diff options
author | Andrej Shadura <andrewsh@debian.org> | 2019-03-09 22:30:32 +0000 |
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committer | Andrej Shadura <andrewsh@debian.org> | 2019-03-09 22:30:32 +0000 |
commit | c36aa2a8fd31ca5e225ff30278e910070cd2c8c1 (patch) | |
tree | bdfe1a5ccb57999d4d664a2a44121a78c88b19d4 /src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java | |
parent | 89aa1958dbaf9052da0c24706308a2ef8cefa96e (diff) |
Import Upstream version 0.5.0~beta2
Diffstat (limited to 'src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java')
-rw-r--r-- | src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java | 236 |
1 files changed, 236 insertions, 0 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java b/src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java new file mode 100644 index 00000000..28e4da32 --- /dev/null +++ b/src/de/lmu/ifi/dbs/elki/visualization/visualizers/scatterplot/density/DensityEstimationOverlay.java @@ -0,0 +1,236 @@ +package de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.density; + +/* + This file is part of ELKI: + Environment for Developing KDD-Applications Supported by Index-Structures + + Copyright (C) 2012 + Ludwig-Maximilians-Universität München + Lehr- und Forschungseinheit für Datenbanksysteme + ELKI Development Team + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + */ +import java.awt.image.BufferedImage; +import java.util.Arrays; +import java.util.Comparator; + +import org.apache.batik.util.SVGConstants; +import org.w3c.dom.Element; + +import de.lmu.ifi.dbs.elki.database.ids.DBID; +import de.lmu.ifi.dbs.elki.math.MathUtil; +import de.lmu.ifi.dbs.elki.math.MeanVariance; +import de.lmu.ifi.dbs.elki.result.HierarchicalResult; +import de.lmu.ifi.dbs.elki.result.KMLOutputHandler; +import de.lmu.ifi.dbs.elki.result.Result; +import de.lmu.ifi.dbs.elki.result.ResultUtil; +import de.lmu.ifi.dbs.elki.utilities.documentation.Reference; +import de.lmu.ifi.dbs.elki.utilities.iterator.IterableIterator; +import de.lmu.ifi.dbs.elki.visualization.VisualizationTask; +import de.lmu.ifi.dbs.elki.visualization.batikutil.ThumbnailRegistryEntry; +import de.lmu.ifi.dbs.elki.visualization.projections.CanvasSize; +import de.lmu.ifi.dbs.elki.visualization.projector.ScatterPlotProjector; +import de.lmu.ifi.dbs.elki.visualization.svg.SVGUtil; +import de.lmu.ifi.dbs.elki.visualization.visualizers.AbstractVisFactory; +import de.lmu.ifi.dbs.elki.visualization.visualizers.Visualization; +import de.lmu.ifi.dbs.elki.visualization.visualizers.scatterplot.AbstractScatterplotVisualization; + +/** + * A simple density estimation visualization, based on a simple kernel-density + * <em>in the projection, not the actual data!</em> + * + * @author Erich Schubert + */ +// TODO: make parameterizable, in particular color map, kernel bandwidth and +// kernel function +public class DensityEstimationOverlay extends AbstractScatterplotVisualization { + /** + * A short name characterizing this Visualizer. + */ + private static final String NAME = "Density estimation overlay"; + + /** + * Density map resolution + */ + private int resolution = 500; + + /** + * The actual image + */ + private BufferedImage img = null; + + /** + * Constructor. + * + * @param task Task + */ + public DensityEstimationOverlay(VisualizationTask task) { + super(task); + incrementalRedraw(); + } + + @Override + protected void redraw() { + if(img == null) { + renderImage(); + } + + CanvasSize canvas = proj.estimateViewport(); + String imguri = ThumbnailRegistryEntry.INTERNAL_PREFIX + ThumbnailRegistryEntry.registerImage(img); + Element itag = svgp.svgElement(SVGConstants.SVG_IMAGE_TAG); + SVGUtil.setAtt(itag, SVGConstants.SVG_IMAGE_RENDERING_ATTRIBUTE, SVGConstants.SVG_OPTIMIZE_SPEED_VALUE); + SVGUtil.setAtt(itag, SVGConstants.SVG_X_ATTRIBUTE, canvas.minx); + SVGUtil.setAtt(itag, SVGConstants.SVG_Y_ATTRIBUTE, canvas.miny); + SVGUtil.setAtt(itag, SVGConstants.SVG_WIDTH_ATTRIBUTE, canvas.maxx - canvas.minx); + SVGUtil.setAtt(itag, SVGConstants.SVG_HEIGHT_ATTRIBUTE, canvas.maxy - canvas.miny); + SVGUtil.setAtt(itag, SVGConstants.SVG_STYLE_ATTRIBUTE, SVGConstants.CSS_OPACITY_PROPERTY + ": .5"); + itag.setAttributeNS(SVGConstants.XLINK_NAMESPACE_URI, SVGConstants.XLINK_HREF_QNAME, imguri); + + layer.appendChild(itag); + } + + @Reference(authors = "D. W. Scott", title = "Multivariate density estimation", booktitle = "Multivariate Density Estimation: Theory, Practice, and Visualization", url = "http://dx.doi.org/10.1002/9780470316849.fmatter") + private double[] initializeBandwidth(double[][] data) { + MeanVariance mv0 = new MeanVariance(); + MeanVariance mv1 = new MeanVariance(); + // For Kernel bandwidth. + for(double[] projected : data) { + mv0.put(projected[0]); + mv1.put(projected[1]); + } + // Set bandwidths according to Scott's rule: + // Note: in projected space, d=2. + double[] bandwidth = new double[2]; + bandwidth[0] = MathUtil.SQRT5 * mv0.getSampleStddev() * Math.pow(rel.size(), -1 / 6.); + bandwidth[1] = MathUtil.SQRT5 * mv1.getSampleStddev() * Math.pow(rel.size(), -1 / 6.); + return bandwidth; + } + + private void renderImage() { + // TODO: SAMPLE? Do region queries? + // Project the data just once, keep a copy. + double[][] data = new double[rel.size()][]; + { + int i = 0; + for(DBID id : rel.iterDBIDs()) { + data[i] = proj.fastProjectDataToRenderSpace(rel.get(id)); + i++; + } + } + double[] bandwidth = initializeBandwidth(data); + // Compare by first component + Comparator<double[]> comp0 = new Comparator<double[]>() { + @Override + public int compare(double[] o1, double[] o2) { + return Double.compare(o1[0], o2[0]); + } + }; + // Compare by second component + Comparator<double[]> comp1 = new Comparator<double[]>() { + @Override + public int compare(double[] o1, double[] o2) { + return Double.compare(o1[1], o2[1]); + } + }; + // TODO: choose comparator order based on smaller bandwidth? + Arrays.sort(data, comp0); + + CanvasSize canvas = proj.estimateViewport(); + double min0 = canvas.minx, max0 = canvas.maxx, ste0 = (max0 - min0) / resolution; + double min1 = canvas.miny, max1 = canvas.maxy, ste1 = (max1 - min1) / resolution; + + double kernf = 9. / (16 * bandwidth[0] * bandwidth[1]); + double maxdens = 0.0; + double[][] dens = new double[resolution][resolution]; + { + // TODO: incrementally update the loff/roff values? + for(int x = 0; x < resolution; x++) { + double xlow = min0 + ste0 * x, xhig = xlow + ste0; + int loff = unflip(Arrays.binarySearch(data, new double[] { xlow - bandwidth[0] }, comp0)); + int roff = unflip(Arrays.binarySearch(data, new double[] { xhig + bandwidth[0] }, comp0)); + // Resort by second component + Arrays.sort(data, loff, roff, comp1); + for(int y = 0; y < resolution; y++) { + double ylow = min1 + ste1 * y, yhig = ylow + ste1; + int boff = unflip(Arrays.binarySearch(data, loff, roff, new double[] { 0, ylow - bandwidth[1] }, comp1)); + int toff = unflip(Arrays.binarySearch(data, loff, roff, new double[] { 0, yhig + bandwidth[1] }, comp1)); + for(int pos = boff; pos < toff; pos++) { + double[] val = data[pos]; + double d0 = (val[0] < xlow) ? (xlow - val[0]) : (val[0] > xhig) ? (val[0] - xhig) : 0; + double d1 = (val[1] < ylow) ? (ylow - val[1]) : (val[1] > yhig) ? (val[1] - yhig) : 0; + d0 = d0 / bandwidth[0]; + d1 = d1 / bandwidth[1]; + dens[x][y] += kernf * (1 - d0 * d0) * (1 - d1 * d1); + } + maxdens = Math.max(maxdens, dens[x][y]); + } + // Restore original sorting, as the intervals overlap + Arrays.sort(data, loff, roff, comp0); + } + } + img = new BufferedImage(resolution, resolution, BufferedImage.TYPE_INT_ARGB); + { + for(int x = 0; x < resolution; x++) { + for(int y = 0; y < resolution; y++) { + int rgb = KMLOutputHandler.getColorForValue(dens[x][y] / maxdens).getRGB(); + img.setRGB(x, y, rgb); + } + } + } + } + + private int unflip(int binarySearch) { + if(binarySearch < 0) { + return (-binarySearch) - 1; + } + else { + return binarySearch; + } + } + + /** + * The visualization factory + * + * @author Erich Schubert + * + * @apiviz.stereotype factory + * @apiviz.uses DensityEstimation2DVisualization oneway - - «create» + */ + public static class Factory extends AbstractVisFactory { + /** + * Constructor, adhering to + * {@link de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable} + */ + public Factory() { + super(); + } + + @Override + public Visualization makeVisualization(VisualizationTask task) { + return new DensityEstimationOverlay(task); + } + + @Override + public void processNewResult(HierarchicalResult baseResult, Result result) { + IterableIterator<ScatterPlotProjector<?>> ps = ResultUtil.filteredResults(result, ScatterPlotProjector.class); + for(ScatterPlotProjector<?> p : ps) { + final VisualizationTask task = new VisualizationTask(NAME, p.getRelation(), p.getRelation(), this); + task.put(VisualizationTask.META_LEVEL, VisualizationTask.LEVEL_DATA + 1); + task.put(VisualizationTask.META_VISIBLE_DEFAULT, false); + baseResult.getHierarchy().add(p, task); + } + } + } +}
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