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Postpone Cell linking to CellRandomAccess.get() #329

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merged 3 commits into from
Feb 11, 2023
Merged

Postpone Cell linking to CellRandomAccess.get() #329

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4aacdb9
fix typos
tpietzsch Feb 6, 2023
6e1b138
Postpone Cell linking to CellRandomAccess.get()
tpietzsch Feb 6, 2023
c2e7570
Do not duplicate type index for CellRandomAccess
tpietzsch Feb 8, 2023
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2 changes: 1 addition & 1 deletion src/main/java/net/imglib2/img/cell/Cell.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ public Cell( final int[] dimensions, final long[] min, final A data )
}

/**
* Get the basic type array that stores this cells pixels.
* Get the basic type array that stores this cell's pixels.
*
* @return underlying basic type array.
*/
Expand Down
32 changes: 31 additions & 1 deletion src/main/java/net/imglib2/img/cell/CellGrid.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,13 @@
package net.imglib2.img.cell;

import java.util.Arrays;
import java.util.Iterator;

import net.imglib2.Cursor;
import net.imglib2.FinalInterval;
import net.imglib2.FlatIterationOrder;
import net.imglib2.Interval;
import net.imglib2.IterableInterval;
import net.imglib2.Localizable;
import net.imglib2.Point;
import net.imglib2.Positionable;
import net.imglib2.RandomAccess;
Expand Down Expand Up @@ -337,6 +337,36 @@ public void getCellPosition( final long[] position, final Positionable cellPos )
cellPos.setPosition( position[ d ] / cellDimensions[ d ], d );
}

/**
* Compute all cell-related coordinates/sizes required by CellRandomAccess.
*
* @param position
* current image position
* @param cellSteps
* allocation steps for cell are written here.
* @param cellMin
* offset of the cell in image coordinates are written here.
* @param cellMax is set to the
* max of the cell in image coordinates are written here.
* @return index within the cell.
*/
int getCellCoordinates( final long[] position, final int[] cellSteps, final long[] cellMin, final long[] cellMax )
{
int steps = 1;
int i = 0;
for ( int d = 0; d < n; ++d )
{
final long gridPos = position[ d ] / cellDimensions[ d ];
final int cellDim = ( gridPos + 1 == numCells[ d ] ) ? borderSize[ d ] : cellDimensions[ d ];
cellMin[ d ] = gridPos * cellDimensions[ d ];
cellMax[ d ] = cellMin[ d ] + cellDim - 1;
cellSteps[ d ] = steps;
i += steps * ( position[ d ] - cellMin[ d ] );
steps *= cellDim;
}
return i;
}

@Override
public int hashCode()
{
Expand Down
100 changes: 36 additions & 64 deletions src/main/java/net/imglib2/img/cell/CellRandomAccess.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@

package net.imglib2.img.cell;

import java.util.Arrays;
import net.imglib2.AbstractLocalizable;
import net.imglib2.Localizable;
import net.imglib2.RandomAccess;
Expand Down Expand Up @@ -64,23 +65,15 @@ public class CellRandomAccess< T extends NativeType< T >, C extends Cell< ? > >

protected final long[] dimensions;

protected int[] currentCellSteps;
protected final int[] currentCellSteps;

protected long[] currentCellMin;
protected final long[] currentCellMin;

protected long[] currentCellMax;
protected final long[] currentCellMax;

protected boolean isOutOfBounds;

protected final long[] oobCellMin;

protected final long[] oobCellMax;

/**
* The current index of the type. It is faster to duplicate this here than
* to access it through type.getIndex().
*/
protected int index;
private boolean typeNeedsUpdate;

protected CellRandomAccess( final CellRandomAccess< T, C > randomAccess )
{
Expand All @@ -95,18 +88,14 @@ protected CellRandomAccess( final CellRandomAccess< T, C > randomAccess )

cellDims = randomAccess.cellDims;
dimensions = randomAccess.dimensions;
currentCellSteps = randomAccess.currentCellSteps;
currentCellMin = randomAccess.currentCellMin;
currentCellMax = randomAccess.currentCellMax;
currentCellSteps = randomAccess.currentCellSteps.clone();
currentCellMin = randomAccess.currentCellMin.clone();
currentCellMax = randomAccess.currentCellMax.clone();

isOutOfBounds = randomAccess.isOutOfBounds;
oobCellMin = randomAccess.oobCellMin;
oobCellMax = randomAccess.oobCellMax;

index = randomAccess.index;
if ( !isOutOfBounds )
type.updateContainer( this );
typeIndex.set( index );
typeIndex.set( randomAccess.typeIndex.get() );
typeNeedsUpdate = true;
}

public CellRandomAccess( final AbstractCellImg< T, ?, C, ? > img )
Expand All @@ -123,14 +112,11 @@ public CellRandomAccess( final AbstractCellImg< T, ?, C, ? > img )
img.getCellGrid().cellDimensions( cellDims );
img.getCellGrid().imgDimensions( dimensions );

currentCellSteps = new int[ n ];
currentCellMin = new long[ n ];
currentCellMax = new long[ n ];

isOutOfBounds = false;
oobCellMin = new long[ n ];
oobCellMax = new long[ n ];
for ( int d = 0; d < n; ++d )
{
oobCellMin[ d ] = Long.MAX_VALUE;
oobCellMax[ d ] = Long.MIN_VALUE;
}

img.getCellGrid().getCellPosition( position, randomAccessOnCells );
updatePosition( false );
Expand All @@ -145,6 +131,11 @@ public C getCell()
@Override
public T get()
{
if ( typeNeedsUpdate )
{
typeNeedsUpdate = false;
type.updateContainer( this );
}
return type;
}

Expand All @@ -157,51 +148,47 @@ public CellRandomAccess< T, C > copy()
@Override
public void fwd( final int d )
{
index += currentCellSteps[ d ];
typeIndex.inc( currentCellSteps[ d ] );
if ( ++position[ d ] > currentCellMax[ d ] )
{
randomAccessOnCells.fwd( d );
updatePosition( position[ d ] >= dimensions[ d ] );
}
typeIndex.set( index );
}

@Override
public void bck( final int d )
{
index -= currentCellSteps[ d ];
typeIndex.dec( currentCellSteps[ d ] );
if ( --position[ d ] < currentCellMin[ d ] )
{
randomAccessOnCells.bck( d );
updatePosition( position[ d ] < 0 );
}
typeIndex.set( index );
}

@Override
public void move( final int distance, final int d )
{
index += distance * currentCellSteps[ d ];
typeIndex.inc( distance * currentCellSteps[ d ] );
position[ d ] += distance;
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
randomAccessOnCells.setPosition( position[ d ] / cellDims[ d ], d );
updatePosition( position[ d ] < 0 || position[ d ] >= dimensions[ d ] );
}
typeIndex.set( index );
}

@Override
public void move( final long distance, final int d )
{
index += ( int ) distance * currentCellSteps[ d ];
typeIndex.inc( ( int ) distance * currentCellSteps[ d ] );
position[ d ] += distance;
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
randomAccessOnCells.setPosition( position[ d ] / cellDims[ d ], d );
updatePosition( position[ d ] < 0 || position[ d ] >= dimensions[ d ] );
}
typeIndex.set( index );
}

@Override
Expand All @@ -212,7 +199,7 @@ public void move( final Localizable localizable )
final long pos = localizable.getLongPosition( d );
if ( pos != 0 )
{
index += ( int ) pos * currentCellSteps[ d ];
typeIndex.inc( ( int ) pos * currentCellSteps[ d ] );
position[ d ] += pos;
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
Expand All @@ -237,7 +224,6 @@ public void move( final Localizable localizable )
}
}
}
typeIndex.set( index );
}

@Override
Expand All @@ -247,7 +233,7 @@ public void move( final int[] distance )
{
if ( distance[ d ] != 0 )
{
index += distance[ d ] * currentCellSteps[ d ];
typeIndex.inc( distance[ d ] * currentCellSteps[ d ] );
position[ d ] += distance[ d ];
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
Expand All @@ -271,7 +257,6 @@ public void move( final int[] distance )
}
}
}
typeIndex.set( index );
}

@Override
Expand All @@ -281,7 +266,7 @@ public void move( final long[] distance )
{
if ( distance[ d ] != 0 )
{
index += ( int ) distance[ d ] * currentCellSteps[ d ];
typeIndex.inc( ( int ) distance[ d ] * currentCellSteps[ d ] );
position[ d ] += distance[ d ];
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
Expand All @@ -305,33 +290,30 @@ public void move( final long[] distance )
}
}
}
typeIndex.set( index );
}

