Revision 6860
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/pom.xml | ||
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<?xml version="1.0" encoding="ISO-8859-1"?> |
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> |
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<modelVersion>4.0.0</modelVersion> |
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<artifactId>org.gvsig.raster.principalcomponents.algorithm</artifactId> |
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<packaging>jar</packaging> |
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<name>org.gvsig.raster.principalcomponents.algorithm</name> |
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<parent> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.raster.principalcomponents</artifactId> |
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<version>2.2.45</version> |
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</parent> |
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<dependencies> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.raster.algorithm</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.i18n</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.tools.lib</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.ui</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.raster.lib.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.raster.lib.impl</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.raster.fmap</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.metadata.lib.basic.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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|
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.geometry.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<!-- |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.geometry.generalpath</artifactId> |
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<scope>runtime</scope> |
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</dependency> |
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--> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.compat.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.compat.se</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.projection.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.projection.cresques.impl</artifactId> |
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<scope>runtime</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.dal.api</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.dal.impl</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.dal.file.lib</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig</groupId> |
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<artifactId>org.gvsig.fmap.dal.spi</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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<dependency> |
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<groupId>org.gvsig.legacy</groupId> |
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<artifactId>jama</artifactId> |
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<scope>compile</scope> |
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</dependency> |
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</dependencies> |
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</project> |
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org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PCAStatisticsProcess.java | ||
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/* gvSIG. Geographic Information System of the Valencian Government |
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* |
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* Copyright (C) 2007-2008 Infrastructures and Transports Department |
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* of the Valencian Government (CIT) |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU General Public License |
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* as published by the Free Software Foundation; either version 2 |
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* of the License, or (at your option) any later version. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU General Public License for more details. |
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* |
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* You should have received a copy of the GNU General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, |
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* MA 02110-1301, USA. |
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* |
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*/ |
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package org.gvsig.raster.principalcomponents.algorithm; |
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import java.awt.geom.Rectangle2D; |
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import java.util.List; |
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import org.cresques.Messages; |
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import org.gvsig.fmap.dal.coverage.RasterLocator; |
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import org.gvsig.fmap.dal.coverage.dataset.Buffer; |
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import org.gvsig.fmap.dal.coverage.datastruct.Extent; |
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import org.gvsig.fmap.dal.coverage.datastruct.NoData; |
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import org.gvsig.fmap.dal.coverage.exception.CloneException; |
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import org.gvsig.fmap.dal.coverage.exception.ProcessInterruptedException; |
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import org.gvsig.fmap.dal.coverage.exception.ROIException; |
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import org.gvsig.fmap.dal.coverage.store.RasterDataStore; |
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import org.gvsig.fmap.dal.exception.CloseException; |
