/*
* Copyright (C) 2011-2013 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 java.util.ArrayList;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.exception.NoDataException;
import org.apache.commons.math3.exception.NullArgumentException;
import org.apache.commons.math3.exception.OutOfRangeException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.ArrayRealVector;
import org.apache.commons.math3.linear.DecompositionSolver;
import org.apache.commons.math3.linear.QRDecomposition;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.RealVector;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
import whitebox.geospatialfiles.ShapeFile;
import whitebox.geospatialfiles.WhiteboxRasterBase;
import whitebox.geospatialfiles.shapefile.MultiPoint;
import whitebox.geospatialfiles.shapefile.MultiPointM;
import whitebox.geospatialfiles.shapefile.MultiPointZ;
import whitebox.geospatialfiles.shapefile.PointM;
import whitebox.geospatialfiles.shapefile.PointZ;
import whitebox.geospatialfiles.shapefile.ShapeFileRecord;
import whitebox.geospatialfiles.shapefile.ShapeType;
import static whitebox.geospatialfiles.shapefile.ShapeType.MULTIPOINT;
import static whitebox.geospatialfiles.shapefile.ShapeType.MULTIPOINTM;
import static whitebox.geospatialfiles.shapefile.ShapeType.MULTIPOINTZ;
import static whitebox.geospatialfiles.shapefile.ShapeType.POINT;
import static whitebox.geospatialfiles.shapefile.ShapeType.POINTM;
import static whitebox.geospatialfiles.shapefile.ShapeType.POINTZ;
import whitebox.geospatialfiles.shapefile.attributes.AttributeTable;
import whitebox.geospatialfiles.shapefile.attributes.DBFField;
import whitebox.geospatialfiles.shapefile.attributes.DBFField.DBFDataType;
/**
* This tool can be used to interpolate a trend surface from a vector points file.
*
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class TrendSurfaceVectorPoints 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 "TrendSurfaceVectorPoints";
}
/**
* 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 "Trend Surface Vector Points";
}
/**
* Used to retrieve a short description of what the plugin tool does.
*
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "Estimates a trend surface from vector points.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
*
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = {"StatisticalTools", "Interpolation"};
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;
WhiteboxRaster output;
int cols, rows;
int progress = 0;
int col, row;
double value;
double gridResolution = 0;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
String inputFieldsString = args[0];
String outputHeader = args[1];
polyOrder = Integer.parseInt(args[2]);
if (polyOrder < 0) {
polyOrder = 0;
}
if (polyOrder > 10) {
polyOrder = 10;
}
// check to see that the inputHeader and outputHeader are not null.
if ((inputFieldsString.length() < 2) || (outputHeader.isEmpty())) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
gridResolution = Double.parseDouble((args[3]));
try {
String[] inputs = inputFieldsString.split(";");
String inputFile = inputs[0];
String fieldName = inputs[1];
ShapeFile shapefile = new ShapeFile(inputFile);
if (shapefile.getShapeType().getBaseType() != ShapeType.POINT) {
showFeedback("The input shapefile must be of a 'point' data type.");
return;
}
AttributeTable table = shapefile.getAttributeTable();
String[] fieldNames = table.getAttributeTableFieldNames();
int fieldNumber = 0;
for (int a = 0; a < fieldNames.length; a++) {
if (fieldNames[a].equals(fieldName)) {
fieldNumber = a;
break;
}
}
// check to make sure that it is a numerical field
DBFField field = table.getField(fieldNumber);
if (field.getDataType() != DBFDataType.FLOAT
&& field.getDataType() != DBFDataType.NUMERIC) {
showFeedback("The selected attribute field must be of a numerical type.");
return;
}
double north = shapefile.getyMax();
double south = shapefile.getyMin();
double east = shapefile.getxMax();
double west = shapefile.getxMin();
rows = (int) (Math.abs(north - south) / gridResolution);
cols = (int) (Math.abs(east - west) / gridResolution);
double noData = -32768.0;
output = new WhiteboxRaster(outputHeader, north, south, east, west,
rows, cols, WhiteboxRasterBase.DataScale.CONTINUOUS,
WhiteboxRasterBase.DataType.FLOAT, 0, noData);
// how many input points are there
ArrayList<Double> xList = new ArrayList<>();
ArrayList<Double> yList = new ArrayList<>();
ArrayList<Double> zList = new ArrayList<>();
double[][] geometry;
for (ShapeFileRecord record : shapefile.records) {
geometry = getXYFromShapefileRecord(record);
Object[] attData = table.getRecord(record.getRecordNumber() - 1);
value = (double) attData[fieldNumber];
for (int i = 0; i < geometry.length; i++) {
xList.add(geometry[i][0]);
yList.add(geometry[i][1]);
zList.add(value);
}
}
int numPoints = xList.size();
double[] x = new double[numPoints];
double[] y = new double[numPoints];
double[] z = new double[numPoints];
for (int a = 0; a < numPoints; a++) {
x[a] = (double)xList.get(a);
y[a] = (double)yList.get(a);
z[a] = (double)zList.get(a);
}
String inputHeaderShort = shapefile.getShortName();
double rsquare = calculateEquation(x, y, z);
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
value = getForwardCoordinates(
output.getXCoordinateFromColumn(col),
output.getYCoordinateFromRow(row));
output.setValue(row, col, value);
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (row * 100.0 / rows);
updateProgress(progress);
}
output.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
output.addMetadataEntry("Created on " + new Date());
output.close();
// returning a header file string displays the image.
