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Implement Command to set a transformation
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166 changes: 166 additions & 0 deletions
166
src/main/java/org/embl/mobie/command/context/SetTransformationCommand.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| /*- | ||
| * #%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; | ||
|
|
||
| import bdv.tools.transformation.TransformedSource; | ||
| import bdv.util.BdvHandle; | ||
| import bdv.viewer.SourceAndConverter; | ||
| import ij.IJ; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.embl.mobie.command.CommandConstants; | ||
| import org.embl.mobie.lib.MoBIEHelper; | ||
| import org.embl.mobie.lib.serialize.transformation.AffineTransformation; | ||
| import org.scijava.Initializable; | ||
| import org.scijava.command.DynamicCommand; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
| import org.scijava.widget.Button; | ||
| import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand; | ||
|
|
||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Set Transformation") | ||
| public class SetTransformationCommand extends DynamicCommand implements BdvPlaygroundActionCommand, Initializable | ||
| { | ||
| static { net.imagej.patcher.LegacyInjector.preinit(); } | ||
|
|
||
| @Parameter | ||
| public BdvHandle bdvHandle; | ||
|
|
||
| @Parameter ( label = "Image", choices = {""} ) | ||
| private String sourceName; | ||
|
|
||
| @Parameter ( label = "3D Affine" ) | ||
| private String transformation = Arrays.toString( new AffineTransform3D().getRowPackedCopy() ); | ||
| private AffineTransform3D previousTransform; | ||
| private TransformedSource< ? > transformedSource; | ||
|
|
||
| public enum AdditionMode | ||
| { | ||
| Concatenate, | ||
| Replace; | ||
| } | ||
|
|
||
| @Parameter ( label = "Addition Mode" ) | ||
| private AdditionMode mode = AdditionMode.Replace; | ||
|
|
||
| @Parameter ( label = "Preview", callback = "apply" ) | ||
| private Button preview; | ||
|
|
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| private List< SourceAndConverter< ? > > sourceAndConverters; | ||
|
|
||
| @Override | ||
| public void initialize() | ||
| { | ||
| sourceAndConverters = MoBIEHelper.getVisibleSacs( bdvHandle ); | ||
|
|
||
| final List< String > imageNames = sourceAndConverters.stream() | ||
| .map( sac -> sac.getSpimSource().getName() ) | ||
| .collect( Collectors.toList() ); | ||
|
|
||
| getInfo().getMutableInput( "sourceName", String.class ) | ||
| .setChoices( imageNames ); | ||
|
|
||
| } | ||
|
|
||
| @Override | ||
| public void run() | ||
| { | ||
| apply(); | ||
| } | ||
|
|
||
| @Override | ||
| public void cancel() | ||
| { | ||
| if ( transformedSource != null ) | ||
| { | ||
| transformedSource.setFixedTransform( previousTransform ); | ||
| bdvHandle.getViewerPanel().requestRepaint(); | ||
| } | ||
| } | ||
|
|
||
| private void apply() | ||
| { | ||
| double[] doubles = parseStringToDoubleArray( transformation ); | ||
| AffineTransform3D additionalTransform = new AffineTransform3D(); | ||
| additionalTransform.set( doubles ); | ||
|
|
||
| if ( additionalTransform.isIdentity() ) | ||
| return; | ||
|
|
||
| // TODO: the below logic will break when the | ||
| // user decides to change the source name | ||
| SourceAndConverter< ? > sourceAndConverter = sourceAndConverters.stream() | ||
| .filter( sac -> sac.getSpimSource().getName().equals( sourceName ) ) | ||
| .findFirst().get(); | ||
|
|
||
| if ( sourceAndConverter.getSpimSource() instanceof TransformedSource ) | ||
| { | ||
| transformedSource = ( TransformedSource< ? > ) sourceAndConverter.getSpimSource(); | ||
