/************************************************************ This example shows how to read and write bitfield datatypes to a dataset. The program first writes bit fields to a dataset with a dataspace of DIM0xDIM1, then closes the file. Next, it reopens the file, reads back the data, and outputs it to the screen. This file is intended for use with HDF5 Library verion 1.6 ************************************************************/ package examples.datatypes; import hdf.hdf5lib.H5; import hdf.hdf5lib.HDF5Constants; import hdf.object.Datatype; import hdf.object.FileFormat; import hdf.object.Group; import hdf.object.h5.H5Datatype; import hdf.object.h5.H5File; import hdf.object.h5.H5ScalarDS; public class H5ObjectEx_T_Bit { private static String FILENAME = "H5ObjectEx_T_Bit.h5"; private static String DATASETNAME = "DS1"; private static final int DIM0 = 4; private static final int DIM1 = 7; private static final int RANK = 2; private static void CreateDataset() { H5File file = null; H5ScalarDS dset = null; long file_id = -1; long dataspace_id = -1; long dataset_id = -1; long[] dims = { DIM0, DIM1 }; int[][] dset_data = new int[DIM0][DIM1]; final H5Datatype typeBitField = new H5Datatype(Datatype.CLASS_BITFIELD, 8, Datatype.ORDER_BE, -1); // Initialize data. for (int indx = 0; indx < DIM0; indx++) for (int jndx = 0; jndx < DIM1; jndx++) { dset_data[indx][jndx] = 0; dset_data[indx][jndx] |= (indx * jndx - jndx) & 0x03; /* Field "A" */ dset_data[indx][jndx] |= (indx & 0x03) << 2; /* Field "B" */ dset_data[indx][jndx] |= (jndx & 0x03) << 4; /* Field "C" */ dset_data[indx][jndx] |= ((indx + jndx) & 0x03) << 6; /* Field "D" */ } // Create a new file using default properties. try { file = new H5File(FILENAME, FileFormat.CREATE); file_id = file.open(); } catch (Exception e) { e.printStackTrace(); } // Create dataspace. Setting maximum size to NULL sets the maximum // size to be the current size. try { dataspace_id = H5.H5Screate_simple(RANK, dims, null); } catch (Exception e) { e.printStackTrace(); } // Create the dataset. try { if ((file_id >= 0) && (dataspace_id >= 0)) dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_B8BE, dataspace_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); dset = new H5ScalarDS(file, DATASETNAME, "/"); Group pgroup = (Group) file.get("/"); pgroup.addToMemberList(dset); } catch (Exception e) { e.printStackTrace(); } // Write the bitfield data to the dataset. try { if (dataset_id >= 0) H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_B8, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); } catch (Exception e) { e.printStackTrace(); } // End access to the dataset and release resources used by it. try { if (dataset_id >= 0) dset.close(dataset_id); } catch (Exception e) { e.printStackTrace(); } // Terminate access to the data space. try { if (dataspace_id >= 0) H5.H5Sclose(dataspace_id); } catch (Exception e) { e.printStackTrace(); } // Close the file. try { file.close(); } catch (Exception e) { e.printStackTrace(); } } private static void ReadDataset() { H5File file = null; H5ScalarDS dset = null; long dataset_id = -1; long dataspace_id = -1; long[] dims = { DIM0, DIM1 }; int[][] dset_data; // Open an existing file. try { file = new H5File(FILENAME, FileFormat.READ); file.open(); } catch (Exception e) { e.printStackTrace(); } // Open an existing dataset. try { dset = (H5ScalarDS) file.get(DATASETNAME); dataset_id = dset.open(); } catch (Exception e) { e.printStackTrace(); } // Get dataspace and allocate memory for read buffer. try { if (dataset_id >= 0) dataspace_id = H5.H5Dget_space(dataset_id); } catch (Exception e) { e.printStackTrace(); } try { if (dataspace_id >= 0) H5.H5Sget_simple_extent_dims(dataspace_id, dims, null); } catch (Exception e) { e.printStackTrace(); } // Allocate array of pointers to two-dimensional arrays (the // elements of the dataset. dset_data = new int[(int) dims[0]][(int) (dims[1])]; // Read data. try { if (dataset_id >= 0) H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_B8, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); } catch (Exception e) { e.printStackTrace(); } // Output the data to the screen. System.out.println(DATASETNAME + ":"); for (int indx = 0; indx < dims[0]; indx++) { System.out.print(" ["); for (int jndx = 0; jndx < dims[1]; jndx++) { System.out.print("{" + (dset_data[indx][jndx] & 0x03) + ", "); System.out.print(((dset_data[indx][jndx] >> 2) & 0x03) + ", "); System.out.print(((dset_data[indx][jndx] >> 4) & 0x03) + ", "); System.out.print(((dset_data[indx][jndx] >> 6) & 0x03) + "}"); } System.out.println("]"); } System.out.println(); // End access to the dataset and release resources used by it. try { if (dataset_id >= 0) dset.close(dataset_id); } catch (Exception e) { e.printStackTrace(); } // Terminate access to the data space. try { if (dataspace_id >= 0) H5.H5Sclose(dataspace_id); } catch (Exception e) { e.printStackTrace(); } // Close the file. try { file.close(); } catch (Exception e) { e.printStackTrace(); } } public static void main(String[] args) { H5ObjectEx_T_Bit.CreateDataset(); // Now we begin the read section of this example. Here we assume // the dataset and array have the same name and rank, but can have // any size. Therefore we must allocate a new array to read in // data using malloc(). H5ObjectEx_T_Bit.ReadDataset(); } }