Merge branch 'JaneliaSciComp:main' into overlap_only_patch

Author: indecisiveuser

install

@@ -124,6 +124,8 @@ install_command detect-interestpoints "net.preibisch.bigstitcher.spark.SparkInte
 install_command match-interestpoints "net.preibisch.bigstitcher.spark.SparkGeometricDescriptorMatching"
 install_command stitching "net.preibisch.bigstitcher.spark.SparkPairwiseStitching"
 install_command solver "net.preibisch.bigstitcher.spark.Solver"
+install_command match-intensities "net.preibisch.bigstitcher.spark.SparkIntensityMatching"
+install_command solve-intensities "net.preibisch.bigstitcher.spark.IntensitySolver"
 install_command create-fusion-container "net.preibisch.bigstitcher.spark.CreateFusionContainer"
 install_command affine-fusion "net.preibisch.bigstitcher.spark.SparkAffineFusion"
 install_command nonrigid-fusion "net.preibisch.bigstitcher.spark.SparkNonRigidFusion"

pom.xml

@@ -96,11 +96,14 @@
 		<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
 		<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
 		-->
-		<imglib2.version>7.1.4</imglib2.version>
-		<imglib2-algorithm.version>0.18.0</imglib2-algorithm.version>
-		<bigdataviewer-core.version>10.6.4</bigdataviewer-core.version>
+		<imglib2.version>8.0.0</imglib2.version>
+		<imglib2-cache.version>1.0.0-beta-20</imglib2-cache.version>
+		<imglib2-algorithm.version>0.18.2</imglib2-algorithm.version>
+		<bigdataviewer-core.version>10.6.5</bigdataviewer-core.version>
+		<bigdataviewer-n5.version>1.0.2</bigdataviewer-n5.version>
+
 		<spim_data.version>2.3.5</spim_data.version>
-		<multiview-reconstruction.version>7.0.5</multiview-reconstruction.version>
+		<multiview-reconstruction.version>8.0.0</multiview-reconstruction.version>
 		<BigStitcher.version>2.5.0</BigStitcher.version>
 
 		<n5-universe.version>2.3.0</n5-universe.version>
@@ -284,6 +287,11 @@
                     <groupId>ome</groupId>
                     <artifactId>formats-gpl</artifactId>
                 </exclusion>
+                <!-- in n5-google-cloud -->
+                <exclusion>
+                    <groupId>javax.annotation</groupId>
+                    <artifactId>javax.annotation-api</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>

src/main/java/net/preibisch/bigstitcher/spark/SparkAffineFusion.java

@@ -52,6 +52,7 @@
 import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.blocks.BlockAlgoUtils;
 import net.imglib2.algorithm.blocks.BlockSupplier;
 import net.imglib2.converter.Converter;
 import net.imglib2.converter.RealUnsignedByteConverter;
@@ -558,7 +559,7 @@ else if ( dataType == DataType.UINT16 )
 						}
 
 						//final RandomAccessibleInterval img;
-						final BlockSupplier blockSupplier;
+						final BlockSupplier< ? > blockSupplier;
 						final FinalInterval interval = new FinalInterval( bbMin, bbMax );
 
 						if ( masks )
@@ -581,7 +582,7 @@ else if ( dataType == DataType.UINT16 )
 							//
 							// PREFETCHING, TODO: should be part of BlkAffineFusion.init
 							//
-							final OverlappingBlocks overlappingBlocks = OverlappingBlocks.find( dataLocal, overlappingViews, fusedBlock );
+							final OverlappingBlocks overlappingBlocks = OverlappingBlocks.find( dataLocal, registrations, overlappingViews, fusedBlock );
 							if ( overlappingBlocks.overlappingViews().isEmpty() )
 								return gridBlock;
 
