/* * Copyright 2010, 2011 Institut Pasteur. * * This file is part of ICY. * * ICY is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * ICY is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with ICY. If not, see <http://www.gnu.org/licenses/>. */ package plugins.tutorial.roi; import icy.gui.dialog.MessageDialog; import icy.gui.frame.progress.AnnounceFrame; import icy.image.IcyBufferedImage; import icy.plugin.abstract_.PluginActionable; import icy.sequence.Sequence; import icy.type.collection.array.Array1DUtil; import plugins.kernel.roi.roi2d.ROI2DArea; /** * This tutorial creates an Area ROI containing pixel of values greater than the mean of the band 0 * of the image (t=0, z=0). It creates a ROI2DArea * * @author Fabrice de Chaumont * @author Stephane Dallongeville */ public class CreateAreaROI extends PluginActionable { @Override public void run() { // Display what this tutorial perform. new AnnounceFrame( "This tutorial creates an Area ROI containing pixel of values greater than the mean of the band 0 of the image (t=0, z=0)."); // Get the current active sequence Sequence sequence = getActiveSequence(); // Check if sequence exists. if (sequence == null) { MessageDialog.showDialog("Please open a sequence to use this plugin.", MessageDialog.WARNING_MESSAGE); return; } // Get the image at t=0 and z=0 IcyBufferedImage image = sequence.getImage(0, 0); // Check if the image exists if (image == null) { MessageDialog.showDialog("No image is present at t=0 and z=0.", MessageDialog.WARNING_MESSAGE); return; } // Get the data of the image for band 0 as a linear buffer, regardless of the type. Object imageData = image.getDataXY(0); // Get a copy of the data in double. double[] dataBuffer = Array1DUtil.arrayToDoubleArray(imageData, image.isSignedDataType()); // Compute mean double total = 0; for (int i = 0; i < dataBuffer.length; i++) total += dataBuffer[i]; double mean = total / dataBuffer.length; // Compute mask boolean[] mask = new boolean[dataBuffer.length]; for (int i = 0; i < dataBuffer.length; i++) // equivalent to if ( dataBuffer[i] > mean ) mask[i]=true; else mask[i]=false; mask[i] = (dataBuffer[i] > mean); // create ROI ROI2DArea roi = new ROI2DArea(); // fill the roi roi.setAsBooleanMask(0, 0, sequence.getWidth(), sequence.getHeight(), mask); // add the roi to the sequence sequence.addROI(roi); } }