org.ujmp.core.doublematrix.impl

Class DenseFileMatrix

java.lang.Object

java.lang.Number

org.ujmp.core.AbstractMatrix

org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix<T>

org.ujmp.core.numbermatrix.stub.AbstractNumberMatrix<java.lang.Double>

org.ujmp.core.doublematrix.stub.AbstractDoubleMatrix

org.ujmp.core.doublematrix.stub.AbstractDoubleMatrixMultiD

org.ujmp.core.doublematrix.stub.AbstractDenseDoubleMatrixMultiD

org.ujmp.core.doublematrix.impl.DenseFileMatrix

All Implemented Interfaces:

java.io.Closeable, java.io.Serializable, java.lang.AutoCloseable, java.lang.Cloneable, java.lang.Comparable<Matrix>, HasMetaData, BaseMatrix, BooleanCalculations, CanPerformCalculations, DenseMatrix, DenseMatrix2D, DenseMatrixMultiD, BaseDoubleMatrix, BasicDoubleCalculations, DoubleCalculations, BasicEntrywiseDoubleCalculations, CreatorDoubleCalculations, EntrywiseDoubleCalculations, HyperbolicDoubleCalculations, MiscEntrywiseDoubleCalculations, RoundingDoubleCalculations, TrigonometricDoubleCalculations, DecompositionDoubleCalculations, DiscretizeCalculations, GeneralDoubleCalculations, MiscGeneralDoubleCalculations, MissingValueDoubleCalculations, StatisticalDoubleCalculations, DenseDoubleMatrix, DenseDoubleMatrix2D, DenseDoubleMatrixMultiD, DoubleMatrix, DoubleMatrix2D, DoubleMatrixMultiD, SparseDoubleMatrix, SparseDoubleMatrix2D, SparseDoubleMatrixMultiD, BaseGenericMatrix<java.lang.Double>, DenseGenericMatrix<java.lang.Double>, DenseGenericMatrix2D<java.lang.Double>, DenseGenericMatrixMultiD<java.lang.Double>, GenericMatrix<java.lang.Double>, GenericMatrix2D<java.lang.Double>, GenericMatrixMultiD<java.lang.Double>, SparseGenericMatrix<java.lang.Double>, SparseGenericMatrix2D<java.lang.Double>, SparseGenericMatrixMultiD<java.lang.Double>, BaseMatrixProperties, Clearable, Conversions, CoordinateFunctions, CoreObject, DistanceMeasures, Erasable, ExtendedMatrixProperties, GettersAndSetters, HasDescription, HasGUIObject, HasId, HasLabel, IntCalculations, Matrix, Matrix2D, MatrixMultiD, BaseNumberMatrix<java.lang.Double>, DenseNumberMatrix<java.lang.Double>, DenseNumberMatrix2D<java.lang.Double>, DenseNumberMatrixMultiD<java.lang.Double>, NumberMatrix<java.lang.Double>, NumberMatrix2D<java.lang.Double>, NumberMatrixMultiD<java.lang.Double>, SparseNumberMatrix<java.lang.Double>, SparseNumberMatrix2D<java.lang.Double>, SparseNumberMatrixMultiD<java.lang.Double>, ObjectCalculations, SparseMatrix, SparseMatrix2D, SparseMatrixMultiD, StringCalculations

Direct Known Subclasses:

WaveMatrix

public class DenseFileMatrix
extends AbstractDenseDoubleMatrixMultiD
implements Erasable, java.io.Closeable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	BOOLEAN
static int	BYTE
static int	CHAR
static int	DOUBLE
static int	FLOAT
static int	INT
static int	INTLITTLEENDIAN
static int	LONG
static int	LONGLITTLEENDIAN
static int	SHORT
static int	SHORTLITTLEENDIAN
static int	UNSIGNEDBYTE
static int	UNSIGNEDSHORT

Fields inherited from interface org.ujmp.core.doublematrix.DenseDoubleMatrix

Factory

Fields inherited from interface org.ujmp.core.Matrix

chol, divideMatrix, divideScalar, eig, inv, lu, minusMatrix, minusScalar, mtimes, plusMatrix, plusScalar, qr, solve, svd, timesMatrix, timesScalar, transpose

