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-rw-r--r--tools/h5dump/h5dump.c34
-rw-r--r--tools/h5dump/testh5dump.sh.in10
-rw-r--r--tools/lib/h5tools.c107
-rw-r--r--tools/testfiles/tindicessub1.ddl2
-rw-r--r--tools/testfiles/tindicessub2.ddl16
-rw-r--r--tools/testfiles/tindicessub3.ddl18
-rw-r--r--tools/testfiles/tindicessub4.ddl58
7 files changed, 166 insertions, 79 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 3bcb40a..70d889f 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -3181,6 +3181,8 @@ parse_subset_params(char *dset)
* Tuesday, 9. January 2001
*
* Modifications:
+ * Pedro Vicente, Tuesday, January 15, 2008
+ * check for block overlap
*
*-------------------------------------------------------------------------
*/
@@ -3253,6 +3255,38 @@ handle_datasets(hid_t fid, char *dset, void *data)
}
}
+
+ /*-------------------------------------------------------------------------
+ * check for block overlap
+ *-------------------------------------------------------------------------
+ */
+
+ if(sset)
+ {
+ hid_t sid = H5Dget_space(dsetid);
+ unsigned int ndims = H5Sget_simple_extent_ndims(sid);
+ unsigned int i;
+
+ for ( i = 0; i < ndims; i++)
+ {
+ if ( sset->count[i] > 1 )
+ {
+
+ if ( sset->stride[i] < sset->block[i] )
+ {
+ error_msg(progname, "wrong subset selection; blocks overlap\n");
+ d_status = EXIT_FAILURE;
+ return;
+
+ }
+
+ }
+
+ }
+ H5Sclose(sid);
+
+ }
+
H5Oget_info(dsetid, &oinfo);
if(oinfo.rc > 1) {
obj_t *found_obj; /* Found object */
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index c0055d6..b7b8429 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -374,17 +374,17 @@ TOOLTEST tindicesyes.ddl taindices.h5
TOOLTEST tindicesno.ddl -y taindices.h5
########## array indices with subsetting
-# 1D case, start at 1, 2 counts of size 3 blocks, separated by stride 10 elements
-TOOLTEST tindicessub1.ddl -d 1d -s 1 -c 2 -k 3 -S 10 taindices.h5
+# 1D case
+TOOLTEST tindicessub1.ddl -d 1d -s 1 -S 10 -c 2 -k 3 taindices.h5
# 2D case
-TOOLTEST tindicessub2.ddl -d 2d -s 1,2 -c 2,3 -k 1,1 -S 2,1 taindices.h5
+TOOLTEST tindicessub2.ddl -d 2d -s 1,2 -S 3,3 -c 3,2 -k 2,2 taindices.h5
# 3D case
-TOOLTEST tindicessub3.ddl -d 3d -s 0,1,2 -c 1,2,3 -k 1,1,1 -S 1,2,1 taindices.h5
+TOOLTEST tindicessub3.ddl -d 3d -s 0,1,2 -S 1,3,3 -c 2,2,2 -k 1,2,2 taindices.h5
# 4D case
-TOOLTEST tindicessub4.ddl -d 4d -s 0,0,1,3 -c 2,2,6,4 taindices.h5
+TOOLTEST tindicessub4.ddl -d 4d -s 0,0,1,2 -c 2,2,3,2 -S 1,1,3,3 -k 1,1,2,2 taindices.h5
# tests for filters
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 77a8bb3..6fc09d7 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -613,7 +613,7 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
}
/*
- * We need to break after each row of a dimension---> we should
+ * We need to break after each row_counter of a dimension---> we should
* break at the end of the each last dimension well that is the
* way the dumper did it before
*/
@@ -707,33 +707,40 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
* Chapter: H5Tools Library
* Purpose: Dump out a subset of a dataset.
* Description:
- * Select a hyperslab from the dataset DSET using the parameters
- * specified in SSET. Dump this out to STREAM.
