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package test.object;
import java.util.Vector;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Attribute;
import ncsa.hdf.object.Dataset;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.Group;
import ncsa.hdf.object.h5.H5Datatype;
import ncsa.hdf.object.h5.H5File;
/**
* Creates an HDF5 file for unit tests.
*
* @author xcao
*
*/
public class H5TestFile {
private final static org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5TestFile.class);
public final static String NAME_FILE_H5 = "TestHDF5.h5";
public final static String NAME_GROUP = "/g0";
public final static String NAME_GROUP_ATTR = "/g0_attr";
public final static String NAME_GROUP_SUB = NAME_GROUP + "/g00";
public final static String NAME_DATASET_INT = "/dataset_int";
public final static String NAME_DATASET_FLOAT = "/dataset_float";
public final static String NAME_DATASET_CHAR = "/dataset_byte";
public final static String NAME_DATASET_STR = "/dataset_str";
public final static String NAME_DATASET_ENUM = "/dataset_enum";
public final static String NAME_DATASET_IMAGE = "/dataset_image";
public final static String NAME_DATASET_IMAGE_PALETTE = "/wave_palete";
public final static String NAME_DATASET_OBJ_REF = "/dataset_obj_ref";
public final static String NAME_DATASET_COMPOUND = "/dataset_comp";
public final static String NAME_DATASET_INT_SUB = NAME_GROUP + "/dataset_int";
public final static String NAME_DATASET_FLOAT_SUB_SUB = NAME_GROUP_SUB + "/dataset_float";
public final static String NAME_DATASET_COMPOUND_SUB = NAME_GROUP + "/dataset_comp";
public final static String NAME_DATATYPE_INT = NAME_GROUP + "/datatype_int";
public final static String NAME_DATATYPE_UINT = NAME_GROUP + "/datatype_uint";
public final static String NAME_DATATYPE_FLOAT = NAME_GROUP + "/datatype_float";
public final static String NAME_DATATYPE_STR = NAME_GROUP + "/datatype_str";
public final static String NAME_HARD_LINK_TO_IMAGE = "a_link_to_the_image";
public final static String OBJ_NAMES[] = { NAME_GROUP, NAME_GROUP_ATTR, NAME_GROUP_SUB, NAME_DATASET_INT,
NAME_DATASET_FLOAT, NAME_DATASET_CHAR, NAME_DATASET_STR, NAME_DATASET_ENUM, NAME_DATASET_IMAGE,
NAME_DATASET_COMPOUND, NAME_DATASET_INT_SUB, NAME_DATASET_FLOAT_SUB_SUB, NAME_DATASET_COMPOUND_SUB,
NAME_DATATYPE_INT, NAME_DATATYPE_UINT, NAME_DATATYPE_FLOAT, NAME_DATATYPE_STR, NAME_DATASET_OBJ_REF };
public final static int OBJ_TYPES[] = { HDF5Constants.H5O_TYPE_GROUP, HDF5Constants.H5O_TYPE_GROUP,
HDF5Constants.H5O_TYPE_GROUP, HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET,
HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET,
HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET,
HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_DATASET, HDF5Constants.H5O_TYPE_NAMED_DATATYPE,
HDF5Constants.H5O_TYPE_NAMED_DATATYPE, HDF5Constants.H5O_TYPE_NAMED_DATATYPE,
HDF5Constants.H5O_TYPE_NAMED_DATATYPE, HDF5Constants.H5O_TYPE_DATASET };
// data space information
public final static int DATATYPE_SIZE = 4;
public final static int RANK = 2;
public final static long DIM1 = 50;
public final static long DIM2 = 10;
public static final long DIM3 = 20;
public final static long[] DIMs = { DIM1, DIM2 };
public final static long[] CHUNKs = { DIM1 / 2, DIM2 / 2 };
public final static int STR_LEN = 20;
public final static int DIM_SIZE = (int) (DIM1 * DIM2);;
/* testing data */
public final static int[] DATA_INT = new int[DIM_SIZE];
public final static long[] DATA_LONG = new long[DIM_SIZE];
public final static float[] DATA_FLOAT = new float[DIM_SIZE];
public final static byte[] DATA_BYTE = new byte[DIM_SIZE];
public final static String[] DATA_STR = new String[DIM_SIZE];
public final static int[] DATA_ENUM = new int[DIM_SIZE];
public final static Vector DATA_COMP = new Vector(3);
public final static byte[] DATA_PALETTE = createWavePalette();
// compound names and datatypes
public final static String[] COMPOUND_MEMBER_NAMES = { "int32", "float32", "string", "uint32" };
public final static H5Datatype[] COMPOUND_MEMBER_DATATYPES = {
new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1),
new H5Datatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1),
new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1),
new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, Datatype.SIGN_NONE) };
// attributes
public final static Attribute ATTRIBUTE_STR = new Attribute("strAttr", new H5Datatype(Datatype.CLASS_STRING,
STR_LEN, -1, -1), new long[] { 1 }, new String[] { "String attribute." });
public final static Attribute ATTRIBUTE_INT_ARRAY = new Attribute("arrayInt", new H5Datatype(
Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1), new long[] { 10 }, new int[] { 1, 2, 3, 4, 5, 6, 7, 8, 9,
10 });
/**
* Creates an HDF5 test file.
