[svn-r13064]

Fix several bugs

1) the parsing of subsetting was using atoi to convert the parameter to an int, which caused problems for numbers greater that int. Substitute with atof

2) the printing of indices in the subsetting case was not being done. Solution: calculate the element position at the start of the subsetting using the algorythm 

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

And pass that position to the function that dumps data, h5tools_dump_simple_data. 

3) several index counters were declared as int, use hsize_t instead

4) modified the test generation program so that it includes test cases for subsetting of 1d, 2d, 3d, and 4d arrays and add these tests to the shell script

1 files changed, 85 insertions, 51 deletions

diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 8279ec9..804f83a 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -563,7 +563,13 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
      if (info->line_ncols > 0)
       ncols = info->line_ncols;
 
-     h5tools_simple_prefix(stream, info, ctx, (hsize_t)0, 0);
+
+    /* pass to the prefix in h5tools_simple_prefix the total position
+      instead of the current stripmine position i; this is necessary
+      to print the array indices */
+     curr_pos = ctx->sm_pos;
+
+     h5tools_simple_prefix(stream, info, ctx, curr_pos, 0);
 
      for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
         /* Render the element */
@@ -703,6 +709,14 @@ h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t contai
  * 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 
+ *      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
  *-------------------------------------------------------------------------
  */
 static herr_t
@@ -710,32 +724,30 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
                            hid_t p_type, struct subset_t *sset,
                            int indentlevel)
 {
-    herr_t              ret;                    /*the value to return   */
-    hid_t  f_space;  /*file data space */
-    int   i;                      /*counters  */
-    hsize_t  zero = 0;               /*vector of zeros */
-    unsigned int flags;   /*buffer extent flags */
-    hsize_t  total_size[H5S_MAX_RANK];/*total size of dataset*/
-
-    /* Print info */
-    h5tools_context_t ctx;   /*print context  */
-    size_t  p_type_nbytes;  /*size of memory type */
-
-    /* Stripmine info */
-    hsize_t  sm_size[H5S_MAX_RANK]; /*stripmine size */
-    hsize_t  sm_nbytes;  /*bytes per stripmine */
-    hsize_t  sm_nelmts;  /*elements per stripmine*/
-    unsigned char      *sm_buf = NULL;  /*buffer for raw data */
-    hid_t  sm_space;  /*stripmine data space */
-
-    hsize_t             count;
+    herr_t            ret;                     /* the value to return */
+    hid_t             f_space;                 /* file data space */
+    hsize_t           i, j;                    /* counters  */
+    hsize_t           zero = 0;                /* vector of zeros */
+    unsigned int      flags;                   /* buffer extent flags */
+    hsize_t           total_size[H5S_MAX_RANK];/* total size of dataset*/
+    hsize_t           elmtno;                  /* elemnt index  */
+    hsize_t           low[H5S_MAX_RANK];       /* low bound of hyperslab */
+    hsize_t           high[H5S_MAX_RANK];      /* higher bound of hyperslab */
+    h5tools_context_t ctx;                     /* print context  */
+    size_t            p_type_nbytes;           /* size of memory type */
+    hsize_t           sm_size[H5S_MAX_RANK];   /* stripmine size */
+    hsize_t           sm_nbytes;               /* bytes per stripmine */
+    hsize_t           sm_nelmts;               /* elements per stripmine*/
+    unsigned char     *sm_buf = NULL;          /* buffer for raw data */
+    hid_t             sm_space;                /* stripmine data space */
+    hsize_t           count;                   /* hyperslab count */
 
     ret = FAIL;     /* be pessimistic */
     f_space = H5Dget_space(dset);
-
+    
     if (f_space == FAIL)
         goto done;
-
+    
     /*
      * check that everything looks okay. the dimensionality must not be too
      * great and the dimensionality of the items selected for printing must
@@ -755,17 +767,17 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
             ctx.p_min_idx[i] = 0;
 
     H5Sget_simple_extent_dims(f_space, total_size, NULL);
- assert(total_size[ctx.ndims - 1]==(hsize_t)((int)(total_size[ctx.ndims - 1])));
-    ctx.size_last_dim = (int)(total_size[ctx.ndims - 1]);
+    ctx.size_last_dim = total_size[ctx.ndims - 1];
 
     count = sset->count[ctx.ndims - 1];
     sset->count[ctx.ndims - 1] = 1;
 
     if(ctx.ndims>0)
-     init_acc_pos(&ctx,total_size);
+        init_acc_pos(&ctx,total_size);
 
+  
     for (; count > 0; sset->start[ctx.ndims - 1] += sset->stride[ctx.ndims - 1],
-                      count--) {
+        count--) {
         /* calculate the potential number of elements we're going to print */
         H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
             sset->start,
@@ -774,6 +786,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
             sset->block);
         sm_nelmts = H5Sget_select_npoints(f_space);
 