+ *
+ * Select a hyperslab from the dataset DSET using the parameters
+ * specified in SSET. Dump this out to STREAM.
*
- * hyperslabs select "count" blocks of size "block",
- * spaced "stride" elements from each other, starting at coordinate
- * "start".
+ * Hyperslabs select "count" blocks of size "block", spaced "stride" elements
+ * from each other, starting at coordinate "start".
*
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
- * Programmer:
- * Bill Wendling, Wednesday, 07. March 2001
- * Modifications:
- * Pedro Vicente, 12 December 2006
- * Add information to print array indices from the element position
- * The algorythm used is
+ *
+ * Original programmer:
+ * Bill Wendling, Wednesday, March 07, 2001
+ *
+ * Rewritten with modified algorithm by:
+ * Pedro Vicente, Wednesday, January 16, 2008, contributions from Quincey Koziol
+ *
+ * Algorithm
+ *
+ * In a inner loop, the parameters from SSET are translated into temporary
+ * variables so that 1 row is printed at a time (getting the coordinate indices
+ * at each row).
+ * We define the stride, count and block to be 1 in the row dimension to achieve
+ * this and advance until all points are printed.
+ * An outer loop for cases where dimensionality is greater than 2D is made.
+ * In each iteration, the 2D block is displayed in the inner loop. The remaining
+ * slower dimensions above the first 2 are incremented one at a time in the outer loop
+ *
+ * The element position is obtained from the matrix according to:
* Given an index I(z,y,x) its position from the beginning of an array
* of sizes A(size_z, size_y,size_x) is given by
* Position of I(z,y,x) = index_z * size_y * size_x
* + index_y * size_x
* + index_x
- *
- * Pedro Vicente, Quincey Koziol, 4 January 2007
- * 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
- *
+ *
*-------------------------------------------------------------------------
*/
static herr_t
@@ -761,13 +768,15 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
hid_t sm_space; /* stripmine data space */
hsize_t count; /* hyperslab count */
hsize_t outer_count; /* offset count */
- unsigned int row_dim; /* index of row dimension */
+ unsigned int row_dim; /* index of row_counter dimension */
int current_outer_dim; /* dimension for start */
hsize_t temp_start[H5S_MAX_RANK];/* temporary start inside offset count loop */
hsize_t max_start[H5S_MAX_RANK]; /* maximum start inside offset count loop */
hsize_t temp_count[H5S_MAX_RANK];/* temporary count inside offset count loop */
hsize_t temp_block[H5S_MAX_RANK];/* temporary block size used in loop */
+ hsize_t temp_stride[H5S_MAX_RANK];/* temporary stride size used in loop */
int reset_dim;
+ hsize_t size_row_block; /* size for blocks along rows */
#if defined (SANITY_CHECK)
hsize_t total_points = 1; /* to print */
@@ -836,6 +845,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
temp_start[ i ] = sset->start[ i ];
