Java Examples for com.vividsolutions.jts.geom.Geometry

/**
     * Factory method creating the appropriate ParamField for the supplied Param.
     * 
     * @param param
     * @return
     */
public static ParamField create(Composite parent, Parameter<?> parameter) {
    if (Double.class.isAssignableFrom(parameter.type)) {
        return new JDoubleField(parent, parameter);
    } else if (URL.class.isAssignableFrom(parameter.type)) {
        if (parameter.metadata != null && parameter.metadata.get(Parameter.EXT) != null) {
            return new JURLField(parent, parameter);
        } else {
            JField field = new JField(parent, parameter);
            field.setSingleLine(true);
            return field;
        }
    } else if (Boolean.class.isAssignableFrom(parameter.type)) {
        JField field = new JField(parent, parameter);
        field.setSingleLine(true);
        return field;
    } else if (Number.class.isAssignableFrom(parameter.type)) {
        JField field = new JField(parent, parameter);
        field.setSingleLine(true);
        return field;
    } else if (File.class.isAssignableFrom(parameter.type)) {
        return new JFileField(parent, parameter);
    } else if (Geometry.class.isAssignableFrom(parameter.type)) {
        return new JGeometryField(parent, parameter);
    } else {
        // We got nothing special hope the converter api can deal
        return new JField(parent, parameter);
    }
}

public void aboutToDisplayPanel() {
    page.removeAll();
    page.setLayout(new GridLayout(0, 2));
    Process process = this.factory.create(name);
    final ProgressListener progress = new ProgressWindow(this.getJProcessWizard());
    Map<String, Object> resultMap;
    try {
        resultMap = process.execute(paramMap, progress);
    } catch (ProcessException ex) {
        Logger.getLogger(ProcessRunPage.class.getName()).log(Level.SEVERE, "Error preparing panel", ex);
        return;
    }
    // when we get here, the processing is over so show the result
    JLabel title = new JLabel(factory.getTitle(name).toString());
    page.add(title);
    JLabel description = new JLabel("Your process results are below:");
    page.add(description);
    for (Entry<String, Object> entry : resultMap.entrySet()) {
        Parameter<?> parameter = new Parameter(entry.getKey(), entry.getValue().getClass(), Text.text("Result"), Text.text("Result of process"));
        JLabel label = new JLabel(entry.getKey());
        page.add(label);
        ParamWidget widget;
        if (Double.class.isAssignableFrom(parameter.type)) {
            widget = new JDoubleField(parameter);
        } else if (Geometry.class.isAssignableFrom(parameter.type)) {
            widget = new JGeometryField(parameter);
        } else {
            // We got nothing special, let's hope the converter api can deal
            widget = new JField(parameter);
        }
        JComponent field = widget.doLayout();
        widget.setValue(entry.getValue());
        page.add(field);
    }
}

/**
     * Factory method creating the appropriate ParamField for the supplied Param.
     * 
     * @param param
     * @return
     */
public static ParamField create(Composite parent, Parameter<?> parameter) {
    if (Double.class.isAssignableFrom(parameter.type)) {
        return new JDoubleField(parent, parameter);
    } else if (URL.class.isAssignableFrom(parameter.type)) {
        if (parameter.metadata != null && parameter.metadata.get(Parameter.EXT) != null) {
            return new JURLField(parent, parameter);
        } else {
            JField field = new JField(parent, parameter);
            field.setSingleLine(true);
            return field;
        }
    } else if (Boolean.class.isAssignableFrom(parameter.type)) {
        JField field = new JField(parent, parameter);
        field.setSingleLine(true);
        return field;
    } else if (Number.class.isAssignableFrom(parameter.type)) {
        JField field = new JField(parent, parameter);
        field.setSingleLine(true);
        return field;
    } else if (File.class.isAssignableFrom(parameter.type)) {
        return new JFileField(parent, parameter);
    } else if (Geometry.class.isAssignableFrom(parameter.type)) {
        return new JGeometryField(parent, parameter);
    } else {
        // We got nothing special hope the converter api can deal
        return new JField(parent, parameter);
    }
}

public static Geometry copyTo(final double x, final double y, final double w, final double h, final Geometry g) {
    if (g.getNumPoints() != 5)
        throw new IllegalArgumentException("Geometry must have 5 points");
    if (!LinearRing.class.isAssignableFrom(g.getClass()))
        throw new IllegalArgumentException("Geometry must be linear ring");
    Coordinate[] coords = g.getCoordinates();
    coords[0].x = x;
    coords[0].y = y;
    coords[1].x = x + w;
    coords[1].y = y;
    coords[2].x = x + w;
    coords[2].y = y + h;
    coords[3].x = x;
    coords[3].y = y + h;
    coords[4].x = x;
    coords[4].y = y;
    return g;
}

@Test
public void testHeterogeneousGeometry() throws Exception {
    GeometryFactory gf = new GeometryFactory();
    Point point = gf.createPoint(new Coordinate(10, 10));
    LineString line = gf.createLineString(new Coordinate[] { new Coordinate(50, 50), new Coordinate(100, 100) });
    Polygon polygon = gf.createPolygon(gf.createLinearRing(new Coordinate[] { new Coordinate(0, 0), new Coordinate(0, 200), new Coordinate(200, 200), new Coordinate(200, 0), new Coordinate(0, 0) }), null);
    SimpleFeatureTypeBuilder ftb = new SimpleFeatureTypeBuilder();
    ftb.setName("test");
    ftb.add("geom", Geometry.class);
    SimpleFeatureType type = ftb.buildFeatureType();
    SimpleFeature f1 = SimpleFeatureBuilder.build(type, new Object[] { point }, null);
    SimpleFeature f2 = SimpleFeatureBuilder.build(type, new Object[] { line }, null);
    SimpleFeature f3 = SimpleFeatureBuilder.build(type, new Object[] { polygon }, null);
    MemoryDataStore ds = new MemoryDataStore();
    ds.createSchema(type);
    ds.addFeatures(new SimpleFeature[] { f1, f2, f3 });
    FeatureSource fs = ds.getFeatureSource("test");
    final WMSMapContent map = new WMSMapContent();
    map.getViewport().setBounds(new ReferencedEnvelope(-250, 250, -250, 250, null));
    map.setMapWidth(300);
    map.setMapHeight(300);
    map.setBgColor(Color.red);
    map.setTransparent(false);
    Style basicStyle = getCatalog().getStyleByName("Default").getStyle();
    map.addLayer(new FeatureLayer(fs, basicStyle));
    SVGStreamingMapOutputFormat producer = new SVGStreamingMapOutputFormat();
    StreamingSVGMap encodeSVG = producer.produceMap(map);
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    encodeSVG.encode(out);
    // System.out.println(out.toString());
    String expectedDoc = "<?xml version=\"1.0\" standalone=\"no\"?>" + //
    "<svg xmlns=\"http://www.w3.org/2000/svg\" " + //
    "    xmlns:xlink=\"http://www.w3.org/1999/xlink\" " + //
    "    stroke=\"green\"  " + //
    "    fill=\"none\"  " + //
    "    stroke-width=\"0.1%\" " + //
    "    stroke-linecap=\"round\" " + //
    "    stroke-linejoin=\"round\" " + //
    "    width=\"300\"  " + //
    "    height=\"300\"  " + //
    "    viewBox=\"-250.0 -250.0 500.0 500.0\"  " + //
    "    preserveAspectRatio=\"xMidYMid meet\"> " + //
    "  <g id=\"test\" class=\"Default\"> " + //
    "    <use x=\"10\" y=\"-10\" xlink:href=\"#point\"/> " + //
    "    <path d=\"M50 -50l50 -50 \"/> " + //
    "    <path d=\"M0 0l0 -200 200 0 0 200 -200 0 Z\"/> " + //
    "  </g> " + "</svg> ";
    DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
    Document expected = builder.parse(new InputSource(new StringReader(expectedDoc)));
    Document result = builder.parse(new ByteArrayInputStream(out.toByteArray()));
    XMLUnit.setIgnoreWhitespace(true);
    XMLUnit.setIgnoreAttributeOrder(true);
    XMLUnit.setIgnoreComments(true);
    XMLAssert.assertXMLEqual(expected, result);
}

@Override
@LogSlow(threshold = 200)
public List<AdminGeo> getGeometries(int adminLevelId) {
    try {
        List<AdminGeo> list = Lists.newArrayList();
        DataInputStream in = new DataInputStream(openWkb(adminLevelId));
        WKBReader wkbReader = new WKBReader(geometryFactory);
        int count = in.readInt();
        for (int i = 0; i != count; ++i) {
            int id = in.readInt();
            LOGGER.info("Reading geometry for admin entity " + id);
            Geometry geometry = wkbReader.read(new DataInputInStream(in));
            list.add(new AdminGeo(id, geometry));
        }
        return list;
    } catch (IOException e) {
        throw new RuntimeException(e);
    } catch (ParseException e) {
        throw new RuntimeException(e);
    }
}

@Test
public void extentOnePoint() throws SQLException {
    union.add(createPoint(3, 5));
    Object result = union.getResult();
    assertThat(result, is(not(nullValue())));
    Geometry envelope = GeoDB.gFromWKB((byte[]) result);
    assertThat(envelope.getArea(), is(0.0));
    assertThat(envelope, is(instanceOf(Point.class)));
    assertThat((Point) envelope, is(equalTo(createPoint(3, 5))));
}

private boolean test(Geometry geom1, Geometry geom2, boolean ignoreSRID) {
    if (geom1 == null) {
        return geom2 == null;
    }
    if (geom1.isEmpty()) {
        return geom2.isEmpty();
    }
    if (!ignoreSRID && !equalSRID(geom1, geom2)) {
        return false;
    }
    if (geom1 instanceof GeometryCollection) {
        if (!(geom2 instanceof GeometryCollection)) {
            return false;
        }
        GeometryCollection expectedCollection = (GeometryCollection) geom1;
        GeometryCollection receivedCollection = (GeometryCollection) geom2;
        for (int partIndex = 0; partIndex < expectedCollection.getNumGeometries(); partIndex++) {
            Geometry partExpected = expectedCollection.getGeometryN(partIndex);
            Geometry partReceived = receivedCollection.getGeometryN(partIndex);
            if (!test(partExpected, partReceived, true)) {
                return false;
            }
        }
        return true;
    } else {
        return testSimpleGeometryEquality(geom1, geom2);
    }
}

/**
     * <p>
     * The operation "distance" shall return the distance between this Geometry and another
     * Geometry. This distance is defined to be the greatest lower bound of the set of distances
     * between all pairs of points that include one each from each of the two Geometries. A
     * "distance" value shall be a positive number associated to distance units such as meters or
     * standard foot. If necessary, the second geometric object shall be transformed into the same
     * coordinate reference system as the first before the distance is calculated.
     * </p>
     * <p>
     * If the geometric objects overlap, or touch, then their distance apart shall be zero. Some
     * current implementations use a "negative" distance for such cases, but the approach is neither
     * consistent between implementations, nor theoretically viable.
     * </p>
     */
public double distance(Geometry gmo) {
    try {
        com.vividsolutions.jts.geom.Geometry jtsThis = JTSAdapter.export(this);
        com.vividsolutions.jts.geom.Geometry jtsThat = JTSAdapter.export(gmo);
        return jtsThis.distance(jtsThat);
    } catch (GeometryException e) {
        LOG.logError(e.getMessage(), e);
        return -1;
    }
}

@Override
protected Envelope getEnvelope(final SimpleFeature entry) {
    // incorporate the bounding box of the entry's envelope
    final Object o;
    if ((persistedType != null) && (reprojectedType != null) && (transform != null)) {
        o = FeatureDataUtils.defaultCRSTransform(entry, persistedType, reprojectedType, transform).getAttribute(getFieldName());
    } else {
        o = entry.getAttribute(getFieldName());
    }
    if ((o != null) && (o instanceof Geometry)) {
        final Geometry geometry = (Geometry) o;
        if (!geometry.isEmpty()) {
            return geometry.getEnvelopeInternal();
        }
    }
    return null;
}

public Geometry read(EndianDataInputStream file, GeometryFactory geometryFactory, int contentLength) throws IOException, InvalidShapefileException {
    //  file.setLittleEndianMode(true);
    //actual number of words read (word = 16bits)
    int actualReadWords = 0;
    int shapeType = file.readIntLE();
    actualReadWords += 2;
    if (shapeType != myShapeType)
        throw new InvalidShapefileException("pointhandler.read() - handler's shapetype doesnt match file's");
    double x = file.readDoubleLE();
    double y = file.readDoubleLE();
    double m, z = Double.NaN;
    actualReadWords += 8;
    if (shapeType == 11) {
        z = file.readDoubleLE();
        actualReadWords += 4;
    }
    if (shapeType >= 11) {
        m = file.readDoubleLE();
        actualReadWords += 4;
    }
    //verify that we have read everything we need
    while (actualReadWords < contentLength) {
        int junk2 = file.readShortBE();
        actualReadWords += 1;
    }
    return geometryFactory.createPoint(new Coordinate(x, y, z));
}

@Test
public void testInside() {
    Geometry box = GeometryHelper.createBoxPolygon(1, 2, 1, 2);
    FastArea fastArea = new FastArea(box, new MemoryStorage());
    assertFalse(fastArea.coversNode(point(0, 0)));
    assertTrue(fastArea.coversNode(point(1, 1)));
    assertTrue(fastArea.coversNode(point(1, 2)));
    assertTrue(fastArea.coversNode(point(1.5, 1.5)));
    assertTrue(fastArea.coversNode(point(1, 1.5)));
}

/* (non-Javadoc)
	 * @see org.n52.ses.enrichment.parser.AIXMAbstractGeometryParser#parseGeometries(org.apache.xmlbeans.XmlObject)
	 */
@Override
protected List<Geometry> parseGeometries(XmlObject xmlO) throws XmlException, ParseException, GMLParseException {
    List<Geometry> geometries = new ArrayList<Geometry>();
    // parse the feature's xml-document
    RunwayDocument runwayDoc = RunwayDocument.Factory.parse(xmlO.xmlText());
    RunwayType runway = runwayDoc.getRunway();
    // parse bounded by
    if (geometries.size() == 0 && runway.isSetBoundedBy()) {
        geometries.add(super.parseBoundedBy(runway.getBoundedBy()));
    }
    return null;
}

@Override
public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
    final Component component = super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
    if (!(component instanceof JLabel)) {
        return component;
    }
    final JLabel label = (JLabel) component;
    if (value instanceof ProductNode) {
        label.setText(((ProductNode) value).getDisplayName());
    } else if (value instanceof Geometry) {
        label.setText(((Geometry) value).toText().substring(0, 48).concat(" ..."));
    } else {
        label.setText("");
    }
    return label;
}

