Java examples for Big Data:HDF
Showing how to use the H5 SCOPY function
/****************************************************************** * Copy.java (for HDF5 tutorial lesson 13) * * -- Showing how to use the H5SCOPY function. * (a java conversion from h5_copy.c) * ******************************************************************/ import ncsa.hdf.hdf5lib.*; import ncsa.hdf.hdf5lib.exceptions.*; public class Copy { public static void main (String []argv) {/* w ww. j av a 2s. c om*/ final String FILE1 = "copy1.h5"; final String FILE2 = "copy2.h5"; final int RANK = 2; final int DIM1 = 3; final int DIM2 = 4; final int NUMP = 2; int file1, file2, dataset1, dataset2; int mid1, mid2, fid1, fid2; long[] fdim = new long[2]; fdim[0] = DIM1; fdim[1] = DIM2; long[] mdim = new long[2]; fdim[0] = DIM1; fdim[1] = DIM2; long[] start = new long[2]; long[] stride = new long[2]; long[] count = new long[2]; long[] block = new long[2]; int[][] buf1 = new int[DIM1][DIM2]; int[][] buf2 = new int[DIM1][DIM2]; int[][] bufnew = new int[DIM1][DIM2]; int[] val = new int[2]; val[0] = 53; val[1] = 59; long[] marray = {2}; long[][] coord = new long[NUMP][RANK]; int ret; int i, j; /***********************************************************************/ /* */ /* Create two files containing identical datasets. Write 0's to one */ /* and 1's to the other. */ /* */ /***********************************************************************/ for ( i = 0; i < DIM1; i++ ) for ( j = 0; j < DIM2; j++ ) buf1[i][j] = 0; for ( i = 0; i < DIM1; i++ ) for ( j = 0; j < DIM2; j++ ) buf2[i][j] = 1; file1 = H5Fcreate_wrap (FILE1, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); file2 = H5Fcreate_wrap (FILE2, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); fid1 = H5Screate_simple_wrap (RANK, fdim, null); fid2 = H5Screate_simple_wrap (RANK, fdim, null); dataset1 = H5Dcreate_wrap (file1, "Copy1", H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), fid1, HDF5Constants.H5P_DEFAULT); dataset2 = H5Dcreate_wrap (file2, "Copy2", H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), fid2, HDF5Constants.H5P_DEFAULT); ret = H5Dwrite_wrap (dataset1, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, buf1); ret = H5Dwrite_wrap (dataset2, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, buf2); ret = H5Dclose_wrap (dataset1); ret = H5Dclose_wrap (dataset2); ret = H5Sclose_wrap (fid1); ret = H5Sclose_wrap (fid2); ret = H5Fclose_wrap (file1); ret = H5Fclose_wrap (file2); /***********************************************************************/ /* */ /* Open the two files. Select two points in one file, write values to */ /* those point locations, then do H5Scopy and write the values to the */ /* other file. Close files. */ /* */ /***********************************************************************/ file1 = H5Fopen_wrap (FILE1, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); file2 = H5Fopen_wrap (FILE2, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); dataset1 = H5Dopen_wrap (file1, "Copy1"); dataset2 = H5Dopen_wrap (file2, "Copy2"); fid1 = H5Dget_space_wrap (dataset1); mid1 = H5Screate_simple_wrap (1, marray, null); coord[0][0] = 0; coord[0][1] = 3; coord[1][0] = 0; coord[1][1] = 1; ret = H5Sselect_elements_wrap (fid1, HDF5Constants.H5S_SELECT_SET, NUMP, coord); ret = H5Dwrite_wrap (dataset1, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), mid1, fid1, HDF5Constants.H5P_DEFAULT, val); fid2 = H5Scopy_wrap (fid1); ret = H5Dwrite_wrap (dataset2, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), mid1, fid2, HDF5Constants.H5P_DEFAULT, val); ret = H5Dclose_wrap (dataset1); ret = H5Dclose_wrap (dataset2); ret = H5Sclose_wrap (fid1); ret = H5Sclose_wrap (fid2); ret = H5Fclose_wrap (file1); ret = H5Fclose_wrap (file2); ret = H5Sclose_wrap (mid1); /***********************************************************************/ /* */ /* Open both files and print the contents of the datasets. */ /* */ /***********************************************************************/ file1 = H5Fopen_wrap (FILE1, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); file2 = H5Fopen_wrap (FILE2, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); dataset1 = H5Dopen_wrap (file1, "Copy1"); dataset2 = H5Dopen_wrap (file2, "Copy2"); ret = H5Dread_wrap (dataset1, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, bufnew); System.out.println ("\nDataset 'Copy1' in file 'copy1.h5' contains: "); for (i = 0;i < DIM1; i++) { for (j = 0;j < DIM2; j++) System.out.print (bufnew[i][j]); System.out.println (); } System.out.println ("\nDataset 'Copy2' in file 'copy2.h5' contains: "); ret = H5Dread_wrap (dataset2, H5.J2C (HDF5CDataTypes.JH5T_NATIVE_INT), HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, bufnew); for (i = 0;i < DIM1; i++) { for (j = 0;j < DIM2; j++) System.out.print (bufnew[i][j]); System.out.println (); } ret = H5Dclose_wrap (dataset1); ret = H5Dclose_wrap (dataset2); ret = H5Fclose_wrap (file1); ret = H5Fclose_wrap (file2); } // 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 ("Copy.H5Fcreate_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Fopen_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Dopen_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Screate_simple_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Dget_space_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.H5Dget_space_wrap() with other Exception: " + e.getMessage()); } return dataspace_id; } // Help function for selecting array elements to be included in // the selection for the space_id dataspace. public static int H5Sselect_elements_wrap (int space_id, int op, int num_elements, long coord2D[][]) { int status = -1; try { status = H5.H5Sselect_elements (space_id, op, num_elements, coord2D); } catch (HDF5Exception hdf5e) { System.out.println ("Copy.H5Sselect_elements_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.H5Sselect_elements_wrap() with other Exception: " + e.getMessage()); } return status; } // Help function for creating a new dataspace which is an exact // copy of the dataspace identified by space_id. public static int H5Scopy_wrap (int space_id) { int dataspace_id = -1; try { dataspace_id = H5.H5Scopy(space_id); } catch (HDF5Exception hdf5e) { System.out.println ("Copy.H5Scopy_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.H5Scopy_wrap() with other Exception: " + e.getMessage()); } return dataspace_id; } // 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 ("Copy.H5Dcreate_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Dwrite_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Dread_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Sclose_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Dclose_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.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 ("Copy.H5Fclose_wrap() with HDF5Exception: " + hdf5e.getMessage()); } catch (Exception e) { System.out.println ("Copy.H5Fclose_wrap() with other exception: " + e.getMessage()); } return status; } }