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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This version represents the developer version, the
"bleeding edge" of development, you could say. New functionality gets added
to this version.
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see m_Colors = new ArrayList();
/**
* Number of rows of the visualization to compute in parallel. We don't want
* to dominate the thread pool that is used for executing all steps and step
* sub-tasks in the KF (this is currently fixed at 50 threads by FlowRunner).
*/
protected int m_maxRowsInParallel = 10;
/** Width of images to generate */
protected int m_imageWidth = 400;
/** Height of images to generate */
protected int m_imageHeight = 400;
/** X axis attribute name/index */
protected String m_xAttName = "/first";
/** Y axis attribute name/index */
protected String m_yAttName = "2";
/** Superimpose the training data on the plot? */
protected boolean m_plotTrainingData = true;
// attribute indices for visualizing on
protected int m_xAttribute;
protected int m_yAttribute;
// min, max and ranges of these attributes
protected double m_minX;
protected double m_minY;
protected double m_maxX;
protected double m_maxY;
protected double m_rangeX;
protected double m_rangeY;
// pixel width and height in terms of attribute values
protected double m_pixHeight;
protected double m_pixWidth;
/** The currently rendering image */
protected transient BufferedImage m_osi;
/** The spec of the scheme being used to render the current image */
protected String m_currentDescription;
/** Completed images */
protected transient Map m_completedImages;
/** Classifiers to use */
protected List m_classifierTemplates;
/** Clusterers to use */
protected List m_clustererTemplates;
/** Copies of trained classifier to use in parallel for prediction */
protected weka.classifiers.Classifier[] m_threadClassifiers;
/** Copies of trained clusterer to use in parallel for prediction */
protected weka.clusterers.Clusterer[] m_threadClusterers;
/** Data generator copies to use in parallel */
protected DataGenerator[] m_threadGenerators;
/** The data generator to use */
protected KDDataGenerator m_dataGenerator;
/** User-specified bandwidth */
protected String m_kBand = "3";
/** User-specified num samples */
protected String m_nSamples = "2";
/** User-specified base for sampling */
protected String m_sBase = "2";
/** Parsed bandwidth */
protected int m_kernelBandwidth = 3;
/** Parsed samples */
protected int m_numSamplesPerRegion = 2;
/** Parsed base */
protected int m_samplesBase = 2;
/** Open interactive view? */
protected transient RenderingUpdateListener m_plotListener;
/** True if we've been reset */
protected boolean m_isReset;
/**
* Constructor
*/
public BoundaryPlotter() {
for (Color element : DEFAULT_COLORS) {
m_Colors.add(new Color(element.getRed(), element.getGreen(), element
.getBlue()));
}
}
/**
* Set the name/index of the X axis attribute
*
* @param xAttName name/index of the X axis attribute
*/
// make programmatic as our dialog will handle these directly, rather than
// deferring to the GOE
@ProgrammaticProperty
@OptionMetadata(displayName = "X attribute",
description = "Attribute to visualize on the x-axis", displayOrder = 1)
public void setXAttName(String xAttName) {
m_xAttName = xAttName;
}
/**
* Get the name/index of the X axis attribute
*
* @return the name/index of the X axis attribute
*/
public String getXAttName() {
return m_xAttName;
}
/**
* Set the name/index of the Y axis attribute
*
* @param attName name/index of the Y axis attribute
*/
// make programmatic as our dialog will handle these directly, rather than
// deferring to the GOE
