/*
* 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.File;
import java.text.DecimalFormat;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool can be used to estimate the Pearson product-moment correlation coefficient (r) between two images.
*
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class ImageCorrelation 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 "ImageCorrelation";
}
/**
* 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 "Image Correlation";
}
/**
* Used to retrieve a short description of what the plugin tool does.
*
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "Performs image correlation on two or more input images.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
*
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = { "StatisticalTools" };
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;
WhiteboxRaster image;
WhiteboxRaster image2;
int cols = 0;
int rows = 0;
double noData = -32768;
double noDataImage2 = -32768;
int numImages;
double z;
float progress = 0;
int col, row;
int a, b, i;
String inputFilesString = null;
String[] imageFiles;
Object[] images;
double[] imageTotals;
long[] imageNs;
double[] imageAverages;
double image1TotalDeviation = 0;
double image2TotalDeviation = 0;
double totalProductDeviations = 0;
double[][] correlationMatrix;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputFilesString = args[0];
imageFiles = inputFilesString.split(";");
numImages = imageFiles.length;
// check to see that the inputHeader and outputHeader are not null.
if (numImages < 2) {
showFeedback("At least two images must be specified for an image correlation.");
return;
}
try {
//initialize the image data arrays
imageTotals = new double[numImages];
imageNs = new long[numImages];
imageAverages = new double[numImages];
correlationMatrix = new double[numImages][numImages];
// initialize the matrix with -99's
for (a = 0; a < numImages; a++) {
for (b = 0; b < numImages; b++) {
correlationMatrix[a][b] = -99;
}
}
double[] data;
double[] data2;
// check that each of the input images has the same number of rows and columns
// and calculate the image averages.
updateProgress("Calculating image averages:", 0);
for (a = 0; a < numImages; a++) {
image = new WhiteboxRaster(imageFiles[a], "r");
noData = image.getNoDataValue();
if (a == 0) {
rows = image.getNumberRows();
cols = image.getNumberColumns();
} else {
if (image.getNumberColumns() != cols ||
image.getNumberRows() != rows) {
showFeedback("All input images must have the same dimensions (rows and columns).");
return;
}
}
for (row = 0; row < rows; row++) {
data = image.getRowValues(row);
for (col = 0; col < cols; col++) {
if (data[col] != noData) {
imageTotals[a] += data[col];
imageNs[a]++;
}
}
if (cancelOp) { cancelOperation(); return; }
}
image.close();
imageAverages[a] = imageTotals[a] / imageNs[a];
progress = a / (numImages - 1) * 100;
updateProgress("Calculating image average:", (int)progress);
}
updateProgress("Calculating the correlation matrix:", 0);
i = 0;
for (a = 0; a < numImages; a++) {
image = new WhiteboxRaster(imageFiles[a], "r");
noData = image.getNoDataValue();
for (b = 0; b <= i; b++) {
if (a == b) {
correlationMatrix[a][b] = 1.0;
} else {
image1TotalDeviation = 0;
image2TotalDeviation = 0;
totalProductDeviations = 0;
image2 = new WhiteboxRaster(imageFiles[b], "r");
noDataImage2 = image2.getNoDataValue();
for (row = 0; row < rows; row++) {
data = image.getRowValues(row);
data2 = image2.getRowValues(row);
for (col = 0; col < cols; col++) {
if (data[col] != noData && data2[col] != noDataImage2) {
image1TotalDeviation += (data[col] - imageAverages[a]) * (data[col] - imageAverages[a]);
image2TotalDeviation += (data2[col] - imageAverages[b]) * (data2[col] - imageAverages[b]);
totalProductDeviations += (data[col] - imageAverages[a]) * (data2[col] - imageAverages[b]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
}
image2.close();
correlationMatrix[a][b] = totalProductDeviations / (Math.sqrt(image1TotalDeviation * image2TotalDeviation));
}
}
i++;
image.close();
progress = a / (numImages - 1) * 100;
updateProgress("Calculating the correlation matrix:", (int)progress);
}
String retstr = null;
retstr = "IMAGE CORRELATION MATRIX\n\n";
String headers = "\t";
for (a = 0; a < numImages; a++) {
headers = headers + "Image" + (a + 1) + "\t";
}
// int lineLength = headers.length();
// String ruledLine = "";
// for (a = 0; a < lineLength; a++) {
// ruledLine += "\u2014";
// }
// ruledLine += "\n";
// retstr += ruledLine;
retstr += headers;
// retstr += ruledLine;
DecimalFormat df = new DecimalFormat("0.0000");
for (a = 0; a < numImages; a++) {
retstr = retstr + "\nImage" + (a + 1) + "\t";
for (b = 0; b < numImages; b++) {
if (correlationMatrix[a][b] != -99) {
if (correlationMatrix[a][b] >= 0) {
retstr = retstr + " " + df.format(correlationMatrix[a][b]) + "\t";
} else {
retstr = retstr + df.format(correlationMatrix[a][b]) + "\t";
}
} else {
retstr = retstr + "\t";
}
}
}
// retstr += ruledLine;
retstr = retstr + "\n\n";
String shortFileName;
int j, k;
for (a = 0; a < numImages; a++) {
j = imageFiles[a].toString().lastIndexOf(File.separator);
k = imageFiles[a].toString().lastIndexOf(".");
shortFileName = imageFiles[a].toString().substring(j + 1, k);
retstr = retstr + "Image" + (a + 1) + " = " + shortFileName + "\n";
}
returnData(retstr);
} 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();
}
}
}