org.jgrasstools.gears.modules.r.summary.OmsZonalStats Maven / Gradle / Ivy
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/*
* This file is part of JGrasstools (http://www.jgrasstools.org)
* (C) HydroloGIS - www.hydrologis.com
*
* JGrasstools 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
* - totalMean
* - userTotalMean
* - totalActiveCells
*
* if {@link #pTotalMean} is != null.
*/
double[] tm_usertm_tactivecells = new double[3];
public static final String MIN = "min";
public static final String MAX = "max";
public static final String AVG = "avg";
public static final String VAR = "var";
public static final String SDEV = "sdev";
public static final String AVGABSDEV = "avgabsdev";
public static final String ACTCELLS = "actcells";
public static final String INVCELLS = "invcells";
@Execute
public void process() throws Exception {
checkNull(inVector, inRaster);
boolean hasUserTotalMean = false;
if (pTotalMean != null) {
hasUserTotalMean = true;
tm_usertm_tactivecells[1] = pTotalMean;
}
ReferencedEnvelope bounds = inVector.getBounds();
CoordinateReferenceSystem crs = bounds.getCoordinateReferenceSystem();
SimpleFeatureBuilder featureBuilder = createFeatureBuilder(crs, hasUserTotalMean);
outVector = new DefaultFeatureCollection();
List geometriesList = FeatureUtilities.featureCollectionToGeometriesList(inVector, true, null);
// pm.message("" + readEnvelope);
GridGeometry2D gridGeometry = inRaster.getGridGeometry();
RandomIter readIter = CoverageUtilities.getRandomIterator(inRaster);
pm.beginTask("Processing polygons...", geometriesList.size());
for( Geometry geometry : geometriesList ) {
double[] polygonStats = polygonStats(geometry, gridGeometry, readIter, hasUserTotalMean, tm_usertm_tactivecells,
pPercentageThres, pm);
if (polygonStats == null) {
continue;
}
Object[] values;
if (!hasUserTotalMean) {
values = new Object[]{geometry, //
polygonStats[0], //
polygonStats[1], //
polygonStats[2], //
polygonStats[3], //
polygonStats[4], //
(int) polygonStats[5], //
(int) polygonStats[6] //
};
} else {
values = new Object[]{geometry, //
polygonStats[0], //
polygonStats[1], //
polygonStats[2], //
polygonStats[3], //
polygonStats[4], //
polygonStats[5], //
(int) polygonStats[6], //
(int) polygonStats[7] //
};
}
featureBuilder.addAll(values);
SimpleFeature feature = featureBuilder.buildFeature(null);
((DefaultFeatureCollection) outVector).add(feature);
pm.worked(1);
}
pm.done();
if (!hasUserTotalMean) {
tm_usertm_tactivecells[0] = tm_usertm_tactivecells[0] / tm_usertm_tactivecells[2];
pm.message("Total mean: " + tm_usertm_tactivecells[0]);
}
}
/**
* @param geometry
* @param gridGeometry
* @param inIter
* @param tm_utm_tac the array holding:
*
* - totalMean
* - userTotalMean
* - totalActiveCells
*
* @param percentageThres
* @param monitor an optional monitor. If null an exception
* is thrown in case of cusps, else an errormessage is given, but
* processing will go on ignoring the geometry.
* @return
* @throws Exception
*/
public static double[] polygonStats( Geometry geometry, GridGeometry2D gridGeometry, RandomIter inIter,
boolean hasUserTotalMean, double[] tm_utm_tac, double percentageThres, IJGTProgressMonitor monitor ) throws Exception {
GeometryFactory gf = GeometryUtilities.gf();
GridEnvelope2D gridRange = gridGeometry.getGridRange2D();
int rows = gridRange.height;
int cols = gridRange.width;
int startX = gridRange.x;
int startY = gridRange.y;
AffineTransform gridToCRS = (AffineTransform) gridGeometry.getGridToCRS();
double xRes = XAffineTransform.getScaleX0(gridToCRS);
double yRes = XAffineTransform.getScaleY0(gridToCRS);
final double delta = xRes / 4.0;
Envelope env = geometry.getEnvelopeInternal();
env.expandBy(xRes, yRes);
double geometryUpperBound = env.getMaxY();
double envArea = env.getWidth() * env.getHeight();
int maxCells = (int) ceil(envArea / (xRes * yRes));
int activeCellCount = 0;
int passiveCellCount = 0;
double min = Double.POSITIVE_INFINITY;
double max = Double.NEGATIVE_INFINITY;
MathTransform gridToCRS2 = gridGeometry.getGridToCRS();
double[] values = new double[maxCells];
LineString previousLine = null;
final Coordinate worldWestCoord = new Coordinate();
final Coordinate worldEastCoord = new Coordinate();
for( int r = startY; r < startY + rows; r++ ) {
// do scan line to fill the polygon
Coordinate gridWestCoord = new Coordinate(startX, r);
JTS.transform(gridWestCoord, worldWestCoord, gridToCRS2);
if (geometryUpperBound < worldWestCoord.y) {
continue;
}
Coordinate gridEastCoord = new Coordinate(startX + cols - 1, r);
JTS.transform(gridEastCoord, worldEastCoord, gridToCRS2);
LineString line = gf.createLineString(new Coordinate[]{worldWestCoord, worldEastCoord});
if (previousLine != null && previousLine.equals(line)) {
previousLine = line;
continue;
}
if (geometry.intersects(line)) {
Geometry internalLines = geometry.intersection(line);
int lineNums = internalLines.getNumGeometries();
for( int l = 0; l < lineNums; l++ ) {
Coordinate[] coords = internalLines.getGeometryN(l).getCoordinates();
if (coords.length == 2) {
for( int j = 0; j < coords.length; j = j + 2 ) {
Coordinate startC = new Coordinate(coords[j].x + delta, coords[j].y);
Coordinate endC = new Coordinate(coords[j + 1].x - delta, coords[j + 1].y);
DirectPosition2D startDP;
DirectPosition2D endDP;
if (startC.x < endC.x) {
startDP = new DirectPosition2D(startC.x, startC.x);
endDP = new DirectPosition2D(endC.x, endC.x);
} else {
startDP = new DirectPosition2D(endC.x, endC.x);
endDP = new DirectPosition2D(startC.x, startC.x);
}
GridCoordinates2D startGridCoord = gridGeometry.worldToGrid(startDP);
GridCoordinates2D endGridCoord = gridGeometry.worldToGrid(endDP);
/*
* the part in between has to be filled
*/
for( int k = startGridCoord.x; k <= endGridCoord.x; k++ ) {
double v = inIter.getSampleDouble(k, r, 0);
if (isNovalue(v)) {
passiveCellCount++;
continue;
}
min = Math.min(min, v);
max = Math.max(max, v);
values[activeCellCount] = v;
activeCellCount++;
if (!hasUserTotalMean) {
tm_utm_tac[0] = tm_utm_tac[0] + v;
tm_utm_tac[2] = tm_utm_tac[2] + 1;
}
}
}
} else {
if (coords.length == 1) {
String message = MessageFormat.format("Found a cusp in: {0}/{1}", coords[0].x, coords[0].y);
if (monitor != null) {
monitor.errorMessage(message);
} else {
throw new ModelsIOException(message, "ZonalStats");
}
} else {
throw new ModelsIOException(MessageFormat.format(
"Found intersection with more than 2 points in: {0}/{1}", coords[0].x, coords[0].y),
"ZonalStats");
}
}
}
}
previousLine = line;
}
int all = activeCellCount + passiveCellCount;
double ratio = 100.0 * activeCellCount / all;
if (ratio < percentageThres) {
return null;
}
double mean = mean(values, activeCellCount);
double sdev = standardDeviation(values, mean, activeCellCount);
double var = variance(values, mean, activeCellCount);
double[] result;
if (hasUserTotalMean) {
double meanAbsoluteDeviation = meanAbsoluteDeviation(values, activeCellCount, tm_utm_tac[1]);
result = new double[]{min, max, mean, var, sdev, meanAbsoluteDeviation, activeCellCount, passiveCellCount};
} else {
result = new double[]{min, max, mean, var, sdev, activeCellCount, passiveCellCount};
}
return result;
}
public static SimpleFeatureBuilder createFeatureBuilder( CoordinateReferenceSystem crs, boolean hasUserTotalMean ) {
SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder();
b.setName("stats");
b.setCRS(crs);
b.add("the_geom", Polygon.class);
b.add(MIN, Double.class);
b.add(MAX, Double.class);
b.add(AVG, Double.class);
b.add(VAR, Double.class);
b.add(SDEV, Double.class);
if (hasUserTotalMean)
b.add(AVGABSDEV, Double.class);
b.add(ACTCELLS, Integer.class);
b.add(INVCELLS, Integer.class);
SimpleFeatureType type = b.buildFeatureType();
return new SimpleFeatureBuilder(type);
}
private static double meanAbsoluteDeviation( double[] values, int count, double userTotalMean ) {
double mean = 0;
for( int i = 0; i < count; i++ ) {
mean = mean + abs(values[i] - userTotalMean);
}
return mean / count;
}
private static double mean( double[] values, int count ) {
double mean = 0;
for( int i = 0; i < count; i++ ) {
mean += values[i];
}
return mean / count;
}
private static double standardDeviation( double[] values, double mean, int count ) {
double sd = variance(values, mean, count);
sd = sqrt(sd);
return sd;
}
private static double variance( double[] values, double mean, int count ) {
double variance = 0;
for( int i = 0; i < count; i++ ) {
variance = variance + pow(values[i] - mean, 2.0);
}
variance = variance / (count);
return variance;
}
protected void processCell( int readCol, int readRow, int writeCol, int writeRow, int readCols, int readRows, int writeCols,
int writeRows ) {
// not used in this case
}
}