[svn-r17505] Description:

	Bring r17416:17496 from trunk to revise_chunks branch

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
                                in debug mode
        Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
                                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                                w/szip filter, in production mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                                in production mode
        Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
        Mac OS X/32 10.5.8 (amazon) in debug mode
        Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
                                in production mode
	

3 files changed, 234 insertions, 94 deletions

diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index beacdbb..c74c9f1 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -81,7 +81,6 @@ static const char   *fp_format = NULL;
 const char          *outfname=NULL;
 
 
-
 /* things to display or which are set via command line parameters */
 static int          display_all       = TRUE;
 static int          display_oid       = FALSE;
@@ -94,6 +93,7 @@ static int          display_dcpl      = FALSE; /*dcpl */
 static int          display_fi        = FALSE; /*file index */
 static int          display_ai        = TRUE;  /*array index */
 static int          display_escape    = FALSE; /*escape non printable characters */
+static int          display_region    = FALSE; /*print region reference data */
 
 /* sort parameters */
 static H5_index_t   sort_by           = H5_INDEX_NAME; /*sort_by [creation_order | name]  */
@@ -388,7 +388,7 @@ struct handler_t {
  * parameters. The long-named ones can be partially spelled. When
  * adding more, make sure that they don't clash with each other.
  */
-static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b*F:s:S:Aq:z:m:";
+static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b*F:s:S:Aq:z:m:R";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "hel", no_arg, 'h' },
@@ -500,6 +500,7 @@ static struct long_options l_opts[] = {
     { "sort_by", require_arg, 'q' },
     { "sort_order", require_arg, 'z' },
     { "format", require_arg, 'm' },
+    { "region", no_arg, 'R' },
     { NULL, 0, '\0' }
 };
 
@@ -655,6 +656,7 @@ usage(const char *prog)
     fprintf(stdout, "     -m T, --format=T     Set the floating point output format\n");
     fprintf(stdout, "     -q Q, --sort_by=Q    Sort groups and attributes by index Q\n");
     fprintf(stdout, "     -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
+    fprintf(stdout, "     -R, --region         Print dataset pointed by region references\n");
     fprintf(stdout, "     -x, --xml            Output in XML using Schema\n");
     fprintf(stdout, "     -u, --use-dtd        Output in XML using DTD\n");
     fprintf(stdout, "     -D U, --xml-dtd=U    Use the DTD or schema at U\n");
@@ -665,14 +667,16 @@ usage(const char *prog)
     fprintf(stdout, " Subsetting is available by using the following options with a dataset\n");
     fprintf(stdout, " attribute. Subsetting is done by selecting a hyperslab from the data.\n");
     fprintf(stdout, " Thus, the options mirror those for performing a hyperslab selection.\n");
-    fprintf(stdout, " The START and COUNT parameters are mandatory if you do subsetting.\n");
-    fprintf(stdout, " The STRIDE and BLOCK parameters are optional and will default to 1 in\n");
-    fprintf(stdout, " each dimension.\n");
+    fprintf(stdout, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n");
+    fprintf(stdout, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n");
+    fprintf(stdout, " each dimension. START is optional and will default to 0 in each dimension.\n");
     fprintf(stdout, "\n");
-    fprintf(stdout, "      -s L, --start=L     Offset of start of subsetting selection\n");
-    fprintf(stdout, "      -S L, --stride=L    Hyperslab stride\n");
-    fprintf(stdout, "      -c L, --count=L     Number of blocks to include in selection\n");
-    fprintf(stdout, "      -k L, --block=L     Size of block in hyperslab\n");
+    fprintf(stdout, "      -s START,  --start=START    Offset of start of subsetting selection\n");
+    fprintf(stdout, "      -S STRIDE, --stride=STRIDE  Hyperslab stride\n");
+    fprintf(stdout, "      -c COUNT,  --count=COUNT    Number of blocks to include in selection\n");
+    fprintf(stdout, "      -k BLOCK,  --block=BLOCK    Size of block in hyperslab\n");
+    fprintf(stdout, "  START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n");
+    fprintf(stdout, "        number of dimensions in the dataspace being queried\n");
     fprintf(stdout, "\n");
     fprintf(stdout, "  D - is the file driver to use in opening the file. Acceptable values\n");
     fprintf(stdout, "        are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n");
@@ -683,8 +687,6 @@ usage(const char *prog)
     fprintf(stdout, "  P - is the full path from the root group to the object.\n");
     fprintf(stdout, "  N - is an integer greater than 1.\n");
     fprintf(stdout, "  T - is a string containing the floating point format, e.g '%%.3f'\n");
-    fprintf(stdout, "  L - is a list of integers the number of which are equal to the\n");
-    fprintf(stdout, "        number of dimensions in the dataspace being queried\n");
     fprintf(stdout, "  U - is a URI reference (as defined in [IETF RFC 2396],\n");
     fprintf(stdout, "        updated by [IETF RFC 2732])\n");
     fprintf(stdout, "  B - is the form of binary output: NATIVE for a memory type, FILE for the\n");
@@ -1189,6 +1191,18 @@ print_datatype(hid_t type,unsigned in_group)
 
