/*
* Copyright (C) 2011-2012 Dr. John Lindsay <jlindsay@uoguelph.ca>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package plugins;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.text.DecimalFormat;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool calculates the Kappa index of agreement (KIA) for two classified raster images.
*
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class KappaIndex implements WhiteboxPlugin {
private WhiteboxPluginHost myHost = null;
private String[] args;
/**
* Used to retrieve the plugin tool's name. This is a short, unique name
* containing no spaces.
*
* @return String containing plugin name.
*/
@Override
public String getName() {
return "KappaIndex";
}
/**
* Used to retrieve the plugin tool's descriptive name. This can be a longer
* name (containing spaces) and is used in the interface to list the tool.
*
* @return String containing the plugin descriptive name.
*/
@Override
public String getDescriptiveName() {
return "Kappa Index of Agreement";
}
/**
* Used to retrieve a short description of what the plugin tool does.
*
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "Calculates the Kappa index of agreement on two categorical images.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
*
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = {"StatisticalTools", "ChangeDetection"};
return ret;
}
/**
* Sets the WhiteboxPluginHost to which the plugin tool is tied. This is the
* class that the plugin will send all feedback messages, progress updates,
* and return objects.
*
* @param host The WhiteboxPluginHost that called the plugin tool.
*/
@Override
public void setPluginHost(WhiteboxPluginHost host) {
myHost = host;
}
/**
* Used to communicate feedback pop-up messages between a plugin tool and
* the main Whitebox user-interface.
*
* @param feedback String containing the text to display.
*/
private void showFeedback(String message) {
if (myHost != null) {
myHost.showFeedback(message);
} else {
System.out.println(message);
}
}
/**
* Used to communicate a return object from a plugin tool to the main
* Whitebox user-interface.
*
* @return Object, such as an output WhiteboxRaster.
*/
private void returnData(Object ret) {
if (myHost != null) {
myHost.returnData(ret);
}
}
private int previousProgress = 0;
private String previousProgressLabel = "";
/**
* Used to communicate a progress update between a plugin tool and the main
* Whitebox user interface.
*
* @param progressLabel A String to use for the progress label.
* @param progress Float containing the progress value (between 0 and 100).
*/
private void updateProgress(String progressLabel, int progress) {
if (myHost != null && ((progress != previousProgress)
|| (!progressLabel.equals(previousProgressLabel)))) {
myHost.updateProgress(progressLabel, progress);
}
previousProgress = progress;
previousProgressLabel = progressLabel;
}
/**
* Used to communicate a progress update between a plugin tool and the main
* Whitebox user interface.
*
* @param progress Float containing the progress value (between 0 and 100).
*/
private void updateProgress(int progress) {
if (myHost != null && progress != previousProgress) {
myHost.updateProgress(progress);
}
previousProgress = progress;
}
/**
* Sets the arguments (parameters) used by the plugin.
*
* @param args An array of string arguments.
*/
@Override
public void setArgs(String[] args) {
this.args = args.clone();
}
private boolean cancelOp = false;
/**
* Used to communicate a cancel operation from the Whitebox GUI.
*
* @param cancel Set to true if the plugin should be canceled.
*/
@Override
public void setCancelOp(boolean cancel) {
cancelOp = cancel;
}
private void cancelOperation() {
showFeedback("Operation cancelled.");
updateProgress("Progress: ", 0);
}
private boolean amIActive = false;
/**
* Used by the Whitebox GUI to tell if this plugin is still running.
*
* @return a boolean describing whether or not the plugin is actively being
* used.
*/
@Override
public boolean isActive() {
return amIActive;
}
/**
* Used to execute this plugin tool.
*/
@Override
public void run() {
amIActive = true;
String inputHeader1 = null;
String inputHeader2 = null;
String outputFile = null;
int minClass;
int maxClass;
int numClasses;
int i1, i2;
int[][] contingency;
double[] data1, data2;
double z1, z2;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputHeader1 = args[0];
inputHeader2 = args[1];
outputFile = args[2];
// check to see that the inputHeader1 and outputFile are not null.
if (inputHeader1 == null || inputHeader2 == null) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
int row, col;
float progress = 0;
WhiteboxRaster image1 = new WhiteboxRaster(inputHeader1, "r");
int rows = image1.getNumberRows();
int cols = image1.getNumberColumns();
double noData1 = image1.getNoDataValue();
WhiteboxRaster image2 = new WhiteboxRaster(inputHeader2, "r");
if (rows != image2.getNumberRows() || cols != image2.getNumberColumns()) {
showFeedback("The input images must have the same dimensions (rows and columns).");
return;
}
double noData2 = image2.getNoDataValue();
minClass = (int)(Math.min(image1.getMinimumValue(), image2.getMinimumValue()));
maxClass = (int)(Math.max(image1.getMaximumValue(), image2.getMaximumValue()));
numClasses = maxClass - minClass + 1;
contingency = new int[numClasses][numClasses];
for (row = 0; row < rows; row++) {
data1 = image1.getRowValues(row);
data2 = image2.getRowValues(row);
for (col = 0; col < cols; col++) {
z1 = data1[col];
z2 = data2[col];
if (z1 != noData1 && z2 != noData2) {
i1 = (int)(z1 - minClass);
i2 = (int)(z2 - minClass);
contingency[i1][i2]++;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
image1.close();
image2.close();
double agreements = 0;
double expectedFrequency = 0;
double N = 0;
double rowTotal = 0;
double colTotal = 0;
double kappa = 0;
double overallAccuracy = 0;
for (int a = 0; a <= numClasses - 1; a++) {
agreements += contingency[a][a];
for (int b = 0; b <= numClasses - 1; b++) {
N += contingency[a][b];
}
}
for (int a = 0; a <= numClasses - 1; a++) {
rowTotal = 0;
colTotal = 0;
for (int b = 0; b <= numClasses - 1; b++) {
colTotal += contingency[a][b];
rowTotal += contingency[b][a];
}
expectedFrequency += (colTotal * rowTotal) / N;
}
kappa = (agreements - expectedFrequency) / (N - expectedFrequency);
overallAccuracy = agreements / N;
File file = new File(outputFile);
FileWriter fw = null;
BufferedWriter bw = null;
PrintWriter out = null;
try {
fw = new FileWriter(file, false);
bw = new BufferedWriter(fw);
out = new PrintWriter(bw, true);
String str;
str = "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">";
out.println(str);
str = "<head>";
out.println(str);
str = "<meta content=\"text/html; charset=iso-8859-1\" http-equiv=\"content-type\"><title>Kappa Index of Agreement Output</title>";
out.println(str);
str = "</head>";
out.println(str);
str = "<body><h1>Kappa Index of Agreement</h1>";
out.println(str);
str = "<b>Input Images:</b> <br><br><b>Classification Image:</b> " + inputHeader1 + "<br><b>Reference Image:</b> " + inputHeader2 + "<br>";
out.println(str);
str = "<br><b>Contingency Table:</b><br>";
out.println(str);
str = "<br><table border=\"1\" cellspacing=\"0\" cellpadding=\"3\">";
out.println(str);
str = "<tr>";
out.println(str);
str = "<th colspan=\"2\" rowspan=\"2\"></th><th colspan=\"" + numClasses + "\">Class Image</th><th rowspan=\"2\">Row<br>Totals</th>";
out.println(str);
str = "</tr>";
out.println(str);
str = "<tr>";
out.println(str);
for (int a = 0; a <= numClasses - 1; a++) {
str = "<th>" + (minClass + a) + "</th>";
out.println(str);
}
str = "</tr>";
out.println(str);
for (int a = 0; a <= numClasses - 1; a++) {
if (a == 0) {
str = "<tr><th rowspan=\"" + numClasses + "\">Ref<br>Image</th> <th>" + (minClass + a) + "</th>";
out.println(str);
} else {
str = "<tr><th>" + (minClass + a) + "</th>";
out.println(str);
}
rowTotal = 0;
for (int b = 0; b <= numClasses - 1; b++) {
rowTotal += contingency[a][b];
str = "<td>" + contingency[a][b] + "</td>";
out.println(str);
}
str = "<td>" + rowTotal + "</td>";
out.println(str);
str = "</tr>";
out.println(str);
}
str = "<tr>";
out.println(str);
str = "<th colspan=\"2\">Col<br>Totals</th>";
out.println(str);
for (int a = 0; a <= numClasses - 1; a++) {
colTotal = 0;
for (int b = 0; b <= numClasses - 1; b++) {
colTotal += contingency[b][a];
}
str = "<td>" + colTotal + "</td>";
out.println(str);
}
str = "<td><b>N</b>=" + N + "</td></tr>";
out.println(str);
str = "</table>";
out.println(str);
str = "<br><b>Class Accuracy Statistics:</b><br><br>";
out.println(str);
str = "<table border=\"1\" cellspacing=\"0\" cellpadding=\"3\">";
out.println(str);
str = "<tr><td><b>Class</b></td><td><b>User's<br>Accuracy</b></td><td><b>Producer's<br>Accuracy</b></td></tr>";
out.println(str);
DecimalFormat df = new DecimalFormat("0.00%");
DecimalFormat df2 = new DecimalFormat("0.000");
for (int a = 0; a <= numClasses - 1; a++) {
rowTotal = 0;
colTotal = 0;
for (int b = 0; b <= numClasses - 1; b++) {
colTotal += contingency[a][b];
rowTotal += contingency[b][a];
}
str = "<tr><td>" + a + "</td><td>" + df.format(contingency[a][a] / colTotal)
+ "</td><td>" + df.format(contingency[a][a] / rowTotal) + "</td></tr>";
out.println(str);
}
str = "</table>";
out.println(str);
str = "<br>Note: User's accuracy refers to the proportion of cells correctly assigned to a class (i.e. the number of cells correctly classified for a category divided by the row total in the contingency table). "
+ "Producer's accuracy is a measure of how much of the land in each category was classified correctly (i.e. the number of cells correctly classified for a category divided by the column total in the contingency table).<br>";
out.println(str);
str = "<br><b>Overall Accuracy</b> = " + df.format(overallAccuracy);
out.println(str);
str = "<br><br><b>Kappa</b> = " + df2.format(kappa);
out.println(str);
str = "</body>";
out.println(str);
} catch (java.io.IOException e) {
System.err.println("Error: " + e.getMessage());
} finally {
if (out != null || bw != null) {
out.flush();
out.close();
}
}
returnData(outputFile);
} catch (OutOfMemoryError oe) {
myHost.showFeedback("An out-of-memory error has occurred during operation.");
} catch (Exception e) {
myHost.showFeedback("An error has occurred during operation. See log file for details.");
myHost.logException("Error in " + getDescriptiveName(), e);
} finally {
updateProgress("Progress: ", 0);
// tells the main application that this process is completed.
amIActive = false;
myHost.pluginComplete();
}
}
// // this is only used for debugging the tool
// public static void main(String[] args) {
// ImageRegression ir = new ImageRegression();
// args = new String[3];
// args[0] = "/Users/johnlindsay/Documents/Data/LandsatData/band1.dep";
// args[1] = "/Users/johnlindsay/Documents/Data/LandsatData/band2_cropped.dep";
// args[2]= "not specified";
//
// ir.setArgs(args);
// ir.run();
//
// }
}