@ProgrammaticProperty
@OptionMetadata(displayName = "Y attribute",
description = "Attribute to visualize on the y-axis", displayOrder = 2)
public void setYAttName(String attName) {
m_yAttName = attName;
}
/**
* Get the name/index of the Y axis attribute
*
* @return the name/index of the Y axis attribute
*/
public String getYAttName() {
return m_yAttName;
}
/**
* Set the base for sampling
*
* @param base the base to use
*/
@OptionMetadata(displayName = "Base for sampling (r)",
description = "The base for sampling", displayOrder = 3)
public void setBaseForSampling(String base) {
m_sBase = base;
}
/**
* Get the base for sampling
*
* @return the base to use
*/
public String getBaseForSampling() {
return m_sBase;
}
/**
* Set the number of locations/samples per pixel
*
* @param num the number of samples to use
*/
@OptionMetadata(displayName = "Num. locations per pixel",
description = "Number of locations per pixel", displayOrder = 4)
public void setNumLocationsPerPixel(String num) {
m_nSamples = num;
}
/**
* Get the number of locations/samples per pixel
*
* @return the number of samples to use
*/
public String getNumLocationsPerPixel() {
return m_nSamples;
}
/**
* Set the kernel bandwidth
*
* @param band the bandwidth
*/
@OptionMetadata(displayName = "Kernel bandwidth (k)",
description = "Kernel bandwidth", displayOrder = 4)
public void setKernelBandwidth(String band) {
m_kBand = band;
}
/**
* Get the kernel bandwidth
*
* @return the bandwidth
*/
public String getKernelBandwidth() {
return m_kBand;
}
/**
* Set the image width (in pixels)
*
* @param width the width to use
*/
@OptionMetadata(displayName = "Image width (pixels)",
description = "Image width in pixels", displayOrder = 5)
public void setImageWidth(int width) {
m_imageWidth = width;
}
/**
* Get the image width (in pixels)
*
* @return the width to use
*/
public int getImageWidth() {
return m_imageWidth;
}
/**
* Set the image height (in pixels)
*
* @param height the height to use
*/
@OptionMetadata(displayName = "Image height (pixels)",
description = "Image height in pixels", displayOrder = 6)
public void setImageHeight(int height) {
m_imageHeight = height;
}
/**
* Get the image height (in pixels)
*
* @return the height to use
*/
public int getImageHeight() {
return m_imageHeight;
}
/**
* Set the maximum number of threads to use when computing image rows
*
* @param max maximum number of rows to compute in parallel
*/
@OptionMetadata(displayName = "Max image rows to compute in parallel",
description = "Use this many tasks for computing rows of the image",
displayOrder = 7)
public void setComputeMaxRowsInParallel(int max) {
if (max > 0) {
m_maxRowsInParallel = max;
}
}
/**
* Get the maximum number of threads to use when computing image rows
*
* @return the maximum number of rows to compute in parallel
*/
public int getComputeMaxRowsInParallel() {
return m_maxRowsInParallel;
}
/**
* Set whether to superimpose the training data points on the plot or not
*
* @param plot true to plot the training data
*/
@OptionMetadata(displayName = "Plot training points",
description = "Superimpose the training data over the top of the plot",
displayOrder = 8)
public void setPlotTrainingData(boolean plot) {
m_plotTrainingData = plot;
}
/**
* Get whether to superimpose the training data points on the plot or not
*
* @return true if plotting the training data
*/
public boolean getPlotTrainingData() {
return m_plotTrainingData;
}
/**
* Initialize the step.
*
* @throws WekaException if a problem occurs during initialization
*/
@Override
public void stepInit() throws WekaException {
List infos =
getStepManager().getIncomingConnectedStepsOfConnectionType(
StepManager.CON_INFO);