Fields inherited from interface org.ujmp.core.BaseMatrix

ALL, COLUMN, LINK, NEW, NONE, ORIG, ROW, X, Y, Z

Fields inherited from interface org.ujmp.core.annotation.HasMetaData

DIMENSIONMETADATA

Fields inherited from interface org.ujmp.core.interfaces.HasLabel

LABEL

Fields inherited from interface org.ujmp.core.interfaces.HasDescription

DESCRIPTION

Fields inherited from interface org.ujmp.core.interfaces.HasId

ID

Fields inherited from interface org.ujmp.core.doublematrix.DoubleMatrix

Factory

Constructor Summary

Constructors

Constructor and Description
DenseFileMatrix(java.io.File file)
DenseFileMatrix(java.io.File file, int dataType, long... size)
DenseFileMatrix(java.io.File file, long... size)
DenseFileMatrix(java.io.File file, long offset, int dataType, boolean readOnly, long... size)
DenseFileMatrix(int bufferSize, java.io.File file, long offset, int dataType, boolean readOnly, long... size)
DenseFileMatrix(long... size)
DenseFileMatrix(Matrix m)

Method Summary

Modifier and Type	Method and Description
void	close()
void	erase()
int	getBitsPerValue()
int	getBufferSize()
long	getBytesPerValue()
int	getDataType()
double	getDouble(long... c) Returns a double representation of an entry in the matrix.
java.io.File	getFile()
long	getFileLength()
static int	getIntLittleEndian(byte[] bytes)
BufferedRandomAccessFile	getRandomAccessFile()
static int	getShortLittleEndian(byte[] bytes)
boolean	isReadOnly()
void	setBufferSize(int bufferSize)
void	setDouble(double value, long... c) Sets an entry in the matrix to a double value.
void	setSize(long... size) Sets the size of the matrix.

Methods inherited from class org.ujmp.core.doublematrix.stub.AbstractDenseDoubleMatrixMultiD

availableCoordinates, clear, containsCoordinates, isSparse

Methods inherited from class org.ujmp.core.doublematrix.stub.AbstractDoubleMatrixMultiD

getDouble, getDouble, setDouble, setDouble

Methods inherited from class org.ujmp.core.doublematrix.stub.AbstractDoubleMatrix

getAsDouble, getNumber, getObject, getValueType, setAsDouble, setNumber, setObject

Methods inherited from class org.ujmp.core.genericmatrix.stub.AbstractGenericMatrix

getAsObject, getObject, getObject, setAsObject, setObject, setObject

Methods inherited from class org.ujmp.core.AbstractMatrix

abs, addMissing, allCoordinates, allValues, and, and, append, appendHorizontally, appendVertically, atimes, bigDecimalValue, bigIntegerValue, booleanValue, bootstrap, bootstrap, ceil, center, charValue, chebyshevDistanceTo, chol, clone, compareTo, containsBigDecimal, containsBigInteger, containsBoolean, containsByte, containsChar, containsDate, containsDouble, containsFloat, containsInt, containsLong, containsMissingValues, containsNull, containsObject, containsShort, containsString, convert, convertEncoding, corrcoef, cos, cosh, cosineSimilarity, cosineSimilarityTo, countMissing, cov, cumprod, cumsum, dateValue, delete, delete, delete, deleteColumns, deleteColumns, deleteColumnsWithMissingValues, deleteRows, deleteRows, deleteRowsWithMissingValues, det, diag, diff, discretize, discretize, discretizeToBoolean, discretizeToColumns, divide, divide, divide, divide, doubleValue, eig, eigSymm, eq, eq, equals, equalsAnnotation, equalsContent, euklideanDistance, euklideanDistanceTo, exp, exportTo, extractAnnotation, eye, fadeIn, fadeOut, fill, fireValueChanged, fireValueChanged, fireValueChanged, flipdim, floatValue, floor, ge, ge, getAbsoluteValueMean, getAbsoluteValueSum, getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsByteArray, getAsChar, getAsDate, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsShort, getAsString, getColumnCount, getColumnForLabel, getColumnLabel, getColumnList, getCoordinatesOfMaximum, getCoordinatesOfMinimum, getCoreObjectId, getDescription, getDimensionCount, getDimensionLabel, getDimensionMetaData, getEuklideanValue, getFactory, getGUIObject, getId, getLabel, getLabelObject, getMaxValue, getMeanValue, getMetaData, getMetaData, getMetaDataDimensionMatrix, getMetaDataDouble, getMetaDataMatrix, getMetaDataString, getMinValue, getPositionForLabel, getPreferredObject, getRMS, getRowCount, getRowForLabel, getRowLabel, getRowList, getSize, getSize, getStdValue, getValueCount, getValueSum, getZCount, ginv, grayScale, gt, gt, importFrom, impute, includeAnnotation, indexOfMax, indexOfMin, intValue, inv, invSPD, invSymm, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isResizable, isRowVector, isScalar, isSingular, isSPD, isSquare, isSymmetric, isTransient, le, le, log, log10, log2, logistic, longValue, lowerCase, lt, lt, lu, manhattenDistance, manhattenDistanceTo, max, mean, min, minkowskiDistance, minkowskiDistanceTo, minus, minus, minus, minus, mtimes, mtimes, mutualInf, nans, ne, ne, nonZeroCoordinates, norm1, norm2, normalize, normF, normInf, not, ones, or, or, pairedTTest, pdet, pinv, pinv, plus, plus, plus, plus, power, power, princomp, prod, qr, rand, randn, rank, removePunctuation, removeWords, replace, replaceMissingBy, replaceRegex, replaceRegex, reshape, round, save, save, select, select, select, selectColumns, selectColumns, selectedCoordinates, selectedCoordinates, selectRows, selectRows, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsByteArray, setAsChar, setAsDate, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsShort, setAsString, setColumnLabel, setContent, setDescription, setDimensionLabel, setDimensionMetaData, setId, setLabel, setMetaData, setMetaData, setMetaDataDimensionMatrix, setRowLabel, share, share, showGUI, shuffle, sign, sin, sinh, solve, solveSPD, solveSymm, sortrows, sqrt, squeeze, standardize, std, stem, stringValue, subMatrix, sum, svd, svd, swap, tan, tanh, tanh, tfIdf, times, times, times, times, toBigDecimalArray, toBigDecimalMatrix, toBigIntegerArray, toBigIntegerMatrix, toBooleanArray, toBooleanMatrix, toByteArray, toByteMatrix, toCharArray, toCharMatrix, toColumnVector, toDateArray, toDoubleArray, toDoubleMatrix, toFloatArray, toFloatMatrix, toHtml, toIntArray, toIntMatrix, toListMatrix, toLongArray, toLongMatrix, toMapMatrix, toObjectArray, toObjectMatrix, toRowVector, toSetMatrix, toShortArray, toShortMatrix, toString, toStringArray, toStringMatrix, trace, translate, transpose, transpose, transpose, tril, triu, unique, uniqueValueCount, upperCase, var, xor, xor, zeros

Methods inherited from class java.lang.Number

byteValue, shortValue

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.ujmp.core.numbermatrix.NumberMatrixMultiD

getNumber, setNumber

Methods inherited from interface org.ujmp.core.genericmatrix.GenericMatrixMultiD

getObject, setObject

Methods inherited from interface org.ujmp.core.Matrix

clone, exportTo, fireValueChanged, fireValueChanged, fireValueChanged, importFrom, save, save, share, share, toHtml

Methods inherited from interface org.ujmp.core.BaseMatrix

getFactory

Methods inherited from interface org.ujmp.core.interfaces.BaseMatrixProperties

allValues, equals, equalsAnnotation, equalsContent, getColumnCount, getColumnList, getDimensionCount, getRowCount, getRowList, getSize, getSize, getValueCount, getValueType, getZCount, isColumnVector, isDiagonal, isEmpty, isMultidimensionalMatrix, isResizable, isRowVector, isScalar, isSingular, isSquare, isSymmetric, isTransient, toString

Methods inherited from interface org.ujmp.core.interfaces.CoreObject

getCoreObjectId

Methods inherited from interface org.ujmp.core.interfaces.HasGUIObject

getGUIObject, showGUI

Methods inherited from interface org.ujmp.core.interfaces.CoordinateFunctions

allCoordinates, getCoordinatesOfMaximum, getCoordinatesOfMinimum, nonZeroCoordinates, selectedCoordinates, selectedCoordinates

Methods inherited from interface org.ujmp.core.interfaces.GettersAndSetters

getAsBigDecimal, getAsBigInteger, getAsBoolean, getAsByte, getAsByteArray, getAsChar, getAsDate, getAsDouble, getAsFloat, getAsInt, getAsLong, getAsMatrix, getAsObject, getAsShort, getAsString, getPreferredObject, setAsBigDecimal, setAsBigInteger, setAsBoolean, setAsByte, setAsByteArray, setAsChar, setAsDate, setAsDouble, setAsFloat, setAsInt, setAsLong, setAsMatrix, setAsObject, setAsShort, setAsString, toBigDecimalArray, toBigIntegerArray, toBooleanArray, toByteArray, toCharArray, toDateArray, toDoubleArray, toFloatArray, toIntArray, toLongArray, toObjectArray, toShortArray, toStringArray

