/*
* 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.util.Date;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
/**
* This tool re-categorizes data in a raster image by grouping cells that form physically discrete, connected areas into unique categories.
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class Clump implements WhiteboxPlugin {
private WhiteboxPluginHost myHost = null;
private String[] args;
double noData = -32768;
WhiteboxRaster image;
WhiteboxRaster output;
double currentPatchNumber = 0;
double currentImageValue = 0;
int maxDepth = 1000;
int depth = 0;
int[] dX = new int[]{1, 1, 1, 0, -1, -1, -1, 0};
int[] dY = new int[]{-1, 0, 1, 1, 1, 0, -1, -1};
int numScanCells = 8;
/**
* 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 "Clump";
}
/**
* 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 "Clump (Group)";
}
/**
* Used to retrieve a short description of what the plugin tool does.
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "Groups cells that form physically discrete areas, assigning "
+ "them unique identifiers.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = { "GISTools" };
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;
int row, col;
float progress = 0;
double maxPatchValue = 0;
int x, y;
boolean blnFoundNeighbour;
boolean blnIncludeDiagNeighbour = false;
boolean blnTreatZerosAsBackground = false;
int i;
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) {
blnIncludeDiagNeighbour = Boolean.parseBoolean(args[i]);
if (!blnIncludeDiagNeighbour) {
dX = new int[]{0, 1, 0, -1};
dY = new int[]{-1, 0, 1, 0};
}
} else if (i == 3) {
blnTreatZerosAsBackground = 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 {
numScanCells = dY.length;
image = new WhiteboxRaster(inputHeader, "r");
int rows = image.getNumberRows();
int cols = image.getNumberColumns();
noData = image.getNoDataValue();
double initialValue = -1;
output = new WhiteboxRaster(outputHeader, "rw", inputHeader, WhiteboxRaster.DataType.FLOAT, initialValue);
output.setDataScale(WhiteboxRaster.DataScale.CATEGORICAL);
output.setPreferredPalette("qual.pal");
if (blnTreatZerosAsBackground) {
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
if (image.getValue(row, col) == 0) {
output.setValue(row, col, 0);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
if (output.getValue(0, 0) == -1) {
output.setValue(0, 0, 1);
}
} else {
output.setValue(0, 0, 0);
}
double patchValue = 0;
double neighbourPatchValue = 0;
double newPatchValue = 0;
double imageValue = 0;
int loopNum = 1;
updateProgress("Loop " + loopNum + ":", 0);
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
imageValue = image.getValue(row, col);
if (imageValue != noData) {
patchValue = output.getValue(row, col);
if (patchValue == initialValue) {
// see if any neighbour has the same value in the input image
blnFoundNeighbour = false;
for (i = 0; i < numScanCells; i++) {
x = col + dX[i];
y = row + dY[i];
neighbourPatchValue = output.getValue(y, x);
if (neighbourPatchValue != initialValue
&& image.getValue(y, x) == imageValue) {
// cell is neighbouring a cell with the same value in image that
// has already been assigned a patch value
output.setValue(row, col, neighbourPatchValue);
newPatchValue = neighbourPatchValue;
blnFoundNeighbour = true;
break;
}
}
if (!blnFoundNeighbour) {
// no neighbouring cell has the same value in Image and has
// already been assigned a value. A new one is needed.
maxPatchValue++;
newPatchValue = maxPatchValue;
output.setValue(row, col, newPatchValue);
}
// recursively scan all connected cells of equal value in Image
depth = 0;
ScanConnectedCells(row, col, imageValue, initialValue, newPatchValue);
}
} else {
output.setValue(row, col, noData);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
// find all cells with neighbouring cells that have the same value in
// the input image but different patch values in the output image.
// Recursively scan them to change the larger patch ID to the lower value.
// Iterate this process until there are no further changes to the image.
boolean somethingDone;
double[] reclass = new double[(int) maxPatchValue + 1];
// this array is used to keep track of the eliminated patches.
do {
loopNum++;
updateProgress("Loop " + loopNum + ":", 0);
somethingDone = false;
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
imageValue = image.getValue(row, col);
if (imageValue != noData) {
patchValue = output.getValue(row, col);
for (i = 0; i < numScanCells; i++) {
x = col + dX[i];
y = row + dY[i];
neighbourPatchValue = output.getValue(y, x);
if (neighbourPatchValue != patchValue
&& image.getValue(y, x) == imageValue) {
// The two patches are equivalent. Find the
// lower valued cell and initiate a recursive
// scan from there.
somethingDone = true;
if (patchValue < neighbourPatchValue) {
reclass[(int)neighbourPatchValue] = -1;
output.setValue(y, x, patchValue);
ScanConnectedCells(y, x, imageValue, neighbourPatchValue, patchValue);
} else {
reclass[(int)patchValue] = -1;
output.setValue(row, col, neighbourPatchValue);
ScanConnectedCells(row, col, imageValue, patchValue, neighbourPatchValue);
patchValue = neighbourPatchValue;
}
}
}
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
} while (somethingDone);
i = 0;
for (int a = 0; a < maxPatchValue + 1; a++) {
if (reclass[a] != -1) {
reclass[a] = i;
i++;
}
}
loopNum++;
updateProgress("Loop " + loopNum + ":", 0);
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
patchValue = output.getValue(row, col);
if (patchValue != noData) {
output.setValue(row, col, reclass[(int)patchValue]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
output.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
output.addMetadataEntry("Created on " + new Date());
image.close();
output.close();
// 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 ScanConnectedCells(int row, int col, double imageValue, double currentPatchValue, double newPatchValue) {
depth++;
int x, y;
if (depth < maxDepth) {
for (int c = 0; c < numScanCells; c++) {
x = col + dX[c];
y = row + dY[c];
if ((output.getValue(y, x) == currentPatchValue) &&
(image.getValue(y, x) == imageValue)) {
// cell should be assigned the new patch value and has the same value in Image
output.setValue(y, x, newPatchValue);
ScanConnectedCells(y, x, imageValue, currentPatchValue, newPatchValue);
}
}
}
depth--;
}
}