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pushed up code from BigStitcher-Spark that can optionally use virtual…
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… downsampling (useful if you only access part of the image and the downsampling steps are not available)
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@StephanPreibisch
StephanPreibisch committed Feb 29, 2024
1 parent 3b071be commit f2a7107
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Showing 3 changed files with 41 additions and 41 deletions.
3 changes: 2 additions & 1 deletion src/main/java/net/preibisch/mvrecon/fiji/plugin/interestpointdetection/DifferenceOfGUI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -485,7 +485,8 @@ protected ImagePlus getImagePlusForInteractive( final String dialogHeader )
RandomAccessibleInterval<RealType<?>> imgGeneric = DownsampleTools.openAndDownsample(
spimData.getSequenceDescription().getImgLoader(),
viewDescription,
new long[] { downsampleXY, downsampleXY, downsampleZ } ).getA();
new long[] { downsampleXY, downsampleXY, downsampleZ },
true ).getA();

if ( imgGeneric == null )
{
Expand Down
73 changes: 36 additions & 37 deletions src/main/java/net/preibisch/mvrecon/process/downsampling/DownsampleTools.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,11 +33,15 @@
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Pair;
import net.imglib2.util.Util;
import net.imglib2.util.ValuePair;
import net.imglib2.view.Views;
import net.preibisch.legacy.io.IOFunctions;
import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint;
import net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x;
import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2;

public class DownsampleTools
{
Expand Down Expand Up @@ -394,7 +398,7 @@ public static AffineTransform3D getMipMapTransform(
{
final AffineTransform3D mmt = new AffineTransform3D();

openAndDownsample( imgLoader, vd, mmt, downsampleFactors, true );
openAndDownsample( imgLoader, vd, mmt, downsampleFactors, true, false );

return mmt;
}
Expand All @@ -406,17 +410,19 @@ public static AffineTransform3D getMipMapTransform(
* @param imgLoader the imgloader
* @param vd the view id
* @param downsampleFactors - specify which downsampling in each dimension (e.g. 1,2,4,8 )
* @param virtualDownsampling - use virtual downsampling if the requested downsamplefactors are not precomputed
* @return opened image and the mipmap transform
*/
@SuppressWarnings({ "rawtypes" })
public static Pair<RandomAccessibleInterval, AffineTransform3D> openAndDownsample(
final BasicImgLoader imgLoader,
final ViewId vd,
final long[] downsampleFactors )
final long[] downsampleFactors,
final boolean virtualDownsampling )
{
final AffineTransform3D mipMapTransform = new AffineTransform3D();

final RandomAccessibleInterval img = openAndDownsample(imgLoader, vd, mipMapTransform, downsampleFactors, false );
final RandomAccessibleInterval img = openAndDownsample(imgLoader, vd, mipMapTransform, downsampleFactors, false, virtualDownsampling );

return new ValuePair<RandomAccessibleInterval, AffineTransform3D>( img, mipMapTransform );
}
Expand All @@ -429,6 +435,7 @@ public static Pair<RandomAccessibleInterval, AffineTransform3D> openAndDownsampl
* @param vd the view id
* @param mipMapTransform - will be filled if downsampling is performed, otherwise identity transform
* @param downsampleFactors - specify which downsampling in each dimension (e.g. 1,2,4,8 )
* @param virtualDownsampling - use virtual downsampling if the requested downsamplefactors are not precomputed
* @param transformOnly - if true does not open any images but only provides the mipMapTransform (METHOD WILL RETURN NULL!)
* @return opened image
*/
Expand All @@ -438,14 +445,9 @@ private static RandomAccessibleInterval openAndDownsample(
final ViewId vd,
final AffineTransform3D mipMapTransform,
long[] downsampleFactors,
final boolean transformOnly ) // only for ImgLib1 legacy code
final boolean transformOnly, // only for ImgLib1 legacy code
final boolean virtualDownsampling )
{