|
|
||
| if ( previousTransform != null ) | ||
| { | ||
| // reset transform to initial state | ||
| transformedSource.setFixedTransform( previousTransform ); | ||
| } | ||
| else | ||
| { | ||
| // remember the previous transform | ||
| // such that we can reset it | ||
| previousTransform = new AffineTransform3D(); | ||
| transformedSource.getFixedTransform( previousTransform ); | ||
| } | ||
|
|
||
| if ( mode.equals( AdditionMode.Replace ) ) | ||
| { | ||
| transformedSource.setFixedTransform( additionalTransform ); | ||
| } | ||
| else if ( mode.equals( AdditionMode.Concatenate ) ) | ||
| { | ||
| AffineTransform3D newTransform = previousTransform.copy().preConcatenate( additionalTransform ); | ||
| transformedSource.setFixedTransform( newTransform ); | ||
| } | ||
|
|
||
| bdvHandle.getViewerPanel().requestRepaint(); | ||
| } | ||
| else | ||
| { | ||
| IJ.error( "Cannot set the transformation of a " + sourceAndConverter.getSpimSource().getClass() ); | ||
| } | ||
| } | ||
|
|
||
| public static double[] parseStringToDoubleArray(String arrayStr) { | ||
| arrayStr = arrayStr.replaceAll("[^0-9.,]", ""); | ||
| String[] items = arrayStr.split(",\\s*"); | ||
| double[] doubles = Arrays.stream(items).mapToDouble(Double::parseDouble).toArray(); | ||
| return doubles; | ||
| } | ||
| } |
84 changes: 84 additions & 0 deletions
84
src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| /*- | ||
| * #%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; | ||
|
|
||
| import bdv.tools.transformation.TransformedSource; | ||
| import bdv.util.BdvHandle; | ||
| import bdv.viewer.Source; | ||
| import bdv.viewer.SourceAndConverter; | ||
| import ij.IJ; | ||
| import net.imglib2.realtransform.AffineTransform3D; | ||
| import org.embl.mobie.MoBIE; | ||
| import org.embl.mobie.command.CommandConstants; | ||
| import org.embl.mobie.lib.MoBIEHelper; | ||
| import org.embl.mobie.lib.bdv.ScreenShotMaker; | ||
| import org.scijava.Initializable; | ||
| import org.scijava.command.DynamicCommand; | ||
| import org.scijava.module.MutableModuleItem; | ||
| import org.scijava.plugin.Parameter; | ||
| import org.scijava.plugin.Plugin; | ||
| import sc.fiji.bdvpg.bdv.BdvHandleHelper; | ||
| import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
||
| @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Log Images Info") | ||
| public class SourcesInfoCommand implements BdvPlaygroundActionCommand | ||
| { | ||
| static { net.imagej.patcher.LegacyInjector.preinit(); } | ||
|
|
||
| public static final String CAPTURE_SIZE_PIXELS = "Capture size [pixels]: "; | ||
|
|
||
| @Parameter | ||
| public BdvHandle bdvHandle; | ||
|
|
||
| @Override | ||
| public void run() | ||
| { | ||
| List< SourceAndConverter< ? > > visibleSacs = MoBIEHelper.getVisibleSacs( bdvHandle ); | ||
| visibleSacs.forEach( sac -> | ||
| { | ||
| Source< ? > source = sac.getSpimSource(); | ||
| IJ.log( "# " + source.getName() ); | ||
| IJ.log( "Number of resolution levels: " + source.getNumMipmapLevels() ); | ||
| IJ.log( "Voxel size: " + Arrays.toString( source.getVoxelDimensions().dimensionsAsDoubleArray() ) ); | ||
|
|
||
| if ( source instanceof TransformedSource ) | ||
| { | ||
| AffineTransform3D transform3D = new AffineTransform3D(); | ||
| ( ( TransformedSource<?> ) source ).getFixedTransform( transform3D ); | ||
| IJ.log( "Additional transform: " + transform3D ); | ||
| source.getSourceTransform( 0, 0, transform3D ); | ||
| IJ.log( "Full transform: " + transform3D ); | ||
| } | ||
| }); | ||
| } | ||
| } |
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