summaryrefslogtreecommitdiffstats
diff options
context:
space:
mode:
authorRobb Matzke <matzke@llnl.gov>1998-01-16 19:52:04 (GMT)
committerRobb Matzke <matzke@llnl.gov>1998-01-16 19:52:04 (GMT)
commit74618e3670ed6c8db4c01dd30d1d7bba70447027 (patch)
tree7cb9ab8c0802eb8a46edc885dd8d6167a3c98d24
parente59138031958a1ceb6105de0e1b222f85f2ac017 (diff)
downloadhdf5-74618e3670ed6c8db4c01dd30d1d7bba70447027.zip
hdf5-74618e3670ed6c8db4c01dd30d1d7bba70447027.tar.gz
hdf5-74618e3670ed6c8db4c01dd30d1d7bba70447027.tar.bz2
[svn-r155] Changes since 19980114
---------------------- ./html/Datasets.html Removed some archaic comments about data spaces. Fixed example code. ./MANIFEST ./html/H5.format.html ./src/H5O.c ./src/H5Oprivate.h ./src/H5Ocstore.c [DELETED] ./src/H5Oistore.c [DELETED] ./src/H5Olayout.c [NEW] ./src/Makefile.in ./test/istore.c Replaced H5O_CSTORE and H5O_ISTORE messages with a more general H5O_LAYOUT message. ./src/H5D.c ./src/H5Dprivate.h ./src/H5Dpublic.h A little more work on the pipeline. Access to the file data is through the new H5F_arr_read() and H5F_arr_write() which do I/O on hyperslabs of byte arrays and don't depend on data layout. This should simplify the I/O pipeline quite a bit. I also added another argument to H5Dread() and H5Dwrite() to describe the hyerslab of the file array on which I/O is occuring. We discussed this at last week's meeting. ./src/H5Farray.c [NEW] Added functions that sit on top of H5F_block_read() and H5F_istore_read() and implement a common set of functions between all layouts. This means I/O of hyperslabs of byte-arrays in the file to arrays of bytes in memory. When operating on arrays of elements (>1byte) then we just add another dimension. That is, a 10x20 array of int32 becomes a 10x20x4 array of bytes. [This is the area I'll be working on most of next week to implement partial I/O for contiguous data and to improve performance for chunked data.] ./src/H5Fistore.c ./src/H5Fprivate.h Replaced the H5F_istore_t data type with the layout message H5O_layout_t which looks almost the same. Eventually I'd like to rename `istore' to `chunked' everywhere and use `istore' for 1-d storage where the chunks are all different sizes like in the small object heap where each object is a chunk. ./src/H5V.c Changed ISTORE to LAYOUT in one place. ./test/dsets.c Fixed for extra argument to H5Dread() and H5Dwrite().
Diffstat
-rw-r--r--MANIFEST4
-rw-r--r--src/H5D.c310
-rw-r--r--src/H5Distore.c121
-rw-r--r--src/H5Dprivate.h8
-rw-r--r--src/H5Dpublic.h8
-rw-r--r--src/H5Farray.c219
-rw-r--r--src/H5Fistore.c121
-rw-r--r--src/H5Fprivate.h20
-rw-r--r--src/H5O.c4
-rw-r--r--src/H5Ocstore.c258
-rw-r--r--src/H5Olayout.c (renamed from src/H5Oistore.c)136
-rw-r--r--src/H5Oprivate.h28
-rw-r--r--src/H5V.c2
-rw-r--r--src/Makefile.in8
-rw-r--r--test/dsets.c11
-rw-r--r--test/istore.c35
16 files changed, 614 insertions, 679 deletions
diff --git a/MANIFEST b/MANIFEST
index e6695d9..f381227 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -47,6 +47,7 @@
./src/H5Eprivate.h
./src/H5Epublic.h
./src/H5F.c
+./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
@@ -77,10 +78,9 @@
./src/H5Mpublic.h
./src/H5O.c
./src/H5Ocont.c
-./src/H5Ocstore.c
./src/H5Odtype.c
./src/H5Oefl.c
-./src/H5Oistore.c
+./src/H5Olayout.c
./src/H5Oname.c
./src/H5Onull.c
./src/H5Oprivate.h
diff --git a/src/H5D.c b/src/H5D.c
index 419b88a..b200e2e 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -40,10 +40,7 @@ struct H5D_t {
H5T_t *type; /*datatype of this dataset */
H5P_t *space; /*dataspace of this dataset */
H5D_create_t create_parms; /*creation parameters */
- union {
- H5O_cstore_t cstore; /*contiguous storage info */
- H5O_istore_t istore; /*chunked storage info */
- } storage;
+ H5O_layout_t layout; /*data layout */
};
/* Default dataset creation template */
@@ -330,15 +327,20 @@ H5Dclose (hid_t dataset_id)
*
* Purpose: Reads (part of) a DATASET from the file into application
* memory BUF. The part of the dataset to read is defined with
- * SPACE_ID (if SPACE_ID is negative then we assume that the
- * caller desires to read the entire dataset). The data points
- * are converted from their file type to the TYPE_ID specified.
+ * MEM_SPACE_ID and FILE_SPACE_ID. The data points are
+ * converted from their file type to the MEM_TYPE_ID specified.
* Additional miscellaneous data transfer properties can be
* passed to this function with the XFER_PARMS_ID argument.
*
- * The SPACE_ID can be the constant H5P_ALL in which case the
- * destination (memory) data space is the same as the source
- * (file) data space defined when the dataset was created.
+ * The FILE_SPACE_ID can be the constant H5P_ALL which indicates
+ * that the entire file data space is to be referenced.
+ *
+ * The MEM_SPACE_ID can be the constant H5P_ALL in which case
+ * the memory data space is the same as the file data space
+ * defined when the dataset was created.
+ *
+ * The number of elements in the memory data space must match
+ * the number of elements in the file data space.
*
* The XFER_PARMS_ID can be the constant H5C_DEFAULT in which
* case the default data transfer properties are used.
@@ -363,12 +365,13 @@ H5Dclose (hid_t dataset_id)
*-------------------------------------------------------------------------
*/
herr_t
-H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
- hid_t xfer_parms_id, void *buf/*out*/)
+H5Dread (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/)
{
H5D_t *dataset = NULL;
- const H5T_t *type = NULL;
- const H5P_t *space = NULL;
+ const H5T_t *mem_type = NULL;
+ const H5P_t *mem_space = NULL;
+ const H5P_t *file_space = NULL;
const H5D_xfer_t *xfer_parms = NULL;
FUNC_ENTER (H5Dread, FAIL);
@@ -380,13 +383,19 @@ H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
NULL==dataset->ent.file) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
- if (H5_DATATYPE!=H5Aatom_group (type_id) ||
- NULL==(type=H5Aatom_object (type_id))) {
+ if (H5_DATATYPE!=H5Aatom_group (mem_type_id) ||
+ NULL==(mem_type=H5Aatom_object (mem_type_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
- if (H5P_ALL!=space_id) {
- if (H5_DATASPACE!=H5Aatom_group (space_id) ||
- NULL==(space=H5Aatom_object (space_id))) {
+ if (H5P_ALL!=mem_space_id) {
+ if (H5_DATASPACE!=H5Aatom_group (mem_space_id) ||
+ NULL==(mem_space=H5Aatom_object (mem_space_id))) {
+ HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
+ }
+ }
+ if (H5P_ALL!=file_space_id) {
+ if (H5_DATASPACE!=H5Aatom_group (file_space_id) ||
+ NULL==(file_space=H5Aatom_object (file_space_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
}
@@ -401,7 +410,8 @@ H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
}
/* read raw data */
- if (H5D_read (dataset, type, space, xfer_parms, buf/*out*/)<0) {
+ if (H5D_read (dataset, mem_type, mem_space, file_space, xfer_parms,
+ buf/*out*/)<0) {
HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "can't read data");
}
@@ -414,17 +424,21 @@ H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
*
* Purpose: Writes (part of) a DATASET from application memory BUF to the
* file. The part of the dataset to write is defined with the
- * SPACE_ID (if SPACE_ID is negative then we assume that the
- * caller desires to write the entire dataset). The data points
- * are converted from their current type (TYPE_ID) to their file
- * data type. Additional miscellaneous data transfer properties
- * can be passed to this function with the XFER_PARMS_ID
- * argument.
- *
- * The SPACE_ID can be the constant H5P_ALL in which case the
- * source (memory) data space is the same as the destination
- * (file) memory space which was defined when the dataset was
- * created.
+ * MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
+ * are converted from their current type (MEM_TYPE_ID) to their
+ * file data type. Additional miscellaneous data transfer
+ * properties can be passed to this function with the
+ * XFER_PARMS_ID argument.
+ *
+ * The FILE_SPACE_ID can be the constant H5P_ALL which indicates
+ * that the entire file data space is to be referenced.
+ *
+ * The MEM_SPACE_ID can be the constant H5P_ALL in which case
+ * the memory data space is the same as the file data space
+ * defined when the dataset was created.
+ *
+ * The number of elements in the memory data space must match
+ * the number of elements in the file data space.
*
* The XFER_PARMS_ID can be the constant H5C_DEFAULT in which
* case the default data transfer properties are used.
