[svn-r1385] Updated H5Rdereference, H5Rget_object_type and H5Rget_region to accept a

location ID (i.e. a file or group ID) as well as the dataset ID.  This should
allow Dave to get the palettes stored in the file correctly and also enable
Bob and/or Bruce's indexing stuff.  This change should be folded into the
documentation for these three functions for the release.
    Also, I fixed a number of bugs in the hyperslab and point selection
iterators for H5Diterate and they are working correctly now.

7 files changed, 96 insertions, 54 deletions

diff --git a/src/H5D.c b/src/H5D.c
index 4a55b64..fb927a3 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -2350,15 +2350,15 @@ H5D_typeof (H5D_t *dset)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5D_get_file
+ * Function:  H5D_get_file
  *
- * Purpose:	Returns the dataset's file pointer.
+ * Purpose:   Returns the dataset's file pointer.
  *
- * Return:	Success:	Ptr to the dataset's file pointer.
+ * Return:    Success:        Ptr to the dataset's file pointer.
  *
- *		Failure:	NULL
+ *            Failure:        NULL
  *
- * Programmer:	Quincey Koziol
+ * Programmer:        Quincey Koziol
  *              Thursday, October 22, 1998
  *
  * Modifications:
diff --git a/src/H5R.c b/src/H5R.c
index bb4b869..924cef3 100644
--- a/src/H5R.c
+++ b/src/H5R.c
@@ -37,9 +37,9 @@ static herr_t		H5R_init_interface(void);
 /* Static functions */
 static herr_t H5R_create(void *ref, H5G_entry_t *loc, const char *name,
         H5R_type_t ref_type, H5S_t *space);
-static hid_t H5R_dereference(H5D_t *dset, H5R_type_t ref_type, void *_ref);
-static H5S_t * H5R_get_region(H5D_t *dset, H5R_type_t ref_type, void *_ref);
-static intn H5R_get_object_type(H5D_t *dset, void *_ref);
+static hid_t H5R_dereference(H5F_t *file, H5R_type_t ref_type, void *_ref);
+static H5S_t * H5R_get_region(H5F_t *file, H5R_type_t ref_type, void *_ref);
+static intn H5R_get_object_type(H5F_t *file, void *_ref);
 
 
 /*--------------------------------------------------------------------------
@@ -319,7 +319,7 @@ done:
     Opens the HDF5 object referenced.
  USAGE
     hid_t H5R_dereference(ref)
-        H5D_t *dset;        IN: Dataset reference object is in.
+        H5F_t *file;        IN: File the object being dereferenced is within
         H5R_type_t ref_type;    IN: Type of reference
         void *ref;          IN: Reference to open.
         
@@ -335,7 +335,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 static hid_t
-H5R_dereference(H5D_t *dset, H5R_type_t ref_type, void *_ref)
+H5R_dereference(H5F_t *file, H5R_type_t ref_type, void *_ref)
 {
     H5D_t *dataset;             /* Pointer to dataset to open */
     H5G_t *group;               /* Pointer to group to open */
@@ -349,12 +349,12 @@ H5R_dereference(H5D_t *dset, H5R_type_t ref_type, void *_ref)
 
     assert(_ref);
     assert(ref_type>H5R_BADTYPE || ref_type<H5R_MAXTYPE);
-    assert(dset);
+    assert(file);
 
     /* Initialize the symbol table entry */
     HDmemset(&ent,0,sizeof(H5G_entry_t));
     ent.type=H5G_NOTHING_CACHED;
-    ent.file=H5D_get_file(dset);
+    ent.file=file;
 
     switch(ref_type) {
         case H5R_OBJECT:
@@ -467,9 +467,10 @@ done:
     Opens the HDF5 object referenced.
  USAGE
     hid_t H5Rdereference(ref)
-        hid_t dataset;      IN: Dataset reference object is in.
+        hid_t id;       IN: Dataset reference object is in or location ID of
+                            object that the dataset is located within.
         H5R_type_t ref_type;    IN: Type of reference to create
-        void *ref;          IN: Reference to open.
+        void *ref;      IN: Reference to open.
         
