Parallel Colt 0.7.2

cern.colt.matrix.tfcomplex.impl
Class DenseFComplexMatrix3D

java.lang.Object
  extended by cern.colt.PersistentObject
      extended by cern.colt.matrix.AbstractMatrix
          extended by cern.colt.matrix.AbstractMatrix3D
              extended by cern.colt.matrix.tfcomplex.FComplexMatrix3D
                  extended by cern.colt.matrix.tfcomplex.impl.DenseFComplexMatrix3D
All Implemented Interfaces:
Serializable, Cloneable

public class DenseFComplexMatrix3D
extends FComplexMatrix3D

Dense 3-d matrix holding complex elements.

Implementation:

Internally holds one single contigous one-dimensional array, addressed in (in decreasing order of significance): slice major, row major, column major. Complex data is represented by 2 float values in sequence, i.e. elements[idx] constitute the real part and elements[idx+1] constitute the imaginary part, where idx = index(0,0,0) + slice * sliceStride + row * rowStride + column * columnStride. Note that this implementation is not synchronized.

Memory requirements:

memory [bytes] = 8*slices()*rows()*2*columns(). Thus, a 100*100*100 matrix uses 16 MB.

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);
         }
     }
 }
 

Author:
Piotr Wendykier (piotr.wendykier@gmail.com)
See Also:
Serialized Form

Constructor Summary
DenseFComplexMatrix3D(float[][][] values)
          Constructs a matrix with a copy of the given values.
DenseFComplexMatrix3D(FloatMatrix3D realPart)
          Constructs a complex matrix with the same size as realPart matrix and fills the real part of this matrix with elements of realPart.
DenseFComplexMatrix3D(int slices, int rows, int columns)
          Constructs a matrix with a given number of slices, rows and columns.
DenseFComplexMatrix3D(int slices, int rows, int columns, float[] elements, int sliceZero, int rowZero, int columnZero, int sliceStride, int rowStride, int columnStride)
          Constructs a view with the given parameters.
 
Method Summary
 float[] aggregate(FComplexFComplexFComplexFunction aggr, FComplexFComplexFunction f)
          Applies a function to each cell and aggregates the results.
 float[] aggregate(FComplexMatrix3D other, FComplexFComplexFComplexFunction aggr, FComplexFComplexFComplexFunction f)
          Applies a function to each corresponding cell of two matrices and aggregates the results.
 FComplexMatrix3D assign(FComplexFComplexFunction function)
          Assigns the result of a function to each cell.
 FComplexMatrix3D assign(FComplexMatrix3D source)
          Replaces all cell values of the receiver with the values of another matrix.
 FComplexMatrix3D assign(FComplexMatrix3D y, FComplexFComplexFComplexFunction function)
          Assigns the result of a function to each cell.
 FComplexMatrix3D assign(FComplexProcedure cond, FComplexFComplexFunction f)
          Assigns the result of a function to all cells that satisfy a condition.
 FComplexMatrix3D assign(FComplexProcedure cond, float[] value)
          Assigns a value to all cells that satisfy a condition.
 FComplexMatrix3D assign(FComplexRealFunction function)
          Assigns the result of a function to the real part of the receiver.
 FComplexMatrix3D assign(float[] values)
          Sets all cells to the state specified by values.
 FComplexMatrix3D assign(float[][][] values)
          Sets all cells to the state specified by values.
 FComplexMatrix3D assign(float re, float im)
          Sets all cells to the state specified by re and im.
 FComplexMatrix3D assignImaginary(FloatMatrix3D other)
          Replaces imaginary part of the receiver with the values of another real matrix.
 FComplexMatrix3D assignReal(FloatMatrix3D other)
          Replaces real part of the receiver with the values of another real matrix.
 int cardinality()
          Returns the number of cells having non-zero values; ignores tolerance.
 float[] elements()
          Returns the elements of this matrix.
 void fft2Slices()
          Computes the 2D discrete Fourier transform (DFT) of each slice of this matrix.
 void fft3()
          Computes the 3D discrete Fourier transform (DFT) of this matrix.
 FloatMatrix3D getImaginaryPart()
          Returns the imaginary part of this matrix
 void getNonZeros(IntArrayList sliceList, IntArrayList rowList, IntArrayList columnList, ArrayList<float[]> valueList)
          Fills the coordinates and values of cells having non-zero values into the specified lists.
 float[] getQuick(int slice, int row, int column)
          Returns the matrix cell value at coordinate [slice,row,column].
 FloatMatrix3D getRealPart()
          Returns the real part of this matrix
 void ifft2Slices(boolean scale)
          Computes the 2D inverse of the discrete Fourier transform (IDFT) of each slice 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.
 FComplexMatrix3D 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.
 void setQuick(int slice, int row, int column, float[] value)
          Sets the matrix cell at coordinate [slice,row,column] to the specified value.
 void setQuick(int slice, int row, int column, float re, float im)
          Sets the matrix cell at coordinate [slice,row,column] to the specified value.
 float[][][] toArray()
          Constructs and returns a 3-dimensional array containing the cell values.
 FComplexMatrix1D vectorize()
          Returns a vector obtained by stacking the columns of each slice of the matrix on top of one another.
 float[] zSum()
          Returns the sum of all cells; Sum( x[i,j,k] ).
 
