private void calculateRaster() {
amIActive = true;
String inputHeader = null;
String outputHeader = null;
int col;
int row;
int numCols;
int numRows;
int a, i;
float progress;
int minValue, maxValue, range;
boolean blnTextOutput = false;
boolean zeroAsBackground = false;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputHeader = args[0];
outputHeader = args[1];
blnTextOutput = Boolean.parseBoolean(args[2]);
zeroAsBackground = Boolean.parseBoolean(args[3]);
// 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);
minValue = (int) (image.getMinimumValue());
maxValue = (int) (image.getMaximumValue());
range = maxValue - minValue;
double[] data;
// find the axis-aligned minimum bounding box.
updateProgress("Loop 1 of 2:", 0);
double[][] boundingBox = new double[6][range + 1];
for (a = 0; a <= range; a++) {
boundingBox[0][a] = Integer.MAX_VALUE; // west
boundingBox[1][a] = Integer.MIN_VALUE; // east
boundingBox[2][a] = Integer.MAX_VALUE; // north
boundingBox[3][a] = Integer.MIN_VALUE; // south
}
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] != noData) {
a = (int) (data[col] - minValue);
if (col < boundingBox[0][a]) {
boundingBox[0][a] = col;
}
if (col > boundingBox[1][a]) {
boundingBox[1][a] = col;
}
if (row < boundingBox[2][a]) {
boundingBox[2][a] = row;
}
if (row > boundingBox[3][a]) {
boundingBox[3][a] = row;
}
boundingBox[5][a]++;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 1 of 2:", (int) progress);
}
updateProgress("Loop 2 of 2:", 0);
double radius;
for (a = 0; a <= range; a++) {
if ((boundingBox[1][a] - boundingBox[0][a] + 1)
> (boundingBox[3][a] - boundingBox[2][a] + 1)) {
radius = (boundingBox[1][a] - boundingBox[0][a] + 1) / 2;
} else {
radius = (boundingBox[3][a] - boundingBox[2][a] + 1) / 2;
}
boundingBox[4][a] = Math.PI * radius * radius;
}
if (zeroAsBackground) {
boundingBox[0 - minValue][4] = 0d;
// sum the column numbers and row numbers of each patch cell
// along with the total number of cells.
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, 1 - boundingBox[5][a] / boundingBox[4][a]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 2 of 2:", (int) progress);
}
} else {
// sum the column numbers and row numbers of each patch cell
// along with the total number of cells.
for (row = 0; row < numRows; row++) {
data = image.getRowValues(row);
for (col = 0; col < numCols; col++) {
if (data[col] != noData) {
a = (int) (data[col] - minValue);
output.setValue(row, col, 1 - boundingBox[5][a] / boundingBox[4][a]);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (numRows - 1));
updateProgress("Loop 2 of 2:", (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 = "Related Circumscribing Circle\nPatch ID\tValue";
for (a = 0; a <= range; a++) {
if (boundingBox[4][a] > 0) {
retstr =
retstr
+ "\n"
+ (a + minValue)
+ "\t"
+ df.format(1 - boundingBox[5][a] / boundingBox[4][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 calculateDistance(WhiteboxRaster outputImage) {
String outputHeader = outputImage.getHeaderFile();
int row, col, whichCell, i, x, y;
double z, z2, zMin, h = 0;
double infVal = Float.POSITIVE_INFINITY;
int[] dX = new int[] {-1, -1, 0, 1, 1, 1, 0, -1};
int[] dY = new int[] {0, -1, -1, -1, 0, 1, 1, 1};
int[] Gx = new int[] {1, 1, 0, 1, 1, 1, 0, 1};
int[] Gy = new int[] {0, 1, 1, 1, 0, 1, 1, 1};
int progress;
int rows = outputImage.getNumberRows();
int cols = outputImage.getNumberColumns();
double noData = outputImage.getNoDataValue();
double gridRes = (outputImage.getCellSizeX() + outputImage.getCellSizeY()) / 2;
WhiteboxRaster Rx =
new WhiteboxRaster(
outputHeader.replace(".dep", "_temp1.dep"),
"rw",
outputHeader,
WhiteboxRaster.DataType.FLOAT,
0);
Rx.isTemporaryFile = true;
WhiteboxRaster Ry =
new WhiteboxRaster(
outputHeader.replace(".dep", "_temp2.dep"),
"rw",
outputHeader,
WhiteboxRaster.DataType.FLOAT,
0);
Ry.isTemporaryFile = true;
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
z = outputImage.getValue(row, col);
if (z != 0) {
zMin = infVal;
whichCell = -1;
for (i = 0; i <= 3; i++) {
x = col + dX[i];
y = row + dY[i];
z2 = outputImage.getValue(y, x);
if (z2 != noData) {
switch (i) {
case 0:
h = 2 * Rx.getValue(y, x) + 1;
break;
case 1:
h = 2 * (Rx.getValue(y, x) + Ry.getValue(y, x) + 1);
break;
case 2:
h = 2 * Ry.getValue(y, x) + 1;
break;
case 3:
h = 2 * (Rx.getValue(y, x) + Ry.getValue(y, x) + 1);
break;
}
z2 += h;
if (z2 < zMin) {
zMin = z2;
whichCell = i;
}
}
}
if (zMin < z) {