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import org.gvsig.raster.algorithm.process.DataProcess; |
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import org.gvsig.raster.algorithm.process.ProcessException; |
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import org.gvsig.raster.roi.ROI; |
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import org.slf4j.Logger; |
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import org.slf4j.LoggerFactory; |
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|
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import Jama.EigenvalueDecomposition; |
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import Jama.Matrix; |
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|
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/** |
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* This Process computes a <code>PCStatsDataStructure</code> Object from bands of two images in a study zone. |
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* <code>PCStatsDataStructure</code> is a object that contains the needed statistics to Principal Components decomposition |
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* of images. |
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* |
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* @author Nacho Brodin (nachobrodin@gmail.com) |
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* |
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*/ |
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public class PCAStatisticsProcess extends DataProcess { |
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public static final String LAYER_ZONA_ESTUDIO = "LAYER_ZONA_ESTUDIO"; |
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public static String BANDS = "BANDS"; |
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public static String PATH = "PATH"; |
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public static String ROI_EPSG = "ROI_EPSG"; |
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public static String WINDOW = "WINDOW"; |
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public static String RASTER_STORE = "RASTER_STORE"; |
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public static String STATS_RESULT = "STATS_RESULT"; |
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private boolean[] bands = null; |
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private RasterDataStore store = null; |
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private Buffer buffer = null; |
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private Buffer roiBuffer = null; |
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private boolean roiBufferCalculated = false; |
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private double autovalors[] = null; |
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private Matrix coVarMatrix = null; |
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private Matrix autoVectorMatrix = null; |
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private double coVar[][] = null; |
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private static Logger logger = LoggerFactory.getLogger(PCAStatisticsProcess.class.getName()); |
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private double[][] maxminmean = null; |
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private Extent extentResult = null; |
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private String path = null; |
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private List<ROI> rois = null; |
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|
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private boolean[] statsByBandCalculated = null; |
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|
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public static void registerParameters() { |
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registerInputParameter(RASTER_STORE, RasterDataStore.class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerInputParameter(BANDS, Boolean[].class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerInputParameter(PATH, String.class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerOutputParameter(STATS_RESULT, PCStatsDataStructure.class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerOutputParameter(PATH, String.class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerOutputParameter(BANDS, Boolean[].class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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registerOutputParameter(ROI_EPSG, String.class, PrincipalComponentsAlgorithmLibrary.PC_STATS_PROCESS_LABEL); |
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} |
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|
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@Override |
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public void init() { |
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store = (RasterDataStore)getParam(RASTER_STORE); |
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bands = (boolean[])getParam(BANDS); |
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path = getStringParam(PATH); |
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} |
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public double[] getAutoValors() { |
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return autovalors; |
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} |
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/** |
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* @return Autovectors Matrix |
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*/ |
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public Matrix getAutoVectorMatrix() { |
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return autoVectorMatrix; |
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} |