* <p>
* The test file contains the following objects:
*
* <pre>
* /dataset_byte Dataset {50, 10}
* /dataset_comp Dataset {50, 10}
* /dataset_enum Dataset {50, 10}
* /dataset_float Dataset {50, 10}
* /dataset_int Dataset {50, 10}
* /dataset_image Dataset {50, 10}
* /dataset_str Dataset {50, 10}
* /g0 Group
* /g0/dataset_int Dataset {50, 10}
* /g0/g00 Group
* /g0/g00/dataset_float Dataset {50, 10}
* /g0_attr Group
* </pre>
*
* @throws Exception
*/
public static final H5File createTestFile(String fileName) throws Exception {
log.debug("createTestFile {}", fileName);
H5File file = null;
Group g0, g1, g00;
final Dataset[] dsets = new Dataset[11];
if ((fileName == null) || (fileName.length() < 1)) {
fileName = NAME_FILE_H5;
}
final H5Datatype typeInt = new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1);
final H5Datatype typeByte = new H5Datatype(Datatype.CLASS_INTEGER, 1, -1, Datatype.SIGN_NONE);
final H5Datatype typeFloat = new H5Datatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1);
final H5Datatype typeStr = new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1);
final H5Datatype typeChar = new H5Datatype(Datatype.CLASS_CHAR, 1, -1, -1);
final H5Datatype typeEnum = new H5Datatype(Datatype.CLASS_ENUM, DATATYPE_SIZE, -1, -1);
final H5Datatype typeRef = new H5Datatype(Datatype.CLASS_REFERENCE, -1, -1, -1);
for (int i = 0; i < DIM_SIZE; i++) {
DATA_INT[i] = i;
DATA_LONG[i] = i;
DATA_FLOAT[i] = i + i / 100.0f;
DATA_BYTE[i] = (byte) Math.IEEEremainder(i, 127);
DATA_STR[i] = "str" + i;
DATA_ENUM[i] = (int) Math.IEEEremainder(i, 2);
}
DATA_COMP.add(0, DATA_INT);
DATA_COMP.add(1, DATA_FLOAT);
DATA_COMP.add(2, DATA_STR);
DATA_COMP.add(3, DATA_LONG);
file = new H5File(fileName, FileFormat.CREATE);
file.open();
g0 = file.createGroup(NAME_GROUP, null);
g1 = file.createGroup(NAME_GROUP_ATTR, null);
g00 = file.createGroup(NAME_GROUP_SUB, null);
g1.writeMetadata(ATTRIBUTE_STR);
g1.writeMetadata(ATTRIBUTE_INT_ARRAY);
dsets[0] = file.createScalarDS(NAME_DATASET_INT, null, typeInt, DIMs, null, CHUNKs, 9, DATA_INT);
dsets[1] = file.createScalarDS(NAME_DATASET_FLOAT, null, typeFloat, DIMs, null, CHUNKs, 9, DATA_FLOAT);
dsets[2] = file.createScalarDS(NAME_DATASET_CHAR, null, typeChar, DIMs, null, CHUNKs, 9, DATA_BYTE);
dsets[3] = file.createScalarDS(NAME_DATASET_STR, null, typeStr, DIMs, null, CHUNKs, 9, DATA_STR);
dsets[4] = file.createScalarDS(NAME_DATASET_ENUM, null, typeEnum, DIMs, null, CHUNKs, 9, DATA_ENUM);
dsets[5] = file.createScalarDS(NAME_DATASET_INT_SUB, g0, typeInt, DIMs, null, CHUNKs, 9, DATA_INT);
dsets[6] = file.createScalarDS(NAME_DATASET_FLOAT_SUB_SUB, g00, typeFloat, DIMs, null, CHUNKs, 9, DATA_FLOAT);
dsets[7] = file.createImage(NAME_DATASET_IMAGE, null, typeByte, DIMs, null, CHUNKs, 9, 1, -1, DATA_BYTE);
dsets[8] = file.createCompoundDS(NAME_DATASET_COMPOUND, null, DIMs, null, CHUNKs, 9, COMPOUND_MEMBER_NAMES,
COMPOUND_MEMBER_DATATYPES, null, DATA_COMP);