@@ -605,6 +606,7 @@ else if ( dataType == DataType.UINT16 )
 									registrations,
 									dataLocal.getSequenceDescription().getViewDescriptions(),
 									fusionType,//fusion.getFusionType(),
+									Double.NaN,
 									null, // map<old,new> will go here
 									1, // linear interpolation
 									coefficients, // intensity correction
@@ -622,7 +624,7 @@ else if ( dataType == DataType.UINT16 )
 							blockMax[ d ] = Math.min( Intervals.zeroMin( interval ).max( d ), blockMin[ d ] + gridBlock[1][ d ] - 1 );
 
 						final RandomAccessibleInterval image;
-						final RandomAccessibleInterval img = BlkAffineFusion.arrayImg( blockSupplier, new FinalInterval( blockMin, blockMax ) );
+						final RandomAccessibleInterval img = BlockAlgoUtils.arrayImg( blockSupplier, new FinalInterval( blockMin, blockMax ) );
 
 						// 5D OME-ZARR CONTAINER
 						if ( storageType == StorageFormat.ZARR )

src/main/java/net/preibisch/bigstitcher/spark/SparkGeometricDescriptorMatching.java

@@ -139,10 +139,13 @@ public enum Method { FAST_ROTATION, FAST_TRANSLATION, PRECISE_TRANSLATION, ICP }
 	@Option(names = { "-rmir", "--ransacMinInlierRatio" }, description = "ransac min inlier ratio (default: 0.1)")
 	protected Double ransacMinInlierRatio = 0.1;
 
-	@Option(names = { "-rmif", "--ransacMinInlierFactor" }, description = "ransac min inlier factor, i.e. how many time the minimal number of matches need to found, e.g. affine needs 4 matches, 3x means at least 12 matches required (default: 3.0)")
-	protected Double ransacMinInlierFactor = 3.0;
+	@Option(names = { "-rmni", "--ransacMinNumInliers" }, description = "ransac minimal number of required inliers (default: 12)")
+	protected Integer ransacMinNumInliers = 12;
+
+	@Option(names = { "-rmc", "--ransacMultiConsensus" }, description = "ransac perform multiconsensus matching (default: false)")
+	protected boolean ransacMultiConsensus = false;
+
 
-	
 	@Option(names = { "-ime", "--icpMaxError" }, description = "ICP max error in pixels (default: 5.0)")
 	protected Double icpMaxError = 5.0;
 
@@ -220,7 +223,8 @@ else if ( ransacIterations == null )
 		final int ransacIterations = this.ransacIterations;
 		final double ransacMaxEpsilon = this.ransacMaxError;
 		final double ransacMinInlierRatio = this.ransacMinInlierRatio;
-		final double ransacMinInlierFactor = this.ransacMinInlierFactor;
+		final int ransacMinNumInliers = this.ransacMinNumInliers;
+		final boolean ransacMultiConsensus = this.ransacMultiConsensus;
 		final double icpMaxError = this.icpMaxError;
 		final int icpMaxIterations = this.icpIterations;
 		final boolean icpUseRANSAC = this.icpUseRANSAC;
@@ -300,7 +304,7 @@ else if ( ransacIterations == null )
 							System.out.println( Group.pvid( element.getKey() ) + ", '" + subElement.getKey() + "' : " + subElement.getValue().size() );
 				}
 
-				final RANSACParameters rp = new RANSACParameters( (float)ransacMaxEpsilon, (float)ransacMinInlierRatio, (float)ransacMinInlierFactor, ransacIterations );
+				final RANSACParameters rp = new RANSACParameters( (float)ransacMaxEpsilon, (float)ransacMinInlierRatio, ransacMinNumInliers, ransacIterations, ransacMultiConsensus );
 				final Model< ? > model = createModelInstance(transformationModel, regularizationModel, lambda);
 
 				final MatcherPairwise< InterestPoint > matcher = createMatcherInstance(
@@ -424,7 +428,7 @@ else if ( ransacIterations == null )
 				groupedInterestpoints.put( task.vB, ipGrouping.group( task.vB ) );
 				IOFunctions.println( task.vA + " <=> " + task.vB + ": Grouping interestpoints for " + task.vB + " (" + ipGrouping.countBefore() + " >>> " + ipGrouping.countAfter() + ")" );
 