@@ -443,12 +457,13 @@ H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
*-------------------------------------------------------------------------
*/
herr_t
-H5Dwrite (hid_t dataset_id, hid_t type_id, hid_t space_id,
- hid_t xfer_parms_id, const void *buf)
+H5Dwrite (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t xfer_parms_id, const void *buf)
{
H5D_t *dataset = NULL;
- const H5T_t *type = NULL;
- const H5P_t *space = NULL;
+ const H5T_t *mem_type = NULL;
+ const H5P_t *mem_space = NULL;
+ const H5P_t *file_space = NULL;
const H5D_xfer_t *xfer_parms = NULL;
FUNC_ENTER (H5Dwrite, FAIL);
@@ -460,13 +475,19 @@ H5Dwrite (hid_t dataset_id, hid_t type_id, hid_t space_id,
NULL==dataset->ent.file) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
- if (H5_DATATYPE!=H5Aatom_group (type_id) ||
- NULL==(type=H5Aatom_object (type_id))) {
+ if (H5_DATATYPE!=H5Aatom_group (mem_type_id) ||
+ NULL==(mem_type=H5Aatom_object (mem_type_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
- if (H5P_ALL!=space_id) {
- if (H5_DATASPACE!=H5Aatom_group (space_id) ||
- NULL==(space=H5Aatom_object (space_id))) {
+ if (H5P_ALL!=mem_space_id) {
+ if (H5_DATASPACE!=H5Aatom_group (mem_space_id) ||
+ NULL==(mem_space=H5Aatom_object (mem_space_id))) {
+ HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
+ }
+ }
+ if (H5P_ALL!=file_space_id) {
+ if (H5_DATASPACE!=H5Aatom_group (file_space_id) ||
+ NULL==(file_space=H5Aatom_object (file_space_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
}
@@ -481,7 +502,8 @@ H5Dwrite (hid_t dataset_id, hid_t type_id, hid_t space_id,
}
/* write raw data */
- if (H5D_write (dataset, type, space, xfer_parms, buf)<0) {
+ if (H5D_write (dataset, mem_type, mem_space, file_space, xfer_parms,
+ buf)<0) {
HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "can't write data");
}
@@ -561,7 +583,7 @@ H5D_create (H5F_t *f, const char *name, const H5T_t *type, const H5P_t *space,
H5D_t *new_dset = NULL;
H5D_t *ret_value = NULL;
size_t nbytes;
- intn ndims;
+ intn i;
FUNC_ENTER (H5D_create, NULL);
@@ -596,55 +618,43 @@ H5D_create (H5F_t *f, const char *name, const H5T_t *type, const H5P_t *space,
/* Total raw data size */
nbytes = H5T_get_size (type) * H5P_get_npoints (space);
+ new_dset->layout.type = new_dset->create_parms.layout;
+ new_dset->layout.ndims = H5P_get_ndims (space) + 1;
+ assert (new_dset->layout.ndims<=NELMTS (new_dset->layout.dim));
+ new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size (type);
- /* Initialize storage */
switch (new_dset->create_parms.layout) {
case H5D_CONTIGUOUS:
- new_dset->storage.cstore.size = nbytes;
- if (H5MF_alloc (f, H5MF_RAW, nbytes,
- &(new_dset->storage.cstore.addr))<0) {
- HGOTO_ERROR (H5E_DATASET, H5E_NOSPACE, NULL,
- "can't allocate raw file storage");
- }
- if (H5O_modify (&(new_dset->ent), H5O_CSTORE, 0, 0,
- &(new_dset->storage.cstore))<0) {
+ if (H5P_get_dims (space, new_dset->layout.dim)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
- "can't update dataset object header");
+ "unable to initialize contiguous storage");
}
break;
case H5D_CHUNKED:
- /*
- * The dimensionality of the chunk should match the dimensionality of
- * the data space. We will add one more dimension here though, to
- * describe the individual bytes of a data point. Therefore, there
- * must be room in the template for one more dimension size.
- */
- ndims = new_dset->create_parms.chunk_ndims;
- if (ndims != H5P_get_ndims (space)) {
+ if (new_dset->create_parms.chunk_ndims != H5P_get_ndims (space)) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"dimensionality of chunks doesn't match the data space");
}
- assert (ndims<NELMTS (new_dset->create_parms.chunk_size));
- new_dset->create_parms.chunk_size[ndims] = H5T_get_size (type);
-
- if (H5F_istore_create (f, &(new_dset->storage.istore), ndims+1,
- new_dset->create_parms.chunk_size)<0) {
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
- "can't initialize chunked storage");
- }
- if (H5O_modify (&(new_dset->ent), H5O_ISTORE, 0, 0,
- &(new_dset->storage.istore))<0) {
- HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
- "can't update dataset object header");
+ for (i=0; i<new_dset->layout.ndims-1; i++) {
+ new_dset->layout.dim[i] = new_dset->create_parms.chunk_size[i];
}
break;
default:
- assert ("not implemented yet" && 0);
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
}
+ /*
+ * Initialize storage
+ */
+ if (H5F_arr_create (f, &(new_dset->layout))<0 ||
+ H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0,
+ &(new_dset->layout))<0) {
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
+ "unable to initialize storage");
+ }
+
/* Give the dataset a name */
if (H5G_insert (name, &(new_dset->ent))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset");
@@ -693,7 +703,6 @@ H5D_open (H5F_t *f, const char *name)
{
H5D_t *dataset = NULL; /*the dataset which was found */
H5D_t *ret_value = NULL; /*return value */
- H5O_istore_t *istore = NULL;
intn i;
FUNC_ENTER (H5D_open, NULL);
@@ -722,31 +731,34 @@ H5D_open (H5F_t *f, const char *name)
}
/*
- * Get the raw data storage info. It's actually stored in two locations:
+ * Get the raw data layout info. It's actually stored in two locations:
* the storage message of the dataset (dataset->storage) and certain
* values are copied to the dataset create template so the user can query
* them.
*/
- if (H5O_read (&(dataset->ent), H5O_CSTORE, 0, &(dataset->storage.cstore))) {
- /* Contiguous storage */
+ if (H5O_read (&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))<0) {
+ HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
+ "unable to read data layout message");
+ }
+ switch (dataset->layout.type) {
+ case H5D_CONTIGUOUS:
dataset->create_parms.layout = H5D_CONTIGUOUS;
-
- } else if (H5O_read (&(dataset->ent), H5O_ISTORE, 0,
- &(dataset->storage.istore))) {
+ break;
+
+ case H5D_CHUNKED:
/*
* Chunked storage. The creation template's dimension is one less than
* the chunk dimension because the chunk includes a dimension for the
* individual bytes of the data type.
*/
- istore = &(dataset->storage.istore);
dataset->create_parms.layout = H5D_CHUNKED;
- dataset->create_parms.chunk_ndims = istore->ndims - 1;
- assert (istore->ndims<=NELMTS (dataset->create_parms.chunk_size));
- for (i=0; i<istore->ndims-1; i++) {
- dataset->create_parms.chunk_size[i] = istore->alignment[i];
+ dataset->create_parms.chunk_ndims = dataset->layout.ndims - 1;
+ for (i=0; i<dataset->layout.ndims-1; i++) {
+ dataset->create_parms.chunk_size[i] = dataset->layout.dim[i];
}
-
- } else {
+ break;
+
+ default:
assert ("not implemented yet" && 0);
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
}
@@ -834,12 +846,8 @@ H5D_close (H5D_t *dataset)
/*-------------------------------------------------------------------------
* Function: H5D_read
*
- * Purpose: Reads (part of) a DATASET into application memory BUF. The
- * SPACE argument determines what part of the dataset to read
- * (the whole thing is read if SPACE is null) and individual
- * data points are translated from their file data type to the
- * specified TYPE. The XFER_PARMS contains additional
- * miscellaneous properties that control the data transfer.
+ * Purpose: Reads (part of) a DATASET into application memory BUF. See
+ * H5Dread() for complete details.
*
* Return: Success: SUCCEED
*
@@ -853,12 +861,13 @@ H5D_close (H5D_t *dataset)
*-------------------------------------------------------------------------
*/
herr_t
-H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
- const H5D_xfer_t *xfer_parms, void *buf/*out*/)
+H5D_read (H5D_t *dataset, const H5T_t *mem_type, const H5P_t *mem_space,
+ const H5P_t *file_space, const H5D_xfer_t *xfer_parms,
+ void *buf/*out*/)
{
size_t nelmts, src_size, dst_size;
- size_t offset[H5O_ISTORE_NDIMS];
- size_t size[H5O_ISTORE_NDIMS];
+ size_t offset[H5O_LAYOUT_NDIMS];
+ size_t size[H5O_LAYOUT_NDIMS];
intn i;
herr_t ret_value = FAIL;
uint8 *conv_buf = NULL; /*data type conv buffer */
@@ -869,25 +878,23 @@ H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
/* check args */
assert (dataset && dataset->ent.file);
- assert (type);
+ assert (mem_type);
assert (xfer_parms);
assert (buf);
- if (H5D_CONTIGUOUS!=dataset->create_parms.layout) {
- HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
- "layout is not supported yet");
- }
- if (space && H5P_cmp (space, dataset->space)) {
+ if ((mem_space && H5P_cmp (mem_space, dataset->space)) ||
+ (file_space && H5P_cmp (file_space, dataset->space))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"space conversion not supported yet");
}
+
/*
* Convert data types to atoms because the conversion functions are
* application-level functions.
*/
if ((src_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (dataset->type)))<0 ||
- (dst_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (type)))<0) {
+ (dst_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (mem_type)))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
@@ -895,39 +902,24 @@ H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
/* Compute the size of the request and allocate scratch buffers */
nelmts = H5P_get_npoints (dataset->space);
src_size = nelmts * H5T_get_size (dataset->type);
- dst_size = nelmts * H5T_get_size (type);
+ dst_size = nelmts * H5T_get_size (mem_type);
conv_buf = H5MM_xmalloc (MAX (src_size, dst_size));
- if (NULL==(conv_func=H5T_find (dataset->type, type))) {
+ if (NULL==(conv_func=H5T_find (dataset->type, mem_type))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
}
/*
* Read data into the data type conversion buffer.
+ * (We only support complete reads currently)
*/
- switch (dataset->create_parms.layout) {
- case H5D_CONTIGUOUS:
- /* Read a block of contiguous data */
- if (H5F_block_read (dataset->ent.file, &(dataset->storage.cstore.addr),
- src_size, conv_buf)<0) {
- HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "read failed");
- }
- break;
-
- case H5D_CHUNKED:
- /* Read one or more chunks from indexed storage */
- for (i=0; i<dataset->storage.istore.ndims; i++) offset[i] = 0;
- H5P_get_dims (dataset->space, size);
- size[dataset->storage.istore.ndims-1] = H5T_get_size (dataset->type);
- if (H5F_istore_read (dataset->ent.file, &(dataset->storage.istore),
- offset, size, conv_buf)<0) {
- HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "read failed");
- }
- break;
-
- default:
- assert ("not implemented yet" && 0);
- HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "not implemented yet");
+ for (i=0; i<dataset->layout.ndims; i++) {
+ offset[i] = 0;
+ size[i] = dataset->layout.dim[i];
+ }
+ if (H5F_arr_read (dataset->ent.file, &(dataset->layout), offset, size,
+ conv_buf)<0) {
+ HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "read failed");
}
/*
@@ -956,12 +948,7 @@ H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
* Function: H5D_write
*
* Purpose: Writes (part of) a DATASET to a file from application memory
- * BUF. The SPACE argument determines what part of the dataset
- * to write (the whole thing is read if SPACE is null) and
- * individual data points are translated from their memory data
- * type (TYPE) to the file data type. The XFER_PARMS contains
- * additional miscellaneous properties that control the data
- * transfer.
+ * BUF. See H5Dwrite() for complete details.
*
* Return: Success: SUCCEED
*
@@ -975,12 +962,13 @@ H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
*-------------------------------------------------------------------------
*/
herr_t
-H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
- const H5D_xfer_t *xfer_parms, const void *buf)
+H5D_write (H5D_t *dataset, const H5T_t *mem_type, const H5P_t *mem_space,
+ const H5P_t *file_space, const H5D_xfer_t *xfer_parms,
+ const void *buf)
{
size_t nelmts, src_size, dst_size;
- size_t offset[H5O_ISTORE_NDIMS];
- size_t size[H5O_ISTORE_NDIMS];
+ size_t offset[H5O_LAYOUT_NDIMS];
+ size_t size[H5O_LAYOUT_NDIMS];
intn i;
herr_t ret_value = FAIL;
uint8 *conv_buf = NULL; /*data type conversion buffer */
@@ -991,7 +979,7 @@ H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
/* check args */
assert (dataset && dataset->ent.file);
- assert (type);
+ assert (mem_type);
assert (xfer_parms);
assert (buf);
@@ -999,7 +987,8 @@ H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
HRETURN_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"layout is not supported yet");
}
- if (space && H5P_cmp (space, dataset->space)) {
+ if ((mem_space && H5P_cmp (mem_space, dataset->space)) ||
+ (file_space && H5P_cmp (file_space, dataset->space))) {
HRETURN_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"space conversion not supported yet");
}
@@ -1008,8 +997,8 @@ H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
* Convert data types to atoms because the conversion functions are
* application-level functions.
