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Diffstat (limited to 'HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java')
| -rw-r--r-- | HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java | 502 |
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diff --git a/HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java b/HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java new file mode 100644 index 0000000..a33faee --- /dev/null +++ b/HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java @@ -0,0 +1,502 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://www.hdfgroup.org/licenses. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/************************************************************ + This example shows how to read and write compound + datatypes to an attribute. The program first writes + compound structures to an attribute with a dataspace of + DIM0, then closes the file. Next, it reopens the file, + reads back the data, and outputs it to the screen. + ************************************************************/ + +import java.nio.ByteBuffer; +import java.nio.ByteOrder; +import java.nio.charset.Charset; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_T_CompoundAttribute { + private static String FILENAME = "H5Ex_T_CompoundAttribute.h5"; + private static String DATASETNAME = "DS1"; + private static String ATTRIBUTENAME = "A1"; + private static final int DIM0 = 4; + private static final int RANK = 1; + protected static final int INTEGERSIZE = 4; + protected static final int DOUBLESIZE = 8; + protected final static int MAXSTRINGSIZE = 80; + + static class Sensor_Datatype { + static int numberMembers = 4; + static int[] memberDims = {1, 1, 1, 1}; + + static String[] memberNames = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"}; + static long[] memberMemTypes = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1, + HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE}; + static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1, + HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE}; + static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE}; + + // Data size is the storage size for the members not the object. + static long getTotalDataSize() + { + long data_size = 0; + for (int indx = 0; indx < numberMembers; indx++) + data_size += memberStorage[indx] * memberDims[indx]; + return DIM0 * data_size; + } + + static long getDataSize() + { + long data_size = 0; + for (int indx = 0; indx < numberMembers; indx++) + data_size += memberStorage[indx] * memberDims[indx]; + return data_size; + } + + static int getOffset(int memberItem) + { + int data_offset = 0; + for (int indx = 0; indx < memberItem; indx++) + data_offset += memberStorage[indx]; + return data_offset; + } + } + + static class Sensor { + public int serial_no; + public String location; + public double temperature; + public double pressure; + + Sensor(int serial_no, String location, double temperature, double pressure) + { + this.serial_no = serial_no; + this.location = location; + this.temperature = temperature; + this.pressure = pressure; + } + + Sensor(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + + Sensor(ByteBuffer databuf, int dbposition) { readBuffer(databuf, dbposition); } + + void writeBuffer(ByteBuffer databuf, int dbposition) + { + databuf.putInt(dbposition + Sensor_Datatype.getOffset(0), serial_no); + byte[] temp_str = location.getBytes(Charset.forName("UTF-8")); + int arraylen = (temp_str.length > MAXSTRINGSIZE) ? MAXSTRINGSIZE : temp_str.length; + for (int ndx = 0; ndx < arraylen; ndx++) + databuf.put(dbposition + Sensor_Datatype.getOffset(1) + ndx, temp_str[ndx]); + for (int ndx = arraylen; ndx < MAXSTRINGSIZE; ndx++) + databuf.put(dbposition + Sensor_Datatype.getOffset(1) + arraylen, (byte)0); + databuf.putDouble(dbposition + Sensor_Datatype.getOffset(2), temperature); + databuf.putDouble(dbposition + Sensor_Datatype.getOffset(3), pressure); + } + + void readBuffer(ByteBuffer databuf, int dbposition) + { + this.serial_no = databuf.getInt(dbposition + Sensor_Datatype.getOffset(0)); + ByteBuffer stringbuf = databuf.duplicate(); + stringbuf.position(dbposition + Sensor_Datatype.getOffset(1)); + stringbuf.limit(dbposition + Sensor_Datatype.getOffset(1) + MAXSTRINGSIZE); + byte[] bytearr = new byte[stringbuf.remaining()]; + stringbuf.get(bytearr); + this.location = new String(bytearr, Charset.forName("UTF-8")).trim(); + this.temperature = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(2)); + this.pressure = databuf.getDouble(dbposition + Sensor_Datatype.getOffset(3)); + } + + List get() + { + List data = new ArrayList<>(); + data.add(this.serial_no); + data.add(this.location); + data.add(this.temperature); + data.add(this.pressure); + return data; + } + + void put(List data) + { + this.serial_no = (int)data.get(0); + this.location = (String)data.get(1); + this.temperature = (double)data.get(2); + this.pressure = (double)data.get(3); + } + + @Override + public String toString() + { + return String.format("Serial number : " + serial_no + "%n" + + "Location : " + location + "%n" + + "Temperature (F) : " + temperature + "%n" + + "Pressure (inHg) : " + pressure + "%n"); + } + } + + private static void CreateDataset() + { + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long filetype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + ArrayList[] object_data = new ArrayList[DIM0]; + byte[] dset_data = null; + + // Initialize data. + object_data[0] = (ArrayList) new Sensor(1153, new String("Exterior (static)"), 53.23, 24.57).get(); + object_data[1] = (ArrayList) new Sensor(1184, new String("Intake"), 55.12, 22.95).get(); + object_data[2] = (ArrayList) new Sensor(1027, new String("Intake manifold"), 103.55, 31.23).get(); + object_data[3] = (ArrayList) new Sensor(1313, new String("Exhaust manifold"), 1252.89, 84.11).get(); + + // Create a new file using default properties. + try { + file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create string datatype. + try { + strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); + if (strtype_id >= 0) + H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the compound datatype for memory. + try { + memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); + if (memtype_id >= 0) { + for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { + long type_id = Sensor_Datatype.memberMemTypes[indx]; + if (type_id == HDF5Constants.H5T_C_S1) + type_id = strtype_id; + H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], + Sensor_Datatype.getOffset(indx), type_id); + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the compound datatype for the file. Because the standard + // types we are using for the file may have different sizes than + // the corresponding native types, we must manually calculate the + // offset of each member. + try { + filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); + if (filetype_id >= 0) { + for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { + long type_id = Sensor_Datatype.memberFileTypes[indx]; + if (type_id == HDF5Constants.H5T_C_S1) + type_id = strtype_id; + H5.H5Tinsert(filetype_id, Sensor_Datatype.memberNames[indx], + Sensor_Datatype.getOffset(indx), type_id); + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create dataset with a scalar dataspace. + try { + dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); + if (dataspace_id >= 0) { + dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + H5.H5Sclose(dataspace_id); + dataspace_id = HDF5Constants.H5I_INVALID_HID; + } + } + 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 attribute. + try { + if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0)) + attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Write the compound data. + try { + if ((attribute_id >= 0) && (memtype_id >= 0)) + H5.H5AwriteVL(attribute_id, memtype_id, (Object[])object_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + // End access to the dataset and release resources used by it. + try { + if (attribute_id >= 0) + H5.H5Aclose(attribute_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (dataset_id >= 0) + H5.H5Dclose(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(); + } + + // Terminate access to the file type. + try { + if (filetype_id >= 0) + H5.H5Tclose(filetype_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Terminate access to the mem type. + try { + if (memtype_id >= 0) + H5.H5Tclose(memtype_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (strtype_id >= 0) + H5.H5Tclose(strtype_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Close the file. + try { + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + private static void ReadDataset() + { + long file_id = HDF5Constants.H5I_INVALID_HID; + long strtype_id = HDF5Constants.H5I_INVALID_HID; + long memtype_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + Sensor[] object_data2 = new Sensor[(int)dims[0]]; + + // Open an existing file. + try { + file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Open an existing dataset. + try { + if (file_id >= 0) + dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (dataset_id >= 0) + attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Get dataspace and allocate memory for read buffer. This is a + // three dimensional dataset when the array datatype is included so + // the dynamic allocation must be done in steps. + try { + if (attribute_id >= 0) + dataspace_id = H5.H5Aget_space(attribute_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(); + } + + // Create string datatype. + try { + strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1); + if (strtype_id >= 0) + H5.H5Tset_size(strtype_id, MAXSTRINGSIZE); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the compound datatype for memory. + try { + memtype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize()); + if (memtype_id >= 0) { + for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) { + long type_id = Sensor_Datatype.memberMemTypes[indx]; + if (type_id == HDF5Constants.H5T_C_S1) + type_id = strtype_id; + H5.H5Tinsert(memtype_id, Sensor_Datatype.memberNames[indx], + Sensor_Datatype.getOffset(indx), type_id); + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + ArrayList[] object_data = new ArrayList[(int)dims[0]]; + + // Read data. + try { + if ((attribute_id >= 0) && (memtype_id >= 0)) + H5.H5AreadVL(attribute_id, memtype_id, (Object[])object_data); + + for (int indx = 0; indx < (int)dims[0]; indx++) { + object_data2[indx] = new Sensor(object_data[indx]); + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + for (int indx = 0; indx < dims[0]; indx++) { + System.out.println(ATTRIBUTENAME + " [" + indx + "]:"); + System.out.println(object_data2[indx].toString()); + } + System.out.println(); + + try { + if (attribute_id >= 0) + H5.H5Aclose(attribute_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (dataset_id >= 0) + H5.H5Dclose(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(); + } + + // Terminate access to the mem type. + try { + if (memtype_id >= 0) + H5.H5Tclose(memtype_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (strtype_id >= 0) + H5.H5Tclose(strtype_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Close the file. + try { + if (file_id >= 0) + H5.H5Fclose(file_id); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + public static void main(String[] args) + { + H5Ex_T_CompoundAttribute.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(). + H5Ex_T_CompoundAttribute.ReadDataset(); + } +} |