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/** |
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* @return Varianze-covarianze Matrix |
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*/ |
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public Matrix getcoVarMatrix() { |
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return coVarMatrix; |
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} |
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|
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public boolean isInsideOfROI(int x, int y, List<ROI> rois, Extent extentResult) { |
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if(roiBufferCalculated) |
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return (roiBuffer.getElemByte(y, x, 0) == 1); |
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if(roiBuffer == null) |
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roiBuffer = createOutputBuffer(buffer.getWidth(), buffer.getHeight(), 1, Buffer.TYPE_BYTE); |
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boolean a = super.isInsideOfROI(x, y, rois, extentResult); |
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roiBuffer.setElem(y, x, 0, a ? (byte)1: (byte)0); |
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return a; |
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} |
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|
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/** |
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* Calculate the Varianze-covarianze Matrix from bands of a Grid |
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* @throws InterruptedException |
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* @throws ProcessInterruptedException |
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*/ |
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private double[][] covarianceOptimize() throws InterruptedException, ProcessInterruptedException { |
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//NoData |
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NoData nd = RasterLocator.getManager().getDataStructFactory().createDefaultNoData(1, Buffer.TYPE_DOUBLE); |
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double nodata = nd.getValue().doubleValue(); |
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double dSum = 0; |
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int iValues = 0; |
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double[][] coV = new double[buffer.getBandCount()][buffer.getBandCount()]; |
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double valorBandai = 0, valorBandaj = 0; |
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maxminmean = new double[buffer.getBandCount()][4]; |
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statsByBandCalculated = new boolean[buffer.getBandCount()]; |
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for (int i = 0; i < statsByBandCalculated.length; i++) { |
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statsByBandCalculated[i] = false; |
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} |
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loadDataStoreStatistics(); |
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int percent = 0; |
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int maxCounter = 0; |
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for (int i = buffer.getBandCount(); i >= 0; i--) { |
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maxCounter += i; |
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} |
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for (int i = 0; i < buffer.getBandCount(); i++) { |
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double meanBufferToOperatei = getMeanValue(i, buffer); |
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for (int j = i; j < buffer.getBandCount(); j++) { |
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iValues = 0; |
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dSum = 0; |
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double meanBufferToOperatej = getMeanValue(j, buffer); |
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for (int row = 0; row < buffer.getHeight(); row++) { |
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for (int col = 0; col < buffer.getWidth(); col++) { |
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if(isInsideOfROI(col, row, rois, extentResult)) { |
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valorBandai = getData(buffer, row, col, i) - meanBufferToOperatei; |
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valorBandaj = getData(buffer, row, col, j) - meanBufferToOperatej; |
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dSum += valorBandai * valorBandaj; |
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iValues++; |
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} |
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} |
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updatePercent(percent, maxCounter); |
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} |
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roiBufferCalculated = true; |
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// Asigno el valor a la matriz |
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if (iValues > 1) |
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coV[i][j] = dSum / (double)(iValues); |
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else |
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coV[i][j] = nodata; |
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percent ++; |
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updatePercent(percent, maxCounter); |
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} |
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} |
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for (int i = 0; i < buffer.getBandCount(); i++) { |