  RETURNS
     Valid ID on success, Negative on failure
@@ -482,24 +483,33 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 hid_t
-H5Rdereference(hid_t dataset, H5R_type_t ref_type, void *_ref)
+H5Rdereference(hid_t id, H5R_type_t ref_type, void *_ref)
 {
-    H5D_t		   *dset = NULL;	/* dataset object */
+    H5G_entry_t *loc = NULL;    /* Symbol table entry */
+    H5D_t *dset = NULL;     /* dataset object */
+    H5F_t *file=NULL;       /* File object */
     hid_t ret_value = FAIL;
 
     FUNC_ENTER(H5Rdereference, FAIL);
-    H5TRACE3("i","iRtx",dataset,ref_type,_ref);
+    H5TRACE3("i","iRtx",id,ref_type,_ref);
 
     /* Check args */
-    if (H5I_DATASET != H5I_get_type(dataset) || NULL == (dset = H5I_object(dataset)))
-        HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+    if (H5I_DATASET == H5I_get_type(id)) {
+        if(NULL == (dset = H5I_object(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+        file=H5D_get_file(dset);
+    } else {
+        if (NULL == (loc = H5G_loc(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
+        file=loc->file;
+    }
     if(ref_type<=H5R_BADTYPE || ref_type>=H5R_MAXTYPE)
         HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type");
     if(_ref==NULL)
         HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer");
 
     /* Create reference */
-    if ((ret_value=H5R_dereference(dset, ref_type, _ref))<0)
+    if ((ret_value=H5R_dereference(file, ref_type, _ref))<0)
         HGOTO_ERROR (H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable dereference object");
 
 done:
@@ -513,8 +523,10 @@ done:
  PURPOSE
     Retrieves a dataspace with the region pointed to selected.
  USAGE
-    H5S_t *H5R_get_region(ref)
-        void *ref;        IN: Reference to open.
+    H5S_t *H5R_get_region(file, ref_type, ref)
+        H5F_t *file;        IN: File the object being dereferenced is within
+        H5R_type_t ref_type;    UNUSED
+        void *ref;          IN: Reference to open.
         
  RETURNS
     Pointer to the dataspace on success, NULL on failure
@@ -528,7 +540,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 static H5S_t *
-H5R_get_region(H5D_t *dset, H5R_type_t UNUSED ref_type, void *_ref)
+H5R_get_region(H5F_t *file, H5R_type_t UNUSED ref_type, void *_ref)
 {
     H5D_t *dataset;             /* Pointer to dataset to open */
     H5G_entry_t ent;            /* Symbol table entry */
@@ -542,12 +554,12 @@ H5R_get_region(H5D_t *dset, H5R_type_t UNUSED ref_type, void *_ref)
 
     assert(_ref);
     assert(ref_type==H5R_DATASET_REGION);
-    assert(dset);
+    assert(file);
 
     /* Initialize the symbol table entry */
     HDmemset(&ent,0,sizeof(H5G_entry_t));
     ent.type=H5G_NOTHING_CACHED;
-    ent.file=H5D_get_file(dset);
+    ent.file=file;
 
     /* Get the heap ID for the dataset region */
     p=(uint8_t *)ref->heapid;
@@ -597,7 +609,10 @@ done:
  PURPOSE
     Retrieves a dataspace with the region pointed to selected.
  USAGE
-    hid_t H5Rget_region(ref)
+    hid_t H5Rget_region(id, ref_type, ref)
+        hid_t id;       IN: Dataset reference object is in or location ID of
+                            object that the dataset is located within.
+        H5R_type_t ref_type;    IN: Type of reference to get region of
         void *ref;        IN: Reference to open.
         
  RETURNS
@@ -612,25 +627,34 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 hid_t
-H5Rget_region(hid_t dataset, H5R_type_t ref_type, void *_ref)
+H5Rget_region(hid_t id, H5R_type_t ref_type, void *_ref)
 {
+    H5G_entry_t *loc = NULL;    /* Symbol table entry */
     H5D_t *dset = NULL;     /* dataset object */
     H5S_t *space = NULL;    /* dataspace object */
+    H5F_t *file=NULL;       /* File object */
     hid_t ret_value = FAIL;
 
     FUNC_ENTER(H5Rget_region, FAIL);
-    H5TRACE3("i","iRtx",dataset,ref_type,_ref);
+    H5TRACE3("i","iRtx",id,ref_type,_ref);
 
     /* Check args */
-    if (H5I_DATASET != H5I_get_type(dataset) || NULL == (dset = H5I_object(dataset)))
-        HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+    if (H5I_DATASET == H5I_get_type(id)) {
+        if(NULL == (dset = H5I_object(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+        file=H5D_get_file(dset);
+    } else {
+        if (NULL == (loc = H5G_loc(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
+        file=loc->file;
+    }
     if(ref_type!=H5R_DATASET_REGION)
         HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type");
     if(_ref==NULL)
         HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer");
 
     /* Get the dataspace with the correct region selected */
-    if ((space=H5R_get_region(dset,ref_type,_ref))==NULL)
+    if ((space=H5R_get_region(file,ref_type,_ref))==NULL)
         HGOTO_ERROR (H5E_REFERENCE, H5E_CANTCREATE, FAIL, "unable to create dataspace");
 
     /* Atomize */
@@ -648,8 +672,8 @@ done:
  PURPOSE
     Retrieves the type of object that an object reference points to
  USAGE
-    intn H5Rget_object_type(dset, ref)
-        H5D_t *dset;        IN: dataset pointer that the reference is located within
+    intn H5R_get_object_type(file, ref)
+        H5F_t *file;        IN: File the object being dereferenced is within
         void *ref;          IN: Reference to query.
         
