edu.umn.cs.spatialHadoop.indexing.RTree.java Source code

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/***********************************************************************
* Copyright (c) 2015 by Regents of the University of Minnesota.
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Apache License, Version 2.0 which 
* accompanies this distribution and is available at
* http://www.opensource.org/licenses/apache2.0.php.
*
*************************************************************************/
package edu.umn.cs.spatialHadoop.indexing;

import java.io.ByteArrayOutputStream;
import java.io.Closeable;
import java.io.DataInput;
import java.io.DataInputStream;
import java.io.DataOutput;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.lang.reflect.Array;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.Map;
import java.util.PriorityQueue;
import java.util.Queue;
import java.util.Stack;
import java.util.Vector;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.Seekable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.Writable;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hadoop.util.GenericOptionsParser;
import org.apache.hadoop.util.IndexedSortable;
import org.apache.hadoop.util.IndexedSorter;
import org.apache.hadoop.util.LineReader;
import org.apache.hadoop.util.QuickSort;

import com.vividsolutions.jts.geom.TopologyException;

import edu.umn.cs.spatialHadoop.OperationsParams;
import edu.umn.cs.spatialHadoop.core.GridInfo;
import edu.umn.cs.spatialHadoop.core.Point;
import edu.umn.cs.spatialHadoop.core.Rectangle;
import edu.umn.cs.spatialHadoop.core.ResultCollector;
import edu.umn.cs.spatialHadoop.core.ResultCollector2;
import edu.umn.cs.spatialHadoop.core.Shape;
import edu.umn.cs.spatialHadoop.core.SpatialAlgorithms;
import edu.umn.cs.spatialHadoop.io.MemoryInputStream;
import edu.umn.cs.spatialHadoop.io.Text2;
import edu.umn.cs.spatialHadoop.io.TextSerializable;

/**
 * A disk-based R-tree that can be loaded using a bulk loading method and
 * never changed afterwards. It works with any shape given in the generic
 * parameter. To load the tree, use the {@link #bulkLoadWrite(byte[], int, int, int, DataOutput, Shape, boolean)}
 * method. To restore the tree from disk, use the {@link #readFields(DataInput)}
 * methods. To do queries against the tree, use the {@link #search(Shape, ResultCollector)},
 *  {@link #knn(double, double, int, ResultCollector2)} or
 *  {@link #spatialJoin(RTree, RTree, ResultCollector2, Reporter)}
 * @author Ahmed Eldawy
 *
 * @param <T>
 */
public class RTree<T extends Shape> implements Writable, Iterable<T>, Closeable {
    /**Logger*/
    private static final Log LOG = LogFactory.getLog(RTree.class);

    /**Size of tree header on disk. Height + Degree + Number of records*/
    public static final int TreeHeaderSize = 4 + 4 + 4;

    /**Size of a node. Offset of first child + dimensions (x, y, width, height)*/
    public static final int NodeSize = 4 + 8 * 4;

    /** An instance of T that can be used to deserialize objects from disk */
    T stockObject;

    /**Height of the tree (number of levels)*/
    private int height;

    /**Degree of internal nodes in the tree*/
    private int degree;

    /**Total number of nodes in the tree*/
    private int nodeCount;

    /**Number of leaf nodes*/
    private int leafNodeCount;

    /**Number of non-leaf nodes*/
    private int nonLeafNodeCount;

    /**Number of elements in the tree*/
    private int elementCount;

    /**Input stream to tree data*/
    private FSDataInputStream data;

    /**The start offset of the tree in the data stream*/
    private long treeStartOffset;

    /**Total tree size (header + structure + data) used to read the data in
     * the last leaf node correctly*/
    private int treeSize;

    /**A cached copy of all nodes (MBRs) in memory indexed by node ID*/
    private Rectangle[] nodes;

    /**A cached copy of data offset for each node.*/
    private int[] dataOffset;

    public RTree() {
    }

    /**
     * Builds the RTree given a serialized list of elements. It uses the given
     * stockObject to deserialize these elements using
     * {@link TextSerializable#fromText(Text)} and build the tree. Also writes the
     * created tree to the disk directly.
     * 
     * @param element_bytes
     *          - serialization of all elements separated by new lines
     * @param offset
     *          - offset of the first byte to use in elements_bytes
     * @param len
     *          - number of bytes to use in elements_bytes
     * @param degree
     *          - Degree of the R-tree to build in terms of number of children per
     *          node
     * @param dataOut
     *          - output stream to write the result to.
     * @param fast_sort
     *          - setting this to <code>true</code> allows the method to run
     *          faster by materializing the offset of each element in the list
     *          which speeds up the comparison. However, this requires an
     *          additional 16 bytes per element. So, for each 1M elements, the
     *          method will require an additional 16 M bytes (approximately).
     */
    public static void bulkLoadWrite(final byte[] element_bytes, final int offset, final int len, final int degree,
            DataOutput dataOut, final Shape stockObject, final boolean fast_sort) {
        try {

            int elementCount = 0;
            // Count number of elements in the given text
            int i_start = offset;
            final Text line = new Text();
            while (i_start < offset + len) {
                int i_end = skipToEOL(element_bytes, i_start);
                // Extract the line without end of line character
                line.set(element_bytes, i_start, i_end - i_start - 1);
                stockObject.fromText(line);
                elementCount++;
                i_start = i_end;
            }
            LOG.info("Bulk loading an RTree with " + elementCount + " elements");

            // It turns out the findBestDegree returns the best degree when the whole
            // tree is loaded to memory when processed. However, as current algorithms
            // process the tree while it's on disk, a higher degree should be selected
            // such that a node fits one file block (assumed to be 4K).
            //final int degree = findBestDegree(bytesAvailable, elementCount);

            int height = Math.max(1, (int) Math.ceil(Math.log(elementCount) / Math.log(degree)));
            int leafNodeCount = (int) Math.pow(degree, height - 1);
            if (elementCount < 2 * leafNodeCount && height > 1) {
                height--;
                leafNodeCount = (int) Math.pow(degree, height - 1);
            }
            int nodeCount = (int) ((Math.pow(degree, height) - 1) / (degree - 1));
            int nonLeafNodeCount = nodeCount - leafNodeCount;

