Java tutorial
/* * 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 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; /** * This tool can be used to interpolate a trend surface from a raster image. * * @author Dr. John Lindsay email: jlindsay@uoguelph.ca */ public class TrendSurface 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 "TrendSurface"; } /** * 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"; } /** * 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 the trend surface of an input raster file."; } /** * 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; String inputHeader = null; String outputHeader = null; WhiteboxRaster image; WhiteboxRaster output; int cols, rows; int progress = 0; int col, row; double value; if (args.length <= 0) { showFeedback("Plugin parameters have not been set."); return; } inputHeader = args[0]; 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 ((inputHeader.isEmpty()) || (outputHeader.isEmpty())) { showFeedback("One or more of the input parameters have not been set properly."); return; } try { image = new WhiteboxRaster(inputHeader, "r"); rows = image.getNumberRows(); cols = image.getNumberColumns(); double noData = image.getNoDataValue(); output = new WhiteboxRaster(outputHeader, "rw", inputHeader, WhiteboxRaster.DataType.FLOAT, 0); int totalNumCells = rows * cols; double[] x = new double[totalNumCells]; double[] y = new double[totalNumCells]; double[] z = new double[totalNumCells]; double[] data; int cellNum = 0; for (row = 0; row < rows; row++) { data = image.getRowValues(row); for (col = 0; col < cols; col++) { if (data[col] != noData) { x[cellNum] = image.getXCoordinateFromColumn(col); y[cellNum] = image.getYCoordinateFromRow(row); z[cellNum] = data[col]; cellNum++; } } if (cancelOp) { cancelOperation(); return; } progress = (int) (row * 100.0 / rows); updateProgress(progress); } String inputHeaderShort = image.getShortHeaderFile(); image.close(); 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(); } } 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 x-coordinate first 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; } }