temp_count[ i ] = sset->count[ i ];
temp_block[ i ] = sset->block[ i ];
+ temp_stride[ i ] = sset->stride[ i ];
max_start[ i ] = 0;
}
@@ -854,34 +864,67 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
for (n = 0; n < outer_count; n++)
{
+ hsize_t row_counter = 0;
+
/* number of read iterations in inner loop, read by rows, to match 2D display */
if (ctx.ndims > 1)
{
-
- /* count is the number of iterations to display all the rows,
- the block size count times */
+
+ /* count is the number of iterations to display all the rows,
+ the block size count times */
count = sset->count[ row_dim ] * sset->block[ row_dim ];
-
- /* always 1 row at a time, that is a block of size 1, 1 time */
+
+ /* always 1 row_counter at a time, that is a block of size 1, 1 time */
temp_count[ row_dim ] = 1;
- temp_block[ row_dim ] = 1;
-
+ temp_block[ row_dim ] = 1;
+
+ /* advance 1 row_counter at a time */
+ if (sset->block[ row_dim ] > 1 )
+ temp_stride[ row_dim ] = 1;
+
+
}
/* for the 1D case */
else
{
count = 1;
}
-
+
+ size_row_block = sset->block[ row_dim ];
+
+
/* display loop */
- for (; count > 0; temp_start[ row_dim ] += sset->stride[ row_dim ],
- count--)
- {
+ for (; count > 0;
+ temp_start[ row_dim ] += temp_stride[ row_dim ],
+ count--)
+ {
+
+
+ /* jump rows if size of block exceeded
+ cases where block > 1 only and stride > block */
+ if ( size_row_block > 1 &&
+ row_counter == size_row_block &&
+ sset->stride[ row_dim ] > sset->block[ row_dim ]
+ )
+ {
+
+ hsize_t increase_rows = sset->stride[ row_dim ] -
+ sset->block[ row_dim ];
+
+ temp_start[ row_dim ] += increase_rows;
+
+ row_counter = 0;
+
+ }
+
+ row_counter++;
+
+
/* calculate the potential number of elements we're going to print */
H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
temp_start,
- sset->stride,
+ temp_stride,
temp_count,
temp_block);
sm_nelmts = H5Sget_select_npoints(f_space);
diff --git a/tools/testfiles/tindicessub1.ddl b/tools/testfiles/tindicessub1.ddl
index 05be904..0173fb5 100644
--- a/tools/testfiles/tindicessub1.ddl
+++ b/tools/testfiles/tindicessub1.ddl
@@ -1,5 +1,5 @@
#############################
-Expected output for 'h5dump -d 1d -s 1 -c 2 -k 3 -S 10 taindices.h5'
+Expected output for 'h5dump -d 1d -s 1 -S 10 -c 2 -k 3 taindices.h5'
#############################
HDF5 "taindices.h5" {
DATASET "1d" {
diff --git a/tools/testfiles/tindicessub2.ddl b/tools/testfiles/tindicessub2.ddl
index 39260bc..7b70d12 100644
--- a/tools/testfiles/tindicessub2.ddl
+++ b/tools/testfiles/tindicessub2.ddl
@@ -1,5 +1,5 @@
#############################
-Expected output for 'h5dump -d 2d -s 1,2 -c 2,3 -k 1,1 -S 2,1 taindices.h5'
+Expected output for 'h5dump -d 2d -s 1,2 -S 3,3 -c 3,2 -k 2,2 taindices.h5'
#############################
HDF5 "taindices.h5" {
DATASET "2d" {
@@ -7,12 +7,16 @@ DATASET "2d" {
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
SUBSET {
START ( 1, 2 );
- STRIDE ( 2, 1 );
- COUNT ( 2, 3 );
- BLOCK ( 1, 1 );
+ STRIDE ( 3, 3 );
+ COUNT ( 3, 2 );
+ BLOCK ( 2, 2 );
DATA {
- (1,2): 12, 13, 14,
- (3,2): 32, 33, 34
+ (1,2): 12, 13, 15, 16,
+ (2,2): 22, 23, 25, 26,
+ (4,2): 42, 43, 45, 46,
+ (5,2): 52, 53, 55, 56,
+ (7,2): 72, 73, 75, 76,
+ (8,2): 82, 83, 85, 86
}
}
}
diff --git a/tools/testfiles/tindicessub3.ddl b/tools/testfiles/tindicessub3.ddl
index 16c71d3..fde8e82 100644
--- a/tools/testfiles/tindicessub3.ddl
+++ b/tools/testfiles/tindicessub3.ddl
@@ -1,5 +1,5 @@
#############################
-Expected output for 'h5dump -d 3d -s 0,1,2 -c 1,2,3 -k 1,1,1 -S 1,2,1 taindices.h5'
+Expected output for 'h5dump -d 3d -s 0,1,2 -S 1,3,3 -c 2,2,2 -k 1,2,2 taindices.h5'
#############################
HDF5 "taindices.h5" {
DATASET "3d" {
@@ -7,12 +7,18 @@ DATASET "3d" {
DATASPACE SIMPLE { ( 2, 10, 10 ) / ( 2, 10, 10 ) }
SUBSET {
START ( 0, 1, 2 );
- STRIDE ( 1, 2, 1 );
- COUNT ( 1, 2, 3 );
- BLOCK ( 1, 1, 1 );
+ STRIDE ( 1, 3, 3 );
+ COUNT ( 2, 2, 2 );
+ BLOCK ( 1, 2, 2 );
DATA {
- (0,1,2): 12, 13, 14,
- (0,3,2): 32, 33, 34
+ (0,1,2): 12, 13, 15, 16,
+ (0,2,2): 22, 23, 25, 26,
+ (0,4,2): 42, 43, 45, 46,
+ (0,5,2): 52, 53, 55, 56
+ (1,1,2): 112, 113, 115, 116,
+ (1,2,2): 122, 123, 125, 126,
+ (1,4,2): 142, 143, 145, 146,
+ (1,5,2): 152, 153, 155, 156
}
}
}
diff --git a/tools/testfiles/tindicessub4.ddl b/tools/testfiles/tindicessub4.ddl
index 99fca01..a57bee6 100644
--- a/tools/testfiles/tindicessub4.ddl
+++ b/tools/testfiles/tindicessub4.ddl
@@ -1,40 +1,40 @@
#############################
-Expected output for 'h5dump -d 4d -s 0,0,1,3 -c 2,2,6,4 taindices.h5'
+Expected output for 'h5dump -d 4d -s 0,0,1,2 -c 2,2,3,2 -S 1,1,3,3 -k 1,1,2,2 taindices.h5'
#############################
HDF5 "taindices.h5" {
DATASET "4d" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 2, 2, 10, 10 ) / ( 2, 2, 10, 10 ) }
SUBSET {
- START ( 0, 0, 1, 3 );
- STRIDE ( 1, 1, 1, 1 );
- COUNT ( 2, 2, 6, 4 );
- BLOCK ( 1, 1, 1, 1 );
+ START ( 0, 0, 1, 2 );
+ STRIDE ( 1, 1, 3, 3 );
+ COUNT ( 2, 2, 3, 2 );
+ BLOCK ( 1, 1, 2, 2 );
DATA {
- (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
+ (0,0,1,2): 12, 13, 15, 16,
+ (0,0,2,2): 22, 23, 25, 26,
+ (0,0,4,2): 42, 43, 45, 46,
+ (0,0,5,2): 52, 53, 55, 56,
+ (0,0,7,2): 72, 73, 75, 76,
+ (0,0,8,2): 82, 83, 85, 86
+ (0,1,1,2): 112, 113, 115, 116,
+ (0,1,2,2): 122, 123, 125, 126,
+ (0,1,4,2): 142, 143, 145, 146,
+ (0,1,5,2): 152, 153, 155, 156,
+ (0,1,7,2): 172, 173, 175, 176,
+ (0,1,8,2): 182, 183, 185, 186
+ (1,0,1,2): 212, 213, 215, 216,
+ (1,0,2,2): 222, 223, 225, 226,
+ (1,0,4,2): 242, 243, 245, 246,
+ (1,0,5,2): 252, 253, 255, 256,
+ (1,0,7,2): 272, 273, 275, 276,
+ (1,0,8,2): 282, 283, 285, 286
+ (1,1,1,2): 312, 313, 315, 316,
+ (1,1,2,2): 322, 323, 325, 326,
+ (1,1,4,2): 342, 343, 345, 346,
+ (1,1,5,2): 352, 353, 355, 356,
+ (1,1,7,2): 372, 373, 375, 376,
+ (1,1,8,2): 382, 383, 385, 386
}
}
}
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