Java examples for Big Data:HDF
Writing and reading a hyperslab for HDF5
/****************************************************************** * HyperSlab.java (for HDF5 tutorial lesson 12) * * -- Writing and reading a hyperslab//w w w . jav a2 s . co m * (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; } }