outputImage.setValue(row, col, zMin);
x = col + dX[whichCell];
y = row + dY[whichCell];
Rx.setValue(row, col, Rx.getValue(y, x) + Gx[whichCell]);
Ry.setValue(row, col, Ry.getValue(y, x) + Gy[whichCell]);
}
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (rows - 1));
updateProgress("Calculating distances: ", progress);
}
for (row = rows - 1; row >= 0; row--) {
for (col = cols - 1; col >= 0; col--) {
z = outputImage.getValue(row, col);
if (z != 0) {
zMin = infVal;
whichCell = -1;
for (i = 4; i <= 7; i++) {
x = col + dX[i];
y = row + dY[i];
z2 = outputImage.getValue(y, x);
if (z2 != noData) {
switch (i) {
case 5:
h = 2 * (Rx.getValue(y, x) + Ry.getValue(y, x) + 1);
break;
case 4:
h = 2 * Rx.getValue(y, x) + 1;
break;
case 6:
h = 2 * Ry.getValue(y, x) + 1;
break;
case 7:
h = 2 * (Rx.getValue(y, x) + Ry.getValue(y, x) + 1);
break;
}
z2 += h;
if (z2 < zMin) {
zMin = z2;
whichCell = i;
}
}
}
if (zMin < z) {
outputImage.setValue(row, col, zMin);
x = col + dX[whichCell];
y = row + dY[whichCell];
Rx.setValue(row, col, Rx.getValue(y, x) + Gx[whichCell]);
Ry.setValue(row, col, Ry.getValue(y, x) + Gy[whichCell]);
}
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * (rows - 1 - row) / (rows - 1));
updateProgress("Calculating distances: ", progress);
}
// for (row = 0; row < rows; row++) {
// for (col = 0; col < cols; col++) {
// z = outputImage.getValue(row, col);
// outputImage.setValue(row, col, Math.sqrt(z) * gridRes);
// }
// if (cancelOp) {
// cancelOperation();
// return;
// }
// progress = (int) (100f * row / (rows - 1));
// updateProgress(progress);
// }
outputImage.flush();
Rx.close();
Ry.close();
}
private void histogramMatching(String inputHeader1, String inputHeader2, String outputHeader) {
// check to see that the inputHeader and outputHeader are not null.
if (inputHeader1.isEmpty() || outputHeader.isEmpty() || inputHeader2.isEmpty()) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
int row, col;
double z;
int progress = 0;
int numCells1 = 0;
int numCells2 = 0;
int i = 0;
WhiteboxRasterInfo inputFile1 = new WhiteboxRasterInfo(inputHeader1);
int rows1 = inputFile1.getNumberRows();
int cols1 = inputFile1.getNumberColumns();
double noData1 = inputFile1.getNoDataValue();
WhiteboxRasterInfo inputFile2 = new WhiteboxRasterInfo(inputHeader2);
int rows2 = inputFile2.getNumberRows();
int cols2 = inputFile2.getNumberColumns();
double noData2 = inputFile2.getNoDataValue();
WhiteboxRaster outputFile =
new WhiteboxRaster(
outputHeader, "rw", inputHeader1, WhiteboxRaster.DataType.FLOAT, noData1);
outputFile.setPreferredPalette(inputFile1.getPreferredPalette());
double minValue1 = inputFile1.getMinimumValue();
double maxValue1 = inputFile1.getMaximumValue();
int numBins1 =
Math.max(
2 * (int) Math.ceil(maxValue1 - minValue1 + 1),
(int) Math.ceil(Math.pow(rows1 * cols1, 1.0 / 3)));
double binSize = (maxValue1 - minValue1) / numBins1;
long[] histogram = new long[numBins1];
int binNum;
int numBinsLessOne1 = numBins1 - 1;
double[] data;
updateProgress("Histogram matching: ", 0);
for (row = 0; row < rows1; row++) {
data = inputFile1.getRowValues(row);
for (col = 0; col < cols1; col++) {
z = data[col];
if (z != noData1) {
numCells1++;
binNum = (int) ((z - minValue1) / binSize);
if (binNum > numBinsLessOne1) {
binNum = numBinsLessOne1;
}
histogram[binNum]++;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (rows1 - 1));
updateProgress("Histogram matching: ", progress);
}
updateProgress("Histogram matching: ", 0);
double[] cdf = new double[numBins1];
cdf[0] = histogram[0];
for (i = 1; i < numBins1; i++) {
cdf[i] = cdf[i - 1] + histogram[i];
}
for (i = 0; i < numBins1; i++) {
cdf[i] = cdf[i] / numCells1;
}
double minValue2 = inputFile2.getMinimumValue();
double maxValue2 = inputFile2.getMaximumValue();
int numBins2 =
Math.max(
2 * (int) Math.ceil(maxValue2 - minValue2 + 1),
(int) Math.ceil(Math.pow(rows2 * cols2, 1.0 / 3)));
int numBinsLessOne2 = numBins2 - 1;
long[] histogram2 = new long[numBins2];
double[][] referenceCDF = new double[numBins2][2];
for (row = 0; row < rows2; row++) {
data = inputFile2.getRowValues(row);
for (col = 0; col < cols2; col++) {
z = data[col];
if (z != noData2) {
numCells2++;
binNum = (int) ((z - minValue2) / binSize);
if (binNum > numBinsLessOne2) {
binNum = numBinsLessOne2;
}
histogram2[binNum]++;
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (rows1 - 1));
updateProgress("Histogram matching: ", progress);
}
// convert the reference histogram to a cdf.