            // Keep track of the offset of each element in the text
            final int[] offsets = new int[elementCount];
            final double[] xs = fast_sort ? new double[elementCount] : null;
            final double[] ys = fast_sort ? new double[elementCount] : null;

            i_start = offset;
            line.clear();
            for (int i = 0; i < elementCount; i++) {
                offsets[i] = i_start;
                int i_end = skipToEOL(element_bytes, i_start);
                if (xs != null) {
                    // Extract the line with end of line character
                    line.set(element_bytes, i_start, i_end - i_start - 1);
                    stockObject.fromText(line);
                    // Sample center of the shape
                    xs[i] = (stockObject.getMBR().x1 + stockObject.getMBR().x2) / 2;
                    ys[i] = (stockObject.getMBR().y1 + stockObject.getMBR().y2) / 2;
                }
                i_start = i_end;
            }

            /**A struct to store information about a split*/
            class SplitStruct extends Rectangle {
                /**Start and end index for this split*/
                int index1, index2;
                /**Direction of this split*/
                byte direction;
                /**Index of first element on disk*/
                int offsetOfFirstElement;

                static final byte DIRECTION_X = 0;
                static final byte DIRECTION_Y = 1;

                SplitStruct(int index1, int index2, byte direction) {
                    this.index1 = index1;
                    this.index2 = index2;
                    this.direction = direction;
                }

                @Override
                public void write(DataOutput out) throws IOException {
                    out.writeInt(offsetOfFirstElement);
                    super.write(out);
                }

                void partition(Queue<SplitStruct> toBePartitioned) {
                    IndexedSortable sortableX;
                    IndexedSortable sortableY;

                    if (fast_sort) {
                        // Use materialized xs[] and ys[] to do the comparisons
                        sortableX = new IndexedSortable() {
                            @Override
                            public void swap(int i, int j) {
                                // Swap xs
                                double tempx = xs[i];
                                xs[i] = xs[j];
                                xs[j] = tempx;
                                // Swap ys
                                double tempY = ys[i];
                                ys[i] = ys[j];
                                ys[j] = tempY;
                                // Swap id
                                int tempid = offsets[i];
                                offsets[i] = offsets[j];
                                offsets[j] = tempid;
                            }

                            @Override
                            public int compare(int i, int j) {
                                if (xs[i] < xs[j])
                                    return -1;
                                if (xs[i] > xs[j])
                                    return 1;
                                return 0;
                            }
                        };

                        sortableY = new IndexedSortable() {
                            @Override
                            public void swap(int i, int j) {
                                // Swap xs
                                double tempx = xs[i];
                                xs[i] = xs[j];
                                xs[j] = tempx;
                                // Swap ys
                                double tempY = ys[i];
                                ys[i] = ys[j];
                                ys[j] = tempY;
                                // Swap id
                                int tempid = offsets[i];
                                offsets[i] = offsets[j];
                                offsets[j] = tempid;
                            }

                            @Override
                            public int compare(int i, int j) {
                                if (ys[i] < ys[j])
                                    return -1;
                                if (ys[i] > ys[j])
                                    return 1;
                                return 0;
                            }
                        };
                    } else {
                        // No materialized xs and ys. Always deserialize objects to compare
                        sortableX = new IndexedSortable() {
                            @Override
                            public void swap(int i, int j) {
                                // Swap id
                                int tempid = offsets[i];
                                offsets[i] = offsets[j];
                                offsets[j] = tempid;
                            }

                            @Override
                            public int compare(int i, int j) {
                                // Get end of line
                                int eol = skipToEOL(element_bytes, offsets[i]);
                                line.set(element_bytes, offsets[i], eol - offsets[i] - 1);
                                stockObject.fromText(line);
                                double xi = (stockObject.getMBR().x1 + stockObject.getMBR().x2) / 2;

                                eol = skipToEOL(element_bytes, offsets[j]);
                                line.set(element_bytes, offsets[j], eol - offsets[j] - 1);
                                stockObject.fromText(line);
                                double xj = (stockObject.getMBR().x1 + stockObject.getMBR().x2) / 2;
                                if (xi < xj)
                                    return -1;
                                if (xi > xj)
                                    return 1;
                                return 0;
                            }
                        };

                        sortableY = new IndexedSortable() {
                            @Override
                            public void swap(int i, int j) {
                                // Swap id
                                int tempid = offsets[i];
                                offsets[i] = offsets[j];
                                offsets[j] = tempid;
                            }

                            @Override
                            public int compare(int i, int j) {
                                int eol = skipToEOL(element_bytes, offsets[i]);
                                line.set(element_bytes, offsets[i], eol - offsets[i] - 1);
                                stockObject.fromText(line);
                                double yi = (stockObject.getMBR().y1 + stockObject.getMBR().y2) / 2;

                                eol = skipToEOL(element_bytes, offsets[j]);
                                line.set(element_bytes, offsets[j], eol - offsets[j] - 1);
                                stockObject.fromText(line);
                                double yj = (stockObject.getMBR().y1 + stockObject.getMBR().y2) / 2;
                                if (yi < yj)
                                    return -1;
                                if (yi > yj)
                                    return 1;
                                return 0;
                            }
                        };
                    }

                    final IndexedSorter sorter = new QuickSort();

                    final IndexedSortable[] sortables = new IndexedSortable[2];
                    sortables[SplitStruct.DIRECTION_X] = sortableX;
                    sortables[SplitStruct.DIRECTION_Y] = sortableY;

                    sorter.sort(sortables[direction], index1, index2);

                    // Partition into maxEntries partitions (equally) and
                    // create a SplitStruct for each partition
                    int i1 = index1;
                    for (int iSplit = 0; iSplit < degree; iSplit++) {
                        int i2 = index1 + (index2 - index1) * (iSplit + 1) / degree;
                        SplitStruct newSplit = new SplitStruct(i1, i2, (byte) (1 - direction));
                        toBePartitioned.add(newSplit);
                        i1 = i2;
                    }
                }
            }

            // All nodes stored in level-order traversal
            Vector<SplitStruct> nodes = new Vector<SplitStruct>();
            final Queue<SplitStruct> toBePartitioned = new LinkedList<SplitStruct>();
            toBePartitioned.add(new SplitStruct(0, elementCount, SplitStruct.DIRECTION_X));

            while (!toBePartitioned.isEmpty()) {
                SplitStruct split = toBePartitioned.poll();
                if (nodes.size() < nonLeafNodeCount) {
                    // This is a non-leaf
                    split.partition(toBePartitioned);
                }
                nodes.add(split);
            }

            if (nodes.size() != nodeCount) {
                throw new RuntimeException(
                        "Expected node count: " + nodeCount + ". Real node count: " + nodes.size());
            }