dsets[9] = file.createCompoundDS(NAME_DATASET_COMPOUND_SUB, null, DIMs, null, CHUNKs, 9, COMPOUND_MEMBER_NAMES,
COMPOUND_MEMBER_DATATYPES, null, DATA_COMP);
dsets[10] = file.createScalarDS(NAME_DATASET_OBJ_REF, null, typeRef, DIMs, null, CHUNKs, 9, null);
// attach attributes to all datasets
for (int i = 0; i < dsets.length; i++) {
dsets[i].writeMetadata(ATTRIBUTE_STR);
dsets[i].writeMetadata(ATTRIBUTE_INT_ARRAY);
}
// create a wave palette and attach it to the image
final Dataset pal = file.createScalarDS(NAME_DATASET_IMAGE_PALETTE, null, typeByte, new long[] { 256, 3 },
null, null, -1, DATA_PALETTE);
long[] oid = pal.getOID();
final Vector attrs = (Vector) dsets[7].getMetadata();
final int n = attrs.size();
for (int i = 0; i < n; i++) {
final Attribute attr = (Attribute) attrs.get(i);
if ("PALETTE".equals(attr.getName())) {
attr.setValue(oid);
dsets[7].writeMetadata(attr);
}
}
Datatype dtype = file.createDatatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1, NAME_DATATYPE_INT);
dtype.writeMetadata(ATTRIBUTE_STR);
dtype.writeMetadata(ATTRIBUTE_INT_ARRAY);
dtype = file.createDatatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, Datatype.SIGN_NONE, NAME_DATATYPE_UINT);
dtype.writeMetadata(ATTRIBUTE_STR);
dtype.writeMetadata(ATTRIBUTE_INT_ARRAY);
dtype = file.createDatatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1, NAME_DATATYPE_FLOAT);
dtype.writeMetadata(ATTRIBUTE_STR);
dtype.writeMetadata(ATTRIBUTE_INT_ARRAY);
dtype = file.createDatatype(Datatype.CLASS_STRING, STR_LEN, -1, -1, NAME_DATATYPE_STR);
dtype.writeMetadata(ATTRIBUTE_STR);
dtype.writeMetadata(ATTRIBUTE_INT_ARRAY);
file.createLink(g0, NAME_HARD_LINK_TO_IMAGE, dsets[7]);
try {
file.close();
}
catch (final Exception ex) {
}
// write object refs to the ref dataset
file.open();
final long[] refs = new long[DIM_SIZE];
// for (int i = 0; i < OBJ_NAMES.length; i++) { --//This gives CORE DUMP when OBJ_NAMES = NAME_DATASET_OBJ_REF,
// as it enters an infinite loop.
for (int i = 0; i < OBJ_NAMES.length - 1; i++) {
oid = file.get(OBJ_NAMES[i]).getOID();
refs[i] = oid[0];
}
dsets[10].write(refs);
try {
file.close();
}
catch (final Exception ex) {
}
return file;
}
/**
* Creates the wave palette of the indexed 256-color table.
* <p>
* The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and
* blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue
* components respectively.
*
* @return the wave palette in the form of byte[3][256]
*/
private static final byte[] createWavePalette() {
final byte[] p = new byte[768]; // 256*3
for (int i = 1; i < 255; i++) {
p[3 * i] = (byte) ((Math.sin(((double) i / 40 - 3.2)) + 1) * 128);
p[3 * i + 1] = (byte) ((1 - Math.sin((i / 2.55 - 3.1))) * 70 + 30);
p[3 * i + 2] = (byte) ((1 - Math.sin(((double) i / 40 - 3.1))) * 128);
}
p[0] = p[1] = p[2] = 0;
p[765] = p[766] = p[767] = (byte) 255;
return p;
}
}
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