[svn-r451] Completely tore out existing dataspace API and replaced with code to match

API defined in the html/Dataspaces.html document.  This code does not include
support for strides, merging selections, or permutations of coordinates yet,
but it's a drop-in replacement for the existing API with the same features.

1 files changed, 455 insertions, 0 deletions

diff --git a/src/H5Spoint.c b/src/H5Spoint.c
new file mode 100644
index 0000000..86b1bc9
--- /dev/null
+++ b/src/H5Spoint.c
@@ -0,0 +1,455 @@
+/*
+ * Copyright (C) 1998 NCSA
+ *                    All rights reserved.
+ *
+ * Programmer:  Quincey Koziol <koziol@ncsa.uiuc.edu>
+ *              Tuesday, June 16, 1998
+ *
+ * Purpose:	Point selection data space I/O functions.
+ */
+#include <H5private.h>
+#include <H5Eprivate.h>
+#include <H5Sprivate.h>
+#include <H5Vprivate.h>
+
+/* Interface initialization */
+#define PABLO_MASK      H5S_point_mask
+#define INTERFACE_INIT  NULL
+static intn             interface_initialize_g = FALSE;
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_init
+ *
+ * Purpose:	Initializes iteration information for point selection.
+ *
+ * Return:	non-negative on success, negative on failure.
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, June 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_point_init (const struct H5O_layout_t __unused__ *layout,
+	       const H5S_t *space, H5S_sel_iter_t *sel_iter)
+{
+    FUNC_ENTER (H5S_point_init, FAIL);
+
+    /* Check args */
+    assert (layout);
+    assert (space && H5S_SEL_POINTS==space->select.type);
+    assert (sel_iter);
+
+    /* Initialize the number of points to iterate over */
+    sel_iter->pnt.elmt_left=space->select.num_elem;
+
+    /* Start at the head of the list of points */
+    sel_iter->pnt.curr=space->select.sel_info.pnt_lst->head;
+    
+    FUNC_LEAVE (SUCCEED);
+}
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_favail
+ *
+ * Purpose:	Figure out the optimal number of elements to transfer to/from the file
+ *
+ * Return:	non-negative number of elements on success, negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, June 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+size_t
+H5S_point_favail (const H5S_t __unused__ *space, const H5S_sel_iter_t *sel_iter, size_t max)
+{
+    FUNC_ENTER (H5S_point_favail, FAIL);
+
+    /* Check args */
+    assert (space && H5S_SEL_POINTS==space->select.type);
+    assert (sel_iter);
+
+    FUNC_LEAVE (MIN(sel_iter->pnt.elmt_left,max));
+}   /* H5S_point_favail() */
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_fgath
+ *
+ * Purpose:	Gathers data points from file F and accumulates them in the
+ *		type conversion buffer BUF.  The LAYOUT argument describes
+ *		how the data is stored on disk and EFL describes how the data
+ *		is organized in external files.  ELMT_SIZE is the size in
+ *		bytes of a datum which this function treats as opaque.
+ *		FILE_SPACE describes the data space of the dataset on disk
+ *		and the elements that have been selected for reading (via
+ *		hyperslab, etc).  This function will copy at most NELMTS elements.
+ *
+ *  Notes: This could be optimized by gathering selected elements near (how
+ *      near?) each other into one I/O request and then moving the correct
+ *      elements into the return buffer
+ *
+ * Return:	Success:	Number of elements copied.
+ *
+ *		Failure:	0
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, June 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+size_t
+H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout,
+		const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
+		size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter,
+		size_t nelmts,
+		const H5D_transfer_t xfer_mode, void *_buf/*out*/)
+{
+    hssize_t	file_offset[H5O_LAYOUT_NDIMS];	/*offset of slab in file*/
+    hsize_t	hsize[H5O_LAYOUT_NDIMS];	/*size of hyperslab	*/
+    hssize_t	zero[H5O_LAYOUT_NDIMS];		/*zero			*/
+    uint8 *buf=(uint8 *)_buf;   /* Alias for pointer arithmetic */
+    intn	i;				/*counters		*/
+    size_t  num_read;       /* number of elements read into buffer */
+
+    FUNC_ENTER (H5S_point_fgath, 0);
+
+    /* Check args */
+    assert (f);
+    assert (layout);
+    assert (elmt_size>0);
+    assert (file_space);
+    assert (file_iter);
+    assert (nelmts>0);
+    assert (buf);
+
+    /* initialize hyperslab size and offset in memory buffer */
+    for(i=0; i<layout->ndims; i++) {
+        hsize[i]=1;     /* hyperslab size is 1, except for last element */
+        zero[i]=0;      /* memory offset is 0 */
+    } /* end for */
+    hsize[layout->ndims] = elmt_size;
+
+    /* Walk though and request each element we need and put it into the buffer */
+    num_read=0;
+    while(num_read<nelmts) {
+        if(file_iter->pnt.elmt_left>0) {
+            /* Copy the location of the point to get */
+            HDmemcpy(file_offset,file_iter->pnt.curr->pnt,layout->ndims);
+            file_offset[layout->ndims] = 0;
+
+            /* Go read the point */
+            if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, file_offset,
+                      xfer_mode, buf/*out*/)<0) {
+                HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error");
+            }
+
+            /* Increment the offset of the buffer */
+            buf+=elmt_size;
+
+            /* Increment the count read */
+            num_read++;
+
+            /* Advance the point iterator */
+            file_iter->pnt.elmt_left--;
+            file_iter->pnt.curr=file_iter->pnt.curr->next;
+        } else {
+            break;      /* out of elements in the selection */
+        } /* end else */
+    } /* end while */
+    
+    FUNC_LEAVE (num_read);
+} /* H5S_point_fgath() */
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_fscat
+ *
+ * Purpose:	Scatters dataset elements from the type conversion buffer BUF
+ *		to the file F where the data points are arranged according to
+ *		the file data space FILE_SPACE and stored according to
+ *		LAYOUT and EFL. Each element is ELMT_SIZE bytes.