            // Now we have our data sorted in the required order. Start building
            // the tree.
            // Store the offset of each leaf node in the tree
            FSDataOutputStream fakeOut = null;
            try {
                fakeOut = new FSDataOutputStream(new java.io.OutputStream() {
                    // Null output stream
                    @Override
                    public void write(int b) throws IOException {
                        // Do nothing
                    }

                    @Override
                    public void write(byte[] b, int off, int len) throws IOException {
                        // Do nothing
                    }

                    @Override
                    public void write(byte[] b) throws IOException {
                        // Do nothing
                    }
                }, null, TreeHeaderSize + nodes.size() * NodeSize);
                for (int i_leaf = nonLeafNodeCount, i = 0; i_leaf < nodes.size(); i_leaf++) {
                    nodes.elementAt(i_leaf).offsetOfFirstElement = (int) fakeOut.getPos();
                    if (i != nodes.elementAt(i_leaf).index1)
                        throw new RuntimeException();
                    double x1, y1, x2, y2;

                    // Initialize MBR to first object
                    int eol = skipToEOL(element_bytes, offsets[i]);
                    fakeOut.write(element_bytes, offsets[i], eol - offsets[i]);
                    line.set(element_bytes, offsets[i], eol - offsets[i] - 1);
                    stockObject.fromText(line);
                    Rectangle mbr = stockObject.getMBR();
                    x1 = mbr.x1;
                    y1 = mbr.y1;
                    x2 = mbr.x2;
                    y2 = mbr.y2;
                    i++;

                    while (i < nodes.elementAt(i_leaf).index2) {
                        eol = skipToEOL(element_bytes, offsets[i]);
                        fakeOut.write(element_bytes, offsets[i], eol - offsets[i]);
                        line.set(element_bytes, offsets[i], eol - offsets[i] - 1);
                        stockObject.fromText(line);
                        mbr = stockObject.getMBR();
                        if (mbr.x1 < x1)
                            x1 = mbr.x1;
                        if (mbr.y1 < y1)
                            y1 = mbr.y1;
                        if (mbr.x2 > x2)
                            x2 = mbr.x2;
                        if (mbr.y2 > y2)
                            y2 = mbr.y2;
                        i++;
                    }
                    nodes.elementAt(i_leaf).set(x1, y1, x2, y2);
                }

            } finally {
                if (fakeOut != null)
                    fakeOut.close();
            }

            // Calculate MBR and offsetOfFirstElement for non-leaves
            for (int i_node = nonLeafNodeCount - 1; i_node >= 0; i_node--) {
                int i_first_child = i_node * degree + 1;
                nodes.elementAt(i_node).offsetOfFirstElement = nodes.elementAt(i_first_child).offsetOfFirstElement;
                int i_child = 0;
                Rectangle mbr;
                mbr = nodes.elementAt(i_first_child + i_child);
                double x1 = mbr.x1;
                double y1 = mbr.y1;
                double x2 = mbr.x2;
                double y2 = mbr.y2;
                i_child++;

                while (i_child < degree) {
                    mbr = nodes.elementAt(i_first_child + i_child);
                    if (mbr.x1 < x1)
                        x1 = mbr.x1;
                    if (mbr.y1 < y1)
                        y1 = mbr.y1;
                    if (mbr.x2 > x2)
                        x2 = mbr.x2;
                    if (mbr.y2 > y2)
                        y2 = mbr.y2;
                    i_child++;
                }
                nodes.elementAt(i_node).set(x1, y1, x2, y2);
            }

            // Start writing the tree
            // write tree header (including size)
            // Total tree size. (== Total bytes written - 8 bytes for the size itself)
            dataOut.writeInt(TreeHeaderSize + NodeSize * nodeCount + len);
            // Tree height
            dataOut.writeInt(height);
            // Degree
            dataOut.writeInt(degree);
            dataOut.writeInt(elementCount);

            // write nodes
            for (SplitStruct node : nodes) {
                node.write(dataOut);
            }
            // write elements
            for (int element_i = 0; element_i < elementCount; element_i++) {
                int eol = skipToEOL(element_bytes, offsets[element_i]);
                dataOut.write(element_bytes, offsets[element_i], eol - offsets[element_i]);
            }

        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    @Override
    public void write(DataOutput out) throws IOException {
        throw new RuntimeException(
                "write is no longer supported. " + "Please use bulkLoadWrite to write the RTree.");
    }

    @Override
    public void readFields(DataInput in) throws IOException {
        // Read the whole tree structure and keep it in memory. Leave data on disk
        // Tree size (Header + structure + data)
        treeSize = in.readInt();

        if (in instanceof Seekable)
            this.treeStartOffset = ((Seekable) in).getPos();
        if (treeSize == 0) {
            height = elementCount = 0;
            return;
        }

        // Read only the tree structure in memory while actual records remain on
        // disk and loaded when necessary
        height = in.readInt();
        if (height == 0)
            return;
        degree = in.readInt();
        elementCount = in.readInt();

        // Keep only tree structure in memory
        nodeCount = (int) ((powInt(degree, height) - 1) / (degree - 1));
        this.nodes = new Rectangle[nodeCount];
        this.dataOffset = new int[nodeCount + 1];

        for (int node_id = 0; node_id < nodeCount; node_id++) {
            this.dataOffset[node_id] = in.readInt();
            this.nodes[node_id] = new Rectangle();
            this.nodes[node_id].readFields(in);
        }
        this.dataOffset[nodeCount] = treeSize;

        if (in instanceof FSDataInputStream) {
            // A random input stream, can keep the data on disk
            this.data = (FSDataInputStream) in;
        } else {
            // A sequential input stream, need to read all data now
            int treeDataSize = this.dataOffset[nodeCount] - this.dataOffset[0];
            // Adjust the offset of data to be zero
            this.treeStartOffset = -this.dataOffset[0];
            byte[] treeData = new byte[treeDataSize];
            in.readFully(treeData, 0, treeDataSize);
            this.data = new FSDataInputStream(new MemoryInputStream(treeData));
        }
        leafNodeCount = (int) Math.pow(degree, height - 1);
        nonLeafNodeCount = nodeCount - leafNodeCount;
    }

    /**
     * Reads and skips the header of the tree returning the total number of
     * bytes skipped from the stream. This is used as a preparatory function to
     * read all elements in the tree without the index part.
     * @param in
     * @return - Total number of bytes read and skipped
     * @throws IOException
     */
    public static int skipHeader(InputStream in) throws IOException {
        DataInput dataIn = in instanceof DataInput ? (DataInput) in : new DataInputStream(in);
        int skippedBytes = 0;
        /*int treeSize = */dataIn.readInt();
        skippedBytes += 4;
        int height = dataIn.readInt();
        skippedBytes += 4;
        if (height == 0) {
            // Empty tree. No results
            return skippedBytes;
        }
        int degree = dataIn.readInt();
        skippedBytes += 4;
        int nodeCount = (int) ((powInt(degree, height) - 1) / (degree - 1));
        /*int elementCount = */dataIn.readInt();
        skippedBytes += 4;
        // Skip all nodes
        dataIn.skipBytes(nodeCount * NodeSize);
        skippedBytes += nodeCount * NodeSize;
        return skippedBytes;
    }

    /**
     * Returns the total size of the header (including the index) in bytes.
     * Assume that the input is aligned to the start offset of the tree (header).
     * Note that the part of the header is consumed from the given input to be
     * able to determine header size.
     * @param in
     * @return
     * @throws IOException
     */
    public static int getHeaderSize(DataInput in) throws IOException {
        int header_size = 0;
        /*int treeSize = */in.readInt();
        header_size += 4;
        int height = in.readInt();
        header_size += 4;
        if (height == 0) {
            // Empty tree. No results
            return header_size;
        }
        int degree = in.readInt();
        header_size += 4;
        int nodeCount = (int) ((Math.pow(degree, height) - 1) / (degree - 1));
        /*int elementCount = */in.readInt();
        header_size += 4;
        // Add the size of all nodes
        header_size += nodeCount * NodeSize;
        return header_size;
    }

    public long getEndOffset() {
        return treeStartOffset + treeSize;
    }

    /**
     * Returns total number of elements
     * @return
     */
    public int getElementCount() {
        return elementCount;
    }

    /**
     * Returns the MBR of the root
     * @return
     */
    public Rectangle getMBR() {
        return nodes[0];
    }

    /**
     * Reads and returns the element with the given index
     * @param i
     * @return
     */
    public T readElement(int i) {
        Iterator<T> iter = iterator();
        while (i-- > 0 && iter.hasNext()) {
            iter.next();
        }
        return iter.next();
    }

    public void setStockObject(T stockObject) {
        this.stockObject = stockObject;
    }

    /**
     * Create rectangles that together pack all points in sample such that
     * each rectangle contains roughly the same number of points. In other words
     * it tries to balance number of points in each rectangle.
     * Works similar to the logic of bulkLoad but does only one level of
     * rectangles.
     * @param gridInfo Used as a hint for number of rectangles per row or column
     * @param sample
     * @return
     */
    public static Rectangle[] packInRectangles(GridInfo gridInfo, final Point[] sample) {
        Rectangle[] rectangles = new Rectangle[gridInfo.columns * gridInfo.rows];
        int iRectangle = 0;
        // Sort in x direction
        final IndexedSortable sortableX = new IndexedSortable() {
            @Override
            public void swap(int i, int j) {
                Point temp = sample[i];
                sample[i] = sample[j];
                sample[j] = temp;
            }

            @Override
            public int compare(int i, int j) {
                if (sample[i].x < sample[j].x)
                    return -1;
                if (sample[i].x > sample[j].x)
                    return 1;
                return 0;
            }
        };

        // Sort in y direction
        final IndexedSortable sortableY = new IndexedSortable() {
            @Override
            public void swap(int i, int j) {
                Point temp = sample[i];
                sample[i] = sample[j];
                sample[j] = temp;
            }

            @Override
            public int compare(int i, int j) {
                if (sample[i].y < sample[j].y)
                    return -1;
                if (sample[i].y > sample[j].y)
                    return 1;
                return 0;
            }
        };

        final QuickSort quickSort = new QuickSort();

        quickSort.sort(sortableX, 0, sample.length);

        int xindex1 = 0;
        double x1 = gridInfo.x1;
        for (int col = 0; col < gridInfo.columns; col++) {
            int xindex2 = sample.length * (col + 1) / gridInfo.columns;

            // Determine extents for all rectangles in this column
            double x2 = col == gridInfo.columns - 1 ? gridInfo.x2 : sample[xindex2 - 1].x;

            // Sort all points in this column according to its y-coordinate
            quickSort.sort(sortableY, xindex1, xindex2);

            // Create rectangles in this column
            double y1 = gridInfo.y1;
            for (int row = 0; row < gridInfo.rows; row++) {
                int yindex2 = xindex1 + (xindex2 - xindex1) * (row + 1) / gridInfo.rows;
                double y2 = row == gridInfo.rows - 1 ? gridInfo.y2 : sample[yindex2 - 1].y;

                rectangles[iRectangle++] = new Rectangle(x1, y1, x2, y2);
                y1 = y2;
            }

            xindex1 = xindex2;
            x1 = x2;
        }
        return rectangles;
    }

    /**
     * An iterator that goes over all elements in the tree in no particular order
     * @author eldawy
     *
     */
    class RTreeIterator implements Iterator<T> {

        /**Current offset in the data stream*/
        int offset;

        /**Temporary text that holds one line to deserialize objects*/
        Text line;

        /**A stock object to read from stream*/
        T _stockObject;

        /**A reader to read lines from the tree*/
        LineReader reader;

        RTreeIterator() throws IOException {
            offset = TreeHeaderSize + NodeSize * RTree.this.nodeCount;
            _stockObject = (T) RTree.this.stockObject.clone();
            line = new Text();
            RTree.this.data.seek(offset + RTree.this.treeStartOffset);
            reader = new LineReader(RTree.this.data);
        }

        @Override
        public boolean hasNext() {
            return offset < RTree.this.treeSize;
        }

        @Override
        public T next() {
            if (!hasNext())
                return null;
            try {
                offset += reader.readLine(line);
                _stockObject.fromText(line);
            } catch (IOException e) {
                e.printStackTrace();
                return null;
            }
            return _stockObject;
        }

        @Override
        public void remove() {
            throw new RuntimeException("Not supported");
        }
    }

    /**
     * Skip bytes until the end of line
     * @param bytes
     * @param startOffset
     * @return
     */
    public static int skipToEOL(byte[] bytes, int startOffset) {
        int eol = startOffset;
        while (eol < bytes.length && (bytes[eol] != '\n' && bytes[eol] != '\r'))
            eol++;
        while (eol < bytes.length && (bytes[eol] == '\n' || bytes[eol] == '\r'))
            eol++;
        return eol;
    }

    @Override
    public Iterator<T> iterator() {
        try {
            return new RTreeIterator();
        } catch (IOException e) {
            e.printStackTrace();
        }
        return null;
    }

    /**
     * Given a block size, record size and a required tree degree, this function
     * calculates the maximum number of records that can be stored in this
     * block taking into consideration the overhead needed by node structure.
     * @param blockSize
     * @param degree
     * @param recordSize
     * @return
     */
    public static int getBlockCapacity(long blockSize, int degree, int recordSize) {
        double a = (double) NodeSize / (degree - 1);
        double ratio = (blockSize + a) / (recordSize + a);
        double break_even_height = Math.log(ratio) / Math.log(degree);
        double h_min = Math.floor(break_even_height);
        double capacity1 = Math.floor(Math.pow(degree, h_min));
        double structure_size = 4 + TreeHeaderSize + a * (capacity1 * degree - 1);
        double capacity2 = Math.floor((blockSize - structure_size) / recordSize);
        return Math.max((int) capacity1, (int) capacity2);
    }

    /**
     * Searches the RTree starting from the given start position. This is either
     * a node number or offset of an element. If it's a node number, it performs
     * the search in the subtree rooted at this node. If it's an offset number,
     * it searches only the object found there.
     * It is assumed that the openQuery() has been called before this function
     * and that endQuery() will be called afterwards.
     * @param query_shape
     * @param output
     * @param start where to start searching
     * @param end where to end searching. Only used when start is an offset of
     *   an object.
     * @return
     * @throws IOException
     */
    protected int search(Shape query_shape, ResultCollector<T> output, int start, int end) throws IOException {
        Rectangle query_mbr = query_shape.getMBR();
        int resultSize = 0;
        // Special case for an empty tree
        if (height == 0)
            return 0;

        Stack<Integer> toBeSearched = new Stack<Integer>();
        // Start from the given node
        toBeSearched.push(start);
        if (start >= nodeCount) {
            toBeSearched.push(end);
        }

        // Holds one data line from tree data
        Text line = new Text2();

        while (!toBeSearched.isEmpty()) {
            int searchNumber = toBeSearched.pop();

            if (searchNumber < nodeCount) {
                // Searching a node
                int nodeID = searchNumber;
                if (query_mbr.isIntersected(nodes[nodeID])) {
                    boolean is_leaf = nodeID >= nonLeafNodeCount;
                    if (is_leaf) {
                        // Check all objects under this node
                        int start_offset = this.dataOffset[nodeID];
                        int end_offset = this.dataOffset[nodeID + 1];
                        toBeSearched.add(start_offset);
                        toBeSearched.add(end_offset);
                    } else {
                        // Add all child nodes
                        for (int iChild = 0; iChild < this.degree; iChild++) {
                            toBeSearched.add(nodeID * this.degree + iChild + 1);
                        }
                    }
                }
            } else {
                // searchNumber is the end offset of data search. Start offset is next
                // in stack
                int end_offset = searchNumber;
                int start_offset = toBeSearched.pop();
                // All data offsets are relative to tree start (typically 4)
                this.data.seek(start_offset + this.treeStartOffset);
                // Should not close the line reader because we do not want to close
                // the underlying data stream now. In case future searches are done
                @SuppressWarnings("resource")
                LineReader lineReader = new LineReader(data);
                while (start_offset < end_offset) {
                    start_offset += lineReader.readLine(line);
                    stockObject.fromText(line);
                    if (stockObject.isIntersected(query_shape)) {
                        resultSize++;
                        if (output != null)
                            output.collect(stockObject);
                    }
                }
            }
        }
        return resultSize;
    }

    /**
     * An iterator used to return all search results
     * @author Ahmed Eldawy
     */
    public class SearchIterator implements Iterable<T>, Iterator<T> {

        /**The last object that has returned by next*/
        private T resultShape;

        /**The next object that will be returned on the following next() call*/
        private T nextResultShape;

        /**MBR of the query shape for fast comparison with nodes*/
        private Rectangle queryMBR;

        /**Shape to search*/
        private Shape queryShape;

        /**Nodes or parts of the file to be searched*/
        private Stack<Integer> toBeSearched = new Stack<Integer>();

        /**Used to deserialize node information*/
        private Rectangle nodeMBR = new Rectangle();

        /**Used to deserialize record information*/
        private Text line = new Text2();

        /**If searching within node, these are the offsets of records in it*/
        private int firstOffset, lastOffset;

        /**If searching within a node, lineReader points to result items*/
        LineReader lineReader;

        public SearchIterator(Shape queryShape) {
            this.queryShape = queryShape;
            this.queryMBR = queryShape.getMBR();
            toBeSearched.push(0); // Start from the root
            this.resultShape = (T) stockObject.clone();
            this.nextResultShape = (T) stockObject.clone();
            prepareNextResult();
        }

        @Override
        public Iterator<T> iterator() {
            return this;
        }

        @Override
        public boolean hasNext() {
            return nextResultShape != null;
        }

        @Override
        public T next() {
            T temp = resultShape;
            resultShape = nextResultShape;
            nextResultShape = temp;
            prepareNextResult();
            return resultShape;
        }

        @Override
        public void remove() {
            throw new RuntimeException("Unsupported method");
        }

        /**
         * Search for next item in result and store it in resultShape.
         * If no more results found, set resultShape to null
         */
        protected void prepareNextResult() {
            try {
                while (lineReader != null && firstOffset < lastOffset) {
                    // Case 1: Searching within a node
                    firstOffset += lineReader.readLine(line);
                    nextResultShape.fromText(line);
                    if (nextResultShape.isIntersected(queryShape)) {
                        return;
                    }
                }
                // Case 2: Searching in nodes
                while (!toBeSearched.isEmpty()) {
                    int searchNumber = toBeSearched.pop();

                    if (searchNumber < nodeCount) {
                        // Searching a node
                        int nodeID = searchNumber;
                        if (queryMBR.isIntersected(nodes[nodeID])) {
                            boolean is_leaf = nodeID >= nonLeafNodeCount;
                            if (is_leaf) {
                                // Check all objects under this node
                                int start_offset = RTree.this.dataOffset[nodeID];
                                int end_offset = RTree.this.dataOffset[nodeID + 1];
                                toBeSearched.add(start_offset);
                                toBeSearched.add(end_offset);
                            } else {
                                // Add all child nodes
                                for (int iChild = 0; iChild < RTree.this.degree; iChild++) {
                                    toBeSearched.add(nodeID * RTree.this.degree + iChild + 1);
                                }
                            }
                        }
                    } else {
                        // searchNumber is the end offset of data search. Start offset is next
                        // in stack
                        lastOffset = searchNumber;
                        firstOffset = toBeSearched.pop();

