cern.colt.matrix.tdouble.impl

Class DenseDoubleMatrix3D

java.lang.Object

cern.colt.PersistentObject

cern.colt.matrix.AbstractMatrix

cern.colt.matrix.AbstractMatrix3D

cern.colt.matrix.tdouble.DoubleMatrix3D

cern.colt.matrix.tdouble.impl.DenseDoubleMatrix3D

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class DenseDoubleMatrix3D
extends DoubleMatrix3D

Dense 3-d matrix holding double elements. First see the package summary and javadoc tree view to get the broad picture.

Implementation:

Internally holds one single contiguous one-dimensional array, addressed in (in decreasing order of significance): slice major, row major, column major. Note that this implementation is not synchronized.

Time complexity:

O(1) (i.e. constant time) for the basic operations get, getQuick, set, setQuick and size,

Applications demanding utmost speed can exploit knowledge about the internal addressing. Setting/getting values in a loop slice-by-slice, row-by-row, column-by-column is quicker than, for example, column-by-column, row-by-row, slice-by-slice. Thus

 for (int slice = 0; slice < slices; slice++) {
     for (int row = 0; row < rows; row++) {
         for (int column = 0; column < columns; column++) {
             matrix.setQuick(slice, row, column, someValue);
         }
     }
 }
 

is quicker than

 for (int column = 0; column < columns; column++) {
     for (int row = 0; row < rows; row++) {
         for (int slice = 0; slice < slices; slice++) {
             matrix.setQuick(slice, row, column, someValue);
         }
     }
 }
 

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DenseDoubleMatrix3D(double[][][] values) Constructs a matrix with a copy of the given values.
DenseDoubleMatrix3D(int slices, int rows, int columns) Constructs a matrix with a given number of slices, rows and columns.
DenseDoubleMatrix3D(int slices, int rows, int columns, double[] elements, int sliceZero, int rowZero, int columnZero, int sliceStride, int rowStride, int columnStride, boolean isView) Constructs a matrix with the given parameters.

