ch.systemsx.cisd.hdf5

Interface IHDF5SimpleReader

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Subinterfaces:

IHDF5Reader, IHDF5SimpleWriter, IHDF5Writer

public interface IHDF5SimpleReader
extends java.io.Closeable

A HDF5 reader which contains only the basic methods. If you feel overwhelmed with all the methods of IHDF5Reader, then assign the reader to a IHDF5SimpleReader variable and let the code completion of your IDE help you find the method you are looking for.

Usage:

 IHDF5SimpleReader reader = HDF5FactoryProvider.get().openForReading(new File("test.h5"));
 float[] f = reader.readFloatArray("/some/path/dataset");
 reader.close();
 

Method Summary

Modifier and Type	Method and Description
void	close() Closes this object and the file referenced by this object.
boolean	exists(java.lang.String objectPath) Returns true, if objectPath exists and false otherwise.
HDF5DataSetInformation	getDataSetInformation(java.lang.String dataSetPath) Returns the information about a data set as a HDF5DataSetInformation object.
java.util.List<java.lang.String>	getGroupMembers(java.lang.String groupPath) Returns the members of groupPath.
boolean	isGroup(java.lang.String objectPath) Returns true if the objectPath exists and represents a group and false otherwise.
byte[]	readAsByteArray(java.lang.String objectPath) Reads the data set objectPath as byte array (of rank 1).
java.util.BitSet	readBitField(java.lang.String objectPath) Reads a bit field (which can be considered the equivalent to a boolean array of rank 1) from the data set objectPath and returns it as a Java BitSet.
boolean	readBoolean(java.lang.String objectPath) Reads a Boolean value from the data set objectPath.
<T> T	readCompound(java.lang.String objectPath, java.lang.Class<T> pojoClass) Reads a compound from the data set objectPath.
<T> T[]	readCompoundArray(java.lang.String objectPath, java.lang.Class<T> pojoClass) Reads a compound array (of rank 1) from the data set objectPath.
java.util.Date	readDate(java.lang.String objectPath) Reads a date value from the data set objectPath.
java.util.Date[]	readDateArray(java.lang.String objectPath) Reads a date array (of rank 1) from the data set objectPath.
double	readDouble(java.lang.String objectPath) Reads a double value from the data set objectPath.
double[]	readDoubleArray(java.lang.String objectPath) Reads a double array (of rank 1) from the data set objectPath.
double[][]	readDoubleMatrix(java.lang.String objectPath) Reads a double matrix (array of arrays) from the data set objectPath.
<T extends java.lang.Enum<T>> T	readEnum(java.lang.String objectPath, java.lang.Class<T> enumClass) Reads an Enum value from the data set objectPath.
<T extends java.lang.Enum<T>> T[]	readEnumArray(java.lang.String objectPath, java.lang.Class<T> enumClass) Reads an Enum value array from the data set objectPath.
java.lang.String[]	readEnumArrayAsString(java.lang.String objectPath) Reads an Enum array (of rank 1) from the data set objectPath.
java.lang.String	readEnumAsString(java.lang.String objectPath) Reads an Enum value from the data set objectPath.
float	readFloat(java.lang.String objectPath) Reads a float value from the data set objectPath.
float[]	readFloatArray(java.lang.String objectPath) Reads a float array (of rank 1) from the data set objectPath.
float[][]	readFloatMatrix(java.lang.String objectPath) Reads a float matrix (array of arrays) from the data set objectPath.
int	readInt(java.lang.String objectPath) Reads a int value from the data set objectPath.
int[]	readIntArray(java.lang.String objectPath) Reads a int array (of rank 1) from the data set objectPath.
int[][]	readIntMatrix(java.lang.String objectPath) Reads a int matrix (array of arrays) from the data set objectPath.
long	readLong(java.lang.String objectPath) Reads a long value from the data set objectPath.
long[]	readLongArray(java.lang.String objectPath) Reads a long array (of rank 1) from the data set objectPath.
long[][]	readLongMatrix(java.lang.String objectPath) Reads a long matrix (array of arrays) from the data set objectPath.
java.lang.String	readString(java.lang.String objectPath) Reads a String from the data set objectPath.
java.lang.String[]	readStringArray(java.lang.String objectPath) Reads a String array (of rank 1) from the data set objectPath.
HDF5TimeDuration	readTimeDuration(java.lang.String objectPath) Reads a time duration value from the data set objectPath.
HDF5TimeDurationArray	readTimeDurationArray(java.lang.String objectPath) Reads a time duration array from the data set objectPath.