             case H5T_REFERENCE:
                 printf("H5T_REFERENCE");
+                /* The BNF document states that the type of reference should be 
+                 * displayed after "H5T_REFERENCE". Therefore add the missing 
+                 * reference type if the region command line option is used. This 
+                 * reference type will not be displayed if the region option is not used. */
+                if(display_region) {
+                    if (H5Tequal(type, H5T_STD_REF_DSETREG)==TRUE) {
+                        printf(" { H5T_STD_REF_DSETREG }");
+                    } 
+                    else {
+                        printf(" { H5T_STD_REF_OBJECT }");
+                    }        
+                }
                 break;
 
             case H5T_ENUM:
@@ -2391,13 +2405,29 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
     outputformat->pindex=display_index;
 
     /* do not print indices for regions */
-    if(obj_data == DATASET_DATA)
-    {
+    if(obj_data == DATASET_DATA) {
         hid_t f_type = H5Dget_type(obj_id);
 
-        if (H5Tequal(f_type, H5T_STD_REF_DSETREG))
-        {
-            outputformat->pindex = 0;
+        if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
+            /* For the region option, correct the display of indices */
+            if (display_region) {
+                if (display_index) {
+                    outputformat->pindex = 1;
+                    outputformat->idx_fmt   = "(%s): ";
+                    outputformat->idx_n_fmt = HSIZE_T_FORMAT;
+                    outputformat->idx_sep   = ",";
+                    outputformat->line_pre  = "%s";
+                }
+                else {
+                    outputformat->pindex = 0;
+                    outputformat->idx_fmt   = "";
+                    outputformat->idx_n_fmt = "";
+                    outputformat->idx_sep   = "";
+                    outputformat->line_pre  = "";
+                }
+            }
+            else
+                outputformat->pindex = 0;
         }
         H5Tclose(f_type);
     }
@@ -2470,13 +2500,15 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index)
         status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, sset, depth);
 
         H5Tclose(f_type);
-    } else {
+    } 
+    else {
         /* need to call h5tools_dump_mem for the attribute data */
         space = H5Aget_space(obj_id);
         space_type = H5Sget_simple_extent_type(space);
         if(space_type == H5S_NULL || space_type == H5S_NO_CLASS) {
             status = SUCCEED;
-        } else {
+        } 
+        else {
             char        string_prefix[64];
             h5tool_format_t    string_dataformat;
 
@@ -3516,21 +3548,13 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis
             }
 
             if (!sset->count) {
-                hsize_t dims[H5S_MAX_RANK];
-                herr_t status = H5Sget_simple_extent_dims(sid, dims, NULL);
                 unsigned int i;
 
-                if (status == FAIL) {
-                    error_msg(progname, "unable to get dataset dimensions\n");
-                    d_status = EXIT_FAILURE;
-                    H5Sclose(sid);
-                    return;
-                }
 
                 sset->count = calloc(ndims, sizeof(hsize_t));
 
                 for (i = 0; i < ndims; i++)
-                    sset->count[i] = dims[i] - sset->start[i];
+                    sset->count[i] = 1;
             }
 
             if (!sset->block) {
@@ -3872,6 +3896,10 @@ parse_command_line(int argc, const char *argv[])
     while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
 parse_start:
         switch ((char)opt) {
+        case 'R':
+            display_region = TRUE;
+            region_output = TRUE;
+            break;
         case 'B':
             display_bb = TRUE;
             last_was_dset = FALSE;
@@ -3981,74 +4009,61 @@ parse_start:
             break;
 
         case 'o':
+            if ( bin_output ) {
+                if (set_output_file(opt_arg, 1) < 0) {
+                    usage(progname);
+                    leave(EXIT_FAILURE);
+                }
+            }
+            else {
+                if (set_output_file(opt_arg, 0) < 0) {
+                    usage(progname);
+                    leave(EXIT_FAILURE);
+                }
+            }
+
+            usingdasho = TRUE;
+            last_was_dset = FALSE;
+            outfname = opt_arg;
+            break;
+
+        case 'b':
+            if ( opt_arg != NULL) {
+                if ( ( bin_form = set_binary_form(opt_arg)) < 0) {
+                    /* failed to set binary form */
+                    usage(progname);
+                    leave(EXIT_FAILURE);
+                }
+            }
+            bin_output = TRUE;
+            if (outfname!=NULL) {
+                if (set_output_file(outfname, 1) < 0)  {
+                    /* failed to set output file */
+                    usage(progname);
+                    leave(EXIT_FAILURE);
+                }
+
+                last_was_dset = FALSE;
+            }
+            break;
 