Method Summary

Modifier and Type	Method and Description
double	aggregate(DoubleDoubleFunction aggr, DoubleFunction f) Applies a function to each cell and aggregates the results.
double	aggregate(DoubleDoubleFunction aggr, DoubleFunction f, DoubleProcedure cond) Applies a function to each cell that satisfies a condition and aggregates the results.
double	aggregate(DoubleDoubleFunction aggr, DoubleFunction f, IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList) Applies a function to all cells with a given indexes and aggregates the results.
double	aggregate(DoubleMatrix3D other, DoubleDoubleFunction aggr, DoubleDoubleFunction f) Applies a function to each corresponding cell of two matrices and aggregates the results.
DoubleMatrix3D	assign(double value) Sets all cells to the state specified by value.
DoubleMatrix3D	assign(double[] values) Sets all cells to the state specified by values.
DoubleMatrix3D	assign(double[][][] values) Sets all cells to the state specified by values.
DoubleMatrix3D	assign(DoubleFunction function) Assigns the result of a function to each cell; x[slice,row,col] = function(x[slice,row,col]).
DoubleMatrix3D	assign(DoubleMatrix3D source) Replaces all cell values of the receiver with the values of another matrix.
DoubleMatrix3D	assign(DoubleMatrix3D y, DoubleDoubleFunction function) Assigns the result of a function to each cell; x[row,col] = function(x[row,col],y[row,col]).
DoubleMatrix3D	assign(DoubleMatrix3D y, DoubleDoubleFunction function, IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList) Assigns the result of a function to all cells with a given indexes
DoubleMatrix3D	assign(DoubleProcedure cond, double value) Assigns a value to all cells that satisfy a condition.
DoubleMatrix3D	assign(DoubleProcedure cond, DoubleFunction f) Assigns the result of a function to all cells that satisfy a condition.
int	cardinality() Returns the number of cells having non-zero values; ignores tolerance.
void	dct2Slices(boolean scale) Computes the 2D discrete cosine transform (DCT-II) of each slice of this matrix.
void	dct3(boolean scale) Computes the 3D discrete cosine transform (DCT-II) of this matrix.
void	dht2Slices() Computes the 2D discrete Hartley transform (DHT) of each slice of this matrix.
void	dht3() Computes the 3D discrete Hartley transform (DHT) of this matrix.
void	dst2Slices(boolean scale) Computes the 2D discrete sine transform (DST-II) of each slice of this matrix.
void	dst3(boolean scale) Computes the 3D discrete sine transform (DST-II) of this matrix.
double[]	elements() Returns the elements of this matrix.
void	fft3() Computes the 3D discrete Fourier transform (DFT) of this matrix.
DenseDComplexMatrix3D	getFft2Slices() Returns new complex matrix which is the 2D discrete Fourier transform (DFT) of each slice of this matrix.
DenseDComplexMatrix3D	getFft3() Returns new complex matrix which is the 3D discrete Fourier transform (DFT) of this matrix.
DenseDComplexMatrix3D	getIfft2Slices(boolean scale) Returns new complex matrix which is the 2D inverse of the discrete Fourier transform (IDFT) of each slice of this matrix.
DenseDComplexMatrix3D	getIfft3(boolean scale) Returns new complex matrix which is the 3D inverse of the discrete Fourier transform (IDFT) of this matrix.
double[]	getMaxLocation() Return maximum value of this matrix together with its location
double[]	getMinLocation() Returns minimum value of this matrix together with its location
void	getNegativeValues(IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList, DoubleArrayList valueList) Fills the coordinates and values of cells having negative values into the specified lists.
void	getNonZeros(IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList, DoubleArrayList valueList) Fills the coordinates and values of cells having non-zero values into the specified lists.
void	getPositiveValues(IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList, DoubleArrayList valueList) Fills the coordinates and values of cells having positive values into the specified lists.
double	getQuick(int slice, int row, int column) Returns the matrix cell value at coordinate [slice,row,column].
void	idct2Slices(boolean scale) Computes the 2D inverse of the discrete cosine transform (DCT-III) of each slice of this matrix.
void	idct3(boolean scale) Computes the 3D inverse of the discrete cosine transform (DCT-III) of this matrix.
void	idht2Slices(boolean scale) Computes the 2D inverse of the discrete Hartley transform (IDHT) of each slice of this matrix.
void	idht3(boolean scale) Computes the 3D inverse of the discrete Hartley transform (IDHT) of this matrix.
void	idst2Slices(boolean scale) Computes the 2D inverse of the discrete sine transform (DST-III) of each slice of this matrix.
void	idst3(boolean scale) Computes the 3D inverse of the discrete sine transform (DST-III) of this matrix.
void	ifft3(boolean scale) Computes the 3D inverse of the discrete Fourier transform (IDFT) of this matrix.
long	index(int slice, int row, int column) Returns the position of the given coordinate within the (virtual or non-virtual) internal 1-dimensional array.
DoubleMatrix3D	like(int slices, int rows, int columns) Construct and returns a new empty matrix of the same dynamic type as the receiver, having the specified number of slices, rows and columns.
DoubleMatrix2D	like2D(int rows, int columns) Construct and returns a new 2-d matrix of the corresponding dynamic type, sharing the same cells.
void	setQuick(int slice, int row, int column, double value) Sets the matrix cell at coordinate [slice,row,column] to the specified value.
double[][][]	toArray() Constructs and returns a 2-dimensional array containing the cell values.
DoubleMatrix1D	vectorize() Returns a vector obtained by stacking the columns of each slice of the matrix on top of one another.
void	zAssign27Neighbors(DoubleMatrix3D B, Double27Function function) 27 neighbor stencil transformation.
double	zSum() Returns the sum of all cells; Sum( x[i,j,k] ).

Methods inherited from class cern.colt.matrix.tdouble.DoubleMatrix3D

copy, equals, equals, get, like, normalize, set, toString, viewColumn, viewColumnFlip, viewDice, viewPart, viewRow, viewRowFlip, viewSelection, viewSelection, viewSlice, viewSliceFlip, viewSorted, viewStrides

Methods inherited from class cern.colt.matrix.AbstractMatrix3D

checkShape, checkShape, columns, columnStride, rows, rowStride, size, slices, sliceStride, toStringShort

Methods inherited from class cern.colt.matrix.AbstractMatrix

ensureCapacity, isView, trimToSize

Methods inherited from class cern.colt.PersistentObject

clone

Methods inherited from class java.lang.Object

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

Constructor Detail

DenseDoubleMatrix3D

public DenseDoubleMatrix3D(double[][][] values)

Constructs a matrix with a copy of the given values. values is required to have the form values[slice][row][column] and have exactly the same number of rows in in every slice and exactly the same number of columns in in every row.

The values are copied. So subsequent changes in values are not reflected in the matrix, and vice-versa.

Parameters:

values - The values to be filled into the new matrix.

Throws:

java.lang.IllegalArgumentException - if for any 1 <= slice < values.length: values[slice].length != values[slice-1].length .

java.lang.IllegalArgumentException - if for any 1 <= row < values[0].length: values[slice][row].length != values[slice][row-1].length .

DenseDoubleMatrix3D

public DenseDoubleMatrix3D(int slices,
                           int rows,
                           int columns)

Constructs a matrix with a given number of slices, rows and columns. All entries are initially 0.

Parameters:

slices - the number of slices the matrix shall have.

rows - the number of rows the matrix shall have.

columns - the number of columns the matrix shall have.