+ *		The caller is requesting that NELMTS elements are copied.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, June 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout,
+		const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
+		size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter,
+		size_t nelmts,
+		const H5D_transfer_t xfer_mode, const void *_buf)
+{
+    hssize_t	file_offset[H5O_LAYOUT_NDIMS];	/*offset of hyperslab	*/
+    hsize_t	hsize[H5O_LAYOUT_NDIMS];	/*size of hyperslab	*/
+    hssize_t	zero[H5O_LAYOUT_NDIMS];		/*zero vector		*/
+    const uint8 *buf=(const uint8 *)_buf;   /* Alias for pointer arithmetic */
+    intn	i;				/*counters		*/
+    size_t  num_written;    /* number of elements written from buffer */
+
+    FUNC_ENTER (H5S_point_fscat, FAIL);
+
+    /* Check args */
+    assert (f);
+    assert (layout);
+    assert (elmt_size>0);
+    assert (file_space);
+    assert (file_iter);
+    assert (nelmts>0);
+    assert (buf);
+
+    /* initialize hyperslab size and offset in memory buffer */
+    for(i=0; i<layout->ndims; i++) {
+        hsize[i]=1;     /* hyperslab size is 1, except for last element */
+        zero[i]=0;      /* memory offset is 0 */
+    } /* end for */
+    hsize[layout->ndims] = elmt_size;
+
+    /* Walk though and request each element we need and put it into the buffer */
+    num_written=0;
+    while(num_written<nelmts) {
+        if(file_iter->pnt.elmt_left>0) {
+            /* Copy the location of the point to get */
+            HDmemcpy(file_offset,file_iter->pnt.curr->pnt,layout->ndims);
+            file_offset[layout->ndims] = 0;
+
+            /* Go read the point */
+            if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero, file_offset,
+                      xfer_mode, buf)<0) {
+                HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error");
+            }
+
+            /* Increment the offset of the buffer */
+            buf+=elmt_size;
+
+            /* Increment the count read */
+            num_written++;
+
+            /* Advance the point iterator */
+            file_iter->pnt.elmt_left--;
+            file_iter->pnt.curr=file_iter->pnt.curr->next;
+        } else {
+            break;      /* out of elements in the selection */
+        } /* end else */
+    } /* end while */
+
+    FUNC_LEAVE (num_written);
+}   /* H5S_point_fscat() */
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_mgath
+ *
+ * Purpose:	Gathers dataset elements from application memory BUF and
+ *		copies them into the data type conversion buffer TCONV_BUF.
+ *		Each element is ELMT_SIZE bytes and arranged in application
+ *		memory according to MEM_SPACE.  
+ *		The caller is requesting that at most NELMTS be gathered.
+ *
+ * Return:	Success:	Number of elements copied.
+ *
+ *		Failure:	0
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, June 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+size_t
+H5S_point_mgath (const void *_buf, size_t elmt_size,
+		const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
+		size_t nelmts, void *_tconv_buf/*out*/)
+{
+    hsize_t	mem_size[H5O_LAYOUT_NDIMS];	/*total size of app buf	*/
+    const uint8 *buf=(const uint8 *)_buf;   /* Get local copies for address arithmetic */
+    uint8 *tconv_buf=(uint8 *)_tconv_buf;
+    hsize_t	acc;				/*accumulator		*/
+    intn	space_ndims;			/*dimensionality of space*/
+    intn	i;				/*counters		*/
+    size_t num_gath;        /* number of elements gathered */
+
+    FUNC_ENTER (H5S_point_mgath, 0);
+
+    /* Check args */
+    assert (buf);
+    assert (elmt_size>0);
+    assert (mem_space && H5S_SEL_POINTS==mem_space->select.type);
+    assert (nelmts>0);
+    assert (tconv_buf);
+
+    if ((space_ndims=H5S_get_dims (mem_space, mem_size, NULL))<0) {
+        HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0,
+		       "unable to retrieve data space dimensions");
+    }
+
+    for(num_gath=0; num_gath<nelmts; num_gath++) {
+        if(mem_iter->pnt.elmt_left>0) {
+            /* Compute the location of the point to get */
+            for(i=0,acc=0; i<space_ndims; i++)
+                acc+=mem_size[i]*mem_iter->pnt.curr->pnt[i];
+
+            /* Copy the elements into the type conversion buffer */
+            *tconv_buf=*(buf+acc);
+
+            /* Increment the offset of the buffers */
+            tconv_buf+=elmt_size;
+
+            /* Advance the point iterator */
+            mem_iter->pnt.elmt_left--;
+            mem_iter->pnt.curr=mem_iter->pnt.curr->next;
+        } else {
+            break;      /* out of elements in the selection */
+        } /* end else */
+    } /* end for */
+
+    FUNC_LEAVE (num_gath);
+}   /* H5S_point_mgath() */
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_point_mscat
+ *
+ * Purpose:	Scatters NELMTS data points from the type conversion buffer
+ *		TCONV_BUF to the application buffer BUF.  Each element is
+ *		ELMT_SIZE bytes and they are organized in application memory
+ *		according to MEM_SPACE.