                        data.seek(firstOffset + treeStartOffset);
                        lineReader = new LineReader(data);
                        while (firstOffset < lastOffset) {
                            firstOffset += lineReader.readLine(line);
                            nextResultShape.fromText(line);
                            if (nextResultShape.isIntersected(queryShape)) {
                                return;
                            }
                        }
                    }
                }
                // No more results in the tree
                nextResultShape = null;

            } catch (IOException e) {
                e.printStackTrace();
                nextResultShape = null;
            }
        }

    }

    /**
     * Searches the tree for all shapes overlapping the queryShape and returns
     * an iterator for all these shapes
     * @param queryShape
     * @return
     */
    public Iterable<T> search(Shape queryShape) {
        return new SearchIterator(queryShape);
    }

    /**
     * Performs a range query over this tree using the given query range.
     * @param query - The query rectangle to use (TODO make it any shape not just rectangle)
     * @param output - Shapes found are reported to this output. If null, results are not reported
     * @return - Total number of records found
     */
    public int search(Shape query, ResultCollector<T> output) {
        int resultCount = 0;

        try {
            resultCount = search(query, output, 0, 0);
        } catch (IOException e) {
            e.printStackTrace();
        }
        return resultCount;
    }

    /**
     * k nearest neighbor query
     * @param qx
     * @param qy
     * @param k
     * @param output
     */
    public int knn(final double qx, final double qy, int k, final ResultCollector2<T, Double> output) {
        double query_area = ((getMBR().x2 - getMBR().x1) * (getMBR().y2 - getMBR().y1)) * k / getElementCount();
        double query_radius = Math.sqrt(query_area / Math.PI);

        boolean result_correct;
        final Vector<Double> distances = new Vector<Double>();
        final Vector<T> shapes = new Vector<T>();
        // Find results in the range and increase this range if needed to ensure
        // correctness of the answer
        do {
            // Initialize result and query range
            distances.clear();
            shapes.clear();
            Rectangle queryRange = new Rectangle();
            queryRange.x1 = qx - query_radius;
            queryRange.y1 = qy - query_radius;
            queryRange.x2 = qx + query_radius;
            queryRange.y2 = qy + query_radius;
            // Retrieve all results in range
            search(queryRange, new ResultCollector<T>() {
                @Override
                public void collect(T shape) {
                    distances.add(shape.distanceTo(qx, qy));
                    shapes.add((T) shape.clone());
                }
            });
            if (shapes.size() < k) {
                // Didn't find k elements in range, double the range to get more items
                if (shapes.size() == getElementCount()) {
                    // Already returned all possible elements
                    result_correct = true;
                } else {
                    query_radius *= 2;
                    result_correct = false;
                }
            } else {
                // Sort items by distance to get the kth neighbor
                IndexedSortable s = new IndexedSortable() {
                    @Override
                    public void swap(int i, int j) {
                        double temp_distance = distances.elementAt(i);
                        distances.set(i, distances.elementAt(j));
                        distances.set(j, temp_distance);

                        T temp_shape = shapes.elementAt(i);
                        shapes.set(i, shapes.elementAt(j));
                        shapes.set(j, temp_shape);
                    }

                    @Override
                    public int compare(int i, int j) {
                        // Note. Equality is not important to check because items with the
                        // same distance can be ordered anyway. 
                        if (distances.elementAt(i) == distances.elementAt(j))
                            return 0;
                        if (distances.elementAt(i) < distances.elementAt(j))
                            return -1;
                        return 1;
                    }
                };
                IndexedSorter sorter = new QuickSort();
                sorter.sort(s, 0, shapes.size());
                if (distances.elementAt(k - 1) > query_radius) {
                    result_correct = false;
                    query_radius = distances.elementAt(k);
                } else {
                    result_correct = true;
                }
            }
        } while (!result_correct);

        int result_size = Math.min(k, shapes.size());
        if (output != null) {
            for (int i = 0; i < result_size; i++) {
                output.collect(shapes.elementAt(i), distances.elementAt(i));
            }
        }
        return result_size;
    }

    protected static <S1 extends Shape, S2 extends Shape> int spatialJoinMemory(final RTree<S1> R,
            final RTree<S2> S, final ResultCollector2<S1, S2> output, final Reporter reporter) throws IOException {
        S1[] rs = (S1[]) Array.newInstance(R.stockObject.getClass(), R.getElementCount());
        int i = 0;
        for (S1 r : R)
            rs[i++] = (S1) r.clone();
        if (i != rs.length)
            throw new RuntimeException(i + "!=" + rs.length);

        S2[] ss = (S2[]) Array.newInstance(S.stockObject.getClass(), S.getElementCount());
        i = 0;
        for (S2 s : S)
            ss[i++] = (S2) s.clone();
        if (i != ss.length)
            throw new RuntimeException(i + "!=" + ss.length);

        return SpatialAlgorithms.SpatialJoin_planeSweep(rs, ss, output, reporter);
    }

    //LRU cache used to avoid deserializing the same records again and again
    static class LruCache<A, B> extends LinkedHashMap<A, B> {
        private static final long serialVersionUID = 702044567572914544L;
        private final int maxEntries;
        private B unusedEntry;

        public LruCache(final int maxEntries) {
            super(maxEntries + 1, 1.0f, true);
            this.maxEntries = maxEntries;
        }

        @Override
        protected boolean removeEldestEntry(final Map.Entry<A, B> eldest) {
            if (super.size() > maxEntries) {
                unusedEntry = eldest.getValue();
                return true;
            }
            return false;
        }

        public B popUnusedEntry() {
            B temp = unusedEntry;
            unusedEntry = null;
            return temp;
        }
    }