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for (int j = 0; j < buffer.getBandCount(); j++) { |
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if(j < i) |
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coV[i][j] = coV[j][i]; |
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} |
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} |
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return coV; |
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} |
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// * Devuelve la media de los valores de los pixeles de un buffer incluidos en la zona de estudio |
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/** |
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* Get the mean of values of pixels from a buffer in a study zone |
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* @param bufferToOperate |
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* @return |
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*/ |
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private double getMeanValue(int band, Buffer bufferToOperate) { |
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if(statsByBandCalculated[band]) |
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return maxminmean[band][2]; |
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|
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double mean = 0; |
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double variance = 0; |
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double min = Double.MAX_VALUE; |
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double max = Double.MIN_VALUE; |
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int valuesCounter = 0; |
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for (int j = 0; j < bufferToOperate.getHeight(); j++) { |
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for (int i = 0; i < bufferToOperate.getWidth(); i++) { |
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if (isInsideOfROI(i, j, rois, extentResult)) { |
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double value = getData(bufferToOperate, j, i, band); |
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|
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if(value < min) { |
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min = value; |
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} |
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if(value > max) { |
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max = value; |
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} |
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mean += value; |
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variance += value * value; |
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valuesCounter++; |
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} |
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} |
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|
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} |
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roiBufferCalculated = true; |
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mean = (mean / valuesCounter); |
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variance = variance / (double) valuesCounter - mean * mean; |
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maxminmean[band][0] = max; |
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maxminmean[band][1] = min; |
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maxminmean[band][2] = mean; |
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maxminmean[band][3] = variance; |
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statsByBandCalculated[band] = true; |
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return mean; |
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} |
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|
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private void loadDataStoreStatistics() { |
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if(isAnalizedEntireLayer(getOutputWindow(), rois, store) && store.getStatistics().isCalculated()) { |
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double[] max = store.getStatistics().getMax(); |
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double[] min = store.getStatistics().getMin(); |
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double[] mean = store.getStatistics().getMean(); |
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double[] variance = store.getStatistics().getVariance(); |
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int iBand = 0; |
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for (int i = 0; i < mean.length; i++) { |
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if(bands[i]) { |
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maxminmean[iBand][0] = max[i]; |
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maxminmean[iBand][1] = min[i]; |
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maxminmean[iBand][2] = mean[i]; |
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maxminmean[iBand][3] = variance[i]; |
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statsByBandCalculated[iBand] = true; |
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iBand ++; |
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} |
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} |
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} |
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} |
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@Override |
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public void process() throws ProcessInterruptedException, ProcessException { |
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insertLineLog(Messages.getText("preparing_buffers")); |
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|
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if(getROIEPSG() != null) { |
