|
HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |
The C Interfaces:
H5Dclose(hid_t dataset_id
)
H5Dclose ends access to a dataset specified by
dataset_id and releases resources used by it.
Further use of the dataset identifier is illegal in calls to
the dataset API.
dataset_id
H5Dcreate(hid_t loc_id,
const char *name,
hid_t type_id,
hid_t space_id,
hid_t create_plist_id
)
H5Dcreate creates a data set with a name,
name, in the file or in the group specified by
the identifier loc_id.
The dataset has the datatype and dataspace identified by
type_id and space_id, respectively.
The specified datatype and dataspace are the datatype and
dataspace of the dataset as it will exist in the file,
which may be different than in application memory.
Dataset creation properties are specified by the argument
create_plist_id.
Dataset names within a group are unique:
H5Dcreate will return an error if a dataset with
the name specified in name already exists at the
location specified in loc_id.
create_plist_id is a H5P_DATASET_CREATE
property list created with H5Pcreate and
initialized with the various functions described above.
H5Dcreate returns an error if the dataset's datatype
includes a variable-length (VL) datatype and the fill value
is undefined, i.e., set to NULL in the
dataset creation property list.
Such a VL datatype may be directly included,
indirectly included as part of a compound or array datatype, or
indirectly included as part of a nested compound or array datatype.
H5Dcreate returns a dataset identifier for success
or a negative value for failure.
The dataset identifier should eventually be closed by
calling H5Dclose to release resources it uses.
Fill values and space allocation:
The HDF5 library provides flexible means
of specifying a fill value,
of specifying when space will be allocated for a dataset, and
of specifying when fill values will be written to a dataset.
For further information on these topics, see the document
Fill Value and Dataset Storage Allocation Issues in HDF5
and the descriptions of the following HDF5 functions in this
HDF5 Reference Manual:
|
H5Dfill H5Pset_fill_value H5Pget_fill_value H5Pfill_value_defined |
H5Pset_fill_time H5Pget_fill_time H5Pset_alloc_time H5Pget_alloc_time |
loc_id
name
type_id
space_id
create_plist_id
H5Dextend(hid_t dataset_id,
const hsize_t * size
)
H5Dextend verifies that the dataset is at least of size
size.
The dimensionality of size is the same as that of
the dataspace of the dataset being changed.
This function cannot be applied to a dataset with fixed dimensions.
Space on disk is immediately allocated for the new dataset extent
if the dataset's space allocation time is set to
H5D_ALLOC_TIME_EARLY.
Fill values will be written to the dataset if the dataset's fill time
is set to H5D_FILL_TIME_IFSET or
H5D_FILL_TIME_ALLOC.
(Also see
H5Pset_fill_time
and
H5Pset_alloc_time.)
dataset_id
size
H5Dfill(
const void *fill,
hid_t fill_type_id,
void *buf,
hid_t buf_type_id,
hid_t space_id
)
H5Dfill explicitly fills
the dataspace selection in memory, space_id,
with the fill value specified in fill.
If fill is NULL,
a fill value of 0 (zero) is used.
fill_type_id specifies the datatype
of the fill value.
buf specifies the buffer in which
the dataspace elements will be written.
buf_type_id specifies the datatype of
those data elements.
Note that if the fill value datatype differs from the memory buffer datatype, the fill value will be converted to the memory buffer datatype before filling the selection.
fill
fill_type_id
buf
buf_type_id
space_id
H5Dget_create_plist(hid_t dataset_id
)
H5Dget_create_plist returns an identifier for a
copy of the dataset creation property list for a dataset.
The creation property list identifier should be released with
the H5Pclose function.
dataset_id
H5Dget_offset(hid_t dset_id)
H5Dget_offset returns the address in the file
of the dataset dset_id.
That address is expressed as the offset in bytes from
the beginning of the file.
dset_id
HADDR_UNDEF, a negative value.
H5Dget_space(hid_t dataset_id
)
H5Dget_space returns an identifier for a copy of the
dataspace for a dataset.
The dataspace identifier should be released with the
H5Sclose function.
dataset_id
H5Dget_space_status(hid_t dset_id,
H5D_space_status_t *status)
H5Dget_space_status determines whether space has been
allocated for the dataset dset_id.
Space allocation status is returned in status,
which will have one of the following values:
| H5D_SPACE_STATUS_NOT_ALLOCATED | Space has not been allocated for this dataset. | |
| H5D_SPACE_STATUS_ALLOCATED | Space has been allocated for this dataset. | |
| H5D_SPACE_STATUS_PART_ALLOCATED | Space has been partially allocated for this dataset. (Used only for datasets with chunked storage.) |
dset_id
status
H5Dget_storage_size(hid_t dataset_id
)
H5Dget_storage_size returns the amount of storage
that is required for the specified dataset, dataset_id.