Methods inherited from class cern.colt.matrix.tfcomplex.FComplexMatrix3D
copy, equals, equals, get, like, set, toString, toString, viewColumn, viewColumnFlip, viewDice, viewPart, viewRow, viewRowFlip, viewSelection, viewSelection, viewSlice, viewSliceFlip, 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

DenseFComplexMatrix3D

public DenseFComplexMatrix3D(float[][][] values)
Constructs a matrix with a copy of the given values. * values is required to have the form re = values[slice][row][2*column], im = values[slice][row][2*column+1] and have exactly the same number of rows 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:
IllegalArgumentException - if for any 1 <= slice < values.length: values[slice].length != values[slice-1].length .
IllegalArgumentException - if for any 1 <= row < values[0].length: values[slice][row].length != values[slice][row-1].length .

DenseFComplexMatrix3D

public DenseFComplexMatrix3D(FloatMatrix3D realPart)
Constructs a complex matrix with the same size as realPart matrix and fills the real part of this matrix with elements of realPart.

Parameters:
realPart - a real matrix whose elements become a real part of this matrix
Throws:
IllegalArgumentException - if (float)slices*columns*rows > Integer.MAX_VALUE.
IllegalArgumentException - if slices<0 || rows<0 || columns<0.

DenseFComplexMatrix3D

public DenseFComplexMatrix3D(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:
IllegalArgumentException - if (float)slices*columns*rows > Integer.MAX_VALUE.
IllegalArgumentException - if slices<0 || rows<0 || columns<0.

DenseFComplexMatrix3D

public DenseFComplexMatrix3D(int slices,
                             int rows,
                             int columns,
                             float[] elements,
                             int sliceZero,
                             int rowZero,
                             int columnZero,
                             int sliceStride,
                             int rowStride,
                             int columnStride)
Constructs a view 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).
Throws:
IllegalArgumentException - if (float)slices*columns*rows > Integer.MAX_VALUE.
IllegalArgumentException - if slices<0 || rows<0 || columns<0.
Method Detail

aggregate

public float[] aggregate(FComplexFComplexFComplexFunction aggr,
                         FComplexFComplexFunction f)
Description copied from class: FComplexMatrix3D
Applies a function to each cell and aggregates the results.

Overrides:
aggregate in class FComplexMatrix3D
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:
FloatFunctions

aggregate

public float[] aggregate(FComplexMatrix3D other,
                         FComplexFComplexFComplexFunction aggr,
                         FComplexFComplexFComplexFunction f)
Description copied from class: FComplexMatrix3D
Applies a function to each corresponding cell of two matrices and aggregates the results.

