[svn-r14437] bug fix for h5dump subsetting (deal with blocks)and new test runs

add a check for block overlap after the command line parsing

* 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
 * 

tested: windows, linux

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
       }
    }
 }