referenceCDF[0][1] = histogram2[0];
for (i = 1; i < numBins2; i++) {
referenceCDF[i][1] = referenceCDF[i - 1][1] + histogram2[i];
}
for (i = 0; i < numBins2; i++) {
referenceCDF[i][0] = minValue2 + (i / (float) numBins2) * (maxValue2 - minValue2);
referenceCDF[i][1] = referenceCDF[i][1] / numCells2;
}
int[] startingVals = new int[11];
double pVal = 0;
for (i = 0; i < numBins2; i++) {
pVal = referenceCDF[i][1];
if (pVal < 0.1) {
startingVals[1] = i;
}
if (pVal < 0.2) {
startingVals[2] = i;
}
if (pVal < 0.3) {
startingVals[3] = i;
}
if (pVal < 0.4) {
startingVals[4] = i;
}
if (pVal < 0.5) {
startingVals[5] = i;
}
if (pVal < 0.6) {
startingVals[6] = i;
}
if (pVal < 0.7) {
startingVals[7] = i;
}
if (pVal < 0.8) {
startingVals[8] = i;
}
if (pVal < 0.9) {
startingVals[9] = i;
}
if (pVal <= 1) {
startingVals[10] = i;
}
}
updateProgress("Histogram matching: ", 0);
int j = 0;
double xVal = 0;
double x1, x2, p1, p2;
for (row = 0; row < rows1; row++) {
data = inputFile1.getRowValues(row);
for (col = 0; col < cols1; col++) {
z = data[col];
if (z != noData1) {
binNum = (int) ((z - minValue1) / binSize);
if (binNum > numBinsLessOne1) {
binNum = numBinsLessOne1;
}
pVal = cdf[binNum];
j = (int) (Math.floor(pVal * 10));
for (i = startingVals[j]; i < numBins2; i++) {
if (referenceCDF[i][1] > pVal) {
if (i > 0) {
x1 = referenceCDF[i - 1][0];
x2 = referenceCDF[i][0];
p1 = referenceCDF[i - 1][1];
p2 = referenceCDF[i][1];
if (p1 != p2) {
xVal = x1 + ((x2 - x1) * ((pVal - p1) / (p2 - p1)));
} else {
xVal = x1;
}
} else {
xVal = referenceCDF[i][0];
}
break;
}
}
outputFile.setValue(row, col, xVal);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (rows1 - 1));
updateProgress("Histogram matching: ", progress);
}
inputFile1.close();
outputFile.close();
} 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);
}
}
@Override
public void run() {
amIActive = true;
int progress;
int row, col, i;
int baseCol, baseRow, appendCol, appendRow;
double x, y, z, zN, zBase, zAppend;
double w1, w2, dist1, dist2, sumDist;
boolean performHistoMatching = true;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
// read the input parameters
String inputBaseHeader = args[0];
String inputHeader = args[1];
String outputHeader = args[2];
String resampleMethod = args[3].toLowerCase().trim();
if (!resampleMethod.equals("nearest neighbour")
&& !resampleMethod.equals("bilinear")
&& !resampleMethod.contains("cubic")) {
showFeedback("Resample method not recognized");
return;
}
if (args[4].toLowerCase().contains("true")) {
performHistoMatching = true;
} else {
performHistoMatching = false;
}
double power = Double.parseDouble(args[5]);
if (power > 15.0) {
power = 15.0;
}
if (power < 1.0) {
power = 1.0;
}
try {
// first perform histogram matching if necessary
if (performHistoMatching) {
String inputHeaderAdjusted = StringUtilities.replaceLast(inputHeader, ".dep", "_temp1.dep");
histogramMatching(inputHeader, inputBaseHeader, inputHeaderAdjusted);
inputHeader = inputHeaderAdjusted;
}
WhiteboxRaster baseRaster = new WhiteboxRaster(inputBaseHeader, "r");
WhiteboxRaster appendRaster = new WhiteboxRaster(inputHeader, "r");
double cellSizeX = baseRaster.getCellSizeX();
double cellSizeY = baseRaster.getCellSizeY();
double baseNoData = baseRaster.getNoDataValue();
double appendNoData = appendRaster.getNoDataValue();
double outputNoData = baseNoData;
int baseCols = baseRaster.getNumberColumns();
int baseRows = baseRaster.getNumberRows();
int appendCols = appendRaster.getNumberColumns();
int appendRows = appendRaster.getNumberRows();
// figure out the north, south, east, and west coordinates and the rows and
// columns of the output image.
double baseNorth = baseRaster.getNorth();
double baseSouth = baseRaster.getSouth();
double baseEast = baseRaster.getEast();
double baseWest = baseRaster.getWest();
double baseNSRange = baseNorth - baseSouth;
double baseEWRange = baseEast - baseWest;
double appendNorth = appendRaster.getNorth();
double appendSouth = appendRaster.getSouth();
double appendEast = appendRaster.getEast();
double appendWest = appendRaster.getWest();
double appendNSRange = appendNorth - appendSouth;
double appendEWRange = appendEast - appendWest;
double north, south, east, west;
if (baseNorth > baseSouth) {
north = Double.NEGATIVE_INFINITY;
south = Double.POSITIVE_INFINITY;
if (baseNorth > north) {
north = baseNorth;
}
if (appendNorth > north) {
north = appendNorth;
}
if (baseSouth < south) {
south = baseSouth;
}
if (appendSouth < south) {
south = appendSouth;
}
} else {
north = Double.POSITIVE_INFINITY;
south = Double.NEGATIVE_INFINITY;
if (baseNorth < north) {
north = baseNorth;
}
if (appendNorth < north) {
north = appendNorth;
}
if (baseSouth > south) {
south = baseSouth;
}
if (appendSouth > south) {
south = appendSouth;
}
}
if (baseEast > baseWest) {
east = Double.NEGATIVE_INFINITY;
west = Double.POSITIVE_INFINITY;
if (baseEast > east) {
east = baseEast;
}
if (appendEast > east) {
east = appendEast;
}
if (baseWest < west) {
west = baseWest;
}
if (appendWest < west) {
west = appendWest;
}
} else {
east = Double.POSITIVE_INFINITY;
west = Double.NEGATIVE_INFINITY;
if (baseEast < east) {
east = baseEast;
}
if (appendEast < east) {
east = appendEast;
}
if (baseWest > west) {
west = baseWest;
}
if (appendWest > west) {
west = appendWest;
}
}
// create the new destination image.
int nRows = (int) Math.round(Math.abs(north - south) / cellSizeY);
int nCols = (int) Math.round(Math.abs(east - west) / cellSizeX);
WhiteboxRaster destination =
new WhiteboxRaster(
outputHeader,
north,
south,
east,
west,
nRows,
nCols,
WhiteboxRasterBase.DataScale.CONTINUOUS,
WhiteboxRasterBase.DataType.FLOAT,
outputNoData,
outputNoData);
int nRowsLessOne = nRows - 1;
// distance to edge images
String distToEdgeBaseHeader =
StringUtilities.replaceLast(inputBaseHeader, ".dep", "_temp1.dep");
WhiteboxRaster distToEdgeBase =
new WhiteboxRaster(
distToEdgeBaseHeader,
"rw",
inputBaseHeader,
WhiteboxRaster.DataType.FLOAT,
Float.POSITIVE_INFINITY);
distToEdgeBase.isTemporaryFile = true;
double[] data;
for (row = 0; row < baseRows; row++) {
data = baseRaster.getRowValues(row);
for (col = 0; col < baseCols; col++) {
if (row == 0 || row == baseRows - 1) {
distToEdgeBase.setValue(row, col, 0.0);
} else if (col == 0 || col == baseCols - 1) {
distToEdgeBase.setValue(row, col, 0.0);
} else {
if (data[col] != baseNoData) {
if (data[col - 1] == baseNoData || data[col + 1] == baseNoData) {
distToEdgeBase.setValue(row, col, 0.0);
}
} else {
distToEdgeBase.setValue(row, col, 0.0);
}
}
}
}
calculateDistance(distToEdgeBase);
String distToEdgeAppendHeader =
whitebox.utilities.StringUtilities.replaceLast(inputBaseHeader, ".dep", "_temp2.dep");
WhiteboxRaster distToEdgeAppend =
new WhiteboxRaster(
distToEdgeAppendHeader,
"rw",
inputHeader,
WhiteboxRaster.DataType.FLOAT,
Float.POSITIVE_INFINITY);
