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Temp fix for the removal of N5CellLoader in recent n5-imglib2
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@tinevez
tinevez committed Oct 17, 2024
1 parent 2a90bea commit 01d532a
Showing 1 changed file with 243 additions and 76 deletions.
319 changes: 243 additions & 76 deletions src/main/java/org/mastodon/mamut/io/loader/util/mobie/ArrayCreator.java
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import org.janelia.saalfeldlab.n5.DataBlock;
import org.janelia.saalfeldlab.n5.DataType;
import org.janelia.saalfeldlab.n5.imglib2.N5CellLoader;
import org.jetbrains.annotations.NotNull;

import net.imglib2.Cursor;
import net.imglib2.FinalInterval;
import net.imglib2.Interval;
import net.imglib2.IterableInterval;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.basictypeaccess.volatiles.array.VolatileByteArray;
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import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
import net.imglib2.img.cell.CellGrid;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.integer.GenericByteType;
import net.imglib2.type.numeric.integer.GenericIntType;
import net.imglib2.type.numeric.integer.GenericLongType;
import net.imglib2.type.numeric.integer.GenericShortType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Cast;
import net.imglib2.util.Intervals;
import net.imglib2.view.IntervalView;
import net.imglib2.view.Views;

public abstract class ArrayCreator< A, T extends NativeType< T > >
{
protected final CellGrid cellGrid;
protected final CellGrid cellGrid;

protected final DataType dataType;
protected final DataType dataType;

protected final BiConsumer< ArrayImg< T, ? >, DataBlock< ? > > copyFromBlock;
protected final BiConsumer< ArrayImg< T, ? >, DataBlock< ? > > copyFromBlock;

public ArrayCreator( final CellGrid cellGrid, final DataType dataType )
{
this.cellGrid = cellGrid;
this.dataType = dataType;
this.copyFromBlock = N5CellLoader.createCopy( dataType );
}
public ArrayCreator( final CellGrid cellGrid, final DataType dataType )
{
this.cellGrid = cellGrid;
this.dataType = dataType;
this.copyFromBlock = createCopy( dataType );
}

@SuppressWarnings( "unchecked" )
@NotNull
public A VolatileDoubleArray( final DataBlock< ? > dataBlock, final long[] cellDims, final int n )
{
switch ( dataType )
{
case UINT8:
case INT8:
final byte[] bytes = new byte[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.bytes( bytes, cellDims ) ), dataBlock );
return ( A ) new VolatileByteArray( bytes, true );
case UINT16:
case INT16:
final short[] shorts = new short[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.shorts( shorts, cellDims ) ), dataBlock );
return ( A ) new VolatileShortArray( shorts, true );
case UINT32:
case INT32:
final int[] ints = new int[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.ints( ints, cellDims ) ), dataBlock );
return ( A ) new VolatileIntArray( ints, true );
case UINT64:
case INT64:
final long[] longs = new long[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.longs( longs, cellDims ) ), dataBlock );
return ( A ) new VolatileLongArray( longs, true );
case FLOAT32:
final float[] floats = new float[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.floats( floats, cellDims ) ), dataBlock );
return ( A ) new VolatileFloatArray( floats, true );
case FLOAT64:
final double[] doubles = new double[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.doubles( doubles, cellDims ) ), dataBlock );
return ( A ) new VolatileDoubleArray( doubles, true );
default:
throw new IllegalArgumentException();
}
}
public A VolatileDoubleArray( final DataBlock< ? > dataBlock, final long[] cellDims, final int n )
{
switch ( dataType )
{
case UINT8:
case INT8:
final byte[] bytes = new byte[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.bytes( bytes, cellDims ) ), dataBlock );
return ( A ) new VolatileByteArray( bytes, true );
case UINT16:
case INT16:
final short[] shorts = new short[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.shorts( shorts, cellDims ) ), dataBlock );
return ( A ) new VolatileShortArray( shorts, true );
case UINT32:
case INT32:
final int[] ints = new int[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.ints( ints, cellDims ) ), dataBlock );
return ( A ) new VolatileIntArray( ints, true );
case UINT64:
case INT64:
final long[] longs = new long[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.longs( longs, cellDims ) ), dataBlock );
return ( A ) new VolatileLongArray( longs, true );
case FLOAT32:
final float[] floats = new float[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.floats( floats, cellDims ) ), dataBlock );
return ( A ) new VolatileFloatArray( floats, true );
case FLOAT64:
final double[] doubles = new double[ n ];
copyFromBlock.accept( Cast.unchecked( ArrayImgs.doubles( doubles, cellDims ) ), dataBlock );
return ( A ) new VolatileDoubleArray( doubles, true );
default:
throw new IllegalArgumentException();
}
}

