cern.colt.matrix.impl
Class SparseObjectMatrix3D

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.ObjectMatrix3D
                  extended by cern.colt.matrix.impl.SparseObjectMatrix3D
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class SparseObjectMatrix3D
extends ObjectMatrix3D

Sparse hashed 3-d matrix holding Object 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 OpenIntObjectHashMap, 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 DenseObjectMatrix2D. 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, OpenIntObjectHashMap, Serialized Form

Field Summary
protected  AbstractIntObjectMap 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
  SparseObjectMatrix3D(int slices, int rows, int columns)
          Constructs a matrix with a given number of slices, rows and columns and default memory usage.
protected SparseObjectMatrix3D(int slices, int rows, int columns, AbstractIntObjectMap elements, int sliceZero, int rowZero, int columnZero, int sliceStride, int rowStride, int columnStride)
          Constructs a view with the given parameters.
  SparseObjectMatrix3D(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.
  SparseObjectMatrix3D(java.lang.Object[][][] values)
          Constructs a matrix with a copy of the given values.
 
Method Summary
 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.
 java.lang.Object getQuick(int slice, int row, int column)
          Returns the matrix cell value at coordinate [slice,row,column].
protected  boolean haveSharedCellsRaw(ObjectMatrix3D 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.
 ObjectMatrix3D 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  ObjectMatrix2D 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, java.lang.Object 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  ObjectMatrix3D viewSelectionLike(int[] sliceOffsets, int[] rowOffsets, int[] columnOffsets)
          Construct and returns a new selection view.
 
Methods inherited from class cern.colt.matrix.ObjectMatrix3D
aggregate, aggregate, assign, 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
 
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 AbstractIntObjectMap elements
Constructor Detail

SparseObjectMatrix3D

public SparseObjectMatrix3D(java.lang.Object[][][] 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.

SparseObjectMatrix3D

public SparseObjectMatrix3D(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 null.

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.

SparseObjectMatrix3D

public SparseObjectMatrix3D(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 null. For details related to memory usage see OpenIntObjectHashMap.

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)slices*columns*rows > Integer.MAX_VALUE.
java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.

SparseObjectMatrix3D

protected SparseObjectMatrix3D(int slices,
                               int rows,
                               int columns,
                               AbstractIntObjectMap 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 (Object)slices*columns*rows > Integer.MAX_VALUE.
java.lang.IllegalArgumentException - if slices<0 || rows<0 || columns<0.
Method Detail

cardinality

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

Overrides:
cardinality in class ObjectMatrix3D

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 java.lang.Object 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 ObjectMatrix3D
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(ObjectMatrix3D other)
Returns true if both matrices share at least one identical cell.

Overrides:
haveSharedCellsRaw in class ObjectMatrix3D

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 ObjectMatrix3D 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 DenseObjectMatrix3D the new matrix must also be of type DenseObjectMatrix3D, if the receiver is an instance of type SparseObjectMatrix3D the new matrix must also be of type SparseObjectMatrix3D, etc. In general, the new matrix should have internal parametrization as similar as possible.

Specified by:
like in class ObjectMatrix3D
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 ObjectMatrix2D 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 DenseObjectMatrix3D the new matrix must also be of type DenseObjectMatrix2D, if the receiver is an instance of type SparseObjectMatrix3D the new matrix must also be of type SparseObjectMatrix2D, etc.

Specified by:
like2D in class ObjectMatrix3D
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,
                     java.lang.Object 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 ObjectMatrix3D
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 ObjectMatrix3D viewSelectionLike(int[] sliceOffsets,
                                           int[] rowOffsets,
                                           int[] columnOffsets)
Construct and returns a new selection view.

Specified by:
viewSelectionLike in class ObjectMatrix3D
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.