/*
* 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 whitebox.interfaces.WhiteboxPluginHost;
import whitebox.interfaces.WhiteboxPlugin;
import java.text.DecimalFormat;
import java.util.ArrayList;
import whitebox.geospatialfiles.shapefile.attributes.AttributeTable;
import whitebox.geospatialfiles.shapefile.attributes.DBFField;
/**
* This tool can be used to estimate the Pearson product-moment correlation coefficient (r) for each pair among a group of attributes associated with the database file of a shapefile.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class CorrelationForAttributes 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 "CorrelationForAttributes";
}
/**
* 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 "Correlation For Attributes";
}
/**
* 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 correlation analysis on attribute fields from a vector database.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = {"StatisticalTools", "DatabaseTools"};
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 shapefile = null;
String inputFieldsString = null;
String[] fieldNames = null;
int numFields;
int progress = 0;
int lastProgress = 0;
int row;
int a, i, j;
double[] fieldAverages;
double[] fieldTotals;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
// read the input parameters
inputFieldsString = args[0];
try {
// deal with the input fields
String[] inputs = inputFieldsString.split(";");
shapefile = inputs[0];
numFields = inputs.length - 1;
fieldNames = new String[numFields];
System.arraycopy(inputs, 1, fieldNames, 0, numFields);
// read the appropriate field from the dbf file into an array
AttributeTable table = new AttributeTable(shapefile.replace(".shp", ".dbf"));
int numRecs = table.getNumberOfRecords();
DBFField[] fields = table.getAllFields();
ArrayList<Integer> PCAFields = new ArrayList<Integer>();
for (j = 0; j < fieldNames.length; j++) {
for (i = 0; i < fields.length; i++) {
if (fields[i].getName().equals(fieldNames[j]) &&
(fields[i].getDataType() == DBFField.DBFDataType.NUMERIC ||
fields[i].getDataType() == DBFField.DBFDataType.FLOAT)) {
PCAFields.add(i);
}
}
}
if (numFields != PCAFields.size()) {
showFeedback("Not all of the specified database fields were found in the file or "
+ "a field of a non-numerical type was selected.");
return;
}
double[][] fieldArray = new double[numRecs][numFields];
Object[] rec;
for (i = 0; i < numRecs; i++) {
rec = table.getRecord(i);
for (j = 0; j < numFields; j++) {
fieldArray[i][j] = (Double)(rec[PCAFields.get(j)]);
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * i / (numRecs - 1));
if (progress != lastProgress) { updateProgress("Reading data:", progress);}
lastProgress = progress;
}
fieldAverages = new double[numFields];
fieldTotals = new double[numFields];
// Calculate the means
for (row = 0; row < numRecs; row++) {
for (i = 0; i < numFields; i++) {
fieldTotals[i] += fieldArray[row][i];
}
}
for (i = 0; i < numFields; i++) {
fieldAverages[i] = fieldTotals[i] / numRecs;
}
// Calculate the covariance matrix and total deviations
double[] fieldTotalDeviation = new double[numFields];
double[][] covariances = new double[numFields][numFields];
double[][] correlationMatrix = new double[numFields][numFields];
for (row = 0; row < numRecs; row++) {
for (i = 0; i < numFields; i++) {
fieldTotalDeviation[i] += (fieldArray[row][i] - fieldAverages[i])
* (fieldArray[row][i] - fieldAverages[i]);
for (a = 0; a < numFields; a++) {
covariances[i][a] += (fieldArray[row][i] - fieldAverages[i])
* (fieldArray[row][a] - fieldAverages[a]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (numRecs - 1));
if (progress != lastProgress) { updateProgress("Calculating covariances:", progress);}
lastProgress = progress;
}
for (i = 0; i < numFields; i++) {
for (a = 0; a < numFields; a++) {
correlationMatrix[i][a] = covariances[i][a] / (Math.sqrt(fieldTotalDeviation[i] * fieldTotalDeviation[a]));
}
}
String ret = "IMAGE CORRELATION MATRIX\n\n";
String headers = "\t";
for (a = 0; a < numFields; a++) {
headers = headers + "Field" + (a + 1) + "\t";
}
ret += headers;
DecimalFormat df = new DecimalFormat("0.0000");
for (a = 0; a < numFields; a++) {
ret += "\nField" + (a + 1) + "\t";
for (int b = 0; b <= a; b++) {
if (correlationMatrix[a][b] != -99) {
if (correlationMatrix[a][b] >= 0) {
ret += " " + df.format(correlationMatrix[a][b]) + "\t";
} else {
ret += df.format(correlationMatrix[a][b]) + "\t";
}
} else {
ret += "\t";
}
}
}
ret += "\n\n";
for (i = 0; i < numFields; i++) {
ret += "Field " + (i + 1) + "\t" + fieldNames[i] + "\n";
}
returnData(ret);
} 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();
}
}
// /**
// * This method is only used during testing.
// * @param args
// */
// // This method is only used during testing.
// public static void main(String[] args) {
//
// // vector-based test
// args = new String[1];
// /*
// * specify the input args array as:
// * args[0] = shapefile input
// * args[1] = input fields string
// * args[2] = standardized (boolean true or false)
// * args[3] = number of components to output
// */
// args[0] = "/Users/johnlindsay/Documents/Research/Contracts/NRCan 2012/Data/alllakesutmdissolve.shp;"
// + "ELONGATION;LINEARITY;COMPLEXITY;AREA;FRACTAL_D;RC_CIRCLE;COMPACT;P-A_RATIO";
//
// CorrelationForAttributes ca = new CorrelationForAttributes();
// ca.setArgs(args);
// ca.run();
// }
}