cern.colt.matrix.impl
Class SparseDoubleMatrix3D

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.SparseDoubleMatrix3D
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class SparseDoubleMatrix3D
extends DoubleMatrix3D

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

Implementation:

Note that this implementation is not synchronized. Uses a OpenIntDoubleHashMap, which is a compact and performant hashing technique.

Memory requirements:

Cells that

worst case: memory [bytes] = (1/minLoadFactor) * nonZeros * 13.
best case: memory [bytes] = (1/maxLoadFactor) * nonZeros * 13.
Where nonZeros = cardinality() is the number of non-zero cells. Thus, a 100 x 100 x 100 matrix with minLoadFactor=0.25 and maxLoadFactor=0.5 and 1000000 non-zero cells consumes between 25 MB and 50 MB. The same 100 x 100 x 100 matrix with 1000 non-zero cells consumes between 25 and 50 KB.

Time complexity:

This class offers expected time complexity O(1) (i.e. constant time) for the basic operations get, getQuick, set, setQuick and size assuming the hash function disperses the elements properly among the buckets. Otherwise, pathological cases, although highly improbable, can occur, degrading performance to O(N) in the worst case. As such this sparse class is expected to have no worse time complexity than its dense counterpart DenseDoubleMatrix2D. However, constant factors are considerably larger.

Cells are internally addressed in (in decreasing order of significance): slice major, row major, column major. Applications demanding utmost speed can exploit this fact. 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:
cern.colt.map, OpenIntDoubleHashMap, Serialized Form

Field Summary
protected  AbstractIntDoubleMap elements
           
 
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
  SparseDoubleMatrix3D(double[][][] values)
          Constructs a matrix with a copy of the given values.
  SparseDoubleMatrix3D(int slices, int rows, int columns)
          Constructs a matrix with a given number of slices, rows and columns and default memory usage.
protected SparseDoubleMatrix3D(int slices, int rows, int columns, AbstractIntDoubleMap elements, int sliceZero, int rowZero, int columnZero, int sliceStride, int rowStride, int columnStride)
          Constructs a view with the given parameters.
  SparseDoubleMatrix3D(int slices, int rows, int columns, int initialCapacity, double minLoadFactor, double maxLoadFactor)
          Constructs a matrix with a given number of slices, rows and columns using memory as specified.
 
Method Summary
 DoubleMatrix3D assign(double value)
          Sets all cells to the state specified by value.
 int cardinality()
          Returns the number of cells having non-zero values.
 void ensureCapacity(int minCapacity)
          Ensures that the receiver can hold at least the specified number of non-zero cells without needing to allocate new internal memory.
 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 at least one identical cell.
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.
 void trimToSize()
          Releases any superfluous memory created by explicitly putting zero values into cells formerly having non-zero values; An application can use this operation to minimize the storage of the receiver.
protected  DoubleMatrix3D viewSelectionLike(int[] sliceOffsets, int[] rowOffsets, int[] columnOffsets)
          Construct and returns a new selection view.
 
Methods inherited from class cern.colt.matrix.DoubleMatrix3D
aggregate, aggregate, assign, assign, assign, assign, copy, equals, equals, get, getContent, getNonZeros, haveSharedCells, like, set, toArray, toString, view, viewColumn, viewColumnFlip, viewDice, viewPart, viewRow, viewRowFlip, viewSelection, viewSelection, viewSlice, viewSliceFlip, viewSorted, viewStrides, zAssign27Neighbors, 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
isView
 
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 AbstractIntDoubleMap elements
Constructor Detail

SparseDoubleMatrix3D

public SparseDoubleMatrix3D(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.

SparseDoubleMatrix3D

public SparseDoubleMatrix3D(int slices,
                            int rows,
                            int columns)
Constructs a matrix with a given number of slices, rows and columns and default memory usage. 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.

SparseDoubleMatrix3D

public SparseDoubleMatrix3D(int slices,
                            int rows,
                            int columns,
                            int initialCapacity,
                            double minLoadFactor,
                            double maxLoadFactor)
Constructs a matrix with a given number of slices, rows and columns using memory as specified. All entries are initially 0. For details related to memory usage see OpenIntDoubleHashMap.

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.
initialCapacity - the initial capacity of the hash map. If not known, set initialCapacity=0 or small.
minLoadFactor - the minimum load factor of the hash map.
maxLoadFactor - the maximum load factor of the hash map.
Throws:
java.lang.IllegalArgumentException - if initialCapacity < 0 || (minLoadFactor < 0.0 || minLoadFactor >= 1.0) || (maxLoadFactor <= 0.0 || maxLoadFactor >= 1.0) || (minLoadFactor >= maxLoadFactor).
java.lang.IllegalArgumentException - if (double)columns*rows > Integer.MAX_VALUE.
java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.

SparseDoubleMatrix3D

protected SparseDoubleMatrix3D(int slices,
                               int rows,
                               int columns,
                               AbstractIntDoubleMap 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 value)
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).

cardinality

public int cardinality()
Returns the number of cells having non-zero values.

Overrides:
cardinality in class DoubleMatrix3D

ensureCapacity

public void ensureCapacity(int minCapacity)
Ensures that the receiver can hold at least the specified number of non-zero cells without needing to allocate new internal memory. If necessary, allocates new internal memory and increases the capacity of the receiver.

This method never need be called; it is for performance tuning only. Calling this method before tt>set()ing a large number of non-zero values boosts performance, because the receiver will grow only once instead of potentially many times and hash collisions get less probable.

Overrides:
ensureCapacity in class AbstractMatrix
Parameters:
minNonZeros - the desired minimum number of non-zero cells.

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 at least one identical cell.

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.

trimToSize

public void trimToSize()
Releases any superfluous memory created by explicitly putting zero values into cells formerly having non-zero values; An application can use this operation to minimize the storage of the receiver.

Background:

Cells that

A sequence like set(s,r,c,5); set(s,r,c,0); sets a cell to non-zero state and later back to zero state. Such as sequence generates obsolete memory that is automatically reclaimed from time to time or can manually be reclaimed by calling trimToSize(). Putting zeros into cells already containing zeros does not generate obsolete memory since no memory was allocated to them in the first place.

Overrides:
trimToSize in class AbstractMatrix

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.