cern.colt.matrix.impl.SparseDoubleMatrix3D

All Implemented Interfaces:: Serializable, 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

are never set to non-zero values do not use any memory.
switch from zero to non-zero state do use memory.
switch back from non-zero to zero state also do use memory. However, their memory is automatically reclaimed from time to time. It can also manually be reclaimed by calling trimToSize().

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

is quicker than

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

Version:

1.0, 09/24/99

See Also:

Field Summary

Fields

Modifier and Type

Field

Description

protected AbstractIntDoubleMap

elements

Fields inherited from class AbstractMatrix3D
columns, columnStride, columnZero, rows, rowStride, rowZero, slices, sliceStride, sliceZero

Fields inherited from class AbstractMatrix
isNoView

Fields inherited from class PersistentObject
serialVersionUID
Constructor Summary

Constructors

Modifier

Constructor

Description

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.

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.

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.
Method Summary

Modifier and Type

Method

Description

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 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 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 AbstractMatrix
isView

Methods inherited from class PersistentObject
clone

Methods inherited from class Object
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- elements
  
  protected AbstractIntDoubleMap elements
Constructor Details
- 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:
  
  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.
- 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:
  
  IllegalArgumentException - if (double)slices*columns*rows > Integer.MAX_VALUE.
  
  IllegalArgumentException - if slicesinvalid input: '<'0 || rowsinvalid input: '<'0 || columnsinvalid input: '<'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:
  
  IllegalArgumentException - if initialCapacity invalid input: '<' 0 || (minLoadFactor invalid input: '<' 0.0 || minLoadFactor >= 1.0) || (maxLoadFactor invalid input: '<'= 0.0 || maxLoadFactor >= 1.0) || (minLoadFactor >= maxLoadFactor).
  
  IllegalArgumentException - if (double)columns*rows > Integer.MAX_VALUE.
  
  IllegalArgumentException - if slicesinvalid input: '<'0 || rowsinvalid input: '<'0 || columnsinvalid input: '<'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:
  
  IllegalArgumentException - if (double)slices*columns*rows > Integer.MAX_VALUE.
  
  IllegalArgumentException - if slicesinvalid input: '<'0 || rowsinvalid input: '<'0 || columnsinvalid input: '<'0.
Method Details
- 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:
  
  minCapacity - the desired minimum number of non-zero (non-null) cells.
  
  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
  
  are never set to non-zero values do not use any memory.
  switch from zero to non-zero state do use memory.
  switch back from non-zero to zero state also do use memory. However, their memory can be reclaimed by calling trimToSize().
  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.

Class SparseDoubleMatrix3D

Field Summary

Fields inherited from class AbstractMatrix3D

Fields inherited from class AbstractMatrix

Fields inherited from class PersistentObject

Constructor Summary

Method Summary

Methods inherited from class DoubleMatrix3D

Methods inherited from class AbstractMatrix3D

Methods inherited from class AbstractMatrix

Methods inherited from class PersistentObject

Methods inherited from class Object

Field Details

elements

Constructor Details

SparseDoubleMatrix3D

SparseDoubleMatrix3D

SparseDoubleMatrix3D

SparseDoubleMatrix3D

Method Details

assign

cardinality

ensureCapacity

getQuick

haveSharedCellsRaw

index

like

like2D

setQuick

trimToSize

viewSelectionLike