-         if ( bin_output )
-         {
-          if (set_output_file(opt_arg, 1) < 0){
-           usage(progname);
-           leave(EXIT_FAILURE);
-          }
-         }
-         else
-         {
-          if (set_output_file(opt_arg, 0) < 0){
-           usage(progname);
-           leave(EXIT_FAILURE);
-          }
-         }
-
-         usingdasho = TRUE;
-         last_was_dset = FALSE;
-         outfname = opt_arg;
-         break;
-
-       case 'b':
-
-        if ( opt_arg != NULL)
-           {
-               if ( ( bin_form = set_binary_form(opt_arg)) < 0)
-               {
-                   /* failed to set binary form */
-                   usage(progname);
-                   leave(EXIT_FAILURE);
-               }
-           }
-           bin_output = TRUE;
-           if (outfname!=NULL) 
-           {
-               if (set_output_file(outfname, 1) < 0)
-               {
-                   /* failed to set output file */
-                   usage(progname);
-                   leave(EXIT_FAILURE);
-               }
-               
-               last_was_dset = FALSE;
-           }
-           
-           break;
-
-       case 'q':
-
-           if ( ( sort_by = set_sort_by(opt_arg)) < 0)
-           {
-               /* failed to set "sort by" form */
-               usage(progname);
-               leave(EXIT_FAILURE);
-           }
-
-           break;
-
-       case 'z':
-
-           if ( ( sort_order = set_sort_order(opt_arg)) < 0)
-           {
-               /* failed to set "sort order" form */
-               usage(progname);
-               leave(EXIT_FAILURE);
-           }
-
-           break;
+        case 'q':
+            if ( ( sort_by = set_sort_by(opt_arg)) < 0) {
+                /* failed to set "sort by" form */
+                usage(progname);
+                leave(EXIT_FAILURE);
+            }
+            break;
+
+        case 'z':
+            if ( ( sort_order = set_sort_order(opt_arg)) < 0) {
+                /* failed to set "sort order" form */
+                usage(progname);
+                leave(EXIT_FAILURE);
+            }
+            break;
+
+            break;
 
         /** begin XML parameters **/
         case 'x':
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index c0d5801..b8ed41d 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -92,6 +92,7 @@
 #define FILE62  "textlinktar.h5"
 #define FILE63  "textlinkfar.h5"
 #define FILE64  "tarray8.h5"
+#define FILE65  "tattrreg.h5"
 
 
 
