Incorporate patch from GE Healthcare (HDFFV-9934)

This is the same patch that had already been integrated to 1.8 branch (pull request #387).
Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.

1 files changed, 100 insertions, 49 deletions

diff --git a/src/H5Dio.c b/src/H5Dio.c
index dfd3f17..572e6cf 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -125,9 +125,13 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 	hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
 {
     H5D_t		   *dset = NULL;
-    const H5S_t		   *mem_space = NULL;
-    const H5S_t		   *file_space = NULL;
-    herr_t                  ret_value = SUCCEED;  /* Return value */
+    const H5S_t	    *mem_space = NULL;
+    const H5S_t	    *file_space = NULL;
+    H5P_genplist_t     *plist;              /* Property list pointer */
+    hsize_t         *direct_offset = NULL;
+    hbool_t         direct_read = FALSE;
+    uint32_t        direct_filters = 0;
+    herr_t          ret_value = SUCCEED;    /* Return value */
 
     FUNC_ENTER_API(FAIL)
     H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id,
@@ -135,28 +139,29 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 
     /* check arguments */
     if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
     if(NULL == dset->oloc.file)
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
 
     if(mem_space_id < 0 || file_space_id < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
 
     if(H5S_ALL != mem_space_id) {
-	if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
-	    HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+        if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
 
-	/* Check for valid selection */
-	if(H5S_SELECT_VALID(mem_space) != TRUE)
-	    HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+        /* Check for valid selection */
+        if(H5S_SELECT_VALID(mem_space) != TRUE)
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
     } /* end if */
+
     if(H5S_ALL != file_space_id) {
-	if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
-	    HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+        if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
 
-	/* Check for valid selection */
-	if(H5S_SELECT_VALID(file_space) != TRUE)
-	    HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+        /* Check for valid selection */
+        if(H5S_SELECT_VALID(file_space) != TRUE)
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
     } /* end if */
 
     /* Get the default dataset transfer property list if the user didn't provide one */
@@ -166,9 +171,55 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
         if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
 
-    /* read raw data */
-    if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
-	HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+    /* Get the dataset transfer property list */
+    if(NULL == (plist = (H5P_genplist_t *)H5I_object(plist_id)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+
+    /* Retrieve the 'direct read' flag */
+    if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &direct_read) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk read")
+
+    if(direct_read) {
+        unsigned u;
+        hsize_t  dims[H5O_LAYOUT_NDIMS];
+        hsize_t  internal_offset[H5O_LAYOUT_NDIMS];
+
+        if(H5D_CHUNKED != dset->shared->layout.type)
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+        /* Get the direct chunk offset property */
+        if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &direct_offset) < 0)
+            HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting direct offset from xfer properties")
+
+        /* The library's chunking code requires the offset terminates with a zero. So transfer the
+         * offset array to an internal offset array */
+        for(u = 0; u < dset->shared->ndims; u++) {
+            /* Make sure the offset doesn't exceed the dataset's dimensions */
+            if(direct_offset[u] > dset->shared->curr_dims[u])
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+
+            /* Make sure the offset fall right on a chunk's boundary */
+            if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+
+            internal_offset[u] = direct_offset[u];
+        } /* end for */
+
+        /* Terminate the offset with a zero */
+        internal_offset[dset->shared->ndims] = 0;
+
+        /* Read the raw chunk */
+        if(H5D__chunk_direct_read(dset, plist_id, internal_offset, &direct_filters, buf) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read chunk directly")
+        /* Set the chunk filter mask property */
+        if(H5P_set(plist, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, &direct_filters) < 0)
+            HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error setting filter mask xfer property")
+    }
+    else {
+        /* read raw data */
+        if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+    }
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -245,28 +296,28 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     /* Check dataspace selections if this is not a direct write */
     if(!direct_write) {
         if(mem_space_id < 0 || file_space_id < 0)
-	    HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
-	if(H5S_ALL != mem_space_id) {
-	    if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
-	        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
-	    /* Check for valid selection */
-	    if(H5S_SELECT_VALID(mem_space) != TRUE)
-		HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
-	} /* end if */
-	if(H5S_ALL != file_space_id) {
-	    if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
-		HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
-	    /* Check for valid selection */
-	    if(H5S_SELECT_VALID(file_space) != TRUE)
-		HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
-	} /* end if */
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+        if(H5S_ALL != mem_space_id) {
+            if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+                HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+            /* Check for valid selection */
+            if(H5S_SELECT_VALID(mem_space) != TRUE)
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
+        } /* end if */
+        if(H5S_ALL != file_space_id) {
+            if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+                HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+            /* Check for valid selection */
+            if(H5S_SELECT_VALID(file_space) != TRUE)
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
+        } /* end if */
     }
 
     if(H5D__pre_write(dset, direct_write, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0) 
-	HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -300,15 +351,15 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
         uint32_t direct_filters;
         hsize_t *direct_offset;
         uint32_t direct_datasize;
-	hsize_t  internal_offset[H5O_LAYOUT_NDIMS];
-	unsigned u;                 /* Local index variable */
+        hsize_t  internal_offset[H5O_LAYOUT_NDIMS];
+        unsigned u;                 /* Local index variable */
 
         /* Get the dataset transfer property list */
         if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
 
         if(H5D_CHUNKED != dset->shared->layout.type)
-	    HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
 
         /* Retrieve parameters for direct chunk write */
         if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0)
@@ -318,19 +369,19 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
         if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write")
 
-	/* The library's chunking code requires the offset terminates with a zero. So transfer the 
+        /* The library's chunking code requires the offset terminates with a zero. So transfer the 
          * offset array to an internal offset array */ 
-	for(u = 0; u < dset->shared->ndims; u++) {
-	    /* Make sure the offset doesn't exceed the dataset's dimensions */
+        for(u = 0; u < dset->shared->ndims; u++) {
+            /* Make sure the offset doesn't exceed the dataset's dimensions */
             if(direct_offset[u] > dset->shared->curr_dims[u])
-		HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
 
             /* Make sure the offset fall right on a chunk's boundary */
-	    if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
-		HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+            if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+                HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
 
-	    internal_offset[u] = direct_offset[u]; 
-	} /* end for */
+            internal_offset[u] = direct_offset[u]; 
+        } /* end for */
 	   
 	/* Terminate the offset with a zero */ 
 	internal_offset[dset->shared->ndims] = 0;
@@ -342,7 +393,7 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
     else {     /* Normal write */
         /* write raw data */
         if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
-	    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+            HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
     } /* end else */
 
 done: