Révision 180
| tmp/org.txm.ca.core/plugin.xml (revision 180) | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<?eclipse version="3.4"?> |
|
| 3 |
<plugin> |
|
| 4 |
<extension |
|
| 5 |
point="org.eclipse.core.runtime.preferences"> |
|
| 6 |
<initializer |
|
| 7 |
class="org.txm.ca.core.preferences.CAPreferences"> |
|
| 8 |
</initializer> |
|
| 9 |
</extension> |
|
| 10 |
<extension |
|
| 11 |
point="org.txm.chartsengine.chartcreator"> |
|
| 12 |
<ChartCreator |
|
| 13 |
class="org.txm.ca.core.chartsengine.jfreechart.themes.highcharts.chartcreators.JFCCAChartCreator" |
|
| 14 |
fileNamePrefix="ca"> |
|
| 15 |
</ChartCreator> |
|
| 16 |
<ChartCreator |
|
| 17 |
chartType="Singular Values" |
|
| 18 |
class="org.txm.ca.core.chartsengine.jfreechart.themes.highcharts.chartcreators.JFCSingularValueChartCreator" |
|
| 19 |
fileNamePrefix="singular_values"> |
|
| 20 |
</ChartCreator> |
|
| 21 |
<ChartCreator |
|
| 22 |
class="org.txm.ca.core.chartsengine.r.RCAChartCreator" |
|
| 23 |
fileNamePrefix="ca"> |
|
| 24 |
</ChartCreator> |
|
| 25 |
<ChartCreator |
|
| 26 |
chartType="SingularValues" |
|
| 27 |
class="org.txm.ca.core.chartsengine.r.RSingularValuesChartCreator" |
|
| 28 |
fileNamePrefix="singular_values"> |
|
| 29 |
</ChartCreator> |
|
| 30 |
</extension> |
|
| 31 |
|
|
| 32 |
</plugin> |
|
| 0 | 33 | |
| tmp/org.txm.ca.core/.settings/org.eclipse.jdt.core.prefs (revision 180) | ||
|---|---|---|
| 1 |
eclipse.preferences.version=1 |
|
| 2 |
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled |
|
| 3 |
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 |
|
| 4 |
org.eclipse.jdt.core.compiler.compliance=1.6 |
|
| 5 |
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error |
|
| 6 |
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error |
|
| 7 |
org.eclipse.jdt.core.compiler.source=1.6 |
|
| 0 | 8 | |
| tmp/org.txm.ca.core/.classpath (revision 180) | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<classpath> |
|
| 3 |
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/> |
|
| 4 |
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/> |
|
| 5 |
<classpathentry kind="src" path="src"/> |
|
| 6 |
<classpathentry kind="output" path="bin"/> |
|
| 7 |
</classpath> |
|
| 0 | 8 | |
| tmp/org.txm.ca.core/META-INF/MANIFEST.MF (revision 180) | ||
|---|---|---|
| 1 |
Manifest-Version: 1.0 |
|
| 2 |
Bundle-ManifestVersion: 2 |
|
| 3 |
Bundle-Name: CA Core |
|
| 4 |
Bundle-SymbolicName: org.txm.ca.core;singleton:=true |
|
| 5 |
Bundle-Version: 1.0.0.qualifier |
|
| 6 |
Bundle-RequiredExecutionEnvironment: JavaSE-1.6 |
|
| 7 |
Require-Bundle: org.txm.chartsengine.core;bundle-version="1.0.0", |
|
| 8 |
org.txm.core;bundle-version="0.7.0", |
|
| 9 |
org.eclipse.core.runtime;bundle-version="3.10.0", |
|
| 10 |
org.txm.chartsengine.r.core;bundle-version="1.0.0", |
|
| 11 |
org.txm.chartsengine.jfreechart.core;bundle-version="1.0.0", |
|
| 12 |
org.txm.lexicaltable.core |
|
| 13 |
Export-Package: org.txm.ca.core.chartsengine.base, |
|
| 14 |
org.txm.ca.core.chartsengine.jfreechart.datasets, |
|
| 15 |
org.txm.ca.core.chartsengine.jfreechart.themes.highcharts.chartcreators, |
|
| 16 |
org.txm.ca.core.chartsengine.jfreechart.themes.highcharts.renderers, |
|
| 17 |
org.txm.ca.core.chartsengine.r, |
|
| 18 |
org.txm.ca.core.functions, |
|
| 19 |
org.txm.ca.core.messages, |
|
| 20 |
org.txm.ca.core.preferences, |
|
| 21 |
org.txm.ca.core.statsengine.r.functions |
|
| 0 | 22 | |
| tmp/org.txm.ca.core/.project (revision 180) | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<projectDescription> |
|
| 3 |
<name>org.txm.ca.core</name> |
|
| 4 |
<comment></comment> |
|
| 5 |
<projects> |
|
| 6 |
</projects> |
|
| 7 |
<buildSpec> |
|
| 8 |
<buildCommand> |
|
| 9 |
<name>org.eclipse.jdt.core.javabuilder</name> |
|
| 10 |
<arguments> |
|
| 11 |
</arguments> |
|
| 12 |
</buildCommand> |
|
| 13 |
<buildCommand> |
|
| 14 |
<name>org.eclipse.pde.ManifestBuilder</name> |
|
| 15 |
<arguments> |
|
| 16 |
</arguments> |
|
| 17 |
</buildCommand> |
|
| 18 |
<buildCommand> |
|
| 19 |
<name>org.eclipse.pde.SchemaBuilder</name> |
|
| 20 |
<arguments> |
|
| 21 |
</arguments> |
|
| 22 |
</buildCommand> |
|
| 23 |
</buildSpec> |
|
| 24 |
<natures> |
|
| 25 |
<nature>org.eclipse.pde.PluginNature</nature> |
|
| 26 |
<nature>org.eclipse.jdt.core.javanature</nature> |
|
| 27 |
</natures> |
|
| 28 |
</projectDescription> |
|
| 0 | 29 | |
| tmp/org.txm.ca.core/src/org/txm/ca/core/preferences/CAPreferences.java (revision 180) | ||
|---|---|---|
| 1 |
package org.txm.ca.core.preferences; |
|
| 2 |
|
|
| 3 |
|
|
| 4 |
import org.eclipse.core.runtime.preferences.DefaultScope; |
|
| 5 |
import org.osgi.framework.FrameworkUtil; |
|
| 6 |
import org.osgi.service.prefs.Preferences; |
|
| 7 |
import org.txm.core.preferences.TXMPreferences; |
|
| 8 |
|
|
| 9 |
/** |
|
| 10 |
* Default preferences initializer. |
|
| 11 |
* |
|
| 12 |
* @author mdecorde |
|
| 13 |
* @author sjacquot |
|
| 14 |
* |
|
| 15 |
*/ |
|
| 16 |
public class CAPreferences extends TXMPreferences {
|
|
| 17 |
|
|
| 18 |
|
|
| 19 |
// auto populate the preference node qualifier from the current bundle id |
|
| 20 |
public static final String PREFERENCES_NODE = FrameworkUtil.getBundle(CAPreferences.class).getSymbolicName(); |
|
| 21 |
|
|
| 22 |
|
|
| 23 |
public static final String PREFERENCES_PREFIX = "ca_"; //$NON-NLS-1$ |
|
| 24 |
|
|
| 25 |
|
|
| 26 |
|
|
| 27 |
/** Lexical table FMIN. */ |
|
| 28 |
public static final String F_MIN = PREFERENCES_PREFIX + "lt_fmin"; //$NON-NLS-1$ |
|
| 29 |
/** Lexical table VMAX. */ |
|
| 30 |
public static final String V_MAX = PREFERENCES_PREFIX + "lt_vmax"; //$NON-NLS-1$ |
|
| 31 |
|
|
| 32 |
/** The Constant SHOWINDIVIDUALS. */ |
|
| 33 |
public static final String SHOW_INDIVIDUALS = PREFERENCES_PREFIX + "chart_show_individuals"; //$NON-NLS-1$ |
|
| 34 |
|
|
| 35 |
/** The Constant SHOWVARIABLES. */ |
|
| 36 |
public static final String SHOW_VARIABLES = PREFERENCES_PREFIX + "chart_show_variables"; //$NON-NLS-1$ |
|
| 37 |
|
|
| 38 |
/** The Constant QUALITYDISPLAY. */ |
|
| 39 |
public static final String QUALITY_DISPLAY_FORMAT = PREFERENCES_PREFIX + "quality_display_format"; //$NON-NLS-1$ |
|
| 40 |
|
|
| 41 |
/** The Constant CONTRIBDISPLAY. */ |
|
| 42 |
public static final String CONTRIB_DISPLAY_FORMAT = PREFERENCES_PREFIX + "contrib_display_format"; //$NON-NLS-1$ |
|
| 43 |
|
|
| 44 |
/** The Constant MASSDISPLAY. */ |
|
| 45 |
public static final String MASS_DISPLAY_FORMAT = PREFERENCES_PREFIX + "mass_display_format"; //$NON-NLS-1$ |
|
| 46 |
|
|
| 47 |
public static final String CHI_DISPLAY_FORMAT = PREFERENCES_PREFIX + "chi_display_format"; //$NON-NLS-1$ |
|
| 48 |
|
|
| 49 |
/** The Constant DISTDISPLAY. */ |
|
| 50 |
public static final String DIST_DISPLAY_FORMAT = PREFERENCES_PREFIX + "dist_display_format"; //$NON-NLS-1$ |
|
| 51 |
|
|
| 52 |
/** The Constant COS2DISPLAY. */ |
|
| 53 |
public static final String COS2_DISPLAY_FORMAT = PREFERENCES_PREFIX + "cos2_display_format"; //$NON-NLS-1$ |
|
| 54 |
|
|
| 55 |
/** The Constant COORDDISPLAY. */ |
|
| 56 |
public static final String COORD_DISPLAY_FORMAT = PREFERENCES_PREFIX + "coord_display_format"; //$NON-NLS-1$ |
|
| 57 |
|
|
| 58 |
|
|
| 59 |
public static final String FIRST_DIMENSION = PREFERENCES_PREFIX + "first_dimension"; //$NON-NLS-1$ |
|
| 60 |
public static final String SECOND_DIMENSION = PREFERENCES_PREFIX + "second_dimension"; //$NON-NLS-1$ |
|
| 61 |
|
|
| 62 |
|
|
| 63 |
/** |
|
| 64 |
* |
|
| 65 |
*/ |
|
| 66 |
public CAPreferences() {
|
|
| 67 |
// TODO Auto-generated constructor stub |
|
| 68 |
} |
|
| 69 |
|
|
| 70 |
@Override |
|
| 71 |
public void initializeDefaultPreferences() {
|
|
| 72 |
Preferences preferences = DefaultScope.INSTANCE.getNode(PREFERENCES_NODE); |
|
| 73 |
|
|
| 74 |
preferences.putInt(F_MIN, 10); |
|
| 75 |
preferences.putInt(V_MAX, 200); |
|
| 76 |
|
|
| 77 |
String defaultFormat = "0.00"; //$NON-NLS-1$ |
|
| 78 |
preferences.put(QUALITY_DISPLAY_FORMAT, defaultFormat); |
|
| 79 |
preferences.put(CONTRIB_DISPLAY_FORMAT, defaultFormat); |
|
| 80 |
preferences.put(MASS_DISPLAY_FORMAT, defaultFormat); |
|
| 81 |
preferences.put(CHI_DISPLAY_FORMAT, defaultFormat); |
|
| 82 |
preferences.put(DIST_DISPLAY_FORMAT, defaultFormat); |
|
| 83 |
preferences.put(COS2_DISPLAY_FORMAT, defaultFormat); |
|
| 84 |
preferences.put(COORD_DISPLAY_FORMAT, defaultFormat); |
|
| 85 |
|
|
| 86 |
|
|
| 87 |
preferences.putBoolean(SHOW_INDIVIDUALS, true); |
|
| 88 |
preferences.putBoolean(SHOW_VARIABLES, true); |
|
| 89 |
|
|
| 90 |
preferences.putInt(FIRST_DIMENSION, 1); |
|
| 91 |
preferences.putInt(SECOND_DIMENSION, 2); |
|
| 92 |
|
|
| 93 |
|
|
| 94 |
// shared charts rendering preferences |
|
| 95 |
super.initializeChartsEngineSharedPreferences(preferences); |
|
| 96 |
} |
|
| 97 |
|
|
| 98 |
} |
|
| 0 | 99 | |
| tmp/org.txm.ca.core/src/org/txm/ca/core/statsengine/r/functions/FactoMineRCA.java (revision 180) | ||
|---|---|---|
| 1 |
// Copyright © 2010-2013 ENS de Lyon. |
|
| 2 |
// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of |
|
| 3 |
// Lyon 2, University of Franche-Comté, University of Nice |
|
| 4 |
// Sophia Antipolis, University of Paris 3. |
|
| 5 |
// |
|
| 6 |
// The TXM platform is free software: you can redistribute it |
|
| 7 |
// and/or modify it under the terms of the GNU General Public |
|
| 8 |
// License as published by the Free Software Foundation, |
|
| 9 |
// either version 2 of the License, or (at your option) any |
|
| 10 |
// later version. |
|
| 11 |
// |
|
| 12 |
// The TXM platform is distributed in the hope that it will be |
|
| 13 |
// useful, but WITHOUT ANY WARRANTY; without even the implied |
|
| 14 |
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR |
|
| 15 |
// PURPOSE. See the GNU General Public License for more |
|
| 16 |
// details. |
|
| 17 |
// |
|
| 18 |
// You should have received a copy of the GNU General |
|
| 19 |
// Public License along with the TXM platform. If not, see |
|
| 20 |
// http://www.gnu.org/licenses. |
|
| 21 |
// |
|
| 22 |
// |
|
| 23 |
// |
|
| 24 |
// $LastChangedDate:$ |
|
| 25 |
// $LastChangedRevision:$ |
|
| 26 |
// $LastChangedBy:$ |
|
| 27 |
// |
|
| 28 |
package org.txm.ca.core.statsengine.r.functions; |
|
| 29 |
|
|
| 30 |
import java.io.File; |
|
| 31 |
import java.util.Arrays; |
|
| 32 |
|
|
| 33 |
import org.rosuda.REngine.REXP; |
|
| 34 |
import org.rosuda.REngine.REXPMismatchException; |
|
| 35 |
import org.txm.Messages; |
|
| 36 |
import org.txm.stat.StatException; |
|
| 37 |
import org.txm.stat.data.LexicalTable; |
|
| 38 |
import org.txm.stat.engine.r.RWorkspace; |
|
| 39 |
import org.txm.stat.engine.r.RWorkspaceException; |
|
| 40 |
import org.txm.stat.engine.r.data.QuantitativeDataStructureImpl; |
|
| 41 |
|
|
| 42 |
// TODO: Auto-generated Javadoc |
|
| 43 |
/** |
|
| 44 |
* Access to the R implementation of the Correspondance Analysis. |
|
| 45 |
* |
|
| 46 |
* @author mdecorde |
|
| 47 |
*/ |
|
| 48 |
public class FactoMineRCA implements ICA {
|
|
| 49 |
|
|
| 50 |
/** The singular values. */ |
|
| 51 |
private double[] valeursPropres = null; |
|
| 52 |
|
|
| 53 |
/** The singular values2. */ |
|
| 54 |
private double[] singularValues = null; |
|
| 55 |
|
|
| 56 |
/** The rowmass. */ |
|
| 57 |
private double[] rowmass = null; |
|
| 58 |
|
|
| 59 |
/** The rowdist. */ |
|
| 60 |
private double[] rowdist = null; |
|
| 61 |
|
|
| 62 |
/** The rowinertia. */ |
|
| 63 |
private double[] rowinertia = null; |
|
| 64 |
|
|
| 65 |
/** The colmass. */ |
|
| 66 |
private double[] colmass = null; |
|
| 67 |
|
|
| 68 |
/** The coldist. */ |
|
| 69 |
private double[] coldist = null; |
|
| 70 |
|
|
| 71 |
/** The colinertia. */ |
|
| 72 |
private double[] colinertia = null; |
|
| 73 |
|
|
| 74 |
/** The rowcos2. */ |
|
| 75 |
private double[][] rowcos2 = null; |
|
| 76 |
|
|
| 77 |
/** The rowcontrib. */ |
|
| 78 |
private double[][] rowcontrib = null; |
|
| 79 |
|
|
| 80 |
/** The colcos2. */ |
|
| 81 |
private double[][] colcos2 = null; |
|
| 82 |
|
|
| 83 |
/** The colcontrib. */ |
|
| 84 |
private double[][] colcontrib = null; |
|
| 85 |
|
|
| 86 |
/** The rw. */ |
|
| 87 |
private final RWorkspace rw = RWorkspace.getRWorkspaceInstance(); |
|
| 88 |
|
|
| 89 |
/** The symbol. */ |
|
| 90 |
private final String symbol = QuantitativeDataStructureImpl.createSymbole(FactoMineRCA.class); |
|
| 91 |
|
|
| 92 |
/** The rowscoords. */ |
|
| 93 |
private double[][] rowscoords; |
|
| 94 |
|
|
| 95 |
/** The colscoords. */ |
|
| 96 |
private double[][] colscoords; |
|
| 97 |
|
|
| 98 |
private LexicalTable table; |
|
| 99 |
|
|
| 100 |
/** |
|
| 101 |
* Create a correspondance analysis on the given table. The correspondance |
|
| 102 |
* analysis is computed as soon as the object is created. |
|
| 103 |
* |
|
| 104 |
* @param table the table |
|
| 105 |
* @throws StatException the stat exception |
|
| 106 |
*/ |
|
| 107 |
public FactoMineRCA(LexicalTable table) throws StatException {
|
|
| 108 |
|
|
| 109 |
if (!rw.containsVariable(table.getSymbol())) {
|
|
| 110 |
throw new StatException(Messages.CA_0); |
|
| 111 |
} |
|
| 112 |
|
|
| 113 |
loadLibrary(); |
|
| 114 |
|
|
| 115 |
this.table = table; |
|
| 116 |
try {
|
|
| 117 |
//rw.callFunctionAndAffect("FactoMineR:CA", new String[] { table.getSymbol() }, symbol); //$NON-NLS-1$
|
|
| 118 |
rw.eval(symbol+" <- FactoMineR::CA("+table.getSymbol()+", graph=FALSE)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 119 |
} catch (RWorkspaceException e) {
|
|
| 120 |
throw new StatException(Messages.CA_2 + e.getMessage(), e); |
|
| 121 |
} |
|
| 122 |
} |
|
| 123 |
|
|
| 124 |
/* (non-Javadoc) |
|
| 125 |
* @see org.txm.stat.engine.r.function.ICA#getColContrib() |
|
| 126 |
*/ |
|
| 127 |
@Override |
|
| 128 |
public double[][] getColContrib() throws StatException {
|
|
| 129 |
if (colcontrib == null) {
|
|
| 130 |
try {
|
|
| 131 |
REXP sv = rw.extractItemFromListByName(symbol, "col$contrib"); //$NON-NLS-1$ |
|
| 132 |
colcontrib = sv.asDoubleMatrix(); |
|
| 133 |
// Arrays.sort(rowdist); |
|
| 134 |
} catch (RWorkspaceException e) {
|
|
| 135 |
throw new StatException(Messages.FactoMineRCA_2 + e.getMessage(), e); |
|
| 136 |
} catch (REXPMismatchException e) {
|
|
| 137 |
// TODO Auto-generated catch block |
|
| 138 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 139 |
} |
|
| 140 |
} |
|
| 141 |
return colcontrib; |
|
| 142 |
} |
|
| 143 |
|
|
| 144 |
/* (non-Javadoc) |
|
| 145 |
* @see org.txm.stat.engine.r.function.ICA#getColCos2() |
|
| 146 |
*/ |
|
| 147 |
@Override |
|
| 148 |
public double[][] getColCos2() throws StatException {
|
|
| 149 |
if (colcos2 == null) {
|
|
| 150 |
try {
|
|
| 151 |
REXP sv = rw.extractItemFromListByName(symbol, "col$cos2"); //$NON-NLS-1$ |
|
| 152 |
colcos2 = sv.asDoubleMatrix(); |
|
| 153 |
// Arrays.sort(rowdist); |
|
| 154 |
} catch (RWorkspaceException e) {
|
|
| 155 |
throw new StatException(Messages.FactoMineRCA_3 + e.getMessage(), e); |
|
| 156 |
} catch (REXPMismatchException e) {
|
|
| 157 |
// TODO Auto-generated catch block |
|
| 158 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 159 |
} |
|
| 160 |
} |
|
| 161 |
return colcos2; |
|
| 162 |
} |
|
| 163 |
|
|
| 164 |
/** |
|
| 165 |
* Get the rows mass. |
|
| 166 |
* |
|
| 167 |
* @return the col dist |
|
| 168 |
* @throws StatException the stat exception |
|
| 169 |
*/ |
|
| 170 |
@Override |
|
| 171 |
public double[] getColDist() throws StatException {
|
|
| 172 |
if (coldist == null) |
|
| 173 |
{
|
|
| 174 |
double[][] colcoords = getColsCoords(); |
|
| 175 |
coldist = new double[colcoords.length]; |
|
| 176 |
for (int i = 0; i < colcoords.length; i++) |
|
| 177 |
for (int c = 0; c < colcoords[i].length; c++) |
|
| 178 |
coldist[i] += Math.pow(colcoords[i][c], 2); |
|
| 179 |
} |
|
| 180 |
return coldist; |
|
| 181 |
} |
|
| 182 |
|
|
| 183 |
/* (non-Javadoc) |
|
| 184 |
* @see org.txm.stat.engine.r.function.ICA#getColsCoords() |
|
| 185 |
*/ |
|
| 186 |
@Override |
|
| 187 |
public double[][] getColsCoords() {
|
|
| 188 |
if (colscoords == null) {
|
|
| 189 |
try {
|
|
| 190 |
REXP exp = rw.extractItemFromListByName(symbol, "col$coord"); //$NON-NLS-1$ |
|
| 191 |
colscoords = exp.asDoubleMatrix(); |
|
| 192 |
|
|
| 193 |
//System.out.println("Avant:");
|
|
| 194 |
// for (int i = 0; i < colscoords.length; i++) |
|
| 195 |
// {
|
|
| 196 |
// for (int c = 0; c < colscoords[i].length; c++) |
|
| 197 |
// {
|
|
| 198 |
// System.out.println(" "+colscoords[i][c]);
|
|
| 199 |
// } |
|
| 200 |
// System.out.println(); |
|
| 201 |
// } |
|
| 202 |
|
|
| 203 |
// multiply coords by sv |
|
| 204 |
// this.getSingularValues(); |
|
| 205 |
// for (int i = 0; i < colscoords.length; i++) |
|
| 206 |
// for (int c = 0; c < colscoords[i].length; c++) |
|
| 207 |
// colscoords[i][c] = colscoords[i][c] * singularValues[c]; |
|
| 208 |
// |
|
| 209 |
// System.out.println("Apres:");
|
|
| 210 |
// for (int i = 0; i < colscoords.length; i++) |
|
| 211 |
// {
|
|
| 212 |
// for (int c = 0; c < colscoords[i].length; c++) |
|
| 213 |
// {
|
|
| 214 |
// System.out.println(" "+colscoords[i][c]);
|
|
| 215 |
// } |
|
| 216 |
// System.out.println(); |
|
| 217 |
// } |
|
| 218 |
|
|
| 219 |
} catch (Exception e) {
|
|
| 220 |
// TODO Auto-generated catch block |
|
| 221 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 222 |
} |
|
| 223 |
} |
|
| 224 |
return colscoords; |
|
| 225 |
} |
|
| 226 |
|
|
| 227 |
/** |
|
| 228 |
* Get the rows mass. |
|
| 229 |
* |
|
| 230 |
* @return the cols inertia |
|
| 231 |
* @throws StatException the stat exception |
|
| 232 |
*/ |
|
| 233 |
@Override |
|
| 234 |
public double[] getColsInertia() throws StatException {
|
|
| 235 |
if (colinertia == null) {
|
|
| 236 |
try {
|
|
| 237 |
REXP sv = rw.extractItemFromListByName(symbol, "col$contrib"); //$NON-NLS-1$ |
|
| 238 |
colinertia = RWorkspace.toDouble(sv); |
|
| 239 |
// Arrays.sort(colinertia); |
|
| 240 |
} catch (RWorkspaceException e) {
|
|
| 241 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 242 |
} |
|
| 243 |
} |
|
| 244 |
return colinertia; |
|
| 245 |
} |
|
| 246 |
|
|
| 247 |
/** |
|
| 248 |
* Get the rows mass. |
|
| 249 |
* |
|
| 250 |
* @return the cols mass |
|
| 251 |
* @throws StatException the stat exception |
|
| 252 |
*/ |
|
| 253 |
@Override |
|
| 254 |
public double[] getColsMass() throws StatException {
|
|
| 255 |
if (colmass == null) {
|
|
| 256 |
try {
|
|
| 257 |
REXP sv = rw.extractItemFromListByName(symbol, "call$marge.col"); //$NON-NLS-1$ |
|
| 258 |
colmass = RWorkspace.toDouble(sv); |
|
| 259 |
// Arrays.sort(colmass); |
|
| 260 |
} catch (RWorkspaceException e) {
|
|
| 261 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 262 |
} |
|
| 263 |
} |
|
| 264 |
return colmass; |
|
| 265 |
} |
|
| 266 |
|
|
| 267 |
/* (non-Javadoc) |
|
| 268 |
* @see org.txm.stat.engine.r.function.ICA#getRowContrib() |
|
| 269 |
*/ |
|
| 270 |
@Override |
|
| 271 |
public double[][] getRowContrib() throws StatException {
|
|
| 272 |
//System.out.println("FACTO: getRowContrib");
|
|
| 273 |
if (rowcontrib == null) {
|
|
| 274 |
try {
|
|
| 275 |
REXP sv = rw.extractItemFromListByName(symbol, "row$contrib"); //$NON-NLS-1$ |
|
| 276 |
rowcontrib = sv.asDoubleMatrix(); |
|
| 277 |
for (int i = 0 ; i < rowcontrib.length ; i++) |
|
| 278 |
for (int j = 0 ; j < rowcontrib[i].length ; j++) |
|
| 279 |
rowcontrib[i][j] = rowcontrib[i][j] / 100.0; |
|
| 280 |
// Arrays.sort(rowdist); |
|
| 281 |
} catch (RWorkspaceException e) {
|
|
| 282 |
throw new StatException(Messages.FactoMineRCA_4 + e.getMessage(), e); |
|
| 283 |
} catch (REXPMismatchException e) {
|
|
| 284 |
// TODO Auto-generated catch block |
|
| 285 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 286 |
} |
|
| 287 |
} |
|
| 288 |
return rowcontrib; |
|
| 289 |
} |
|
| 290 |
|
|
| 291 |
/* (non-Javadoc) |
|
| 292 |
* @see org.txm.stat.engine.r.function.ICA#getRowCos2() |
|
| 293 |
*/ |
|
| 294 |
@Override |
|
| 295 |
public double[][] getRowCos2() throws StatException {
|
|
| 296 |
if (rowcos2 == null) {
|
|
| 297 |
try {
|
|
| 298 |
REXP sv = rw.extractItemFromListByName(symbol, "row$cos2"); //$NON-NLS-1$ |
|
| 299 |
rowcos2 = sv.asDoubleMatrix(); |
|
| 300 |
// Arrays.sort(rowdist); |
|
| 301 |
} catch (RWorkspaceException e) {
|
|
| 302 |
throw new StatException(Messages.FactoMineRCA_5 + e.getMessage(), e); |
|
| 303 |
} catch (REXPMismatchException e) {
|
|
| 304 |
// TODO Auto-generated catch block |
|
| 305 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 306 |
} |
|
| 307 |
} |
|
| 308 |
return rowcos2; |
|
| 309 |
} |
|
| 310 |
|
|
| 311 |
/** |
|
| 312 |
* Get the rows mass. |
|
| 313 |
* |
|
| 314 |
* @return the row dist |
|
| 315 |
* @throws StatException the stat exception |
|
| 316 |
*/ |
|
| 317 |
@Override |
|
| 318 |
public double[] getRowDist() throws StatException {
|
|
| 319 |
if (rowdist == null) |
|
| 320 |
{
|
|
| 321 |
double[][] rowcoords = getRowsCoords(); |
|
| 322 |
rowdist = new double[rowcoords.length]; |
|
| 323 |
for (int i = 0; i < rowcoords.length; i++) |
|
| 324 |
for (int c = 0; c < rowcoords[i].length; c++) |
|
| 325 |
rowdist[i] += Math.pow(rowcoords[i][c], 2); |
|
| 326 |
} |
|
| 327 |
return rowdist; |
|
| 328 |
} |
|
| 329 |
|
|
| 330 |
/* (non-Javadoc) |
|
| 331 |
* @see org.txm.stat.engine.r.function.ICA#getRowsCoords() |
|
| 332 |
*/ |
|
| 333 |
@Override |
|
| 334 |
public double[][] getRowsCoords() {
|
|
| 335 |
if (rowscoords == null) {
|
|
| 336 |
try {
|
|
| 337 |
REXP sv = rw.extractItemFromListByName(symbol, "row$coord"); //$NON-NLS-1$ |
|
| 338 |
rowscoords = sv.asDoubleMatrix(); |
|
| 339 |
|
|
| 340 |
// this.getSingularValues(); |
|
| 341 |
// //System.out.println("Apres:");
|
|
| 342 |
// for (int i = 0; i < rowscoords.length; i++) |
|
| 343 |
// {
|
|
| 344 |
// for (int c = 0; c < rowscoords[i].length; c++) |
|
| 345 |
// {
|
|
| 346 |
// rowscoords[i][c] = rowscoords[i][c] * singularValues[c]; |
|
| 347 |
// // System.out.println(" "+rowscoords[i][c]);
|
|
| 348 |
// } |
|
| 349 |
// //System.out.println(); |
|
| 350 |
// } |
|
| 351 |
|
|
| 352 |
} catch (Exception e) {
|
|
| 353 |
// TODO Auto-generated catch block |
|
| 354 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 355 |
} |
|
| 356 |
} |
|
| 357 |
return rowscoords; |
|
| 358 |
} |
|
| 359 |
|
|
| 360 |
/** |
|
| 361 |
* Get the rows mass. |
|
| 362 |
* |
|
| 363 |
* @return the rows inertia |
|
| 364 |
* @throws StatException the stat exception |
|
| 365 |
*/ |
|
| 366 |
@Override |
|
| 367 |
public double[] getRowsInertia() throws StatException {
|
|
| 368 |
if (rowinertia == null) {
|
|
| 369 |
try {
|
|
| 370 |
REXP sv = rw.extractItemFromListByName(symbol, "row$contrib"); //$NON-NLS-1$ |
|
| 371 |
rowinertia = RWorkspace.toDouble(sv); |
|
| 372 |
// Arrays.sort(rowinertia); |
|
| 373 |
} catch (RWorkspaceException e) {
|
|
| 374 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 375 |
} |
|
| 376 |
} |
|
| 377 |
return rowinertia; |
|
| 378 |
} |
|
| 379 |
|
|
| 380 |
/** |
|
| 381 |
* Get the rows mass. |
|
| 382 |
* |
|
| 383 |
* @return the rows mass |
|
| 384 |
* @throws StatException the stat exception |
|
| 385 |
*/ |
|
| 386 |
@Override |
|
| 387 |
public double[] getRowsMass() throws StatException {
|
|
| 388 |
if (rowmass == null) {
|
|
| 389 |
try {
|
|
| 390 |
REXP sv = rw.extractItemFromListByName(symbol, "call$marge.row"); //$NON-NLS-1$ |
|
| 391 |
rowmass = RWorkspace.toDouble(sv); |
|
| 392 |
// Arrays.sort(rowmass); |
|
| 393 |
} catch (RWorkspaceException e) {
|
|
| 394 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 395 |
} |
|
| 396 |
} |
|
| 397 |
return rowmass; |
|
| 398 |
} |
|
| 399 |
|
|
| 400 |
/** |
|
| 401 |
* Get the singular values. |
|
| 402 |
* |
|
| 403 |
* @return the singular values |
|
| 404 |
* @throws StatException the stat exception |
|
| 405 |
*/ |
|
| 406 |
@Override |
|
| 407 |
public double[] getSingularValues() throws StatException {
|
|
| 408 |
if (singularValues == null) {
|
|
| 409 |
getValeursPropres(); |
|
| 410 |
singularValues = new double[valeursPropres.length]; |
|
| 411 |
for(int i = 0 ; i < valeursPropres.length ; i++) |
|
| 412 |
singularValues[i] = Math.pow(valeursPropres[i], 0.5); |
|
| 413 |
} |
|
| 414 |
return singularValues; |
|
| 415 |
} |
|
| 416 |
|
|
| 417 |
/* (non-Javadoc) |
|
| 418 |
* @see org.txm.stat.engine.r.function.ICA#getSymbol() |
|
| 419 |
*/ |
|
| 420 |
@Override |
|
| 421 |
public String getSymbol() {
|
|
| 422 |
return symbol; |
|
| 423 |
} |
|
| 424 |
|
|
| 425 |
/** |
|
| 426 |
* Gets the valeurs propres. |
|
| 427 |
* |
|
| 428 |
* @return the singular values pow 2 |
|
| 429 |
* @throws StatException the stat exception |
|
| 430 |
*/ |
|
| 431 |
@Override |
|
| 432 |
public double[] getValeursPropres() throws StatException {
|
|
| 433 |
if (valeursPropres == null) {
|
|
| 434 |
try {
|
|
| 435 |
REXP sv = rw.eval(symbol+"$eig$eigenvalue"); //$NON-NLS-1$ |
|
| 436 |
valeursPropres = RWorkspace.toDouble(sv); |
|
| 437 |
// remove last singular value |
|
| 438 |
if (valeursPropres.length == table.getNColumns()) |
|
| 439 |
valeursPropres = Arrays.copyOfRange(valeursPropres, 0, valeursPropres.length -1); |
|
| 440 |
// Arrays.sort(singularValues); |
|
| 441 |
} catch (RWorkspaceException e) {
|
|
| 442 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 443 |
} |
|
| 444 |
} |
|
| 445 |
return valeursPropres; |
|
| 446 |
|
|
| 447 |
} |
|
| 448 |
|
|
| 449 |
/* (non-Javadoc) |
|
| 450 |
* @see org.txm.stat.engine.r.function.ICA#loadLibrary() |
|
| 451 |
*/ |
|
| 452 |
@Override |
|
| 453 |
public boolean loadLibrary(){
|
|
| 454 |
try {
|
|
| 455 |
rw.voidEval("library(FactoMineR)"); //$NON-NLS-1$
|
|
| 456 |
} catch (RWorkspaceException e) {
|
|
| 457 |
System.out.println(Messages.CA_16+ e); |
|
| 458 |
return false; |
|
| 459 |
} |
|
| 460 |
return true; |
|
| 461 |
} |
|
| 462 |
|
|
| 463 |
|
|
| 464 |
/** |
|
| 465 |
* Draw in the given file a plot of the factorial map. |
|
| 466 |
* |
|
| 467 |
* @param file the file |
|
| 468 |
* @param encoding the encoding |
|
| 469 |
* @param colseparator the colseparator |
|
| 470 |
* @param txtseparator the txtseparator |
|
| 471 |
* @return true, if successful |
|
| 472 |
*/ |
|
| 473 |
@Override |
|
| 474 |
public boolean toTxt(File file, String encoding, String colseparator, String txtseparator) {
|
|
| 475 |
try {
|
|
| 476 |
RWorkspace rw = RWorkspace.getRWorkspaceInstance(); |
|
| 477 |
rw.eval("sink(file=\"" + file.getAbsolutePath().replace("\\", "\\\\")+"\")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 478 |
rw.eval("print("+symbol+")"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 479 |
|
|
| 480 |
rw.eval("print("+symbol+"$eig)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 481 |
|
|
| 482 |
rw.eval("print("+symbol+"$col)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 483 |
|
|
| 484 |
rw.eval("print("+symbol+"$col$coord)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 485 |
|
|
| 486 |
rw.eval("print("+symbol+"$col$cos2)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 487 |
|
|
| 488 |
rw.eval("print("+symbol+"$col$contrib)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 489 |
|
|
| 490 |
rw.eval("print("+symbol+"$row)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 491 |
|
|
| 492 |
rw.eval("print("+symbol+"$row$coord)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 493 |
|
|
| 494 |
rw.eval("print("+symbol+"$row$cos2)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 495 |
|
|
| 496 |
rw.eval("print("+symbol+"$row$contrib)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 497 |
// rw.eval("print("+symbol+"$call)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 498 |
// rw.eval("print("+symbol+"$call$marge.col)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 499 |
// rw.eval("print("+symbol+"$call$marge.row)"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 500 |
rw.eval("sink()"); //$NON-NLS-1$
|
|
| 501 |
} catch (StatException e) {
|
|
| 502 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 503 |
return false; |
|
| 504 |
} |
|
| 505 |
return true; |
|
| 506 |
} |
|
| 507 |
|
|
| 508 |
|
|
| 509 |
@Override |
|
| 510 |
public int getRowsCount() {
|
|
| 511 |
return this.table.getRowsCount(); |
|
| 512 |
} |
|
| 513 |
|
|
| 514 |
@Override |
|
| 515 |
public int getColumnsCount() {
|
|
| 516 |
return this.table.getColumnsCount(); |
|
| 517 |
} |
|
| 518 |
} |
|
| 0 | 519 | |
| tmp/org.txm.ca.core/src/org/txm/ca/core/statsengine/r/functions/ICA.java (revision 180) | ||
|---|---|---|
| 1 |
// Copyright © 2010-2013 ENS de Lyon. |
|
| 2 |
// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of |
|
| 3 |
// Lyon 2, University of Franche-Comté, University of Nice |
|
| 4 |
// Sophia Antipolis, University of Paris 3. |
|
| 5 |
// |
|
| 6 |
// The TXM platform is free software: you can redistribute it |
|
| 7 |
// and/or modify it under the terms of the GNU General Public |
|
| 8 |
// License as published by the Free Software Foundation, |
|
| 9 |
// either version 2 of the License, or (at your option) any |
|
| 10 |
// later version. |
|
| 11 |
// |
|
| 12 |
// The TXM platform is distributed in the hope that it will be |
|
| 13 |
// useful, but WITHOUT ANY WARRANTY; without even the implied |
|
| 14 |
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR |
|
| 15 |
// PURPOSE. See the GNU General Public License for more |
|
| 16 |
// details. |
|
| 17 |
// |
|
| 18 |
// You should have received a copy of the GNU General |
|
| 19 |
// Public License along with the TXM platform. If not, see |
|
| 20 |
// http://www.gnu.org/licenses. |
|
| 21 |
// |
|
| 22 |
// |
|
| 23 |
// |
|
| 24 |
// $LastChangedDate:$ |
|
| 25 |
// $LastChangedRevision:$ |
|
| 26 |
// $LastChangedBy:$ |
|
| 27 |
// |
|
| 28 |
package org.txm.ca.core.statsengine.r.functions; |
|
| 29 |
|
|
| 30 |
import java.io.File; |
|
| 31 |
|
|
| 32 |
import org.txm.stat.StatException; |
|
| 33 |
|
|
| 34 |
// TODO: Auto-generated Javadoc |
|
| 35 |
/** |
|
| 36 |
* The Interface ICA. |
|
| 37 |
*/ |
|
| 38 |
public interface ICA {
|
|
| 39 |
|
|
| 40 |
/** |
|
| 41 |
* Gets the col contrib. |
|
| 42 |
* |
|
| 43 |
* @return the col contrib |
|
| 44 |
* @throws StatException the stat exception |
|
| 45 |
*/ |
|
| 46 |
public double[][] getColContrib() throws StatException; |
|
| 47 |
|
|
| 48 |
/** |
|
| 49 |
* Gets the col cos2. |
|
| 50 |
* |
|
| 51 |
* @return the col cos2 |
|
| 52 |
* @throws StatException the stat exception |
|
| 53 |
*/ |
|
| 54 |
public double[][] getColCos2() throws StatException; |
|
| 55 |
|
|
| 56 |
/** |
|
| 57 |
* Gets the col dist. |
|
| 58 |
* |
|
| 59 |
* @return the col dist |
|
| 60 |
* @throws StatException the stat exception |
|
| 61 |
*/ |
|
| 62 |
public double[] getColDist() throws StatException; |
|
| 63 |
|
|
| 64 |
/** |
|
| 65 |
* Gets the cols coords. |
|
| 66 |
* |
|
| 67 |
* @return the cols coords |
|
| 68 |
*/ |
|
| 69 |
public double[][] getColsCoords(); |
|
| 70 |
|
|
| 71 |
/** |
|
| 72 |
* Get the rows mass. |
|
| 73 |
* |
|
| 74 |
* @return the cols inertia |
|
| 75 |
* @throws StatException the stat exception |
|
| 76 |
*/ |
|
| 77 |
public double[] getColsInertia() throws StatException; |
|
| 78 |
|
|
| 79 |
/** |
|
| 80 |
* Get the rows mass. |
|
| 81 |
* |
|
| 82 |
* @return the cols mass |
|
| 83 |
* @throws StatException the stat exception |
|
| 84 |
*/ |
|
| 85 |
public double[] getColsMass() throws StatException; |
|
| 86 |
|
|
| 87 |
/** |
|
| 88 |
* Gets the row contrib. |
|
| 89 |
* |
|
| 90 |
* @return the row contrib |
|
| 91 |
* @throws StatException the stat exception |
|
| 92 |
*/ |
|
| 93 |
public double[][] getRowContrib() throws StatException; |
|
| 94 |
|
|
| 95 |
/** |
|
| 96 |
* Gets the row cos2. |
|
| 97 |
* |
|
| 98 |
* @return the row cos2 |
|
| 99 |
* @throws StatException the stat exception |
|
| 100 |
*/ |
|
| 101 |
public double[][] getRowCos2() throws StatException; |
|
| 102 |
|
|
| 103 |
/** |
|
| 104 |
* Gets the row dist. |
|
| 105 |
* |
|
| 106 |
* @return the row dist |
|
| 107 |
* @throws StatException the stat exception |
|
| 108 |
*/ |
|
| 109 |
public double[] getRowDist() throws StatException; |
|
| 110 |
|
|
| 111 |
/** |
|
| 112 |
* Gets the rows coords. |
|
| 113 |
* |
|
| 114 |
* @return the rows coords |
|
| 115 |
*/ |
|
| 116 |
public double[][] getRowsCoords(); |
|
| 117 |
|
|
| 118 |
/** |
|
| 119 |
* Get the rows mass. |
|
| 120 |
* |
|
| 121 |
* @return the rows inertia |
|
| 122 |
* @throws StatException the stat exception |
|
| 123 |
*/ |
|
| 124 |
public double[] getRowsInertia() throws StatException; |
|
| 125 |
|
|
| 126 |
/** |
|
| 127 |
* Get the rows mass. |
|
| 128 |
* |
|
| 129 |
* @return the rows mass |
|
| 130 |
* @throws StatException the stat exception |
|
| 131 |
*/ |
|
| 132 |
public double[] getRowsMass() throws StatException; |
|
| 133 |
|
|
| 134 |
/** |
|
| 135 |
* Get the singular values. |
|
| 136 |
* |
|
| 137 |
* @return the singular values |
|
| 138 |
* @throws StatException the stat exception |
|
| 139 |
*/ |
|
| 140 |
public double[] getSingularValues() throws StatException; |
|
| 141 |
|
|
| 142 |
|
|
| 143 |
/** |
|
| 144 |
* Gets the number of rows. |
|
| 145 |
* @return the number of rows |
|
| 146 |
*/ |
|
| 147 |
public int getRowsCount(); |
|
| 148 |
|
|
| 149 |
|
|
| 150 |
/** |
|
| 151 |
* Gets the number of columns. |
|
| 152 |
* @return the number of columns |
|
| 153 |
*/ |
|
| 154 |
public int getColumnsCount(); |
|
| 155 |
|
|
| 156 |
|
|
| 157 |
/** |
|
| 158 |
* Gets the symbol. |
|
| 159 |
* |
|
| 160 |
* @return the symbol |
|
| 161 |
*/ |
|
| 162 |
public String getSymbol(); |
|
| 163 |
|
|
| 164 |
/** |
|
| 165 |
* Gets the valeurs propres. |
|
| 166 |
* |
|
| 167 |
* @return the valeurs propres |
|
| 168 |
* @throws StatException the stat exception |
|
| 169 |
*/ |
|
| 170 |
public double[] getValeursPropres() throws StatException; |
|
| 171 |
|
|
| 172 |
/** |
|
| 173 |
* Load library. |
|
| 174 |
* |
|
| 175 |
* @return true, if successful |
|
| 176 |
*/ |
|
| 177 |
public boolean loadLibrary(); |
|
| 178 |
|
|
| 179 |
|
|
| 180 |
|
|
| 181 |
/** |
|
| 182 |
* Draw in the given file a plot of the factorial map. |
|
| 183 |
* |
|
| 184 |
* @param file the file |
|
| 185 |
* @param encoding the encoding |
|
| 186 |
* @param colseparator the colseparator |
|
| 187 |
* @param txtseparator the txtseparator |
|
| 188 |
* @return true, if successful |
|
| 189 |
*/ |
|
| 190 |
public boolean toTxt(File file, String encoding, String colseparator, String txtseparator); |
|
| 191 |
} |
|
| 0 | 192 | |
| tmp/org.txm.ca.core/src/org/txm/ca/core/statsengine/r/functions/CA.java (revision 180) | ||
|---|---|---|
| 1 |
// Copyright © 2010-2013 ENS de Lyon. |
|
| 2 |
// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of |
|
| 3 |
// Lyon 2, University of Franche-Comté, University of Nice |
|
| 4 |
// Sophia Antipolis, University of Paris 3. |
|
| 5 |
// |
|
| 6 |
// The TXM platform is free software: you can redistribute it |
|
| 7 |
// and/or modify it under the terms of the GNU General Public |
|
| 8 |
// License as published by the Free Software Foundation, |
|
| 9 |
// either version 2 of the License, or (at your option) any |
|
| 10 |
// later version. |
|
| 11 |
// |
|
| 12 |
// The TXM platform is distributed in the hope that it will be |
|
| 13 |
// useful, but WITHOUT ANY WARRANTY; without even the implied |
|
| 14 |
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR |
|
| 15 |
// PURPOSE. See the GNU General Public License for more |
|
| 16 |
// details. |
|
| 17 |
// |
|
| 18 |
// You should have received a copy of the GNU General |
|
| 19 |
// Public License along with the TXM platform. If not, see |
|
| 20 |
// http://www.gnu.org/licenses. |
|
| 21 |
// |
|
| 22 |
// |
|
| 23 |
// |
|
| 24 |
// $LastChangedDate: 2014-06-10 15:10:24 +0200 (Tue, 10 Jun 2014) $ |
|
| 25 |
// $LastChangedRevision: 2771 $ |
|
| 26 |
// $LastChangedBy: sjacquot $ |
|
| 27 |
// |
|
| 28 |
package org.txm.ca.core.statsengine.r.functions; |
|
| 29 |
|
|
| 30 |
import java.io.File; |
|
| 31 |
|
|
| 32 |
import org.rosuda.REngine.REXP; |
|
| 33 |
import org.txm.Messages; |
|
| 34 |
import org.txm.stat.StatException; |
|
| 35 |
import org.txm.stat.data.LexicalTable; |
|
| 36 |
import org.txm.stat.engine.r.RWorkspace; |
|
| 37 |
import org.txm.stat.engine.r.RWorkspaceException; |
|
| 38 |
import org.txm.stat.engine.r.data.QuantitativeDataStructureImpl; |
|
| 39 |
|
|
| 40 |
/** |
|
| 41 |
* Access to the R implementation of the Correspondance Analysis. |
|
| 42 |
* |
|
| 43 |
* @author sloiseau, mdecorde, sjacquot |
|
| 44 |
*/ |
|
| 45 |
public class CA implements ICA {
|
|
| 46 |
|
|
| 47 |
/** The singular values. */ |
|
| 48 |
private double[] singularValues = null; |
|
| 49 |
|
|
| 50 |
/** The singular values2. */ |
|
| 51 |
private double[] singularValues2 = null; |
|
| 52 |
|
|
| 53 |
/** The rowmass. */ |
|
| 54 |
private double[] rowmass = null; |
|
| 55 |
|
|
| 56 |
/** The rowdist. */ |
|
| 57 |
private double[] rowdist = null; |
|
| 58 |
|
|
| 59 |
/** The rowinertia. */ |
|
| 60 |
private double[] rowinertia = null; |
|
| 61 |
|
|
| 62 |
/** The rowcos2. */ |
|
| 63 |
private double[][] rowcos2 = null; |
|
| 64 |
|
|
| 65 |
/** The rowcontrib. */ |
|
| 66 |
private double[][] rowcontrib = null; |
|
| 67 |
|
|
| 68 |
/** The colmass. */ |
|
| 69 |
private double[] colmass = null; |
|
| 70 |
|
|
| 71 |
/** The coldist. */ |
|
| 72 |
private double[] coldist = null; |
|
| 73 |
|
|
| 74 |
/** The colinertia. */ |
|
| 75 |
private double[] colinertia = null; |
|
| 76 |
|
|
| 77 |
/** The colcos2. */ |
|
| 78 |
private double[][] colcos2 = null; |
|
| 79 |
|
|
| 80 |
/** The colcontrib. */ |
|
| 81 |
private double[][] colcontrib = null; |
|
| 82 |
|
|
| 83 |
/** The rw. */ |
|
| 84 |
private final RWorkspace rw = RWorkspace.getRWorkspaceInstance(); |
|
| 85 |
|
|
| 86 |
/** The symbol. */ |
|
| 87 |
private final String symbol = QuantitativeDataStructureImpl.createSymbole(CA.class); |
|
| 88 |
|
|
| 89 |
/** The rowscoords. */ |
|
| 90 |
private double[][] rowscoords; |
|
| 91 |
|
|
| 92 |
/** The colscoords. */ |
|
| 93 |
private double[][] colscoords; |
|
| 94 |
|
|
| 95 |
/** |
|
| 96 |
* The lexical table. |
|
| 97 |
*/ |
|
| 98 |
private LexicalTable table; |
|
| 99 |
|
|
| 100 |
/** |
|
| 101 |
* Create a correspondance analysis on the given table. The correspondance |
|
| 102 |
* analysis is computed as soon as the object is created. |
|
| 103 |
* |
|
| 104 |
* @param table the table |
|
| 105 |
* @throws StatException the stat exception |
|
| 106 |
*/ |
|
| 107 |
public CA(LexicalTable table) throws StatException {
|
|
| 108 |
|
|
| 109 |
|
|
| 110 |
|
|
| 111 |
if (!rw.containsVariable(table.getSymbol())) {
|
|
| 112 |
throw new StatException(Messages.CA_0); |
|
| 113 |
} |
|
| 114 |
|
|
| 115 |
loadLibrary(); |
|
| 116 |
this.table = table; |
|
| 117 |
|
|
| 118 |
try {
|
|
| 119 |
rw.callFunctionAndAffect( |
|
| 120 |
"ca", new String[] { table.getSymbol() }, symbol); //$NON-NLS-1$
|
|
| 121 |
} catch (RWorkspaceException e) {
|
|
| 122 |
throw new StatException(Messages.CA_2 + e.getMessage(), e); |
|
| 123 |
} |
|
| 124 |
} |
|
| 125 |
|
|
| 126 |
/* (non-Javadoc) |
|
| 127 |
* @see org.txm.stat.engine.r.function.ICA#getColContrib() |
|
| 128 |
*/ |
|
| 129 |
@Override |
|
| 130 |
public double[][] getColContrib() throws StatException {
|
|
| 131 |
|
|
| 132 |
double[][] colcoords = getColsCoords(); |
|
| 133 |
double[] sv = this.getValeursPropres(); |
|
| 134 |
double[] mass = this.getColsMass(); |
|
| 135 |
|
|
| 136 |
colcontrib = new double[colcoords.length][3]; |
|
| 137 |
|
|
| 138 |
for (int i = 0; i < colcoords.length; i++) {
|
|
| 139 |
for(int c = 0 ; c < 3 ; c++) |
|
| 140 |
{
|
|
| 141 |
colcontrib[i][c] = 100.0 * mass[i] * (colcoords[i][c] * colcoords[i][c]) / (sv[c]); |
|
| 142 |
} |
|
| 143 |
} |
|
| 144 |
return colcontrib; |
|
| 145 |
} |
|
| 146 |
|
|
| 147 |
/* (non-Javadoc) |
|
| 148 |
* @see org.txm.stat.engine.r.function.ICA#getColCos2() |
|
| 149 |
*/ |
|
| 150 |
@Override |
|
| 151 |
public double[][] getColCos2() {
|
|
| 152 |
if (colcos2 == null) |
|
| 153 |
{
|
|
| 154 |
double[][] colcoords = getColsCoords(); |
|
| 155 |
double[] dist = getColDist(); |
|
| 156 |
colcos2 = new double[colcoords.length][3]; |
|
| 157 |
|
|
| 158 |
for (int i = 0; i < colcoords.length; i++) {
|
|
| 159 |
|
|
| 160 |
double distt = dist[i]; |
|
| 161 |
|
|
| 162 |
colcos2[i][0] = Math.pow(colcoords[i][0], 2) / distt; |
|
| 163 |
colcos2[i][1] = Math.pow(colcoords[i][1], 2) / distt; |
|
| 164 |
colcos2[i][2] = Math.pow(colcoords[i][2], 2) / distt; |
|
| 165 |
} |
|
| 166 |
} |
|
| 167 |
return colcos2; |
|
| 168 |
} |
|
| 169 |
|
|
| 170 |
/* (non-Javadoc) |
|
| 171 |
* @see org.txm.stat.engine.r.function.ICA#getColDist() |
|
| 172 |
*/ |
|
| 173 |
@Override |
|
| 174 |
public double[] getColDist() {
|
|
| 175 |
if (coldist == null) |
|
| 176 |
{
|
|
| 177 |
double[][] colcoords = getColsCoords(); |
|
| 178 |
coldist = new double[colcoords.length]; |
|
| 179 |
for (int i = 0; i < colcoords.length; i++) |
|
| 180 |
for (int c = 0; c < colcoords[i].length; c++) |
|
| 181 |
coldist[i] += Math.pow(colcoords[i][c], 2); |
|
| 182 |
} |
|
| 183 |
return coldist; |
|
| 184 |
} |
|
| 185 |
|
|
| 186 |
/* (non-Javadoc) |
|
| 187 |
* @see org.txm.stat.engine.r.function.ICA#getColsCoords() |
|
| 188 |
*/ |
|
| 189 |
@Override |
|
| 190 |
public double[][] getColsCoords() {
|
|
| 191 |
if (colscoords == null) {
|
|
| 192 |
try {
|
|
| 193 |
REXP exp = rw.extractItemFromListByName(symbol, "colcoord"); //$NON-NLS-1$ |
|
| 194 |
colscoords = exp.asDoubleMatrix(); |
|
| 195 |
|
|
| 196 |
// multiply coords by sv |
|
| 197 |
this.getSingularValues(); |
|
| 198 |
for (int i = 0; i < colscoords.length; i++) |
|
| 199 |
for (int c = 0; c < colscoords[i].length; c++) |
|
| 200 |
colscoords[i][c] = colscoords[i][c] * singularValues[c]; |
|
| 201 |
} catch (Exception e) {
|
|
| 202 |
// TODO Auto-generated catch block |
|
| 203 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 204 |
} |
|
| 205 |
} |
|
| 206 |
return colscoords; |
|
| 207 |
} |
|
| 208 |
|
|
| 209 |
/** |
|
| 210 |
* Get the rows mass. |
|
| 211 |
* |
|
| 212 |
* @return the cols dist |
|
| 213 |
* @throws StatException the stat exception |
|
| 214 |
*/ |
|
| 215 |
public double[] getColsDist() throws StatException {
|
|
| 216 |
if (coldist == null) {
|
|
| 217 |
try {
|
|
| 218 |
REXP sv = rw.extractItemFromListByName(symbol, "coldist"); //$NON-NLS-1$ |
|
| 219 |
coldist = RWorkspace.toDouble(sv); |
|
| 220 |
// Arrays.sort(coldist); |
|
| 221 |
} catch (RWorkspaceException e) {
|
|
| 222 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 223 |
} |
|
| 224 |
} |
|
| 225 |
return coldist; |
|
| 226 |
} |
|
| 227 |
|
|
| 228 |
/** |
|
| 229 |
* Get the rows mass. |
|
| 230 |
* |
|
| 231 |
* @return the cols inertia |
|
| 232 |
* @throws StatException the stat exception |
|
| 233 |
*/ |
|
| 234 |
@Override |
|
| 235 |
public double[] getColsInertia() throws StatException {
|
|
| 236 |
if (colinertia == null) {
|
|
| 237 |
try {
|
|
| 238 |
REXP sv = rw.extractItemFromListByName(symbol, "colinertia"); //$NON-NLS-1$ |
|
| 239 |
colinertia = RWorkspace.toDouble(sv); |
|
| 240 |
// Arrays.sort(colinertia); |
|
| 241 |
} catch (RWorkspaceException e) {
|
|
| 242 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 243 |
} |
|
| 244 |
} |
|
| 245 |
return colinertia; |
|
| 246 |
} |
|
| 247 |
|
|
| 248 |
/** |
|
| 249 |
* Get the rows mass. |
|
| 250 |
* |
|
| 251 |
* @return the cols mass |
|
| 252 |
* @throws StatException the stat exception |
|
| 253 |
*/ |
|
| 254 |
@Override |
|
| 255 |
public double[] getColsMass() throws StatException {
|
|
| 256 |
if (colmass == null) {
|
|
| 257 |
try {
|
|
| 258 |
REXP sv = rw.extractItemFromListByName(symbol, "colmass"); //$NON-NLS-1$ |
|
| 259 |
colmass = RWorkspace.toDouble(sv); |
|
| 260 |
// Arrays.sort(colmass); |
|
| 261 |
} catch (RWorkspaceException e) {
|
|
| 262 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 263 |
} |
|
| 264 |
} |
|
| 265 |
return colmass; |
|
| 266 |
} |
|
| 267 |
|
|
| 268 |
/* (non-Javadoc) |
|
| 269 |
* @see org.txm.stat.engine.r.function.ICA#getRowContrib() |
|
| 270 |
*/ |
|
| 271 |
@Override |
|
| 272 |
public double[][] getRowContrib() throws StatException {
|
|
| 273 |
if (rowcontrib != null) |
|
| 274 |
return rowcontrib; |
|
| 275 |
|
|
| 276 |
double[][] rowcoords = getRowsCoords(); |
|
| 277 |
double[] sv = this.getValeursPropres(); |
|
| 278 |
double[] mass = this.getRowsMass(); |
|
| 279 |
|
|
| 280 |
rowcontrib = new double[rowcoords.length][3]; |
|
| 281 |
|
|
| 282 |
for (int i = 0; i < rowcoords.length; i++) {
|
|
| 283 |
for(int c = 0 ; c <3 ; c++) |
|
| 284 |
{
|
|
| 285 |
rowcontrib[i][c] = 100.0 * mass[i] * (rowcoords[i][c] * rowcoords[i][c]) / (sv[c]); |
|
| 286 |
} |
|
| 287 |
} |
|
| 288 |
return rowcontrib; |
|
| 289 |
} |
|
| 290 |
|
|
| 291 |
/* (non-Javadoc) |
|
| 292 |
* @see org.txm.stat.engine.r.function.ICA#getRowCos2() |
|
| 293 |
*/ |
|
| 294 |
@Override |
|
| 295 |
public double[][] getRowCos2() {
|
|
| 296 |
if (rowcos2 == null) |
|
| 297 |
{
|
|
| 298 |
double[][] rowcoords = getRowsCoords(); |
|
| 299 |
double[] dist = getRowDist(); |
|
| 300 |
|
|
| 301 |
rowcos2 = new double[rowcoords.length][3]; |
|
| 302 |
|
|
| 303 |
for (int i = 0; i < rowcoords.length; i++) {
|
|
| 304 |
|
|
| 305 |
double distt = dist[i]; |
|
| 306 |
|
|
| 307 |
rowcos2[i][0] = Math.pow(rowcoords[i][0], 2) / distt; |
|
| 308 |
rowcos2[i][1] = Math.pow(rowcoords[i][1], 2) / distt; |
|
| 309 |
rowcos2[i][2] = Math.pow(rowcoords[i][2], 2) / distt; |
|
| 310 |
} |
|
| 311 |
} |
|
| 312 |
return rowcos2; |
|
| 313 |
} |
|
| 314 |
|
|
| 315 |
/* (non-Javadoc) |
|
| 316 |
* @see org.txm.stat.engine.r.function.ICA#getRowDist() |
|
| 317 |
*/ |
|
| 318 |
@Override |
|
| 319 |
public double[] getRowDist() {
|
|
