A basic and inefficient program to replace a polygon's area in a raster with a new value using GeoTools.

UpdateByPolygon.java

package com.ianturton.cookbook.raster;

import java.awt.image.WritableRaster;
import java.io.File;
import java.io.IOException;

import javax.media.jai.RasterFactory;

import org.geotools.coverage.CoverageFactoryFinder;
import org.geotools.coverage.grid.GridCoordinates2D;
import org.geotools.coverage.grid.GridCoverage2D;
import org.geotools.coverage.grid.GridCoverageFactory;
import org.geotools.coverage.grid.InvalidGridGeometryException;
import org.geotools.coverage.grid.io.AbstractGridCoverage2DReader;
import org.geotools.coverage.grid.io.AbstractGridFormat;
import org.geotools.coverage.grid.io.GridFormatFinder;
import org.geotools.factory.Hints;
import org.geotools.gce.geotiff.GeoTiffFormat;
import org.geotools.geometry.Envelope2D;
import org.opengis.coverage.grid.GridCoverageWriter;
import org.opengis.coverage.grid.GridEnvelope;
import org.opengis.geometry.DirectPosition;
import org.opengis.referencing.operation.TransformException;

import com.vividsolutions.jts.geom.Coordinate;
import com.vividsolutions.jts.geom.GeometryFactory;
import com.vividsolutions.jts.geom.Polygon;

public class UpdateByPolygon {

  private GridCoverage2D coverage;
  private GridCoverage2D output;
  static final GeometryFactory gf = new GeometryFactory();

  public void loadRaster(File in) {
    AbstractGridFormat format = GridFormatFinder.findFormat(in);
    Hints hints = null;
    if (format instanceof GeoTiffFormat) {
      hints = new Hints(Hints.FORCE_LONGITUDE_FIRST_AXIS_ORDER, Boolean.TRUE);
    }
    AbstractGridCoverage2DReader reader = format.getReader(in,hints);

    coverage = null;
    try {
      coverage = reader.read(null);
    } catch (IOException giveUp) {
      throw new RuntimeException(giveUp);
    }
    reader.dispose();
  }

  public void writeRaster(File out) {
    try {
      AbstractGridFormat format = new GeoTiffFormat();
      Hints hints = null;
      if (format instanceof GeoTiffFormat) {
        hints = new Hints(Hints.FORCE_LONGITUDE_FIRST_AXIS_ORDER, Boolean.TRUE);
      }
      GridCoverageWriter writer = format.getWriter(out,hints);
      try {
        writer.write(output, null);
        writer.dispose();
      } catch (IllegalArgumentException | IOException e) {
        e.printStackTrace();
      }
    } catch (InvalidGridGeometryException e) {
      e.printStackTrace();
    }
  }

  /**
   * Set pixels inside the polygon to value
   * 
   * @param poly
   * @param value
   * @throws TransformException
   */
  public void intersect(Polygon poly, double[] value) throws TransformException {
    GridEnvelope gridRange = coverage.getGridGeometry().getGridRange();
    WritableRaster writableRaster = RasterFactory.createBandedRaster(java.awt.image.DataBuffer.TYPE_DOUBLE,
        gridRange.getSpan(0), gridRange.getSpan(1), coverage.getNumSampleDimensions(), null);
    Hints hints = new Hints(Hints.FORCE_LONGITUDE_FIRST_AXIS_ORDER, Boolean.TRUE);
    GridCoverageFactory factory = CoverageFactoryFinder.getGridCoverageFactory(hints);
    Envelope2D envelope = coverage.getEnvelope2D();
    
    output = factory.create("Result", writableRaster, envelope);
    double[] dest = new double[3];
    GridEnvelope gridRange2D = coverage.getGridGeometry().getGridRange();

    for (int i = gridRange2D.getLow(0); i < gridRange2D.getHigh(0); i++) {
      for (int j = gridRange2D.getLow(1); j < gridRange2D.getHigh(1); j++) {
        GridCoordinates2D coord = new GridCoordinates2D(i, j);
        DirectPosition p = coverage.getGridGeometry().gridToWorld(coord);

        if (poly.contains(gf.createPoint(new Coordinate(p.getOrdinate(0), p.getOrdinate(1))))) {
          writableRaster.setDataElements(i, j, value);
        } else {
          coverage.evaluate(coord, dest);
          writableRaster.setDataElements(i, j, dest);
        }

      }
    }
  }

  /**
   * @return the output
   */
  public GridCoverage2D getOutput() {
    return output;
  }
  
  public static void main(String[] args) throws TransformException {
    UpdateByPolygon updater = new UpdateByPolygon();
    updater.loadRaster(new File("world2.tif"));
    Coordinate[] coordinates = new Coordinate[] {new Coordinate(0,0),new Coordinate(0,10),new Coordinate(10,10), new Coordinate(10,0),new Coordinate(0,0)};
    updater.intersect(gf.createPolygon(gf.createLinearRing(coordinates)), new double[] {0,0,0});
    updater.writeRaster(new File("world3.tif"));
  }
}