public A createEmptyArray( final long[] gridPosition )
{
final long[] cellDims = getCellDims( gridPosition );
final int n = ( int ) ( cellDims[ 0 ] * cellDims[ 1 ] * cellDims[ 2 ] );
switch ( dataType )
{
case UINT8:
case INT8:
return Cast.unchecked( new VolatileByteArray( new byte[ n ], true ) );
case UINT16:
case INT16:
return Cast.unchecked( new VolatileShortArray( new short[ n ], true ) );
case UINT32:
case INT32:
return Cast.unchecked( new VolatileIntArray( new int[ n ], true ) );
case UINT64:
case INT64:
return Cast.unchecked( new VolatileLongArray( new long[ n ], true ) );
case FLOAT32:
return Cast.unchecked( new VolatileFloatArray( new float[ n ], true ) );
case FLOAT64:
return Cast.unchecked( new VolatileDoubleArray( new double[ n ], true ) );
default:
throw new IllegalArgumentException();
}
}
public A createEmptyArray( final long[] gridPosition )
{
final long[] cellDims = getCellDims( gridPosition );
final int n = ( int ) ( cellDims[ 0 ] * cellDims[ 1 ] * cellDims[ 2 ] );
switch ( dataType )
{
case UINT8:
case INT8:
return Cast.unchecked( new VolatileByteArray( new byte[ n ], true ) );
case UINT16:
case INT16:
return Cast.unchecked( new VolatileShortArray( new short[ n ], true ) );
case UINT32:
case INT32:
return Cast.unchecked( new VolatileIntArray( new int[ n ], true ) );
case UINT64:
case INT64:
return Cast.unchecked( new VolatileLongArray( new long[ n ], true ) );
case FLOAT32:
return Cast.unchecked( new VolatileFloatArray( new float[ n ], true ) );
case FLOAT64:
return Cast.unchecked( new VolatileDoubleArray( new double[ n ], true ) );
default:
throw new IllegalArgumentException();
}
}

public long[] getCellDims( final long[] gridPosition )
{
return null;
}
public long[] getCellDims( final long[] gridPosition )
{
return null;
}

private static < T extends NativeType< T >, I extends RandomAccessibleInterval< T > & IterableInterval< T > > BiConsumer< I, DataBlock< ? > > createCopy(
final DataType dataType )
{
switch ( dataType )
{
case INT8:
case UINT8:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final byte[] data = ( byte[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends GenericByteType< ? > > c = ( Cursor< ? extends GenericByteType< ? > > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().setByte( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
case INT16:
case UINT16:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final short[] data = ( short[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends GenericShortType< ? > > c = ( Cursor< ? extends GenericShortType< ? > > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().setShort( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
case INT32:
case UINT32:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final int[] data = ( int[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends GenericIntType< ? > > c = ( Cursor< ? extends GenericIntType< ? > > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().setInt( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
case INT64:
case UINT64:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final long[] data = ( long[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends GenericLongType< ? > > c = ( Cursor< ? extends GenericLongType< ? > > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().setLong( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
case FLOAT32:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final float[] data = ( float[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends FloatType > c = ( Cursor< ? extends FloatType > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().set( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
case FLOAT64:
return ( a, b ) -> {
if ( sizeEquals( a, b ) )
{
final double[] data = ( double[] ) b.getData();
@SuppressWarnings( "unchecked" )
final Cursor< ? extends DoubleType > c = ( Cursor< ? extends DoubleType > ) a.cursor();
for ( int i = 0; i < data.length; ++i )
c.next().set( data[ i ] );
}
else
copyIntersection( a, b, dataType );
};
default:
throw new IllegalArgumentException( "Type " + dataType.name() + " not supported!" );
}
}

private static boolean sizeEquals( final Interval a, final DataBlock< ? > b )
{
final int[] dataBlockSize = b.getSize();
for ( int d = 0; d < dataBlockSize.length; ++d )
{
if ( a.dimension( d ) != dataBlockSize[ d ] )
return false;
}
return true;
}

private static < T extends NativeType< T >, I extends RandomAccessibleInterval< T > & IterableInterval< T > > void copyIntersection(
final I a,
final DataBlock< ? > b,
final DataType dataType )
{
@SuppressWarnings( "unchecked" )
final ArrayImg< T, ? > block = dataBlock2ArrayImg( b, dataType );
final IntervalView< T > za = Views.zeroMin( a );
final FinalInterval intersection = Intervals.intersect( block, za );
final Cursor< T > c = Views.interval( za, intersection ).cursor();
final Cursor< T > d = Views.interval( block, intersection ).cursor();
while ( c.hasNext() )
c.next().set( d.next() );
}

@SuppressWarnings( "rawtypes" )
private static ArrayImg dataBlock2ArrayImg(
final DataBlock< ? > dataBlock,
final DataType dataType )
{
final int[] dataBlockSize = dataBlock.getSize();
final long[] dims = new long[ dataBlockSize.length ];
for ( int d = 0; d < dataBlockSize.length; ++d )
dims[ d ] = dataBlockSize[ d ];
switch ( dataType )
{
case INT8:
return ArrayImgs.bytes( ( byte[] ) dataBlock.getData(), dims );
case UINT8:
return ArrayImgs.unsignedBytes( ( byte[] ) dataBlock.getData(), dims );
case INT16:
return ArrayImgs.shorts( ( short[] ) dataBlock.getData(), dims );
case UINT16:
return ArrayImgs.unsignedShorts( ( short[] ) dataBlock.getData(), dims );
case INT32:
return ArrayImgs.ints( ( int[] ) dataBlock.getData(), dims );
case UINT32:
return ArrayImgs.unsignedInts( ( int[] ) dataBlock.getData(), dims );
case INT64:
return ArrayImgs.longs( ( long[] ) dataBlock.getData(), dims );
case UINT64:
return ArrayImgs.unsignedLongs( ( long[] ) dataBlock.getData(), dims );
case FLOAT32:
return ArrayImgs.floats( ( float[] ) dataBlock.getData(), dims );
case FLOAT64:
return ArrayImgs.doubles( ( double[] ) dataBlock.getData(), dims );
default:
return null;
}
}
}

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