+       
         /*
          * start (0, 0)
          * block (2, 2)
@@ -801,7 +814,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
          * a hyperslab whose size is manageable.
          */
         sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
-
+        
         if (ctx.ndims > 0)
             for (i = ctx.ndims; i > 0; --i) {
                 sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
@@ -825,17 +838,38 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
 
         /* Print the data */
         flags = START_OF_DATA;
-
+        
         if (count == 1)
             flags |= END_OF_DATA;
-
+        
         for (i = 0; i < ctx.ndims; i++) {
             ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]);
         }
 
+        /* print array indices. get the lower bound of the hyperslab and calulate
+           the element position at the start of hyperslab */
+        H5Sget_select_bounds(f_space,low,high);
+        elmtno=0;
+        for (i = 0; i < ctx.ndims-1; i++) 
+        {
+            hsize_t offset = 1; /* accumulation of the previous dimensions */
+            for (j = i+1; j < ctx.ndims; j++) 
+                offset *= total_size[j];
+            elmtno+= low[i] * offset;
+        }
+        elmtno+= low[ctx.ndims - 1];
+        
+       /* initialize the current stripmine position; this is necessary to print the array
+          indices */
+        ctx.sm_pos = elmtno;
+
         h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
                                  p_type, sm_buf);
         free(sm_buf);
+
+        /* we need to jump to next line and update the index */
+        ctx.need_prefix = 1;
+
         ctx.continuation++;
     }
 
@@ -845,9 +879,9 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset
         putc('\n', stream);
         fputs(OPT(info->line_sep, ""), stream);
     }
-
+    
     ret = SUCCEED;
-
+    
 done_close:
     H5Sclose(f_space);
 done:
@@ -876,33 +910,33 @@ static int
 h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, hid_t dset,
                          hid_t p_type, int indentlevel)
 {
-    hid_t  f_space;  /*file data space */
-    hsize_t  elmtno;   /*counter  */
-    int   i;   /*counter  */
-    int   carry;   /*counter carry value */
-    hsize_t  zero[8];  /*vector of zeros */
-    unsigned int flags;   /*buffer extent flags */
-    hsize_t  total_size[H5S_MAX_RANK];/*total size of dataset*/
+    hid_t               f_space;                  /* file data space */
+    hsize_t             elmtno;                   /* counter  */
+    hsize_t             i;                        /* counter  */
+    int                 carry;                    /* counter carry value */
+    hsize_t             zero[8];                  /* vector of zeros */
+    unsigned int        flags;                    /* buffer extent flags */
+    hsize_t             total_size[H5S_MAX_RANK]; /* total size of dataset*/
 
     /* Print info */
-    h5tools_context_t ctx;   /*print context  */
-    size_t  p_type_nbytes;  /*size of memory type */
-    hsize_t  p_nelmts;  /*total selected elmts */
+    h5tools_context_t   ctx;                      /* print context  */
+    size_t              p_type_nbytes;            /* size of memory type */
+    hsize_t             p_nelmts;                 /* total selected elmts */
 
     /* Stripmine info */
-    hsize_t  sm_size[H5S_MAX_RANK]; /*stripmine size */
-    hsize_t  sm_nbytes;  /*bytes per stripmine */
-    hsize_t  sm_nelmts;  /*elements per stripmine*/
-    unsigned char      *sm_buf = NULL;  /*buffer for raw data */
-    hid_t  sm_space;  /*stripmine data space */
+    hsize_t             sm_size[H5S_MAX_RANK];    /* stripmine size */
+    hsize_t             sm_nbytes;                /* bytes per stripmine */
+    hsize_t             sm_nelmts;                /* elements per stripmine*/
+    unsigned char       *sm_buf = NULL;           /* buffer for raw data */
+    hid_t               sm_space;                 /* stripmine data space */
 
     /* Hyperslab info */
-    hsize_t  hs_offset[H5S_MAX_RANK];/*starting offset */
-    hsize_t  hs_size[H5S_MAX_RANK]; /*size this pass */
-    hsize_t  hs_nelmts;  /*elements in request */
+    hsize_t            hs_offset[H5S_MAX_RANK];   /* starting offset */
+    hsize_t            hs_size[H5S_MAX_RANK];     /* size this pass */
+    hsize_t            hs_nelmts;                 /* elements in request */
 
     /* VL data special information */
-    unsigned int        vl_data = 0;            /*contains VL datatypes */
+    unsigned int       vl_data = 0;               /* contains VL datatypes */
 
     f_space = H5Dget_space(dset);
 
@@ -918,7 +952,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, hid_t dset,
     ctx.indent_level = indentlevel;
     ctx.need_prefix = 1;
     ctx.ndims = H5Sget_simple_extent_ndims(f_space);
-
+    
     if ((size_t)ctx.ndims > NELMTS(sm_size)) {
         H5Sclose(f_space);
         return FAIL;