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try { |
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rois = store.getRois(getROIEPSG()); |
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} catch (ROIException e2) { |
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logger.error(Messages.getText("error_getting_rois"), e2); |
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} |
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} |
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|
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try { |
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store = store.cloneDataStore(); |
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} catch (CloneException e1) { |
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throw new ProcessException("Error cloning the sources", e1); |
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} |
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|
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//Calculo de datos de entrada |
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extentResult = getExtentResult(getOutputWindow(), rois, store); |
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Rectangle2D sourcePxBBox = getSourcePxBox(extentResult, store); |
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buffer = createSourceBuffer(store, sourcePxBBox, bands); |
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|
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insertLineLog(Messages.getText("calc_stats")); |
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|
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try { |
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coVar = covarianceOptimize(); |
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} catch (InterruptedException e) { |
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logger.error(Messages.getText("error_covarianza_optimize"), e); |
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} |
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// Calculo de autovectores: |
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coVarMatrix = new Matrix(coVar); |
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EigenvalueDecomposition eigenvalueDecomp = new EigenvalueDecomposition(coVarMatrix); |
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//Autovectores |
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autoVectorMatrix = eigenvalueDecomp.getV(); |
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|
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// Autovalores |
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autovalors = eigenvalueDecomp.getRealEigenvalues(); |
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|
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PCStatsDataStructure resultStatistics = new PCStatsDataStructure(autoVectorMatrix, autovalors, coVarMatrix); |
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resultStatistics.setMaxMinMean(maxminmean); |
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|
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roiBuffer.dispose(); |
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//Object[] dataROI = new Object[]{vectROI, (int)shift[0].getX(), (int)shift[0].getY()}; |
|
311 |
addOutputValue(STATS_RESULT, resultStatistics); |
|
312 |
addOutputValue(PATH, path); |
|
313 |
addOutputValue(BANDS, bands); |
|
314 |
addOutputValue(ROI_EPSG, getROIEPSG()); |
|
315 |
try { |
|
316 |
store.close(); |
|
317 |
} catch (CloseException e) { |
|
318 |
throw new ProcessException("Error closing the sources", e); |
|
319 |
} |
|
320 |
} |
|
321 |
|
|
322 |
|
|
323 |
public String getTitle() { |
|
324 |
return null; |
|
325 |
} |
|
326 |
} |
|
0 | 327 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PCStatistics.java | ||
---|---|---|
1 |
/* gvSIG. Geographic Information System of the Valencian Government |
|
2 |
* |
|
3 |
* Copyright (C) 2007-2008 Infrastructures and Transports Department |
|
4 |
* of the Valencian Government (CIT) |
|
5 |
* |
|
6 |
* This program is free software; you can redistribute it and/or |
|
7 |
* modify it under the terms of the GNU General Public License |
|
8 |
* as published by the Free Software Foundation; either version 2 |
|
9 |
* of the License, or (at your option) any later version. |
|
10 |
* |
|
11 |
* This program is distributed in the hope that it will be useful, |
|
12 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
|
13 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|
14 |
* GNU General Public License for more details. |
|
15 |
* |
|
16 |
* You should have received a copy of the GNU General Public License |
|
17 |
* along with this program; if not, write to the Free Software |
|
18 |
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, |
|
19 |
* MA 02110-1301, USA. |
|
20 |
* |
|
21 |
*/ |
|
22 |
|
|
23 |
package org.gvsig.raster.principalcomponents.algorithm; |
|
24 |
|
|
25 |
import Jama.Matrix; |
|
26 |
|
|
27 |
/** |
|
28 |
* Represents statistics needed to generate a transformated raster by PCA method |
|
29 |
* @author seriznue |
|
30 |
*/ |
|
31 |
public class PCStatistics { |
|
32 |
|
|
33 |
private Matrix autoVectorsMatrix = null; |
|
34 |
private Matrix coVarMatrix = null; |
|
35 |
private double autovalues[] = null; |
|
36 |
|
|
37 |
/** |
|
38 |
* Constructor. |
|
39 |
* |
|
40 |
* @param autoVectorsMatrix Matrix of autovectors. |
|
41 |
* @param autovalues Array of eigenvalues. |
|
42 |
* @param coVarMatrix Matrix of Covariance. |
|
43 |
*/ |
|
44 |
public PCStatistics(Matrix autoVectorsMatrix, double[] autovalues, Matrix coVarMatrix) { |
|
45 |
this.autoVectorsMatrix = autoVectorsMatrix; |
|
46 |
this.autovalues = autovalues; |
|
47 |
this.coVarMatrix = coVarMatrix; |
|
48 |
} |
|
49 |
|
|
50 |
|
|
51 |
public Matrix getAutoVectorsMatrix() { |
|
52 |
return autoVectorsMatrix; |
|
53 |
} |
|
54 |
|
|
55 |
|
|
56 |
public void setAutoVectorsMatrix(Matrix autoVectorsMatrix) { |
|
57 |
this.autoVectorsMatrix = autoVectorsMatrix; |
|
58 |
} |
|
59 |
|
|
60 |
|
|
61 |
public Matrix getCoVarMatrix() { |
|
62 |
return coVarMatrix; |
|
63 |
} |
|
64 |
|
|
65 |
|
|
66 |
public void setCoVarMatrix(Matrix coVarMatrix) { |
|
67 |
this.coVarMatrix = coVarMatrix; |
|
68 |
} |
|
69 |
|
|
70 |
|
|
71 |
public double[] getAutovalues() { |
|
72 |
return autovalues; |
|
73 |
} |
|
74 |
|
|
75 |
|
|
76 |
public void setAutovalors(double[] autovalors) { |
|
77 |
this.autovalues = autovalors; |
|
78 |
} |
|
79 |
|
|
80 |
} |
|
0 | 81 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PrincipalComponentsAlgorithmLibrary.java | ||
---|---|---|
1 |
package org.gvsig.raster.principalcomponents.algorithm; |
|
2 |
|
|
3 |
import org.gvsig.i18n.Messages; |
|
4 |
import org.gvsig.raster.algorithm.RasterBaseAlgorithmLibrary; |
|
5 |
import org.gvsig.tools.library.AbstractLibrary; |
|
6 |
import org.gvsig.tools.library.LibraryException; |
|
7 |
|
|
8 |
/** |
|
9 |
* Initialization of PrincipalComponentsAlgorithmLibrary library. |
|
10 |
*/ |
|
11 |
public class PrincipalComponentsAlgorithmLibrary extends AbstractLibrary { |
|
12 |
public static final String PC_PROCESS_LABEL = "PrincipalComponentsProcess"; |
|
13 |
public static final String PC_STATS_PROCESS_LABEL = "StatsPrincipalComponentsProcess"; |
|
14 |
|
|
15 |
@Override |
|
16 |
protected void doInitialize() throws LibraryException { |
|
17 |
// Nothing to do |
|
18 |
} |
|
19 |
|
|
20 |
@Override |
|
21 |
protected void doPostInitialize() throws LibraryException { |
|
22 |
//Registers the process and its parameters |
|
23 |
RasterBaseAlgorithmLibrary.register(PC_STATS_PROCESS_LABEL, PCAStatisticsProcess.class); |
|
24 |
PCAStatisticsProcess.registerParameters(); |
|
25 |
RasterBaseAlgorithmLibrary.register(PC_PROCESS_LABEL, PrincipalComponentsProcess.class); |
|
26 |
PrincipalComponentsProcess.registerParameters(); |
|
27 |
|
|
28 |
Messages.addResourceFamily( |
|
29 |
"org.gvsig.raster.principalcomponents.algorithm", |
|
30 |
PrincipalComponentsAlgorithmLibrary.class.getClassLoader(), |
|
31 |
PrincipalComponentsAlgorithmLibrary.class.getClass().getName()); |
|
32 |
//registerGeoProcess(new RasterReprojectAlgorithmLibrary()); |
|
33 |
|
|
34 |
Messages.addResourceFamily("org.gvsig.raster.principalcomponents.algorithm.i18n.text", |
|
35 |
PrincipalComponentsAlgorithmLibrary.class.getClassLoader(), |
|
36 |
PrincipalComponentsAlgorithmLibrary.class.getClass().getName()); |
|
37 |
} |
|
38 |
} |
|
0 | 39 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PrincipalComponentsException.java | ||
---|---|---|
1 |
package org.gvsig.raster.principalcomponents.algorithm; |
|
2 |
|
|
3 |
import org.gvsig.raster.algorithm.process.ProcessException; |
|
4 |
|
|
5 |
|
|
6 |
/** |
|
7 |
* This exception is thrown if happen problems processing data with this algorithm. |
|
8 |
*/ |
|
9 |
public class PrincipalComponentsException extends ProcessException { |
|
10 |
private static final long serialVersionUID = -3022090543908771484L; |
|
11 |
|
|
12 |
public PrincipalComponentsException(String msg){ |
|
13 |
super(msg); |
|
14 |
} |
|
15 |
|
|
16 |
public PrincipalComponentsException(String msg, Throwable e){ |
|
17 |
super(msg, e); |
|
18 |
} |
|
19 |
} |
|
0 | 20 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PrincipalComponentsProcess.java | ||
---|---|---|
1 |
package org.gvsig.raster.principalcomponents.algorithm; |
|
2 |
|
|
3 |
import java.awt.geom.Rectangle2D; |
|
4 |
import java.util.List; |
|
5 |
|
|
6 |
import org.gvsig.fmap.dal.coverage.RasterLocator; |
|
7 |
import org.gvsig.fmap.dal.coverage.dataset.Buffer; |
|
8 |
import org.gvsig.fmap.dal.coverage.datastruct.Extent; |
|
9 |
import org.gvsig.fmap.dal.coverage.datastruct.NoData; |
|
10 |
import org.gvsig.fmap.dal.coverage.exception.CloneException; |
|
11 |
import org.gvsig.fmap.dal.coverage.exception.ProcessInterruptedException; |
|
12 |
import org.gvsig.fmap.dal.coverage.exception.ROIException; |
|
13 |
import org.gvsig.fmap.dal.coverage.store.RasterDataStore; |
|
14 |
import org.gvsig.i18n.Messages; |
|
15 |
import org.gvsig.raster.algorithm.process.DataProcess; |
|
16 |
import org.gvsig.raster.algorithm.process.ProcessException; |
|
17 |
import org.gvsig.raster.roi.ROI; |
|
18 |
|
|
19 |
import Jama.Matrix; |
|
20 |
|
|
21 |
/** |
|
22 |
* PCA Process |
|
23 |
* @author Nacho Brodin (nachobrodin@gmail.com) |
|
24 |
*/ |
|
25 |
public class PrincipalComponentsProcess extends DataProcess { |
|
26 |
public static String RASTER_STORE = "RASTER_STORE"; |
|
27 |
public static String PATH = "PATH"; |
|
28 |
public static String FILENAME = "FILENAME"; |
|
29 |
|
|
30 |
public static final String BUFFERS = "BUFFERS"; |
|
31 |
public static final String SELECTEDPCS = "SELECTEDPCS"; |
|
32 |
public static final String PCSTATISTICS = "PCSTATISTICS"; |
|
33 |
public static final String GRAPHIC_DATA = "GRAPHIC_DATA"; |
|
34 |
public static final String BANDS = "BANDS"; |
|
35 |
|
|
36 |
private RasterDataStore store = null; |
|
37 |
private String filename = null; |
|
38 |
|
|
39 |
private PCStatsDataStructure pcStatistics = null; |
|
40 |
private List<ROI> rois = null; |
|
41 |
private Extent extentResult = null; |
|
42 |
private boolean[] selectedPCs = null; |
|
43 |
private boolean[] bands = null; |
|
44 |
private int[] selectedBands = null; |
|
45 |
private NoData nodata = null; |
|
46 |
|
|
47 |
|
|
48 |
public static void registerParameters() { |
|
49 |
registerInputParameter(RASTER_STORE, RasterDataStore.class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
50 |
registerInputParameter(PCSTATISTICS, PCStatsDataStructure.class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
51 |
registerInputParameter(PATH, String.class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
52 |
registerInputParameter(SELECTEDPCS, Boolean[].class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
53 |
registerInputParameter(BANDS, Boolean[].class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
54 |
|
|
55 |
registerOutputParameter(FILENAME, String.class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
56 |
registerOutputParameter(GRAPHIC_DATA, Double[].class, PrincipalComponentsAlgorithmLibrary.PC_PROCESS_LABEL); |
|
57 |
} |
|
58 |
|
|
59 |
public void init() { |
|
60 |
store = getParam(RASTER_STORE) != null ? (RasterDataStore)getParam(RASTER_STORE) : null; |
|
61 |
filename = getStringParam(PATH); |
|
62 |
selectedPCs = (boolean[]) getParam(SELECTEDPCS); |
|
63 |
bands = (boolean[]) getParam(BANDS); |
|
64 |
pcStatistics = (PCStatsDataStructure) getParam(PCSTATISTICS); |
|
65 |
} |
|
66 |
|
|
67 |
public void process() throws ProcessInterruptedException, ProcessException { |
|
68 |
insertLineLog(Messages.getText("processing_pc")); |
|
69 |
try { |
|
70 |
if (store == null) |
|
71 |
throw new PrincipalComponentsException(Messages.getText("need_a_input")); |
|
72 |
|
|
73 |
if(getROIEPSG() != null) { |
|
74 |
try { |
|
75 |
rois = store.getRois(getROIEPSG()); |
|
76 |
} catch (ROIException e2) { |
|
77 |
logger.error(Messages.getText("error_getting_rois"), e2); |
|
78 |
} |
|
79 |
} |
|
80 |
|
|
81 |
try { |
|
82 |
store = ((RasterDataStore)store).cloneDataStore(); |
|
83 |
} catch (CloneException e) { |
|
84 |
new PrincipalComponentsException("Error cloning the input DataStore", e); |
|
85 |
} |
|
86 |
|
|
87 |
extentResult = getExtentResult(getOutputWindow(), rois, store); |
|
88 |
Rectangle2D sourcePxBBox = getSourcePxBox(extentResult, store); |
|
89 |
|
|
90 |
double cellSize = store.getCellSize(); |
|
91 |
|
|
92 |
nodata = RasterLocator.getManager().getDataStructFactory().createDefaultNoData(1, Buffer.TYPE_DOUBLE); |
|
93 |
double nodataValue = nodata.getValue().doubleValue(); |
|
94 |
|
|
95 |
int numberOfOutputBands = getNumberOfOutputBands(selectedPCs); |
|
96 |
|
|
97 |
Buffer outputBuffer = createOutputBuffer((int)sourcePxBBox.getWidth(), (int)sourcePxBBox.getHeight(), numberOfOutputBands); |
|
98 |
Buffer sourceBuffer = createSourceBuffer(store, sourcePxBBox, bands); |
|
99 |
|
|
100 |
// Matriz Autovectores |
|
101 |
// Colocamos la matriz en el orden correcto: |
|
102 |
/* |
|
103 |
* b3 b2 b1 c1 c2 c3 | | | | Cambio de orden de columnas de la matriz |
|
104 |
* transpuesta ___ \ / V c1 c2 c3 b1 b2 b3 |
|
105 |
*/ |
|
106 |
Matrix autovect = changeColumns((pcStatistics.getAutoVectorsMatrix().transpose())); |
|
107 |
insertLineLog(Messages.getText("writting_in_buffer")); |
|
108 |
|
|
109 |
for (int i = 0; i < sourceBuffer.getHeight(); i++) { |
|
110 |
for (int j = 0; j < sourceBuffer.getWidth(); j++) { |
|
111 |
|
|
112 |
if (isInsideOfROI(j, i, rois, extentResult)) { |
|
113 |
for (int iComponent = 0; iComponent < sourceBuffer.getBandCount(); iComponent++) { |
|
114 |
if(selectedPCs[iComponent]) { |
|
115 |
double valor = 0; |
|
116 |
for (int iBand = 0; iBand < sourceBuffer.getBandCount(); iBand++) { |
|
117 |
valor += getData(sourceBuffer, i, j, iBand) * autovect.get(iBand, iComponent); |
|
118 |
} |
|
119 |
int indexBandResult = indexBandResult(selectedPCs, iComponent); |
|
120 |
outputBuffer.setElem(i, j, indexBandResult, (double) valor); |
|
121 |
} |
|
122 |
} |
|
123 |
|
|
124 |
} else { |
|
125 |
for (int iBand = 0; iBand < outputBuffer.getBandCount(); iBand++) { |
|
126 |
outputBuffer.setElem(i, j, iBand, nodataValue); |
|
127 |
} |
|
128 |
} |
|
129 |
} |
|
130 |
updatePercent((int)(i * 100 / sourcePxBBox.getHeight()), 100); |
|
131 |
} |
|
132 |
|
|
133 |
super.exportRaster(filename, outputBuffer, cellSize, extentResult.getULX(), |
|
134 |
extentResult.getULY(), nodata, store.getProjection()); |
|
135 |
|
|
136 |
addOutputValue(FILENAME, filename); |
|
137 |
addOutputValue(GRAPHIC_DATA, filename); |
|
138 |
} catch (PrincipalComponentsException e) { |
|
139 |
if (incrementableTask != null) |
|
140 |
incrementableTask.processFinalize(); |
|
141 |
messageBoxError("principal_components", null, e); |
|
142 |
} |
|
143 |
} |
|
144 |
|
|
145 |
|
|
146 |
/** |
|
147 |
* Gets the number of the selected bands |
|
148 |
* @param bandsPCs |
|
149 |
* @return |
|
150 |
*/ |
|
151 |
private int getNumberOfOutputBands(boolean[] b) { |
|
152 |
int bandCount = 0; |
|
153 |
for (int i = 0; i < b.length; i++) { |
|
154 |
if(b[i]) |
|
155 |
bandCount++; |
|
156 |
} |
|
157 |
return bandCount; |
|
158 |
} |
|
159 |
|
|
160 |
/** |
|
161 |
* Gets the band index of the result buffer |
|
162 |
* @param bandsPCs |
|
163 |
* @param indexIn |
|
164 |
* @return |
|
165 |
*/ |
|
166 |
private int indexBandResult(boolean[] bandsPCs, int indexIn) { |
|
167 |
if(selectedBands == null) { |
|
168 |
selectedBands = new int[bandsPCs.length]; |
|
169 |
int indexOut = 0; |
|
170 |
for (int i = 0; i < bandsPCs.length; i++) { |
|
171 |
if(bandsPCs[i]) { |
|
172 |
selectedBands[i] = indexOut; |
|
173 |
indexOut++; |
|
174 |
} else |
|
175 |
selectedBands[i] = -1; |
|
176 |
} |
|
177 |
} |
|
178 |
return selectedBands[indexIn]; |
|
179 |
} |
|
180 |
|
|
181 |
public double getScaleFactor(Buffer buffer, int sizePreview) { |
|
182 |
double x = 0, y = 0; |
|
183 |
x = 200.0 / buffer.getWidth(); |
|
184 |
y = 200.0 / buffer.getHeight(); |
|
185 |
|
|
186 |
if (x > y) { |
|
187 |
return y; |
|
188 |
} else { |
|
189 |
return x; |
|
190 |
} |
|
191 |
} |
|
192 |
|
|
193 |
private Matrix changeColumns(Matrix m) { |
|
194 |
Matrix result = new Matrix(m.getRowDimension(), m.getColumnDimension()); |
|
195 |
int k = m.getColumnDimension() - 1; |
|
196 |
for (int i = 0; i < m.getRowDimension(); i++) { |
|
197 |
for (int j = 0; j < m.getColumnDimension(); j++) { |
|
198 |
result.set(i, j, m.get(k - i, j)); |
|
199 |
} |
|
200 |
} |
|
201 |
return result; |
|
202 |
} |
|
203 |
|
|
204 |
public String getTitle() { |
|
205 |
return Messages.getText("..."); |
|
206 |
} |
|
207 |
} |
|
0 | 208 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/java/org/gvsig/raster/principalcomponents/algorithm/PCStatsDataStructure.java | ||
---|---|---|
1 |
/* gvSIG. Geographic Information System of the Valencian Government |
|
2 |
* |
|
3 |
* Copyright (C) 2007-2008 Infrastructures and Transports Department |
|
4 |
* of the Valencian Government (CIT) |
|
5 |
* |
|
6 |
* This program is free software; you can redistribute it and/or |
|
7 |
* modify it under the terms of the GNU General Public License |
|
8 |
* as published by the Free Software Foundation; either version 2 |
|
9 |
* of the License, or (at your option) any later version. |
|
10 |
* |
|
11 |
* This program is distributed in the hope that it will be useful, |
|
12 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
|
13 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|
14 |
* GNU General Public License for more details. |
|
15 |
* |
|
16 |
* You should have received a copy of the GNU General Public License |
|
17 |
* along with this program; if not, write to the Free Software |
|
18 |
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, |
|
19 |
* MA 02110-1301, USA. |
|
20 |
* |
|
21 |
*/ |
|
22 |
|
|
23 |
package org.gvsig.raster.principalcomponents.algorithm; |
|
24 |
|
|
25 |
import Jama.Matrix; |
|
26 |
|
|
27 |
/** |
|
28 |
* Represents statistics needed to generate a transformated raster by PCA method |
|
29 |
* @author seriznue |
|
30 |
*/ |
|
31 |
public class PCStatsDataStructure { |
|
32 |
|
|
33 |
private Matrix autoVectorsMatrix = null; |
|
34 |
private Matrix coVarMatrix = null; |
|
35 |
private double autovalues[] = null; |
|
36 |
private double[][] maxminmean = null; |
|
37 |
|
|
38 |
/** |
|
39 |
* Constructor. |
|
40 |
* |
|
41 |
* @param autoVectorsMatrix Matrix of autovectors. |
|
42 |
* @param autovalues Array of eigenvalues. |
|
43 |
* @param coVarMatrix Matrix of Covariance. |
|
44 |
*/ |
|
45 |
public PCStatsDataStructure(Matrix autoVectorsMatrix, double[] autovalues, Matrix coVarMatrix) { |
|
46 |
this.autoVectorsMatrix = autoVectorsMatrix; |
|
47 |
this.autovalues = autovalues; |
|
48 |
this.coVarMatrix = coVarMatrix; |
|
49 |
} |
|
50 |
|
|
51 |
|
|
52 |
public Matrix getAutoVectorsMatrix() { |
|
53 |
return autoVectorsMatrix; |
|
54 |
} |
|
55 |
|
|
56 |
|
|
57 |
public void setAutoVectorsMatrix(Matrix autoVectorsMatrix) { |
|
58 |
this.autoVectorsMatrix = autoVectorsMatrix; |
|
59 |
} |
|
60 |
|
|
61 |
public double[][] getMaxMinMean() { |
|
62 |
return maxminmean; |
|
63 |
} |
|
64 |
|
|
65 |
public void setMaxMinMean(double[][] maxminmean) { |
|
66 |
this.maxminmean = maxminmean; |
|
67 |
} |
|
68 |
|
|
69 |
|
|
70 |
public Matrix getCoVarMatrix() { |
|
71 |
return coVarMatrix; |
|
72 |
} |
|
73 |
|
|
74 |
|
|
75 |
public void setCoVarMatrix(Matrix coVarMatrix) { |
|
76 |
this.coVarMatrix = coVarMatrix; |
|
77 |
} |
|
78 |
|
|
79 |
|
|
80 |
public double[] getAutovalues() { |
|
81 |
return autovalues; |
|
82 |
} |
|
83 |
|
|
84 |
|
|
85 |
public void setAutovalors(double[] autovalors) { |
|
86 |
this.autovalues = autovalors; |
|
87 |
} |
|
88 |
|
|
89 |
} |
|
0 | 90 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/resources-plugin/org/gvsig/raster/principalcomponents/algorithm/i18n/text.properties | ||
---|---|---|
1 |
layers_dont_intersect=Las capas no intersectan |
|
2 |
roi_not_inside=La zona de estudio no esta contenida en la extensi?n de las capas |
|
3 |
calc_stats="Calculando estad?sticas para PCA" |
|
4 |
error_covarianza_optimize="Error en el covarianceOptimize() : C?lculo de la matriz varianza covarianza de las bandas de un Grid." |
|
5 |
preparing_buffers=Preparando buffers |
|
0 | 6 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/resources-plugin/org/gvsig/raster/principalcomponents/algorithm/i18n/text_en.properties | ||
---|---|---|
1 |
layers_dont_intersect=Layers do not intersect |
|
2 |
roi_not_inside=The region of interest are not inside the extension of the layers |
|
3 |
calc_stats="Calculating statistics to PCA" |
|
4 |
error_covarianza_optimize="Error in covarianceOptimize." |
|
5 |
preparing_buffers=Preparing buffers |
|
0 | 6 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/resources/META-INF/services/org.gvsig.tools.library.Library | ||
---|---|---|
1 |
org.gvsig.raster.principalcomponents.algorithm.PrincipalComponentsAlgorithmLibrary |
|
0 | 2 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/resources/org/gvsig/raster/principalcomponents/algorithm/i18n/text.properties | ||
---|---|---|
1 |
layers_dont_intersect=Las capas no intersectan |
|
2 |
roi_not_inside=La zona de estudio no esta contenida en la extensi?n de las capas |
|
3 |
calc_stats="Calculando estad?sticas para PCA" |
|
4 |
error_covarianza_optimize="Error en el covarianceOptimize() : C?lculo de la matriz varianza covarianza de las bandas de un Grid." |
|
5 |
preparing_buffers=Preparando buffers |
|
6 |
writting_in_buffer=Escribiendo en buffer de salida |
|
7 |
processing_pc=Procesando Componentes Principales |
|
8 |
principal_components=Componentes Principales |
|
0 | 9 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.algorithm/src/main/resources/org/gvsig/raster/principalcomponents/algorithm/i18n/text_en.properties | ||
---|---|---|
1 |
layers_dont_intersect=Layers do not intersect |
|
2 |
roi_not_inside=The region of interest are not inside the extension of the layers |
|
3 |
calc_stats="Calculating statistics to PCA" |
|
4 |
error_covarianza_optimize="Error in covarianceOptimize." |
|
5 |
preparing_buffers=Preparing buffers |
|
6 |
writting_in_buffer=Writing in the output buffer |
|
7 |
processing_pc=Processing Principal Components |
|
8 |
principal_components=Principal Components |
|
0 | 9 |
org.gvsig.raster.principalcomponents/tags/org.gvsig.raster.principalcomponents-2.2.45/org.gvsig.raster.principalcomponents.swing/org.gvsig.raster.principalcomponents.swing.impl/src/main/resources/org/gvsig/raster/principalcomponents/swing/impl/i18n/text.properties | ||
---|---|---|
1 |
components_selection=Selecci?n de componentes |
|
2 |
autovalor=Autovalor |
|
3 |
by_band=Por banda |
|
4 |
var_covar=Matriz varianza-covarianza |
|
5 |
autovector=Autovector |
|
6 |
generate=Generar |
|
7 |
stats=Estadisticas |
|
8 |
use_rois=Usar regiones de inter?s de la capa |
Also available in: Unified diff