Method Detail

close

void close()

Closes this object and the file referenced by this object. This object must not be used after being closed.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

exists

boolean exists(java.lang.String objectPath)

Returns true, if objectPath exists and false otherwise.

isGroup

boolean isGroup(java.lang.String objectPath)

Returns true if the objectPath exists and represents a group and false otherwise.

getDataSetInformation

HDF5DataSetInformation getDataSetInformation(java.lang.String dataSetPath)

Returns the information about a data set as a HDF5DataSetInformation object. It is a failure condition if the dataSetPath does not exist or does not identify a data set.

Parameters:

dataSetPath - The name (including path information) of the data set to return information about.

getGroupMembers

java.util.List<java.lang.String> getGroupMembers(java.lang.String groupPath)

Returns the members of groupPath. The order is not well defined.

Parameters:

groupPath - The path of the group to get the members for.

Throws:

java.lang.IllegalArgumentException - If groupPath is not a group.

readAsByteArray

byte[] readAsByteArray(java.lang.String objectPath)

Reads the data set objectPath as byte array (of rank 1).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readBoolean

boolean readBoolean(java.lang.String objectPath)
             throws HDF5JavaException

Reads a Boolean value from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a boolean type.

readBitField

java.util.BitSet readBitField(java.lang.String objectPath)
                       throws HDF5DatatypeInterfaceException

Reads a bit field (which can be considered the equivalent to a boolean array of rank 1) from the data set objectPath and returns it as a Java BitSet.

Note that the storage form of the bit array is a long[]. However, it is marked in HDF5 to be interpreted bit-wise. Thus a data set written by IHDF5LongWriter.writeArray(String, long[]) cannot be read back by this method but will throw a HDF5DatatypeInterfaceException.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The BitSet read from the data set.

Throws:

HDF5DatatypeInterfaceException - If the objectPath is not of bit field type.

readInt

int readInt(java.lang.String objectPath)

Reads a int value from the data set objectPath. This method doesn't check the data space but simply reads the first value.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The value read from the data set.

readIntArray

int[] readIntArray(java.lang.String objectPath)

Reads a int array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readIntMatrix

int[][] readIntMatrix(java.lang.String objectPath)

Reads a int matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readLong

long readLong(java.lang.String objectPath)

Reads a long value from the data set objectPath. This method doesn't check the data space but simply reads the first value.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The value read from the data set.

readLongArray

long[] readLongArray(java.lang.String objectPath)

Reads a long array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readLongMatrix

long[][] readLongMatrix(java.lang.String objectPath)

Reads a long matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readFloat

float readFloat(java.lang.String objectPath)

Reads a float value from the data set objectPath. This method doesn't check the data space but simply reads the first value.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The value read from the data set.

readFloatArray

float[] readFloatArray(java.lang.String objectPath)

Reads a float array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readFloatMatrix

float[][] readFloatMatrix(java.lang.String objectPath)

Reads a float matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readDouble

double readDouble(java.lang.String objectPath)

Reads a double value from the data set objectPath. This method doesn't check the data space but simply reads the first value.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The value read from the data set.

readDoubleArray

double[] readDoubleArray(java.lang.String objectPath)

Reads a double array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readDoubleMatrix

double[][] readDoubleMatrix(java.lang.String objectPath)

Reads a double matrix (array of arrays) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readDate

java.util.Date readDate(java.lang.String objectPath)
                 throws HDF5JavaException

Reads a date value from the data set objectPath. It needs to have been written by IHDF5SimpleWriter.writeDate(String, Date).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The time stamp as Date.