//if ( !transformOnly )
// IOFunctions.println(
// "(" + new Date(System.currentTimeMillis()) + "): "
// + "Requesting Img from ImgLoader (tp=" + vd.getTimePointId() + ", setup=" + vd.getViewSetupId() + "), downsampling: " + Util.printCoordinates( downsampleFactors ) );

long dsx = downsampleFactors[0];
long dsy = downsampleFactors[1];
long dsz = (downsampleFactors.length > 2) ? downsampleFactors[ 2 ] : 1;
Expand Down Expand Up @@ -485,31 +487,14 @@ private static RandomAccessibleInterval openAndDownsample(

if ( !transformOnly )
{
//IOFunctions.println(
// "(" + new Date(System.currentTimeMillis()) + "): " +
// "Using precomputed Multiresolution Images [" + fx + "x" + fy + "x" + fz + "], " +
// "Remaining downsampling [" + dsx + "x" + dsy + "x" + dsz + "]" );

//if ( openAsFloat )
// input = ImgLib2Tools.convertVirtual( (RandomAccessibleInterval)mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel ) );
//else
input = mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel );
input = mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel );
}
}
else
{
if ( !transformOnly )
{
//IOFunctions.println(
// "(" + new Date(System.currentTimeMillis()) + "): " +
// "Using precomputed Multiresolution Images [1x1x1], " +
// "Remaining downsampling [" + dsx + "x" + dsy + "x" + dsz + "]" );

// we only need to do the complete opening when we do not perform additional downsampling below
//if ( openAsFloat )
// input = ImgLib2Tools.convertVirtual( (RandomAccessibleInterval)imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() ) );
//else
input = imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() );
input = imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() );
}

if ( mipMapTransform != null )
Expand All @@ -521,7 +506,7 @@ private static RandomAccessibleInterval openAndDownsample(
// the additional downsampling (performed below)
final AffineTransform3D additonalDS = new AffineTransform3D();
additonalDS.set( dsx, 0.0, 0.0, 0.0, 0.0, dsy, 0.0, 0.0, 0.0, 0.0, dsz, 0.0 );

// we need to concatenate since when correcting for the downsampling we first multiply by whatever
// the manual downsampling did, and just then by the scaling+offset of the HDF5
//
Expand All @@ -534,15 +519,29 @@ private static RandomAccessibleInterval openAndDownsample(

if ( !transformOnly )
{
// note: every pixel is read exactly once, therefore caching the virtual input would not give any advantages
for ( ;dsx > 1; dsx /= 2 )
input = Downsample.simple2x( input, new boolean[]{ true, false, false } );
if ( virtualDownsampling )
{
for ( ;dsx > 1; dsx /= 2 )
input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 0 );

for ( ;dsy > 1; dsy /= 2 )
input = Downsample.simple2x( input, new boolean[]{ false, true, false } );
for ( ;dsy > 1; dsy /= 2 )
input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 1 );

for ( ;dsz > 1; dsz /= 2 )
input = Downsample.simple2x( input, new boolean[]{ false, false, true } );
for ( ;dsz > 1; dsz /= 2 )
input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 2 );
}
else
{
// note: every pixel is read exactly once, therefore caching the virtual input would not give any advantages
for ( ;dsx > 1; dsx /= 2 )
input = Downsample.simple2x( input, new boolean[]{ true, false, false } );

for ( ;dsy > 1; dsy /= 2 )
input = Downsample.simple2x( input, new boolean[]{ false, true, false } );

for ( ;dsz > 1; dsz /= 2 )
input = Downsample.simple2x( input, new boolean[]{ false, false, true } );
}
}

return input;
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/net/preibisch/mvrecon/process/interestpointdetection/methods/dog/DoG.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,15 +142,15 @@ public static void addInterestPoints( final HashMap< ViewId, List< InterestPoint

final ExecutorService service = Threads.createFixedExecutorService( Threads.numThreads() );

// TODO: downsampling is not virtual!
// downsampling is not virtual!
@SuppressWarnings({"rawtypes" })
final Pair<RandomAccessibleInterval, AffineTransform3D> input =
DownsampleTools.openAndDownsample(
dog.imgloader,
vd,
new long[] { dog.downsampleXY, dog.downsampleXY, dog.downsampleZ } );
new long[] { dog.downsampleXY, dog.downsampleXY, dog.downsampleZ },
false );

@SuppressWarnings("unchecked")
List< InterestPoint > ips = DoGImgLib2.computeDoG(
Views.extendMirrorSingle( input.getA() ),
null, // mask
Expand Down

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