For chunked datasets, this is the number of allocated chunks times
the chunk size.
The return value may be zero if no data has been stored.
dataset_id
H5Dget_type(hid_t dataset_id
)
H5Dget_type returns an identifier for a copy of the
datatype for a dataset.
The datatype should be released with the H5Tclose function.
If a dataset has a named datatype, then an identifier to the opened datatype is returned. Otherwise, the returned datatype is read-only. If atomization of the datatype fails, then the datatype is closed.
dataset_id
H5Diterate(
void *buf,
hid_t type_id,
hid_t space_id,
H5D_operator_t operator,
void *operator_data
)
H5Diterate iterates over all the elements selected
in a memory buffer. The callback function is called once for each
element selected in the dataspace.
The selection in the dataspace is modified so that any elements
already iterated over are removed from the selection if the
iteration is interrupted (by the H5D_operator_t
function returning non-zero) before the iteration is complete;
the iteration may then be re-started by the user where it left off.
buf
type_id
buf.
space_id
buf.
Also contains the selection to iterate over.
operator
buf iterated over.
operator_data
H5Dopen(hid_t loc_id,
const char *name
)
H5Dopen opens an existing dataset for access in the file
or group specified in loc_id. name is
a dataset name and is used to identify the dataset in the file.
loc_id
name
H5Dread(hid_t dataset_id,
hid_t mem_type_id,
hid_t mem_space_id,
hid_t file_space_id,
hid_t xfer_plist_id,
void * buf
)
H5Dread reads a (partial) dataset, specified by its
identifier dataset_id, from the
file into an application memory buffer buf.
Data transfer properties are defined by the argument
xfer_plist_id.
The memory datatype of the (partial) dataset is identified by
the identifier mem_type_id.
The part of the dataset to read is defined by
mem_space_id and file_space_id.
file_space_id is used to specify only the selection within
the file dataset's dataspace. Any dataspace specified in file_space_id
is ignored by the library and the dataset's dataspace is always used.
file_space_id can be the constant H5S_ALL.
which indicates that the entire file dataspace, as defined by the
current dimensions of the dataset, is to be selected.
mem_space_id is used to specify both the memory dataspace
and the selection within that dataspace.
mem_space_id can be the constant H5S_ALL,
in which case the file dataspace is used for the memory dataspace and
the selection defined with file_space_id is used for the
selection within that dataspace.
If raw data storage space has not been allocated for the dataset
and a fill value has been defined, the returned buffer buf
is filled with the fill value.
The behavior of the library for the various combinations of valid
dataspace identifiers and H5S_ALL for the mem_space_id and the
file_space_id parameters is described below:
mem_space_id
|
file_space_id
|
Behavior |
|---|---|---|
| valid dataspace identifier | valid dataspace identifier |
mem_space_id specifies the memory dataspace and the
selection within it.
file_space_id specifies the selection within the file
dataset's dataspace.
|
H5S_ALL
|
valid dataspace identifier |
The file dataset's dataspace is used for the memory dataspace and the
selection specified with file_space_id specifies the
selection within it.
The combination of the file dataset's dataspace and the selection from
file_space_id is used for memory also.
|
| valid dataspace identifier |
H5S_ALL
|
mem_space_id specifies the memory dataspace and the
selection within it.
The selection within the file dataset's dataspace is set to the "all"
selection.
|
H5S_ALL
|
H5S_ALL
|
The file dataset's dataspace is used for the memory dataspace and the selection within the memory dataspace is set to the "all" selection. The selection within the file dataset's dataspace is set to the "all" selection. |
Setting an H5S_ALL selection indicates that the entire dataspace, as
defined by the current dimensions of a dataspace, will be selected.
The number of elements selected in the memory dataspace must match the
number of elements selected in the file dataspace.
xfer_plist_id can be the constant H5P_DEFAULT.
in which case the default data transfer properties are used.
Data is automatically converted from the file datatype and dataspace to the memory datatype and dataspace at the time of the read. See the Data Conversion section of The Data Type Interface (H5T) in the HDF5 User's Guide for a discussion of data conversion, including the range of conversions currently supported by the HDF5 libraries.
dataset_id
mem_type_id
mem_space_id
file_space_id
xfer_plist_id
buf
H5Dvlen_get_buf_size(hid_t dataset_id,
hid_t type_id,
hid_t space_id,
hsize_t *size
)
H5Dvlen_get_buf_size determines the number of bytes
required to store the VL data from the dataset, using the
space_id for the selection in the dataset on
disk and the type_id for the memory representation
of the VL data in memory.
