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doc/html/Tutor/examples/java/HyperSlab.java Normal file
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/******************************************************************
* HyperSlab.java (for HDF5 tutorial lesson 12)
*
* -- Writing and reading a hyperslab
* (a java conversion from h5_hyperslab.c)
*
******************************************************************/
import ncsa.hdf.hdf5lib.*;
import ncsa.hdf.hdf5lib.exceptions.*;
public class HyperSlab
{
public static void main (String []argv)
{
final String FILE = "sds.h5";
final String DATASETNAME = "IntArray";
final int NX_SUB = 3; /* hyperslab dimensions */
final int NY_SUB = 4;
final int NX = 7; /* output buffer dimensions */
final int NY = 7;
final int NZ = 3;
final int RANK = 2;
final int RANK_OUT = 3;
final int X = 5; /* dataset dimensions */
final int Y = 6;
long[] dimsf = new long[2]; /* dataset dimensions */
int[][] data = new int[X][Y]; /* data to write */
/*
* Data and output buffer initialization.
*/
int file, dataset; /* handles */
int dataspace;
int memspace;
long[] dimsm = new long[3]; /* memory space dimensions */
long[] dims_out = new long[2]; /* dataset dimensions */
int status;
int[][][] data_out = new int[NX][NY][NZ]; /* output buffer */
long[] count = new long[2]; /* size of the hyperslab in the file */
long[] offset = new long[2]; /* hyperslab offset in the file */
long[] count_out = new long[3]; /* size of the hyperslab in memory */
long[] offset_out = new long[3]; /* hyperslab offset in memory */
int i, j, k, status_n, rank;
/*********************************************************
This writes data to the HDF5 file.
*********************************************************/
/*
* Data and output buffer initialization.
*/
for (j = 0; j < X; j++)
{
for (i = 0; i < Y; i++)
data[j][i] = i + j;
}
/*
* 0 1 2 3 4 5
* 1 2 3 4 5 6
* 2 3 4 5 6 7
* 3 4 5 6 7 8
* 4 5 6 7 8 9
*/
/*
* Create a new file using H5F_ACC_TRUNC access,
* the default file creation properties, and the default file
* access properties.
*/
file = H5Fcreate_wrap (FILE, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = X;
dimsf[1] = Y;
dataspace = H5Screate_simple_wrap (RANK, dimsf, null);
/*
* Create a new dataset within the file using defined dataspace and
* default dataset creation properties.
*/
dataset = H5Dcreate_wrap
(file, DATASETNAME, H5.J2C (HDF5CDataTypes.JH5T_STD_I32BE),
dataspace, HDF5Constants.H5P_DEFAULT);
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite_wrap
(dataset, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT),
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose_wrap (dataspace);
H5Dclose_wrap (dataset);
H5Fclose_wrap (file);
/*************************************************************
This reads the hyperslab from the sds.h5 file just
created, into a 2-dimensional plane of the 3-dimensional
array.
************************************************************/
for (j = 0; j < NX; j++)
{
for (i = 0; i < NY; i++)
{
for (k = 0; k < NZ ; k++)
data_out[j][i][k] = 0;
}
}
/*
* Open the file and the dataset.
*/
file = H5Fopen_wrap (FILE, HDF5Constants.H5F_ACC_RDONLY,
HDF5Constants.H5P_DEFAULT);
dataset = H5Dopen_wrap (file, DATASETNAME);
dataspace = H5Dget_space_wrap (dataset); /* dataspace handle */
rank = H5Sget_simple_extent_ndims_wrap (dataspace);
status_n = H5Sget_simple_extent_dims_wrap (dataspace, dims_out, null);
System.out.println ("Rank: " + rank);
System.out.println ("Dimensions: "+ dims_out[0] + " x " + dims_out[1]);
/*
* Define hyperslab in the dataset.
*/
offset[0] = 1;
offset[1] = 2;
count[0] = NX_SUB;
count[1] = NY_SUB;
status = H5Sselect_hyperslab_wrap (dataspace,
HDF5Constants.H5S_SELECT_SET,
offset, null, count, null);
/*
* Define the memory dataspace.
*/
dimsm[0] = NX;
dimsm[1] = NY;
dimsm[2] = NZ;
memspace = H5Screate_simple_wrap (RANK_OUT, dimsm, null);
/*
* Define memory hyperslab.
*/
offset_out[0] = 3;
offset_out[1] = 0;
offset_out[2] = 0;
count_out[0] = NX_SUB;
count_out[1] = NY_SUB;
count_out[2] = 1;
status = H5Sselect_hyperslab_wrap (memspace,
HDF5Constants.H5S_SELECT_SET,
offset_out, null, count_out, null);
/*
* Read data from hyperslab in the file into the hyperslab in
* memory and display.
*/
status =
H5Dread_wrap (dataset, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT),
memspace, dataspace, HDF5Constants.H5P_DEFAULT,
data_out);
System.out.println ("Data:");
for (j = 0; j < NX; j++)
{
for (i = 0; i < NY; i++)
System.out.print (data_out[j][i][0]);
System.out.println ();
}
System.out.println ();
/*
* 0 0 0 0 0 0 0
* 0 0 0 0 0 0 0
* 0 0 0 0 0 0 0
* 3 4 5 6 0 0 0
* 4 5 6 7 0 0 0
* 5 6 7 8 0 0 0
* 0 0 0 0 0 0 0
*/
/*
* Close and release resources.