*/
- if ((src_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (dataset->type)))<0 ||
- (dst_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (type)))<0) {
+ if ((src_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (mem_type)))<0 ||
+ (dst_id=H5Aregister_atom (H5_DATATYPE, H5T_copy (dataset->type)))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
@@ -1017,10 +1006,10 @@ H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
/* Compute the size of the request and allocate scratch buffers */
nelmts = H5P_get_npoints (dataset->space);
- src_size = nelmts * H5T_get_size (type);
+ src_size = nelmts * H5T_get_size (mem_type);
dst_size = nelmts * H5T_get_size (dataset->type);
conv_buf = H5MM_xmalloc (MAX (src_size, dst_size));
- if (NULL==(conv_func=H5T_find (type, dataset->type))) {
+ if (NULL==(conv_func=H5T_find (mem_type, dataset->type))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
}
@@ -1041,30 +1030,15 @@ H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
/*
* Write data into the file.
+ * (We only support complete writes currently.)
*/
- switch (dataset->create_parms.layout) {
- case H5D_CONTIGUOUS:
- /* Write a contiguous chunk of data */
- if (H5F_block_write (dataset->ent.file, &(dataset->storage.cstore.addr),
- dst_size, conv_buf)<0) {
- HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "write failed");
- }
- break;
-
- case H5D_CHUNKED:
- /* Write one or more chunks to indexed storage */
- for (i=0; i<dataset->storage.istore.ndims; i++) offset[i] = 0;
- H5P_get_dims (dataset->space, size);
- size[dataset->storage.istore.ndims-1] = H5T_get_size (dataset->type);
- if (H5F_istore_write (dataset->ent.file, &(dataset->storage.istore),
- offset, size, conv_buf)<0) {
- HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "write failed");
- }
- break;
-
- default:
- assert ("not implemented yet" && 0);
- HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "not implemented yet");
+ for (i=0; i<dataset->layout.ndims; i++) {
+ offset[i] = 0;
+ size[i] = dataset->layout.dim[i];
+ }
+ if (H5F_arr_write (dataset->ent.file, &(dataset->layout), offset, size,
+ conv_buf)<0) {
+ HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "write failed");
}
ret_value = SUCCEED;
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 15c7d4d..fa53b91 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -6,6 +6,7 @@
* Wednesday, October 8, 1997
*/
#include <H5private.h>
+#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5MFprivate.h>
@@ -48,7 +49,7 @@ static herr_t H5F_istore_decode_key (H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_encode_key (H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
-static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore,
+static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_layout_t *layout,
H5F_isop_t op,
const size_t offset_f[],
const size_t size[],
@@ -72,14 +73,14 @@ static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore,
*/
typedef struct H5F_istore_key_t {
uintn file_number; /*external file number */
- size_t offset[H5O_ISTORE_NDIMS]; /*logical offset to start*/
- size_t size[H5O_ISTORE_NDIMS]; /*logical chunk size */
+ size_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
+ size_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */
} H5F_istore_key_t;
typedef struct H5F_istore_ud1_t {
H5F_istore_key_t key; /*key values */
haddr_t addr; /*file address of chunk */
- H5O_istore_t mesg; /*storage message */
+ H5O_layout_t mesg; /*layout message */
} H5F_istore_ud1_t;
/* inherits B-tree like properties from H5B */
@@ -127,7 +128,7 @@ H5F_istore_sizeof_rkey (H5F_t *f, const void *_udata)
size_t nbytes;
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
nbytes = 4 + /*external file number */
udata->mesg.ndims * 4 + /*dimension indices */
@@ -168,7 +169,7 @@ H5F_istore_decode_key (H5F_t *f, H5B_t *bt, uint8 *raw, void *_key)
assert (bt);
assert (raw);
assert (key);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
+ assert (ndims>0 && ndims<=H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE (raw, key->file_number);
@@ -213,7 +214,7 @@ H5F_istore_encode_key (H5F_t *f, H5B_t *bt, uint8 *raw, void *_key)
assert (bt);
assert (raw);
assert (key);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
+ assert (ndims>0 && ndims<=H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE (raw, key->file_number);
@@ -261,7 +262,7 @@ H5F_istore_cmp2 (H5F_t *f, void *_lt_key, void *_udata, void *_rt_key)
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
/* Compare the offsets but ignore the other fields */
cmp = H5V_vector_cmp (udata->mesg.ndims, lt_key->offset, rt_key->offset);
@@ -312,7 +313,7 @@ H5F_istore_cmp3 (H5F_t *f, void *_lt_key, void *_udata, void *_rt_key)
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
if (H5V_vector_lt (udata->mesg.ndims, udata->key.offset, lt_key->offset)) {
cmp = -1;
@@ -363,7 +364,7 @@ H5F_istore_new_node (H5F_t *f, H5B_ins_t op,
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>=0 && udata->mesg.ndims<H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>=0 && udata->mesg.ndims<H5O_LAYOUT_NDIMS);
assert (addr);
/* Allocate new storage */
@@ -543,8 +544,8 @@ H5F_istore_insert (H5F_t *f, const haddr_t *addr,
*/
md_key->file_number = udata->key.file_number;
for (i=0, nbytes=1; i<udata->mesg.ndims; i++) {
- assert (0==udata->key.offset[i] % udata->mesg.alignment[i]);
- assert (udata->key.size[i] == udata->mesg.alignment[i]);
+ assert (0==udata->key.offset[i] % udata->mesg.dim[i]);
+ assert (udata->key.size[i] == udata->mesg.dim[i]);
md_key->offset[i] = udata->key.offset[i];
md_key->size[i] = udata->key.size[i];
nbytes *= udata->key.size[i];
@@ -603,18 +604,18 @@ H5F_istore_insert (H5F_t *f, const haddr_t *addr,
*-------------------------------------------------------------------------
*/
static herr_t
-H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
+H5F_istore_copy_hyperslab (H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
const size_t offset_f[], const size_t size[],
const size_t offset_m[], const size_t size_m[],
void *buf)
{
intn i, carry;
- size_t idx_cur[H5O_ISTORE_NDIMS];
- size_t idx_min[H5O_ISTORE_NDIMS];
- size_t idx_max[H5O_ISTORE_NDIMS];
- size_t sub_size[H5O_ISTORE_NDIMS];
- size_t offset_wrt_chunk[H5O_ISTORE_NDIMS];
- size_t sub_offset_m[H5O_ISTORE_NDIMS];
+ size_t idx_cur[H5O_LAYOUT_NDIMS];
+ size_t idx_min[H5O_LAYOUT_NDIMS];
+ size_t idx_max[H5O_LAYOUT_NDIMS];
+ size_t sub_size[H5O_LAYOUT_NDIMS];
+ size_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
+ size_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
uint8 *chunk=NULL;
H5F_istore_ud1_t udata;
@@ -625,60 +626,60 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
/* check args */
assert (f);
- assert (istore);
- assert (H5F_addr_defined (&(istore->btree_addr)));
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (H5F_addr_defined (&(layout->addr)));
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (H5F_ISTORE_READ==op || H5F_ISTORE_WRITE==op);
assert (size);
assert (size_m);
assert (buf);
#ifndef NDEBUG
- for (i=0; i<istore->ndims; i++) {
+ for (i=0; i<layout->ndims; i++) {
assert (!offset_f || offset_f[i]>=0);/*neg domains unsupported */
assert (!offset_m || offset_m[i]>=0);/*mem array offset never neg */
assert (size[i]>=0); /*size may be zero, implies no-op */
assert (size_m[i]>0); /*destination must exist */
/*hyperslab must fit in BUF*/
assert ((offset_m?offset_m[i]:0)+size[i]<=size_m[i]);
- assert (istore->alignment[i]>0);
+ assert (layout->dim[i]>0);
}
#endif
/* Initialize indices */
- for (i=0; i<istore->ndims; i++) {
- idx_min[i] = (offset_f?offset_f[i]:0) / istore->alignment[i];
- idx_max[i] = ((offset_f?offset_f[i]:0)+size[i]-1)/istore->alignment[i]+1;
+ for (i=0; i<layout->ndims; i++) {
+ idx_min[i] = (offset_f?offset_f[i]:0) / layout->dim[i];
+ idx_max[i] = ((offset_f?offset_f[i]:0)+size[i]-1)/layout->dim[i]+1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
- for (i=0, chunk_size=1; i<istore->ndims; i++) {
- chunk_size *= istore->alignment[i];
+ for (i=0, chunk_size=1; i<layout->ndims; i++) {
+ chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc (chunk_size);
/* Initialize non-changing part of udata */
- udata.mesg = *istore;
+ udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
/* Read/Write chunk or create it if it doesn't exist */
- udata.mesg.ndims = istore->ndims;
+ udata.mesg.ndims = layout->ndims;
H5F_addr_undef (&(udata.addr));
udata.key.file_number = 0;
- for (i=0; i<istore->ndims; i++) {
+ for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
- udata.key.offset[i] = idx_cur[i] * istore->alignment[i];
- udata.key.size[i] = istore->alignment[i];
+ udata.key.offset[i] = idx_cur[i] * layout->dim[i];
+ udata.key.size[i] = layout->dim[i];
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX ((offset_f?offset_f[i]:0),
udata.key.offset[i]) -
udata.key.offset[i];
- sub_size[i] = MIN ((idx_cur[i]+1)*istore->alignment[i],
+ sub_size[i] = MIN ((idx_cur[i]+1)*layout->dim[i],
(offset_f?offset_f[i]:0)+size[i]) -
(udata.key.offset[i]+offset_wrt_chunk[i]);
@@ -689,10 +690,10 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
}
if (H5F_ISTORE_WRITE==op) {
- status = H5B_insert (f, H5B_ISTORE, &(istore->btree_addr), &udata);
+ status = H5B_insert (f, H5B_ISTORE, &(layout->addr), &udata);
assert (status>=0);
} else {
- status = H5B_find (f, H5B_ISTORE, &(istore->btree_addr), &udata);
+ status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
}
/*
@@ -700,8 +701,8 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
* partial chunk then load the chunk from disk.
