/*- * #%L * Scenery-backed 3D visualization package for ImageJ. * %% * Copyright (C) 2016 - 2018 SciView developers. * %% * 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.iview.commands.edit; import static sc.iview.commands.MenuWeights.EDIT; import static sc.iview.commands.MenuWeights.EDIT_ADD_LABEL_IMAGE; import net.imagej.Dataset; import net.imagej.mesh.Mesh; import net.imagej.ops.OpService; import net.imglib2.Cursor; import net.imglib2.Dimensions; import net.imglib2.RandomAccessibleInterval; import net.imglib2.img.Img; import net.imglib2.roi.labeling.ImgLabeling; import net.imglib2.roi.labeling.LabelRegion; import net.imglib2.roi.labeling.LabelRegions; import net.imglib2.roi.labeling.LabelingType; import net.imglib2.type.numeric.RealType; import net.imglib2.type.numeric.integer.IntType; import net.imglib2.util.Util; import net.imglib2.view.Views; import org.scijava.command.Command; import org.scijava.plugin.Menu; import org.scijava.plugin.Parameter; import org.scijava.plugin.Plugin; import sc.iview.SciView; /** * Adds a label image to the scene. * * @author Robert Haase, Scientific Computing Facility, MPI-CBG Dresden */ @Plugin(type = Command.class, menuRoot = "SciView", // menu = { @Menu(label = "Edit", weight = EDIT), // @Menu(label = "Add Label Image", weight = EDIT_ADD_LABEL_IMAGE) }) public class AddLabelImage<T extends RealType<T>> implements Command { @Parameter private OpService ops; @Parameter private SciView sciView; @Parameter private Dataset currentImage; @Override public void run() { // interpret the current image as a label image and convert it to ImgLabeling @SuppressWarnings("unchecked") Img<T> labelMap = ( Img<T> ) currentImage.getImgPlus(); final Dimensions dims = labelMap; final IntType t = new IntType(); final RandomAccessibleInterval<IntType> img = Util.getArrayOrCellImgFactory( dims, t ).create( dims, t ); ImgLabeling<Integer, IntType> labeling = new ImgLabeling<>( img ); final Cursor<LabelingType<Integer>> labelCursor = Views.flatIterable( labeling ).cursor(); for( final T input : Views.flatIterable( labelMap ) ) { final LabelingType<Integer> element = labelCursor.next(); if( input.getRealFloat() != 0 ) { element.add( ( int ) input.getRealFloat() ); } } // take the regions, process them to meshes and put it in the viewer LabelRegions<Integer> labelRegions = new LabelRegions<>( labeling ); Object[] regionsArr = labelRegions.getExistingLabels().toArray(); for( int i = 0; i < labelRegions.getExistingLabels().size(); i++ ) { LabelRegion<Integer> lr = labelRegions.getLabelRegion( ( Integer ) regionsArr[i] ); Mesh mesh = ops.geom().marchingCubes( lr ); sciView.addMesh( mesh ); } } }