Overrides:
aggregate in class FComplexMatrix3D
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:
FloatFunctions

assign

public FComplexMatrix3D assign(FComplexFComplexFunction function)
Description copied from class: FComplexMatrix3D
Assigns the result of a function to each cell.

Overrides:
assign in class FComplexMatrix3D
Parameters:
function - a function object taking as argument the current cell's value.
Returns:
this (for convenience only).
See Also:
FComplexFunctions

assign

public FComplexMatrix3D assign(FComplexProcedure cond,
                               FComplexFComplexFunction f)
Description copied from class: FComplexMatrix3D
Assigns the result of a function to all cells that satisfy a condition.

Overrides:
assign in class FComplexMatrix3D
Parameters:
cond - a condition.
f - a function object.
Returns:
this (for convenience only).
See Also:
FComplexFunctions

assign

public FComplexMatrix3D assign(FComplexProcedure cond,
                               float[] value)
Description copied from class: FComplexMatrix3D
Assigns a value to all cells that satisfy a condition.

Overrides:
assign in class FComplexMatrix3D
Parameters:
cond - a condition.
value - a value (re=value[0], im=value[1]).
Returns:
this (for convenience only).

assign

public FComplexMatrix3D assign(FComplexRealFunction function)
Description copied from class: FComplexMatrix3D
Assigns the result of a function to the real part of the receiver. The imaginary part of the receiver is reset to zero.

Overrides:
assign in class FComplexMatrix3D
Parameters:
function - a function object taking as argument the current cell's value.
Returns:
this (for convenience only).
See Also:
FComplexFunctions

assign

public FComplexMatrix3D assign(FComplexMatrix3D source)
Description copied from class: FComplexMatrix3D
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 FComplexMatrix3D
Parameters:
source - the source matrix to copy from (may be identical to the receiver).
Returns:
this (for convenience only).

assign

public FComplexMatrix3D assign(FComplexMatrix3D y,
                               FComplexFComplexFComplexFunction function)
Description copied from class: FComplexMatrix3D
Assigns the result of a function to each cell.

Overrides:
assign in class FComplexMatrix3D
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:
FComplexFunctions

assign

public FComplexMatrix3D assign(float re,
                               float im)
Description copied from class: FComplexMatrix3D
Sets all cells to the state specified by re and im.

Overrides:
assign in class FComplexMatrix3D
Parameters:
re - the real part of the value to be filled into the cells.
im - the imagiary part of the value to be filled into the cells.
Returns:
this (for convenience only).

assign

public FComplexMatrix3D assign(float[] values)
Description copied from class: FComplexMatrix3D
Sets all cells to the state specified by values. values is required to have the form re = values[slice*silceStride+row*rowStride+2*column], im = values[slice*silceStride+row*rowStride+2*column+1] 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 FComplexMatrix3D
Parameters:
values - the values to be filled into the cells.
Returns:
this (for convenience only).

assign

public FComplexMatrix3D assign(float[][][] values)
Description copied from class: FComplexMatrix3D
Sets all cells to the state specified by values. values is required to have the form re = values[slice][row][2*column], im = values[slice][row][2*column+1] 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 FComplexMatrix3D
Parameters:
values - the values to be filled into the cells.
Returns:
this (for convenience only).

assignImaginary

public FComplexMatrix3D assignImaginary(FloatMatrix3D other)
Description copied from class: FComplexMatrix3D
Replaces imaginary part of the receiver with the values of another real matrix. The real part of the receiver remains unchanged. Both matrices must have the same size.

Overrides:
assignImaginary in class FComplexMatrix3D
Parameters:
other - the source matrix to copy from
Returns:
this (for convenience only).

assignReal

public FComplexMatrix3D assignReal(FloatMatrix3D other)
Description copied from class: FComplexMatrix3D
Replaces real part of the receiver with the values of another real matrix. The imaginary part of the receiver remains unchanged. Both matrices must have the same size.

Overrides:
assignReal in class FComplexMatrix3D
Parameters:
other - the source matrix to copy from
Returns:
this (for convenience only).

cardinality

public int cardinality()
Description copied from class: FComplexMatrix3D
Returns the number of cells having non-zero values; ignores tolerance.

Overrides:
cardinality in class FComplexMatrix3D
Returns:
the number of cells having non-zero values.

fft2Slices

public void fft2Slices()
Computes the 2D discrete Fourier transform (DFT) of each slice of this matrix. Throws IllegalArgumentException if the column size or a the row size of a slice is not a power of 2 number.


fft3

public void fft3()
Computes the 3D discrete Fourier transform (DFT) of this matrix. Throws IllegalArgumentException if the slice size or the row size or the column size of this matrix is not a power of 2 number.


elements

public float[] elements()
Description copied from class: FComplexMatrix3D
Returns the elements of this matrix.

Specified by:
elements in class FComplexMatrix3D
Returns:
the elements

getImaginaryPart

public FloatMatrix3D getImaginaryPart()
Description copied from class: FComplexMatrix3D
Returns the imaginary part of this matrix

Specified by:
getImaginaryPart in class FComplexMatrix3D
Returns:
the imaginary part

getNonZeros

public void getNonZeros(IntArrayList sliceList,
                        IntArrayList rowList,
                        IntArrayList columnList,
                        ArrayList<float[]> valueList)
Description copied from class: FComplexMatrix3D
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).

Overrides:
getNonZeros in class FComplexMatrix3D
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 float[] getQuick(int slice,
                        int row,
                        int column)
Description copied from class: FComplexMatrix3D
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 FComplexMatrix3D
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.

getRealPart

public FloatMatrix3D getRealPart()
Description copied from class: FComplexMatrix3D
Returns the real part of this matrix

Specified by:
getRealPart in class FComplexMatrix3D
Returns:
the real part

ifft2Slices

public void ifft2Slices(boolean scale)
Computes the 2D inverse of the discrete Fourier transform (IDFT) of each slice of this matrix. Throws IllegalArgumentException if the column size or the row size of a slice is not a power of 2 number.

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

Parameters:
scale - if true then scaling is performed

like

public FComplexMatrix3D like(int slices,
                             int rows,
                             int columns)
Description copied from class: FComplexMatrix3D
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 DenseComplexMatrix3D the new matrix must also be of type DenseComplexMatrix3D. In general, the new matrix should have internal parametrization as similar as possible.

Specified by:
like in class FComplexMatrix3D
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.

setQuick

public void setQuick(int slice,
                     int row,
                     int column,
                     float re,
                     float im)
Description copied from class: FComplexMatrix3D
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 FComplexMatrix3D
Parameters:
slice - the index of the slice-coordinate.
row - the index of the row-coordinate.
column - the index of the column-coordinate.
re - the real part of the value to be filled into the specified cell.
im - the imaginary part of the value to be filled into the specified cell.

setQuick

public void setQuick(int slice,
                     int row,
                     int column,
                     float[] value)
Description copied from class: FComplexMatrix3D
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 FComplexMatrix3D
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 float[][][] toArray()
Description copied from class: FComplexMatrix3D
Constructs and returns a 3-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 FComplexMatrix3D
Returns:
an array filled with the values of the cells.

vectorize

public FComplexMatrix1D vectorize()
Description copied from class: FComplexMatrix3D
Returns a vector obtained by stacking the columns of each slice of the matrix on top of one another.

Specified by:
vectorize in class FComplexMatrix3D
Returns:
a vector obtained by stacking the columns of each slice of the matrix on top of one another.

zSum

public float[] zSum()
Description copied from class: FComplexMatrix3D
Returns the sum of all cells; Sum( x[i,j,k] ).

Overrides:
zSum in class FComplexMatrix3D
Returns:
the sum.

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.

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