*/
if (H5F_ISTORE_READ==op ||
- !H5V_vector_zerop (istore->ndims, offset_wrt_chunk) ||
- !H5V_vector_eq (istore->ndims, sub_size, udata.key.size)) {
+ !H5V_vector_zerop (layout->ndims, offset_wrt_chunk) ||
+ !H5V_vector_eq (layout->ndims, sub_size, udata.key.size)) {
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
assert (0==udata.key.file_number);
if (H5F_block_read (f, &(udata.addr), chunk_size, chunk)<0) {
@@ -715,7 +716,7 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
/* Transfer data to/from the chunk */
if (H5F_ISTORE_WRITE==op) {
- H5V_hyper_copy (istore->ndims, sub_size,
+ H5V_hyper_copy (layout->ndims, sub_size,
udata.key.size, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
assert (0==udata.key.file_number);
@@ -724,13 +725,13 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
"unable to write raw storage chunk");
}
} else {
- H5V_hyper_copy (istore->ndims, sub_size,
+ H5V_hyper_copy (layout->ndims, sub_size,
size_m, sub_offset_m, buf,
udata.key.size, offset_wrt_chunk, chunk);
}
/* Increment indices */
- for (i=istore->ndims-1, carry=1; i>=0 && carry; --i) {
+ for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
@@ -763,19 +764,19 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_read (H5F_t *f, const H5O_istore_t *istore,
+H5F_istore_read (H5F_t *f, const H5O_layout_t *layout,
const size_t offset[], const size_t size[], void *buf)
{
FUNC_ENTER (H5F_istore_read, FAIL);
/* Check args */
assert (f);
- assert (istore);
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (size);
assert (buf);
- if (H5F_istore_copy_hyperslab (f, istore, H5F_ISTORE_READ,
+ if (H5F_istore_copy_hyperslab (f, layout, H5F_ISTORE_READ,
offset, size, H5V_ZERO, size, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
"hyperslab output failure");
@@ -803,7 +804,7 @@ H5F_istore_read (H5F_t *f, const H5O_istore_t *istore,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
+H5F_istore_write (H5F_t *f, const H5O_layout_t *layout,
const size_t offset[], const size_t size[],
const void *buf)
{
@@ -811,12 +812,12 @@ H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
/* Check args */
assert (f);
- assert (istore);
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (size);
assert (buf);
- if (H5F_istore_copy_hyperslab (f, istore, H5F_ISTORE_WRITE,
+ if (H5F_istore_copy_hyperslab (f, layout, H5F_ISTORE_WRITE,
offset, size, H5V_ZERO, size, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"hyperslab output failure");
@@ -850,8 +851,7 @@ H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_create (H5F_t *f, struct H5O_istore_t *istore/*out*/,
- uintn ndims, const size_t alignment[])
+H5F_istore_create (H5F_t *f, H5O_layout_t *layout/*out*/)
{
H5F_istore_ud1_t udata;
int i;
@@ -860,23 +860,18 @@ H5F_istore_create (H5F_t *f, struct H5O_istore_t *istore/*out*/,
/* Check args */
assert (f);
- assert (istore);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
- assert (alignment);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
#ifndef NDEBUG
- for (i=0; i<ndims; i++) {
- assert (alignment[i]>0);
+ for (i=0; i<layout->ndims; i++) {
+ assert (layout->dim[i]>0);
}
#endif
- udata.mesg.ndims = istore->ndims = ndims;
- if (H5B_create (f, H5B_ISTORE, &udata, &(istore->btree_addr)/*out*/)<0) {
+ udata.mesg.ndims = layout->ndims;
+ if (H5B_create (f, H5B_ISTORE, &udata, &(layout->addr)/*out*/)<0) {
HRETURN_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree");
}
- for (i=0; i<ndims; i++) {
- istore->alignment[i] = alignment[i];
- }
-
FUNC_LEAVE (SUCCEED);
}
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 9c4ffeb..07f6d9c 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -55,9 +55,11 @@ H5D_t *H5D_create (H5F_t *f, const char *name, const H5T_t *type,
const H5P_t *space, const H5D_create_t *create_parms);
H5D_t *H5D_open (H5F_t *f, const char *name);
herr_t H5D_close (H5D_t *dataset);
-herr_t H5D_read (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
- const H5D_xfer_t *xfer_parms, void *buf/*out*/);
-herr_t H5D_write (H5D_t *dataset, const H5T_t *type, const H5P_t *space,
+herr_t H5D_read (H5D_t *dataset, const H5T_t *mem_type, const H5P_t *mem_space,
+ const H5P_t *file_space, const H5D_xfer_t *xfer_parms,
+ void *buf/*out*/);
+herr_t H5D_write (H5D_t *dataset, const H5T_t *mem_type,
+ const H5P_t *mem_space, const H5P_t *file_space,
const H5D_xfer_t *xfer_parms, const void *buf);
hid_t H5D_find_name (hid_t file_id, group_t UNUSED, const char *name);
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 417146b..303a18d 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -42,10 +42,10 @@ hid_t H5Dcreate (hid_t file_id, const char *name, hid_t type_id,
hid_t space_id, hid_t create_parms_id);
hid_t H5Dopen (hid_t file_id, const char *name);
herr_t H5Dclose (hid_t dataset_id);
-herr_t H5Dread (hid_t dataset_id, hid_t type_id, hid_t space_id,
- hid_t xfer_parms_id, void *buf/*out*/);
-herr_t H5Dwrite (hid_t dataset_id, hid_t type_id, hid_t space_id,
- hid_t xfer_parms_id, const void *buf);
+herr_t H5Dread (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/);
+herr_t H5Dwrite (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
+ hid_t file_space_id, hid_t xfer_parms_id, const void *buf);
#ifdef __cplusplus
}
diff --git a/src/H5Farray.c b/src/H5Farray.c
new file mode 100644
index 0000000..88dae0b
--- /dev/null
+++ b/src/H5Farray.c
@@ -0,0 +1,219 @@
+/*
+ * Copyright (C) 1998 Spizella Software
+ * All rights reserved.
+ *
+ * Programmer: Robb Matzke <robb@arborea.spizella.com>
+ * Thursday, January 15, 1998
+ *
+ * Purpose: Provides I/O facilities for multi-dimensional arrays of bytes
+ * stored with various layout policies.
+ */
+#include <H5private.h>
+#include <H5Dprivate.h>
+#include <H5Eprivate.h>
+#include <H5Fprivate.h>
+#include <H5MFprivate.h>
+#include <H5Oprivate.h>
+
+/* Interface initialization */
+#define PABLO_MASK H5F_arr_mask
+#define INTERFACE_INIT NULL
+static intn interface_initialize_g = FALSE;
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5F_arr_create
+ *
+ * Purpose: Creates an array of bytes. When called to create an array of
+ * some type, the fastest varying dimension corresponds to an
+ * instance of that type. That is, a 10x20 array of int32 is
+ * really a 10x20x4 array of bytes.
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Robb Matzke
+ * Friday, January 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
+{
+ intn i;
+ size_t nbytes;
+
+ FUNC_ENTER (H5F_arr_create, FAIL);
+
+ /* check args */
+ assert (f);
+ assert (layout);
+ H5F_addr_undef (&(layout->addr)); /*just in case we fail*/
+
+ switch (layout->type) {
+ case H5D_CONTIGUOUS:
+ /* Reserve space in the file for the entire array */
+ for (i=0, nbytes=1; i<layout->ndims; i++) nbytes *= layout->dim[i];
+ assert (nbytes>0);
+ if (H5MF_alloc (f, H5MF_RAW, nbytes, &(layout->addr)/*out*/)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_NOSPACE, FAIL,
+ "unable to reserve file space");
+ }
+ break;
+
+ case H5D_CHUNKED:
+ /* Create the root of the B-tree that describes chunked storage */
+ if (H5F_istore_create (f, layout/*out*/)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_CANTINIT, FAIL,
+ "unable to initialize chunked storage");
+ }
+ break;
+
+ default:
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
+ }
+
+ FUNC_LEAVE (SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5F_arr_read
+ *
+ * Purpose: Reads a hyperslab of a file byte array into a byte array in
+ * memory which has the same dimensions as the hyperslab.
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Robb Matzke
+ * Friday, January 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t offset[], const size_t size[],
+ void *buf/*out*/)
+{
+ intn i;
+ size_t nbytes;
+ size_t zero_offset[H5O_LAYOUT_NDIMS];
+
+ FUNC_ENTER (H5F_arr_read, FAIL);
+
+ /* Check args */
+ assert (f);
+ assert (layout);
+ if (!offset) {
+ HDmemset (zero_offset, 0, sizeof zero_offset);
+ offset = zero_offset;
+ }
+ assert (size);
+ assert (buf);
+
+ switch (layout->type) {
+ case H5D_CONTIGUOUS:
+ /*
+ * We currently only support complete I/O.
+ */
+ for (i=0; i<layout->ndims; i++) {
+ assert (0==offset[i]);
+ assert (size[i]==layout->dim[i]);
+ }
+ for (i=0, nbytes=1; i<layout->ndims; i++) nbytes *= layout->dim[i];
+ if (H5F_block_read (f, &(layout->addr), nbytes, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "block read failed");
+ }
+ break;
+
+ case H5D_CHUNKED:
+ if (H5F_istore_read (f, layout, offset, size, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
+ }
+ break;
+
+ default:
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
+ }
+
+ FUNC_LEAVE (SUCCEED);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5F_arr_write
+ *
+ * Purpose: Writes an array to a hyperslab of a file byte array. The
+ * memory array and the hyperslab are the same size.
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Robb Matzke
+ * Friday, January 16, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t offset[], const size_t size[],
+ const void *buf)
+{
+ intn i;
+ size_t nbytes;
+
+ FUNC_ENTER (H5F_arr_write, FAIL);
+
+ /* Check args */
+ assert (f);
+ assert (layout);
+ assert (offset);
+ assert (size);
+ assert (buf);
+
+ switch (layout->type) {
+ case H5D_CONTIGUOUS:
+ /*
+ * We currently only support complete I/O.