distToEdgeAppend.isTemporaryFile = true;
for (row = 0; row < appendRows; row++) {
data = appendRaster.getRowValues(row);
for (col = 0; col < appendCols; col++) {
if (row == 0 || row == appendRows - 1) {
distToEdgeAppend.setValue(row, col, 0.0);
} else if (col == 0 || col == appendCols - 1) {
distToEdgeAppend.setValue(row, col, 0.0);
} else {
if (data[col] != appendNoData) {
if (data[col - 1] == appendNoData || data[col + 1] == appendNoData) {
distToEdgeAppend.setValue(row, col, 0.0);
}
} else {
distToEdgeAppend.setValue(row, col, 0.0);
}
}
}
}
calculateDistance(distToEdgeAppend);
if (resampleMethod.contains("nearest")) {
for (row = 0; row < nRows; row++) {
for (col = 0; col < nCols; col++) {
x = destination.getXCoordinateFromColumn(col);
y = destination.getYCoordinateFromRow(row);
baseCol = baseRaster.getColumnFromXCoordinate(x);
baseRow = baseRaster.getRowFromYCoordinate(y);
appendCol = appendRaster.getColumnFromXCoordinate(x);
appendRow = appendRaster.getRowFromYCoordinate(y);
zBase = baseRaster.getValue(baseRow, baseCol);
zAppend = appendRaster.getValue(appendRow, appendCol);
if (zBase != baseNoData && zAppend == appendNoData) {
destination.setValue(row, col, zBase);
} else if (zBase == baseNoData && zAppend != appendNoData) {
destination.setValue(row, col, zAppend);
} else if (zBase == baseNoData && zAppend == appendNoData) {
destination.setValue(row, col, outputNoData);
} else { // two valid values.
// find the distance to the nearest edge in the base image
dist1 = distToEdgeBase.getValue(baseRow, baseCol); // baseCol;
dist2 = distToEdgeAppend.getValue(appendRow, appendCol); // appendCol;
sumDist = Math.pow(dist1, power) + Math.pow(dist2, power);
w1 = Math.pow(dist1, power) / sumDist;
w2 = Math.pow(dist2, power) / sumDist;
z = w1 * zBase + w2 * zAppend;
destination.setValue(row, col, z);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / nRowsLessOne);
updateProgress("Resampling images: ", progress);
}
} else {
if (destination.getDataType() != WhiteboxRaster.DataType.DOUBLE
&& destination.getDataType() != WhiteboxRaster.DataType.FLOAT) {
showFeedback(
"The destination image is not of an appropriate data"
+ " type (i.e. double or float) to perform this operation.");
return;
}
double dX, dY;
double srcRow, srcCol;
double originRow, originCol;
double rowN, colN;
double sumOfDist;
double[] shiftX;
double[] shiftY;
int numNeighbours = 0;
double[][] neighbour;
if (resampleMethod.contains("cubic")) {
shiftX = new double[] {-1, 0, 1, 2, -1, 0, 1, 2, -1, 0, 1, 2, -1, 0, 1, 2};
shiftY = new double[] {-1, -1, -1, -1, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2};
numNeighbours = 16;
neighbour = new double[numNeighbours][2];
} else { // resampleMethod is "bilinear"
shiftX = new double[] {0, 1, 0, 1};
shiftY = new double[] {0, 0, 1, 1};
numNeighbours = 4;
neighbour = new double[numNeighbours][2];
}
for (row = 0; row < nRows; row++) {
for (col = 0; col < nCols; col++) {
x = destination.getXCoordinateFromColumn(col);
y = destination.getYCoordinateFromRow(row);
baseCol = baseRaster.getColumnFromXCoordinate(x);
baseRow = baseRaster.getRowFromYCoordinate(y);
// what are the exact col and row of the image?