-				final RANSACParameters rp = new RANSACParameters( (float)ransacMaxEpsilon, (float)ransacMinInlierRatio, (float)ransacMinInlierFactor, ransacIterations );
+				final RANSACParameters rp = new RANSACParameters( (float)ransacMaxEpsilon, (float)ransacMinInlierRatio, ransacMinNumInliers, ransacIterations, ransacMultiConsensus );
 				final Model< ? > model = createModelInstance(transformationModel, regularizationModel, lambda);
 
 				final MatcherPairwise< GroupedInterestPoint< ViewId > > matcher = createMatcherInstance(
@@ -609,7 +613,7 @@ else if ( registrationMethod == Method.PRECISE_TRANSLATION )
 					rp.getMinInlierRatio(),
 					rp.getMaxEpsilon(),
 					rp.getNumIterations(),
-					Math.round( rp.getMinInlierFactor() * model.getMinNumMatches() ) );
+					rp.getMinNumMatches() );
 			matcher = new IterativeClosestPointPairwise<>( ip );
 		}
 

src/main/java/net/preibisch/bigstitcher/spark/SparkIntensityMatching.java

@@ -34,6 +34,11 @@
 
 public class SparkIntensityMatching extends AbstractSelectableViews
 {
+	public enum IntensityMatchingMethod
+	{
+		RANSAC, HISTOGRAM
+	}
+
 	@Option(names = { "--numCoefficients" }, description = "number of coefficients per dimension (default: 8,8,8)")
 	private String numCoefficientsString = "8,8,8";
 
@@ -52,19 +57,23 @@ public class SparkIntensityMatching extends AbstractSelectableViews
 	@Option(names = { "--minNumCandidates" }, description = "minimum number of (non-discarded) overlapping pixels required to match overlapping coefficient regions (default: 1000)")
 	private int minNumCandidates = 1000;
 
+	@Option(names = {"--method"}, defaultValue = "RANSAC", showDefaultValue = CommandLine.Help.Visibility.ALWAYS,
+			description = "Method to match intensities between overlapping views: RANSAC or HISTOGRAM")
+	private IntensityMatchingMethod intensityMatchingMethod;
+
 	@CommandLine.Option(names = { "--numIterations" }, description = "number of RANSAC iterations (default: 1000)")
 	private int iterations = 1000;
 
-	@CommandLine.Option(names = { "--maxEpsilon" }, description = "maximal allowed transfer error (default: 5.1)")
+	@CommandLine.Option(names = { "--maxEpsilon" }, description = "maximal allowed transfer error (default: 5.1, only for RANSAC method)")
 	private double maxEpsilon = 0.02 * 255;
 
-	@CommandLine.Option(names = { "--minInlierRatio" }, description = "minimal ratio of of inliers to number of candidates (default: 0.1)")
+	@CommandLine.Option(names = { "--minInlierRatio" }, description = "minimal ratio of of inliers to number of candidates (default: 0.1, only for RANSAC method)")
 	private double minInlierRatio = 0.1;
 
-	@CommandLine.Option(names = { "--minNumInliers" }, description = "minimally required absolute number of inliers (default: 10)")
+	@CommandLine.Option(names = { "--minNumInliers" }, description = "minimally required absolute number of inliers (default: 10, only for RANSAC method)")
 	private int minNumInliers = 10;
 
-	@CommandLine.Option(names = { "--maxTrust" }, description = "reject candidates with a cost larger than maxTrust * median cost (default: 3)")
+	@CommandLine.Option(names = { "--maxTrust" }, description = "reject candidates with a cost larger than maxTrust * median cost (default: 3, only for RANSAC method)")
 	private double maxTrust = 3.0;
 
 	private SpimData2 dataGlobal;
@@ -100,6 +109,7 @@ public Void call() throws Exception
 		final double minInlierRatio = this.minInlierRatio;
 		final int minNumInliers = this.minNumInliers;
 		final double maxTrust = this.maxTrust;
+		final IntensityMatchingMethod method = this.intensityMatchingMethod;
 
 		new ViewPairCoefficientMatchesIO( outputURI ).writeCoefficientsSize( coefficientsSize );
 