  RETURNS
@@ -664,7 +688,7 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 static intn
-H5R_get_object_type(H5D_t *dset, void *_ref)
+H5R_get_object_type(H5F_t *file, void *_ref)
 {
     H5G_entry_t ent;            /* Symbol table entry */
     hobj_ref_t *ref=(hobj_ref_t *)_ref; /* Only object references currently supported */
@@ -674,12 +698,12 @@ H5R_get_object_type(H5D_t *dset, void *_ref)
     FUNC_ENTER(H5R_get_object_type, H5G_UNKNOWN);
 
     assert(ref);
-    assert(dset);
+    assert(file);
 
     /* Initialize the symbol table entry */
     HDmemset(&ent,0,sizeof(H5G_entry_t));
     ent.type=H5G_NOTHING_CACHED;
-    ent.file=H5D_get_file(dset);
+    ent.file=file;
 
     /* Get the object oid */
     p=(uint8_t *)ref->oid;
@@ -700,8 +724,9 @@ done:
  PURPOSE
     Retrieves the type of object that an object reference points to
  USAGE
-    intn H5Rget_object_type(ref)
-        hid_t dataset;      IN: dataset the reference is located within
+    intn H5Rget_object_type(id, ref)
+        hid_t id;       IN: Dataset reference object is in or location ID of
+                            object that the dataset is located within.
         void *ref;          IN: Reference to query.
         
  RETURNS
@@ -716,24 +741,32 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 int
-H5Rget_object_type(hid_t dataset, void *_ref)
+H5Rget_object_type(hid_t id, void *_ref)
 {
+    H5G_entry_t *loc = NULL;    /* Symbol table entry */
     H5D_t *dset = NULL;     /* dataset object */
+    H5F_t *file=NULL;       /* File object */
     hid_t ret_value = H5G_UNKNOWN;
 
     FUNC_ENTER(H5Rget_object_type, H5G_UNKNOWN);
-    H5TRACE2("Is","ix",dataset,_ref);
+    H5TRACE2("Is","ix",id,_ref);
 
     /* Check args */
-    if (H5I_DATASET != H5I_get_type(dataset) ||
-	NULL == (dset = H5I_object(dataset)))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5G_UNKNOWN, "not a dataset");
+    if (H5I_DATASET == H5I_get_type(id)) {
+        if(NULL == (dset = H5I_object(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
+        file=H5D_get_file(dset);
+    } else {
+        if (NULL == (loc = H5G_loc(id)))
+            HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
+        file=loc->file;
+    }
     if(_ref==NULL)
         HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, H5G_UNKNOWN,
 		     "invalid reference pointer");
 
     /* Get the object information */
-    if ((ret_value=H5R_get_object_type(dset,_ref))<0) {
+    if ((ret_value=H5R_get_object_type(file,_ref))<0) {
 	HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, H5G_UNKNOWN,
 		    "unable to determine object type");
     }
diff --git a/src/H5Sall.c b/src/H5Sall.c
index 18d8f52..9109589 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -9,6 +9,7 @@
  */
 #include <H5private.h>
 #include <H5Eprivate.h>
+#include <H5Iprivate.h>
 #include <H5Sprivate.h>
 #include <H5Vprivate.h>
 #include <H5Dprivate.h>
@@ -967,7 +968,7 @@ H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op
     assert(buf);
     assert(space);
     assert(operator);
-    assert(H5I_DATATYPE != H5I_get_type(type_id));
+    assert(H5I_DATATYPE == H5I_get_type(type_id));
 
     /* Get the dataspace extent rank */
     rank=space->extent.u.simple.rank;
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index ecef87c..50704bd 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -2992,7 +2992,7 @@ H5S_hyper_select_iterate_mem (intn dim, H5S_hyper_iter_info_t *iter_info)
     size_t i;                   /* Counters */
     intn j;
 
-    FUNC_ENTER (H5S_hyper_mwrite, 0);
+    FUNC_ENTER (H5S_hyper_select_iterate_mem, 0);
 
     assert(iter_info);
 
@@ -3010,6 +3010,8 @@ H5S_hyper_select_iterate_mem (intn dim, H5S_hyper_iter_info_t *iter_info)
         /*  (Which means that we've got a list of the regions in the fastest */
         /*   changing dimension and should input those regions) */
         if((dim+2)==iter_info->space->extent.u.simple.rank) {
+            HDmemcpy(iter_info->mem_offset, iter_info->iter->hyp.pos,(iter_info->space->extent.u.simple.rank*sizeof(hssize_t)));
+            iter_info->mem_offset[iter_info->space->extent.u.simple.rank]=0;
 