srcRow = (baseNorth - y) / baseNSRange * (baseRows - 0.5);
srcCol = (x - baseWest) / baseEWRange * (baseCols - 0.5);
originRow = Math.floor(srcRow);
originCol = Math.floor(srcCol);
sumOfDist = 0;
for (i = 0; i < numNeighbours; i++) {
rowN = originRow + shiftY[i];
colN = originCol + shiftX[i];
neighbour[i][0] = baseRaster.getValue((int) rowN, (int) colN);
dY = rowN - srcRow;
dX = colN - srcCol;
if ((dX + dY) != 0 && neighbour[i][0] != baseNoData) {
neighbour[i][1] = 1 / (dX * dX + dY * dY);
sumOfDist += neighbour[i][1];
} else if (neighbour[i][0] == baseNoData) {
neighbour[i][1] = 0;
} else { // dist is zero
neighbour[i][1] = 99999999;
sumOfDist += neighbour[i][1];
}
}
if (sumOfDist > 0) {
z = 0;
for (i = 0; i < numNeighbours; i++) {
z += neighbour[i][0] * neighbour[i][1] / sumOfDist;
}
zBase = z;
} else {
zBase = baseNoData;
}
appendCol = appendRaster.getColumnFromXCoordinate(x);
appendRow = appendRaster.getRowFromYCoordinate(y);
srcRow = (appendNorth - y) / appendNSRange * (appendRows - 0.5);
srcCol = (x - appendWest) / appendEWRange * (appendCols - 0.5);
originRow = Math.floor(srcRow);
originCol = Math.floor(srcCol);
sumOfDist = 0;
for (i = 0; i < numNeighbours; i++) {
rowN = originRow + shiftY[i];
colN = originCol + shiftX[i];
neighbour[i][0] = appendRaster.getValue((int) rowN, (int) colN);
dY = rowN - srcRow;
dX = colN - srcCol;
if ((dX + dY) != 0 && neighbour[i][0] != appendNoData) {
neighbour[i][1] = 1 / (dX * dX + dY * dY);
sumOfDist += neighbour[i][1];
} else if (neighbour[i][0] == appendNoData) {
neighbour[i][1] = 0;
} else { // dist is zero
neighbour[i][1] = 99999999;
sumOfDist += neighbour[i][1];
}
}
if (sumOfDist > 0) {
z = 0;
for (i = 0; i < numNeighbours; i++) {
z += (neighbour[i][0] * neighbour[i][1]) / sumOfDist;
}
zAppend = z;
} else {
zAppend = appendNoData;
}
if (zBase != baseNoData && zAppend == appendNoData) {
destination.setValue(row, col, zBase);
} else if (zBase == baseNoData && zAppend != appendNoData) {
destination.setValue(row, col, zAppend);
} else if (zBase == baseNoData && zAppend == appendNoData) {
destination.setValue(row, col, outputNoData);
} else { // two valid values.
// find the distance to the nearest edge in the base image
dist1 = distToEdgeBase.getValue(baseRow, baseCol); // baseCol;
dist2 = distToEdgeAppend.getValue(appendRow, appendCol); // appendCol;
sumDist = dist1 + dist2;
w1 = dist1 / sumDist;
w2 = dist2 / sumDist;
z = w1 * zBase + w2 * zAppend;
destination.setValue(row, col, z);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / nRowsLessOne);
updateProgress("Resampling images: ", progress);
}
}
destination.addMetadataEntry("Created by the " + getDescriptiveName() + " tool.");
destination.addMetadataEntry("Created on " + new Date());
destination.close();
distToEdgeBase.close();
distToEdgeAppend.close();
baseRaster.close();
if (performHistoMatching) {
File header = new File(inputHeader);
if (header.exists()) {
header.delete();
}
File dataFile = new File(StringUtilities.replaceLast(inputHeader, ".dep", ".tas"));
if (dataFile.exists()) {
dataFile.delete();
}
} else {
appendRaster.close();
}
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();
}
}
/** Used to execute this plugin tool. */
@Override
public void run() {
/*
* This transformation has been taken from:
* http://ij.ms3d.de/pdf/ihs_transforms.pdf
* in reference to Haydn, Dalke, and Henkel (1982)
* Note: 0 <= I <= 3, 0 <= H <= 3, 0 <= S <= 1
*/
amIActive = true;
String redHeader, greenHeader, blueHeader, intensityHeader, saturationHeader, hueHeader;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
redHeader = args[0];
greenHeader = args[1];
blueHeader = args[2];
intensityHeader = args[3];
hueHeader = args[4];
saturationHeader = args[5];
// check to see that the inputHeader and outputHeader are not null.
