/*
* 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.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool performs a type of adaptive filter on a raster image, which can be used to reduce the level of random noise (shot noise) in an image.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class FilterAdaptive 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 "FilterAdaptive";
}
/**
* 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 "Adaptive Filter";
}
/**
* 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 adaptive filter on an image.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = { "Filters" };
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;
int row, col, x, y;
double z;
float progress = 0;
int a;
int filterSizeX = 3;
int filterSizeY = 3;
double n;
double sum;
double sumOfTheSquares;
double average;
double stdDev;
int dX[];
int dY[];
int midPointX;
int midPointY;
int numPixelsInFilter;
boolean filterRounded = false;
double[] filterShape;
boolean reflectAtBorders = false;
double threshold = 0;
double centreValue = 0;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
for (int i = 0; i < args.length; i++) {
if (i == 0) {
inputHeader = args[i];
} else if (i == 1) {
outputHeader = args[i];
} else if (i == 2) {
filterSizeX = Integer.parseInt(args[i]);
} else if (i == 3) {
filterSizeY = Integer.parseInt(args[i]);
} else if (i == 4) {
threshold = Double.parseDouble(args[i]);
} else if (i == 5) {
filterRounded = Boolean.parseBoolean(args[i]);
} else if (i == 6) {
reflectAtBorders = Boolean.parseBoolean(args[i]);
}
}
// 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 {
WhiteboxRaster inputFile = new WhiteboxRaster(inputHeader, "r");
inputFile.isReflectedAtEdges = reflectAtBorders;
int rows = inputFile.getNumberRows();
int cols = inputFile.getNumberColumns();
double noData = inputFile.getNoDataValue();
WhiteboxRaster outputFile = new WhiteboxRaster(outputHeader, "rw", inputHeader, WhiteboxRaster.DataType.FLOAT, noData);
outputFile.setPreferredPalette(inputFile.getPreferredPalette());
//the filter dimensions must be odd numbers such that there is a middle pixel
if (Math.floor(filterSizeX / 2d) == (filterSizeX / 2d)) {
showFeedback("Filter dimensions must be odd numbers. The specified filter x-dimension" +
" has been modified.");
filterSizeX++;
}
if (Math.floor(filterSizeY / 2d) == (filterSizeY / 2d)) {
showFeedback("Filter dimensions must be odd numbers. The specified filter y-dimension" +
" has been modified.");
filterSizeY++;
}
numPixelsInFilter = filterSizeX * filterSizeY;
dX = new int[numPixelsInFilter];
dY = new int[numPixelsInFilter];
filterShape = new double[numPixelsInFilter];
//fill the filter DX and DY values
midPointX = (int)Math.floor(filterSizeX / 2);
midPointY = (int)Math.floor(filterSizeY / 2);
if (!filterRounded) {
a = 0;
for (row = 0; row < filterSizeY; row++) {
for (col = 0; col < filterSizeX; col++) {
dX[a] = col - midPointX;
dY[a] = row - midPointY;
filterShape[a] = 1;
a++;
}
}
} else {
//see which pixels in the filter lie within the largest ellipse
//that fits in the filter box
double aSqr = midPointX * midPointX;
double bSqr = midPointY * midPointY;
a = 0;
for (row = 0; row < filterSizeY; row++) {
for (col = 0; col < filterSizeX; col++) {
dX[a] = col - midPointX;
dY[a] = row - midPointY;
z = (dX[a] * dX[a]) / aSqr + (dY[a] * dY[a]) / bSqr;
if (z > 1) {
filterShape[a] = 0;
} else {
filterShape[a] = 1;
}
a++;
}
}
}
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
centreValue = inputFile.getValue(row, col);
if (centreValue != noData) {
n = 0;
sum = 0;
sumOfTheSquares = 0;
for (a = 0; a < numPixelsInFilter; a++) {
x = col + dX[a];
y = row + dY[a];
if ((x != midPointX) && (y != midPointY)) {
z = inputFile.getValue(y, x);
if (z != noData) {
n += filterShape[a];
sum += z * filterShape[a];
sumOfTheSquares += (z * filterShape[a]) * z;
}
}
}
if (n > 2) {
average = sum / n;
stdDev = (sumOfTheSquares / n) - (average * average);
if (stdDev > 0) {
stdDev = Math.sqrt(stdDev);
}
if (Math.abs((centreValue - average) / stdDev) > threshold) {
outputFile.setValue(row, col, average);
} else {
outputFile.setValue(row, col, centreValue);
}
}
} else {
outputFile.setValue(row, col, noData);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((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();
}
}
}