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NicoKiaruNicoKiaru
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adds a way to change the background value of sources
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‎pom.xml‎

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<groupId>sc.fiji</groupId>
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<artifactId>bigdataviewer-playground</artifactId>
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<version>0.11.3-SNAPSHOT</version>
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<version>0.12.0-SNAPSHOT</version>
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<name>bigdataviewer-playground</name>
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<description>BigDataViewer Actions and GUI</description>

‎src/main/java/bdv/util/OutOfBoundsColorChangedSource.java‎

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package bdv.util;
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import bdv.viewer.Interpolation;
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import bdv.viewer.Source;
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import mpicbg.spim.data.sequence.VoxelDimensions;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.RealRandomAccessible;
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import net.imglib2.realtransform.AffineTransform3D;
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import net.imglib2.type.numeric.NumericType;
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import net.imglib2.view.ExtendedRandomAccessibleInterval;
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import net.imglib2.view.Views;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class OutOfBoundsColorChangedSource<T extends NumericType<T>> implements Source<T> {
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protected static final Logger logger = LoggerFactory.getLogger(
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OutOfBoundsColorChangedSource.class);
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transient protected final DefaultInterpolators<T> interpolators =
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new DefaultInterpolators<>();
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/**
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* Origin source of type {@link T}
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*/
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final Source<T> origin;
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final T outOfBoundsValue;
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public OutOfBoundsColorChangedSource(Source<T> source, T outOfBoundsValue)
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{
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this.origin = source;
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this.outOfBoundsValue = outOfBoundsValue;
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}
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@Override
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public boolean isPresent(int t) {
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return origin.isPresent(t);
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}
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@Override
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public RandomAccessibleInterval<T> getSource(int t, int level) {
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return origin.getSource(t, level);
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}
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@Override
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public RealRandomAccessible<T> getInterpolatedSource(int t, int level, Interpolation method) {
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ExtendedRandomAccessibleInterval<T, RandomAccessibleInterval<T>> eView =
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Views.extendValue(getSource(t, level), outOfBoundsValue);
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return Views.interpolate(eView, interpolators.get(method));
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}
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@Override
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public void getSourceTransform(int t, int level, AffineTransform3D transform) {
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origin.getSourceTransform(t, level, transform);
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}
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@Override
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public T getType() {
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return origin.getType();
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}
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@Override
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public String getName() {
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return origin.getName();
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}
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@Override
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public VoxelDimensions getVoxelDimensions() {
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return origin.getVoxelDimensions();
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}
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@Override
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public int getNumMipmapLevels() {
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return origin.getNumMipmapLevels();
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}
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}

‎src/main/java/sc/fiji/bdvpg/sourceandconverter/transform/SourceOutOfBoundsColorChanger.java‎