@Override
public void setPosition( final int pos, final int d )
{
index += ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ];
typeIndex.inc( ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ] );
position[ d ] = pos;
if ( pos < currentCellMin[ d ] || pos > currentCellMax[ d ] )
{
randomAccessOnCells.setPosition( pos / cellDims[ d ], d );
updatePosition( position[ d ] < 0 || position[ d ] >= dimensions[ d ] );
}
typeIndex.set( index );
}

@Override
public void setPosition( final long pos, final int d )
{
index += ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ];
typeIndex.inc( ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ] );
position[ d ] = pos;
if ( pos < currentCellMin[ d ] || pos > currentCellMax[ d ] )
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
randomAccessOnCells.setPosition( pos / cellDims[ d ], d );
updatePosition( position[ d ] < 0 || position[ d ] >= dimensions[ d ] );
}
typeIndex.set( index );
}

@Override
Expand All @@ -342,7 +324,7 @@ public void setPosition( final Localizable localizable )
final long pos = localizable.getLongPosition( d );
if ( pos != position[ d ] )
{
index += ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ];
typeIndex.inc( ( int ) ( pos - position[ d ] ) * currentCellSteps[ d ] );
position[ d ] = pos;
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
Expand All @@ -367,7 +349,6 @@ public void setPosition( final Localizable localizable )
}
}
}
typeIndex.set( index );
}

@Override
Expand All @@ -377,7 +358,7 @@ public void setPosition( final int[] pos )
{
if ( pos[ d ] != position[ d ] )
{
index += ( int ) ( pos[ d ] - position[ d ] ) * currentCellSteps[ d ];
typeIndex.inc( ( int ) ( pos[ d ] - position[ d ] ) * currentCellSteps[ d ] );
if ( pos[ d ] < currentCellMin[ d ] || pos[ d ] > currentCellMax[ d ] )
{
setPos2( pos, d );
Expand All @@ -386,7 +367,6 @@ public void setPosition( final int[] pos )
position[ d ] = pos[ d ];
}
}
typeIndex.set( index );
}

private void setPos2( final int[] pos, final int d0 )
Expand Down Expand Up @@ -414,7 +394,7 @@ public void setPosition( final long[] pos )
{
if ( pos[ d ] != position[ d ] )
{
index += ( int ) ( pos[ d ] - position[ d ] ) * currentCellSteps[ d ];
typeIndex.inc( ( int ) ( pos[ d ] - position[ d ] ) * currentCellSteps[ d ] );
position[ d ] = pos[ d ];
if ( position[ d ] < currentCellMin[ d ] || position[ d ] > currentCellMax[ d ] )
{
Expand All @@ -438,7 +418,6 @@ public void setPosition( final long[] pos )
}
}
}
typeIndex.set( index );
}

/**
Expand All @@ -452,8 +431,8 @@ private void updatePosition( final boolean movedOutOfBounds )
if ( movedOutOfBounds )
{
isOutOfBounds = true;
currentCellMin = oobCellMin;
currentCellMax = oobCellMax;
Arrays.fill( currentCellMin, Long.MAX_VALUE );
Arrays.fill( currentCellMax, Long.MIN_VALUE );
}
else
{
Expand All @@ -470,15 +449,8 @@ private void updatePosition( final boolean movedOutOfBounds )
isOutOfBounds = false;
grid.getCellPosition( position, randomAccessOnCells );
}

final C cell = getCell();

currentCellSteps = cell.steps;
currentCellMin = cell.min;
currentCellMax = cell.max;

index = cell.globalPositionToIndex( position );
type.updateContainer( this );
typeIndex.set( grid.getCellCoordinates( position, currentCellSteps, currentCellMin, currentCellMax ) );
typeNeedsUpdate = true;
}
}
}
2 changes: 1 addition & 1 deletion src/main/java/net/imglib2/img/cell/LazyCellImg.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
/**
* A {@link AbstractCellImg} that obtains its Cells lazily when they are
* accessed. Cells are obtained by a {@link Get} method that is provided by the
* user. Typically this is some kind of cache.
* user. Typically, this is some kind of cache.
*
* @param <T>
* the pixel type
Expand Down