if (infos.size() == 0) {
throw new WekaException(
"One or more classifiers/clusterers need to be supplied via an 'info' "
+ "connection type");
}
m_classifierTemplates = new ArrayList();
m_clustererTemplates = new ArrayList();
for (StepManager m : infos) {
Step info = m.getInfoStep();
if (info instanceof weka.knowledgeflow.steps.Classifier) {
m_classifierTemplates.add(((weka.knowledgeflow.steps.Classifier) info)
.getClassifier());
} else if (info instanceof weka.knowledgeflow.steps.Clusterer) {
weka.clusterers.Clusterer c =
((weka.knowledgeflow.steps.Clusterer) info).getClusterer();
if (!(c instanceof DensityBasedClusterer)) {
throw new WekaException("Clusterer "
+ c.getClass().getCanonicalName()
+ " is not a DensityBasedClusterer");
}
m_clustererTemplates.add((DensityBasedClusterer) c);
}
}
m_completedImages = new LinkedHashMap();
if (m_nSamples != null && m_nSamples.length() > 0) {
String nSampes = environmentSubstitute(m_nSamples);
try {
m_numSamplesPerRegion = Integer.parseInt(nSampes);
} catch (NumberFormatException ex) {
getStepManager().logWarning(
"Unable to parse '" + nSampes + "' for num "
+ "samples per region parameter, using default: "
+ m_numSamplesPerRegion);
}
}
if (m_sBase != null && m_sBase.length() > 0) {
String sBase = environmentSubstitute(m_sBase);
try {
m_samplesBase = Integer.parseInt(sBase);
} catch (NumberFormatException ex) {
getStepManager().logWarning(
"Unable to parse '" + sBase + "' for "
+ "the base for sampling parameter, using default: "
+ m_samplesBase);
}
}
if (m_kBand != null && m_kBand.length() > 0) {
String kBand = environmentSubstitute(m_kBand);
try {
m_kernelBandwidth = Integer.parseInt(kBand);
} catch (NumberFormatException ex) {
getStepManager().logWarning(
"Unable to parse '" + kBand + "' for kernel "
+ "bandwidth parameter, using default: " + m_kernelBandwidth);
}
}
/*
* m_osi = new BufferedImage(m_imageWidth, m_imageHeight,
* BufferedImage.TYPE_INT_RGB);
*/
m_isReset = true;
}
protected void computeMinMaxAtts(Instances trainingData) {
m_minX = Double.MAX_VALUE;
m_minY = Double.MAX_VALUE;
m_maxX = Double.MIN_VALUE;
m_maxY = Double.MIN_VALUE;
boolean allPointsLessThanOne = true;
if (trainingData.numInstances() == 0) {
m_minX = m_minY = 0.0;
m_maxX = m_maxY = 1.0;
} else {
for (int i = 0; i < trainingData.numInstances(); i++) {
Instance inst = trainingData.instance(i);
double x = inst.value(m_xAttribute);
double y = inst.value(m_yAttribute);
if (!Utils.isMissingValue(x) && !Utils.isMissingValue(y)) {
if (x < m_minX) {
m_minX = x;
}
if (x > m_maxX) {
m_maxX = x;
}
if (y < m_minY) {
m_minY = y;
}
if (y > m_maxY) {
m_maxY = y;
}
if (x > 1.0 || y > 1.0) {
allPointsLessThanOne = false;
}
}
}
}
if (m_minX == m_maxX) {
m_minX = 0;
}
if (m_minY == m_maxY) {
m_minY = 0;
}
if (m_minX == Double.MAX_VALUE) {
m_minX = 0;
}
if (m_minY == Double.MAX_VALUE) {
m_minY = 0;
}
if (m_maxX == Double.MIN_VALUE) {
m_maxX = 1;
}
if (m_maxY == Double.MIN_VALUE) {
m_maxY = 1;
}
if (allPointsLessThanOne) {
// m_minX = m_minY = 0.0;
m_maxX = m_maxY = 1.0;
}
m_rangeX = (m_maxX - m_minX);
m_rangeY = (m_maxY - m_minY);
m_pixWidth = m_rangeX / m_imageWidth;
m_pixHeight = m_rangeY / m_imageHeight;
}
protected int getAttIndex(String attName, Instances data)
throws WekaException {
attName = environmentSubstitute(attName);
int index = -1;
if (attName.equalsIgnoreCase("first") || attName.equalsIgnoreCase("/first")) {
index = 0;
} else if (attName.equalsIgnoreCase("last")
|| attName.equalsIgnoreCase("/last")) {
index = data.numAttributes() - 1;
} else {
Attribute a = data.attribute(attName);
if (a != null) {
index = a.index();
} else {
// try parsing as a number
try {
index = Integer.parseInt(attName);
index--;
} catch (NumberFormatException ex) {
}
}
}
if (index == -1) {
throw new WekaException("Unable to find attribute '" + attName
+ "' in the data " + "or to parse it as an index");
}
return index;
}
protected void initDataGenerator(Instances trainingData) throws WekaException {
boolean[] attsToWeightOn;
// build DataGenerator
attsToWeightOn = new boolean[trainingData.numAttributes()];
attsToWeightOn[m_xAttribute] = true;
attsToWeightOn[m_yAttribute] = true;
m_dataGenerator = new KDDataGenerator();
m_dataGenerator.setWeightingDimensions(attsToWeightOn);
m_dataGenerator.setKernelBandwidth(m_kernelBandwidth);
try {
m_dataGenerator.buildGenerator(trainingData);
} catch (Exception ex) {
throw new WekaException(ex);
}
}
@Override
public synchronized void processIncoming(Data data) throws WekaException {
getStepManager().processing();
Instances training = data.getPrimaryPayload();
Integer setNum =
data.getPayloadElement(StepManager.CON_AUX_DATA_SET_NUM, 1);
Integer maxSetNum =
data.getPayloadElement(StepManager.CON_AUX_DATA_MAX_SET_NUM, 1);
m_xAttribute = getAttIndex(m_xAttName, training);
m_yAttribute = getAttIndex(m_yAttName, training);
computeMinMaxAtts(training);
initDataGenerator(training);
for (Classifier c : m_classifierTemplates) {
if (isStopRequested()) {
getStepManager().interrupted();
return;
}
// do classifiers
doScheme(c, null, training, setNum, maxSetNum);
}
for (DensityBasedClusterer c : m_clustererTemplates) {
if (isStopRequested()) {
getStepManager().interrupted();
return;
}
doScheme(null, c, training, setNum, maxSetNum);
}
if (isStopRequested()) {
getStepManager().interrupted();
} else {
getStepManager().finished();
}
}
protected void doScheme(Classifier classifier, DensityBasedClusterer clust,
Instances trainingData, int setNum, int maxSetNum) throws WekaException {
try {
m_osi =
new BufferedImage(m_imageWidth, m_imageHeight,
BufferedImage.TYPE_INT_RGB);
m_currentDescription =
makeSchemeSpec(classifier != null ? classifier : clust, setNum,
maxSetNum);
// notify listeners
getStepManager()
.logBasic("Starting new plot for " + m_currentDescription);
if (m_plotListener != null) {
m_plotListener.newPlotStarted(m_currentDescription);
}
Graphics m = m_osi.getGraphics();
m.fillRect(0, 0, m_imageWidth, m_imageHeight);
Classifier toTrainClassifier = null;
weka.clusterers.DensityBasedClusterer toTrainClusterer = null;
if (classifier != null) {
toTrainClassifier =
(Classifier) AbstractClassifier.makeCopy(classifier);
toTrainClassifier.buildClassifier(trainingData);
} else {
int tempClassIndex = trainingData.classIndex();
trainingData.setClassIndex(-1);
toTrainClusterer =
(DensityBasedClusterer) weka.clusterers.AbstractClusterer
.makeCopy((weka.clusterers.Clusterer) clust);
toTrainClusterer.buildClusterer(trainingData);
trainingData.setClassIndex(tempClassIndex);
}
// populate the thread classifiers ready for parallel processing
if (toTrainClassifier != null) {
m_threadClassifiers =
AbstractClassifier.makeCopies(toTrainClassifier, m_maxRowsInParallel);
} else {
m_threadClusterers =
AbstractClusterer.makeCopies(toTrainClusterer, m_maxRowsInParallel);
}
m_threadGenerators = new DataGenerator[m_maxRowsInParallel];
SerializedObject so = new SerializedObject(m_dataGenerator);
for (int i = 0; i < m_maxRowsInParallel; i++) {
m_threadGenerators[i] = (DataGenerator) so.getObject();
}
int taskCount = 0;
List>> results =
new ArrayList>>();
for (int i = 0; i < m_imageHeight; i++) {
if (taskCount < m_maxRowsInParallel) {
getStepManager().logDetailed(
"Launching task to compute image row " + i);
SchemeRowTask t = new SchemeRowTask(this);
t.setResourceIntensive(isResourceIntensive());
t.m_classifier = null;