+ */
+ for (i=0; i<layout->ndims; i++) {
+ assert (0==offset[i]);
+ assert (size[i]==layout->dim[i]);
+ }
+ for (i=0, nbytes=1; i<layout->ndims; i++) nbytes *= layout->dim[i];
+ if (H5F_block_write (f, &(layout->addr), nbytes, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "block write failed");
+ }
+ break;
+
+ case H5D_CHUNKED:
+ if (H5F_istore_write (f, layout, offset, size, buf)<0) {
+ HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
+ }
+ break;
+
+ default:
+ assert ("not implemented yet" && 0);
+ HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL,
+ "unsupported storage layout");
+ break;
+ }
+
+ FUNC_LEAVE (SUCCEED);
+}
+
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 15c7d4d..fa53b91 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -6,6 +6,7 @@
* Wednesday, October 8, 1997
*/
#include <H5private.h>
+#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5Fprivate.h>
#include <H5MFprivate.h>
@@ -48,7 +49,7 @@ static herr_t H5F_istore_decode_key (H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_encode_key (H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
-static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore,
+static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_layout_t *layout,
H5F_isop_t op,
const size_t offset_f[],
const size_t size[],
@@ -72,14 +73,14 @@ static herr_t H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore,
*/
typedef struct H5F_istore_key_t {
uintn file_number; /*external file number */
- size_t offset[H5O_ISTORE_NDIMS]; /*logical offset to start*/
- size_t size[H5O_ISTORE_NDIMS]; /*logical chunk size */
+ size_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
+ size_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */
} H5F_istore_key_t;
typedef struct H5F_istore_ud1_t {
H5F_istore_key_t key; /*key values */
haddr_t addr; /*file address of chunk */
- H5O_istore_t mesg; /*storage message */
+ H5O_layout_t mesg; /*layout message */
} H5F_istore_ud1_t;
/* inherits B-tree like properties from H5B */
@@ -127,7 +128,7 @@ H5F_istore_sizeof_rkey (H5F_t *f, const void *_udata)
size_t nbytes;
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
nbytes = 4 + /*external file number */
udata->mesg.ndims * 4 + /*dimension indices */
@@ -168,7 +169,7 @@ H5F_istore_decode_key (H5F_t *f, H5B_t *bt, uint8 *raw, void *_key)
assert (bt);
assert (raw);
assert (key);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
+ assert (ndims>0 && ndims<=H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE (raw, key->file_number);
@@ -213,7 +214,7 @@ H5F_istore_encode_key (H5F_t *f, H5B_t *bt, uint8 *raw, void *_key)
assert (bt);
assert (raw);
assert (key);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
+ assert (ndims>0 && ndims<=H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE (raw, key->file_number);
@@ -261,7 +262,7 @@ H5F_istore_cmp2 (H5F_t *f, void *_lt_key, void *_udata, void *_rt_key)
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
/* Compare the offsets but ignore the other fields */
cmp = H5V_vector_cmp (udata->mesg.ndims, lt_key->offset, rt_key->offset);
@@ -312,7 +313,7 @@ H5F_istore_cmp3 (H5F_t *f, void *_lt_key, void *_udata, void *_rt_key)
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>0 && udata->mesg.ndims<=H5O_LAYOUT_NDIMS);
if (H5V_vector_lt (udata->mesg.ndims, udata->key.offset, lt_key->offset)) {
cmp = -1;
@@ -363,7 +364,7 @@ H5F_istore_new_node (H5F_t *f, H5B_ins_t op,
assert (lt_key);
assert (rt_key);
assert (udata);
- assert (udata->mesg.ndims>=0 && udata->mesg.ndims<H5O_ISTORE_NDIMS);
+ assert (udata->mesg.ndims>=0 && udata->mesg.ndims<H5O_LAYOUT_NDIMS);
assert (addr);
/* Allocate new storage */
@@ -543,8 +544,8 @@ H5F_istore_insert (H5F_t *f, const haddr_t *addr,
*/
md_key->file_number = udata->key.file_number;
for (i=0, nbytes=1; i<udata->mesg.ndims; i++) {
- assert (0==udata->key.offset[i] % udata->mesg.alignment[i]);
- assert (udata->key.size[i] == udata->mesg.alignment[i]);
+ assert (0==udata->key.offset[i] % udata->mesg.dim[i]);
+ assert (udata->key.size[i] == udata->mesg.dim[i]);
md_key->offset[i] = udata->key.offset[i];
md_key->size[i] = udata->key.size[i];
nbytes *= udata->key.size[i];
@@ -603,18 +604,18 @@ H5F_istore_insert (H5F_t *f, const haddr_t *addr,
*-------------------------------------------------------------------------
*/
static herr_t
-H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
+H5F_istore_copy_hyperslab (H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
const size_t offset_f[], const size_t size[],
const size_t offset_m[], const size_t size_m[],
void *buf)
{
intn i, carry;
- size_t idx_cur[H5O_ISTORE_NDIMS];
- size_t idx_min[H5O_ISTORE_NDIMS];
- size_t idx_max[H5O_ISTORE_NDIMS];
- size_t sub_size[H5O_ISTORE_NDIMS];
- size_t offset_wrt_chunk[H5O_ISTORE_NDIMS];
- size_t sub_offset_m[H5O_ISTORE_NDIMS];
+ size_t idx_cur[H5O_LAYOUT_NDIMS];
+ size_t idx_min[H5O_LAYOUT_NDIMS];
+ size_t idx_max[H5O_LAYOUT_NDIMS];
+ size_t sub_size[H5O_LAYOUT_NDIMS];
+ size_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
+ size_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
uint8 *chunk=NULL;
H5F_istore_ud1_t udata;
@@ -625,60 +626,60 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
/* check args */
assert (f);
- assert (istore);
- assert (H5F_addr_defined (&(istore->btree_addr)));
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (H5F_addr_defined (&(layout->addr)));
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (H5F_ISTORE_READ==op || H5F_ISTORE_WRITE==op);
assert (size);
assert (size_m);
assert (buf);
#ifndef NDEBUG
- for (i=0; i<istore->ndims; i++) {
+ for (i=0; i<layout->ndims; i++) {
assert (!offset_f || offset_f[i]>=0);/*neg domains unsupported */
assert (!offset_m || offset_m[i]>=0);/*mem array offset never neg */
assert (size[i]>=0); /*size may be zero, implies no-op */
assert (size_m[i]>0); /*destination must exist */
/*hyperslab must fit in BUF*/
assert ((offset_m?offset_m[i]:0)+size[i]<=size_m[i]);
- assert (istore->alignment[i]>0);
+ assert (layout->dim[i]>0);
}
#endif
/* Initialize indices */
- for (i=0; i<istore->ndims; i++) {
- idx_min[i] = (offset_f?offset_f[i]:0) / istore->alignment[i];
- idx_max[i] = ((offset_f?offset_f[i]:0)+size[i]-1)/istore->alignment[i]+1;
+ for (i=0; i<layout->ndims; i++) {
+ idx_min[i] = (offset_f?offset_f[i]:0) / layout->dim[i];
+ idx_max[i] = ((offset_f?offset_f[i]:0)+size[i]-1)/layout->dim[i]+1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
- for (i=0, chunk_size=1; i<istore->ndims; i++) {
- chunk_size *= istore->alignment[i];
+ for (i=0, chunk_size=1; i<layout->ndims; i++) {
+ chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc (chunk_size);
/* Initialize non-changing part of udata */
- udata.mesg = *istore;
+ udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
/* Read/Write chunk or create it if it doesn't exist */
- udata.mesg.ndims = istore->ndims;
+ udata.mesg.ndims = layout->ndims;
H5F_addr_undef (&(udata.addr));
udata.key.file_number = 0;
- for (i=0; i<istore->ndims; i++) {
+ for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
- udata.key.offset[i] = idx_cur[i] * istore->alignment[i];
- udata.key.size[i] = istore->alignment[i];
+ udata.key.offset[i] = idx_cur[i] * layout->dim[i];
+ udata.key.size[i] = layout->dim[i];
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX ((offset_f?offset_f[i]:0),
udata.key.offset[i]) -
udata.key.offset[i];
- sub_size[i] = MIN ((idx_cur[i]+1)*istore->alignment[i],
+ sub_size[i] = MIN ((idx_cur[i]+1)*layout->dim[i],
(offset_f?offset_f[i]:0)+size[i]) -
(udata.key.offset[i]+offset_wrt_chunk[i]);
@@ -689,10 +690,10 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
}
if (H5F_ISTORE_WRITE==op) {
- status = H5B_insert (f, H5B_ISTORE, &(istore->btree_addr), &udata);
+ status = H5B_insert (f, H5B_ISTORE, &(layout->addr), &udata);
assert (status>=0);
} else {
- status = H5B_find (f, H5B_ISTORE, &(istore->btree_addr), &udata);
+ status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
}
/*
@@ -700,8 +701,8 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
* partial chunk then load the chunk from disk.
*/
if (H5F_ISTORE_READ==op ||
- !H5V_vector_zerop (istore->ndims, offset_wrt_chunk) ||
- !H5V_vector_eq (istore->ndims, sub_size, udata.key.size)) {
+ !H5V_vector_zerop (layout->ndims, offset_wrt_chunk) ||
+ !H5V_vector_eq (layout->ndims, sub_size, udata.key.size)) {
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
assert (0==udata.key.file_number);
if (H5F_block_read (f, &(udata.addr), chunk_size, chunk)<0) {
@@ -715,7 +716,7 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
/* Transfer data to/from the chunk */
if (H5F_ISTORE_WRITE==op) {
- H5V_hyper_copy (istore->ndims, sub_size,
+ H5V_hyper_copy (layout->ndims, sub_size,
udata.key.size, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
assert (0==udata.key.file_number);
@@ -724,13 +725,13 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
"unable to write raw storage chunk");
}
} else {
- H5V_hyper_copy (istore->ndims, sub_size,
+ H5V_hyper_copy (layout->ndims, sub_size,
size_m, sub_offset_m, buf,
udata.key.size, offset_wrt_chunk, chunk);
}
/* Increment indices */
- for (i=istore->ndims-1, carry=1; i>=0 && carry; --i) {
+ for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
@@ -763,19 +764,19 @@ H5F_istore_copy_hyperslab (H5F_t *f, const H5O_istore_t *istore, H5F_isop_t op,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_read (H5F_t *f, const H5O_istore_t *istore,
+H5F_istore_read (H5F_t *f, const H5O_layout_t *layout,
const size_t offset[], const size_t size[], void *buf)
{
FUNC_ENTER (H5F_istore_read, FAIL);
/* Check args */
assert (f);
- assert (istore);
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (size);
assert (buf);
- if (H5F_istore_copy_hyperslab (f, istore, H5F_ISTORE_READ,
+ if (H5F_istore_copy_hyperslab (f, layout, H5F_ISTORE_READ,
offset, size, H5V_ZERO, size, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
"hyperslab output failure");
@@ -803,7 +804,7 @@ H5F_istore_read (H5F_t *f, const H5O_istore_t *istore,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
+H5F_istore_write (H5F_t *f, const H5O_layout_t *layout,
const size_t offset[], const size_t size[],
const void *buf)
{
@@ -811,12 +812,12 @@ H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
/* Check args */
assert (f);
- assert (istore);
- assert (istore->ndims>0 && istore->ndims<=H5O_ISTORE_NDIMS);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (size);
assert (buf);
- if (H5F_istore_copy_hyperslab (f, istore, H5F_ISTORE_WRITE,
+ if (H5F_istore_copy_hyperslab (f, layout, H5F_ISTORE_WRITE,