@@ -156,8 +166,18 @@ public Void call() throws Exception
 		viewPairRDD.foreach( views -> {
 			final SpimData2 dataLocal = Spark.getSparkJobSpimData2( xmlURI );
 			System.out.println( "(" + new Date( System.currentTimeMillis() ) + "): " + views._1().getViewSetupId() + "<>" + views._2().getViewSetupId() );
-			final ViewPairCoefficientMatches matches = IntensityCorrection.match( dataLocal, views._1(), views._2(), renderScale, coefficientsSize,
-					minIntensityThreshold, maxIntensityThreshold, minNumCandidates, iterations, maxEpsilon, minInlierRatio, minNumInliers, maxTrust );
+
+			final ViewPairCoefficientMatches matches;
+			if ( method == IntensityMatchingMethod.RANSAC )
+			{
+				matches = IntensityCorrection.matchRansac( dataLocal, views._1(), views._2(), renderScale, coefficientsSize,
+						minIntensityThreshold, maxIntensityThreshold, minNumCandidates, iterations, maxEpsilon, minInlierRatio, minNumInliers, maxTrust );
+			}
+			else // method == IntensityMatchingMethod.HISTOGRAM
+			{
+				matches = IntensityCorrection.matchHistograms( dataLocal, views._1(), views._2(), renderScale, coefficientsSize,
+						minIntensityThreshold, maxIntensityThreshold, minNumCandidates );
+			}
 			final ViewPairCoefficientMatchesIO matchWriter = new ViewPairCoefficientMatchesIO(outputURI);
 			matchWriter.write( matches );
 		} );

src/main/java/net/preibisch/bigstitcher/spark/SparkInterestPointDetection.java

@@ -91,6 +91,7 @@
 import net.preibisch.mvrecon.process.downsampling.Downsample;
 import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x;
+import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
 import net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools;
 import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2;
 import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters;
@@ -242,13 +243,20 @@ public Void call() throws Exception
 		// assemble all pairs for parallelization with Spark
 		final ArrayList< Tuple2< ViewId, ViewId > > metadataJobs = new ArrayList<>();
 
+		final HashMap< ViewId, AffineTransform3D > registrations =
+				TransformVirtual.adjustAllTransforms(
+						viewIdsGlobal,
+						dataGlobal.getViewRegistrations().getViewRegistrations(),
+						Double.NaN,
+						Double.NaN );
+
 		for ( final ViewId viewDesc : viewIdsGlobal )
 		{
 			final ViewId viewId = new ViewId( viewDesc.getTimePointId(), viewDesc.getViewSetupId() );
 
 			if ( onlyOverlappingRegions )
 			{
-				for ( final ViewId otherViewId : OverlappingViews.findAllOverlappingViewsFor( viewId, dataGlobal, viewIdsGlobal ) )
+				for ( final ViewId otherViewId : OverlappingViews.findAllOverlappingViewsFor( viewId, dataGlobal, registrations, viewIdsGlobal ) )
 				{
 					if ( !otherViewId.equals( viewId ) )
 					{
@@ -514,7 +522,7 @@ public Void call() throws Exception
 
 				// here we put in the inverse mipmap transform and pretend its a fusion so we can re-use Tobi's code
 				// that finds which blocks need to be prefetched from an input image
-				final List< PrefetchPixel< ? > > prefetchBlocks = ViewUtil.findOverlappingBlocks( data, viewId, input.getB().inverse(), processInterval, maxKernelSize );
+				final List< PrefetchPixel< ? > > prefetchBlocks = ViewUtil.findOverlappingBlocks( data, viewId, processInterval, input.getB().inverse(), maxKernelSize );
 
 				System.out.println( "Prefetching " + prefetchBlocks.size() + " blocks for " + Group.pvid(viewId) + ", " + Util.printInterval( processInterval ) );
 

src/main/java/net/preibisch/bigstitcher/spark/SparkNonRigidFusion.java

@@ -331,7 +331,8 @@ else if ( uint16 )
 						final ViewId viewId = Spark.deserializeViewIds(serializedViewIds, i);
 
 						// expand by 50 to be conservative for non-rigid overlaps
-						final Interval boundingBox = ViewUtil.getTransformedBoundingBox( dataLocal, viewId );
+						dataLocal.getViewRegistrations().getViewRegistration( viewId ).updateModel();
+						final Interval boundingBox = ViewUtil.getTransformedBoundingBox( dataLocal, viewId, dataLocal.getViewRegistrations().getViewRegistration( viewId ).getModel() );
 						final Interval bounds = Intervals.expand( boundingBox, 50 );
 						// TODO: estimate the "50" from the distance of corresponding, transformed interest points
 