//~ Methods ----------------------------------------------------------------
/**
     * DOCUMENT ME!
     *
     * @param   args  the command line arguments
     *
     * @throws  Throwable  DOCUMENT ME!
     */
public static void main(final String[] args) throws Throwable {
    // NOI18N
    final String domain = "WUNDA_BLAU";
    // security alles unsinn :-)
    System.setSecurityManager(new RMISecurityManager() {

        @Override
        public void checkConnect(final String host, final int port) {
        }

        @Override
        public void checkConnect(final String host, final int port, final Object context) {
        }
    });
    // rmi registry lokaliseren
    final java.rmi.registry.Registry rmiRegistry = LocateRegistry.getRegistry(1099);
    // lookup des callservers
    // NOI18N
    final Remote r = (Remote) Naming.lookup("rmi://localhost/callServer");
    // ich weiss, dass die server von callserver implementiert werden
    final SearchService ss = (SearchService) r;
    final CatalogueService cat = (CatalogueService) r;
    final MetaService meta = (MetaService) r;
    final UserService us = (UserService) r;
    //        System.out.println("server contacted :: "+r);
    // Benutzergruppe anlegen (muss auf dem Server existieren)
    // UserGroup ug = new UserGroup(0,"Administratoren",domain );
    // user anlegen muss auf dem server existieren
    // User u = new User(0,  "admin",domain, ug );
    // oder mit login
    // ug_domain,ug_name,u_domain,u_name,password
    // NOI18N
    final User u = us.getUser(domain, "Administratoren", domain, "admin", "x");
    // NOI18N
    System.out.println(u + "  user token retrieved");
    // meta.getC
    // Beispiel:
    // hole alle Klassen einer Dom\u00E4ne
    // hole dir dann f\u00FCr jede Klasse ein ObjektTemplate
    // MetaClass[] cs = meta.getClasses(u,domain);
    //
    // for(int i=0;i<cs.length;i++)
    // {
    // System.out.println("NEW instance ::"+meta.getInstance(u,cs[i]));
    //
    // }
    // System.out.println("!!getInstance durchgelaufen !!");
    // Beispiel:
    // Template f\u00FCr eine Object der ersten Klasse
    // MetaObject mo = meta.getInstance(u,cs[0]);
    // NOI18N
    final MetaObject mo = meta.getMetaObject(u, 5646, 6, "WUNDA_BLAU");
    // NOI18N
    System.out.println("metaobject::" + mo);
    // alle attribute des Objects
    // ObjectAttribute[] attribs = mo.getAttribs();
    // NOI18N
    final java.util.Collection col1 = mo.getTraversedAttributesByType(Class.forName(""));
    // NOI18N
    final java.util.Collection col2 = mo.getAttributesByType(Class.forName("com.vividsolutions.jts.geom.Geometry"));
    final java.util.Collection col3 = // NOI18N
    mo.getAttributesByType(// NOI18N
    Class.forName("com.vividsolutions.jts.geom.Geometry"), 1);
    final java.util.Collection col4 = // NOI18N
    mo.getAttributesByType(// NOI18N
    Class.forName("com.vividsolutions.jts.geom.Geometry"), 2);
    final java.util.Collection col5 = // NOI18N
    mo.getAttributesByType(// NOI18N
    Class.forName("com.vividsolutions.jts.geom.Geometry"), 3);
    Iterator iter = col1.iterator();
    // NOI18N
    System.out.println("!!!!!!!!!!!! traversiert !!!!!!!!!!!!!!!!!!!");
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }
    iter = col2.iterator();
    // NOI18N
    System.out.println("!!!!!!!!!!!! level 0 !!!!!!!!!!!!!!!!!!!");
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }
    iter = col3.iterator();
    // NOI18N
    System.out.println("!!!!!!!!!!!! level 1 !!!!!!!!!!!!!!!!!!!");
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }
    iter = col4.iterator();
    // NOI18N
    System.out.println("!!!!!!!!!!!! level 2 !!!!!!!!!!!!!!!!!!!");
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }
    iter = col5.iterator();
    // NOI18N
    System.out.println("!!!!!!!!!!!! level 3 !!!!!!!!!!!!!!!!!!!");
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }
}

@Test
public void testDimensionSequence() throws Exception {
    Geometry geom = wKTReader.read("POINT(0 0)");
    CoordinateSequenceDimensionFilter cd = new CoordinateSequenceDimensionFilter();
    geom.apply(cd);
    assertTrue(cd.getDimension() == 2);
    geom = wKTReader.read("LINESTRING(0 0, 0 0 1)");
    cd = new CoordinateSequenceDimensionFilter();
    geom.apply(cd);
    assertTrue(cd.getDimension() == 3);
}

/**
     * Used to execute this plugin tool.
     */
@Override
public void run() {
    amIActive = true;
    String inputFile;
    String outputFile;
    int progress;
    int i, j, n, FID;
    int oneHundredthTotal;
    int numRecs;
    ShapeType shapeType;
    double bufferSize = 0;
    GeometryFactory factory = new GeometryFactory();
    com.vividsolutions.jts.geom.Geometry geometriesToBuffer = null;
    if (args.length <= 0) {
        showFeedback("Plugin parameters have not been set.");
        return;
    }
    inputFile = args[0];
    outputFile = args[1];
    bufferSize = Double.parseDouble(args[2]);
    if (bufferSize < 0) {
        showFeedback("The buffer size has not been set properly.");
        return;
    }
    // check to see that the inputHeader and outputHeader are not null.
    if ((inputFile == null) || (outputFile == null)) {
        showFeedback("One or more of the input parameters have not been set properly.");
        return;
    }
    try {
        // set up the input shapefile.
        ShapeFile input = new ShapeFile(inputFile);
        shapeType = input.getShapeType();
        numRecs = input.getNumberOfRecords();
        oneHundredthTotal = numRecs / 100;
        // set up the output files of the shapefile and the dbf
        ShapeFile output = new ShapeFile(outputFile, ShapeType.POLYGON);
        output.setProjectionStringFromOtherShapefile(input);
        DBFField fields[] = new DBFField[1];
        fields[0] = new DBFField();
        fields[0].setName("FID");
        fields[0].setDataType(DBFField.DBFDataType.NUMERIC);
        fields[0].setFieldLength(10);
        fields[0].setDecimalCount(0);
        String DBFName = output.getDatabaseFile();
        DBFWriter writer = new DBFWriter(new File(DBFName));
        writer.setFields(fields);
        if (shapeType.getBaseType() == ShapeType.POLYGON) {
            progress = 0;
            ArrayList<com.vividsolutions.jts.geom.Polygon> polygons = new ArrayList<>();
            com.vividsolutions.jts.geom.Geometry[] recJTSPoly = null;
            n = 0;
            for (ShapeFileRecord record : input.records) {
                if (record.getShapeType() != ShapeType.NULLSHAPE) {
                    recJTSPoly = record.getGeometry().getJTSGeometries();
                    for (int a = 0; a < recJTSPoly.length; a++) {
                        polygons.add((com.vividsolutions.jts.geom.Polygon) recJTSPoly[a]);
                    }
                }
                n++;
                if (n >= oneHundredthTotal) {
                    n = 0;
                    if (cancelOp) {
                        cancelOperation();
                        return;
                    }
                    progress++;
                    updateProgress("Reading shapefile data:", progress);
                }
            }
            // create an array of polygons
            com.vividsolutions.jts.geom.Polygon[] polygonArray = new com.vividsolutions.jts.geom.Polygon[polygons.size()];
            for (i = 0; i < polygons.size(); i++) {
                polygonArray[i] = polygons.get(i);
            }
            polygons.clear();
            geometriesToBuffer = factory.createMultiPolygon(polygonArray);
        } else if (shapeType.getBaseType() == ShapeType.POLYLINE) {
            ArrayList<LineString> lineStringList = new ArrayList<>();
            com.vividsolutions.jts.geom.Geometry[] recJTSPoly = null;
            progress = 0;
            n = 0;
            for (ShapeFileRecord record : input.records) {
                if (record.getShapeType() != ShapeType.NULLSHAPE) {
                    recJTSPoly = record.getGeometry().getJTSGeometries();
                    for (int a = 0; a < recJTSPoly.length; a++) {
                        lineStringList.add((com.vividsolutions.jts.geom.LineString) recJTSPoly[a]);
                    }
                }
                n++;
                if (n >= oneHundredthTotal) {
                    n = 0;
                    if (cancelOp) {
                        cancelOperation();
                        return;
                    }
                    progress++;
                    updateProgress("Reading shapefile data:", progress);
                }
            }
            // create an array of polygons
            com.vividsolutions.jts.geom.LineString[] lineStringArray = new com.vividsolutions.jts.geom.LineString[lineStringList.size()];
            for (i = 0; i < lineStringList.size(); i++) {
                lineStringArray[i] = lineStringList.get(i);
            }
            lineStringList.clear();
            geometriesToBuffer = factory.createMultiLineString(lineStringArray);
        } else if (shapeType.getBaseType() == ShapeType.POINT || shapeType.getBaseType() == ShapeType.MULTIPOINT) {
            ArrayList<com.vividsolutions.jts.geom.Point> pointList = new ArrayList<>();
            com.vividsolutions.jts.geom.Geometry[] recJTSPoly = null;
            n = 0;
            progress = 0;
            for (ShapeFileRecord record : input.records) {
                if (record.getShapeType() != ShapeType.NULLSHAPE) {
                    recJTSPoly = record.getGeometry().getJTSGeometries();
                    for (int a = 0; a < recJTSPoly.length; a++) {
                        pointList.add((com.vividsolutions.jts.geom.Point) recJTSPoly[a]);
                    }
                }
                n++;
                if (n >= oneHundredthTotal) {
                    n = 0;
                    if (cancelOp) {
                        cancelOperation();
                        return;
                    }
                    progress++;
                    updateProgress("Reading shapefile data:", progress);
                }
            }
            // create an array of polygons
            com.vividsolutions.jts.geom.Point[] pointArray = new com.vividsolutions.jts.geom.Point[pointList.size()];
            for (i = 0; i < pointList.size(); i++) {
                pointArray[i] = pointList.get(i);
            }
            pointList.clear();
            geometriesToBuffer = factory.createMultiPoint(pointArray);
        }
        updateProgress("Buffering data (progress will not be updated):", -1);
        com.vividsolutions.jts.geom.Geometry buffer = geometriesToBuffer.buffer(bufferSize);
        progress = 0;
        updateProgress("Creating new shapefile:", -1);
        if (buffer instanceof com.vividsolutions.jts.geom.MultiPolygon) {
            MultiPolygon mpBuffer = (MultiPolygon) buffer;
            FID = 0;
            n = 0;
            for (int a = 0; a < mpBuffer.getNumGeometries(); a++) {
                com.vividsolutions.jts.geom.Geometry g = mpBuffer.getGeometryN(a);
                if (g instanceof com.vividsolutions.jts.geom.Polygon) {
                    com.vividsolutions.jts.geom.Polygon bufferPoly = (com.vividsolutions.jts.geom.Polygon) g;
                    ArrayList<ShapefilePoint> pnts = new ArrayList<>();
                    int[] parts = new int[bufferPoly.getNumInteriorRing() + 1];
                    Coordinate[] buffCoords = bufferPoly.getExteriorRing().getCoordinates();
                    if (!Topology.isLineClosed(buffCoords)) {
                        System.out.println("Exterior ring not closed.");
                    }
                    if (Topology.isClockwisePolygon(buffCoords)) {
                        for (i = 0; i < buffCoords.length; i++) {
                            pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                        }
                    } else {
                        for (i = buffCoords.length - 1; i >= 0; i--) {
                            pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                        }
                    }
                    for (int b = 0; b < bufferPoly.getNumInteriorRing(); b++) {
                        parts[b + 1] = pnts.size();
                        buffCoords = bufferPoly.getInteriorRingN(b).getCoordinates();
                        if (!Topology.isLineClosed(buffCoords)) {
                            System.out.println("Interior ring not closed.");
                        }
                        if (Topology.isClockwisePolygon(buffCoords)) {
                            for (i = buffCoords.length - 1; i >= 0; i--) {
                                pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                            }
                        } else {
                            for (i = 0; i < buffCoords.length; i++) {
                                pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                            }
                        }
                    }
                    PointsList pl = new PointsList(pnts);
                    whitebox.geospatialfiles.shapefile.Polygon wbPoly = new whitebox.geospatialfiles.shapefile.Polygon(parts, pl.getPointsArray());
                    output.addRecord(wbPoly);
                    FID++;
                    Object[] rowData = new Object[1];
                    rowData[0] = new Double(FID);
                    writer.addRecord(rowData);
                    if (cancelOp) {
                        cancelOperation();
                        return;
                    }
                    n++;
                    progress = (int) (n * 100.0 / mpBuffer.getNumGeometries());
                    updateProgress("Creating new shapefile:", progress);
                } else {
                // I'm really hoping this is never hit.
                }
            }
        } else if (buffer instanceof com.vividsolutions.jts.geom.Polygon) {
            com.vividsolutions.jts.geom.Polygon pBuffer = (com.vividsolutions.jts.geom.Polygon) buffer;
            com.vividsolutions.jts.geom.Geometry g = pBuffer.getGeometryN(0);
            if (g instanceof com.vividsolutions.jts.geom.Polygon) {
                ArrayList<ShapefilePoint> pnts = new ArrayList<>();
                int[] parts = new int[pBuffer.getNumInteriorRing() + 1];
                Coordinate[] buffCoords = pBuffer.getExteriorRing().getCoordinates();
                if (Topology.isClockwisePolygon(buffCoords)) {
                    for (i = 0; i < buffCoords.length; i++) {
                        pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                    }
                } else {
                    for (i = buffCoords.length - 1; i >= 0; i--) {
                        pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                    }
                }
                for (int b = 0; b < pBuffer.getNumInteriorRing(); b++) {
                    parts[b + 1] = pnts.size();
                    buffCoords = pBuffer.getInteriorRingN(b).getCoordinates();
                    if (Topology.isClockwisePolygon(buffCoords)) {
                        for (i = buffCoords.length - 1; i >= 0; i--) {
                            pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                        }
                    } else {
                        for (i = 0; i < buffCoords.length; i++) {
                            pnts.add(new ShapefilePoint(buffCoords[i].x, buffCoords[i].y));
                        }
                    }
                }
                PointsList pl = new PointsList(pnts);
                whitebox.geospatialfiles.shapefile.Polygon wbPoly = new whitebox.geospatialfiles.shapefile.Polygon(parts, pl.getPointsArray());
                output.addRecord(wbPoly);
                Object[] rowData = new Object[1];
                rowData[0] = new Double(1);
                writer.addRecord(rowData);
            } else {
            // I'm really hoping this is never hit.
            }
        }
        output.write();
        writer.write();
        // returning a header file string displays the image.
        returnData(outputFile);
    } 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();
    }
}