@@ -1852,6 +1853,126 @@ static void gent_datareg(void)
     free(drbuf);
 }
 
+static void gent_attrreg(void)
+{
+    /*some code is taken from enum.c in the test dir */
+
+    hid_t  fid1;        /* HDF5 File IDs  */
+    hid_t  dset1;       /* Dataset ID   */
+    hid_t  dset2;       /* Dereferenced dataset ID */
+    hid_t  sid1;        /* Dataspace ID #1  */
+    hid_t  sid2;        /* Dataspace ID #2  */
+    hid_t  sid3;        /* Dataspace ID #3  */
+    hid_t  attr1;       /* Attribute ID  */
+    hsize_t  dims1[] = {SPACE1_DIM1};
+    hsize_t  dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
+    hsize_t  start[SPACE2_RANK];     /* Starting location of hyperslab */
+    hsize_t  stride[SPACE2_RANK];    /* Stride of hyperslab */
+    hsize_t  count[SPACE2_RANK];     /* Element count of hyperslab */
+    hsize_t  block[SPACE2_RANK];     /* Block size of hyperslab */
+    hsize_t  coord1[POINT1_NPOINTS][SPACE2_RANK]; /* Coordinates for point selection */
+    hdset_reg_ref_t      *wbuf;      /* buffer to write to disk */
+    hdset_reg_ref_t      *rbuf;      /* buffer read from disk */
+    uint8_t    *dwbuf;      /* Buffer for writing numeric data to disk */
+    uint8_t    *drbuf;      /* Buffer for reading numeric data from disk */
+    uint8_t    *tu8;        /* Temporary pointer to uint8 data */
+    int        i;           /* counting variables */
+
+    /* Allocate write & read buffers */
+    wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
+    rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
+    dwbuf=malloc(sizeof(uint8_t)*SPACE2_DIM1*SPACE2_DIM2);
+    drbuf=calloc(sizeof(uint8_t),SPACE2_DIM1*SPACE2_DIM2);
+
+    /* Create file */
+    fid1 = H5Fcreate(FILE65, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+    /* Create dataspace for datasets */
+    sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);
+
+    /* Create a dataset */
+    dset2 = H5Dcreate2(fid1, "Dataset2", H5T_STD_U8BE, sid2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+    for(tu8 = dwbuf, i = 0; i < SPACE2_DIM1 * SPACE2_DIM2; i++)
+        *tu8++=i*3;
+
+    /* Write selection to disk */
+    H5Dwrite(dset2, H5T_NATIVE_UCHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, dwbuf);
+
+    /* Close Dataset */
+    H5Dclose(dset2);
+
+    /*
+     * Create dataset with a null dataspace to serve as the parent for
+     * the attribute.
+     */
+    sid1 = H5Screate (H5S_NULL);
+    dset1 = H5Dcreate2 (fid1, "Dataset1", H5T_STD_I32LE, sid1, H5P_DEFAULT,
+                H5P_DEFAULT, H5P_DEFAULT);
+    H5Sclose (sid1);
+
+    /* Create references */
+
+    /* Select 6x6 hyperslab for first reference */
+    start[0] = 2; start[1] = 2;
+    stride[0] = 1; stride[1] = 1;
+    count[0] = 6; count[1] = 6;
+    block[0] = 1; block[1] = 1;
+    H5Sselect_hyperslab(sid2, H5S_SELECT_SET, start, stride, count, block);
+
+    H5Sget_select_npoints(sid2);
+
+    /* Store first dataset region */
+    H5Rcreate(&wbuf[0], fid1, "/Dataset2", H5R_DATASET_REGION, sid2);
+
+    /* Select sequence of ten points for second reference */
+    coord1[0][0]=6; coord1[0][1]=9;
+    coord1[1][0]=2; coord1[1][1]=2;
+    coord1[2][0]=8; coord1[2][1]=4;
+    coord1[3][0]=1; coord1[3][1]=6;
+    coord1[4][0]=2; coord1[4][1]=8;
+    coord1[5][0]=3; coord1[5][1]=2;
+    coord1[6][0]=0; coord1[6][1]=4;
+    coord1[7][0]=9; coord1[7][1]=0;
+    coord1[8][0]=7; coord1[8][1]=1;
+    coord1[9][0]=3; coord1[9][1]=3;
+    H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(hsize_t *)coord1);
+
+    H5Sget_select_npoints(sid2);
+
+    /* Store second dataset region */
+    H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
+
+    /* Create dataspace for the attribute */
+    sid3 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
+
+    /* Create the attribute and write the region references to it. */
+    attr1 = H5Acreate2 (dset1, "Attribute1", H5T_STD_REF_DSETREG, sid3, H5P_DEFAULT,
+                    H5P_DEFAULT);
+    H5Awrite (attr1, H5T_STD_REF_DSETREG, wbuf);
+
+    /* Close attribute dataspace */
+    H5Sclose(sid3);
+
+    /* Close attribute */
+    H5Aclose (attr1);
+
+    /* Close Dataset */
+    H5Dclose(dset1);
+
+    /* Close uint8 dataset dataspace */
+    H5Sclose(sid2);
+
+    /* Close file */
+    H5Fclose(fid1);
+
+    /* Free memory buffers */
+    free(wbuf);
+    free(rbuf);
+    free(dwbuf);
+    free(drbuf);
+}
+
 /*taken from Elena's compound test file*/
 static void gent_nestcomp(void)
 {
@@ -6351,6 +6472,7 @@ int main(void)
     gent_enum();
     gent_objref();
     gent_datareg();
+    gent_attrreg();
     gent_nestcomp();
     gent_opaque();
     gent_bitfields();
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index 5bf7f75..3ffff50 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -489,6 +489,9 @@ fi
 
 # test for dataset region references 
 TOOLTEST tdatareg.ddl tdatareg.h5
+TOOLTEST tdataregR.ddl -R tdatareg.h5
+TOOLTEST tattrreg.ddl tattrreg.h5
+TOOLTEST tattrregR.ddl -R tattrreg.h5
 
 # tests for group creation order
 # "1" tracked, "2" name, root tracked