offset, size, H5V_ZERO, size, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"hyperslab output failure");
@@ -850,8 +851,7 @@ H5F_istore_write (H5F_t *f, const H5O_istore_t *istore,
*-------------------------------------------------------------------------
*/
herr_t
-H5F_istore_create (H5F_t *f, struct H5O_istore_t *istore/*out*/,
- uintn ndims, const size_t alignment[])
+H5F_istore_create (H5F_t *f, H5O_layout_t *layout/*out*/)
{
H5F_istore_ud1_t udata;
int i;
@@ -860,23 +860,18 @@ H5F_istore_create (H5F_t *f, struct H5O_istore_t *istore/*out*/,
/* Check args */
assert (f);
- assert (istore);
- assert (ndims>0 && ndims<=H5O_ISTORE_NDIMS);
- assert (alignment);
+ assert (layout && H5D_CHUNKED==layout->type);
+ assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
#ifndef NDEBUG
- for (i=0; i<ndims; i++) {
- assert (alignment[i]>0);
+ for (i=0; i<layout->ndims; i++) {
+ assert (layout->dim[i]>0);
}
#endif
- udata.mesg.ndims = istore->ndims = ndims;
- if (H5B_create (f, H5B_ISTORE, &udata, &(istore->btree_addr)/*out*/)<0) {
+ udata.mesg.ndims = layout->ndims;
+ if (H5B_create (f, H5B_ISTORE, &udata, &(layout->addr)/*out*/)<0) {
HRETURN_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "can't create B-tree");
}
- for (i=0; i<ndims; i++) {
- istore->alignment[i] = alignment[i];
- }
-
FUNC_LEAVE (SUCCEED);
}
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 8ec0ab6..acf2e80 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -395,7 +395,7 @@ typedef struct H5F_t {
case 2: UINT16DECODE(p,l); break; \
}
-struct H5O_istore_t; /*forward decl for prototype arguments*/
+struct H5O_layout_t; /*forward decl for prototype arguments*/
/* library variables */
extern const H5F_create_t H5F_create_dflt;
@@ -408,13 +408,21 @@ herr_t H5F_close (H5F_t *f);
herr_t H5F_debug (H5F_t *f, const haddr_t *addr, FILE *stream, intn indent,
intn fwidth);
+/* Functions that operate on array storage */
+herr_t H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/);
+herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t offset[], const size_t size[],
+ void *buf/*out*/);
+herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
+ const size_t offset[], const size_t size[],
+ const void *buf);
+
/* Functions that operate on indexed storage */
-herr_t H5F_istore_create (H5F_t *f, struct H5O_istore_t *istore,
- uintn ndims, const size_t alignment[]);
-herr_t H5F_istore_read (H5F_t *f, const struct H5O_istore_t *mesg,
+herr_t H5F_istore_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/);
+herr_t H5F_istore_read (H5F_t *f, const struct H5O_layout_t *layout,
const size_t offset[], const size_t size[],
- void *buf);
-herr_t H5F_istore_write (H5F_t *f, const struct H5O_istore_t *mesg,
+ void *buf/*out*/);
+herr_t H5F_istore_write (H5F_t *f, const struct H5O_layout_t *layout,
const size_t offset[], const size_t size[],
const void *buf);
diff --git a/src/H5O.c b/src/H5O.c
index 9bb050c..18c6b10 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -55,10 +55,10 @@ static const H5O_class_t *const message_type_g[] = {
NULL, /*0x0002 Data space (fiber bundle?) */
H5O_DTYPE, /*0x0003 Data Type */
NULL, /*0x0004 Not assigned */
- H5O_CSTORE, /*0x0005 Contiguous Data Storage */
+ NULL, /*0x0005 Not assigned */
NULL, /*0x0006 Data storage -- compact object */
NULL, /*0x0007 Data storage -- external object */
- H5O_ISTORE, /*0x0008 Indexed Data Storage */
+ H5O_LAYOUT, /*0x0008 Data Layout */
H5O_EFL, /*0x0009 External File List */
NULL, /*0x000A Not assigned */
NULL, /*0x000B Data storage -- compressed object */
diff --git a/src/H5Ocstore.c b/src/H5Ocstore.c
deleted file mode 100644
index 5cc3215..0000000
--- a/src/H5Ocstore.c
+++ /dev/null
@@ -1,258 +0,0 @@
-/****************************************************************************
-* NCSA HDF *
-* Software Development Group *
-* National Center for Supercomputing Applications *
-* University of Illinois at Urbana-Champaign *
-* 605 E. Springfield, Champaign IL 61820 *
-* *
-* For conditions of distribution and use, see the accompanying *
-* hdf/COPYING file. *
-* *
-****************************************************************************/
-
-/*LINTLIBRARY */
-/*+
- FILE
- H5Ocstore.c
- HDF5 Contiguous Data Storage Object Header Message routines
-
- EXPORTED ROUTINES
-
- LIBRARY-SCOPED ROUTINES
-
- LOCAL ROUTINES
- + */
-
-#include <H5private.h>
-#include <H5Eprivate.h>
-#include <H5Gprivate.h>
-#include <H5MMprivate.h>
-#include <H5Oprivate.h>
-
-#define PABLO_MASK H5O_cstore_mask
-
-/* PRIVATE PROTOTYPES */
-static void *H5O_cstore_decode (H5F_t *f, size_t raw_size, const uint8 *p);
-static herr_t H5O_cstore_encode (H5F_t *f, size_t size, uint8 *p,
- const void *_mesg);
-static void *H5O_cstore_copy (const void *_mesg, void *_dest);
-static size_t H5O_cstore_size (H5F_t *f, const void *_mesg);
-static herr_t H5O_cstore_debug (H5F_t *f, const void *_mesg,
- FILE *stream, intn indent, intn fwidth);
-
-/* This message derives from H5O */
-const H5O_class_t H5O_CSTORE[1] = {{
- H5O_CSTORE_ID, /* message id number */
- "cstore", /* message name for debugging */
- sizeof (H5O_cstore_t), /* native message size */
- H5O_cstore_decode, /* decode message */
- H5O_cstore_encode, /* encode message */
- H5O_cstore_copy, /* copy the native value */
- H5O_cstore_size, /* size of symbol table entry */
- NULL, /* default reset method */
- H5O_cstore_debug, /* debug the message */
-}};
-
-/* Interface initialization */
-static hbool_t interface_initialize_g = FALSE;
-#define INTERFACE_INIT NULL
-
-/*--------------------------------------------------------------------------
- NAME
- H5O_cstore_decode
- PURPOSE
- Decode a contiguous data storage and return a pointer to a memory
- struct with the decoded information
- USAGE
- void *H5O_cstore_decode(f, raw_size, p)
- H5F_t *f; IN: pointer to the HDF5 file struct
- size_t raw_size; IN: size of the raw information buffer
- const uint8 *p; IN: the raw information buffer
- RETURNS
- Pointer to the new message in native order on success, NULL on failure
- DESCRIPTION
- This function decodes the "raw" disk form of a contiguous data storage
- message into a struct in memory native format. The struct is allocated
- within this function using malloc() and is returned to the caller.
---------------------------------------------------------------------------*/
-static void *
-H5O_cstore_decode (H5F_t *f, size_t raw_size, const uint8 *p)
-{
- H5O_cstore_t *store=NULL; /* New contiguous storage structure */
-
- FUNC_ENTER (H5O_cstore_decode, NULL);
-
- /* check args */
- assert (f);
- assert (raw_size == H5F_SIZEOF_ADDR(f)+H5F_SIZEOF_SIZE(f));
- assert (p);
-
- /* decode */
- if((store = H5MM_xcalloc (1, sizeof(H5O_cstore_t)))!=NULL)
- {
- H5F_addr_decode (f, &p,&(store->addr));
- H5F_decode_length(f,p,store->size);
- } /* end if */
-
-#ifdef LATER
-done:
-#endif /* LATER */
- if(store == NULL)
- { /* Error condition cleanup */
-
- } /* end if */
-
- /* Normal function cleanup */
-
- FUNC_LEAVE (store);
-}
-
-/*--------------------------------------------------------------------------
- NAME
- H5O_cstore_encode
- PURPOSE
- Encode a contiguous data storage message
- USAGE
- herr_t H5O_cstore_encode(f, raw_size, p, mesg)
- H5F_t *f; IN: pointer to the HDF5 file struct
- size_t raw_size; IN: size of the raw information buffer
- const uint8 *p; IN: the raw information buffer
- const void *mesg; IN: Pointer to the contiguous storage struct
- RETURNS
- SUCCEED/FAIL
- DESCRIPTION
- This function encodes the native memory form of the contiguous data
- storage message in the "raw" disk form.
---------------------------------------------------------------------------*/
-static herr_t
-H5O_cstore_encode (H5F_t *f, size_t raw_size, uint8 *p, const void *mesg)
-{
- const H5O_cstore_t *store = (const H5O_cstore_t *)mesg;
-
- FUNC_ENTER (H5O_cstore_encode, FAIL);
-
- /* check args */
- assert (f);
- assert (raw_size == H5F_SIZEOF_ADDR(f)+H5F_SIZEOF_SIZE(f));
- assert (p);
- assert (store);
-
- /* encode */
- H5F_addr_encode (f, &p, &(store->addr));
- H5F_encode_length(f,p,store->size);
-
- FUNC_LEAVE (SUCCEED);
-}
-
-/*--------------------------------------------------------------------------
- NAME
- H5O_cstore_copy
- PURPOSE
- Copies a message from MESG to DEST, allocating DEST if necessary.
- USAGE
- void *H5O_cstore_copy(mesg, dest)
- const void *mesg; IN: Pointer to the source contiguous storage
- struct
- const void *dest; IN: Pointer to the destination contiguous
- storage struct
- RETURNS
- Pointer to DEST on success, NULL on failure
- DESCRIPTION
- This function copies a native (memory) contiguous storage message,
- allocating the destination structure if necessary.
---------------------------------------------------------------------------*/
-static void *
-H5O_cstore_copy (const void *mesg, void *dest)
-{
- const H5O_cstore_t *src = (const H5O_cstore_t *)mesg;
- H5O_cstore_t *dst = (H5O_cstore_t *)dest;
-
- FUNC_ENTER (H5O_cstore_copy, NULL);
-
- /* check args */
- assert (src);
- if (!dst)
- dst = H5MM_xcalloc (1, sizeof(H5O_cstore_t));
-
- /* copy */
- HDmemcpy(dst,src,sizeof(H5O_cstore_t));
-
- FUNC_LEAVE ((void*)dst);
-}
-
-/*--------------------------------------------------------------------------
- NAME
- H5O_cstore_size
- PURPOSE
- Return the raw message size in bytes
- USAGE
- void *H5O_cstore_copy(f, mesg)
- H5F_t *f; IN: pointer to the HDF5 file struct
- const void *mesg; IN: Pointer to the source contiguous storage
- struct
- RETURNS
- Size of message on success, FAIL on failure
- DESCRIPTION
- This function returns the size of the raw contiguous storage message on
- success. (Not counting the message type or size fields, only the data
- portion of the message). It doesn't take into account alignment.
---------------------------------------------------------------------------*/
-static size_t
-H5O_cstore_size (H5F_t *f, const void *mesg)
-{
- size_t ret_value;
-
- FUNC_ENTER (H5O_cstore_size, FAIL);
-
- /* All contiguous data storage messages have the same data */
- ret_value=H5F_SIZEOF_ADDR(f)+H5F_SIZEOF_SIZE(f);
-
- FUNC_LEAVE (ret_value);
-}
-
-/*--------------------------------------------------------------------------
- NAME
- H5O_cstore_debug
- PURPOSE
- Prints debugging information for a contiguous storage message
- USAGE
- void *H5O_cstore_debug(f, mesg, stream, indent, fwidth)
- H5F_t *f; IN: pointer to the HDF5 file struct
- const void *mesg; IN: Pointer to the source contiguous storage
- struct
- FILE *stream; IN: Pointer to the stream for output data
- intn indent; IN: Amount to indent information by
- intn fwidth; IN: Field width (?)
- RETURNS
- SUCCEED/FAIL
- DESCRIPTION
- This function prints debugging output to the stream passed as a
- parameter.
---------------------------------------------------------------------------*/
-static herr_t
-H5O_cstore_debug (H5F_t *f, const void *mesg, FILE *stream,
- intn indent, intn fwidth)
-{
- const H5O_cstore_t *store = (const H5O_cstore_t *)mesg;
-
- FUNC_ENTER (H5O_cstore_debug, FAIL);
-
- /* check args */
- assert (f);
- assert (store);
- assert (stream);
- assert (indent>=0);
- assert (fwidth>=0);
-
- fprintf (stream, "%*s%-*s ", indent, "", fwidth,
- "Address:");
- H5F_addr_print (stream, &(store->addr));
- fprintf (stream, "\n");
-
- fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth,
- "Size (bytes):",
- (unsigned long)(store->size));
-
- FUNC_LEAVE (SUCCEED);
-}
-
diff --git a/src/H5Oistore.c b/src/H5Olayout.c
index ea65578..0d1ed2e 100644
--- a/src/H5Oistore.c
+++ b/src/H5Olayout.c
@@ -2,47 +2,49 @@
* Copyright (C) 1997 NCSA
* All rights reserved.
*
- * Programmer: Robb Matzke <matzke@llnl.gov>
- * Wednesday, October 8, 1997
+ * Programmer: Robb Matzke <matzke@llnl.gov>
+ * Wednesday, October 8, 1997
+ *
+ * Purpose: Messages related to data layout.
*/
#include <H5private.h>
+#include <H5Dprivate.h>
#include <H5Eprivate.h>
#include <H5MMprivate.h>
#include <H5Oprivate.h>
-#define PABLO_MASK H5O_istore_mask
-
/* PRIVATE PROTOTYPES */
-static void *H5O_istore_decode (H5F_t *f, size_t raw_size, const uint8 *p);
-static herr_t H5O_istore_encode (H5F_t *f, size_t size, uint8 *p,
+static void *H5O_layout_decode (H5F_t *f, size_t raw_size, const uint8 *p);
+static herr_t H5O_layout_encode (H5F_t *f, size_t size, uint8 *p,
const void *_mesg);
-static void *H5O_istore_copy (const void *_mesg, void *_dest);
-static size_t H5O_istore_size (H5F_t *f, const void *_mesg);
-static herr_t H5O_istore_debug (H5F_t *f, const void *_mesg, FILE *stream,
+static void *H5O_layout_copy (const void *_mesg, void *_dest);
+static size_t H5O_layout_size (H5F_t *f, const void *_mesg);
+static herr_t H5O_layout_debug (H5F_t *f, const void *_mesg, FILE *stream,
intn indent, intn fwidth);
/* This message derives from H5O */
-const H5O_class_t H5O_ISTORE[1] = {{
- H5O_ISTORE_ID, /*message id number */
- "istore", /*message name for debugging */
- sizeof(H5O_istore_t), /*native message size */
- H5O_istore_decode, /*decode message */
- H5O_istore_encode, /*encode message */
- H5O_istore_copy, /*copy the native value */
- H5O_istore_size, /*size of message on disk */
+const H5O_class_t H5O_LAYOUT[1] = {{
+ H5O_LAYOUT_ID, /*message id number */
+ "layout", /*message name for debugging */
+ sizeof(H5O_layout_t), /*native message size */
+ H5O_layout_decode, /*decode message */
+ H5O_layout_encode, /*encode message */
+ H5O_layout_copy, /*copy the native value */
+ H5O_layout_size, /*size of message on disk */
NULL, /*reset method */
- H5O_istore_debug, /*debug the message */
+ H5O_layout_debug, /*debug the message */
}};
/* Interface initialization */
+#define PABLO_MASK H5O_layout_mask
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT NULL
/*-------------------------------------------------------------------------
- * Function: H5O_istore_decode
+ * Function: H5O_layout_decode
*
- * Purpose: Decode an indexed storage message and return a pointer to a
+ * Purpose: Decode an data layout message and return a pointer to a
* new one created with malloc().
*
* Return: Success: Ptr to new message in native order.
@@ -57,38 +59,41 @@ static hbool_t interface_initialize_g = FALSE;
*-------------------------------------------------------------------------
*/
static void *
-H5O_istore_decode (H5F_t *f, size_t raw_size, const uint8 *p)
+H5O_layout_decode (H5F_t *f, size_t raw_size, const uint8 *p)
{
- H5O_istore_t *mesg = NULL;
+ H5O_layout_t *mesg = NULL;
intn i;
- FUNC_ENTER (H5O_istore_decode, NULL);
+ FUNC_ENTER (H5O_layout_decode, NULL);
/* check args */
assert (f);
assert (p);
/* decode */
- mesg = H5MM_xcalloc (1, sizeof(H5O_istore_t));
- H5F_addr_decode (f, &p, &(mesg->btree_addr));
+ mesg = H5MM_xcalloc (1, sizeof(H5O_layout_t));
+ H5F_addr_decode (f, &p, &(mesg->addr));
mesg->ndims = *p++;
- assert (raw_size == H5O_istore_size (f, mesg));
+ assert (raw_size == H5O_layout_size (f, mesg));
+
+ /* Layout class */
+ mesg->type = *p++;
+ assert (H5D_CONTIGUOUS==mesg->type || H5D_CHUNKED==mesg->type);
/* Reserved bytes */
- p += 7;
+ p += 6;
- /* Read the min_corner, max_corner, and alignment values */
+ /* Read the size */
for (i=0; i<mesg->ndims; i++) {
- UINT32DECODE (p, mesg->alignment[i]);
+ UINT32DECODE (p, mesg->dim[i]);
}
FUNC_LEAVE (mesg);
}
-
/*-------------------------------------------------------------------------
- * Function: H5O_istore_encode
+ * Function: H5O_layout_encode
*
* Purpose: Encodes a message.
*
@@ -104,41 +109,43 @@ H5O_istore_decode (H5F_t *f, size_t raw_size, const uint8 *p)
*-------------------------------------------------------------------------
*/
static herr_t
-H5O_istore_encode (H5F_t *f, size_t raw_size, uint8 *p, const void *_mesg)
+H5O_layout_encode (H5F_t *f, size_t raw_size, uint8 *p, const void *_mesg)
{
- const H5O_istore_t *mesg = (const H5O_istore_t *)_mesg;
+ const H5O_layout_t *mesg = (const H5O_layout_t *)_mesg;
int i;
- FUNC_ENTER (H5O_istore_encode, FAIL);
+ FUNC_ENTER (H5O_layout_encode, FAIL);
/* check args */
assert (f);
assert (mesg);
- assert (mesg->ndims>0 && mesg->ndims<=H5O_ISTORE_NDIMS);
- assert (raw_size == H5O_istore_size (f, _mesg));
+ assert (mesg->ndims>0 && mesg->ndims<=H5O_LAYOUT_NDIMS);
+ assert (raw_size == H5O_layout_size (f, _mesg));
assert (p);
- /* encode B-tree offset */
- H5F_addr_encode (f, &p, &(mesg->btree_addr));
+ /* data or B-tree address */
+ H5F_addr_encode (f, &p, &(mesg->addr));
/* number of dimensions */
*p++ = mesg->ndims;
+ /* layout class */
+ *p++ = mesg->type;
+
/* reserved bytes should be zero */
- for (i=0; i<7; i++) *p++ = 0;
+ for (i=0; i<6; i++) *p++ = 0;
- /* min_corner, max_corner, and alignment */
+ /* dimension size */
for (i=0; i<mesg->ndims; i++) {
- UINT32ENCODE (p, mesg->alignment[i]);
+ UINT32ENCODE (p, mesg->dim[i]);
}
FUNC_LEAVE (SUCCEED);
}
-
/*-------------------------------------------------------------------------
- * Function: H5O_istore_copy
+ * Function: H5O_layout_copy
*
* Purpose: Copies a message from _MESG to _DEST, allocating _DEST if
* necessary.
@@ -155,16 +162,16 @@ H5O_istore_encode (H5F_t *f, size_t raw_size, uint8 *p, const void *_mesg)
*-------------------------------------------------------------------------
*/
static void *
-H5O_istore_copy (const void *_mesg, void *_dest)
+H5O_layout_copy (const void *_mesg, void *_dest)
{
- const H5O_istore_t *mesg = (const H5O_istore_t *)_mesg;
- H5O_istore_t *dest = (H5O_istore_t *)_dest;
+ const H5O_layout_t *mesg = (const H5O_layout_t *)_mesg;
+ H5O_layout_t *dest = (H5O_layout_t *)_dest;
- FUNC_ENTER (H5O_istore_copy, NULL);
+ FUNC_ENTER (H5O_layout_copy, NULL);
/* check args */
assert (mesg);
- if (!dest) dest = H5MM_xcalloc (1, sizeof(H5O_istore_t));
+ if (!dest) dest = H5MM_xcalloc (1, sizeof(H5O_layout_t));
/* copy */
*dest = *mesg;
@@ -172,10 +179,9 @@ H5O_istore_copy (const void *_mesg, void *_dest)
FUNC_LEAVE ((void*)dest);
}
-
/*-------------------------------------------------------------------------
- * Function: H5O_istore_size
+ * Function: H5O_layout_size
*
* Purpose: Returns the size of the raw message in bytes not counting the
* message type or size fields, but only the data fields. This
@@ -193,30 +199,30 @@ H5O_istore_copy (const void *_mesg, void *_dest)
*-------------------------------------------------------------------------
*/
static size_t
-H5O_istore_size (H5F_t *f, const void *_mesg)
+H5O_layout_size (H5F_t *f, const void *_mesg)
{
- const H5O_istore_t *mesg = (const H5O_istore_t *)_mesg;
+ const H5O_layout_t *mesg = (const H5O_layout_t *)_mesg;
size_t ret_value = FAIL;
- FUNC_ENTER (H5O_istore_size, FAIL);
+ FUNC_ENTER (H5O_layout_size, FAIL);
/* check args */
assert (f);
assert (mesg);
- assert (mesg->ndims>0 && mesg->ndims<=H5O_ISTORE_NDIMS);
+ assert (mesg->ndims>0 && mesg->ndims<=H5O_LAYOUT_NDIMS);
ret_value = H5F_SIZEOF_ADDR (f) + /* B-tree address */
1 + /* max dimension index */
- 7 + /* reserved bytes */
+ 1 + /* layout class number */
+ 6 + /* reserved bytes */
mesg->ndims * 4; /* alignment */
FUNC_LEAVE (ret_value);
}
-
/*-------------------------------------------------------------------------
- * Function: H5O_istore_debug
+ * Function: H5O_layout_debug
*
* Purpose: Prints debugging info for a message.