@@ -351,12 +352,14 @@ else if ( uint16 )
 
 					for ( final ViewId viewId : allViews )
 					{
-						final Interval boundingBoxView = ViewUtil.getTransformedBoundingBox( dataLocal, viewId );
+						dataLocal.getViewRegistrations().getViewRegistration( viewId ).updateModel();
+						final Interval boundingBoxView = ViewUtil.getTransformedBoundingBox( dataLocal, viewId, dataLocal.getViewRegistrations().getViewRegistration( viewId ).getModel() );
 						final Interval boundsView = Intervals.expand( boundingBoxView, 25 );
 
 						for ( final ViewId fusedId : viewsToFuse )
 						{
-							final Interval boundingBoxFused = ViewUtil.getTransformedBoundingBox( dataLocal, fusedId );
+							dataLocal.getViewRegistrations().getViewRegistration( fusedId ).updateModel();
+							final Interval boundingBoxFused = ViewUtil.getTransformedBoundingBox( dataLocal, fusedId, dataLocal.getViewRegistrations().getViewRegistration( fusedId ).getModel() );
 							final Interval boundsFused = Intervals.expand( boundingBoxFused, 25 );
 
 							if ( ViewUtil.overlaps( boundsView, boundsFused ))

src/main/java/net/preibisch/bigstitcher/spark/abstractcmdline/AbstractBasic.java

@@ -36,6 +36,8 @@
 
 public abstract class AbstractBasic extends AbstractInfrastructure implements Callable<Void>, Serializable
 {
+	static { net.preibisch.legacy.io.IOFunctions.printIJLog = false;  }
+
 	private static final long serialVersionUID = -4916959775650710928L;
 
 	@Option(names = { "-x", "--xml" }, required = true, description = "Path to the existing BigStitcher project xml, e.g. -x /home/project.xml or -x s3://mybucket/data/dataset.xml or -x file:/home/project.xml")

src/main/java/net/preibisch/bigstitcher/spark/fusion/OverlappingBlocks.java

@@ -22,6 +22,7 @@
 package net.preibisch.bigstitcher.spark.fusion;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutorService;
@@ -30,6 +31,7 @@
 import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.sequence.ViewId;
 import net.imglib2.Interval;
+import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.util.Intervals;
 import net.preibisch.bigstitcher.spark.util.ViewUtil;
 import net.preibisch.bigstitcher.spark.util.ViewUtil.PrefetchPixel;
@@ -46,7 +48,9 @@ public class OverlappingBlocks
 	 * {@code interval}.
 	 *
 	 * @param data
-	 * 		has all images and transformations
+	 * 		has all image sizes
+	 * @param registrations
+	 * 		registrations, maybe updated to reflect anisotropy
 	 * @param viewIds
 	 * 		which views to check
 	 * @param interval
@@ -55,6 +59,7 @@ public class OverlappingBlocks
 	 */
 	public static OverlappingBlocks find(
 			final SpimData data,
+			final HashMap< ViewId, AffineTransform3D > registrations,
 			final List<ViewId> viewIds,
 			Interval interval )
 	{
@@ -66,11 +71,11 @@ public static OverlappingBlocks find(
 
 		for ( final ViewId viewId : viewIds )
 		{
-			final Interval bounds = ViewUtil.getTransformedBoundingBox( data, viewId );
+			final Interval bounds = ViewUtil.getTransformedBoundingBox( data, viewId, registrations.get( viewId ) );
 			if ( ViewUtil.overlaps( expandedInterval, bounds ) )
 			{
 				// determine which Cells exactly we need to compute the fused block
-				final List< PrefetchPixel< ? > > blocks = ViewUtil.findOverlappingBlocks( data, viewId, interval );
+				final List< PrefetchPixel< ? > > blocks = ViewUtil.findOverlappingBlocks( data, viewId, interval, registrations.get( viewId ) );
 				if ( !blocks.isEmpty() )
 				{
 					prefetch.addAll( blocks );