0,0,1,3 -c 2,2,6,4 taindices.h5'
|
||||
#############################
|
||||
HDF5 "taindices.h5" {
|
||||
DATASET "4d" {
|
||||
@ -8,10 +8,33 @@ DATASET "4d" {
|
||||
SUBSET {
|
||||
START ( 0, 0, 1, 3 );
|
||||
STRIDE ( 1, 1, 1, 1 );
|
||||
COUNT ( 1, 1, 1, 1 );
|
||||
COUNT ( 2, 2, 6, 4 );
|
||||
BLOCK ( 1, 1, 1, 1 );
|
||||
DATA {
|
||||
(0,0,1,3): 13
|
||||
(0,0,1,3): 13, 14, 15, 16,
|
||||
(0,0,2,3): 23, 24, 25, 26,
|
||||
(0,0,3,3): 33, 34, 35, 36,
|
||||
(0,0,4,3): 43, 44, 45, 46,
|
||||
(0,0,5,3): 53, 54, 55, 56,
|
||||
(0,0,6,3): 63, 64, 65, 66
|
||||
(0,1,1,3): 113, 114, 115, 116,
|
||||
(0,1,2,3): 123, 124, 125, 126,
|
||||
(0,1,3,3): 133, 134, 135, 136,
|
||||
(0,1,4,3): 143, 144, 145, 146,
|
||||
(0,1,5,3): 153, 154, 155, 156,
|
||||
(0,1,6,3): 163, 164, 165, 166
|
||||
(1,0,1,3): 213, 214, 215, 216,
|
||||
(1,0,2,3): 223, 224, 225, 226,
|
||||
(1,0,3,3): 233, 234, 235, 236,
|
||||
(1,0,4,3): 243, 244, 245, 246,
|
||||
(1,0,5,3): 253, 254, 255, 256,
|
||||
(1,0,6,3): 263, 264, 265, 266
|
||||
(1,1,1,3): 313, 314, 315, 316,
|
||||
(1,1,2,3): 323, 324, 325, 326,
|
||||
(1,1,3,3): 333, 334, 335, 336,
|
||||
(1,1,4,3): 343, 344, 345, 346,
|
||||
(1,1,5,3): 353, 354, 355, 356,
|
||||
(1,1,6,3): 363, 364, 365, 366
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user