Methods inherited from interface org.ujmp.core.doublematrix.calculation.basic.BasicDoubleCalculations

atimes, divide, divide, divide, divide, minus, minus, minus, minus, mtimes, mtimes, plus, plus, plus, plus, times, times, times, times

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.basic.BasicEntrywiseDoubleCalculations

abs, exp, log, log10, log2, logistic, power, power, sign, sqrt

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.rounding.RoundingDoubleCalculations

ceil, floor, round

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.hyperbolic.HyperbolicDoubleCalculations

cosh, sinh, tanh, tanh

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.trigonometric.TrigonometricDoubleCalculations

cos, sin, tan

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.creators.CreatorDoubleCalculations

eye, nans, ones, rand, randn, zeros

Methods inherited from interface org.ujmp.core.doublematrix.calculation.entrywise.misc.MiscEntrywiseDoubleCalculations

grayScale

Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.statistical.StatisticalDoubleCalculations

corrcoef, cov, cumprod, cumsum, diff, indexOfMax, indexOfMin, max, mean, min, mutualInf, pairedTTest, prod, std, sum, var

Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.decomposition.DecompositionDoubleCalculations

chol, eig, eigSymm, ginv, inv, invSPD, invSymm, lu, pinv, pinv, princomp, qr, solve, solveSPD, solveSymm, svd, svd

Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.missingvalues.MissingValueDoubleCalculations

addMissing, countMissing, deleteColumnsWithMissingValues, deleteRowsWithMissingValues, impute

Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.misc.MiscGeneralDoubleCalculations

append, appendHorizontally, appendVertically, center, fadeIn, fadeOut, normalize, replaceMissingBy, standardize

Methods inherited from interface org.ujmp.core.doublematrix.calculation.general.discretize.DiscretizeCalculations

discretize, discretize, discretizeToBoolean, discretizeToColumns

Methods inherited from interface org.ujmp.core.booleanmatrix.calculation.BooleanCalculations

and, and, eq, eq, ge, ge, gt, gt, le, le, lt, lt, ne, ne, not, or, or, xor, xor

Methods inherited from interface org.ujmp.core.stringmatrix.calculation.StringCalculations

convertEncoding, lowerCase, removePunctuation, removeWords, replaceRegex, replaceRegex, stem, tfIdf, translate, upperCase

Methods inherited from interface org.ujmp.core.objectmatrix.calculation.ObjectCalculations

bootstrap, bootstrap, convert, delete, delete, delete, deleteColumns, deleteColumns, deleteRows, deleteRows, diag, extractAnnotation, fill, flipdim, includeAnnotation, replace, reshape, select, select, select, selectColumns, selectColumns, selectRows, selectRows, shuffle, sortrows, squeeze, subMatrix, swap, toColumnVector, toRowVector, transpose, transpose, transpose, tril, triu, unique, uniqueValueCount

Methods inherited from interface org.ujmp.core.interfaces.DistanceMeasures

chebyshevDistanceTo, cosineSimilarity, cosineSimilarityTo, euklideanDistance, euklideanDistanceTo, manhattenDistance, manhattenDistanceTo, minkowskiDistance, minkowskiDistanceTo

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.ujmp.core.annotation.HasMetaData

getColumnForLabel, getColumnLabel, getDimensionLabel, getDimensionMetaData, getMetaData, getMetaData, getMetaDataDimensionMatrix, getMetaDataDouble, getMetaDataMatrix, getMetaDataString, getPositionForLabel, getRowForLabel, getRowLabel, setColumnLabel, setDimensionLabel, setDimensionMetaData, setMetaData, setMetaData, setMetaDataDimensionMatrix, setRowLabel

Methods inherited from interface org.ujmp.core.interfaces.HasLabel

getLabel, getLabelObject, setLabel

Methods inherited from interface org.ujmp.core.interfaces.HasDescription

getDescription, setDescription

Methods inherited from interface org.ujmp.core.interfaces.HasId

getId, setId

Methods inherited from interface org.ujmp.core.interfaces.Conversions

toBigDecimalMatrix, toBigIntegerMatrix, toBooleanMatrix, toByteMatrix, toCharMatrix, toDoubleMatrix, toFloatMatrix, toIntMatrix, toListMatrix, toLongMatrix, toMapMatrix, toObjectMatrix, toSetMatrix, toShortMatrix, toStringMatrix

Methods inherited from interface org.ujmp.core.interfaces.ExtendedMatrixProperties

bigDecimalValue, bigIntegerValue, booleanValue, byteValue, charValue, containsBigDecimal, containsBigInteger, containsBoolean, containsByte, containsChar, containsDate, containsDouble, containsFloat, containsInt, containsLong, containsMissingValues, containsNull, containsObject, containsShort, containsString, dateValue, det, doubleValue, floatValue, getAbsoluteValueMean, getAbsoluteValueSum, getEuklideanValue, getMaxValue, getMeanValue, getMinValue, getRMS, getStdValue, getValueSum, intValue, isSPD, longValue, norm1, norm2, normF, normInf, pdet, rank, setContent, shortValue, stringValue, trace

Methods inherited from interface org.ujmp.core.genericmatrix.GenericMatrix2D

getObject, getObject, setObject, setObject

Field Detail

BYTE

public static final int BYTE

See Also:

Constant Field Values

CHAR

public static final int CHAR

See Also:

Constant Field Values

DOUBLE

public static final int DOUBLE

See Also:

Constant Field Values

FLOAT

public static final int FLOAT

See Also:

Constant Field Values

INT

public static final int INT

See Also:

Constant Field Values

LONG

public static final int LONG

See Also:

Constant Field Values

SHORT

public static final int SHORT

See Also:

Constant Field Values

UNSIGNEDBYTE

public static final int UNSIGNEDBYTE

See Also:

Constant Field Values

UNSIGNEDSHORT

public static final int UNSIGNEDSHORT

See Also:

Constant Field Values

SHORTLITTLEENDIAN

public static final int SHORTLITTLEENDIAN

See Also:

Constant Field Values

INTLITTLEENDIAN

public static final int INTLITTLEENDIAN

See Also:

Constant Field Values

LONGLITTLEENDIAN

public static final int LONGLITTLEENDIAN

See Also:

Constant Field Values

BOOLEAN

public static final int BOOLEAN

See Also:

Constant Field Values

Constructor Detail

DenseFileMatrix

public DenseFileMatrix(java.io.File file,
                       long... size)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(java.io.File file)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(java.io.File file,
                       int dataType,
                       long... size)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(java.io.File file,
                       long offset,
                       int dataType,
                       boolean readOnly,
                       long... size)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(int bufferSize,
                       java.io.File file,
                       long offset,
                       int dataType,
                       boolean readOnly,
                       long... size)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(long... size)
                throws java.io.IOException

Throws:

java.io.IOException

DenseFileMatrix

public DenseFileMatrix(Matrix m)
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

getBufferSize

public int getBufferSize()

setBufferSize

public void setBufferSize(int bufferSize)

getRandomAccessFile

public BufferedRandomAccessFile getRandomAccessFile()

getFile

public java.io.File getFile()

getBytesPerValue

public long getBytesPerValue()

getBitsPerValue

public int getBitsPerValue()

getFileLength

public long getFileLength()

getDataType

public int getDataType()

getDouble

public double getDouble(long... c)

Description copied from interface: DoubleMatrixMultiD

Returns a double representation of an entry in the matrix. The stored value will be converted to a double as good as possible.

Specified by:

getDouble in interface DoubleMatrixMultiD

Parameters:

c - location of the entry

Returns:

a double representation of the entry @

setSize

public void setSize(long... size)

Description copied from interface: BaseMatrixProperties

Sets the size of the matrix. This is an optional method that is not implemented for all matrices. If this method is not implemented, a MatrixException is thrown.

Specified by:

setSize in interface BaseMatrixProperties

Overrides:

setSize in class AbstractMatrix

Parameters:

size - the new size of the matrix

setDouble

public void setDouble(double value,
                      long... c)

Description copied from interface: DoubleMatrixMultiD

Sets an entry in the matrix to a double value. If the matrix cannot store double values, the value will be represented as good as possible.

Specified by:

setDouble in interface DoubleMatrixMultiD

Parameters:

value - double value

c - location of the entry @

isReadOnly

public boolean isReadOnly()

Specified by:

isReadOnly in interface BaseMatrixProperties

Overrides:

isReadOnly in class AbstractMatrix

getShortLittleEndian

public static final int getShortLittleEndian(byte[] bytes)

getIntLittleEndian

public static final int getIntLittleEndian(byte[] bytes)

erase

public void erase()
           throws java.io.IOException

Specified by:

erase in interface Erasable

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException