cern.colt.matrix.impl
Class DenseDoubleMatrix3D

java.lang.Object
  extended by cern.colt.PersistentObject
      extended by cern.colt.matrix.impl.AbstractMatrix
          extended by cern.colt.matrix.impl.AbstractMatrix3D
              extended by cern.colt.matrix.DoubleMatrix3D
                  extended by cern.colt.matrix.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 contigous one-dimensional array, addressed in (in decreasing order of significance): slice major, row major, column major. Note that this implementation is not synchronized.

Memory requirements:

memory [bytes] = 8*slices()*rows()*columns(). Thus, a 100*100*100 matrix uses 8 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:
wolfgang.hoschek@cern.ch
See Also:
Serialized Form

Field Summary
protected  double[] elements
          The elements of this matrix.
 
Fields inherited from class cern.colt.matrix.impl.AbstractMatrix3D
columns, columnStride, columnZero, rows, rowStride, rowZero, slices, sliceStride, sliceZero
 
Fields inherited from class cern.colt.matrix.impl.AbstractMatrix
isNoView
 
Fields inherited from class cern.colt.PersistentObject
serialVersionUID
 
Constructor Summary
  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.
protected DenseDoubleMatrix3D(int slices, int rows, int columns, double[] elements, int sliceZero, int rowZero, int columnZero, int sliceStride, int rowStride, int columnStride)
          Constructs a view with the given parameters.
 
Method Summary
 DoubleMatrix3D assign(double[][][] values)
          Sets all cells to the state specified by values.
 DoubleMatrix3D assign(DoubleMatrix3D source)
          Replaces all cell values of the receiver with the values of another matrix.
 double getQuick(int slice, int row, int column)
          Returns the matrix cell value at coordinate [slice,row,column].
protected  boolean haveSharedCellsRaw(DoubleMatrix3D other)
          Returns true if both matrices share common cells.
protected  int 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.
protected  DoubleMatrix2D like2D(int rows, int columns, int rowZero, int columnZero, int rowStride, int columnStride)
          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.
protected  DoubleMatrix3D viewSelectionLike(int[] sliceOffsets, int[] rowOffsets, int[] columnOffsets)
          Construct and returns a new selection view.
 void zAssign27Neighbors(DoubleMatrix3D B, Double27Function function)
          27 neighbor stencil transformation.
 
Methods inherited from class cern.colt.matrix.DoubleMatrix3D
aggregate, aggregate, assign, assign, assign, cardinality, copy, equals, equals, get, getContent, getNonZeros, haveSharedCells, like, set, toArray, toString, view, viewColumn, viewColumnFlip, viewDice, viewPart, viewRow, viewRowFlip, viewSelection, viewSelection, viewSlice, viewSliceFlip, viewSorted, viewStrides, zSum
 
Methods inherited from class cern.colt.matrix.impl.AbstractMatrix3D
_columnOffset, _columnRank, _rowOffset, _rowRank, _sliceOffset, _sliceRank, checkBox, checkColumn, checkColumnIndexes, checkRow, checkRowIndexes, checkShape, checkShape, checkSlice, checkSliceIndexes, columns, rows, setUp, setUp, shape, size, slices, toStringShort, vColumnFlip, vDice, vPart, vRowFlip, vSliceFlip, vStrides
 
Methods inherited from class cern.colt.matrix.impl.AbstractMatrix
ensureCapacity, isView, trimToSize
 
Methods inherited from class cern.colt.PersistentObject
clone
 
Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

elements

protected double[] elements
The elements of this matrix. elements are stored in slice major, then row major, then column major, in order of significance, i.e. index==slice*sliceStride+ row*rowStride + column*columnStride i.e. {slice0 row0..m}, {slice1 row0..m}, ..., {sliceN row0..m} with each row storead as {row0 column0..m}, {row1 column0..m}, ..., {rown column0..m}

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

protected DenseDoubleMatrix3D(int slices,
                              int rows,
                              int columns,
                              double[] 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).
columnnStride - the number of elements between two columns, i.e. index(k,i,j+1)-index(k,i,j).
Throws:
java.lang.IllegalArgumentException - if (double)slices*columns*rows > Integer.MAX_VALUE.
java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.
Method Detail

assign

public DoubleMatrix3D assign(double[][][] values)
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).
Throws:
java.lang.IllegalArgumentException - if values.length != slices() || for any 0 <= slice < slices(): values[slice].length != rows().
java.lang.IllegalArgumentException - if for any 0 <= column < columns(): values[slice][row].length != columns().

assign

public DoubleMatrix3D assign(DoubleMatrix3D source)
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).
Throws:
java.lang.IllegalArgumentException - if slices() != source.slices() || rows() != source.rows() || columns() != source.columns()

getQuick

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

haveSharedCellsRaw

protected boolean haveSharedCellsRaw(DoubleMatrix3D other)
Returns true if both matrices share common cells. More formally, returns true if other != null and at least one of the following conditions is met

Overrides:
haveSharedCellsRaw in class DoubleMatrix3D

index

protected int index(int slice,
                    int row,
                    int column)
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)
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

protected DoubleMatrix2D like2D(int rows,
                                int columns,
                                int rowZero,
                                int columnZero,
                                int rowStride,
                                int columnStride)
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.
rowZero - the position of the first element.
columnZero - the position of the first element.
rowStride - the number of elements between two rows, i.e. index(i+1,j)-index(i,j).
columnStride - the number of elements between two columns, i.e. index(i,j+1)-index(i,j).
Returns:
a new matrix of the corresponding dynamic type.

setQuick

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

viewSelectionLike

protected DoubleMatrix3D viewSelectionLike(int[] sliceOffsets,
                                           int[] rowOffsets,
                                           int[] columnOffsets)
Construct and returns a new selection view.

Specified by:
viewSelectionLike in class DoubleMatrix3D
Parameters:
sliceOffsets - the offsets of the visible elements.
rowOffsets - the offsets of the visible elements.
columnOffsets - the offsets of the visible elements.
Returns:
a new view.

zAssign27Neighbors

public void zAssign27Neighbors(DoubleMatrix3D B,
                               Double27Function function)
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.
Throws:
java.lang.NullPointerException - if function==null.
java.lang.IllegalArgumentException - if rows() != B.rows() || columns() != B.columns() || slices() != B.slices() .