Throws:

HDF5JavaException - If the objectPath does not denote a time stamp.

readDateArray

java.util.Date[] readDateArray(java.lang.String objectPath)
                        throws HDF5JavaException

Reads a date array (of rank 1) from the data set objectPath. It needs to have been written by IHDF5SimpleWriter.writeDateArray(String, Date[]).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The time stamp as Date.

Throws:

HDF5JavaException - If the objectPath does not denote a time stamp.

readTimeDuration

HDF5TimeDuration readTimeDuration(java.lang.String objectPath)
                           throws HDF5JavaException

Reads a time duration value from the data set objectPath. It needs to have been written by IHDF5SimpleWriter.writeTimeDuration(String, HDF5TimeDuration).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The time duration in seconds.

Throws:

HDF5JavaException - If the objectPath is not tagged as a type variant that corresponds to a time duration.

readTimeDurationArray

HDF5TimeDurationArray readTimeDurationArray(java.lang.String objectPath)
                                     throws HDF5JavaException

Reads a time duration array from the data set objectPath. It needs to have been written by IHDF5SimpleWriter.writeTimeDurationArray(String, HDF5TimeDurationArray).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The time duration in seconds.

Throws:

HDF5JavaException - If the objectPath is not defined as type variant HDF5DataTypeVariant.TIMESTAMP_MILLISECONDS_SINCE_START_OF_THE_EPOCH.

readString

java.lang.String readString(java.lang.String objectPath)
                     throws HDF5JavaException

Reads a String from the data set objectPath. Considers '\0' as end of string. This needs to be a string type.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a string type.

readStringArray

java.lang.String[] readStringArray(java.lang.String objectPath)
                            throws HDF5JavaException

Reads a String array (of rank 1) from the data set objectPath. The elements of this data set need to be a string type.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

Throws:

HDF5JavaException

readCompound

<T> T readCompound(java.lang.String objectPath,
                   java.lang.Class<T> pojoClass)
            throws HDF5JavaException

Reads a compound from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

pojoClass - The class to return the result in. Use HDF5CompoundDataMap to get it in a map, HDF5CompoundDataList to get it in a list, and Object[] to get it in an array, or use a pojo (Data Transfer Object), in which case the compound members will be mapped to Java fields.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a compound data set.

See Also:

CompoundType, CompoundElement

readCompoundArray

<T> T[] readCompoundArray(java.lang.String objectPath,
                          java.lang.Class<T> pojoClass)
                   throws HDF5JavaException

Reads a compound array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

pojoClass - The class to return the result in. Use HDF5CompoundDataMap to get it in a map, HDF5CompoundDataList to get it in a list, and Object[] to get it in an array, or use a pojo (Data Transfer Object), in which case the compound members will be mapped to Java fields.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not a compound data set.

See Also:

CompoundType, CompoundElement

readEnum

<T extends java.lang.Enum<T>> T readEnum(java.lang.String objectPath,
                                         java.lang.Class<T> enumClass)
                                  throws HDF5JavaException

Reads an Enum value from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

enumClass - the Enum class to represent the values of.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not of enumType or if enumClass is incompatible with the HDF5 enumeration type of objectPath.

readEnumAsString

java.lang.String readEnumAsString(java.lang.String objectPath)
                           throws HDF5JavaException

Reads an Enum value from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set as a String.

Throws:

HDF5JavaException - If the objectPath is not an enum type.

readEnumArray

<T extends java.lang.Enum<T>> T[] readEnumArray(java.lang.String objectPath,
                                                java.lang.Class<T> enumClass)
                                         throws HDF5JavaException

Reads an Enum value array from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

enumClass - the Enum class to represent the values of.

Returns:

The data read from the data set.

Throws:

HDF5JavaException - If the objectPath is not of enumType.

readEnumArrayAsString

java.lang.String[] readEnumArrayAsString(java.lang.String objectPath)
                                  throws HDF5JavaException

Reads an Enum array (of rank 1) from the data set objectPath.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set as an array of Strings.

Throws:

HDF5JavaException - If the objectPath is not an enum type.