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A multidimensional, type-agnostic image processing library.
/*
* #%L
* ImgLib2: a general-purpose, multidimensional image processing library.
* %%
* Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
* John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
* Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
* Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
* Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
* Jean-Yves Tinevez and Michael Zinsmaier.
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package net.imglib2.img.sparse;
/**
* N-dimensional equivalent of a quad/oct-tree.
*
* @author Tobias Pietzsch
*/
public final class Ntree< T extends Comparable< T >>
{
public static final class NtreeNode< T >
{
private T value;
private final NtreeNode< T > parent;
private NtreeNode< T >[] children;
public NtreeNode( final NtreeNode< T > parent, final T value )
{
this.parent = parent;
this.value = value;
}
boolean hasChildren()
{
return children != null;
}
public T getValue()
{
return value;
}
public void setValue( final T value )
{
this.value = value;
}
public NtreeNode< T >[] getChildren()
{
return children;
}
public void setChildren( final NtreeNode< T >[] children )
{
this.children = children;
}
}
/**
* number of dimensions.
*/
final int n;
/**
* maximum depth of the tree.
*/
final int numTreeLevels;
/**
* how many children (if any) each node has.
*/
final int numChildren;
/**
* Root of the tree
*/
NtreeNode< T > root;
/**
* dimensions of tree
*/
final long[] dimensions;
/**
* Create a ntree structure capable of representing an array of the given
* dimensions. Initially, the tree contains only a root node and represents
* an array of uniform values.
*
* @param dimensions
* of the array
* @param value
* uniform value of all pixels in the array
*/
public Ntree( final long[] dimensions, final T value )
{
this.n = dimensions.length;
this.dimensions = dimensions.clone();
// set the maximum number of levels in the ntree.
// This is how many times to split the maximum dimension
// in half to arrive at a single pixel
long maxdim = 0;
for ( int d = 0; d < n; ++d )
maxdim = Math.max( maxdim, dimensions[ d ] );
this.numTreeLevels = ( int ) Math.ceil( Math.log( maxdim ) / Math.log( 2 ) ) + 1;
this.numChildren = 1 << n;
this.root = new NtreeNode<>( null, value );
}
/**
* helper method for the copy constructor {@link #Ntree(Ntree)} to create a
* deep copy of the tree.
*/
@SuppressWarnings( "unchecked" )
private NtreeNode< T > copyRecursively( final NtreeNode< T > node, final NtreeNode< T > newParent )
{
final NtreeNode< T > copy = new NtreeNode<>( newParent, node.getValue() );
if ( node.hasChildren() )
{
copy.children = new NtreeNode[ numChildren ];
for ( int i = 0; i < numChildren; ++i )
{
copy.children[ i ] = copyRecursively( node.children[ i ], copy );
}
}
return copy;
}
/**
* Copy constructor. Create a deep copy of ntree.
*/
Ntree( final Ntree< T > ntree )
{
dimensions = ntree.dimensions;
n = ntree.n;
numTreeLevels = ntree.numTreeLevels;
numChildren = ntree.numChildren;
root = copyRecursively( ntree.root, null );
}
/**
* Get the lowest-level node containing position. Note that position is not
* necessarily the only pixel inside the node. So use this for read-access
* to pixel values only.
*
* @param position
* a position inside the image.
* @return the lowest-level node containing position.
*/
synchronized NtreeNode< T > getNode( final long[] position )
{
NtreeNode< T > current = root;
for ( int l = numTreeLevels - 2; l >= 0; --l )
{
if ( !current.hasChildren() )
break;
final long bitmask = 1 << l;
int childindex = 0;
for ( int d = 0; d < n; ++d )
if ( ( position[ d ] & bitmask ) != 0 )
childindex |= 1 << d;
current = current.children[ childindex ];
}
return current;
}
/**
* Create a node containing only position (if it does not exist already).
* This may insert nodes at several levels in the tree.
*
* @param position
* a position inside the image.
* @return node containing exactly position.
*/
@SuppressWarnings( "unchecked" )
synchronized NtreeNode< T > createNode( final long[] position )
{
NtreeNode< T > current = root;
for ( int l = numTreeLevels - 2; l >= 0; --l )
{
if ( !current.hasChildren() )
{
current.children = new NtreeNode[ numChildren ];
for ( int i = 0; i < numChildren; ++i )
current.children[ i ] = new NtreeNode<>( current, current.getValue() );
}
final long bitmask = 1 << l;
int childindex = 0;
for ( int d = 0; d < n; ++d )
if ( ( position[ d ] & bitmask ) != 0 )
childindex |= 1 << d;
current = current.children[ childindex ];
}
return current;
}
/**
* Set the value at position and get the lowest-level node containing
* position. Note that position is not necessarily the only pixel inside the
* node, if the value matches neighboring values. If necessary, new nodes
* will be created. If possible, nodes will be merged.
*
* @param position
* a position inside the image.
* @param value
* value to store at position.
* @return node containing position.
*/
@SuppressWarnings( "unchecked" )
synchronized NtreeNode< T > createNodeWithValue( final long[] position, final T value )
{
NtreeNode< T > current = root;
for ( int l = numTreeLevels - 2; l >= 0; --l )
{
if ( !current.hasChildren() )
{
if ( current.getValue().compareTo( value ) == 0 )
return current;
current.children = new NtreeNode[ numChildren ];
for ( int i = 0; i < numChildren; ++i )
current.children[ i ] = new NtreeNode<>( current, current.getValue() );
}
final long bitmask = 1 << l;
int childindex = 0;
for ( int d = 0; d < n; ++d )
if ( ( position[ d ] & bitmask ) != 0 )
childindex |= 1 << d;
current = current.children[ childindex ];
}
if ( current.getValue().compareTo( value ) == 0 )
return current;
current.setValue( value );
return mergeUpwards( current );
}
/**
* If all the children of our parent have the same value remove them all.
* Call recursively for parent.
*
* @param node
* the starting node (whose parents should be tested
* recursively).
* @return node that the starting node was ultimately merged into.
*/
NtreeNode< T > mergeUpwards( final NtreeNode< T > node )
{
final NtreeNode< T > parent = node.parent;
if ( parent == null )
return node;
final NtreeNode< T > child0 = parent.children[ 0 ];
if ( child0.hasChildren() )
return node;
for ( int i = 1; i < numChildren; ++i )
{
final NtreeNode< T > child = parent.children[ i ];
if ( child.hasChildren() || child0.getValue().compareTo( child.getValue() ) != 0 )
return node;
}
parent.setValue( child0.getValue() );
parent.children = null;
return mergeUpwards( parent );
}
/**
* Returns the root node of the ntree
*
* @return root node
*/
public NtreeNode< T > getRootNode()
{
return root;
}
}