/*
* 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.ShapeFile;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.geospatialfiles.shapefile.*;
import whitebox.geospatialfiles.shapefile.attributes.DBFField;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool calculates the linearity index of polygon features based on a regression analysis.
*
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class LinearityIndex 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 "LinearityIndex";
}
/**
* 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 "Linearity Index";
}
/**
* Used to retrieve a short description of what the plugin tool does.
*
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "The LinearityIndex tool can be used to find patches that are "
+ "linear in shape, i.e. well-described by a straight line.";
}
/**
* 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;
}
private void calculateRaster() {
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[][] regressionData = new double[6][range + 1];
double[] rSquare = new double[range + 1];
//double[][] totals = new double[3][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);
double[] data;
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);
}
// Calculate the patch orientation.
updateProgress("Calculating patch linearity:", 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);
regressionData[0][a]++; // N
regressionData[1][a] += (col - minRowAndCol[1][a]); // sigma X
regressionData[2][a] += (row - minRowAndCol[0][a]); // sigma Y
regressionData[3][a] += (col - minRowAndCol[1][a]) * (row - minRowAndCol[0][a]); // sigma XY
regressionData[4][a] += (col - minRowAndCol[1][a]) * (col - minRowAndCol[1][a]); // sigma Xsqr
regressionData[5][a] += (row - minRowAndCol[0][a]) * (row - minRowAndCol[0][a]); // sigma Ysqr
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Calculating patch linearity:", (int) progress);
}
double sigmaX;
double sigmaY;
double N;
double sigmaXY;
double sigmaXsqr;
double sigmaYsqr;
double mean = 0;
double Sxx, Syy, Sxy;
//double radians2Deg = (180 / Math.PI);
for (a = 0; a <= range; a++) {
if (regressionData[0][a] > 1) {
N = regressionData[0][a];
sigmaX = regressionData[1][a];
mean = sigmaX / N;
sigmaY = regressionData[2][a];
sigmaXY = regressionData[3][a];
sigmaXsqr = regressionData[4][a];
sigmaYsqr = regressionData[5][a];
Sxx = (sigmaXsqr / N - mean * mean);
Syy = (sigmaYsqr / N - (sigmaY / N) * (sigmaY / N));
Sxy = (sigmaXY / N - (sigmaX * sigmaY) / (N * N));
z = (sigmaXsqr - mean * sigmaX);
if (Math.sqrt(Sxx * Syy) != 0) {
rSquare[a] = ((Sxy / Math.sqrt(Sxx * Syy)) * (Sxy / Math.sqrt(Sxx * Syy)));
}
}
}
// Creat output image.
updateProgress("Creating output image:", 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, rSquare[a]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Creating output image:", (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 = "Linearity Index\nPatch ID\tLinearity";
for (a = 0; a <= range; a++) {
if (regressionData[0][a] > 0) {
retstr = retstr + "\n" + (a + minValue) + "\t" + df.format(rSquare[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();
}
}
private void calculateVector() {
/*
* Notice that this tool assumes that each record in the shapefile is an
* individual polygon. The feature can contain multiple parts only if it
* has holes, i.e. islands. A multipart record cannot contain multiple
* and seperate features. This is because it complicates the calculation
* of feature area and perimeter.
*/
amIActive = true;
// Declare the variable.
String inputFile = null;
int progress;
int recNum;
int v;
double sigmaX;
double sigmaY;
double N;
double sigmaXY;
double sigmaXsqr;
double sigmaYsqr;
double mean;
double midX;
double midY;
double Sxx, Syy, Sxy;
double z = 0;
double x, y;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputFile = args[0];
// check to see that the inputHeader and outputHeader are not null.
if (inputFile == null) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
ShapeFile input = new ShapeFile(inputFile);
double numberOfRecords = input.getNumberOfRecords();
if (input.getShapeType().getBaseType() != ShapeType.POLYGON) {
showFeedback("This function can only be applied to polygon type shapefiles.");
return;
}
/*
* create a new field in the input file's database to hold the
* fractal dimension. Put it at the end of the database.
*/
DBFField field = new DBFField();
field = new DBFField();
field.setName("LINEARITY");
field.setDataType(DBFField.DBFDataType.NUMERIC);
field.setFieldLength(10);
field.setDecimalCount(4);
input.getAttributeTable().addField(field);
// initialize the shapefile.
ShapeType inputType = input.getShapeType();
double[][] vertices = null;
double[] regressionData;
double rSquared;
for (ShapeFileRecord record : input.records) {
midX = 0;
midY = 0;
switch (inputType) {
case POLYGON:
whitebox.geospatialfiles.shapefile.Polygon recPolygon =
(whitebox.geospatialfiles.shapefile.Polygon) (record.getGeometry());
vertices = recPolygon.getPoints();
midX = recPolygon.getXMin() + (recPolygon.getXMax() - recPolygon.getXMin()) / 2;
midY = recPolygon.getYMin() + (recPolygon.getYMax() - recPolygon.getYMin()) / 2;
break;
case POLYGONZ:
PolygonZ recPolygonZ = (PolygonZ) (record.getGeometry());
vertices = recPolygonZ.getPoints();
midX = recPolygonZ.getXMin() + (recPolygonZ.getXMax() - recPolygonZ.getXMin()) / 2;
midY = recPolygonZ.getYMin() + (recPolygonZ.getYMax() - recPolygonZ.getYMin()) / 2;
break;
case POLYGONM:
PolygonM recPolygonM = (PolygonM) (record.getGeometry());
vertices = recPolygonM.getPoints();
midX = recPolygonM.getXMin() + (recPolygonM.getXMax() - recPolygonM.getXMin()) / 2;
midY = recPolygonM.getYMin() + (recPolygonM.getYMax() - recPolygonM.getYMin()) / 2;
break;
}
// initialize variables
regressionData = new double[5];
rSquared = 0;
N = vertices.length;
for (v = 0; v < N; v++) {
x = vertices[v][0] - midX;
y = vertices[v][1] - midY;
regressionData[0] += x; // sigma X
regressionData[1] += y; // sigma Y
regressionData[2] += x * y; // sigma XY
regressionData[3] += x * x; // sigma Xsqr
regressionData[4] += y * y; // sigma Ysqr
}
sigmaX = regressionData[0];
mean = sigmaX / N;
sigmaY = regressionData[1];
sigmaXY = regressionData[2];
sigmaXsqr = regressionData[3];
sigmaYsqr = regressionData[4];
Sxx = (sigmaXsqr / N - mean * mean);
Syy = (sigmaYsqr / N - (sigmaY / N) * (sigmaY / N));
Sxy = (sigmaXY / N - (sigmaX * sigmaY) / (N * N));
if (Math.sqrt(Sxx * Syy) != 0) {
rSquared = ((Sxy / Math.sqrt(Sxx * Syy)) * (Sxy / Math.sqrt(Sxx * Syy)));
}
recNum = record.getRecordNumber() - 1;
Object[] recData = input.getAttributeTable().getRecord(recNum);
recData[recData.length - 1] = new Double(rSquared);
input.getAttributeTable().updateRecord(recNum, recData);
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (record.getRecordNumber() / numberOfRecords * 100);
updateProgress(progress);
}
// returning the database file will result in it being opened in the Whitebox GUI.
returnData(input.getDatabaseFile());
} 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 to execute this plugin tool.
*/
@Override
public void run() {
amIActive = true;
String inputFile = args[0];
if (inputFile.toLowerCase().contains(".dep")) {
calculateRaster();
} else if (inputFile.toLowerCase().contains(".shp")) {
calculateVector();
} else {
showFeedback("There was a problem reading the input file.");
}
}
}