    /**
     * Performs a spatial join between records in two R-trees
     * @param R
     * @param S
     * @param output
     * @return
     * @throws IOException
     * SuppresWarnings("resource") is used because we create LineReaders on the
     * internal data stream of both R and S. We do not want to close the
     * LineReader because it will subsequently close the internal data stream
     * of R and S which is something we want to avoid because both R and S are
     * not created by this function and it should not free these resources.
     */
    protected static <S1 extends Shape, S2 extends Shape> int spatialJoinDisk(final RTree<S1> R, final RTree<S2> S,
            final ResultCollector2<S1, S2> output, final Reporter reporter) throws IOException {
        PriorityQueue<Long> nodesToJoin = new PriorityQueue<Long>(R.nodeCount + S.nodeCount);

        // Start with the two roots
        nodesToJoin.add(0L);

        // Caches to keep the retrieved data records. Helpful when it reaches the
        // leaves and starts to read objects from the two trees
        LruCache<Integer, Shape[]> r_records_cache = new LruCache<Integer, Shape[]>(R.degree * 2);
        LruCache<Integer, Shape[]> s_records_cache = new LruCache<Integer, Shape[]>(S.degree * R.degree * 4);

        Text line = new Text2();

        int result_count = 0;

        LineReader r_lr = null, s_lr = null;
        // Last offset read from r and s
        int r_last_offset = 0;
        int s_last_offset = 0;

        while (!nodesToJoin.isEmpty()) {
            long nodes_to_join = nodesToJoin.remove();
            int r_node = (int) (nodes_to_join >>> 32);
            int s_node = (int) (nodes_to_join & 0xFFFFFFFF);

            // Compute the overlap between the children of the two nodes
            // If a node is non-leaf, its children are other nodes
            // If a node is leaf, its children are data records
            boolean r_leaf = r_node >= R.nonLeafNodeCount;
            boolean s_leaf = s_node >= S.nonLeafNodeCount;

            if (!r_leaf && !s_leaf) {
                // Both are internal nodes, read child nodes under them
                // Find overlaps using a simple cross join (TODO: Use plane-sweep)
                for (int i = 0; i < R.degree; i++) {
                    int new_r_node = r_node * R.degree + i + 1;
                    for (int j = 0; j < S.degree; j++) {
                        int new_s_node = s_node * S.degree + j + 1;
                        if (R.nodes[new_r_node].isIntersected(S.nodes[new_s_node])) {
                            long new_pair = (((long) new_r_node) << 32) | new_s_node;
                            nodesToJoin.add(new_pair);
                        }
                    }
                }
            } else if (r_leaf && !s_leaf) {
                // R is a leaf node while S is an internal node
                // Compare the leaf node in R against all child nodes of S
                for (int j = 0; j < S.degree; j++) {
                    int new_s_node = s_node * S.degree + j + 1;
                    if (R.nodes[r_node].isIntersected(S.nodes[new_s_node])) {
                        long new_pair = (((long) r_node) << 32) | new_s_node;
                        nodesToJoin.add(new_pair);
                    }
                }
            } else if (!r_leaf && s_leaf) {
                // R is an internal node while S is a leaf node
                // Compare child nodes of R against the leaf node in S
                for (int i = 0; i < R.degree; i++) {
                    int new_r_node = r_node * R.degree + i + 1;
                    if (R.nodes[new_r_node].isIntersected(S.nodes[s_node])) {
                        long new_pair = (((long) new_r_node) << 32) | s_node;
                        nodesToJoin.add(new_pair);
                    }
                }
            } else if (r_leaf && s_leaf) {
                // Both are leaf nodes, join objects under them
                int r_start_offset = R.dataOffset[r_node];
                int r_end_offset = R.dataOffset[r_node + 1];
                int s_start_offset = S.dataOffset[s_node];
                int s_end_offset = S.dataOffset[s_node + 1];

                // Read or retrieve r_records
                Shape[] r_records = r_records_cache.get(r_start_offset);
                if (r_records == null) {
                    int cache_key = r_start_offset;
                    r_records = r_records_cache.popUnusedEntry();
                    if (r_records == null) {
                        r_records = new Shape[R.degree * 2];
                    }

                    // Need to read it from stream
                    if (r_last_offset != r_start_offset) {
                        long seekTo = r_start_offset + R.treeStartOffset;
                        R.data.seek(seekTo);
                        r_lr = new LineReader(R.data);
                    }
                    int record_i = 0;
                    while (r_start_offset < r_end_offset) {
                        r_start_offset += r_lr.readLine(line);
                        if (r_records[record_i] == null)
                            r_records[record_i] = R.stockObject.clone();
                        r_records[record_i].fromText(line);
                        record_i++;
                    }
                    r_last_offset = r_start_offset;
                    // Nullify other records
                    while (record_i < r_records.length)
                        r_records[record_i++] = null;
                    r_records_cache.put(cache_key, r_records);
                }

                // Read or retrieve s_records
                Shape[] s_records = s_records_cache.get(s_start_offset);
                if (s_records == null) {
                    int cache_key = s_start_offset;

                    // Need to read it from stream
                    if (s_lr == null || s_last_offset != s_start_offset) {
                        // Need to reposition s_lr (LineReader of S)
                        long seekTo = s_start_offset + S.treeStartOffset;
                        S.data.seek(seekTo);
                        s_lr = new LineReader(S.data);
                    }
                    s_records = s_records_cache.popUnusedEntry();
                    if (s_records == null) {
                        s_records = new Shape[S.degree * 2];
                    }
                    int record_i = 0;
                    while (s_start_offset < s_end_offset) {
                        s_start_offset += s_lr.readLine(line);
                        if (s_records[record_i] == null)
                            s_records[record_i] = S.stockObject.clone();
                        s_records[record_i].fromText(line);
                        record_i++;
                    }
                    // Nullify other records
                    while (record_i < s_records.length)
                        s_records[record_i++] = null;
                    // Put in cache
                    s_records_cache.put(cache_key, s_records);
                    s_last_offset = s_start_offset;
                }

                // Do Cartesian product between records to find overlapping pairs
                for (int i_r = 0; i_r < r_records.length && r_records[i_r] != null; i_r++) {
                    for (int i_s = 0; i_s < s_records.length && s_records[i_s] != null; i_s++) {
                        if (r_records[i_r].isIntersected(s_records[i_s])
                                && !r_records[i_r].equals(s_records[i_s])) {
                            result_count++;
                            if (output != null) {
                                output.collect((S1) r_records[i_r], (S2) s_records[i_s]);
                            }
                        }
                    }
                }
            }
            if (reporter != null)
                reporter.progress();
        }
        return result_count;
    }

    public static <S1 extends Shape, S2 extends Shape> int spatialJoin(final RTree<S1> R, final RTree<S2> S,
            final ResultCollector2<S1, S2> output, final Reporter reporter) throws IOException {
        try {
            if (R.treeStartOffset >= 0 && S.treeStartOffset >= 0) {
                // Both trees are read from disk
                return spatialJoinDisk(R, S, output, reporter);
            } else {
                return spatialJoinMemory(R, S, output, reporter);
            }
        } catch (TopologyException e) {
            e.printStackTrace();
            return 0;
        }
    }

    /**
     * Calculate the storage overhead required to build an RTree for the given
     * number of nodes.
     * @return - storage overhead in bytes
     */
    public static int calculateStorageOverhead(int elementCount, int degree) {
        // Update storage overhead
        int height = Math.max(1, (int) Math.ceil(Math.log(elementCount) / Math.log(degree)));
        int leafNodeCount = (int) Math.pow(degree, height - 1);
        if (elementCount <= 2 * leafNodeCount && height > 1) {
            height--;
            leafNodeCount = (int) Math.pow(degree, height - 1);
        }
        int nodeCount = (int) ((Math.pow(degree, height) - 1) / (degree - 1));
        int storage_overhead = 4 + TreeHeaderSize + nodeCount * NodeSize;
        return storage_overhead;
    }

    /**
     * Find log to the base 2 quickly
     * @param x
     * @return
     */
    public static int log2Floor(int x) {
        if (x == 0)
            return -1;
        int pos = 0;
        if ((x & 0xFFFF0000) != 0) {
            pos += 16;
            x >>>= 16;
        }
        if ((x & 0xFF00) != 0) {
            pos += 8;
            x >>>= 8;
        }
        if ((x & 0xF0) != 0) {
            pos += 4;
            x >>>= 4;
        }
        if ((x & 0xC) != 0) {
            pos += 2;
            x >>>= 2;
        }
        if ((x & 0x2) != 0) {
            pos++;
            x >>>= 1;
        }

        return pos;
    }

    public static int powInt(int base, int exponent) {
        int pow = 1;
        while (exponent != 0) {
            if ((exponent & 1) != 0)
                pow *= base;
            exponent >>>= 1;
            base *= base;
        }
        return pow;
    }

    private static final double LogLookupTable[];

    static {
        int count = 100;
        LogLookupTable = new double[count];
        for (int i = 0; i < count; i++) {
            LogLookupTable[i] = Math.log(i);
        }
    }

    public static double fastLog(int x) {
        if (x < LogLookupTable.length) {
            return LogLookupTable[x];
        }
        return Math.log(x);
    }

    public static double fastPow(double a, double b) {
        final long tmp = (long) (9076650 * (a - 1) / (a + 1 + 4 * (Math.sqrt(a))) * b + 1072632447);
        return Double.longBitsToDouble(tmp << 32);
    }

    /**
     * Find the best (minimum) degree that can index the given number of records
     * such that the whole tree structure can be stored in the given bytes
     * available.
     * @param bytesAvailable
     * @param recordCount
     * @return
     */
    public static int findBestDegree(int bytesAvailable, int recordCount) {
        // Maximum number of nodes that can be stored in the bytesAvailable
        int maxNodeCount = (bytesAvailable - TreeHeaderSize) / NodeSize;
        // Calculate maximum possible tree height to store the given record count
        int h_max = log2Floor(recordCount / 2);
        // Minimum height is always 1 (degree = recordCount)
        int h_min = 2;
        // Best degree is the minimum degree
        int d_best = Integer.MAX_VALUE;
        double log_recordcount_e = Math.log(recordCount / 2);
        double log_recordcount_2 = log_recordcount_e / fastLog(2);
        // Find the best height among all possible heights
        for (int h = h_min; h <= h_max; h++) {
            // Find the minimum degree for the given height (h)
            // This approximation is good enough for our case.
            // Not proven but tested with millions of random cases
            int d_min = (int) Math.ceil(fastPow(2.0, log_recordcount_2 / (h + 1)));
            // Some heights are invalid, recalculate the height to ensure it's valid
            int h_recalculated = (int) Math.floor(log_recordcount_e / fastLog(d_min));
            if (h != h_recalculated)
                continue;
            int nodeCount = (int) ((powInt(d_min, h + 1) - 1) / (d_min - 1));
            if (nodeCount < maxNodeCount && d_min < d_best)
                d_best = d_min;
        }

        return d_best;
    }

    public static int calculateTreeStorage(int elementCount, int degree) {
        int height = Math.max(1, (int) Math.ceil(Math.log(elementCount) / Math.log(degree)));
        int leafNodeCount = (int) Math.pow(degree, height - 1);
        if (elementCount < 2 * leafNodeCount && height > 1) {
            height--;
            leafNodeCount = (int) Math.pow(degree, height - 1);
        }
        int nodeCount = (int) ((Math.pow(degree, height) - 1) / (degree - 1));
        return TreeHeaderSize + nodeCount * NodeSize;
    }

    @Override
    public void close() throws IOException {
        if (data != null)
            data.close();
    }

    public void toWKT(PrintStream out) throws IOException {
        out.println("NodeID\tBoundaries");
        for (int nodeID = 0; nodeID < this.nodeCount; nodeID++) {
            out.printf("%d\t%s\n", nodeID, nodes[nodeID].toWKT());
        }
    }

    /**
     * A main method that creates a single R-tree out of a single file.
     * @param args
     * @throws IOException 
     */
    public static void main(String[] args) throws IOException {
        final OperationsParams params = new OperationsParams(new GenericOptionsParser(args));
        if (!params.checkInputOutput())
            throw new RuntimeException("Input-output combination not correct");
        Path inPath = params.getInputPath();
        Path outPath = params.getOutputPath();
        Shape shape = params.getShape("shape");

        // Read the whole input file as one byte array
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        byte[] buffer = new byte[1024 * 1024];
        FileSystem inFS = inPath.getFileSystem(params);
        FSDataInputStream in = inFS.open(inPath);
        int bytesRead;
        while ((bytesRead = in.read(buffer)) >= 0) {
            baos.write(buffer, 0, bytesRead);
        }
        in.close();
        baos.close();

        // Create the R-tree and write to output
        byte[] inputData = baos.toByteArray();
        FileSystem outFS = outPath.getFileSystem(params);
        FSDataOutputStream out = outFS.create(outPath);
        RTree.bulkLoadWrite(inputData, 0, inputData.length, 4, out, shape, true);
        out.close();
    }
}