/*
* 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.text.DecimalFormat;
import java.util.Date;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This can be used to calculate the radius of gyration (RoG) for the polygon features within a raster image.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class RadiusOfGyration implements WhiteboxPlugin {
private WhiteboxPluginHost myHost;
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 "RadiusOfGyration";
}
/**
* 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 "Radius Of Gyration";
}
/**
* 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 distance "
+ "of cells from their polygon's centroid.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = { "PatchShapeTools" };
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 feedback) {
if (myHost != null) {
myHost.showFeedback(feedback);
} else {
System.out.println(feedback);
}
}
/**
* 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);
}
}
/**
* 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) {
myHost.updateProgress(progressLabel, progress);
} else {
System.out.println(progressLabel + " " + progress + "%");
}
}
/**
* 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) {
myHost.updateProgress(progress);
} else {
System.out.println("Progress: " + 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 col;
int row;
int numCols;
int numRows;
int a;
int i;
float progress;
int range;
boolean blnTextOutput = false;
double z;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
for (i = 0; i < args.length; i++) {
if (i == 0) {
inputHeader = args[i];
} else if (i == 1) {
outputHeader = args[i];
} else if (i == 2) {
blnTextOutput = 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 image = new WhiteboxRaster(inputHeader, "r");
numRows = image.getNumberRows();
numCols = image.getNumberColumns();
double noData = image.getNoDataValue();
WhiteboxRaster output = new WhiteboxRaster(outputHeader, "rw", inputHeader, WhiteboxRaster.DataType.FLOAT, noData);
output.setPreferredPalette("spectrum.pal");
output.setDataScale(WhiteboxRaster.DataScale.CONTINUOUS);
int minValue = (int)(image.getMinimumValue());
int maxValue = (int)(image.getMaximumValue());
range = maxValue - minValue;
double[] data;
double[][] totals = new double[4][range + 1];
double[] radius = new double[range + 1];
double[][] centroid = new double[2][range + 1];
double[] DFCSum = new double[range + 1];
long[][] minRowAndCol = new long[2][range + 1];
for (a = 0; a <= range; a++) {
minRowAndCol[0][a] = Long.MAX_VALUE;
minRowAndCol[1][a] = Long.MAX_VALUE;
}
updateProgress("Finding patch min row and columns:", 0);
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] > 0) {
a = (int)(data[col] - minValue);
if (row < minRowAndCol[0][a]) {
minRowAndCol[0][a] = row;
}
if (col < minRowAndCol[1][a]) {
minRowAndCol[1][a] = col;
}
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Finding patch min row and columns:", (int) progress);
}
updateProgress("Loop 1 of 3:", 0);
// sum the column numbers and row numbers of each patch cell along
// with the total number of cells.
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] > 0) {
a = (int) (data[col] - minValue);
totals[0][a] += (col - minRowAndCol[1][a]);
totals[1][a] += (row - minRowAndCol[0][a]);
totals[2][a]++;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 1 of 3:", (int) progress);
}
for (a = 0; a <= range; a++) {
if (totals[2][a] > 0) {
centroid[0][a] = totals[0][a] / totals[2][a] + minRowAndCol[1][a];
centroid[1][a] = totals[1][a] / totals[2][a] + minRowAndCol[0][a];
radius[a] = Math.sqrt((totals[2][a]) / Math.PI) - 0.5;
}
}
updateProgress("Loop 2 of 3:", 0);
double d;
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] > 0) {
a = (int) (data[col] - minValue);
d = Math.sqrt(Math.pow((col - centroid[0][a]), 2d)
+ Math.pow((row - centroid[1][a]), 2));
DFCSum[a] += (double) d;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 2 of 3:", (int) progress);
}
for (a = 0; a <= range; a++) {
if (totals[2][a] > 0) {
DFCSum[a] = DFCSum[a] / totals[2][a];
}
}
updateProgress("Loop 3 of 3:", 0);
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] > 0) {
a = (int)(data[col] - minValue);
output.setValue(row, col, DFCSum[a]);
} else {
output.setValue(row, col, noData);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 3 of 3:", (int) progress);
}
output.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
output.addMetadataEntry("Created on " + new Date());
image.close();
output.close();
if (blnTextOutput) {
DecimalFormat df;
df = new DecimalFormat("0.0000");
String retstr = "Radius of Gyration\nPatch ID\tValue";
for (a = 0; a <= range; a++) {
if (DFCSum[a] > 0) {
retstr = retstr + "\n" + (a + minValue) + "\t"
+ df.format(DFCSum[a]);
}
}
returnData(retstr);
}
// 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();
}
}
}