+ *
+ * Return:	Success:	SUCCEED
+ *
+ *		Failure:	FAIL
+ *
+ * Programmer:	Quincey Koziol
+ *              Wednesday, June 17, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_point_mscat (const void *_tconv_buf, size_t elmt_size,
+		const H5S_t *mem_space, H5S_sel_iter_t *mem_iter,
+		size_t nelmts, void *_buf/*out*/)
+{
+    hsize_t	mem_size[H5O_LAYOUT_NDIMS];	/*total size of app buf	*/
+    uint8 *buf=(uint8 *)_buf;   /* Get local copies for address arithmetic */
+    const uint8 *tconv_buf=(const uint8 *)_tconv_buf;
+    hsize_t	acc;				/*accumulator		*/
+    intn	space_ndims;			/*dimensionality of space*/
+    intn	i;				/*counters		*/
+    size_t num_scat;        /* Number of elements scattered */
+
+    FUNC_ENTER (H5S_point_mscat, FAIL);
+
+    /* Check args */
+    assert (tconv_buf);
+    assert (elmt_size>0);
+    assert (mem_space && H5S_SEL_POINTS==mem_space->select.type);
+    assert (nelmts>0);
+    assert (buf);
+
+    /*
+     * Retrieve hyperslab information to determine what elements are being
+     * selected (there might be other selection methods in the future).  We
+     * only handle hyperslabs with unit sample because there's currently no
+     * way to pass sample information to H5V_hyper_copy().
+     */
+    if ((space_ndims=H5S_get_dims (mem_space, mem_size, NULL))<0) {
+        HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL,
+		       "unable to retrieve data space dimensions");
+    }
+
+    for(num_scat=0; num_scat<nelmts; num_scat++) {
+        if(mem_iter->pnt.elmt_left>0) {
+            /* Compute the location of the point to get */
+            for(i=0,acc=0; i<space_ndims; i++)
+                acc+=mem_size[i]*mem_iter->pnt.curr->pnt[i];
+
+            /* Copy the elements into the type conversion buffer */
+            *(buf+acc)=*tconv_buf;
+
+            /* Increment the offset of the buffers */
+            tconv_buf+=elmt_size;
+
+            /* Advance the point iterator */
+            mem_iter->pnt.elmt_left--;
+            mem_iter->pnt.curr=mem_iter->pnt.curr->next;
+        } else {
+            break;      /* out of elements in the selection */
+        } /* end else */
+    } /* end for */
+
+    FUNC_LEAVE (SUCCEED);
+}   /* H5S_point_mscat() */
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5S_point_release
+ PURPOSE
+    Release point selection information for a dataspace
+ USAGE
+    herr_t H5S_point_release(space)
+        H5S_t *space;       IN: Pointer to dataspace
+ RETURNS
+    SUCCEED/FAIL
+ DESCRIPTION
+    Releases all point selection information for a dataspace
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5S_point_release (H5S_t *space)
+{
+    intn i;     /* Counters */
+
+    FUNC_ENTER (H5S_point_release, FAIL);
+
+    /* Check args */
+    assert (space);
+
+done:
+    FUNC_LEAVE (SUCCEED);
+}   /* H5S_point_release() */
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5S_point_npoints
+ PURPOSE
+    Compute number of elements in current selection
+ USAGE
+    hsize_t H5S_point_npoints(space)
+        H5S_t *space;       IN: Pointer to dataspace
+ RETURNS
+    The number of elements in selection on success, 0 on failure
+ DESCRIPTION
+    Compute number of elements in current selection.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+hsize_t
+H5S_hyper_npoints (H5S_t *space)
+{
+    FUNC_ENTER (H5S_hyper_npoints, 0);
+
+    /* Check args */
+    assert (space);
+
+    FUNC_LEAVE (space->select.num_elem);
+}   /* H5S_hyper_npoints() */