if (redHeader.isEmpty()
|| greenHeader.isEmpty()
|| blueHeader == null
|| intensityHeader.isEmpty()
|| hueHeader.isEmpty()
|| saturationHeader.isEmpty()) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
int row, col;
double redVal, greenVal, blueVal;
// double redRange, greenRange, blueRange;
// double redMin, greenMin, blueMin;
double r, g, b;
double i, s, h, m;
float progress;
WhiteboxRasterInfo red = new WhiteboxRasterInfo(redHeader);
int rows = red.getNumberRows();
int cols = red.getNumberColumns();
WhiteboxRasterInfo green = new WhiteboxRasterInfo(greenHeader);
if (green.getNumberRows() != rows || green.getNumberColumns() != cols) {
showFeedback("All input images must have the same dimensions.");
return;
}
WhiteboxRasterInfo blue = new WhiteboxRasterInfo(blueHeader);
if (blue.getNumberRows() != rows || blue.getNumberColumns() != cols) {
showFeedback("All input images must have the same dimensions.");
return;
}
double redNoData = red.getNoDataValue();
double greenNoData = green.getNoDataValue();
double blueNoData = blue.getNoDataValue();
WhiteboxRaster intensity =
new WhiteboxRaster(
intensityHeader, "rw", redHeader, WhiteboxRaster.DataType.FLOAT, redNoData);
WhiteboxRaster hue =
new WhiteboxRaster(hueHeader, "rw", redHeader, WhiteboxRaster.DataType.FLOAT, redNoData);
WhiteboxRaster saturation =
new WhiteboxRaster(
saturationHeader, "rw", redHeader, WhiteboxRaster.DataType.FLOAT, redNoData);
// redMin = red.getDisplayMinimum();
// greenMin = green.getDisplayMinimum();
// blueMin = blue.getDisplayMinimum();
//
// redRange = red.getDisplayMaximum() - redMin;
// greenRange = green.getDisplayMaximum() - greenMin;
// blueRange = blue.getDisplayMaximum() - blueMin;
double overallMin =
Math.min(
Math.min(red.getDisplayMinimum(), green.getDisplayMinimum()),
blue.getDisplayMinimum());
double overallMax =
Math.max(
Math.max(red.getDisplayMaximum(), green.getDisplayMaximum()),
blue.getDisplayMaximum());
double range = overallMax - overallMin;
double[] dataRed, dataGreen, dataBlue;
for (row = 0; row < rows; row++) {
dataRed = red.getRowValues(row);
dataGreen = green.getRowValues(row);
dataBlue = blue.getRowValues(row);
for (col = 0; col < cols; col++) {
redVal = dataRed[col];
greenVal = dataGreen[col];
blueVal = dataBlue[col];
if ((redVal != redNoData) && (greenVal != greenNoData) && (blueVal != blueNoData)) {
r = (redVal - overallMin) / range;
if (r < 0) {
r = 0;
}
if (r > 1) {
r = 1;
}
g = (greenVal - overallMin) / range;
if (g < 0) {
g = 0;
}
if (g > 1) {
g = 1;
}
b = (blueVal - overallMin) / range;
if (b < 0) {
b = 0;
}
if (b > 1) {
b = 1;
}
m = Math.min(Math.min(r, g), b);
i = r + g + b;
if (i == 3) {
h = 0;
} else if (m == b) {
h = (g - b) / (i - 3 * b);
} else if (m == r) {
h = (b - r) / (i - 3 * r) + 1;
} else { // m == g
h = (r - g) / (i - 3 * g) + 2;
}
if (h <= 1) {
s = (i - 3 * b) / i;
} else if (h <= 2) {
s = (i - 3 * r) / i;
} else { // H <= 3
s = (i - 3 * g) / i;
}
intensity.setValue(row, col, i);
hue.setValue(row, col, h);
saturation.setValue(row, col, s);
} else {
intensity.setValue(row, col, redNoData);
hue.setValue(row, col, redNoData);
saturation.setValue(row, col, redNoData);
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (float) (100f * row / (rows - 1));
updateProgress((int) progress);
}
intensity.addMetadataEntry("Created by the " + getDescriptiveName() + " tool.");
intensity.addMetadataEntry("Created on " + new Date());
intensity.close();
hue.addMetadataEntry("Created by the " + getDescriptiveName() + " tool.");
hue.addMetadataEntry("Created on " + new Date());
hue.close();
saturation.addMetadataEntry("Created by the " + getDescriptiveName() + " tool.");
saturation.addMetadataEntry("Created on " + new Date());
saturation.close();
red.close();
green.close();
blue.close();
// returning a header file string displays the image.
returnData(intensityHeader);
returnData(hueHeader);
returnData(saturationHeader);
} 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 streamsHeader;
String pointerHeader;
String outputFileName;
int row, col, x, y;
double xCoord, yCoord;
int progress;
int c;
int[] dX = new int[] {1, 1, 1, 0, -1, -1, -1, 0};
int[] dY = new int[] {-1, 0, 1, 1, 1, 0, -1, -1};
double[] inflowingVals = new double[] {16, 32, 64, 128, 1, 2, 4, 8};
boolean flag;
double flowDir;
double previousFlowDir;
double linkLength;
double streamValue;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
streamsHeader = args[0];
pointerHeader = args[1];
outputFileName = args[2];
// check to see that the inputHeader and outputHeader are not null.
if ((streamsHeader == null) || (pointerHeader == null) || (outputFileName == null)) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
try {
WhiteboxRaster streams = new WhiteboxRaster(streamsHeader, "r");
int rows = streams.getNumberRows();
int cols = streams.getNumberColumns();
double noData = streams.getNoDataValue();
double gridResX = streams.getCellSizeX();
double gridResY = streams.getCellSizeY();
double diagGridRes = Math.sqrt(gridResX * gridResX + gridResY * gridResY);
double[] gridLengths =
new double[] {
diagGridRes,
gridResX,
diagGridRes,
gridResY,
diagGridRes,
gridResX,
diagGridRes,
gridResY
};
double east = streams.getEast() - gridResX / 2.0;
double west = streams.getWest() + gridResX / 2.0;
double EWRange = east - west;
double north = streams.getNorth() - gridResY / 2.0;
double south = streams.getSouth() + gridResY / 2.0;
double NSRange = north - south;
WhiteboxRaster pntr = new WhiteboxRaster(pointerHeader, "r");
if (pntr.getNumberRows() != rows || pntr.getNumberColumns() != cols) {
showFeedback("The input images must be of the same dimensions.");
return;
}
DBFField fields[] = new DBFField[3];
fields[0] = new DBFField();
fields[0].setName("FID");
fields[0].setDataType(DBFField.DBFDataType.NUMERIC);
fields[0].setFieldLength(10);
fields[0].setDecimalCount(0);
fields[1] = new DBFField();
fields[1].setName("STRM_VAL");
fields[1].setDataType(DBFField.DBFDataType.NUMERIC);
fields[1].setFieldLength(10);
fields[1].setDecimalCount(3);
fields[2] = new DBFField();
fields[2].setName("Length");
fields[2].setDataType(DBFField.DBFDataType.NUMERIC);
fields[2].setFieldLength(10);
fields[2].setDecimalCount(3);
// set up the output files of the shapefile and the dbf
ShapeFile output = new ShapeFile(outputFileName, ShapeType.POLYLINE, fields);
byte numNeighbouringStreamCells;
int FID = 0;
for (row = 0; row < rows; row++) {
for (col = 0; col < cols; col++) {
streamValue = streams.getValue(row, col);
if (streamValue > 0) {
// see if it is a headwater location
numNeighbouringStreamCells = 0;
for (c = 0; c < 8; c++) {
x = col + dX[c];
y = row + dY[c];
if (streams.getValue(y, x) > 0 && pntr.getValue(y, x) == inflowingVals[c]) {
numNeighbouringStreamCells++;
}
}
if (numNeighbouringStreamCells != 1) {
// it's the start of a link.
FID++;
linkLength = 0;
int[] parts = {0};
PointsList points = new PointsList();
x = col;
y = row;
previousFlowDir = -99;
flag = true;
do {
// find the downslope neighbour
flowDir = pntr.getValue(y, x);
if (flowDir > 0) {
if (flowDir != previousFlowDir) {
// it's a bend in the stream so add this point
xCoord = west + ((double) x / cols) * EWRange;
yCoord = north - ((double) y / rows) * NSRange;
points.addPoint(xCoord, yCoord);
previousFlowDir = flowDir;
}
// update the row and column values to the
// cell that the flowpath leads to.
c = (int) (Math.log(flowDir) / LnOf2);
if (c > 7) {
showFeedback(
"An unexpected value has "
+ "been identified in the pointer "
+ "image. This tool requires a "
+ "pointer grid that has been "
+ "created using either the D8 "
+ "or Rho8 tools.");
return;
}
x += dX[c];
y += dY[c];
linkLength += gridLengths[c];
if (streams.getValue(y, x) <= 0) { // it's not a stream cell
flag = false;
} else {
// is it a confluence
numNeighbouringStreamCells = 0;
int x2, y2;
for (int d = 0; d < 8; d++) {
x2 = x + dX[d];
y2 = y + dY[d];
if (streams.getValue(y2, x2) > 0
&& pntr.getValue(y2, x2) == inflowingVals[d]) {
numNeighbouringStreamCells++;
}
}
if (numNeighbouringStreamCells > 1) {
// It's a confluence and you should stop here.
flag = false;
}
}
} else {
flag = false;
}
if (!flag) {
// it's the end of the stream link so
// add the point.
xCoord = west + ((double) x / cols) * EWRange;
yCoord = north - ((double) y / rows) * NSRange;
points.addPoint(xCoord, yCoord);
}
} while (flag);
// add the line to the shapefile.
PolyLine line = new PolyLine(parts, points.getPointsArray());
Object[] rowData = new Object[3];
rowData[0] = new Double(FID);
rowData[1] = new Double(streamValue);
rowData[2] = new Double(linkLength / 1000.0);
output.addRecord(line, rowData);
}
}
}
if (cancelOp) {
cancelOperation();
return;
}
progress = (int) (100f * row / (rows - 1));
updateProgress(progress);
}
output.write();
pntr.close();
streams.close();
// returning a header file string displays the image.
returnData(outputFileName);
} 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();
}
}