*/
H5Dclose_wrap (dataset);
H5Sclose_wrap (dataspace);
H5Sclose_wrap (memspace);
H5Fclose_wrap (file);
}
// Help function for creating a new file
public static int H5Fcreate_wrap (String name, int flags,
int create_id, int access_id)
{
int file_id = -1; // file identifier
try
{
// Create a new file using default file properties.
file_id = H5.H5Fcreate (name, flags, create_id, access_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Fcreate_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Fcreate_wrap() with other Exception: "
+ e.getMessage());
}
return file_id;
}
// Help function for opening an existing file
public static int H5Fopen_wrap (String name, int flags, int access_id)
{
int file_id = -1; // file identifier
try
{
// Create a new file using default file properties.
file_id = H5.H5Fopen (name, flags, access_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Fopen_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Fopen_wrap() with other Exception: "
+ e.getMessage());
}
return file_id;
}
// Help function for opening an existing dataset
public static int H5Dopen_wrap (int loc_id, String name)
{
int dataset_id = -1; // dataset identifier
try
{
// Opening an existing dataset
dataset_id = H5.H5Dopen (loc_id, name);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dopen_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dopen_wrap() with other Exception: "
+ e.getMessage());
}
return dataset_id;
}
// Help function for creating a new simple dataspace and opening it
// for access
public static int H5Screate_simple_wrap (int rank, long dims[],
long maxdims[])
{
int dataspace_id = -1; // dataspace identifier
try
{
// Create the data space for the dataset.
dataspace_id = H5.H5Screate_simple (rank, dims, maxdims);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Screate_simple_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Screate_simple_wrap() with other Exception: "
+ e.getMessage());
}
return dataspace_id;
}
// Help function for getting an identifier for a copy of
// the dataspace for a dataset
public static int H5Dget_space_wrap (int dataset_id)
{
int dataspace_id = -1;
try
{
// Returning an identifier for a copy of the dataspace for a dataset
dataspace_id = H5.H5Dget_space (dataset_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dget_space_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dget_space_wrap() with other Exception: "
+ e.getMessage());
}
return dataspace_id;
}
// Help function for determining the dimensionality (or rank) of
// a dataspace
public static int H5Sget_simple_extent_ndims_wrap (int space_id)
{
int rank = -1;
try
{
// Determine the dimensionality (or rank) of a dataspace.
rank = H5.H5Sget_simple_extent_ndims (space_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Sget_simple_extent_ndims_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Sget_simple_extent_ndims_wrap() with other Exception: "
+ e.getMessage());
}
return rank;
}
// Help function for returning the size and maximum sizes of each
// dimension of a dataspace through the dims and maxdims parameters.
public static int H5Sget_simple_extent_dims_wrap (int space_id,
long dims[],
long maxdims[])
{
int dimension_number = -1;
try
{
dimension_number = H5.H5Sget_simple_extent_dims (space_id, dims,
maxdims);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Sget_simple_extent_dims_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Sget_simple_extent_dims_wrap() with other Exception: "
+ e.getMessage());
}
return dimension_number;
}
// Help function for selecting a hyperslab region to add to the
// current selected region for the dataspace specified by space_id.
public static int H5Sselect_hyperslab_wrap (int space_id, int op,
long start[], long stride[],
long count[], long block[])
{
int status = -1;
try
{
status = H5.H5Sselect_hyperslab (space_id, op, start, stride,
count, block);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Sselect_hyperslab_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Sselect_hyperslab_wrap() with other Exception: "
+ e.getMessage());
}
return status;
}
// Help function for creating a dataset
public static int H5Dcreate_wrap (int loc_id, String name, int type_id,
int space_id, int create_plist_id)
{
int dataset_id = -1; // dataset identifier
try
{
// Create the dataset
dataset_id = H5.H5Dcreate (loc_id, name, type_id, space_id,
create_plist_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dcreate_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dcreate_wrap() with other Exception: "
+ e.getMessage());
}
return dataset_id;
}
// Help function for writing the dataset
public static int H5Dwrite_wrap (int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id,
int xfer_plist_id, Object buf)
{
int status = -1;
try
{
// Write the dataset.
status = H5.H5Dwrite (dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dwrite_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dwrite_wrap() with other exception: "
+ e.getMessage());
}
return status;
}
// Help function for reading the dataset
public static int H5Dread_wrap (int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id,
int xfer_plist_id, Object obj)
{
int status = -1;
try
{
// Read the dataset.
status = H5.H5Dread (dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, obj);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dread_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dread_wrap() with other exception: "
+ e.getMessage());
}
return status;
}
// Help function for terminating access to the data space.
public static int H5Sclose_wrap (int dataspace_id)
{
int status = -1;
try
{
// Terminate access to the data space.
status = H5.H5Sclose (dataspace_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Sclose_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Sclose_wrap() with other exception: "
+ e.getMessage());
}
return status;
}
// Help function for ending access to the dataset and releasing
// resources used by it.
public static int H5Dclose_wrap (int dataset_id)
{
int status = -1;
try
{
// End access to the dataset and release resources used by it.
status = H5.H5Dclose (dataset_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Dclose_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Dclose_wrap() with other exception: "
+ e.getMessage());
}
return status;
}
// Help function for terminating access to the file.
public static int H5Fclose_wrap (int file_id)
{
int status = -1;
try
{
// Terminate access to the file.
status = H5.H5Fclose (file_id);
}
catch (HDF5Exception hdf5e)
{
System.out.println
("HyperSlab.H5Fclose_wrap() with HDF5Exception: "
+ hdf5e.getMessage());
}
catch (Exception e)
{
System.out.println
("HyperSlab.H5Fclose_wrap() with other exception: "
+ e.getMessage());
}
return status;
}
}