/*
* 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.util.ArrayList;
import java.util.Date;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.geospatialfiles.WhiteboxRasterBase.DataScale;
import whitebox.geospatialfiles.WhiteboxRasterInfo;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool can be used to perform an inverse principal component analysis (PCA) on a set of PCA component images created using the Principal Component Analysis tool.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class InversePrincipalComponentAnalysis 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 "InversePrincipalComponentAnalysis";
}
/**
* 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 "Inverse Principal Component Analysis";
}
/**
* 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 an inverse principal component analysis on PCA components.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = {"ImageTransformations"};
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 inputFilesString = null;
String[] imageFiles = null;
String outputName = null;
String workingDirectory = null;
WhiteboxRasterInfo[] components = null;
WhiteboxRaster ouptut = null;
int nCols = 0;
int nRows = 0;
double z;
int numImages = 0;
int numFiles, numComponents;
int progress = 0;
int col, row;
int a, i, j;
double[] imageAverages;
double[] imageTotals;
double[] imageNumPixels;
double[][] data;
double[] noDataValues;
String pathSep = File.separator;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
// read the input parameters
inputFilesString = args[0];
outputName = args[1];
if (outputName.toLowerCase().contains(".dep")) {
outputName = outputName.replace(".dep", "");
}
try {
// deal with the input images
imageFiles = inputFilesString.split(";");
numFiles = imageFiles.length;
components = new WhiteboxRasterInfo[numFiles];
imageAverages = new double[numFiles];
imageTotals = new double[numFiles];
imageNumPixels = new double[numFiles];
noDataValues = new double[numFiles];
data = new double[numFiles][];
int[] componentNumbers = new int[numFiles];
double[][] eigenvectors = null;
//ArrayList<double[]> eigenvectors = new ArrayList<double[]>();
for (i = 0; i < numFiles; i++) {
boolean isComponent = false;
components[i] = new WhiteboxRasterInfo(imageFiles[i]);
noDataValues[i] = components[i].getNoDataValue();
if (i == 0) {
nCols = components[i].getNumberColumns();
nRows = components[i].getNumberRows();
File file = new File(imageFiles[i]);
workingDirectory = file.getParent();
} else {
if (components[i].getNumberColumns() != nCols
|| components[i].getNumberRows() != nRows) {
showFeedback("All input components must have the same dimensions (rows and columns).");
return;
}
}
ArrayList<String> metadata = components[i].getMetadata();
for (String entry: metadata) {
if (entry.toLowerCase().contains("principal component num")) {
componentNumbers[i] = Integer.parseInt(entry.replace("Principal Component Num.:", "").trim()) - 1; // zero based
}
if (entry.toLowerCase().contains("eigenvector")) {
String[] eigenStr = entry.replace("Eigenvector:", "").
replace("[", "").replace("]", "").split(",");
if (i == 0) {
numImages = eigenStr.length;
eigenvectors = new double[numImages][numImages];
}
for (a = 0; a < numImages; a++) {
eigenvectors[componentNumbers[i]][a] = Double.parseDouble(eigenStr[a].trim());
}
isComponent = true;
}
}
if (!isComponent) {
showFeedback("At least one of the input images does not appear to have been created by the PrincipalComponentAnalysis tool. " +
"This tool will not operate correctly.");
return;
}
}
int[] componentPointers = new int[numImages];
for (i = 0; i < numFiles; i++) {
componentPointers[componentNumbers[i]] = i;
}
for (j = 0; j < numImages; j++) {
// now set up the output image
String outputHeader = workingDirectory + pathSep + outputName + (j + 1) + ".dep";
if (new File(outputHeader).exists()) {
(new File(outputHeader)).delete();
}
if (new File(outputHeader.replace(".dep", ".tas")).exists()) {
(new File(outputHeader.replace(".dep", ".tas"))).delete();
}
WhiteboxRaster output = new WhiteboxRaster(outputHeader, "rw",
imageFiles[0], WhiteboxRaster.DataType.FLOAT, 0);
output.setDataScale(DataScale.CONTINUOUS);
for (row = 0; row < nRows; row++) {
for (i = 0; i < numFiles; i++) {
data[i] = components[i].getRowValues(row);
}
for (col = 0; col < nCols; col++) {
if (data[0][col] != noDataValues[0]) {
z = 0;
for (i = 0; i < numFiles; i++) {
z += data[i][col] * eigenvectors[componentPointers[i]][j];
}
output.setValue(row, col, z);
} else {
output.setValue(row, col, noDataValues[0]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (nRows - 1));
updateProgress("Creating image " + (j + 1) + ":", progress);
}
output.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
output.addMetadataEntry("Created on " + new Date());
output.close();
}
for (i = 0; i < numFiles; i++) {
components[i].close();
}
String outputHeader = workingDirectory + pathSep + outputName + "1.dep";
returnData(outputHeader);
} 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();
}
}
public static class PrincipalComponent implements Comparable<PrincipalComponent> {
public double eigenValue;
public double[] eigenVector;
public PrincipalComponent(double eigenValue, double[] eigenVector) {
this.eigenValue = eigenValue;
this.eigenVector = eigenVector;
}
@Override
public int compareTo(PrincipalComponent o) {
int ret = 0;
if (eigenValue > o.eigenValue) {
ret = -1;
} else if (eigenValue < o.eigenValue) {
ret = 1;
}
return ret;
}
@Override
public String toString() {
String ret = "Principle Component, eigenvalue: " + eigenValue + ", eigenvector: [";
for (int i = 0; i < eigenVector.length; i++) {
ret += eigenVector[i] + ", ";
}
ret += "]";
return ret;
}
}
// // this is only used for debugging the tool
// public static void main(String[] args) {
// InversePrincipalComponentAnalysis ipca = new InversePrincipalComponentAnalysis();
// args = new String[2];
// args[0] = "/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp1.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp3.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp2.dep";
// //args[0] = "/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp1.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp3.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp2.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp4.dep;/Users/johnlindsay/Documents/Data/LandsatData/PCA_comp5.dep";
// args[1] = "invPCA_band";
//
// ipca.setArgs(args);
// ipca.run();
//
// }
}