Add CroppedSource

src/main/java/bdv/util/CroppedSource.java

@@ -0,0 +1,149 @@
+/*-
+ * #%L
+ * BigDataViewer-Playground
+ * %%
+ * Copyright (C) 2019 - 2021 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package bdv.util;
+
+//import bdv.SpimSource;
+import bdv.img.WarpedSource;
+import bdv.tools.transformation.TransformedSource;
+import bdv.viewer.Interpolation;
+import bdv.viewer.Source;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import net.imglib2.FinalInterval;
+import net.imglib2.FinalRealInterval;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.RealInterval;
+import net.imglib2.RealRandomAccessible;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.realtransform.RealViews;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.util.Intervals;
+import net.imglib2.view.ExtendedRandomAccessibleInterval;
+import net.imglib2.view.IntervalView;
+import net.imglib2.view.Views;
+import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+
+public class CroppedSource< T extends NumericType<T> & NativeType<T>> implements Source<T>
+{
+    private final Source<T> wrappedSource;
+    private final String name;
+    private final RealInterval crop;
+    private final boolean cropMinToZero;
+    protected final DefaultInterpolators< T > interpolators;
+    private HashMap< Integer, Interval > levelToVoxelInterval;
+
+    public CroppedSource( Source<T> source, String name, RealInterval crop, boolean cropMinToZero )
+    {
+        this.wrappedSource = source;
+        this.name = name;
+        this.crop = crop;
+        this.cropMinToZero = cropMinToZero;
+        this.interpolators = new DefaultInterpolators();
+
+        initCropIntervals( source, crop );
+    }
+
+
+    private void initCropIntervals( Source< T > source, RealInterval crop )
+    {
+        final AffineTransform3D transform3D = new AffineTransform3D();
+        levelToVoxelInterval = new HashMap<>();
+        for ( int l = 0; l < source.getNumMipmapLevels(); l++ )
+        {
+            source.getSourceTransform( 0, l, transform3D );
+            final Interval voxelInterval = Intervals.smallestContainingInterval( transform3D.inverse().estimateBounds( crop ) );
+            levelToVoxelInterval.put( l, voxelInterval );
+        }
+    }
+
+    public Source<?> getWrappedSource() {
+        return wrappedSource;
+    }
+
+    @Override
+    public boolean isPresent(int t) {
+        return wrappedSource.isPresent(t);
+    }
+
+    @Override
+    public RandomAccessibleInterval<T> getSource(int t, int level)
+    {
+        final IntervalView< T > intervalView = Views.interval( wrappedSource.getSource( t, level ), levelToVoxelInterval.get( level ) );
+
+        if ( cropMinToZero )
+            return Views.zeroMin( intervalView );
+        else
+            return intervalView;
+    }
+
+    @Override
+    public RealRandomAccessible<T> getInterpolatedSource(int t, int level, Interpolation method)
+    {
+        ExtendedRandomAccessibleInterval<T, RandomAccessibleInterval< T >>
+                zeroExtendedCrop = Views.extendZero( getSource( t, level ) );
+        RealRandomAccessible< T > realRandomAccessible = Views.interpolate( zeroExtendedCrop, interpolators.get(method) );
+        return realRandomAccessible;
+    }
+
+    @Override
+    public void getSourceTransform(int t, int level, AffineTransform3D transform)
+    {
+        wrappedSource.getSourceTransform( t, level, transform );
+    }
+
+    @Override
+    public T getType() {
+        return wrappedSource.getType();
+    }
+
+    @Override
+    public String getName()
+    {
+        return name;
+    }
+
+    @Override
+    public VoxelDimensions getVoxelDimensions() {
+        return wrappedSource.getVoxelDimensions();
+    }
+
+    @Override
+    public int getNumMipmapLevels() {
+        return wrappedSource.getNumMipmapLevels();
+    }
+
+}

src/test/src/sc/fiji/bdvpg/CroppingDemo.java

@@ -0,0 +1,106 @@
+/*-
+ * #%L
+ * BigDataViewer-Playground
+ * %%
+ * Copyright (C) 2019 - 2021 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package sc.fiji.bdvpg;
+
+import bdv.util.BdvFunctions;
+import bdv.util.BdvHandle;
+import bdv.util.CroppedSource;
+import bdv.viewer.Source;
+import bdv.viewer.SourceAndConverter;
+import mpicbg.spim.data.generic.AbstractSpimData;
+import net.imagej.ImageJ;
+import net.imglib2.FinalRealInterval;
+import net.imglib2.cache.img.DiskCachedCellImgOptions;
+import net.imglib2.converter.Converter;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.ARGBType;
+import org.junit.After;
+import org.junit.Test;
+import sc.fiji.bdvpg.bdv.navigate.ViewerTransformAdjuster;
+import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
+import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
+import sc.fiji.bdvpg.sourceandconverter.display.BrightnessAdjuster;
+import sc.fiji.bdvpg.sourceandconverter.display.BrightnessAutoAdjuster;
+import sc.fiji.bdvpg.sourceandconverter.display.ColorChanger;
+import sc.fiji.bdvpg.sourceandconverter.importer.EmptySourceAndConverterCreator;
+import sc.fiji.bdvpg.sourceandconverter.importer.MandelbrotSourceGetter;
+import sc.fiji.bdvpg.sourceandconverter.importer.SourceAndConverterFromSpimDataCreator;
+import sc.fiji.bdvpg.sourceandconverter.transform.SourceAffineTransformer;
+import sc.fiji.bdvpg.sourceandconverter.transform.SourceResampler;
+import sc.fiji.bdvpg.spimdata.importer.SpimDataFromXmlImporter;
+
+import java.util.Set;
+
+import static net.imglib2.cache.img.DiskCachedCellImgOptions.options;
+
+public class CroppingDemo
+{
+    static ImageJ ij;
+
+    static public void main(String... args) {
+
+        // create the ImageJ application context with all available services
+        ij = new ImageJ();
+        ij.ui().showUI();
+
+        demo();
+    }
+
+    @Test
+    public void demoRunOk() {
+        main(new String[]{""});
+    }
+
+    @After
+    public void closeFiji() {
+        TestHelper.closeFijiAndBdvs(ij);
+    }
+
+    public static void demo() {
+
+        final SourceAndConverterBdvDisplayService displayService = SourceAndConverterServices.getSourceAndConverterDisplayService();
+
+        // open and show source
+        SpimDataFromXmlImporter importer = new SpimDataFromXmlImporter("src/test/resources/mri-stack-multilevel.xml");
+        AbstractSpimData asd = importer.get();
+        final SourceAndConverterFromSpimDataCreator creator = new SourceAndConverterFromSpimDataCreator( asd );
+        final SourceAndConverter sac = creator.getSetupIdToSourceAndConverter().get( 0 );
+        displayService.show( sac );
+        new ViewerTransformAdjuster( displayService.getActiveBdv(), sac ).run();
+        new BrightnessAutoAdjuster( sac, 0 ).run();
+
+        // crop and show
+        final CroppedSource croppedSource = new CroppedSource( sac.getSpimSource(), "crop", new FinalRealInterval( new double[]{ 60, 60, 60 }, new double[]{ 110, 110, 110 } ), false );
+        final SourceAndConverter croppedSAC = new SourceAndConverter<>( croppedSource, sac.getConverter() );
+        displayService.show( croppedSAC );
+        new ViewerTransformAdjuster( displayService.getActiveBdv(), croppedSAC ).run();
+        new BrightnessAutoAdjuster( croppedSAC, 0 ).run();
+    }
+}