Throws:

java.lang.IllegalArgumentException - if (double)slices*columns*rows > Integer.MAX_VALUE.

java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.

DenseDoubleMatrix3D

public DenseDoubleMatrix3D(int slices,
                           int rows,
                           int columns,
                           double[] elements,
                           int sliceZero,
                           int rowZero,
                           int columnZero,
                           int sliceStride,
                           int rowStride,
                           int columnStride,
                           boolean isView)

Constructs a matrix with the given parameters.

Parameters:

slices - the number of slices the matrix shall have.

rows - the number of rows the matrix shall have.

columns - the number of columns the matrix shall have.

elements - the cells.

sliceZero - the position of the first element.

rowZero - the position of the first element.

columnZero - the position of the first element.

sliceStride - the number of elements between two slices, i.e. index(k+1,i,j)-index(k,i,j).

rowStride - the number of elements between two rows, i.e. index(k,i+1,j)-index(k,i,j).

columnStride - the number of elements between two columns, i.e. index(k,i,j+1)-index(k,i,j).

isView - if true then a matrix view is constructed

Throws:

java.lang.IllegalArgumentException - if (double)slices*columns*rows > Integer.MAX_VALUE.

java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.

Method Detail

aggregate

public double aggregate(DoubleDoubleFunction aggr,
                        DoubleFunction f)

Description copied from class: DoubleMatrix3D

Applies a function to each cell and aggregates the results. Returns a value v such that v==a(size()) where a(i) == aggr( a(i-1), f(get(slice,row,column)) ) and terminators are a(1) == f(get(0,0,0)), a(0)==Double.NaN.

Example:

         cern.jet.math.Functions F = cern.jet.math.Functions.functions;
         2 x 2 x 2 matrix
         0 1
         2 3
 
         4 5
         6 7
 
         // Sum( x[slice,row,col]*x[slice,row,col] ) 
         matrix.aggregate(F.plus,F.square);
         --> 140
 
 

For further examples, see the package doc.

Overrides:

aggregate in class DoubleMatrix3D

Parameters:

aggr - an aggregation function taking as first argument the current aggregation and as second argument the transformed current cell value.

f - a function transforming the current cell value.

Returns:

the aggregated measure.

See Also:

DoubleFunctions

aggregate

public double aggregate(DoubleDoubleFunction aggr,
                        DoubleFunction f,
                        DoubleProcedure cond)

Description copied from class: DoubleMatrix3D

Applies a function to each cell that satisfies a condition and aggregates the results.

Overrides:

aggregate in class DoubleMatrix3D

Parameters:

aggr - an aggregation function taking as first argument the current aggregation and as second argument the transformed current cell value.

f - a function transforming the current cell value.

cond - a condition.

Returns:

the aggregated measure.

See Also:

DoubleFunctions

aggregate

public double aggregate(DoubleDoubleFunction aggr,
                        DoubleFunction f,
                        IntArrayList sliceList,
                        IntArrayList rowList,
                        IntArrayList columnList)

Description copied from class: DoubleMatrix3D

Applies a function to all cells with a given indexes and aggregates the results.

Overrides:

aggregate in class DoubleMatrix3D

Parameters:

aggr - an aggregation function taking as first argument the current aggregation and as second argument the transformed current cell value.

f - a function transforming the current cell value.

sliceList - slice indexes.

rowList - row indexes.

columnList - column indexes.

Returns:

the aggregated measure.

See Also:

DoubleFunctions

aggregate

public double aggregate(DoubleMatrix3D other,
                        DoubleDoubleFunction aggr,
                        DoubleDoubleFunction f)

Description copied from class: DoubleMatrix3D

Applies a function to each corresponding cell of two matrices and aggregates the results. Returns a value v such that v==a(size()) where a(i) == aggr( a(i-1), f(get(slice,row,column),other.get(slice,row,column)) ) and terminators are a(1) == f(get(0,0,0),other.get(0,0,0)), a(0)==Double.NaN.

Example:

         cern.jet.math.Functions F = cern.jet.math.Functions.functions;
         x = 2 x 2 x 2 matrix
         0 1
         2 3
 
         4 5
         6 7
 
         y = 2 x 2 x 2 matrix
         0 1
         2 3
 
         4 5
         6 7
 
         // Sum( x[slice,row,col] * y[slice,row,col] ) 
         x.aggregate(y, F.plus, F.mult);
         --> 140
 
         // Sum( (x[slice,row,col] + y[slice,row,col])ˆ2 )
         x.aggregate(y, F.plus, F.chain(F.square,F.plus));
         --> 560
 
 

For further examples, see the package doc.

Overrides:

aggregate in class DoubleMatrix3D

aggr - an aggregation function taking as first argument the current aggregation and as second argument the transformed current cell values.

f - a function transforming the current cell values.

Returns:

the aggregated measure.

