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Merge pull request #1079 from mobie/sift
Add 2D SIFT Alignment
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src/main/java/org/embl/mobie/command/context/AutomaticRegistrationCommand.java
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| /*- | ||
| * #%L | ||
| * Fiji viewer for MoBIE projects | ||
| * %% | ||
| * Copyright (C) 2018 - 2023 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 org.embl.mobie.command.context; | ||
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|
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| import bdv.tools.transformation.TransformedSource; | ||
| import bdv.util.BdvHandle; | ||
| import bdv.viewer.SourceAndConverter; | ||
| import ij.CompositeImage; | ||
| import ij.IJ; | ||
| import ij.ImagePlus; | ||
| import ij.ImageStack; | ||
| import ij.gui.Roi; | ||
| import ij.plugin.filter.ThresholdToSelection; | ||
| import ij.process.ByteProcessor; | ||
| import ij.process.ImageConverter; | ||
| import ij.process.ImageProcessor; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.embl.mobie.command.CommandConstants; | ||
| import org.embl.mobie.lib.MoBIEHelper; | ||
| import org.embl.mobie.lib.align.TurboReg2DAligner; | ||
| import org.embl.mobie.lib.bdv.ScreenShotMaker; | ||
| import org.embl.mobie.lib.align.SIFT2DAligner; | ||
| import org.scijava.Initializable; | ||
| import org.scijava.command.DynamicCommand; | ||
| import org.scijava.command.Interactive; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
| import org.scijava.widget.Button; | ||
| import sc.fiji.bdvpg.bdv.BdvHandleHelper; | ||
| import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand; | ||
|
|
||
| import java.awt.*; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.concurrent.ExecutionException; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Automatic") | ||
| public class AutomaticRegistrationCommand extends DynamicCommand implements BdvPlaygroundActionCommand, Interactive, Initializable | ||
| { | ||
| public static final String TRANSLATION = "Translation"; | ||
| public static final String RIGID = "Rigid"; | ||
| public static final String SIMILARITY = "Similarity"; | ||
| public static final String AFFINE = "Affine"; | ||
|
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| static { net.imagej.patcher.LegacyInjector.preinit(); } | ||
|
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| @Parameter | ||
| public BdvHandle bdvHandle; | ||
|
|
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| @Parameter ( label = "Registration Method", choices = {"TurboReg", "SIFT"} ) | ||
| private String registrationMethod = "SIFT"; | ||
|
|
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| @Parameter(label="Registration Voxel Size", persist = false, min = "0.0", style="format:#.00000") | ||
| public Double voxelSize = 1D; | ||
|
|
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| @Parameter ( label = "Transformation", choices = { TRANSLATION, RIGID, SIMILARITY, AFFINE } ) | ||
| private String transformationType = TRANSLATION; | ||
|
|
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| @Parameter ( label = "Image A (fixed)", choices = {""} ) | ||
| private String imageA; | ||
|
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| @Parameter ( label = "Image B (transformed)", choices = {""} ) | ||
| private String imageB; | ||
|
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| @Parameter ( label = "Show Intermediates" ) | ||
| private Boolean showIntermediates = false; | ||
|
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| @Parameter ( label = "Compute Alignment", callback = "compute") | ||
| private Button compute; | ||
|
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| @Parameter ( label = "Toggle Alignment", callback = "toggle") | ||
| private Button toggle; | ||
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| private AffineTransform3D previousTransform; | ||
| private AffineTransform3D newTransform; | ||
| private TransformedSource< ? > transformedSource; | ||
| private boolean isAligned; | ||
| private List< SourceAndConverter< ? > > sourceAndConverters; | ||
| private AffineTransform3D alignmentTransform3D; | ||
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||
| @Override | ||
| public void initialize() | ||
| { | ||
| sourceAndConverters = MoBIEHelper.getVisibleSacs( bdvHandle ); | ||
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|
||
| if ( sourceAndConverters.size() < 2 ) | ||
| { | ||
| IJ.showMessage( "There must be at least two images visible." ); | ||
| return; | ||
| } | ||
|
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| final List< String > imageNames = sourceAndConverters.stream() | ||
| .map( sac -> sac.getSpimSource().getName() ) | ||
| .collect( Collectors.toList() ); | ||
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| getInfo().getMutableInput( "imageA", String.class ) | ||
| .setChoices( imageNames ); | ||
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| getInfo().getMutableInput( "imageB", String.class ) | ||
| .setChoices( imageNames ); | ||
|
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| getInfo().getMutableInput("voxelSize", Double.class) | ||
| .setValue( this, 2 * BdvHandleHelper.getViewerVoxelSpacing( bdvHandle ) ); | ||
| } | ||
|
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||
| @Override | ||
| public void run() | ||
| { | ||
| // | ||
| } | ||
|
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| private void compute() | ||
| { | ||
| SourceAndConverter< ? > sacA = sourceAndConverters.stream() | ||