             /* Iterate over data from regions */
             for(i=0; i<num_regions && user_ret==0; i++) {
@@ -3028,6 +3030,9 @@ H5S_hyper_select_iterate_mem (intn dim, H5S_hyper_iter_info_t *iter_info)
 
                     /* Subtract the element from the selected region (not implemented yet) */
 
+                    /* Increment the coordinate offset */
+                    iter_info->mem_offset[iter_info->space->extent.u.simple.rank-1]=j;
+
                     /* Advance the pointer in the buffer */
                     tmp_buf=((char *)tmp_buf+iter_info->elem_size);
                 } /* end for */
@@ -3122,7 +3127,7 @@ H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t
     assert(buf);
     assert(space);
     assert(operator);
-    assert(H5I_DATATYPE != H5I_get_type(type_id));
+    assert(H5I_DATATYPE == H5I_get_type(type_id));
 
     /* Initialize these before any errors can occur */
     HDmemset(&iter,0,sizeof(H5S_sel_iter_t));
@@ -3159,8 +3164,6 @@ H5S_hyper_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t
     HDmemcpy(iter_info.mem_size, space->extent.u.simple.size, space->extent.u.simple.rank*sizeof(hsize_t));
     iter_info.mem_size[space->extent.u.simple.rank]=iter_info.elem_size;
     /* Copy the location of the region in the file */
-    HDmemcpy(iter_info.mem_offset, iter.hyp.pos,(space->extent.u.simple.rank*sizeof(hssize_t)));
-    iter_info.mem_offset[space->extent.u.simple.rank]=0;
     iter_info.op=operator;
     iter_info.op_data=operator_data;
 
diff --git a/src/H5Snone.c b/src/H5Snone.c
index 508be0e..cb5ede3 100644
--- a/src/H5Snone.c
+++ b/src/H5Snone.c
@@ -133,7 +133,7 @@ H5S_none_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t o
     assert(buf);
     assert(space);
     assert(operator);
-    assert(H5I_DATATYPE != H5I_get_type(type_id));
+    assert(H5I_DATATYPE == H5I_get_type(type_id));
 
     FUNC_LEAVE (ret_value);
 }   /* H5S_hyper_select_iterate() */
diff --git a/src/H5Spoint.c b/src/H5Spoint.c
index 583aab7..4d248b8 100644
--- a/src/H5Spoint.c
+++ b/src/H5Spoint.c
@@ -1149,6 +1149,7 @@ H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t
         void *operator_data)
 {
     hsize_t	mem_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */
+    hsize_t	mem_offset[H5O_LAYOUT_NDIMS];   /* Point offset */
     hsize_t offset;             /* offset of region in buffer */
     void *tmp_buf;              /* temporary location of the element in the buffer */
     H5S_pnt_node_t *node;   /* Point node */
@@ -1160,7 +1161,7 @@ H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t
     assert(buf);
     assert(space);
     assert(operator);
-    assert(H5I_DATATYPE != H5I_get_type(type_id));
+    assert(H5I_DATATYPE == H5I_get_type(type_id));
 
     /* Get the dataspace extent rank */
     rank=space->extent.u.simple.rank;
@@ -1172,8 +1173,12 @@ H5S_point_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t
     /* Iterate through the node, checking the bounds on each element */
     node=space->select.sel_info.pnt_lst->head;
     while(node!=NULL && ret_value==0) {
+        /* Set up the location of the point */
+        HDmemcpy(mem_offset, node->pnt, rank*sizeof(hssize_t));
+        mem_offset[rank]=0;
+
         /* Get the offset in the memory buffer */
-        offset=H5V_array_offset(rank+1,mem_size,node->pnt);
+        offset=H5V_array_offset(rank+1,mem_size,mem_offset);
         tmp_buf=((char *)buf+offset);
 
         ret_value=(*operator)(tmp_buf,type_id,rank,node->pnt,operator_data);
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 1379617..c36cc03 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -1725,7 +1725,7 @@ H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t operat
     assert(buf);
     assert(space);
     assert(operator);
-    assert(H5I_DATATYPE != H5I_get_type(type_id));
+    assert(H5I_DATATYPE == H5I_get_type(type_id));
 
     switch(space->select.type) {
         case H5S_SEL_POINTS:         /* Sequence of points selected */
@@ -1749,6 +1749,6 @@ H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t operat
             break;
     }
 
-    FUNC_LEAVE(SUCCEED);
+    FUNC_LEAVE(ret_value);
 }   /* end H5S_select_iterate() */