*
@@ -232,13 +238,13 @@ H5O_istore_size (H5F_t *f, const void *_mesg)
*-------------------------------------------------------------------------
*/
static herr_t
-H5O_istore_debug (H5F_t *f, const void *_mesg, FILE *stream, intn indent,
+H5O_layout_debug (H5F_t *f, const void *_mesg, FILE *stream, intn indent,
intn fwidth)
{
- const H5O_istore_t *mesg = (const H5O_istore_t *)_mesg;
+ const H5O_layout_t *mesg = (const H5O_layout_t *)_mesg;
intn i;
- FUNC_ENTER (H5O_istore_debug, FAIL);
+ FUNC_ENTER (H5O_layout_debug, FAIL);
/* check args */
assert (f);
@@ -248,20 +254,20 @@ H5O_istore_debug (H5F_t *f, const void *_mesg, FILE *stream, intn indent,
assert (fwidth>=0);
fprintf (stream, "%*s%-*s ", indent, "", fwidth,
- "B-tree address:");
- H5F_addr_print (stream, &(mesg->btree_addr));
+ H5D_CHUNKED==mesg->type?"B-tree address:":"Data address:");
+ H5F_addr_print (stream, &(mesg->addr));
fprintf (stream, "\n");
fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth,
"Number of dimensions:",
(unsigned long)(mesg->ndims));
- /* Alignment */
+ /* Size */
fprintf (stream, "%*s%-*s {", indent, "", fwidth,
- "Alignment:");
+ "Size:");
for (i=0; i<mesg->ndims; i++) {
fprintf (stream, "%s%lu", i?", ":"",
- (unsigned long)(mesg->alignment[i]));
+ (unsigned long)(mesg->dim[i]));
}
fprintf (stream, "}\n");
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index fade4b4..cf23fc6 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -109,28 +109,18 @@ extern const H5O_class_t H5O_DTYPE[1];
/* operates on an H5T_t struct */
/*
- * Contiguous Data Storage Message.
+ * Data Layout Message
*/
-#define H5O_CSTORE_ID 0x0005
-extern const H5O_class_t H5O_CSTORE[1];
+#define H5O_LAYOUT_ID 0x0008
+#define H5O_LAYOUT_NDIMS 32
+extern const H5O_class_t H5O_LAYOUT[1];
-typedef struct H5O_cstore_t {
- haddr_t addr;
- size_t size;
-} H5O_cstore_t;
-
-/*
- * Indexed Data Storage Message.
- */
-#define H5O_ISTORE_ID 0x0008
-#define H5O_ISTORE_NDIMS 32
-extern const H5O_class_t H5O_ISTORE[1];
-
-typedef struct H5O_istore_t {
- haddr_t btree_addr; /*file address of B-tree */
+typedef struct H5O_layout_t {
+ int type; /*type of layout, H5D_layout_t */
+ haddr_t addr; /*file address of data or B-tree*/
uintn ndims; /*num dimensions in stored data */
- size_t alignment[H5O_ISTORE_NDIMS]; /*algn in logical space */
-} H5O_istore_t;
+ size_t dim[H5O_LAYOUT_NDIMS]; /*size of data or chunk */
+} H5O_layout_t;
/*
* External File List Message
diff --git a/src/H5V.c b/src/H5V.c
index d079399..c9c156c 100644
--- a/src/H5V.c
+++ b/src/H5V.c
@@ -11,7 +11,7 @@
#include <H5Oprivate.h>
#include <H5Vprivate.h>
-#define H5V_HYPER_NDIMS H5O_ISTORE_NDIMS
+#define H5V_HYPER_NDIMS H5O_LAYOUT_NDIMS
#define PABLO_MASK H5V_mask
static hbool_t interface_initialize_g = TRUE;
#define INTERFACE_INIT NULL
diff --git a/src/Makefile.in b/src/Makefile.in
index b0dc57f..7bb2f81 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -14,10 +14,10 @@ LIB=libhdf5.a
PROGS=debug
# Source and object files for the library (lexicographically)...
-LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5C.c H5D.c H5E.c H5F.c H5Fcore.c H5Ffamily.c \
- H5Fistore.c H5Flow.c H5Fsec2.c H5Fsplit.c H5Fstdio.c H5G.c H5Gent.c \
- H5Gnode.c H5Gstab.c H5H.c H5M.c H5MF.c H5MM.c H5O.c H5Ocont.c \
- H5Ocstore.c H5Odtype.c H5Oefl.c H5Oistore.c H5Oname.c H5Onull.c \
+LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5C.c H5D.c H5E.c H5F.c H5Farray.c H5Fcore.c \
+ H5Ffamily.c H5Fistore.c H5Flow.c H5Fsec2.c H5Fsplit.c H5Fstdio.c \
+ H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5H.c H5M.c H5MF.c H5MM.c H5O.c \
+ H5Ocont.c H5Odtype.c H5Oefl.c H5Olayout.c H5Oname.c H5Onull.c \
H5Osdspace.c H5Ostab.c H5P.c H5T.c H5Tconv.c H5Tinit.c H5V.c
LIB_OBJ=$(LIB_SRC:.c=.o)
diff --git a/test/dsets.c b/test/dsets.c
index 45aff80..9e024af 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -231,7 +231,8 @@ test_simple_io (hid_t file)
assert (dataset>=0);
/* Write the data to the dataset */
- status = H5Dwrite (dataset, H5T_NATIVE_INT, H5P_ALL, H5C_DEFAULT, points);
+ status = H5Dwrite (dataset, H5T_NATIVE_INT, H5P_ALL, H5P_ALL,
+ H5C_DEFAULT, points);
if (status<0) {
puts ("*FAILED*");
if (!isatty (1)) {
@@ -242,7 +243,8 @@ test_simple_io (hid_t file)
}
/* Read the dataset back */
- status = H5Dread (dataset, H5T_NATIVE_INT, H5P_ALL, H5C_DEFAULT, check);
+ status = H5Dread (dataset, H5T_NATIVE_INT, H5P_ALL, H5P_ALL,
+ H5C_DEFAULT, check);
if (status<0) {
puts ("*FAILED*");
if (!isatty (1)) {
@@ -321,7 +323,8 @@ test_tconv (hid_t file)
assert (dataset>=0);
/* Write the data to the dataset */
- status = H5Dwrite (dataset, H5T_NATIVE_INT32, H5P_ALL, H5C_DEFAULT, out);
+ status = H5Dwrite (dataset, H5T_NATIVE_INT32, H5P_ALL, H5P_ALL,
+ H5C_DEFAULT, out);
assert (status>=0);
/* Create a new type with the opposite byte order */
@@ -339,7 +342,7 @@ test_tconv (hid_t file)
}
/* Read data with byte order conversion */
- status = H5Dread (dataset, type, H5P_ALL, H5C_DEFAULT, in);
+ status = H5Dread (dataset, type, H5P_ALL, H5P_ALL, H5C_DEFAULT, in);
assert (status>=0);
/* Check */
diff --git a/test/istore.c b/test/istore.c
index 74154fc..8f246c8 100644
--- a/test/istore.c
+++ b/test/istore.c
@@ -99,8 +99,7 @@ print_array (uint8 *array, size_t nx, size_t ny, size_t nz)
static int
new_object (H5F_t *f, const char *name, size_t ndims, H5G_entry_t *ent/*out*/)
{
- H5O_istore_t istore;
- size_t alignment[H5O_ISTORE_NDIMS];
+ H5O_layout_t layout;
intn i;
/* Create the object header */
@@ -113,16 +112,18 @@ new_object (H5F_t *f, const char *name, size_t ndims, H5G_entry_t *ent/*out*/)
return -1;
}
- /* Add the indexed-storage message */
+ /* create chunked storage */
+ layout.type = H5D_CHUNKED;
+ layout.ndims = ndims;
for (i=0; i<ndims; i++) {
if (i<NELMTS (align_g)) {
- alignment[i] = align_g[i];
+ layout.dim[i] = align_g[i];
} else {
- alignment[i] = 2;
+ layout.dim[i] = 2;
}
}
- H5F_istore_create (f, &istore, ndims, alignment);
- if (H5O_modify (ent, H5O_ISTORE, H5O_NEW_MESG, 0, &istore)<0) {
+ H5F_arr_create (f, &layout/*in,out*/);
+ if (H5O_modify (ent, H5O_LAYOUT, H5O_NEW_MESG, 0, &layout)<0) {
printf ("*FAILED*\n");
if (!isatty (1)) {
AT();
@@ -174,7 +175,7 @@ test_create (H5F_t *f, const char *prefix)
printf ("%-70s", "Testing istore create");
- for (i=1; i<=H5O_ISTORE_NDIMS; i++) {
+ for (i=1; i<=H5O_LAYOUT_NDIMS; i++) {
sprintf (name, "%s_%02d", prefix, i);
if (new_object (f, name, i, &handle)<0) return FAIL;
}
@@ -216,7 +217,7 @@ test_extend (H5F_t *f, const char *prefix,
size_t size[3];
size_t whole_size[3];
size_t nelmts;
- H5O_istore_t istore;
+ H5O_layout_t layout;
if (!nz) {
if (!ny) {
@@ -250,7 +251,7 @@ test_extend (H5F_t *f, const char *prefix,
}
goto error;
}
- if (NULL==H5O_read (&handle, H5O_ISTORE, 0, &istore)) {
+ if (NULL==H5O_read (&handle, H5O_LAYOUT, 0, &layout)) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -258,7 +259,7 @@ test_extend (H5F_t *f, const char *prefix,
}
goto error;
}
- if (ndims!=istore.ndims) {
+ if (ndims!=layout.ndims) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -312,7 +313,7 @@ test_extend (H5F_t *f, const char *prefix,
memset (buf, 128+ctr, nelmts);
/* Write to disk */
- if (H5F_istore_write (f, &istore, offset, size, buf)<0) {
+ if (H5F_arr_write (f, &layout, offset, size, buf)<0) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -323,7 +324,7 @@ test_extend (H5F_t *f, const char *prefix,
/* Read from disk */
memset (check, 0xff, nelmts);
- if (H5F_istore_read (f, &istore, offset, size, check)<0) {
+ if (H5F_arr_read (f, &layout, offset, size, check)<0) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -357,7 +358,7 @@ test_extend (H5F_t *f, const char *prefix,
/* Now read the entire array back out and check it */
memset (buf, 0xff, nx*ny*nz);
- if (H5F_istore_read (f, &istore, H5V_ZERO, whole_size, buf)<0) {
+ if (H5F_arr_read (f, &layout, H5V_ZERO, whole_size, buf)<0) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -426,7 +427,7 @@ test_sparse (H5F_t *f, const char *prefix, size_t nblocks,
char dims[64], s[256], name[256];
size_t offset[3], size[3], total=0;
H5G_entry_t handle;
- H5O_istore_t istore;
+ H5O_layout_t layout;
uint8 *buf = NULL;
if (!nz) {
@@ -458,7 +459,7 @@ test_sparse (H5F_t *f, const char *prefix, size_t nblocks,
}
goto error;
}
- if (NULL==H5O_read (&handle, H5O_ISTORE, 0, &istore)) {
+ if (NULL==H5O_read (&handle, H5O_LAYOUT, 0, &layout)) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
@@ -477,7 +478,7 @@ test_sparse (H5F_t *f, const char *prefix, size_t nblocks,
memset (buf, 128+ctr, nx*ny*nz);
/* write to disk */
- if (H5F_istore_write (f, &istore, offset, size, buf)<0) {
+ if (H5F_arr_write (f, &layout, offset, size, buf)<0) {
puts ("*FAILED*");
if (!isatty (1)) {
AT ();
generated by cgit v0.12 at 2024-08-25 14:53:20 (GMT)