/*
* 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.util.Date;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPluginHost;
import whitebox.interfaces.WhiteboxPlugin;
/**
* This tool performs a Gaussian stretch on a raster image, which fits the observed histogram of the input image to a normal Gaussian histogram.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class GaussianStretch 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 "GaussianStretch";
}
/**
* 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 "Gaussian Contrast Stretch";
}
/**
* 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 a Gausian contrast stretch on an input image.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = { "ImageEnhancement" };
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 inputHeader = null;
String outputHeader = null;
double cutoffsInSD = 3;
int numOutputBins = 1024;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputHeader = args[0];
outputHeader = args[1];
cutoffsInSD = Double.parseDouble(args[2]);
numOutputBins = Integer.parseInt(args[3]);
// check to see that the inputHeader and outputHeader are not null.
if ((inputHeader == null) || (outputHeader == null)) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
int row, col;
double z;
float progress = 0;
int numCells = 0;
int i = 0;
WhiteboxRaster inputFile = new WhiteboxRaster(inputHeader, "r");
int rows = inputFile.getNumberRows();
int cols = inputFile.getNumberColumns();
double noData = inputFile.getNoDataValue();
WhiteboxRaster outputFile = new WhiteboxRaster(outputHeader, "rw", inputHeader, WhiteboxRaster.DataType.INTEGER, noData);
outputFile.setPreferredPalette(inputFile.getPreferredPalette());
int numBins = 50000;
double minValue = inputFile.getMinimumValue();
double maxValue = inputFile.getMaximumValue();
double binSize = (maxValue - minValue) / numBins;
long[] histogram = new long[numBins];
int binNum;
int numBinsLessOne = numBins - 1;
double[] data;
updateProgress("Loop 1 of 3: ", 0);
for (row = 0; row < rows; row++) {
data = inputFile.getRowValues(row);
for (col = 0; col < cols; col++) {
z = data[col];
if (z != noData) {
numCells++;
binNum = (int)((z - minValue) / binSize);
if (binNum > numBinsLessOne) { binNum = numBinsLessOne; }
histogram[binNum]++;
}
}
if (cancelOp) { cancelOperation(); return; }
progress = (float) (100f * row / (rows - 1));
updateProgress("Loop 1 of 3: ", (int)progress);
}
updateProgress("Loop 2 of 3: ", 0);
double[] cdf = new double[numBins];
cdf[0] = histogram[0];
for (i = 1; i < numBins; i++) {
cdf[i] = cdf[i - 1] + histogram[i];
}
histogram = null;
for (i = 0; i < numBins; i++) {
cdf[i] = cdf[i] / numCells;
}
// create the reference distribution
double[] referenceCDF = new double[numOutputBins];
double rootOf2Pi = Math.sqrt(2 * Math.PI);
double exponent;
double x;
for (i = 0; i < numOutputBins; i++) {
x = (double)i / (numOutputBins - 1) * 2 * cutoffsInSD - cutoffsInSD;
exponent = -x * x / 2;
referenceCDF[i] = Math.pow(Math.E, exponent) / rootOf2Pi;
}
// convert the reference histogram to a cdf.
for (i = 1; i < numOutputBins; i++) {
referenceCDF[i] += referenceCDF[i - 1];
}
double totalFrequency = referenceCDF[numOutputBins - 1];
for (i = 0; i < numOutputBins; i++) {
referenceCDF[i] = referenceCDF[i] / totalFrequency;
}
int[] startingVals = new int[11];
double pVal = 0;
for (i = 0; i < numOutputBins; i++) {
pVal = referenceCDF[i];
if (pVal < 0.1) {
startingVals[1] = i;
}
if (pVal < 0.2) {
startingVals[2] = i;
}
if (pVal < 0.3) {
startingVals[3] = i;
}
if (pVal < 0.4) {
startingVals[4] = i;
}
if (pVal < 0.5) {
startingVals[5] = i;
}
if (pVal < 0.6) {
startingVals[6] = i;
}
if (pVal < 0.7) {
startingVals[7] = i;
}
if (pVal < 0.8) {
startingVals[8] = i;
}
if (pVal < 0.9) {
startingVals[9] = i;
}
if (pVal <= 1) {
startingVals[10] = i;
}
}
updateProgress("Loop 3 of 3: ", 0);
int j = 0;
double xVal = 0;
double x1, x2, p1, p2;
for (row = 0; row < rows; row++) {
data = inputFile.getRowValues(row);
for (col = 0; col < cols; col++) {
z = data[col];
if (z != noData) {
binNum = (int)((z - minValue) / binSize);
if (binNum > numBinsLessOne) { binNum = numBinsLessOne; }
pVal = cdf[binNum];
j = (int)(Math.floor(pVal * 10));
for (i = startingVals[j]; i < numOutputBins; i++) {
if (referenceCDF[i] > pVal) {
if (i > 0) {
xVal = i - 1;
} else {
xVal = i;
}
break;
} else if (referenceCDF[i] == pVal) {
xVal = i;
}
}
outputFile.setValue(row, col, xVal);
}
}
if (cancelOp) { cancelOperation(); return; }
progress = (float) (100f * row / (rows - 1));
updateProgress("Loop 3 of 3: ", (int)progress);
}
outputFile.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
outputFile.addMetadataEntry("Created on " + new Date());
inputFile.close();
outputFile.close();
// returning a header file string displays the image.
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();
}
}
// // used for debugging the tool
// public static void main(String[] args) {
// GaussianStretch gs = new GaussianStretch();
// args = new String[4];
// args[0] = "/Users/johnlindsay/Documents/Teaching/GEOG3420/Winter 2012/Labs/Lab1/Data/LE70180302002142EDC00/band3.dep";
// args[1] = "/Users/johnlindsay/Documents/Teaching/GEOG3420/Winter 2012/Labs/Lab1/Data/LE70180302002142EDC00/tmp1.dep";
// args[2] = "3";
// args[3] = "255";
//
// gs.setArgs(args);
// gs.run();
// }
}