| .filter( sac -> sac.getSpimSource().getName().equals( imageA ) ) | ||
| .findFirst().get(); | ||
|
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| SourceAndConverter< ? > sacB = sourceAndConverters.stream() | ||
| .filter( sac -> sac.getSpimSource().getName().equals( imageB ) ) | ||
| .findFirst().get(); | ||
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||
| if ( ! ( sacB.getSpimSource() instanceof TransformedSource ) ) | ||
| { | ||
| IJ.log("Cannot apply transformations to image of type " + sacB.getSpimSource().getClass() ); | ||
| return; | ||
| } | ||
|
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| // create two 2D ImagePlus that are to be aligned | ||
| // | ||
| ScreenShotMaker screenShotMaker = new ScreenShotMaker( bdvHandle, sacA.getSpimSource().getVoxelDimensions().unit() ); | ||
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| screenShotMaker.run( Arrays.asList( sacA, sacB ), voxelSize ); | ||
| CompositeImage compositeImage = screenShotMaker.getCompositeImagePlus(); | ||
| AffineTransform3D canvasToGlobalTransform = screenShotMaker.getCanvasToGlobalTransform(); | ||
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| ImageStack stack = compositeImage.getStack(); | ||
| ImagePlus impA = new ImagePlus( imageA + " (fixed)", stack.getProcessor( 1 ) ); | ||
| ImagePlus impB = new ImagePlus( imageB + " (moving)", stack.getProcessor( 2 ) ); | ||
|
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| // set the display ranges and burn them in by converting to uint8 | ||
| // this is important for the intensity based registration methods | ||
| compositeImage.setPosition( 1 ); | ||
| impA.getProcessor().setMinAndMax( compositeImage.getDisplayRangeMin(), compositeImage.getDisplayRangeMax() ); | ||
| new ImageConverter( impA ).convertToGray8(); | ||
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| compositeImage.setPosition( 2 ); | ||
| impB.getProcessor().setMinAndMax( compositeImage.getDisplayRangeMin(), compositeImage.getDisplayRangeMax() ); | ||
| new ImageConverter( impB ).convertToGray8(); | ||
|
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| // set the rois within which the images contain valid pixel values | ||
| // those are used by some registration methods, e.g. turboReg | ||
| Roi[] rois = screenShotMaker.getMasks(); | ||
| impA.setRoi( rois[ 0 ] ); | ||
| impB.setRoi( rois[ 1 ] ); | ||
|
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||
| // compute the transformation that aligns the two images in 2D | ||
| // | ||
| AffineTransform3D localRegistration = new AffineTransform3D(); | ||
| if ( registrationMethod.equals( "SIFT" ) ) | ||
| { | ||
| SIFT2DAligner sift2DAligner = new SIFT2DAligner( impA, impB, transformationType ); | ||
| if ( ! sift2DAligner.run( showIntermediates ) ) return; | ||
| localRegistration = sift2DAligner.getAlignmentTransform(); | ||
| } | ||
| else if ( registrationMethod.equals( "TurboReg" ) ) | ||
| { | ||
| TurboReg2DAligner turboReg2DAligner = new TurboReg2DAligner( impA, impB, transformationType ); | ||
| turboReg2DAligner.run( showIntermediates ); | ||
| localRegistration = turboReg2DAligner.getAlignmentTransform(); | ||
| if ( showIntermediates ) | ||
| { | ||
| impA.show(); | ||
| impB.show(); | ||
| } | ||
| } | ||
|
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| // convert the transformation that aligns the images in 2D | ||
| // to the global 3D coordinate system | ||
| AffineTransform3D globalRegistration = new AffineTransform3D(); | ||
|
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| // global to target canvas... | ||
| globalRegistration.preConcatenate( canvasToGlobalTransform.inverse() ); | ||
|
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| // ...registration within canvas... | ||
| globalRegistration.preConcatenate( localRegistration ); | ||
|
|
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| // ...canvas back to global | ||
| globalRegistration.preConcatenate( canvasToGlobalTransform ); | ||
|
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| // apply the transformation to imageB | ||
| // | ||
| transformedSource = ( TransformedSource< ? > ) sacB.getSpimSource(); | ||
| previousTransform = new AffineTransform3D(); | ||
| transformedSource.getFixedTransform( previousTransform ); | ||
| newTransform = previousTransform.copy(); | ||
| newTransform.preConcatenate( globalRegistration ); | ||
| transformedSource.setFixedTransform( newTransform ); | ||
| IJ.log( "Transforming " + transformedSource.getName() ); | ||
| IJ.log( "Previous Transform: " + previousTransform ); | ||
| IJ.log( "Additional SIFT Transform: " + globalRegistration ); | ||
| IJ.log( "Combined Transform: " + newTransform ); | ||
| isAligned = true; | ||
| bdvHandle.getViewerPanel().requestRepaint(); | ||
| } | ||
|
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| private void toggle() | ||
| { | ||
| if ( transformedSource == null ) | ||
| { | ||
| IJ.showMessage( "Please first [ Compute Alignment ]." ); | ||
| return; | ||
| } | ||
|
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| if ( isAligned ) | ||
| { | ||
| transformedSource.setFixedTransform( previousTransform ); | ||
| } | ||
| else | ||
| { | ||
| transformedSource.setFixedTransform( newTransform ); | ||
| } | ||
|
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| bdvHandle.getViewerPanel().requestRepaint(); | ||
| isAligned = ! isAligned; | ||
| } | ||
|
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|
|
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| } |
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