t.m_clusterer = null;
if (toTrainClassifier != null) {
t.m_classifier = m_threadClassifiers[taskCount];
} else {
t.m_clusterer =
(DensityBasedClusterer) m_threadClusterers[taskCount];
}
t.m_rowNum = i;
t.m_xAtt = m_xAttribute;
t.m_yAtt = m_yAttribute;
t.m_imageWidth = m_imageWidth;
t.m_imageHeight = m_imageHeight;
t.m_pixWidth = m_pixWidth;
t.m_pixHeight = m_pixHeight;
t.m_dataGenerator = m_threadGenerators[taskCount];
t.m_trainingData = trainingData;
t.m_minX = m_minX;
t.m_maxX = m_maxX;
t.m_minY = m_minY;
t.m_maxY = m_maxY;
t.m_numOfSamplesPerRegion = m_numSamplesPerRegion;
t.m_samplesBase = m_samplesBase;
results.add(getStepManager().getExecutionEnvironment().submitTask(t));
taskCount++;
} else {
// wait for running tasks
for (Future> r : results) {
double[][] rowProbs = r.get().getResult().m_rowProbs;
for (int j = 0; j < m_imageWidth; j++) {
plotPoint(m_osi, j, r.get().getResult().m_rowNumber, rowProbs[j],
j == m_imageWidth - 1);
}
getStepManager().statusMessage(
"Completed row " + r.get().getResult().m_rowNumber);
getStepManager().logDetailed(
"Completed image row " + r.get().getResult().m_rowNumber);
}
results.clear();
taskCount = 0;
if (i != m_imageHeight - 1) {
i--;
}
if (isStopRequested()) {
return;
}
}
}
if (results.size() > 0) {
// wait for running tasks
for (Future> r : results) {
double[][] rowProbs = r.get().getResult().m_rowProbs;
for (int i = 0; i < m_imageWidth; i++) {
plotPoint(m_osi, i, r.get().getResult().m_rowNumber, rowProbs[i],
i == m_imageWidth - 1);
}
getStepManager().statusMessage(
"Completed row " + r.get().getResult().m_rowNumber);
getStepManager().logDetailed(
"Completed image row " + r.get().getResult().m_rowNumber);
}
if (isStopRequested()) {
return;
}
}
if (m_plotTrainingData) {
plotTrainingData(trainingData);
}
m_completedImages.put(m_currentDescription, m_osi);
Data imageOut = new Data(StepManager.CON_IMAGE, m_osi);
imageOut.setPayloadElement(StepManager.CON_AUX_DATA_TEXT_TITLE,
m_currentDescription);
getStepManager().outputData(imageOut);
} catch (Exception ex) {
throw new WekaException(ex);
}
}
protected String makeSchemeSpec(Object scheme, int setNum, int maxSetNum) {
String name = scheme.getClass().getCanonicalName();
name = name.substring(name.lastIndexOf('.') + 1, name.length());
if (scheme instanceof OptionHandler) {
name += " " + Utils.joinOptions(((OptionHandler) scheme).getOptions());
}
if (maxSetNum != 1) {
name += " (set " + setNum + " of " + maxSetNum + ")";
}
return name;
}
protected void plotPoint(BufferedImage osi, int x, int y, double[] probs,
boolean update) {
Graphics osg = osi.getGraphics();
osg.setPaintMode();
float[] colVal = new float[3];
float[] tempCols = new float[3];
for (int k = 0; k < probs.length; k++) {
Color curr = m_Colors.get(k % m_Colors.size());
curr.getRGBColorComponents(tempCols);
for (int z = 0; z < 3; z++) {
colVal[z] += probs[k] * tempCols[z];
}
}
for (int z = 0; z < 3; z++) {
if (colVal[z] < 0) {
colVal[z] = 0;
} else if (colVal[z] > 1) {
colVal[z] = 1;
}
}
osg.setColor(new Color(colVal[0], colVal[1], colVal[2]));
osg.fillRect(x, y, 1, 1);
if (update) {
// end of row
// generate an update event for interactive viewer to consume
if (m_plotListener != null) {
m_plotListener.currentPlotRowCompleted(y);
}
}
}
public void plotTrainingData(Instances trainingData) {
Graphics2D osg = (Graphics2D) m_osi.getGraphics();
// Graphics g = m_plotPanel.getGraphics();
osg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
double xval = 0;
double yval = 0;
for (int i = 0; i < trainingData.numInstances(); i++) {
if (!trainingData.instance(i).isMissing(m_xAttribute)
&& !trainingData.instance(i).isMissing(m_yAttribute)) {
xval = trainingData.instance(i).value(m_xAttribute);
yval = trainingData.instance(i).value(m_yAttribute);
int panelX = convertToImageX(xval);
int panelY = convertToImageY(yval);
Color colorToPlotWith = Color.white;
if (trainingData.classIndex() > 0) {
colorToPlotWith =
m_Colors.get((int) trainingData.instance(i).value(
trainingData.classIndex())
% m_Colors.size());
}
if (colorToPlotWith.equals(Color.white)) {
osg.setColor(Color.black);
} else {
osg.setColor(Color.white);
}
osg.fillOval(panelX - 3, panelY - 3, 7, 7);
osg.setColor(colorToPlotWith);
osg.fillOval(panelX - 2, panelY - 2, 5, 5);
}
}
if (m_plotListener != null) {
m_plotListener.renderingImageUpdate();
}
}
private int convertToImageX(double xval) {
double temp = (xval - m_minX) / m_rangeX;
temp = temp * m_imageWidth;
return (int) temp;
}
private int convertToImageY(double yval) {
double temp = (yval - m_minY) / m_rangeY;
temp = temp * m_imageHeight;
temp = m_imageHeight - temp;
return (int) temp;
}
/**
* Get a list of incoming connection types that this step can accept. Ideally
* (and if appropriate), this should take into account the state of the step
* and any existing incoming connections. E.g. a step might be able to accept
* one (and only one) incoming batch data connection.
*
* @return a list of incoming connections that this step can accept given its
* current state
*/
@Override
public List getIncomingConnectionTypes() {
return Arrays.asList(StepManager.CON_DATASET, StepManager.CON_TRAININGSET,
StepManager.CON_INFO);
}
/**
* Get a list of outgoing connection types that this step can produce. Ideally
* (and if appropriate), this should take into account the state of the step
* and the incoming connections. E.g. depending on what incoming connection is
* present, a step might be able to produce a trainingSet output, a testSet
* output or neither, but not both.
*
* @return a list of outgoing connections that this step can produce
*/
@Override
public List getOutgoingConnectionTypes() {
return Arrays.asList(StepManager.CON_IMAGE);
}
/**
* Get the completed images
*
* @return a map of completed images
*/
public Map getImages() {
return m_completedImages;
}
/**
* Get the currently rendering image
*
* @return the current image
*/
public BufferedImage getCurrentImage() {
return m_osi;
}
/**
* Set a listener to receive rendering updates
*
* @param l the {@code RenderingUpdateListener} to add
*/
public void setRenderingListener(RenderingUpdateListener l) {
m_plotListener = l;
}
/**
* Remove the rendering update listener
*
* @param l the {@code RenderingUpdateListener} to remove
*/
public void removeRenderingListener(RenderingUpdateListener l) {
if (l == m_plotListener) {
m_plotListener = null;
}
}
/**
* When running in a graphical execution environment a step can make one or
* more popup Viewer components available. These might be used to display
* results, graphics etc. Returning null indicates that the step has no such
* additional graphical views. The map returned by this method should be keyed
* by action name (e.g. "View results"), and values should be fully qualified
* names of the corresponding StepInteractiveView implementation. Furthermore,
* the contents of this map can (and should) be dependent on whether a
* particular viewer should be made available - i.e. if execution hasn't
* occurred yet, or if a particular incoming connection type is not present,
* then it might not be possible to view certain results.
*
* Viewers can implement StepInteractiveView directly (in which case they need
* to extends JPanel), or extends the AbstractInteractiveViewer class. The
* later extends JPanel, uses a BorderLayout, provides a "Close" button and a
* method to add additional buttons.
*
* @return a map of viewer component names, or null if this step has no
* graphical views
*/
@Override
public Map getInteractiveViewers() {
Map views = new LinkedHashMap();
if (m_plotListener == null) {
views.put("Show plots",
"weka.gui.knowledgeflow.steps.BoundaryPlotterInteractiveView");
}
return views;
}
/**
* Return the fully qualified name of a custom editor component (JComponent)
* to use for editing the properties of the step. This method can return null,
* in which case the system will dynamically generate an editor using the
* GenericObjectEditor
*
* @return the fully qualified name of a step editor component
*/
@Override
public String getCustomEditorForStep() {
return "weka.gui.knowledgeflow.steps.BoundaryPlotterStepEditorDialog";
}
/**
* Get the map of completed images
*
* @return the map of completed images
*/
@Override
public Object retrieveData() {
return ImageViewer.bufferedImageMapToSerializableByteMap(m_completedImages);
}
/**
* Set a map of images.
*
* @param data the images to set
* @throws WekaException if a problem occurs
*/
@Override
@SuppressWarnings("unchecked")
public void restoreData(Object data) throws WekaException {
if (!(data instanceof Map)) {
throw new IllegalArgumentException("Argument must be a Map");
}
try {
m_completedImages =
ImageViewer
.byteArrayImageMapToBufferedImageMap((Map) data);
} catch (IOException ex) {
throw new WekaException(ex);
}
}
/**
* Interface for something that wants to be informed of rendering progress
* updates
*/
public interface RenderingUpdateListener {
/**
* Called when a new plot is started
*
* @param description the description/title of the plot
*/
void newPlotStarted(String description);
/**
* Called when rendering of a row in the current plot has completed
*
* @param row the index of the row that was completed
*/
void currentPlotRowCompleted(int row);
/**
* Called when a change (other than rendering a row) to the current plot has
* occurred.
*/
void renderingImageUpdate();
}
/**
* Holds computed image data for a row of an image
*/
protected static class RowResult {
/** Probabilities for the pixels in a row of the image */
protected double[][] m_rowProbs;
/** The row number of this result */
protected int m_rowNumber;
}
/**
* A task for computing a row of an image using a trained model
*/
protected static class SchemeRowTask extends StepTask implements
Serializable {
private static final long serialVersionUID = -4144732293602550066L;
protected int m_xAtt;
protected int m_yAtt;
protected int m_rowNum;
protected int m_imageWidth;
protected int m_imageHeight;
protected double m_pixWidth;
protected double m_pixHeight;
protected weka.classifiers.Classifier m_classifier;
protected weka.clusterers.DensityBasedClusterer m_clusterer;
protected DataGenerator m_dataGenerator;
protected Instances m_trainingData;
protected double m_minX;
protected double m_maxX;
protected double m_minY;
protected double m_maxY;
protected int m_numOfSamplesPerRegion;
protected double m_samplesBase;
private Random m_random;
private int m_numOfSamplesPerGenerator;
private boolean[] m_attsToWeightOn;
private double[] m_weightingAttsValues;
private double[] m_vals;
private double[] m_dist;
Instance m_predInst;
public SchemeRowTask(Step source) {
super(source);
}
@Override
public void process() throws Exception {
RowResult result = new RowResult();
result.m_rowNumber = m_rowNum;
result.m_rowProbs = new double[m_imageWidth][0];
m_random = new Random(m_rowNum * 11);
m_dataGenerator.setSeed(m_rowNum * 11);
m_numOfSamplesPerGenerator =
(int) Math.pow(m_samplesBase, m_trainingData.numAttributes() - 3);
if (m_trainingData == null) {
throw new Exception("No training data set");
}
if (m_classifier == null && m_clusterer == null) {
throw new Exception("No scheme set");
}
if (m_dataGenerator == null) {
throw new Exception("No data generator set");
}
if (m_trainingData.attribute(m_xAtt).isNominal()
|| m_trainingData.attribute(m_yAtt).isNominal()) {
throw new Exception("Visualization dimensions must be numeric");
}
m_attsToWeightOn = new boolean[m_trainingData.numAttributes()];
m_attsToWeightOn[m_xAtt] = true;
m_attsToWeightOn[m_yAtt] = true;
// generate samples
m_weightingAttsValues = new double[m_attsToWeightOn.length];
m_vals = new double[m_trainingData.numAttributes()];
m_predInst = new DenseInstance(1.0, m_vals);
m_predInst.setDataset(m_trainingData);
getLogHandler().logDetailed("Computing row number: " + m_rowNum);
for (int j = 0; j < m_imageWidth; j++) {
double[] preds = calculateRegionProbs(j, m_rowNum);
result.m_rowProbs[j] = preds;
}
getExecutionResult().setResult(result);
}
private double[] calculateRegionProbs(int j, int i) throws Exception {
double[] sumOfProbsForRegion =
new double[m_classifier != null ? m_trainingData.classAttribute()
.numValues() : ((weka.clusterers.Clusterer) m_clusterer)
.numberOfClusters()];
double sumOfSums = 0;
for (int u = 0; u < m_numOfSamplesPerRegion; u++) {
double[] sumOfProbsForLocation =
new double[m_classifier != null ? m_trainingData.classAttribute()
.numValues() : ((weka.clusterers.Clusterer) m_clusterer)
.numberOfClusters()];
m_weightingAttsValues[m_xAtt] = getRandomX(j);
m_weightingAttsValues[m_yAtt] = getRandomY(m_imageHeight - i - 1);
m_dataGenerator.setWeightingValues(m_weightingAttsValues);
double[] weights = m_dataGenerator.getWeights();
double sumOfWeights = Utils.sum(weights);
sumOfSums += sumOfWeights;
int[] indices = Utils.sort(weights);
// Prune 1% of weight mass
int[] newIndices = new int[indices.length];
double sumSoFar = 0;
double criticalMass = 0.99 * sumOfWeights;
int index = weights.length - 1;
int counter = 0;
for (int z = weights.length - 1; z >= 0; z--) {
newIndices[index--] = indices[z];
sumSoFar += weights[indices[z]];
counter++;
if (sumSoFar > criticalMass) {
break;
}
}
indices = new int[counter];
System.arraycopy(newIndices, index + 1, indices, 0, counter);
for (int z = 0; z < m_numOfSamplesPerGenerator; z++) {
m_dataGenerator.setWeightingValues(m_weightingAttsValues);
double[][] values = m_dataGenerator.generateInstances(indices);
for (int q = 0; q < values.length; q++) {
if (values[q] != null) {
System.arraycopy(values[q], 0, m_vals, 0, m_vals.length);
m_vals[m_xAtt] = m_weightingAttsValues[m_xAtt];
m_vals[m_yAtt] = m_weightingAttsValues[m_yAtt];
// classify/cluster the instance
m_dist =
m_classifier != null ? m_classifier
.distributionForInstance(m_predInst) : m_clusterer
.distributionForInstance(m_predInst);
for (int k = 0; k < sumOfProbsForLocation.length; k++) {
sumOfProbsForLocation[k] += (m_dist[k] * weights[q]);
}
}
}
}
for (int k = 0; k < sumOfProbsForRegion.length; k++) {
sumOfProbsForRegion[k] +=
(sumOfProbsForLocation[k] / m_numOfSamplesPerGenerator);
}
}
if (sumOfSums > 0) {
// average
Utils.normalize(sumOfProbsForRegion, sumOfSums);
} else {
throw new Exception(
"Arithmetic underflow. Please increase value of kernel bandwidth " +
"parameter (k).");
}
// cache
double[] tempDist = new double[sumOfProbsForRegion.length];
System.arraycopy(sumOfProbsForRegion, 0, tempDist, 0,
sumOfProbsForRegion.length);
return tempDist;
}
/**
* Return a random x attribute value contained within the pix'th horizontal
* pixel
*
* @param pix the horizontal pixel number
* @return a value in attribute space
*/
private double getRandomX(int pix) {
double minPix = m_minX + (pix * m_pixWidth);
return minPix + m_random.nextDouble() * m_pixWidth;
}
/**
* Return a random y attribute value contained within the pix'th vertical
* pixel
*
* @param pix the vertical pixel number
* @return a value in attribute space
*/
private double getRandomY(int pix) {
double minPix = m_minY + (pix * m_pixHeight);
return minPix + m_random.nextDouble() * m_pixHeight;
}
}
}
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