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/*-
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* #%L
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* BigDataViewer-Playground
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* %%
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* Copyright (C) 2019 - 2025 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package sc.fiji.bdvpg.sourceandconverter.transform;
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import bdv.util.OutOfBoundsColorChangedSource;
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import bdv.viewer.Source;
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import bdv.viewer.SourceAndConverter;
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import net.imglib2.Volatile;
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import net.imglib2.type.NativeType;
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import net.imglib2.type.numeric.ARGBType;
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import net.imglib2.type.numeric.NumericType;
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import net.imglib2.type.numeric.integer.UnsignedByteType;
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import net.imglib2.type.numeric.integer.UnsignedShortType;
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import net.imglib2.type.numeric.real.FloatType;
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import net.imglib2.type.volatiles.VolatileARGBType;
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import net.imglib2.type.volatiles.VolatileFloatType;
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import net.imglib2.type.volatiles.VolatileUnsignedByteType;
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import net.imglib2.type.volatiles.VolatileUnsignedShortType;
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import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
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import java.util.function.Function;
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public class SourceOutOfBoundsColorChanger<T extends NumericType<T> & NativeType<T>>
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implements Runnable, Function<SourceAndConverter<T>, SourceAndConverter<T>>
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{
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final SourceAndConverter<T> sac_in;
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final T outOfBoundsColor;
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public SourceOutOfBoundsColorChanger(final SourceAndConverter<T> sac_in,
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final T outOfBoundsColor)
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{
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this.outOfBoundsColor = outOfBoundsColor;
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this.sac_in = sac_in;
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}
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@Override
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public void run() {
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}
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public SourceAndConverter<T> get() {
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return apply(sac_in);
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}
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@Override
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public SourceAndConverter<T> apply(final SourceAndConverter<T> src) {
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final Source<T> srcNewBg = new OutOfBoundsColorChangedSource<>(src.getSpimSource(), outOfBoundsColor);
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SourceAndConverter<T> sac;
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if (src.asVolatile() != null) {
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SourceAndConverter<? extends Volatile<T>> vsac;
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Source<? extends Volatile<T>> vsrcNewBg;
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// Rah...
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Volatile<T> vOutOfBoundsColor;
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if (outOfBoundsColor instanceof UnsignedShortType) {
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vOutOfBoundsColor = (Volatile<T>) new VolatileUnsignedShortType(((UnsignedShortType) outOfBoundsColor).get());
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} else if (outOfBoundsColor instanceof UnsignedByteType) {
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vOutOfBoundsColor = (Volatile<T>) new VolatileUnsignedByteType(((UnsignedByteType) outOfBoundsColor).get());
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} else if (outOfBoundsColor instanceof ARGBType) {
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vOutOfBoundsColor = (Volatile<T>) new VolatileARGBType(((ARGBType) outOfBoundsColor).get());
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} else if (outOfBoundsColor instanceof FloatType) {
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vOutOfBoundsColor = (Volatile<T>) new VolatileFloatType(((FloatType) outOfBoundsColor).get());
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} else {
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throw new RuntimeException("Sorry, can't find matching volatile type of pixel class "+outOfBoundsColor.getClass().getSimpleName()+". Please contribute to bdv-playground SourceOutOfBoundsColorChanger class");
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}
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vsrcNewBg = new OutOfBoundsColorChangedSource(src.asVolatile().getSpimSource(), (NumericType) vOutOfBoundsColor);
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vsac = new SourceAndConverter(vsrcNewBg, SourceAndConverterHelper
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.cloneConverter(src.asVolatile().getConverter(), src.asVolatile()));
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sac = new SourceAndConverter<>(srcNewBg, SourceAndConverterHelper
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.cloneConverter(src.getConverter(), src), vsac);
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}
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else {
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sac = new SourceAndConverter<>(srcNewBg, SourceAndConverterHelper
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.cloneConverter(src.getConverter(), src));
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}
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return sac;
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}
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}

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

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/*-
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* #%L
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* BigDataViewer-Playground
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* %%
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* Copyright (C) 2019 - 2025 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package sc.fiji.bdvpg;
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import bdv.util.BdvHandle;
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import bdv.viewer.SourceAndConverter;
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import mpicbg.spim.data.generic.AbstractSpimData;
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import net.imagej.ImageJ;
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import net.imglib2.type.numeric.integer.UnsignedShortType;
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import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
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import sc.fiji.bdvpg.scijava.services.SourceAndConverterService;
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import sc.fiji.bdvpg.services.SourceAndConverterServices;
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import sc.fiji.bdvpg.sourceandconverter.transform.SourceOutOfBoundsColorChanger;
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import sc.fiji.bdvpg.spimdata.importer.SpimDataFromXmlImporter;
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public class SourceBgChangerDemo {
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static ImageJ ij;
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public static void main(String... args) {
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// Initializes static SourceService and Display Service
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ij = new ImageJ();
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TestHelper.startFiji(ij);
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// Creates a BdvHandle
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BdvHandle bdvHandle =
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ij.get(SourceAndConverterBdvDisplayService.class).getActiveBdv();
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final String filePath = "src/test/resources/mri-stack.xml";
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// Import SpimData
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SpimDataFromXmlImporter importer = new SpimDataFromXmlImporter(filePath);
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//importer.run();
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final AbstractSpimData<?> spimData = importer.get();
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SourceAndConverter<UnsignedShortType> sac = (SourceAndConverter<UnsignedShortType>) ij.get(SourceAndConverterService.class)
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.getSourceAndConverterFromSpimdata(spimData)
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.get(0);
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SourceAndConverter<UnsignedShortType> sourceBgModified = new SourceOutOfBoundsColorChanger<>(sac, new UnsignedShortType(2000)).get();
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SourceAndConverterServices.getBdvDisplayService().show(bdvHandle,sourceBgModified);
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//new TimepointAdapterAdder(bdvh).run();
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}
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}

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