| 320 |
if (rowdist == null) |
|
| 321 |
{
|
|
| 322 |
double[][] rowcoords = getRowsCoords(); |
|
| 323 |
rowdist = new double[rowcoords.length]; |
|
| 324 |
for (int i = 0; i < rowcoords.length; i++) |
|
| 325 |
for (int c = 0; c < rowcoords[i].length; c++) |
|
| 326 |
rowdist[i] += Math.pow(rowcoords[i][c], 2); |
|
| 327 |
} |
|
| 328 |
return rowdist; |
|
| 329 |
} |
|
| 330 |
|
|
| 331 |
/* (non-Javadoc) |
|
| 332 |
* @see org.txm.stat.engine.r.function.ICA#getRowsCoords() |
|
| 333 |
*/ |
|
| 334 |
@Override |
|
| 335 |
public double[][] getRowsCoords() {
|
|
| 336 |
if (rowscoords == null) {
|
|
| 337 |
try {
|
|
| 338 |
REXP sv = rw.extractItemFromListByName(symbol, "rowcoord"); //$NON-NLS-1$ |
|
| 339 |
rowscoords = sv.asDoubleMatrix(); |
|
| 340 |
|
|
| 341 |
this.getSingularValues(); |
|
| 342 |
for (int i = 0; i < rowscoords.length; i++) |
|
| 343 |
for (int c = 0; c < rowscoords[i].length; c++) |
|
| 344 |
rowscoords[i][c] = rowscoords[i][c] * singularValues[c]; |
|
| 345 |
} catch (Exception e) {
|
|
| 346 |
// TODO Auto-generated catch block |
|
| 347 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 348 |
} |
|
| 349 |
} |
|
| 350 |
return rowscoords; |
|
| 351 |
} |
|
| 352 |
|
|
| 353 |
/** |
|
| 354 |
* Get the rows mass. |
|
| 355 |
* |
|
| 356 |
* @return the rows dist |
|
| 357 |
* @throws StatException the stat exception |
|
| 358 |
*/ |
|
| 359 |
public double[] getRowsDist() throws StatException {
|
|
| 360 |
if (rowdist == null) {
|
|
| 361 |
try {
|
|
| 362 |
REXP sv = rw.extractItemFromListByName(symbol, "rowdist"); //$NON-NLS-1$ |
|
| 363 |
rowdist = RWorkspace.toDouble(sv); |
|
| 364 |
// Arrays.sort(rowdist); |
|
| 365 |
} catch (RWorkspaceException e) {
|
|
| 366 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 367 |
} |
|
| 368 |
} |
|
| 369 |
return rowdist; |
|
| 370 |
} |
|
| 371 |
|
|
| 372 |
/** |
|
| 373 |
* Get the rows mass. |
|
| 374 |
* |
|
| 375 |
* @return the rows inertia |
|
| 376 |
* @throws StatException the stat exception |
|
| 377 |
*/ |
|
| 378 |
@Override |
|
| 379 |
public double[] getRowsInertia() throws StatException {
|
|
| 380 |
if (rowinertia == null) {
|
|
| 381 |
try {
|
|
| 382 |
REXP sv = rw.extractItemFromListByName(symbol, "rowinertia"); //$NON-NLS-1$ |
|
| 383 |
rowinertia = RWorkspace.toDouble(sv); |
|
| 384 |
// Arrays.sort(rowinertia); |
|
| 385 |
} catch (RWorkspaceException e) {
|
|
| 386 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 387 |
} |
|
| 388 |
} |
|
| 389 |
return rowinertia; |
|
| 390 |
} |
|
| 391 |
|
|
| 392 |
/** |
|
| 393 |
* Get the rows mass. |
|
| 394 |
* |
|
| 395 |
* @return the rows mass |
|
| 396 |
* @throws StatException the stat exception |
|
| 397 |
*/ |
|
| 398 |
@Override |
|
| 399 |
public double[] getRowsMass() throws StatException {
|
|
| 400 |
if (rowmass == null) {
|
|
| 401 |
try {
|
|
| 402 |
REXP sv = rw.extractItemFromListByName(symbol, "rowmass"); //$NON-NLS-1$ |
|
| 403 |
rowmass = RWorkspace.toDouble(sv); |
|
| 404 |
// Arrays.sort(rowmass); |
|
| 405 |
} catch (RWorkspaceException e) {
|
|
| 406 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 407 |
} |
|
| 408 |
} |
|
| 409 |
return rowmass; |
|
| 410 |
} |
|
| 411 |
|
|
| 412 |
/** |
|
| 413 |
* Get the singular values. |
|
| 414 |
* |
|
| 415 |
* @return the singular values |
|
| 416 |
* @throws StatException the stat exception |
|
| 417 |
*/ |
|
| 418 |
@Override |
|
| 419 |
public double[] getSingularValues() throws StatException {
|
|
| 420 |
if (singularValues == null) {
|
|
| 421 |
try {
|
|
| 422 |
REXP sv = rw.extractItemFromListByName(symbol, "sv"); //$NON-NLS-1$ |
|
| 423 |
singularValues = RWorkspace.toDouble(sv); |
|
| 424 |
// Arrays.sort(singularValues); |
|
| 425 |
} catch (RWorkspaceException e) {
|
|
| 426 |
throw new StatException(Messages.CA_4 + e.getMessage(), e); |
|
| 427 |
} |
|
| 428 |
} |
|
| 429 |
return singularValues; |
|
| 430 |
} |
|
| 431 |
|
|
| 432 |
/** |
|
| 433 |
* Gets the valeurs propres. |
|
| 434 |
* |
|
| 435 |
* @return the singular valeurs pow 2 |
|
| 436 |
* @throws StatException the stat exception |
|
| 437 |
*/ |
|
| 438 |
@Override |
|
| 439 |
public double[] getValeursPropres() throws StatException {
|
|
| 440 |
if (singularValues2 == null) {
|
|
| 441 |
getSingularValues(); |
|
| 442 |
singularValues2 = new double[singularValues.length]; |
|
| 443 |
for(int i = 0 ; i < singularValues.length ; i++) |
|
| 444 |
singularValues2[i] = Math.pow(singularValues[i], 2); |
|
| 445 |
} |
|
| 446 |
return singularValues2; |
|
| 447 |
} |
|
| 448 |
|
|
| 449 |
/* (non-Javadoc) |
|
| 450 |
* @see org.txm.stat.engine.r.function.ICA#getSymbol() |
|
| 451 |
*/ |
|
| 452 |
@Override |
|
| 453 |
public String getSymbol() {
|
|
| 454 |
return symbol; |
|
| 455 |
} |
|
| 456 |
|
|
| 457 |
/* (non-Javadoc) |
|
| 458 |
* @see org.txm.stat.engine.r.function.ICA#loadLibrary() |
|
| 459 |
*/ |
|
| 460 |
@Override |
|
| 461 |
public boolean loadLibrary() {
|
|
| 462 |
try {
|
|
| 463 |
rw.voidEval("library(ca)"); //$NON-NLS-1$
|
|
| 464 |
} catch (RWorkspaceException e) {
|
|
| 465 |
System.out.println(Messages.CA_16 + e); |
|
| 466 |
return false; |
|
| 467 |
} |
|
| 468 |
return true; |
|
| 469 |
} |
|
| 470 |
|
|
| 471 |
|
|
| 472 |
|
|
| 473 |
/** |
|
| 474 |
* Draw in the given file a plot of the factorial map. |
|
| 475 |
* |
|
| 476 |
* @param file the file |
|
| 477 |
* @param encoding the encoding |
|
| 478 |
* @param colseparator the colseparator |
|
| 479 |
* @param txtseparator the txtseparator |
|
| 480 |
* @return true, if successful |
|
| 481 |
*/ |
|
| 482 |
@Override |
|
| 483 |
public boolean toTxt(File file, String encoding, String colseparator, String txtseparator) {
|
|
| 484 |
try {
|
|
| 485 |
RWorkspace rw = RWorkspace.getRWorkspaceInstance(); |
|
| 486 |
rw.eval("sink(file=\"" + file.getAbsolutePath().replace("\\", "\\\\")+"\")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 487 |
rw.eval("print("+symbol+")"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 488 |
rw.eval("sink()"); //$NON-NLS-1$
|
|
| 489 |
} catch (StatException e) {
|
|
| 490 |
org.txm.utils.logger.Log.printStackTrace(e); |
|
| 491 |
return false; |
|
| 492 |
} |
|
| 493 |
return true; |
|
| 494 |
} |
|
| 495 |
|
|
| 496 |
@Override |
|
| 497 |
public int getRowsCount() {
|
|
| 498 |
return this.table.getRowsCount(); |
|
| 499 |
} |
|
| 500 |
|
|
| 501 |
@Override |
|
| 502 |
public int getColumnsCount() {
|
|
| 503 |
return this.table.getColumnsCount(); |
|
| 504 |
} |
|
| 505 |
} |
|
| 0 | 506 | |
Formats disponibles : Unified diff