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Merge pull request #309 from imglib/grid
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@tpietzsch
tpietzsch authored Feb 24, 2022
2 parents c1d225f + ae1c8c2 commit 9ae38fb
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Showing 4 changed files with 912 additions and 20 deletions.
199 changes: 179 additions & 20 deletions 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 @@ -35,9 +35,20 @@

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.Point;
import net.imglib2.Positionable;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.util.IntervalIndexer;
import net.imglib2.util.Intervals;
import net.imglib2.util.Util;
import net.imglib2.view.RandomAccessibleIntervalCursor;

/**
* Defines {@link AbstractCellImg} geometry and translates between image, cell,
Expand All @@ -59,6 +70,13 @@ public class CellGrid

private final int hashcode;

/**
* @param dimensions
* the dimensions of the image (in pixels, not in cells).
* @param cellDimensions
* the dimensions of a standard cell (in pixels). Cells on the max border
* of the image may be cut off and have different dimensions.
*/
public CellGrid(
final long[] dimensions,
final int[] cellDimensions )
Expand All @@ -75,6 +93,8 @@ public CellGrid(
borderSize[ d ] = ( int ) ( dimensions[ d ] - ( numCells[ d ] - 1 ) * cellDimensions[ d ] );
}
hashcode = 31 * Arrays.hashCode( dimensions ) + Arrays.hashCode( cellDimensions );

cellIntervals = new CellIntervals();
}

public CellGrid( final CellGrid grid )
Expand All @@ -85,24 +105,35 @@ public CellGrid( final CellGrid grid )
numCells = grid.numCells.clone();
borderSize = grid.borderSize.clone();
hashcode = grid.hashcode;
cellIntervals = new CellIntervals();
}

public int numDimensions()
{
return n;
}

/**
* Get the number of cells in each dimension as a new long[].
*/
public long[] getGridDimensions()
{
return numCells.clone();
}

public void gridDimensions( final long[] s )
/**
* Write the number of cells in each dimension into the provided {@code
* dimensions} array.
*/
public void gridDimensions( final long[] dimensions )
{
for ( int i = 0; i < n; ++i )
s[ i ] = numCells[ i ];
dimensions[ i ] = numCells[ i ];
}

/**
* Get the number of cells in dimension {@code d}.
*/
public long gridDimension( final int d )
{
return numCells[ d ];
Expand All @@ -118,10 +149,9 @@ public long[] getImgDimensions()
}

/**
* Write the number of pixels in each dimension into long[]. Note, that this
* is the number of pixels in all cells combined, not the number of cells!
*
* @param dimensions
* Write the number of pixels in each dimension into the provided {@code
* dimensions} array. Note, that this is the number of pixels in all cells
* combined, not the number of cells!
*/
public void imgDimensions( final long[] dimensions )
{
Expand All @@ -130,22 +160,27 @@ public void imgDimensions( final long[] dimensions )
}

/**
* Get the number of pixels in a given dimension <em>d</em>. Note, that this
* is the number of pixels in all cells combined, not the number of cells!
*
* @param d
* Get the number of pixels in dimension {@code d}. Note, that this is the number
* of pixels in all cells combined, not the number of cells!
*/
public long imgDimension( final int d )
{
return dimensions[ d ];
}

/**
* Write the number of pixels in a standard cell in each dimension into
* long[]. Cells on the max border of the image may be cut off and have
* different dimensions.
*
* @param dimensions
* Get the number of pixels in a standard cell in each dimension as a new int[].
* Cells on the borders of the image may be cut off and have different dimensions.
*/
public int[] getCellDimensions()
{
return cellDimensions.clone();
}

/**
* Write the number of pixels in a standard cell in each dimension into the
* provided {@code dimensions} array. Cells on the max border of the image may be
* cut off and have different dimensions.
*/
public void cellDimensions( final int[] dimensions )
{
Expand All @@ -154,11 +189,8 @@ public void cellDimensions( final int[] dimensions )
}

/**
* Get the number of pixels in a standard cell in a given dimension
* <em>d</em>. Cells on the max border of the image may be cut off and have
* different dimensions.
*
* @param d
* Get the number of pixels in a standard cell in dimension {@code d}. Cells on the
* max border of the image may be cut off and have different dimensions.
*/
public int cellDimension( final int d )
{
Expand Down Expand Up @@ -219,6 +251,17 @@ public void getCellDimensions( final long[] cellGridPosition, final long[] cellM
}
}

public void getCellInterval( final long[] cellGridPosition, final long[] cellMin, final long[] cellMax )
{
for ( int d = 0; d < n; ++d )
{
final long gridPos = cellGridPosition[ d ];
final int cellDim = ( gridPos + 1 == numCells[ d ] ) ? borderSize[ d ] : cellDimensions[ d ];
cellMin[ d ] = gridPos * cellDimensions[ d ];
cellMax[ d ] = cellMin[ d ] + cellDim - 1;
}
}

/**
* From the position of a cell in the grid, compute the size of the cell in
* dimension {@code d}. The size will be the standard
Expand Down Expand Up @@ -319,4 +362,120 @@ public String toString()
+ "( dims = " + Util.printCoordinates( dimensions )
+ ", cellDims = " + Util.printCoordinates( cellDimensions ) + " )";
}

private class CellIntervalsRA extends Point implements RandomAccess< Interval >
{
private final long[] min = new long[ CellGrid.this.n ];

private final long[] max = new long[ CellGrid.this.n ];

private final Interval interval = FinalInterval.wrap( min, max );

@Override
public Interval get()
{
getCellInterval( position, min, max );
return interval;
}

CellIntervalsRA()
{
super( CellGrid.this.n );
}

CellIntervalsRA( CellIntervalsRA ra )
{
super( ra );
}

@Override
public RandomAccess< Interval > copyRandomAccess()
{
return copy();
}

@Override
public RandomAccess< Interval > copy()
{
return new CellIntervalsRA( this );
}
}

public class CellIntervals implements RandomAccessibleInterval< Interval >, IterableInterval< Interval >
{
private final long size = Intervals.numElements( numCells );

@Override
public int numDimensions()
{
return n;
}

@Override
public long min( final int d )
{
return 0;
}

@Override
public long max( final int d )
{
return numCells[ d ] - 1;
}

@Override
public RandomAccess< Interval > randomAccess()
{
return new CellIntervalsRA();
}

@Override
public RandomAccess< Interval > randomAccess( final Interval interval )
{
return randomAccess();
}

@Override
public Cursor< Interval > cursor()
{
return new RandomAccessibleIntervalCursor<>( this );
}

@Override
public Cursor< Interval > localizingCursor()
{
return cursor();
}

@Override
public long size()
{
return size;
}

@Override
public Interval firstElement()
{
return cursor().next();
}

@Override
public FlatIterationOrder iterationOrder()
{
return new FlatIterationOrder( this );
}

@Override
public Iterator< Interval > iterator()
{
return cursor();
}
}

private final CellIntervals cellIntervals;

public CellIntervals cellIntervals()
{
return cellIntervals;
}
}
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