/**
	 * 
	 */
public ArrayList<Geometry> parseGeometries(InputStream inputStream) {
    try {
        // Get a SAXParser from the SAXPArserFactory.
        SAXParserFactory saxParserFac = SAXParserFactory.newInstance();
        SAXParser saxParser = saxParserFac.newSAXParser();
        // Get the XMLReader of the SAXParser we created.
        XMLReader xmlReader = saxParser.getXMLReader();
        // Create a new ContentHandler and apply it to the XML-Reader.
        GeoRSSHandler georssHandler = new GeoRSSHandler();
        xmlReader.setContentHandler(georssHandler);
        // Parse the georss content
        xmlReader.parse(new InputSource(inputStream));
        return georssHandler.getParsedGeometries();
    } catch (Exception e) {
        Util.printErrorMessage(e.toString());
        return null;
    }
}

private void countGeoms(Geometry g) {
    if (g != null) {
        if (GeometryCollection.class.isInstance(g)) {
            int n = g.getNumGeometries();
            for (int i = 0; i < n; i++) {
                countGeoms(g.getGeometryN(i));
            }
        } else if (Point.class.isInstance(g)) {
            pointsCount++;
        } else if (LineString.class.isInstance(g)) {
            linestringsCount++;
        } else if (Polygon.class.isInstance(g)) {
            pointsCount++;
        }
    }
}

public void write(JSONWriter writer, Properties options) throws JSONException {
    writer.object();
    writer.key("description");
    writer.value("first geometry has at least one point in common with second geometry (opposite of disjoint)");
    writer.key("params");
    writer.value("Geometry a, Geometry b");
    writer.key("returns");
    writer.value("true/false");
    writer.endObject();
}

public Object parse(ElementInstance instance, Node node, Object value) throws Exception {
    try {
        if (node.hasAttribute("srsName")) {
            CRS.decode(node.getAttributeValue("srsName").toString());
        }
    } catch (NoSuchAuthorityCodeException e) {
        throw new WFSException("Invalid Authority Code: " + e.getAuthorityCode(), "InvalidParameterValue");
    }
    Geometry geometry = (Geometry) super.parse(instance, node, value);
    if (geometry != null) {
        //1. ensure a crs is set
        if (geometry.getUserData() == null) {
            //no crs set for the geometry, did we inherit one from a parent?
            if (crs != null) {
                geometry.setUserData(crs);
            } else {
            // for the moment we don't do anything since we miss the information
            // to infer the CRS from the feature type
            }
        }
        //2. ensure the coordinates of the geometry fall into valid space defined by crs
        CoordinateReferenceSystem crs = (CoordinateReferenceSystem) geometry.getUserData();
        if (crs != null)
            try {
                JTS.checkCoordinatesRange(geometry, crs);
            } catch (PointOutsideEnvelopeException e) {
                throw new WFSException(e, "InvalidParameterValue");
            }
    }
    return geometry;
}

public Object parse(ElementInstance instance, Node node, Object value) throws Exception {
    try {
        if (node.hasAttribute("srsName")) {
            CRS.decode(node.getAttributeValue("srsName").toString());
        }
    } catch (NoSuchAuthorityCodeException e) {
        throw new WFSException("Invalid Authority Code: " + e.getAuthorityCode(), "InvalidParameterValue");
    }
    Geometry geometry = (Geometry) super.parse(instance, node, value);
    if (geometry != null) {
        //1. ensure a crs is set
        if (geometry.getUserData() == null) {
            //no crs set for the geometry, did we inherit one from a parent?
            if (crs != null) {
                geometry.setUserData(crs);
            } else {
            // for the moment we don't do anything since we miss the information
            // to infer the CRS from the feature type
            }
        }
        //2. ensure the coordinates of the geometry fall into valid space defined by crs
        CoordinateReferenceSystem crs = (CoordinateReferenceSystem) geometry.getUserData();
        if (crs != null)
            try {
                JTS.checkCoordinatesRange(geometry, crs);
            } catch (PointOutsideEnvelopeException e) {
                throw new WFSException(e, "InvalidParameterValue");
            }
    }
    return geometry;
}

public Map<String, Object> execute(Map<String, Object> input, ProgressListener monitor) {
    if (started)
        throw new IllegalStateException("Process can only be run once");
    started = true;
    if (monitor == null)
        monitor = new NullProgressListener();
    try {
        monitor.started();
        monitor.setTask(Text.text("Grabbing arguments"));
        monitor.progress(10.0f);
        Object value = input.get(BufferFactory.GEOM1.key);
        if (value == null) {
            throw new NullPointerException("geom1 parameter required");
        }
        if (!(value instanceof Geometry)) {
            throw new ClassCastException("geom1 requied Geometry, not " + value);
        }
        Geometry geom1 = (Geometry) value;
        value = input.get(BufferFactory.BUFFER.key);
        if (value == null) {
            throw new ClassCastException("geom1 requied Geometry, not " + value);
        }
        if (!(value instanceof Number)) {
            throw new ClassCastException("buffer requied number, not " + value);
        }
        Double buffer = ((Number) value).doubleValue();
        monitor.setTask(Text.text("Processing Buffer"));
        monitor.progress(25.0f);
        if (monitor.isCanceled()) {
            // user has canceled this operation
            return null;
        }
        Geometry resultGeom = geom1.buffer(buffer);
        monitor.setTask(Text.text("Encoding result"));
        monitor.progress(90.0f);
        Map<String, Object> result = new HashMap<String, Object>();
        result.put(BufferFactory.RESULT.key, resultGeom);
        // same as 100.0f
        monitor.complete();
        return result;
    } catch (Exception eek) {
        monitor.exceptionOccurred(eek);
        return null;
    } finally {
        monitor.dispose();
    }
}

public static Map<Triple, Geometry> geomize(Iterable<Triple> triples, LookupService<Node, Geometry> lookupServiceSubjects, LookupService<Node, Geometry> lookupServiceObjects) {
    Map<Triple, Geometry> result = new HashMap<Triple, Geometry>();
    Set<Node> subjects = new HashSet<Node>();
    Set<Node> objects = new HashSet<Node>();
    for (Triple triple : triples) {
        subjects.add(triple.getSubject());
        objects.add(triple.getObject());
    }
    Map<Node, Geometry> mapSubjects = lookupServiceSubjects.apply(subjects);
    Map<Node, Geometry> mapObjects = lookupServiceObjects.apply(objects);
    System.out.println("mapSubjects: " + mapSubjects);
    System.out.println("mapObjects: " + mapObjects);
    GeometryFactory gf = new GeometryFactory(new PrecisionModel(PrecisionModel.FLOATING), 4326);
    for (Triple triple : triples) {
        Geometry gs = mapSubjects.get(triple.getSubject());
        Geometry go = mapObjects.get(triple.getObject());
        if (gs == null || go == null) {
            continue;
        }
        Coordinate[] coordinates = DistanceOp.nearestPoints(gs, go);
        //            Point ps = GeometryFactory.createPointFromInternalCoord(points[0], gs);
        //            Point po = GeometryFactory.createPointFromInternalCoord(points[1], go);
        LineString lineString = gf.createLineString(coordinates);
        result.put(triple, lineString);
    }
    return result;
}

@Override
public Object asJSON(Object value) {
    Geometry geometry = null;
    if (value instanceof Geometry) {
        geometry = (Geometry) value;
    } else if (value instanceof byte[]) {
        byte[] bytes = (byte[]) value;
        // mysql sprinkles 4 mystery bytes on top of the GIS data.
        bytes = Arrays.copyOfRange(bytes, 4, bytes.length);
        final WKBReader reader = new WKBReader();
        try {
            geometry = reader.read(bytes);
        } catch (ParseException e) {
            throw new RuntimeException("Could not parse geometry: " + e);
        }
    } else {
        throw new RuntimeException("Could not parse geometry column value: " + value);
    }
    return geometry.toText();
}

/**
     *@inheritDoc
     */
public boolean execute(PlugInContext context) throws Exception {
    RasterImageLayer rLayer = (RasterImageLayer) LayerTools.getSelectedLayerable(context, RasterImageLayer.class);
    if (rLayer == null) {
        //$NON-NLS-1$
        context.getWorkbenchFrame().warnUser(I18N.get("pirol.plugIns.EditAttributeByFormulaPlugIn.no-layer-selected"));
        return false;
    }
    Geometry fence = SelectionTools.getFenceGeometry(context);
    Envelope envWanted = fence.getEnvelopeInternal();
    rLayer.setEnvelope(envWanted);
    return true;
}

public SimpleFeature next() throws NoSuchElementException {
    SimpleFeature feature = delegate.next();
    for (Object attribute : feature.getAttributes()) {
        if (attribute instanceof Geometry) {
            Geometry geometry = (Geometry) attribute;
            attribute = geometry.reverse();
        }
        builder.add(attribute);
    }
    return builder.buildFeature(feature.getID());
}

public void insert(int id, Geometry geometry) {
    for (int i = 0; i < bufferWidths.length; i++) {
        Geometry exp = geometry.buffer(bufferWidths[i]);
        Envelope env = exp.getEnvelopeInternal();
        synchronized (indexes[i]) {
            indexes[i].insert(env, id);
            expanded[i].put(id, exp);
        }
        synchronized (geometries) {
            geometries.put(id, geometry);
        }
    }
}

@Test
public void testConvertForward() throws Exception {
    System.out.println("TEST " + getCurrentMethodName());
    final GeomFromWktConverter conv = new GeomFromWktConverter();
    final String wkt = "POINT(1.13 2)";
    Geometry resGeom = conv.convertForward(wkt, new String[] { "4326" });
    assertNotNull(resGeom);
    assertEquals(4326, resGeom.getSRID());
    assertEquals(1, resGeom.getCoordinates().length);
    assertEquals(new Coordinate(1.13, 2), resGeom.getCoordinates()[0]);
    assertEquals("Point", resGeom.getGeometryType());
    final String ewkt = "SRID=3021;POINT(1.13 2)";
    resGeom = conv.convertForward(ewkt, new String[] { "4326" });
    assertNotNull(resGeom);
    assertEquals(3021, resGeom.getSRID());
    assertEquals(1, resGeom.getCoordinates().length);
    assertEquals(new Coordinate(1.13, 2), resGeom.getCoordinates()[0]);
    assertEquals("Point", resGeom.getGeometryType());
}

com.vividsolutions.jts.geom.Geometry decode(Geometry g) {
    switch(g.getType()) {
        case POINT:
            return decodePoint(g);
        case LINESTRING:
            return decodeLine(g);
        case POLYGON:
            return decodePolygon(g);
        case MULTIPOINT:
            return decodeMultiPoint(g);
        case MULTILINESTRING:
            return decodeMultiLine(g);
        case MULTIPOLYGON:
            return decodeMultiPolygon(g);
        case GEOMETRYCOLLECTION:
            return decodeCollection(g);
        default:
            throw new UnsupportedOperationException();
    }
}

@Override
public G unmarshal(String val) throws Exception {
    WKTReader wktReader = new WKTReader();
    Geometry the_geom = wktReader.read(val);
    if (the_geom.getSRID() == 0) {
        the_geom.setSRID(4326);
    }
    try {
        return (G) the_geom;
    } catch (ClassCastException e) {
        throw new ParseException("WKT val is a " + the_geom.getClass().getName());
    }
}

/**
    * @see liquibase.datatype.LiquibaseDataType#objectToSql(java.lang.Object,
    *      liquibase.database.Database)
    */
@Override
public String objectToSql(final Object value, final Database database) {
    final String returnValue;
    if (value instanceof Geometry) {
        // TODO: Tailor the output for the database.
        returnValue = ((Geometry) value).toText();
    } else if (value instanceof String) {
        returnValue = value.toString();
    } else if (value instanceof DatabaseFunction) {
        returnValue = value.toString();
    } else if (value == null || value.toString().equalsIgnoreCase("null")) {
        returnValue = null;
    } else {
        throw new UnexpectedLiquibaseException("Cannot convert type " + value.getClass() + " to a Geometry value");
    }
    return returnValue;
}

public Geometry parseGeometry(JsonParser parser) throws JsonParseException, IOException {
    if (parser.getCurrentToken() != JsonToken.START_OBJECT)
        return null;
    String typeName = null;
    ArrayNode coordinates = null;
    while (parser.nextToken() != JsonToken.END_OBJECT) {
        String name = parser.getCurrentName();
        if ("type".equals(name)) {
            parser.nextToken();
            typeName = parser.getText();
        } else if ("coordinates".equals(name)) {
            parser.nextToken();
            coordinates = parser.readValueAsTree();
        } else {
            parser.nextToken();
            parser.skipChildren();
        }
    }
    Geometry geometry = null;
    if (typeName.equals("Point")) {
        geometry = geometryFactory.createPoint(new Coordinate(coordinates.get(0).asDouble(), coordinates.get(1).asDouble()));
    } else if (typeName.equals("MultiPoint")) {
        geometry = geometryFactory.createMultiPoint(parseLineString(coordinates));
    } else if (typeName.equals("LineString")) {
        geometry = geometryFactory.createLineString(parseLineString(coordinates));
    } else if (typeName.equals("MultiLineString")) {
        geometry = geometryFactory.createMultiLineString(parseLineStrings(coordinates));
    } else if (typeName.equals("Polygon")) {
        geometry = parsePolygonCoordinates(coordinates);
    } else if (typeName.equals("MultiPolygon")) {
        geometry = geometryFactory.createMultiPolygon(parsePolygons(coordinates));
    } else if (typeName.equals("GeometryCollection")) {
        geometry = geometryFactory.createGeometryCollection(parseGeometries(coordinates));
    }
    return geometry;
}

/**
     * Get polygons covering the components of the graph. The largest component (in terms of number
     * of nodes) will not overlap any other components (it will have holes); the others may overlap
     * each other.
     *
     * @param modes
     * @return
     */
@Secured({ "ROLE_USER" })
@GET
@Path("/polygons")
@Produces({ MediaType.APPLICATION_JSON })
public GraphComponentPolygons getComponentPolygons(@DefaultValue("TRANSIT,WALK") @QueryParam("modes") TraverseModeSet modes, @QueryParam("date") String date, @QueryParam("time") String time, @DefaultValue("") @QueryParam("bannedRoutes") String bannedRoutes, @QueryParam("routerId") String routerId) {
    RoutingRequest options = new RoutingRequest(modes);
    if (bannedRoutes.length() > 0) {
        options.setBannedRoutes(bannedRoutes);
    }
    Graph graph = graphService.getGraph(routerId);
    long dateTime = DateUtils.toDate(date, time, graph.getTimeZone()).getTime();
    if (cachedPolygons == null || dateTime != cachedDateTime || !options.equals(cachedOptions)) {
        cachedOptions = options;
        cachedDateTime = dateTime;
        cachedPolygons = AnalysisUtils.getComponentPolygons(graph, options, dateTime);
    }
    GraphComponentPolygons out = new GraphComponentPolygons();
    out.components = new ArrayList<GraphComponent>();
    for (Geometry geometry : cachedPolygons) {
        GraphComponent component = new GraphComponent();
        component.polygon = geometry;
        out.components.add(component);
    }
    return out;
}

public static GeometryElement marshalFrom(Attribute attribute) throws CatalogTransformerException {
    GeometryElement element = new GeometryElement();
    element.setName(attribute.getName());
    if (attribute.getValue() != null) {
        for (Serializable value : attribute.getValues()) {
            if (!(value instanceof String)) {
                continue;
            }
            String wkt = (String) value;
            WKTReader wktReader = new WKTReader(geometryFactory);
            Geometry jtsGeometry = null;
            try {
                jtsGeometry = wktReader.read(wkt);
            } catch (ParseException e) {
                throw new CatalogTransformerException("Could not transform Metacard to XML.  Invalid WKT.", e);
            }
            JTSToGML311GeometryConverter converter = new JTSToGML311GeometryConverter();
            @SuppressWarnings("unchecked") JAXBElement<AbstractGeometryType> gmlElement = (JAXBElement<AbstractGeometryType>) converter.createElement(jtsGeometry);
            GeometryElement.Value geoValue = new GeometryElement.Value();
            geoValue.setGeometry(gmlElement);
            ((GeometryElement) element).getValue().add(geoValue);
        }
    }
    return element;
}

public Geometry parseGeometry(JsonParser parser) throws JsonParseException, IOException {
    if (parser.getCurrentToken() != JsonToken.START_OBJECT)
        return null;
    String typeName = null;
    ArrayNode coordinates = null;
    while (parser.nextToken() != JsonToken.END_OBJECT) {
        String name = parser.getCurrentName();
        if ("type".equals(name)) {
            parser.nextToken();
            typeName = parser.getText();
        } else if ("coordinates".equals(name)) {
            parser.nextToken();
            coordinates = parser.readValueAsTree();
        } else {
            parser.nextToken();
            parser.skipChildren();
        }
    }
    Geometry geometry = null;
    if (typeName.equals("Point")) {
        geometry = geometryFactory.createPoint(new Coordinate(coordinates.get(0).asDouble(), coordinates.get(1).asDouble()));
    } else if (typeName.equals("MultiPoint")) {
        geometry = geometryFactory.createMultiPoint(parseLineString(coordinates));
    } else if (typeName.equals("LineString")) {
        geometry = geometryFactory.createLineString(parseLineString(coordinates));
    } else if (typeName.equals("MultiLineString")) {
        geometry = geometryFactory.createMultiLineString(parseLineStrings(coordinates));
    } else if (typeName.equals("Polygon")) {
        geometry = parsePolygonCoordinates(coordinates);
    } else if (typeName.equals("MultiPolygon")) {
        geometry = geometryFactory.createMultiPolygon(parsePolygons(coordinates));
    } else if (typeName.equals("GeometryCollection")) {
        geometry = geometryFactory.createGeometryCollection(parseGeometries(coordinates));
    }
    return geometry;
}

/**
     * Inject in Esper Configuration geospatial methods and classes
     * @param configuration
     */
public static void registerConfiguration(Configuration configuration) {
    // Inject methods to create Geometry variables
    configuration.addPlugInSingleRowFunction("polygon", Geospatial.class.getName(), "createPolygon");
    configuration.addPlugInSingleRowFunction("point", Geospatial.class.getName(), "createPoint");
    configuration.addPlugInSingleRowFunction("geometry", Geospatial.class.getName(), "readGeometry");
    // Register Geometry class
    configuration.addImport(Geometry.class.getName());
}

public void visit(final Feature feature) {
    final Geometry geometry = (Geometry) feature.getProperty(m_geometryName).getValue();
    if (point.within(geometry)) {
        m_found = true;
        for (final ColumnInterface column : columnList) {
            final Property property = feature.getProperty(column.getQualifier());
            if (property != null) {
                column.setWeight(column.toDouble(property.getValue()));
            }
        }
    }
}

/**
     * Project geometry.
     *
     * @param originalGeom
     *            the original geom
     * @param srcCRSCode
     *            the src crs code
     * @param trgCRSCode
     *            the trg crs code
     * @return the geometry
     * @throws NoSuchAuthorityCodeException
     *             the no such authority code exception
     * @throws FactoryException
     *             the factory exception
     * @throws MismatchedDimensionException
     *             the mismatched dimension exception
     * @throws TransformException
     *             the transform exception
     */
public static Geometry projectGeometry(Geometry originalGeom, String srcCRSCode, String trgCRSCode) throws NoSuchAuthorityCodeException, FactoryException, MismatchedDimensionException, TransformException {
    Geometry projectedGeometry = null;
    final MathTransform transform = CRS.findMathTransform(CRS.decode(srcCRSCode, true), CRS.decode(trgCRSCode, true), true);
    // converting geometries into a linear system
    try {
        projectedGeometry = JTS.transform(originalGeom, transform);
    } catch (Exception e) {
        GeometryFactory geometryFactory = new GeometryFactory(new PrecisionModel(PrecisionModel.FLOATING), 4326);
        WKTReader reader = new WKTReader(geometryFactory);
        try {
            Polygon worldCutPolygon = (Polygon) reader.read("POLYGON((-180 -89.9, -180 89.9, 180 89.9, 180 -89.9, -180 -89.9))");
            projectedGeometry = JTS.transform(originalGeom.intersection(worldCutPolygon), transform);
        } catch (Exception ex) {
            throw new RuntimeException(ex);
        }
    }
    return projectedGeometry;
}

/**
     * Creates and returns a geometry out of bounds (a point if bounds.getSpan(0) ==
     * bounds.getSpan(1) == 0D, a polygon otherwise), setting the bounds
     * {@link BoundingBox#getCoordinateReferenceSystem() CRS} as the geometry's
     * {@link Geometry#getUserData() user data}.
     * 
     * @param bounds the bounding box to build from
     * @return the newly constructed geometry
     */
public static Geometry toGeometry(final BoundingBox bounds) {
    if (bounds == null) {
        return null;
    }
    Geometry geom;
    if (bounds.getSpan(0) == 0D && bounds.getSpan(1) == 0D) {
        geom = gfac.createPoint(new Coordinate(bounds.getMinX(), bounds.getMinY()));
    } else {
        geom = JTS.toGeometry(bounds, gfac);
    }
    geom.setUserData(bounds.getCoordinateReferenceSystem());
    return geom;
}

@Override
public void execute(final GeometryUtilsRequest request, final GeometryUtilsResponse response) throws Exception {
    if (request.getGeometries() != null && request.getGeometries().length > 0) {
        int geomCount = request.getGeometries().length;
        log.debug("GeometryUtilsCommand for " + geomCount + " geometries.");
        if (request.getActionFlags() == 0) {
            response.setGeometries(request.getGeometries());
        }
        // convert to internal
        Geometry[] lastResult = new Geometry[geomCount];
        org.geomajas.geometry.Geometry[] dtoGeoms = request.getGeometries();
        for (int i = 0; i < geomCount; i++) {
            lastResult[i] = converter.toInternal(dtoGeoms[i]);
        }
        List<Geometry[]> intermediateResults = new ArrayList<Geometry[]>();
        // do merge before buffer
        if ((request.getActionFlags() & GeometryUtilsRequest.ACTION_MERGE) > 0) {
            lastResult = merge(lastResult);
            intermediateResults.add(lastResult);
        }
        if ((request.getActionFlags() & GeometryUtilsRequest.ACTION_BUFFER) > 0) {
            lastResult = buffer(lastResult, request.getBuffer(), request.getBufferQuadrantSegments());
            intermediateResults.add(lastResult);
        }
        // -- other actions here
        // ----------------------------------------------------------
        List<org.geomajas.geometry.Geometry> dtoResult = new ArrayList<org.geomajas.geometry.Geometry>();
        if (request.isIntermediateResults()) {
            for (Geometry[] geometries : intermediateResults) {
                for (Geometry geometry : geometries) {
                    dtoResult.add(converter.toDto(geometry));
                }
            }
        } else {
            for (Geometry geometry : lastResult) {
                dtoResult.add(converter.toDto(geometry));
            }
        }
        response.setGeometries(dtoResult.toArray(new org.geomajas.geometry.Geometry[dtoResult.size()]));
    }
}

public Coordinate[] edit(Coordinate[] coordinates, Geometry geom) {
    if (coordinates.length == 0)
        return null;
    Coordinate[] reducedCoords = new Coordinate[coordinates.length];
    // copy coordinates and reduce
    for (int i = 0; i < coordinates.length; i++) {
        Coordinate coord = new Coordinate(coordinates[i]);
        targetPM.makePrecise(coord);
        reducedCoords[i] = coord;
    }
    // remove repeated points, to simplify returned geometry as much as possible
    CoordinateList noRepeatedCoordList = new CoordinateList(reducedCoords, false);
    Coordinate[] noRepeatedCoords = noRepeatedCoordList.toCoordinateArray();
    /**
		 * Check to see if the removal of repeated points collapsed the coordinate
		 * List to an invalid length for the type of the parent geometry. It is not
		 * necessary to check for Point collapses, since the coordinate list can
		 * never collapse to less than one point. If the length is invalid, return
		 * the full-length coordinate array first computed, or null if collapses are
		 * being removed. (This may create an invalid geometry - the client must
		 * handle this.)
		 */
    int minLength = 0;
    if (geom instanceof LineString)
        minLength = 2;
    if (geom instanceof LinearRing)
        minLength = 4;
    Coordinate[] collapsedCoords = reducedCoords;
    if (removeCollapsed)
        collapsedCoords = null;
    // return null or orginal length coordinate array
    if (noRepeatedCoords.length < minLength) {
        return collapsedCoords;
    }
    // ok to return shorter coordinate array
    return noRepeatedCoords;
}

public Object parse(ElementInstance instance, Node node, Object value) throws Exception {
    try {
        if (node.hasAttribute("srsName")) {
            CRS.decode(node.getAttributeValue("srsName").toString());
        }
    } catch (NoSuchAuthorityCodeException e) {
        throw new WFSException("Invalid Authority Code: " + e.getAuthorityCode(), "InvalidParameterValue");
    }
    Geometry geometry = (Geometry) super.parse(instance, node, value);
    if (geometry != null) {
        //1. ensure a crs is set
        if (geometry.getUserData() == null) {
            //no crs set for the geometry, did we inherit one from a parent?
            if (crs != null) {
                geometry.setUserData(crs);
            } else {
            // for the moment we don't do anything since we miss the information
            // to infer the CRS from the feature type
            }
        }
        //2. ensure the coordinates of the geometry fall into valid space defined by crs
        CoordinateReferenceSystem crs = (CoordinateReferenceSystem) geometry.getUserData();
        if (crs != null)
            try {
                JTS.checkCoordinatesRange(geometry, crs);
            } catch (PointOutsideEnvelopeException e) {
                throw new WFSException(e, "InvalidParameterValue");
            }
    }
    return geometry;
}

@Test
public void testExecuteBuffer() throws Exception {
    String xml = "<wps:Execute service='WPS' version='1.0.0' xmlns:wps='http://www.opengis.net/wps/1.0.0' " + "xmlns:ows='http://www.opengis.net/ows/1.1'>" + "<ows:Identifier>JTS:buffer</ows:Identifier>" + "<wps:DataInputs>" + "<wps:Input>" + "<ows:Identifier>geom</ows:Identifier>" + "<wps:Data>" + "<wps:ComplexData mimeType=\"application/wkt\">" + "<![CDATA[POINT(0 0)]]>" + "</wps:ComplexData>" + "</wps:Data>" + "</wps:Input>" + "<wps:Input>" + "<ows:Identifier>distance</ows:Identifier>" + "<wps:Data>" + "<wps:LiteralData>1</wps:LiteralData>" + "</wps:Data>" + "</wps:Input>" + "<wps:Input>" + "<ows:Identifier>capStyle</ows:Identifier>" + "<wps:Data>" + "<wps:LiteralData>Round</wps:LiteralData>" + "</wps:Data>" + "</wps:Input>" + "</wps:DataInputs>" + "<wps:ResponseForm>" + "    <wps:RawDataOutput mimeType=\"application/wkt\">" + "        <ows:Identifier>result</ows:Identifier>" + "    </wps:RawDataOutput>" + "  </wps:ResponseForm>" + "</wps:Execute>";
    MockHttpServletResponse response = postAsServletResponse("wps", xml);
    // System.out.println(response.getOutputStreamContent());
    assertEquals("application/wkt", response.getContentType());
    Geometry g = new WKTReader().read(response.getOutputStreamContent());
    assertTrue(g instanceof Polygon);
}

/**
     * Creates and returns a geometry out of bounds (a point if bounds.getSpan(0) ==
     * bounds.getSpan(1) == 0D, a polygon otherwise), setting the bounds
     * {@link BoundingBox#getCoordinateReferenceSystem() CRS} as the geometry's
     * {@link Geometry#getUserData() user data}.
     * 
     * @param bounds the bounding box to build from
     * @return the newly constructed geometry
     */
public static Geometry toGeometry(final BoundingBox bounds) {
    if (bounds == null) {
        return null;
    }
    Geometry geom;
    if (bounds.getSpan(0) == 0D && bounds.getSpan(1) == 0D) {
        geom = gfac.createPoint(new Coordinate(bounds.getMinX(), bounds.getMinY()));
    } else {
        geom = JTS.toGeometry(bounds, gfac);
    }
    geom.setUserData(bounds.getCoordinateReferenceSystem());
    return geom;
}

/**
	 * @see eu.esdihumboldt.hale.io.jdbc.spatialite.internal.AbstractSpatiaLiteSupport#getGeometryType(java.lang.Object)
	 */
@Override
protected Class<? extends Geometry> getGeometryType(Object type) {
    Integer geomType = Integer.class.cast(type);
    Class<? extends Geometry> geometryClass = null;
    int geomSelector = geomType % 1000;
    switch(geomSelector) {
        case 1:
            geometryClass = Point.class;
            break;
        case 2:
            geometryClass = LineString.class;
            break;
        case 3:
            geometryClass = Polygon.class;
            break;
        case 4:
            geometryClass = MultiPoint.class;
            break;
        case 5:
            geometryClass = MultiLineString.class;
            break;
        case 6:
            geometryClass = MultiPolygon.class;
            break;
        case 7:
            geometryClass = GeometryCollection.class;
            break;
        case 0:
            geometryClass = Geometry.class;
            break;
        default:
            // should never happen
            break;
    }
    return geometryClass;
}

@Override
public void run() {
    logger.debug("starting");
    try {
        CopyManager copyManager = new CopyManager(connection);
        StringBuilder queryBuilder = new StringBuilder("copy ");
        queryBuilder.append(destination);
        queryBuilder.append(" (");
        for (int i = 0; i < columnNames.length; i++) {
            if (i != 0) {
                queryBuilder.append(", ");
            }
            queryBuilder.append(columnNames[i]);
        }
        if (columnNames.length > 0) {
            queryBuilder.append(", ");
        }
        queryBuilder.append("geometry) from stdin csv");
        CopyIn copyIn = copyManager.copyIn(queryBuilder.toString());
        CopyInOutputStream outputStream = new CopyInOutputStream(copyIn);
        Writer writer = new OutputStreamWriter(outputStream, "utf-8");
        PrintWriter printWriter = new PrintWriter(writer);
        logger.debug("database connection established");
        long featureCounter = 0;
        for (; ; ) {
            Event event = eventQueue.take();
            logger.debug("event received");
            if (event instanceof GeometryResult) {
                GeometryResult geometryResult = (GeometryResult) event;
                Geometry geometry = geometryResult.getGeometry();
                String[] columnValues = geometryResult.getColumnValues();
                for (int i = 0; i < geometry.getNumGeometries(); i++) {
                    String wkt = wktWriter.write(geometry.getGeometryN(i));
                    org.postgis.Geometry pgGeometry = PGgeometry.geomFromString(wkt);
                    pgGeometry.setSrid(28992);
                    featureCounter++;
                    for (int j = 0; j < columnValues.length; j++) {
                        if (j != 0) {
                            printWriter.print(',');
                        }
                        String columnValue = columnValues[j];
                        if (columnValue != null) {
                            printWriter.print('"');
                            printWriter.print(columnValue);
                            printWriter.print('"');
                        }
                    }
                    if (columnValues.length > 0) {
                        printWriter.print(',');
                    }
                    printWriter.print('"');
                    printWriter.print(binaryWriter.writeHexed(pgGeometry));
                    printWriter.println('"');
                }
                semaphore.release();
                logger.debug("geometry received (" + semaphore.availablePermits() + ")");
            } else if (event instanceof Finalize) {
                logger.debug("finalize event received");
                break;
            } else {
                logger.debug("Unknown event type: " + event.getClass().getCanonicalName());
            }
        }
        printWriter.close();
        logger.debug("finished: " + featureCounter + " geometries written");
        semaphore.release();
    } catch (Exception e) {
        logger.debug("couldn't write generalized geometrie", e);
    }
}

/**
     * Create a JTS Polygon form a GMLShape.
     * @param shape
     *            The shape to convert.
     * @return Polygon geometry.
     * @throws ValidationException
     */
public static Geometry shapeToPolygon(GMLShape shape) throws ValidationException {
    LineSequencer seq = new LineSequencer();
    for (GMLDirectedEdge e : shape.getEdges()) {
        Coordinate[] coord = new Coordinate[2];
        coord[0] = nodeToCoordinate(e.getStartNode());
        coord[1] = nodeToCoordinate(e.getEndNode());
        if (coord[0].equals(coord[1])) {
            throw new ValidationException(e.getEdge().getID(), "Zero length edge.");
        }
        seq.add(geomFactory.createLineString(coord));
    }
    try {
        if (!seq.isSequenceable()) {
            throw new ValidationException(shape.getID(), "Outline is not a single line.");
        }
    } catch (AssertionFailedException e) {
        throw new ValidationException(shape.getID(), "Could not get outline: " + e.getMessage());
    }
    Geometry line = seq.getSequencedLineStrings();
    CoordinateList coord = new CoordinateList(line.getCoordinates());
    coord.closeRing();
    // CHECKSTYLE:OFF:MagicNumber
    if (coord.size() < 4) {
        // CHECKSTYLE:ON:MagicNumber
        throw new ValidationException(shape.getID(), "Degenerate Shape");
    }
    Geometry ring = geomFactory.createLinearRing(coord.toCoordinateArray());
    return geomFactory.createPolygon((LinearRing) ring, null);
}

public static void main(String[] args) throws ParseException, NoSuchAuthorityCodeException, FactoryException, IOException, SchemaException, java.text.ParseException {
    String wktGeometry = "POLYGON ((-61.6866679999999974 17.0244409999999995, -61.8872220000000013 17.1052740000000014, -61.7944490000000002 17.1633299999999984, -61.6866679999999974 17.0244409999999995)) POLYGON ((-61.7291719999999984 17.6086080000000003, -61.8530579999999972 17.5830540000000006, -61.8730619999999973 17.7038879999999992, -61.7291719999999984 17.6086080000000003))";
    WKTReader wktR = new WKTReader();
    Geometry geom = wktR.read(wktGeometry);
    // write JTS to string
    GMLWriter gmlW = new GMLWriter(true);
    gmlW.setSrsName("<http://www.opengis.net/def/crs/EPSG/0/4326>");
    String gml = gmlW.write(geom);
    System.out.println(gml);
    GeometryBuilder gb = new GeometryBuilder(gml);
    WKTParser wktp = new WKTParser(gb);
    wktp.parse(wktGeometry);
}

public void load(File blockShapefile, Geometry boundary) throws IOException, FactoryException {
    System.out.println("loading " + blockShapefile.getName());
    PreparedPolygon preparedBoundary = null;
    if (boundary != null)
        preparedBoundary = new PreparedPolygon((Polygonal) boundary);
    Map map = new HashMap();
    map.put("url", blockShapefile.toURI().toURL());
    DataStore dataStore = DataStoreFinder.getDataStore(map);
    SimpleFeatureSource featureSource = dataStore.getFeatureSource(dataStore.getTypeNames()[0]);
    SimpleFeatureType schema = featureSource.getSchema();
    CoordinateReferenceSystem shpCRS = schema.getCoordinateReferenceSystem();
    MathTransform transform = CRS.findMathTransform(shpCRS, wgsCRS, true);
    SimpleFeatureCollection collection = featureSource.getFeatures();
    SimpleFeatureIterator iterator = collection.features();
    Integer skippedFeatures = 0;
    Integer clipedFeatures = 0;
    try {
        while (iterator.hasNext()) {
            try {
                SimpleFeature feature = iterator.next();
                String geoId = (String) feature.getAttribute("GEOID10");
                Long areaLand = (Long) feature.getAttribute("ALAND10");
                Long areaWater = (Long) feature.getAttribute("AWATER10");
                Double percentLand = (double) (areaLand / (areaLand + areaWater));
                Geometry geom = JTS.transform((Geometry) feature.getDefaultGeometry(), transform);
                Point centroid = geom.getCentroid();
                if (preparedBoundary == null || (preparedBoundary.contains(centroid)))
                    lodesBlocks.put(geoId, new IndicatorItem(geoId, geom, percentLand));
                else
                    clipedFeatures++;
            } catch (Exception e) {
                skippedFeatures++;
                System.out.println(e.toString());
                continue;
            }
        }
    } finally {
        iterator.close();
    }
    dataStore.dispose();
    System.out.println("Features imported: " + lodesBlocks.size() + "(" + skippedFeatures + " skipped, " + clipedFeatures + " outside survey area)");
}

private static GeometryCollection geometryCollectionFromVertices(Graph graph) {
    GeometryFactory gf = GeometryUtils.getGeometryFactory();
    Collection<Vertex> vertices = graph.getVertices();
    Geometry[] points = new Geometry[vertices.size()];
    int i = 0;
    for (Vertex v : vertices) {
        points[i++] = gf.createPoint(v.getCoordinate());
    }
    GeometryCollection geometries = new GeometryCollection(points, gf);
    return geometries;
}

public static Gson createFeatureGson() {
    Type resourceListType = new TypeToken<List<Resource>>() {
    }.getType();
    Type attributeListType = new TypeToken<List<Attribute>>() {
    }.getType();
    return new GsonBuilder().disableHtmlEscaping().registerTypeAdapter(// GeoStore compliant typeAdapter
    resourceListType, new GeoStoreResourceTypeAdapter()).registerTypeAdapter(attributeListType, new GeoStoreAttributeTypeAdapter()).registerTypeHierarchyAdapter(// GeoJson serializer/deserializer
    Geometry.class, new GeometryJsonSerializer()).registerTypeHierarchyAdapter(Geometry.class, new GeometryJsonDeserializer()).create();
}

public BooleanWritable evaluate(Text geometryAsWKT, Double latitude, Double longitude) {
    isContained.set(false);
    try {
        // sanitize the input
        if (geometryAsWKT == null || latitude == null || longitude == null || latitude > 90 || latitude < -90 || longitude > 180 || longitude < -180) {
            return isContained;
        }
        String geoWKTStr = geometryAsWKT.toString();
        Geometry geom = geometryCache.get(geoWKTStr);
        if (geom == null) {
            geom = wktReader.read(geoWKTStr);
            geometryCache.put(geoWKTStr, geom);
        }
        // support any geometry - up to the user to make a sensible query
        Geometry point = geometryFactory.createPoint(new Coordinate(longitude, latitude));
        isContained.set(geom.contains(point));
    } catch (ParseException e) {
        LOG.error("Invalid geometry received: {}", geometryAsWKT.toString(), e);
    } catch (Exception e) {
        LOG.error("Error applying UDF", e);
    }
    return isContained;
}

@Test
public void noIntersection() throws Exception {
    String kml = Tests.getKml("multipolygon.kml");
    KmlFeature feature = KmlFeature.parse(kml);
    Geometry multi = feature.geometry;
    Geometry noIntersect = Tests.createPolygon(COORDS_NO_INTERSECT);
    double area = multi.intersection(noIntersect).getArea();
    Assert.assertEquals(0d, area, 0d);
}

@Override
public String resolve(double x, double y) {
    System.out.println("x=" + x + ", y=" + y);
    FeatureIterator<Feature> iterator = collection.features();
    while (iterator.hasNext()) {
        SimpleFeature feature = (SimpleFeature) iterator.next();
        Geometry geom = (Geometry) feature.getDefaultGeometry();
        GeometryFactory geometryFactory = JTSFactoryFinder.getGeometryFactory();
        Coordinate coord = new Coordinate(x, y);
        Point point = geometryFactory.createPoint(coord);
        //System.out.println("checking "+point.toString());
        if (geom.contains(point)) {
            return feature.getAttribute(this.nameField).toString();
        }
    }
    return null;
}

@Override
public String resolve(double x, double y) {
    System.out.println("x=" + x + ", y=" + y);
    FeatureIterator<Feature> iterator = collection.features();
    while (iterator.hasNext()) {
        SimpleFeature feature = (SimpleFeature) iterator.next();
        Geometry geom = (Geometry) feature.getDefaultGeometry();
        GeometryFactory geometryFactory = JTSFactoryFinder.getGeometryFactory();
        Coordinate coord = new Coordinate(x, y);
        Point point = geometryFactory.createPoint(coord);
        //System.out.println("checking "+point.toString());
        if (geom.contains(point)) {
            return feature.getAttribute(this.nameField).toString();
        }
    }
    return null;
}

@Override
public <T> String encode(T object) throws EncodeException {
    if (object instanceof Geometry) {
        GeoJtsConverter converter = new GeoJtsConverter();
        GeoObject geo = converter.fromJts((Geometry) object);
        GeoJsonEncoder encoder = GeoJsonEncoder.create();
        return encoder.encode(geo);
    } else {
        throw new EncodeException("Cannot encode " + object.getClass().getSimpleName() + " as GeoJSON");
    }
}

Geometry randomGeometry(int points) {
    //a circle
    JtsSpatialContext ctx = (JtsSpatialContext) super.ctx;
    GeometricShapeFactory gsf = new GeometricShapeFactory(ctx.getGeometryFactory());
    gsf.setCentre(new Coordinate(0, 0));
    //diameter
    gsf.setSize(180);
    gsf.setNumPoints(points);
    return gsf.createCircle();
}

/**
	 * Check the target geometry compatibility for dissolve operation.
	 * 
	 * @return
	 */
@Override
public boolean validGeometryCompatible(ILayer sourceLayer) {
    SimpleFeatureType sourceType = sourceLayer.getSchema();
    GeometryDescriptor firstGeomAttr = sourceType.getGeometryDescriptor();
    Class<? extends Geometry> sourceGeomClass = (Class<? extends Geometry>) firstGeomAttr.getType().getBinding();
    Class<? extends Geometry> targetGeomClass = null;
    if (targetLayer != null) {
        SimpleFeatureType targetType = targetLayer.getSchema();
        GeometryDescriptor secondGeomAttr = targetType.getGeometryDescriptor();
        targetGeomClass = (Class<? extends Geometry>) secondGeomAttr.getType().getBinding();
    } else {
        targetGeomClass = this.targetGeometryClass;
    }
    if (targetGeomClass.equals(Geometry.class)) {
        return true;
    }
    if ((sourceGeomClass.equals(Polygon.class) || sourceGeomClass.equals(MultiPolygon.class)) && (!targetGeomClass.equals(Polygon.class) && !targetGeomClass.equals(MultiPolygon.class))) {
        return false;
    }
    if ((sourceGeomClass.equals(LineString.class) || sourceGeomClass.equals(MultiLineString.class)) && (!targetGeomClass.equals(LineString.class) && !targetGeomClass.equals(MultiLineString.class))) {
        return false;
    }
    if ((sourceGeomClass.equals(Point.class) || sourceGeomClass.equals(MultiPoint.class)) && (!targetGeomClass.equals(Point.class) && !targetGeomClass.equals(MultiPoint.class))) {
        return false;
    }
    return true;
}

protected void addPolygon(Task t, Geometry g, MeshBucket ml, LineBucket ll) {
    mGeom.clear();
    mGeom.startPolygon();
    CoordinatePath p = CoordinatePath.create(g);
    if (mMinX > 0 || mMinY > 0)
        p.generalize(mMinX, mMinY);
    if (transformPath(t.position, mGeom, p) < 3)
        return;
    if (!mClipper.clip(mGeom))
        return;
    mSimpVW.simplify(mGeom, 0.1f);
    mSimpDP.simplify(mGeom, 0.5f);
    ll.addLine(mGeom);
    ml.addMesh(mGeom);
}

public static GeometryElement marshalFrom(Attribute attribute) throws CatalogTransformerException {
    GeometryElement element = new GeometryElement();
    element.setName(attribute.getName());
    if (attribute.getValue() != null) {
        for (Serializable value : attribute.getValues()) {
            if (!(value instanceof String)) {
                continue;
            }
            String wkt = (String) value;
            WKTReader wktReader = new WKTReader(geometryFactory);
            Geometry jtsGeometry = null;
            try {
                jtsGeometry = wktReader.read(wkt);
            } catch (ParseException e) {
                throw new CatalogTransformerException("Could not transform Metacard to XML.  Invalid WKT.", e);
            }
            JTSToGML311GeometryConverter converter = new JTSToGML311GeometryConverter();
            @SuppressWarnings("unchecked") JAXBElement<AbstractGeometryType> gmlElement = (JAXBElement<AbstractGeometryType>) converter.createElement(jtsGeometry);
            GeometryElement.Value geoValue = new GeometryElement.Value();
            geoValue.setGeometry(gmlElement);
            ((GeometryElement) element).getValue().add(geoValue);
        }
    }
    return element;
}

public static com.vividsolutions.jts.geom.Geometry getGeometry(PositionType position) {
    Geometry g = null;
    if (position.getPoint() != null) {
        if (position.getPoint().getCoord() != null && position.getPoint().getCoord().getX() != null) {
            g = geomFact.createPoint(new Coordinate(position.getPoint().getCoord().getX().doubleValue(), position.getPoint().getCoord().getY().doubleValue()));
        } else if (position.getPoint().getPos() != null && position.getPoint().getPos().getValue() != null && position.getPoint().getPos().getValue().size() == 2) {
            g = geomFact.createPoint(new Coordinate(position.getPoint().getPos().getValue().get(0), position.getPoint().getPos().getValue().get(1)));
        }
    } else if (position.getPolygon() != null) {
        PolygonType polygon = position.getPolygon();
        List<LinearRing> interiorRings = new LinkedList<LinearRing>();
        polygon.getInterior();
        // TODO
        LinearRing[] holes = interiorRings.toArray(new LinearRing[] {});
        List<Coordinate> coordinateList = new LinkedList<Coordinate>();
        AbstractRingPropertyType exterior = polygon.getExterior().getValue();
        LinearRingType ring = (LinearRingType) exterior.getRing().getValue();
        for (CoordType coord : ring.getCoord()) {
            coordinateList.add(new Coordinate(coord.getX().doubleValue(), coord.getY().doubleValue()));
        }
        Coordinate[] coordinates = coordinateList.toArray(new Coordinate[] {});
        LinearRing shell = geomFact.createLinearRing(coordinates);
        g = geomFact.createPolygon(shell, holes);
    }
    return g;
}

public static void read(final URL input, GeomVectorField field, final Bag masked) throws FileNotFoundException {
    try {
        Map<String, Serializable> connectParameters = new HashMap<String, Serializable>();
        connectParameters.put("url", input);
        DataStore dataStore = DataStoreFinder.getDataStore(connectParameters);
        // we are now connected
        String[] typeNames = dataStore.getTypeNames();
        String typeName = typeNames[0];
        FeatureSource<SimpleFeatureType, SimpleFeature> featureSource;
        FeatureCollection<SimpleFeatureType, SimpleFeature> collection;
        FeatureIterator<SimpleFeature> iterator;
        featureSource = dataStore.getFeatureSource(typeName);
        collection = featureSource.getFeatures();
        iterator = collection.features();
        try {
            while (iterator.hasNext()) {
                SimpleFeature feature = iterator.next();
                Geometry geometry = (Geometry) feature.getDefaultGeometry();
                MasonGeometry mg = new MasonGeometry(geometry);
                mg.addAttributes(readAttributes(feature, masked));
                field.addGeometry(mg);
            }
        } finally {
            if (iterator != null) {
                iterator.close();
            }
        }
    } catch (Exception e) {
        System.out.println("Exception in GeoToolsImportor::ingest:");
        e.printStackTrace();
    }
}

/**
     * Returns the {@link JtsGeometry} represented by the specified WKT text.
     *
     * @param context the JTS spatial context
     * @param string the WKT text
     * @return the parsed geometry
     */
public static JtsGeometry geometryFromWKT(JtsSpatialContext context, String string) {
    if (StringUtils.isBlank(string)) {
        throw new IndexException("Shape shouldn't be blank");
    }
    try {
        GeometryFactory geometryFactory = context.getGeometryFactory();
        WKTReader reader = new WKTReader(geometryFactory);
        Geometry geometry = reader.read(string);
        return context.makeShape(geometry);
    } catch (ParseExceptionIllegalArgumentException |  e) {
        throw new IndexException(e, "Shape '%s' is not parseable", string);
    }
}

@Override
public Icon getLeafObjectNodeIcon(final ObjectTreeNode otn) {
    try {
        final CidsBean bean = otn.getMetaObject().getBean();
        final Geometry geom = (Geometry) bean.getProperty("area.geo_field");
        final Envelope env = geom.getEnvelopeInternal();
        final double scale = Math.min(16 / env.getWidth(), 16 / env.getHeight());
        final double xoff = 0 - (scale * env.getMinX());
        final double yoff = env.getMaxY() * scale;
        final AffineTransform at = new AffineTransform(scale, 0, 0, -scale, xoff, yoff);
        final LiteShape shape = new LiteShape(geom, at, false);
        final int dw = (int) Math.ceil(geom.getEnvelopeInternal().getWidth() * scale);
        final int dh = (int) Math.ceil(geom.getEnvelopeInternal().getHeight() * scale);
        final BufferedImage biShape = new BufferedImage(dw, dh, BufferedImage.TYPE_INT_ARGB);
        final Graphics2D g2dShape = (Graphics2D) biShape.getGraphics();
        final Paint paint = new Color(153, 153, 255);
        g2dShape.setPaint(paint);
        g2dShape.fill(shape);
        g2dShape.setPaint(Color.BLACK);
        g2dShape.draw(shape);
        final BufferedImage bi = new BufferedImage(16, 16, BufferedImage.TYPE_INT_ARGB);
        final Graphics2D g2d = (Graphics2D) bi.getGraphics();
        final int x = (bi.getWidth() - biShape.getWidth()) / 2;
        final int y = (bi.getHeight() - biShape.getHeight()) / 2;
        g2d.drawImage(biShape, x, y, null);
        return new ImageIcon(bi);
    } catch (final Exception e) {
        LOG.error("cannot create catchment area icon", e);
        return null;
    }
}

@Override
public Object visit(final Literal expression, final Object extraData) {
    Object obj = expression.getValue();
    try {
        if (obj instanceof BoundingBox) {
            BoundingBox bbox = (BoundingBox) obj;
            if (CRS.equalsIgnoreMetadata(bbox.getCoordinateReferenceSystem(), baseCrs)) {
                final Envelope e = CRS.transform(bbox, replacementCrs);
                final BoundingBox rbbox = new DefaultBoundingBox(replacementCrs);
                rbbox.setBounds(new DefaultBoundingBox(e));
                obj = rbbox;
            }
        } else if (obj instanceof Geometry) {
            Geometry geo = (Geometry) obj;
            geo = (Geometry) geo.clone();
            final CoordinateReferenceSystem geoCrs = JTS.findCoordinateReferenceSystem(geo);
            if (geoCrs == null) {
                JTS.setCRS(geo, replacementCrs);
            } else if (CRS.equalsIgnoreMetadata(geoCrs, baseCrs)) {
                geo = JTS.transform(geo, CRS.findMathTransform(baseCrs, replacementCrs));
                JTS.setCRS(geo, replacementCrs);
            }
            obj = geo;
        }
    } catch (FactoryExceptionTransformException |  ex) {
        Logging.getLogger("org.constellation.wfs.ws").log(Level.SEVERE, null, ex);
    }
    return getFactory(extraData).literal(obj);
}

public Coordinate[] edit(Coordinate[] coordinates, Geometry geom) {
    if (coordinates.length == 0)
        return null;
    Coordinate[] reducedCoords = new Coordinate[coordinates.length];
    // copy coordinates and reduce
    for (int i = 0; i < coordinates.length; i++) {
        Coordinate coord = new Coordinate(coordinates[i]);
        targetPM.makePrecise(coord);
        reducedCoords[i] = coord;
    }
    // remove repeated points, to simplify returned geometry as much as possible
    CoordinateList noRepeatedCoordList = new CoordinateList(reducedCoords, false);
    Coordinate[] noRepeatedCoords = noRepeatedCoordList.toCoordinateArray();
    /**
		 * Check to see if the removal of repeated points collapsed the coordinate
		 * List to an invalid length for the type of the parent geometry. It is not
		 * necessary to check for Point collapses, since the coordinate list can
		 * never collapse to less than one point. If the length is invalid, return
		 * the full-length coordinate array first computed, or null if collapses are
		 * being removed. (This may create an invalid geometry - the client must
		 * handle this.)
		 */
    int minLength = 0;
    if (geom instanceof LineString)
        minLength = 2;
    if (geom instanceof LinearRing)
        minLength = 4;
    Coordinate[] collapsedCoords = reducedCoords;
    if (removeCollapsed)
        collapsedCoords = null;
    // return null or orginal length coordinate array
    if (noRepeatedCoords.length < minLength) {
        return collapsedCoords;
    }
    // ok to return shorter coordinate array
    return noRepeatedCoords;
}

@Override
public Map toJsonMap() {
    Map map = new HashMap();
    if (TYPE.equals(getGeometry().getGeometryType())) {
        map.put(TYPE_KEY, TYPE);
        List<List> listOfPolygons = new ArrayList<List>();
        for (int i = 0; i < getGeometry().getNumGeometries(); i++) {
            List polygon = buildJsonPolygon((com.vividsolutions.jts.geom.Polygon) getGeometry().getGeometryN(i));
            listOfPolygons.add(polygon);
        }
        map.put(COORDINATES_KEY, listOfPolygons);
    } else {
        throw new UnsupportedOperationException("Geometry is not a " + TYPE);
    }
    return map;
}

/**
	 *
	 */
@Test
public final void testCompareGeography() throws Exception {
    List<Geometry> list = new ArrayList<Geometry>();
    list.add(Location.EUROPE.getEnvelope());
    list.add(Location.AFRICA.getEnvelope());
    list.add(Location.CHINA.getEnvelope());
    list.add(Location.MACARONESIA.getEnvelope());
    list.add(Location.EASTERN_CANADA.getEnvelope());
    list.add(Location.FRA.getEnvelope());
    list.add(Location.ABT.getEnvelope());
    list.add(Location.GRB.getEnvelope());
    list.add(Location.IRE.getEnvelope());
    list.add(Location.ALG.getEnvelope());
    GeometryCollection geometryCollection = new GeometryCollection(list.toArray(new Geometry[list.size()]), new GeometryFactory());
    Coordinate[] envelope = geometryCollection.getEnvelope().getCoordinates();
    for (Coordinate c : envelope) {
        logger.debug(Math.round(c.x) + " " + Math.round(c.y));
    }
}

public static Geometry parseGeometry(JSONObject geom) {
    if (geom != null) {
        String type = geom.optString("type").toLowerCase();
        JSONArray coords = geom.getJSONArray("coordinates");
        switch(type) {
            case "point":
                return factory.createPoint(new Coordinate(coords.getDouble(0), coords.getDouble(1)));
            case "linestring":
                return getLineStringGeometry(coords);
            case "polygon":
                return getPolygonGeometry(coords);
            case "multipolygon":
                return getMultiPolygonGeometry(coords);
        }
    }
    return null;
}

/*
     * (non-Javadoc) @see javax.xml.bind.annotation.adapters.XmlAdapter#unmarshal(java.lang.Object)
     */
@Override
public MultiPolygon unmarshal(String val) throws ParseException {
    WKTReader wktReader = new WKTReader();
    Geometry the_geom = wktReader.read(val);
    if (the_geom.getSRID() == 0) {
        the_geom.setSRID(4326);
    }
    try {
        return (MultiPolygon) the_geom;
    } catch (ClassCastException e) {
        throw new ParseException("WKT val is a " + the_geom.getClass().getName());
    }
}

@Override
public <T> BooleanBuilder createPredicateByAnd(PathBuilder<T> entity, Map<String, Object> searchArgs) {
    BooleanBuilder predicate = super.createPredicateByAnd(entity, searchArgs);
    if (searchArgs == null || searchArgs.isEmpty()) {
        return predicate;
    }
    // Build the predicate
    for (Entry<String, Object> entry : searchArgs.entrySet()) {
        String key = entry.getKey();
        // searchArgs can contain dtt_bbox attribute
        if (key.equals(DatatablesUtilsBeanGeoImpl.BOUNDING_BOX_PARAM)) {
            // Getting bbox to Search
            String bBoxToSearch = ((String[]) entry.getValue())[0];
            Geometry bBoxGeometry = null;
            try {
                bBoxGeometry = getConversionService().convert(bBoxToSearch, Geometry.class);
            } catch (Exception e) {
                try {
                    bBoxGeometry = getConversionService().convert(String.format("POLYGON((%s))", bBoxToSearch), Geometry.class);
                } catch (Exception e1) {
                    throw new RuntimeException(String.format("Error getting map Bounding Box on QuerydslUtils from string: '%s'", bBoxToSearch), e);
                }
            }
            // Getting fields to filter using bbox
            if (searchArgs.get(DatatablesUtilsBeanGeoImpl.BOUNDING_BOX_FIELDS_PARAM) != null && bBoxGeometry != null) {
                String bBoxFields = ((String[]) searchArgs.get(DatatablesUtilsBeanGeoImpl.BOUNDING_BOX_FIELDS_PARAM))[0];
                String[] separatedFields = StringUtils.split(bBoxFields, ",");
                for (String field : separatedFields) {
                    predicate.or(createIntersectsExpression(entity, field, bBoxGeometry));
                }
            }
        }
    }
    return predicate;
}

@Override
public Geometry getGeometry(int columnIndex) throws SQLException {
    Object field = getObject(columnIndex);
    if (field == null) {
        return (Geometry) field;
    }
    if (field instanceof Geometry) {
        return (Geometry) field;
    } else {
        throw new SQLException("The column " + getMetaData().getColumnName(columnIndex) + " is not a Geometry");
    }
}

public void testVectorTransformer() throws Exception {
    SimpleFeatureTypeBuilder b = new SimpleFeatureTypeBuilder();
    b.setName("test");
    b.setCRS(DefaultGeographicCRS.WGS84);
    b.add("the_geom", Point.class);
    b.add("id", Integer.class);
    DefaultFeatureCollection newCollection = new DefaultFeatureCollection();
    SimpleFeatureType type = b.buildFeatureType();
    SimpleFeatureBuilder builder = new SimpleFeatureBuilder(type);
    Point point = GeometryUtilities.gf().createPoint(new Coordinate(0, 0));
    Object[] values = new Object[] { point, 1 };
    builder.addAll(values);
    SimpleFeature feature = builder.buildFeature(type.getTypeName() + ".0");
    newCollection.add(feature);
    OmsVectorTransformer transformer = new OmsVectorTransformer();
    transformer.inVector = newCollection;
    transformer.pTransX = 1.0;
    transformer.pTransY = -1.0;
    transformer.process();
    SimpleFeatureCollection outFeatures = transformer.outVector;
    Geometry g = FeatureUtilities.featureCollectionToGeometriesList(outFeatures, false, null).get(0);
    Coordinate coord = g.getCoordinate();
    assertEquals(coord.x, 1.0, 0.00001);
    assertEquals(coord.y, -1.0, 0.00001);
}

/**
   * The score is a linear function of the symmetric difference: 1 if the shapes perfectly
   * overlap; 0 if the shapes do not overlap at all.
   * @param target the feature to match
   * @param candidate the feature to compare with the target
   * @return candidates with a score greater than 0 (typically all the candidates).
   */
public double match(Geometry target, Geometry candidate) {
    Geometry targetGeom = (Geometry) target.clone();
    Geometry candidateGeom = (Geometry) candidate.clone();
    if (targetGeom.isEmpty() || candidateGeom.isEmpty()) {
        //avoid div by 0 in centre-of-mass calc [Jon Aquino]
        return 0;
    }
    return MatcherUtil.toScoreFromSymDiffArea(targetGeom.getArea(), candidateGeom.getArea(), targetGeom.symDifference(candidateGeom).getArea());
}

@Override
public Style load(final MfClientHttpRequestFactory requestFactory, final FeatureSource featureSource) {
    if (featureSource == null) {
        throw new IllegalArgumentException("Feature source cannot be null");
    }
    String geomType = Geometry.class.getSimpleName().toLowerCase();
    if (featureSource.getSchema() != null) {
        geomType = featureSource.getSchema().getGeometryDescriptor().getType().getBinding().getSimpleName();
    }
    String styleRef = styleString;
    if (styleRef == null) {
        styleRef = geomType;
    }
    final StyleParser styleParser = AbstractFeatureSourceLayerPlugin.this.parser;
    return template.getStyle(styleRef).or(styleParser.loadStyle(template.getConfiguration(), requestFactory, styleRef)).or(template.getConfiguration().getDefaultStyle(geomType));
}

@Override
public KmlItem buildKmlItem() throws SQLException {
    logger.info("Preparing visualizations: " + this.getClass().getSimpleName());
    TimeKmlItem kmlItem;
    if (interpolated)
        kmlItem = getInterpolatedTimeKmlItem();
    else
        kmlItem = getNonInterpolatedTimeKmlItem();
    String sql = "SELECT " + " * FROM " + schemaName + "." + tableName + " " + whereClause + " ORDER BY from_time";
    ResultSet resultSet = connection.executeQueryWithFetchSize(sql, 10000);
    while (resultSet.next()) {
        String id = getRecordId(resultSet);
        Geometry geom = getGeometry(resultSet, "geom");
        Timestamp timestamp = resultSet.getTimestamp("from_time");
        kmlItem.addTimeGeometry(id, convertJTSCoordinatesToKmlCoordinates(geom.getCoordinates()), timestamp.getTime(), descriptionFactory.createDescription(resultSet));
    }
    //logger.info(this.getClass().getSimpleName()+" finishes building.");
    return kmlItem;
}

@RequestMapping()
public ModelAndView index() {
    GeometryFactory gf = new GeometryFactory();
    List<Polygon> polygons = new ArrayList<Polygon>();
    Map<String, CoordinateBounds> agencies = _agencyService.getAgencyIdsAndCoverageAreas();
    for (CoordinateBounds cb : agencies.values()) {
        Envelope e = new Envelope(cb.getMinLon(), cb.getMaxLon(), cb.getMinLat(), cb.getMaxLat());
        Polygon p = (Polygon) gf.toGeometry(e);
        polygons.add(p);
    }
    MultiPolygon mp = gf.createMultiPolygon(polygons.toArray(new Polygon[0]));
    Geometry hull = mp.convexHull();
    Envelope env = hull.getEnvelopeInternal();
    ModelAndView mv = new ModelAndView("bounding-box.jspx");
    mv.addObject("minY", env.getMinY());
    mv.addObject("minX", env.getMinX());
    mv.addObject("maxY", env.getMaxY());
    mv.addObject("maxX", env.getMaxX());
    mv.addObject("hullWKT", hull.toText());
    return mv;
}

/**
	 * takes a polygon outline, "subtracts" a collection of other polygon outlines,
	 * and returns a collection of polygons that covers the difference area.
	 * 
	 * The result polygons should cover the area that was
	 * within the original polygon (excluding its holes),
	 * but not within a subtracted polygon.
	 * 
	 * @return
	 * 	 polygons without self-intersections, but maybe with holes
	 */
public static final Collection<PolygonWithHolesXZ> subtractPolygons(SimplePolygonXZ basePolygon, List<? extends SimplePolygonXZ> subtractPolygons) {
    List<Geometry> remainingGeometry = Collections.singletonList((Geometry) polygonXZToJTSPolygon(basePolygon));
    for (SimplePolygonXZ subtractPolygon : subtractPolygons) {
        Polygon jtsSubtractPolygon = polygonXZToJTSPolygon(subtractPolygon);
        if (!jtsSubtractPolygon.isValid())
            continue;
        List<Geometry> newRemainingGeometry = new ArrayList<Geometry>(1);
        for (Geometry g : remainingGeometry) {
            Geometry newG = g.difference(jtsSubtractPolygon);
            if (newG instanceof GeometryCollection) {
                for (int i = 0; i < ((GeometryCollection) newG).getNumGeometries(); i++) {
                    newRemainingGeometry.add(((GeometryCollection) newG).getGeometryN(i));
                }
            } else {
                newRemainingGeometry.add(newG);
            }
        }
        remainingGeometry = newRemainingGeometry;
    }
    Collection<PolygonWithHolesXZ> result = new ArrayList<PolygonWithHolesXZ>();
    for (Geometry g : remainingGeometry) {
        result.addAll(polygonsXZFromJTSGeometry(g));
    }
    return result;
}

@Test
public void testUpdatePointDataSource() throws Exception {
    final BindingContext bindingContext = new BindingContext();
    bindingContext.getPropertySet().addProperties(Property.create("pointDataSource", VectorDataNode.class));
    bindingContext.getPropertySet().addProperties(Property.create("dataField", AttributeDescriptor.class));
    final CorrelativeFieldSelector correlativeFieldSelector = new CorrelativeFieldSelector(bindingContext);
    final Product product = new Product("name", "type", 10, 10);
    product.getVectorDataGroup().add(new VectorDataNode("a", createFeatureType(Geometry.class)));
    product.getVectorDataGroup().add(new VectorDataNode("b", createFeatureType(Point.class)));
    assertEquals(0, correlativeFieldSelector.pointDataSourceList.getItemCount());
    assertEquals(0, correlativeFieldSelector.dataFieldList.getItemCount());
    correlativeFieldSelector.updatePointDataSource(product);
    assertEquals(3, correlativeFieldSelector.pointDataSourceList.getItemCount());
    assertEquals(0, correlativeFieldSelector.dataFieldList.getItemCount());
    correlativeFieldSelector.pointDataSourceProperty.setValue(product.getVectorDataGroup().get("b"));
    assertEquals(3, correlativeFieldSelector.dataFieldList.getItemCount());
}

@Test
public final void should_have_SpatialFilteringProfileParameter() throws OwsExceptionReport {
    OmObservation omObservation = new OmObservation();
    NamedValue<Geometry> namedValue = new NamedValue<Geometry>();
    namedValue.setName(new ReferenceType(OmConstants.PARAM_NAME_SAMPLING_GEOMETRY));
    namedValue.setValue(new GeometryValue(JTSHelper.createGeometryFromWKT("POINT (34.5 76.4)", Constants.EPSG_WGS84)));
    // test no parameter is set
    assertFalse(omObservation.isSetParameter());
    assertFalse(omObservation.isSetSpatialFilteringProfileParameter());
    omObservation.addParameter(namedValue);
    // test with set SpatialFilteringProfile parameter
    assertTrue(omObservation.isSetParameter());
    assertTrue(omObservation.isSetSpatialFilteringProfileParameter());
    assertThat(omObservation.getSpatialFilteringProfileParameter(), is(equalTo(namedValue)));
}

@Override
protected void doEvaluate(TExecutionContext context, LazyList<? extends ValueSource> inputs, ValueTarget output) {
    String wkt = inputs.get(0).getString();
    WKTReader reader = (WKTReader) context.preptimeObjectAt(READER_CONTEXT_POS);
    try {
        Geometry geometry = reader.read(wkt);
        output.putObject(geometry);
    } catch (ParseException e) {
        throw new InvalidSpatialObjectException(e.getMessage());
    }
}

private LatLon findCenterPoint() {
    try {
        Geometry geom = JTSConst.toGeometry(this);
        if (!geom.isValid())
            return null;
        if (geom instanceof Polygonal) {
            return JTSConst.toLatLon(geom.getInteriorPoint());
        } else if (geom instanceof Lineal) {
            LengthIndexedLine lil = new LengthIndexedLine(geom);
            return JTSConst.toLatLon(lil.extractPoint(geom.getLength() / 2.0));
        }
    } catch (IllegalArgumentException e) {
        return null;
    }
    return null;
}

private LatLon findCenterPoint() {
    try {
        Geometry geom = JTSConst.toGeometry(this);
        if (!geom.isValid())
            return null;
        if (geom instanceof Polygonal) {
            return JTSConst.toLatLon(geom.getInteriorPoint());
        } else if (geom instanceof Lineal) {
            LengthIndexedLine lil = new LengthIndexedLine(geom);
            return JTSConst.toLatLon(lil.extractPoint(geom.getLength() / 2.0));
        }
    } catch (IllegalArgumentException e) {
        return null;
    }
    return null;
}

public static Polygon get(Geometry geom, GeometryFactory gf) {
    Geometry hull_ = (new ConvexHull(geom)).getConvexHull();
    if (!(hull_ instanceof Polygon))
        return null;
    Polygon convHull = (Polygon) hull_;
    Coordinate c = geom.getCentroid().getCoordinate();
    Coordinate[] coords = convHull.getExteriorRing().getCoordinates();
    double minArea = Double.MAX_VALUE, minAngle = 0.0;
    Polygon ssr = null;
    Coordinate ci = coords[0], cii;
    for (int i = 0; i < coords.length - 1; i++) {
        cii = coords[i + 1];
        double angle = Math.atan2(cii.y - ci.y, cii.x - ci.x);
        Polygon rect = (Polygon) Rotation.get(convHull, c, -1.0 * angle, gf).getEnvelope();
        double area = rect.getArea();
        if (area < minArea) {
            minArea = area;
            ssr = rect;
            minAngle = angle;
        }
        ci = cii;
    }
    return Rotation.get(ssr, c, minAngle, gf);
}

/**
	 * @throws RuntimeException
	 *             if an error occurs while writing the stream to disk or
	 *             unzipping the written file
	 * @see org.n52.wps.io.IParser#parse(java.io.InputStream)
	 */
@Override
public GTVectorDataBinding parse(InputStream stream, String mimeType, String schema) {
    try {
        String fileName = "tempfile" + UUID.randomUUID() + ".zip";
        String tmpDirPath = System.getProperty("java.io.tmpdir");
        File tempFile = new File(tmpDirPath + File.separatorChar + fileName);
        // mark tempFile for final delete
        finalizeFiles.add(tempFile);
        try {
            FileOutputStream outputStream = new FileOutputStream(tempFile);
            byte buf[] = new byte[4096];
            int len;
            while ((len = stream.read(buf)) > 0) {
                outputStream.write(buf, 0, len);
            }
            outputStream.close();
            stream.close();
        } catch (FileNotFoundException e) {
            System.gc();
            LOGGER.error(e.getMessage(), e);
            throw new RuntimeException(e);
        } catch (IOException e) {
            LOGGER.error(e.getMessage(), e);
            System.gc();
            throw new RuntimeException(e);
        }
        // mark for final delete
        finalizeFiles.add(tempFile);
        stream.close();
        List<File> wktFiles = IOUtils.unzip(tempFile, "wkt");
        // mark for final delete
        finalizeFiles.addAll(wktFiles);
        if (wktFiles == null || wktFiles.size() == 0) {
            throw new RuntimeException("Cannot find a shapefile inside the zipped file.");
        }
        //set namespace namespace
        List<Geometry> geometries = new ArrayList<Geometry>();
        //please not that only 1 geometry is returned. If multiple geometries are included, perhaps use the read(String wktstring) method
        for (int i = 0; i < wktFiles.size(); i++) {
            File wktFile = wktFiles.get(i);
            Reader fileReader = new FileReader(wktFile);
            WKTReader2 wktReader = new WKTReader2();
            com.vividsolutions.jts.geom.Geometry geometry = wktReader.read(fileReader);
            geometries.add(geometry);
        }
        CoordinateReferenceSystem coordinateReferenceSystem = CRS.decode("EPSG:4326");
        SimpleFeatureCollection inputFeatureCollection = createFeatureCollection(geometries, coordinateReferenceSystem);
        return new GTVectorDataBinding(inputFeatureCollection);
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
        throw new RuntimeException("An error has occurred while accessing provided data", e);
    } catch (ParseException e) {
        LOGGER.error(e.getMessage(), e);
        throw new RuntimeException("An error has occurred while accessing provided data", e);
    } catch (NoSuchAuthorityCodeException e) {
        LOGGER.error(e.getMessage(), e);
        throw new RuntimeException("An error has occurred while accessing provided data", e);
    } catch (FactoryException e) {
        LOGGER.error(e.getMessage(), e);
        throw new RuntimeException("An error has occurred while accessing provided data", e);
    }
}

@Test
public void NoShapeDoubleShapeTest() {
    PointSequence points = PointCollectionFactory.create(new double[] { 8, 9, 9, 10, 10, 11 }, DimensionalFlag.d2D, CrsId.UNDEFINED);
    LineString shape2 = new LineString(points);
    points = PointCollectionFactory.create(new double[] { 5, 6, 6, 7, 7, 8 }, DimensionalFlag.d2D, CrsId.UNDEFINED);
    LineString shape = new LineString(points);
    Object noShape = new TestFeatureNoShape("Antwerpen", 128, new String[] { "Belgium", "Flanders" }, 5, "sub", "subsub");
    Object doubleShape = new TestFeatureDoubleShape("Antwerpen", 128, new String[] { "Belgium", "Flanders" }, shape, 5, shape2, "sub");
    reader = EntityClassReader.getClassReaderFor(noShape.getClass());
    try {
        Geometry test = reader.getGeometry(noShape);
        Assert.assertNull(test);
    } catch (InvalidObjectReaderException e) {
        Assert.fail("No Exception should be thrown when no one geometry is present");
    }
    reader = EntityClassReader.getClassReaderFor(doubleShape.getClass());
    try {
        Geometry geom = reader.getGeometry(doubleShape);
        Assert.assertTrue(geom == shape2 || geom == shape);
    } catch (InvalidObjectReaderException e) {
        Assert.fail("No Exception should be thrown when more than one geometry is present");
    }
}

@Override
public void marshal(Object value, HierarchicalStreamWriter writer, MarshallingContext context) {
    Geometry geometry = (Geometry) value;
    GMLWriter gmlWriter = new GMLWriter();
    String gmlXml = gmlWriter.write(geometry);
    // Copy the GML XML into the writer
    XmlPullParser parser = null;
    try {
        parser = XppFactory.createDefaultParser();
        new HierarchicalStreamCopier().copy(new XppReader(new StringReader(gmlXml), parser), writer);
    } catch (XmlPullParserException e) {
        LOGGER.warn(ERROR_SERIALIZING_MSG, e);
    }
}

/**
    * Test the getBoundariesWKT() operation of the NominatimGeocoder.
    * The test consists in a call with "france" as search query that shall
    * contains paris, noumea, and shall not contains berlin.
    * @throws ParseException
    */
@Test
public void getBoundariesWKTFrance() throws ParseException {
    XmlDocument document = getDocument("france.xml");
    String wkt_france = this.geocoder.computeWKT(document);
    Assert.assertNotNull(wkt_france, "France geometry not found.");
    document = getDocument("paris.xml");
    String wkt_paris = this.geocoder.computeWKT(document);
    Assert.assertNotNull(wkt_paris, "Paris geometry not found.");
    WKTReader reader = new WKTReader();
    Geometry france = reader.read(wkt_france);
    Geometry paris = reader.read(wkt_paris);
    // Test paris place is inside "France"
    Assert.assertTrue(france.contains(paris), "Paris geometry is not inside france");
    // Check Noumea france territory in also inside france
    document = getDocument("noumea.xml");
    String wkt_noumea = this.geocoder.computeWKT(document);
    Assert.assertNotNull(wkt_noumea, "Nouméa geometry not found.");
    Geometry noumea = reader.read(wkt_noumea);
    Assert.assertTrue(france.contains(noumea), "Nouméa geometry is not inside france");
    // Check berlin is outside france
    document = getDocument("berlin.xml");
    String wkt_berlin = this.geocoder.computeWKT(document);
    Assert.assertNotNull(wkt_berlin, "Berlin geometry not found.");
    Geometry berlin = reader.read(wkt_berlin);
    Assert.assertFalse(france.contains(berlin), "Berlin geometry is found inside france");
}

private Geometry retrieveGeometryForLayer(List<GeometryFilterInfo> geometryFilterInfos, String layerName) throws ParseException {
    for (GeometryFilterInfo wcsGeometryFilterInfo : geometryFilterInfos) {
        if (layerName.equals(wcsGeometryFilterInfo.getLayerName())) {
            String geometryString = wcsGeometryFilterInfo.getGeometryString();
            if (geometryString != null)
                return parseGeometry(geometryString);
        }
    }
    return null;
}

@Override
public Shape build() {
    final Geometry geometry;
    if (wrapdateline) {
        ArrayList<LineString> parts = new ArrayList<>();
        for (BaseLineStringBuilder<?> line : lines) {
            BaseLineStringBuilder.decompose(FACTORY, line.coordinates(false), parts);
        }
        if (parts.size() == 1) {
            geometry = parts.get(0);
        } else {
            LineString[] lineStrings = parts.toArray(new LineString[parts.size()]);
            geometry = FACTORY.createMultiLineString(lineStrings);
        }
    } else {
        LineString[] lineStrings = new LineString[lines.size()];
        Iterator<BaseLineStringBuilder<?>> iterator = lines.iterator();
        for (int i = 0; iterator.hasNext(); i++) {
            lineStrings[i] = FACTORY.createLineString(iterator.next().coordinates(false));
        }
        geometry = FACTORY.createMultiLineString(lineStrings);
    }
    return jtsGeometry(geometry);
}

@Override
public SimpleFeatureType buildFeatureType() {
    if (attributes != null) {
        String defaultGeometryName = null;
        for (ElasticAttribute attribute : attributes) {
            if (attribute.isUse()) {
                final String attributeName;
                if (attribute.getUseShortName()) {
                    attributeName = attribute.getShortName();
                } else {
                    attributeName = attribute.getName();
                }
                AttributeDescriptor att = null;
                if (Geometry.class.isAssignableFrom(attribute.getType())) {
                    final Integer srid = attribute.getSrid();
                    try {
                        if (srid != null) {
                            attributeBuilder.setCRS(CRS.decode("EPSG:" + srid));
                            attributeBuilder.setName(attributeName);
                            attributeBuilder.setBinding(attribute.getType());
                            att = attributeBuilder.buildDescriptor(attributeName, attributeBuilder.buildGeometryType());
                            final ElasticGeometryType geometryType = attribute.getGeometryType();
                            att.getUserData().put(GEOMETRY_TYPE, geometryType);
                            if (attribute.isDefaultGeometry() != null && attribute.isDefaultGeometry()) {
                                defaultGeometryName = attributeName;
                            }
                        }
                    } catch (Exception e) {
                        String msg = "Error occured determing srid for " + attribute.getName();
                        LOGGER.log(Level.WARNING, msg, e);
                    }
                } else {
                    attributeBuilder.setName(attributeName);
                    attributeBuilder.setBinding(attribute.getType());
                    att = attributeBuilder.buildDescriptor(attributeName, attributeBuilder.buildType());
                }
                if (att != null && attribute.getDateFormat() != null) {
                    att.getUserData().put(DATE_FORMAT, attribute.getDateFormat());
                }
                if (att != null) {
                    att.getUserData().put(FULL_NAME, attribute.getName());
                    att.getUserData().put(ANALYZED, attribute.getAnalyzed());
                    att.getUserData().put(NESTED, attribute.isNested());
                    add(att);
                }
            }
        }
        if (defaultGeometryName != null) {
            setDefaultGeometry(defaultGeometryName);
        }
    }
    return super.buildFeatureType();
}

@Override
public Shape build() {
    final Geometry geometry;
    if (wrapdateline) {
        ArrayList<LineString> parts = new ArrayList<>();
        for (LineStringBuilder line : lines) {
            LineStringBuilder.decompose(FACTORY, line.coordinates(false), parts);
        }
        if (parts.size() == 1) {
            geometry = parts.get(0);
        } else {
            LineString[] lineStrings = parts.toArray(new LineString[parts.size()]);
            geometry = FACTORY.createMultiLineString(lineStrings);
        }
    } else {
        LineString[] lineStrings = new LineString[lines.size()];
        Iterator<LineStringBuilder> iterator = lines.iterator();
        for (int i = 0; iterator.hasNext(); i++) {
            lineStrings[i] = FACTORY.createLineString(iterator.next().coordinates(false));
        }
        geometry = FACTORY.createMultiLineString(lineStrings);
    }
    return jtsGeometry(geometry);
}

/**
	 * Decode a geojson file for the sampling state
	 */
public ArrayList<BoundingBox> decodeForSampling(String file) throws IOException, JSONException {
    MfGeoFactory mfFactory = new MfGeoFactory() {

        public MfFeature createFeature(String id, MfGeometry geometry, JSONObject properties) {
            return new SamplingFeatureTemplate(id, geometry, properties);
        }
    };
    MfGeoJSONReader reader = new MfGeoJSONReader(mfFactory);
    ArrayList<BoundingBox> data = new ArrayList<BoundingBox>();
    File f = new File(file);
    InputStream in = new FileInputStream(f);
    String str = IOUtils.toString(in);
    in.close();
    //decode geojson file given as a String
    MfGeo result = reader.decode(str);
    MfFeatureCollection collection = (MfFeatureCollection) result;
    //all the geojson features
    ArrayList<MfFeature> coll = (ArrayList<MfFeature>) collection.getCollection();
    SamplingFeatureTemplate feature;
    MfGeometry featureGeometry;
    Geometry jts;
    Polygon polygon;
    double north;
    double east;
    double south;
    double west;
    BoundingBox b;
    for (MfFeature mf : coll) {
        feature = (SamplingFeatureTemplate) mf;
        //get the feature geometry
        featureGeometry = feature.getMfGeometry();
        jts = featureGeometry.getInternalGeometry();
        //feature geometry is a polygon
        polygon = (Polygon) jts;
        //get the bbox coordinates
        north = polygon.getExteriorRing().getPointN(0).getCoordinate().y;
        east = polygon.getExteriorRing().getPointN(1).getCoordinate().x;
        south = polygon.getExteriorRing().getPointN(2).getCoordinate().y;
        west = polygon.getExteriorRing().getPointN(3).getCoordinate().x;
        b = new BoundingBox(north, east, south, west);
        data.add(b);
    }
    //Set the matrix indices
    //First row and col indices are equal to 1
    int size = (int) Math.sqrt(data.size());
    int i = 1;
    int j = 1;
    for (BoundingBox box : data) {
        box.setRow(i);
        box.setColumn(j);
        j++;
        if (//row complete, continue with the next row
        j > size) {
            i++;
            j = 1;
        }
    }
    return data;
}

public static GeometryRasterMaskBuilder buildSampleFilterMatrix(final TileLayer layer, final String gridsetId, final int maxMaskLevel) throws Exception {
    final Geometry entries[] = createSampleEntries();
    final GridSubset gridSubset = layer.getGridSubset(layer.getGridSubsets().iterator().next());
    final int[] metaTilingFactors = layer.getMetaTilingFactors();
    GeometryRasterMaskBuilder matrix = new GeometryRasterMaskBuilder(gridSubset, metaTilingFactors, maxMaskLevel);
    try {
        for (Geometry geom : entries) {
            matrix.setMasksForGeometry(geom);
        }
    } finally {
        matrix.disposeGraphics();
    }
    logImages(new File("target"), matrix);
    return matrix;
}

@Override
protected void visitLiteralGeometry(Literal expression) throws IOException {
    // evaluate the literal and store it for later
    Geometry geom = (Geometry) evaluateLiteral(expression, Geometry.class);
    if (geom instanceof LinearRing) {
        //postgis does not handle linear rings, convert to just a line string
        geom = geom.getFactory().createLineString(((LinearRing) geom).getCoordinateSequence());
    }
    out.write("GeomFromText('");
    out.write(geom.toText());
    if (currentSRID == null && currentGeometry != null) {
        // if we don't know at all, use the srid of the geometry we're comparing against
        // (much slower since that has to be extracted record by record as opposed to 
        // being a constant)
        out.write("', SRID(\"" + currentGeometry.getLocalName() + "\"))");
    } else {
        out.write("', " + currentSRID + ")");
    }
}

@SuppressWarnings("unchecked")
public List<Project> getProjects(String wktFilter) throws Exception {
    final Session s = openSession();
    s.getTransaction().begin();
    final Geometry filter = wktToGeometry(wktFilter);
    final Query query = s.createQuery("FROM Project p WHERE WITHIN(p.location, :filter) = TRUE");
    query.setParameter("filter", filter);
    final List<Project> projects = query.list();
    s.getTransaction().commit();
    s.close();
    return projects;
}

/**
     * Creates a new instance of VectorBinarizeOpImage in the rendered layer.
     * 
     * @param paramBlock parameter block with parameters minx, miny, width height, geometry and coordtype
     * 
     * @param renderHints optional rendering hints which may be used to pass an {@code ImageLayout} object containing a {@code SampleModel} to use
     *        when creating destination tiles
     */
public RenderedImage create(ParameterBlock paramBlock, RenderingHints renderHints) {
    int minx = paramBlock.getIntParameter(VectorBinarizeDescriptor.MINX_ARG);
    int miny = paramBlock.getIntParameter(VectorBinarizeDescriptor.MINY_ARG);
    int width = paramBlock.getIntParameter(VectorBinarizeDescriptor.WIDTH_ARG);
    int height = paramBlock.getIntParameter(VectorBinarizeDescriptor.HEIGHT_ARG);
    Object obj = paramBlock.getObjectParameter(VectorBinarizeDescriptor.GEOM_ARG);
    PreparedGeometry pg = null;
    if (obj instanceof Polygonal) {
        // defensively copy the input Geometry
        Geometry g = (Geometry) ((Geometry) obj).clone();
        pg = PreparedGeometryFactory.prepare(g);
    } else if (obj instanceof PreparedGeometry) {
        pg = (PreparedGeometry) obj;
    } else {
        throw new IllegalArgumentException("The geometry must be a JTS polygon or multipolygon");
    }
    // get the tile size from the image layout
    Dimension tileSize = null;
    if (renderHints != null && renderHints.containsKey(JAI.KEY_IMAGE_LAYOUT)) {
        ImageLayout il = (ImageLayout) renderHints.get(JAI.KEY_IMAGE_LAYOUT);
        if (il != null) {
            tileSize = new Dimension(il.getTileWidth(null), il.getTileHeight(null));
        }
    }
    if (tileSize == null) {
        tileSize = JAI.getDefaultTileSize();
    }
    // sample model wise we only build bw images
    SampleModel sm = new MultiPixelPackedSampleModel(DataBuffer.TYPE_BYTE, tileSize.width, tileSize.height, 1);
    boolean antiAliasing = VectorBinarizeOpImage.DEFAULT_ANTIALIASING;
    Object antiAlias = paramBlock.getObjectParameter(VectorBinarizeDescriptor.ANTIALIASING_ARG);
    if (antiAlias != null && antiAlias instanceof Boolean) {
        antiAliasing = ((Boolean) antiAlias).booleanValue();
    }
    return new VectorBinarizeOpImage(sm, renderHints, minx, miny, width, height, pg, antiAliasing);
}