*size is returned with the number of bytes
required to store the VL data in memory.
dataset_id
type_id
space_id
size
H5Dvlen_get_buf_size;
corresponding functionality is provided by the FORTRAN function
h5dvlen_get_max_len_f.
H5Dvlen_reclaim(hid_t type_id,
hid_t space_id,
hid_t plist_id,
void *buf
)
H5Dvlen_reclaim reclaims memory buffers created to
store VL datatypes.
The type_id must be the datatype stored in the buffer.
The space_id describes the selection for the memory buffer
to free the VL datatypes within.
The plist_id is the dataset transfer property list which
was used for the I/O transfer to create the buffer.
And buf is the pointer to the buffer to be reclaimed.
The VL structures (hvl_t) in the user's buffer are
modified to zero out the VL information after the memory has been reclaimed.
If nested VL datatypes were used to create the buffer, this routine frees them from the bottom up, releasing all the memory without creating memory leaks.
type_id
space_id
plist_id
buf
H5Dwrite(hid_t dataset_id,
hid_t mem_type_id,
hid_t mem_space_id,
hid_t file_space_id,
hid_t xfer_plist_id,
const void * buf
)
H5Dwrite writes a (partial) dataset, specified by its
identifier dataset_id, from the
application memory buffer buf into the file.
Data transfer properties are defined by the argument
xfer_plist_id.
The memory datatype of the (partial) dataset is identified by
the identifier mem_type_id.
The part of the dataset to write is defined by
mem_space_id and file_space_id.
file_space_id is used to specify only the selection within
the file dataset's dataspace. Any dataspace specified in file_space_id
is ignored by the library and the dataset's dataspace is always used.
file_space_id can be the constant H5S_ALL.
which indicates that the entire file dataspace, as defined by the
current dimensions of the dataset, is to be selected.
mem_space_id is used to specify both the memory dataspace
and the selection within that dataspace.
mem_space_id can be the constant H5S_ALL,
in which case the file dataspace is used for the memory dataspace and
the selection defined with file_space_id is used for the
selection within that dataspace.
The behavior of the library for the various combinations of valid
dataspace IDs and H5S_ALL for the mem_space_id and the
file_space_id parameters is described below:
mem_space_id
|
file_space_id
|
Behavior |
|---|---|---|
| valid dataspace identifier | valid dataspace identifier |
mem_space_id specifies the memory dataspace and the
selection within it.
file_space_id specifies the selection within the file
dataset's dataspace.
|
| H5S_ALL | valid dataspace identifier |
The file dataset's dataspace is used for the memory dataspace and the
selection specified with file_space_id specifies the
selection within it.
The combination of the file dataset's dataspace and the selection from
file_space_id is used for memory also.
|
| valid dataspace identifier | H5S_ALL |
mem_space_id specifies the memory dataspace and the
selection within it.
The selection within the file dataset's dataspace is set to the "all"
selection.
|
| H5S_ALL | H5S_ALL | The file dataset's dataspace is used for the memory dataspace and the selection within the memory dataspace is set to the "all" selection. The selection within the file dataset's dataspace is set to the "all" selection. |
Setting an "all" selection indicates that the entire dataspace, as defined by the current dimensions of a dataspace, will be selected. The number of elements selected in the memory dataspace must match the number of elements selected in the file dataspace.
xfer_plist_id can be the constant H5P_DEFAULT.
in which case the default data transfer properties are used.
Writing to an dataset will fail if the HDF5 file was not opened with write access permissions.
Data is automatically converted from the memory datatype and dataspace to the file datatype and dataspace at the time of the write. See the Data Conversion section of The Data Type Interface (H5T) in the HDF5 User's Guide for a discussion of data conversion, including the range of conversions currently supported by the HDF5 libraries.
If the dataset's space allocation time is set to
H5D_ALLOC_TIME_LATE or H5D_ALLOC_TIME_INCR
and the space for the dataset has not yet been allocated,
that space is allocated when the first raw data is written to the
dataset.
Unused space in the dataset will be written with fill values at the
same time if the dataset's fill time is set to
H5D_FILL_TIME_IFSET or H5D_FILL_TIME_ALLOC.
(Also see
H5Pset_fill_time
and
H5Pset_alloc_time.)
If a dataset's storage layout is 'compact', care must be taken when writing data to the dataset in parallel. A compact dataset's raw data is cached in memory and may be flushed to the file from any of the parallel processes, so parallel applications should always attempt to write identical data to the dataset from all processes.
dataset_id
mem_type_id
mem_space_id
file_space_id
xfer_plist_id
buf
|
HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |