diff options
author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2023-11-27 21:30:15 (GMT) |
---|---|---|
committer | GitHub <noreply@github.com> | 2023-11-27 21:30:15 (GMT) |
commit | fc88fcde1091cf12c1e88c783a14ee0f1cffe31c (patch) | |
tree | 91b88b62cd30ed37ee9227e43989e95035be43c3 /HDF5Examples/JAVA/H5T/110 | |
parent | a067bf71f57723d2dfca7dfe2ffd9ea502eccd4f (diff) | |
download | hdf5-fc88fcde1091cf12c1e88c783a14ee0f1cffe31c.zip hdf5-fc88fcde1091cf12c1e88c783a14ee0f1cffe31c.tar.gz hdf5-fc88fcde1091cf12c1e88c783a14ee0f1cffe31c.tar.bz2 |
Develop merge examples (#3851)
* Merge examples repo into library
* Change grepTest to be more fault-tolerant
* Update examples macro file
* Exclude all Fortran examples from doxygen
Diffstat (limited to 'HDF5Examples/JAVA/H5T/110')
-rw-r--r-- | HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReference.java | 341 | ||||
-rw-r--r-- | HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReferenceAttribute.java | 381 |
2 files changed, 722 insertions, 0 deletions
diff --git a/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReference.java b/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReference.java new file mode 100644 index 0000000..0e147d8 --- /dev/null +++ b/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReference.java @@ -0,0 +1,341 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 object references + to a dataset. The program first creates objects in the + file and writes references to those objects to a dataset + with a dataspace of DIM0, then closes the file. Next, it + reopens the file, dereferences the references, and outputs + the names of their targets to the screen. + ************************************************************/ + +import java.util.EnumSet; +import java.util.HashMap; +import java.util.Map; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_T_ObjectReference { + private static String FILENAME = "H5Ex_T_ObjectReference.h5"; + private static String DATASETNAME = "DS1"; + private static String DATASETNAME2 = "DS2"; + private static String GROUPNAME = "G1"; + private static final int DIM0 = 2; + private static final int RANK = 1; + + // Values for the status of space allocation + enum H5G_obj { + H5G_UNKNOWN(HDF5Constants.H5O_TYPE_UNKNOWN), /* Unknown object type */ + H5G_GROUP(HDF5Constants.H5O_TYPE_GROUP), /* Object is a group */ + H5G_DATASET(HDF5Constants.H5O_TYPE_DATASET), /* Object is a dataset */ + H5G_TYPE(HDF5Constants.H5O_TYPE_NAMED_DATATYPE); /* Object is a named data type */ + private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>(); + + static + { + for (H5G_obj s : EnumSet.allOf(H5G_obj.class)) + lookup.put(s.getCode(), s); + } + + private int code; + + H5G_obj(int layout_type) { this.code = layout_type; } + + public int getCode() { return this.code; } + + public static H5G_obj get(int code) { return lookup.get(code); } + } + + private static void writeObjRef() + { + long file_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long filespace_id = HDF5Constants.H5I_INVALID_HID; + long group_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + byte[][] dset_data = new byte[DIM0][8]; + + // 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 dataset with a scalar dataspace. + try { + dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); + if ((file_id >= 0) && (dataspace_id >= 0)) { + dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + dataset_id = HDF5Constants.H5I_INVALID_HID; + H5.H5Sclose(dataspace_id); + dataspace_id = HDF5Constants.H5I_INVALID_HID; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create a group in the file. + try { + if (file_id >= 0) + group_id = H5.H5Gcreate(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + if (group_id >= 0) + H5.H5Gclose(group_id); + group_id = HDF5Constants.H5I_INVALID_HID; + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create references to the previously created objects. Passing -1 + // as space_id causes this parameter to be ignored. Other values + // besides valid dataspaces result in an error. + try { + if (file_id >= 0) { + byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1); + byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1); + for (int indx = 0; indx < 8; indx++) { + dset_data[0][indx] = rbuf0[indx]; + dset_data[1][indx] = rbuf1[indx]; + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create dataspace. Setting maximum size to NULL sets the maximum + // size to be the current size. + try { + filespace_id = H5.H5Screate_simple(RANK, dims, null); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create the dataset. + try { + if ((file_id >= 0) && (filespace_id >= 0)) + dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF_OBJ, filespace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Write the object references to it. + try { + if (dataset_id >= 0) + H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, 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) + H5.H5Dclose(dataset_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (filespace_id >= 0) + H5.H5Sclose(filespace_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 readObjRef() + { + long file_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + int object_type = -1; + long object_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + byte[][] dset_data; + + // 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(); + } + + // 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 byte[(int)dims[0]][8]; + + // Read the data using the default properties. + try { + if (dataset_id >= 0) { + H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, + HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data); + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Output the data to the screen. + for (int indx = 0; indx < dims[0]; indx++) { + System.out.println(DATASETNAME + "[" + indx + "]:"); + System.out.print(" ->"); + // Open the referenced object, get its name and type. + try { + if (dataset_id >= 0) { + object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5R_OBJECT, dset_data[indx]); + object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]); + } + String obj_name = null; + if (object_type >= 0) { + // Get the length of the name and retrieve the name. + obj_name = H5.H5Iget_name(object_id); + } + if ((object_id >= 0) && (object_type >= -1)) { + switch (H5G_obj.get(object_type)) { + case H5G_GROUP: + System.out.print("H5G_GROUP"); + try { + if (object_id >= 0) + H5.H5Gclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + case H5G_DATASET: + System.out.print("H5G_DATASET"); + try { + if (object_id >= 0) + H5.H5Dclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + case H5G_TYPE: + System.out.print("H5G_TYPE"); + try { + if (object_id >= 0) + H5.H5Tclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + default: + System.out.print("UNHANDLED"); + } + } + // Print the name. + System.out.println(": " + obj_name); + } + catch (Exception e) { + e.printStackTrace(); + } + } + + // End access to the dataset and release resources used by it. + try { + if (dataspace_id >= 0) + H5.H5Sclose(dataspace_id); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_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) + { + // Check if gzip compression is available and can be used for both + // compression and decompression. Normally we do not perform error + // checking in these examples for the sake of clarity, but in this + // case we will make an exception because this filter is an + // optional part of the hdf5 library. + H5Ex_T_ObjectReference.writeObjRef(); + H5Ex_T_ObjectReference.readObjRef(); + } +} diff --git a/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReferenceAttribute.java b/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReferenceAttribute.java new file mode 100644 index 0000000..9818dba --- /dev/null +++ b/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReferenceAttribute.java @@ -0,0 +1,381 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 object references + to an attribute. The program first creates objects in the + file and writes references to those objects to an + attribute with a dataspace of DIM0, then closes the file. + Next, it reopens the file, dereferences the references, + and outputs the names of their targets to the screen. + ************************************************************/ + +import java.util.EnumSet; +import java.util.HashMap; +import java.util.Map; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; + +public class H5Ex_T_ObjectReferenceAttribute { + private static String FILENAME = "H5Ex_T_ObjectReferenceAttribute.h5"; + private static String DATASETNAME = "DS1"; + private static String ATTRIBUTENAME = "A1"; + private static String DATASETNAME2 = "DS2"; + private static String GROUPNAME = "G1"; + private static final int DIM0 = 2; + private static final int RANK = 1; + + // Values for the status of space allocation + enum H5G_obj { + H5G_UNKNOWN(HDF5Constants.H5O_TYPE_UNKNOWN), /* Unknown object type */ + H5G_GROUP(HDF5Constants.H5O_TYPE_GROUP), /* Object is a group */ + H5G_DATASET(HDF5Constants.H5O_TYPE_DATASET), /* Object is a dataset */ + H5G_TYPE(HDF5Constants.H5O_TYPE_NAMED_DATATYPE); /* Object is a named data type */ + private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>(); + + static + { + for (H5G_obj s : EnumSet.allOf(H5G_obj.class)) + lookup.put(s.getCode(), s); + } + + private int code; + + H5G_obj(int layout_type) { this.code = layout_type; } + + public int getCode() { return this.code; } + + public static H5G_obj get(int code) { return lookup.get(code); } + } + + private static void CreateDataset() + { + long file_id = HDF5Constants.H5I_INVALID_HID; + long dataspace_id = HDF5Constants.H5I_INVALID_HID; + long group_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + byte[][] dset_data = new byte[DIM0][8]; + + // 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 dataset with a scalar dataspace. + try { + dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR); + if (dataspace_id >= 0) { + dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT); + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + dataset_id = HDF5Constants.H5I_INVALID_HID; + H5.H5Sclose(dataspace_id); + dataspace_id = HDF5Constants.H5I_INVALID_HID; + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create a group in the file. + try { + if (file_id >= 0) + group_id = H5.H5Gcreate(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + if (group_id >= 0) + H5.H5Gclose(group_id); + group_id = HDF5Constants.H5I_INVALID_HID; + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create references to the previously created objects. Passing -1 + // as space_id causes this parameter to be ignored. Other values + // besides valid dataspaces result in an error. + try { + if (file_id >= 0) { + byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1); + byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1); + for (int indx = 0; indx < 8; indx++) { + dset_data[0][indx] = rbuf0[indx]; + dset_data[1][indx] = rbuf1[indx]; + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + + // Create dataset with a scalar dataspace to serve as the parent + // for the attribute. + 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 and write the array data to it. + try { + if ((dataset_id >= 0) && (dataspace_id >= 0)) + attribute_id = + H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_REF_OBJ, dataspace_id, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception e) { + e.printStackTrace(); + } + + // Write the dataset. + try { + if (attribute_id >= 0) + H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_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(); + } + + // 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 dataspace_id = HDF5Constants.H5I_INVALID_HID; + long dataset_id = HDF5Constants.H5I_INVALID_HID; + long attribute_id = HDF5Constants.H5I_INVALID_HID; + int object_type = -1; + long object_id = HDF5Constants.H5I_INVALID_HID; + long[] dims = {DIM0}; + byte[][] dset_data; + + // 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. + 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(); + } + + // Allocate array of pointers to two-dimensional arrays (the + // elements of the dataset. + dset_data = new byte[(int)dims[0]][8]; + + // Read data. + try { + if (attribute_id >= 0) + H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data); + } + 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.print(" ->"); + // Open the referenced object, get its name and type. + try { + if (dataset_id >= 0) { + object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, + HDF5Constants.H5R_OBJECT, dset_data[indx]); + object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]); + } + String obj_name = null; + if (object_type >= 0) { + // Get the length of the name and retrieve the name. + obj_name = H5.H5Iget_name(object_id); + } + if ((object_id >= 0) && (object_type >= -1)) { + switch (H5G_obj.get(object_type)) { + case H5G_GROUP: + System.out.print("H5G_GROUP"); + try { + if (object_id >= 0) + H5.H5Gclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + case H5G_DATASET: + System.out.print("H5G_DATASET"); + try { + if (object_id >= 0) + H5.H5Dclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + case H5G_TYPE: + System.out.print("H5G_TYPE"); + try { + if (object_id >= 0) + H5.H5Tclose(object_id); + } + catch (Exception e) { + e.printStackTrace(); + } + break; + default: + System.out.print("UNHANDLED"); + } + } + // Print the name. + System.out.println(": " + obj_name); + } + 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(); + } + + // 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_ObjectReferenceAttribute.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_ObjectReferenceAttribute.ReadDataset(); + } +} |