See Also:

DoubleFunctions

assign

public DoubleMatrix3D assign(DoubleFunction function)

Description copied from class: DoubleMatrix3D

Assigns the result of a function to each cell; x[slice,row,col] = function(x[slice,row,col]).

Example:

         matrix = 1 x 2 x 2 matrix
         0.5 1.5      
         2.5 3.5
 
         // change each cell to its sine
         matrix.assign(cern.jet.math.Functions.sin);
         -->
         1 x 2 x 2 matrix
         0.479426  0.997495 
         0.598472 -0.350783
 
 

For further examples, see the package doc.

Overrides:

assign in class DoubleMatrix3D

Parameters:

function - a function object taking as argument the current cell's value.

Returns:

this (for convenience only).

See Also:

DoubleFunctions

assign

public DoubleMatrix3D assign(DoubleProcedure cond,
                             DoubleFunction f)

Description copied from class: DoubleMatrix3D

Assigns the result of a function to all cells that satisfy a condition.

Overrides:

assign in class DoubleMatrix3D

Parameters:

cond - a condition.

f - a function object.

Returns:

this (for convenience only).

See Also:

DoubleFunctions

assign

public DoubleMatrix3D assign(DoubleProcedure cond,
                             double value)

Description copied from class: DoubleMatrix3D

Assigns a value to all cells that satisfy a condition.

Overrides:

assign in class DoubleMatrix3D

Parameters:

cond - a condition.

value - a value.

Returns:

this (for convenience only).

assign

public DoubleMatrix3D assign(double value)

Description copied from class: DoubleMatrix3D

Sets all cells to the state specified by value.

Overrides:

assign in class DoubleMatrix3D

Parameters:

value - the value to be filled into the cells.

Returns:

this (for convenience only).

assign

public DoubleMatrix3D assign(double[] values)

Description copied from class: DoubleMatrix3D

Sets all cells to the state specified by values. values is required to have the form values[slice*row*column].

The values are copied. So subsequent changes in values are not reflected in the matrix, and vice-versa.

Overrides:

assign in class DoubleMatrix3D

Parameters:

values - the values to be filled into the cells.

Returns:

this (for convenience only).

assign

public DoubleMatrix3D assign(double[][][] values)

Description copied from class: DoubleMatrix3D

Sets all cells to the state specified by values. values is required to have the form values[slice][row][column] and have exactly the same number of slices, rows and columns as the receiver.

The values are copied. So subsequent changes in values are not reflected in the matrix, and vice-versa.

Overrides:

assign in class DoubleMatrix3D

Parameters:

values - the values to be filled into the cells.

Returns:

this (for convenience only).

assign

public DoubleMatrix3D assign(DoubleMatrix3D source)

Description copied from class: DoubleMatrix3D

Replaces all cell values of the receiver with the values of another matrix. Both matrices must have the same number of slices, rows and columns. If both matrices share the same cells (as is the case if they are views derived from the same matrix) and intersect in an ambiguous way, then replaces as if using an intermediate auxiliary deep copy of other.

Overrides:

assign in class DoubleMatrix3D

Parameters:

source - the source matrix to copy from (may be identical to the receiver).

Returns:

this (for convenience only).

assign

public DoubleMatrix3D assign(DoubleMatrix3D y,
                             DoubleDoubleFunction function)

Description copied from class: DoubleMatrix3D

Assigns the result of a function to each cell; x[row,col] = function(x[row,col],y[row,col]).

Example:

         // assign x[row,col] = x[row,col]<sup>y[row,col]</sup>
         m1 = 1 x 2 x 2 matrix 
         0 1 
         2 3
 
         m2 = 1 x 2 x 2 matrix 
         0 2 
         4 6
 
         m1.assign(m2, cern.jet.math.Functions.pow);
         -->
         m1 == 1 x 2 x 2 matrix
         1   1 
         16 729
 
 

For further examples, see the package doc.

Overrides:

assign in class DoubleMatrix3D

Parameters:

y - the secondary matrix to operate on.

function - a function object taking as first argument the current cell's value of this, and as second argument the current cell's value of y,

Returns:

this (for convenience only).

See Also:

DoubleFunctions

assign

public DoubleMatrix3D assign(DoubleMatrix3D y,
                             DoubleDoubleFunction function,
                             IntArrayList sliceList,
                             IntArrayList rowList,
                             IntArrayList columnList)

Description copied from class: DoubleMatrix3D

Assigns the result of a function to all cells with a given indexes

Overrides:

assign in class DoubleMatrix3D

Parameters:

y - the secondary matrix to operate on.

function - a function object taking as first argument the current cell's value of this, and as second argument the current cell's value of y, *

sliceList - slice indexes.

rowList - row indexes.

columnList - column indexes.

Returns:

this (for convenience only).

See Also:

DoubleFunctions

cardinality

public int cardinality()

Description copied from class: DoubleMatrix3D

Returns the number of cells having non-zero values; ignores tolerance.

Overrides:

cardinality in class DoubleMatrix3D

Returns:

the number of cells having non-zero values.

dct2Slices

public void dct2Slices(boolean scale)

Computes the 2D discrete cosine transform (DCT-II) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

dct3

public void dct3(boolean scale)

Computes the 3D discrete cosine transform (DCT-II) of this matrix.

Parameters:

scale - if true then scaling is performed

dht2Slices

public void dht2Slices()

Computes the 2D discrete Hartley transform (DHT) of each slice of this matrix.

dht3

public void dht3()

Computes the 3D discrete Hartley transform (DHT) of this matrix.

dst2Slices

public void dst2Slices(boolean scale)

Computes the 2D discrete sine transform (DST-II) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

dst3

public void dst3(boolean scale)

Computes the 3D discrete sine transform (DST-II) of this matrix.

Parameters:

scale - if true then scaling is performed

elements

public double[] elements()

Description copied from class: DoubleMatrix3D

Returns the elements of this matrix.

Specified by:

elements in class DoubleMatrix3D

Returns:

the elements

fft3

public void fft3()

Computes the 3D discrete Fourier transform (DFT) of this matrix. The physical layout of the output data is as follows:

 this[k1][k2][2*k3] = Re[k1][k2][k3]
                 = Re[(n1-k1)%n1][(n2-k2)%n2][n3-k3], 
 this[k1][k2][2*k3+1] = Im[k1][k2][k3]
                   = -Im[(n1-k1)%n1][(n2-k2)%n2][n3-k3], 
     0<=k1<n1, 0<=k2<n2, 0<k3<n3/2, 
 this[k1][k2][0] = Re[k1][k2][0]
              = Re[(n1-k1)%n1][n2-k2][0], 
 this[k1][k2][1] = Im[k1][k2][0]
              = -Im[(n1-k1)%n1][n2-k2][0], 
 this[k1][n2-k2][1] = Re[(n1-k1)%n1][k2][n3/2]
                 = Re[k1][n2-k2][n3/2], 
 this[k1][n2-k2][0] = -Im[(n1-k1)%n1][k2][n3/2]
                 = Im[k1][n2-k2][n3/2], 
     0<=k1<n1, 0<k2<n2/2, 
 this[k1][0][0] = Re[k1][0][0]
             = Re[n1-k1][0][0], 
 this[k1][0][1] = Im[k1][0][0]
             = -Im[n1-k1][0][0], 
 this[k1][n2/2][0] = Re[k1][n2/2][0]
                = Re[n1-k1][n2/2][0], 
 this[k1][n2/2][1] = Im[k1][n2/2][0]
                = -Im[n1-k1][n2/2][0], 
 this[n1-k1][0][1] = Re[k1][0][n3/2]
                = Re[n1-k1][0][n3/2], 
 this[n1-k1][0][0] = -Im[k1][0][n3/2]
                = Im[n1-k1][0][n3/2], 
 this[n1-k1][n2/2][1] = Re[k1][n2/2][n3/2]
                   = Re[n1-k1][n2/2][n3/2], 
 this[n1-k1][n2/2][0] = -Im[k1][n2/2][n3/2]
                   = Im[n1-k1][n2/2][n3/2], 
     0<k1<n1/2, 
 this[0][0][0] = Re[0][0][0], 
 this[0][0][1] = Re[0][0][n3/2], 
 this[0][n2/2][0] = Re[0][n2/2][0], 
 this[0][n2/2][1] = Re[0][n2/2][n3/2], 
 this[n1/2][0][0] = Re[n1/2][0][0], 
 this[n1/2][0][1] = Re[n1/2][0][n3/2], 
 this[n1/2][n2/2][0] = Re[n1/2][n2/2][0], 
 this[n1/2][n2/2][1] = Re[n1/2][n2/2][n3/2]
 

This method computes only half of the elements of the real transform. The other half satisfies the symmetry condition. If you want the full real forward transform, use getFft3. To get back the original data, use ifft3.

Throws:

java.lang.IllegalArgumentException - if the slice size or the row size or the column size of this matrix is not a power of 2 number.

getFft2Slices

public DenseDComplexMatrix3D getFft2Slices()

Returns new complex matrix which is the 2D discrete Fourier transform (DFT) of each slice of this matrix.

Returns:

the 2D discrete Fourier transform (DFT) of each slice of this matrix.

getFft3

public DenseDComplexMatrix3D getFft3()

Returns new complex matrix which is the 3D discrete Fourier transform (DFT) of this matrix.

Returns:

the 3D discrete Fourier transform (DFT) of this matrix.

getIfft2Slices

public DenseDComplexMatrix3D getIfft2Slices(boolean scale)

Returns new complex matrix which is the 2D inverse of the discrete Fourier transform (IDFT) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

Returns:

the 2D inverse of the discrete Fourier transform (IDFT) of each slice of this matrix.

getIfft3

public DenseDComplexMatrix3D getIfft3(boolean scale)

Returns new complex matrix which is the 3D inverse of the discrete Fourier transform (IDFT) of this matrix.

Parameters:

scale - if true then scaling is performed

Returns:

the 3D inverse of the discrete Fourier transform (IDFT) of this matrix.

getMaxLocation

public double[] getMaxLocation()

Description copied from class: DoubleMatrix3D

Return maximum value of this matrix together with its location

Overrides:

getMaxLocation in class DoubleMatrix3D

Returns:

{ maximum_value, slice_location, row_location, column_location };

getMinLocation

public double[] getMinLocation()

Description copied from class: DoubleMatrix3D

Returns minimum value of this matrix together with its location

Overrides:

getMinLocation in class DoubleMatrix3D

Returns:

{ minimum_value, slice_location, row_location, column_location };

getNegativeValues

public void getNegativeValues(IntArrayList sliceList,
                              IntArrayList rowList,
                              IntArrayList columnList,
                              DoubleArrayList valueList)

Description copied from class: DoubleMatrix3D

Fills the coordinates and values of cells having negative values into the specified lists. Fills into the lists, starting at index 0. After this call returns the specified lists all have a new size, the number of non-zero values.

Overrides:

getNegativeValues in class DoubleMatrix3D

Parameters:

sliceList - the list to be filled with slice indexes, can have any size.

rowList - the list to be filled with row indexes, can have any size.

columnList - the list to be filled with column indexes, can have any size.

valueList - the list to be filled with values, can have any size.

getNonZeros

public void getNonZeros(IntArrayList sliceList,
                        IntArrayList rowList,
                        IntArrayList columnList,
                        DoubleArrayList valueList)

Description copied from class: DoubleMatrix3D

Fills the coordinates and values of cells having non-zero values into the specified lists. Fills into the lists, starting at index 0. After this call returns the specified lists all have a new size, the number of non-zero values.

In general, fill order is unspecified. This implementation fill like: for (slice = 0..slices-1) for (row = 0..rows-1) for (column = 0..colums-1) do ... . However, subclasses are free to us any other order, even an order that may change over time as cell values are changed. (Of course, result lists indexes are guaranteed to correspond to the same cell). For an example, see DoubleMatrix3D.getNonZeros(IntArrayList,IntArrayList,IntArrayList,DoubleArrayList).

Overrides:

getNonZeros in class DoubleMatrix3D

Parameters:

sliceList - the list to be filled with slice indexes, can have any size.

rowList - the list to be filled with row indexes, can have any size.

columnList - the list to be filled with column indexes, can have any size.

valueList - the list to be filled with values, can have any size.

getPositiveValues

public void getPositiveValues(IntArrayList sliceList,
                              IntArrayList rowList,
                              IntArrayList columnList,
                              DoubleArrayList valueList)

Description copied from class: DoubleMatrix3D

Fills the coordinates and values of cells having positive values into the specified lists. Fills into the lists, starting at index 0. After this call returns the specified lists all have a new size, the number of non-zero values.

Overrides:

getPositiveValues in class DoubleMatrix3D

Parameters:

sliceList - the list to be filled with slice indexes, can have any size.

rowList - the list to be filled with row indexes, can have any size.

columnList - the list to be filled with column indexes, can have any size.

valueList - the list to be filled with values, can have any size.

getQuick

public double getQuick(int slice,
                       int row,
                       int column)

Description copied from class: DoubleMatrix3D

Returns the matrix cell value at coordinate [slice,row,column].

Provided with invalid parameters this method may return invalid objects without throwing any exception. You should only use this method when you are absolutely sure that the coordinate is within bounds. Precondition (unchecked): slice<0 || slice>=slices() || row<0 || row>=rows() || column<0 || column>=column().

Specified by:

getQuick in class DoubleMatrix3D

Parameters:

slice - the index of the slice-coordinate.

row - the index of the row-coordinate.

column - the index of the column-coordinate.

Returns:

the value at the specified coordinate.

idct2Slices

public void idct2Slices(boolean scale)

Computes the 2D inverse of the discrete cosine transform (DCT-III) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

idct3

public void idct3(boolean scale)

Computes the 3D inverse of the discrete cosine transform (DCT-III) of this matrix.

Parameters:

scale - if true then scaling is performed

idht2Slices

public void idht2Slices(boolean scale)

Computes the 2D inverse of the discrete Hartley transform (IDHT) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

idht3

public void idht3(boolean scale)

Computes the 3D inverse of the discrete Hartley transform (IDHT) of this matrix.

Parameters:

scale - if true then scaling is performed

idst2Slices

public void idst2Slices(boolean scale)

Computes the 2D inverse of the discrete sine transform (DST-III) of each slice of this matrix.

Parameters:

scale - if true then scaling is performed

idst3

public void idst3(boolean scale)

Computes the 3D inverse of the discrete sine transform (DST-III) of this matrix.

Parameters:

scale - if true then scaling is performed

ifft3

public void ifft3(boolean scale)

Computes the 3D inverse of the discrete Fourier transform (IDFT) of this matrix. The physical layout of the input data has to be as follows:

 this[k1][k2][2*k3] = Re[k1][k2][k3]
                 = Re[(n1-k1)%n1][(n2-k2)%n2][n3-k3], 
 this[k1][k2][2*k3+1] = Im[k1][k2][k3]
                   = -Im[(n1-k1)%n1][(n2-k2)%n2][n3-k3], 
     0<=k1<n1, 0<=k2<n2, 0<k3<n3/2, 
 this[k1][k2][0] = Re[k1][k2][0]
              = Re[(n1-k1)%n1][n2-k2][0], 
 this[k1][k2][1] = Im[k1][k2][0]
              = -Im[(n1-k1)%n1][n2-k2][0], 
 this[k1][n2-k2][1] = Re[(n1-k1)%n1][k2][n3/2]
                 = Re[k1][n2-k2][n3/2], 
 this[k1][n2-k2][0] = -Im[(n1-k1)%n1][k2][n3/2]
                 = Im[k1][n2-k2][n3/2], 
     0<=k1<n1, 0<k2<n2/2, 
 this[k1][0][0] = Re[k1][0][0]
             = Re[n1-k1][0][0], 
 this[k1][0][1] = Im[k1][0][0]
             = -Im[n1-k1][0][0], 
 this[k1][n2/2][0] = Re[k1][n2/2][0]
                = Re[n1-k1][n2/2][0], 
 this[k1][n2/2][1] = Im[k1][n2/2][0]
                = -Im[n1-k1][n2/2][0], 
 this[n1-k1][0][1] = Re[k1][0][n3/2]
                = Re[n1-k1][0][n3/2], 
 this[n1-k1][0][0] = -Im[k1][0][n3/2]
                = Im[n1-k1][0][n3/2], 
 this[n1-k1][n2/2][1] = Re[k1][n2/2][n3/2]
                   = Re[n1-k1][n2/2][n3/2], 
 this[n1-k1][n2/2][0] = -Im[k1][n2/2][n3/2]
                   = Im[n1-k1][n2/2][n3/2], 
     0<k1<n1/2, 
 this[0][0][0] = Re[0][0][0], 
 this[0][0][1] = Re[0][0][n3/2], 
 this[0][n2/2][0] = Re[0][n2/2][0], 
 this[0][n2/2][1] = Re[0][n2/2][n3/2], 
 this[n1/2][0][0] = Re[n1/2][0][0], 
 this[n1/2][0][1] = Re[n1/2][0][n3/2], 
 this[n1/2][n2/2][0] = Re[n1/2][n2/2][0], 
 this[n1/2][n2/2][1] = Re[n1/2][n2/2][n3/2]
 

This method computes only half of the elements of the real transform. The other half satisfies the symmetry condition. If you want the full real inverse transform, use getIfft3.

Parameters:

scale - if true then scaling is performed

Throws:

java.lang.IllegalArgumentException - if the slice size or the row size or the column size of this matrix is not a power of 2 number.

index

public long index(int slice,
                  int row,
                  int column)

Description copied from class: AbstractMatrix3D

Returns the position of the given coordinate within the (virtual or non-virtual) internal 1-dimensional array.

Overrides:

index in class AbstractMatrix3D

Parameters:

slice - the index of the slice-coordinate.

row - the index of the row-coordinate.

column - the index of the third-coordinate.

like

public DoubleMatrix3D like(int slices,
                           int rows,
                           int columns)

Description copied from class: DoubleMatrix3D

Construct and returns a new empty matrix of the same dynamic type as the receiver, having the specified number of slices, rows and columns. For example, if the receiver is an instance of type DenseDoubleMatrix3D the new matrix must also be of type DenseDoubleMatrix3D, if the receiver is an instance of type SparseDoubleMatrix3D the new matrix must also be of type SparseDoubleMatrix3D, etc. In general, the new matrix should have internal parametrization as similar as possible.

Specified by:

like in class DoubleMatrix3D

Parameters:

slices - the number of slices the matrix shall have.

rows - the number of rows the matrix shall have.

columns - the number of columns the matrix shall have.

Returns:

a new empty matrix of the same dynamic type.

like2D

public DoubleMatrix2D like2D(int rows,
                             int columns)

Description copied from class: DoubleMatrix3D

Construct and returns a new 2-d matrix of the corresponding dynamic type, sharing the same cells. For example, if the receiver is an instance of type DenseDoubleMatrix3D the new matrix must also be of type DenseDoubleMatrix2D, if the receiver is an instance of type SparseDoubleMatrix3D the new matrix must also be of type SparseDoubleMatrix2D, etc.

Specified by:

like2D in class DoubleMatrix3D

Parameters:

rows - the number of rows the matrix shall have.

columns - the number of columns the matrix shall have.

Returns:

a new matrix of the corresponding dynamic type.

setQuick

public void setQuick(int slice,
                     int row,
                     int column,
                     double value)

Description copied from class: DoubleMatrix3D

Sets the matrix cell at coordinate [slice,row,column] to the specified value.

Provided with invalid parameters this method may access illegal indexes without throwing any exception. You should only use this method when you are absolutely sure that the coordinate is within bounds. Precondition (unchecked): slice<0 || slice>=slices() || row<0 || row>=rows() || column<0 || column>=column().

Specified by:

setQuick in class DoubleMatrix3D

Parameters:

slice - the index of the slice-coordinate.

row - the index of the row-coordinate.

column - the index of the column-coordinate.

value - the value to be filled into the specified cell.

toArray

public double[][][] toArray()

Description copied from class: DoubleMatrix3D

Constructs and returns a 2-dimensional array containing the cell values. The returned array values has the form values[slice][row][column] and has the same number of slices, rows and columns as the receiver.

The values are copied. So subsequent changes in values are not reflected in the matrix, and vice-versa.

Overrides:

toArray in class DoubleMatrix3D

Returns:

an array filled with the values of the cells.

vectorize

public DoubleMatrix1D vectorize()

Description copied from class: DoubleMatrix3D

Returns a vector obtained by stacking the columns of each slice of the matrix on top of one another.

Specified by:

vectorize in class DoubleMatrix3D

Returns:

a vector obtained by stacking the columns of each slice of the matrix on top of one another.

zAssign27Neighbors

public void zAssign27Neighbors(DoubleMatrix3D B,
                               Double27Function function)

Description copied from class: DoubleMatrix3D

27 neighbor stencil transformation. For efficient finite difference operations. Applies a function to a moving 3 x 3 x 3 window. Does nothing if rows() < 3 || columns() < 3 || slices() < 3.

         B[k,i,j] = function.apply(
            A[k-1,i-1,j-1], A[k-1,i-1,j], A[k-1,i-1,j+1],
            A[k-1,i,  j-1], A[k-1,i,  j], A[k-1,i,  j+1],
            A[k-1,i+1,j-1], A[k-1,i+1,j], A[k-1,i+1,j+1],
 
            A[k  ,i-1,j-1], A[k  ,i-1,j], A[k  ,i-1,j+1],
            A[k  ,i,  j-1], A[k  ,i,  j], A[k  ,i,  j+1],
            A[k  ,i+1,j-1], A[k  ,i+1,j], A[k  ,i+1,j+1],
 
            A[k+1,i-1,j-1], A[k+1,i-1,j], A[k+1,i-1,j+1],
            A[k+1,i,  j-1], A[k+1,i,  j], A[k+1,i,  j+1],
            A[k+1,i+1,j-1], A[k+1,i+1,j], A[k+1,i+1,j+1]
            )
 
         x x x -     - x x x     - - - - 
         x o x -     - x o x     - - - - 
         x x x -     - x x x ... - x x x 
         - - - -     - - - -     - x o x 
         - - - -     - - - -     - x x x
 
 

Make sure that cells of this and B do not overlap. In case of overlapping views, behaviour is unspecified.

Example:

 
 final double alpha = 0.25; final double beta = 0.75;
 
 cern.colt.function.Double27Function f = new
 cern.colt.function.Double27Function() {    public final
 double apply(       double a000, double
 a001, double a002,       double a010,
 double a011, double a012,       double
 a020, double a021, double a022,
 
       double a100, double a101, double
 a102,       double a110, double a111,
 double a112,       double a120, double
 a121, double a122,
 
       double a200, double a201, double
 a202,       double a210, double a211,
 double a212,       double a220, double
 a221, double a222) {
          return beta*a111 +
 alpha*(a000 + ... + a222);       } };
 A.zAssign27Neighbors(B,f);
 
 

Overrides:

zAssign27Neighbors in class DoubleMatrix3D

Parameters:

B - the matrix to hold the results.

function - the function to be applied to the 27 cells.

zSum

public double zSum()

Description copied from class: DoubleMatrix3D

Returns the sum of all cells; Sum( x[i,j,k] ).

Overrides:

zSum in class DoubleMatrix3D

Returns:

the sum.