returnData(outputHeader);
// text return
StringBuilder sb = new StringBuilder();
sb.append("TREND SURFACE ANALYSIS OUTPUT\n\n");
sb.append("Input File:\t").append(inputHeaderShort).append("\n");
sb.append("Polynomial Order:\t").append(polyOrder).append("\n\n");
sb.append("Coefficent #\t").append("Value\n");
for (int a = 0; a < regressCoefficents.length; a++) {
sb.append((a + 1)).append("\t").append(regressCoefficents[a]).append("\n");
}
sb.append("\nR-square:\t").append(rsquare);
returnData(sb.toString());
} 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 solve the equation.
*/
private int numCoefficients = 0;
private int polyOrder = 1;
private double[] regressCoefficents;
public double calculateEquation(double[] X, double[] Y,
double[] Z) {
try {
int m, i, j, k;
int n = Z.length;
// How many coefficients are there?
numCoefficients = 0;
for (j = 0; j <= polyOrder; j++) {
for (k = 0; k <= (polyOrder - j); k++) {
numCoefficients++;
}
}
// Solve the forward transformation equations
double[][] forwardCoefficientMatrix = new double[n][numCoefficients];
for (i = 0; i < n; i++) {
m = 0;
for (j = 0; j <= polyOrder; j++) {
for (k = 0; k <= (polyOrder - j); k++) {
forwardCoefficientMatrix[i][m] = Math.pow(X[i], j) * Math.pow(Y[i], k);
m++;
}
}
}
RealMatrix coefficients =
new Array2DRowRealMatrix(forwardCoefficientMatrix, false);
//DecompositionSolver solver = new SingularValueDecomposition(coefficients).getSolver();
DecompositionSolver solver = new QRDecomposition(coefficients).getSolver();
// do the z-coordinate
RealVector constants = new ArrayRealVector(Z, false);
RealVector solution = solver.solve(constants);
regressCoefficents = new double[numCoefficients];
for (int a = 0; a < numCoefficients; a++) {
regressCoefficents[a] = solution.getEntry(a);
}
double[] residuals = new double[n];
double SSresid = 0;
for (i = 0; i < n; i++) {
double yHat = 0.0;
for (j = 0; j < numCoefficients; j++) {
yHat += forwardCoefficientMatrix[i][j] * regressCoefficents[j];
}
residuals[i] = Z[i] - yHat;
SSresid += residuals[i] * residuals[i];
}
double sum = 0;
double SS = 0;
for (i = 0; i < n; i++) {
SS += Z[i] * Z[i];
sum += Z[i];
}
double variance = (SS - (sum * sum) / n) / n;
double SStotal = (n - 1) * variance;
double rsq = 1 - SSresid / SStotal;
return rsq;
} catch (DimensionMismatchException | NoDataException | NullArgumentException | OutOfRangeException e) {
showFeedback("Error in TrendSurface.calculateEquation: "
+ e.toString());
return -1;
}
}
private double getForwardCoordinates(double x, double y) {
double ret = 0;
int j, k, m;
double term;
m = 0;
for (j = 0; j <= polyOrder; j++) {
for (k = 0; k <= (polyOrder - j); k++) {
term = Math.pow(x, j) * Math.pow(y, k);
ret += term * regressCoefficents[m];
m++;
}
}
return ret;
}
private double[][] getXYFromShapefileRecord(ShapeFileRecord record) {
double[][] ret;
ShapeType shapeType = record.getShapeType();
switch (shapeType) {
case POINT:
whitebox.geospatialfiles.shapefile.Point recPoint =
(whitebox.geospatialfiles.shapefile.Point) (record.getGeometry());
ret = new double[1][2];
ret[0][0] = recPoint.getX();
ret[0][1] = recPoint.getY();
break;
case POINTZ:
PointZ recPointZ = (PointZ) (record.getGeometry());
ret = new double[1][2];
ret[0][0] = recPointZ.getX();
ret[0][1] = recPointZ.getY();
break;
case POINTM:
PointM recPointM = (PointM) (record.getGeometry());
ret = new double[1][2];
ret[0][0] = recPointM.getX();
ret[0][1] = recPointM.getY();
break;
case MULTIPOINT:
MultiPoint recMultiPoint = (MultiPoint) (record.getGeometry());
return recMultiPoint.getPoints();
case MULTIPOINTZ:
MultiPointZ recMultiPointZ = (MultiPointZ) (record.getGeometry());
return recMultiPointZ.getPoints();
case MULTIPOINTM:
MultiPointM recMultiPointM = (MultiPointM) (record.getGeometry());
return recMultiPointM.getPoints();
default:
ret = new double[1][2];
ret[1][0] = -1;
ret[1][1] = -1;
break;
}
return ret;
}
}