edu.stanford.rsl.conrad.segmentation.MetaFeatureExtractor.java Source code

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Here is the source code for edu.stanford.rsl.conrad.segmentation.MetaFeatureExtractor.java

Source

/*
 * Copyright (C) 2017 Andreas Maier
 * CONRAD is developed as an Open Source project under the GNU General Public License (GPL).
 */
package edu.stanford.rsl.conrad.segmentation;

import ij.gui.GenericDialog;

import java.util.ArrayList;

import edu.stanford.rsl.conrad.data.numeric.Grid2D;
import edu.stanford.rsl.conrad.utils.CONRAD;
import weka.core.Attribute;
import weka.core.Instances;

public class MetaFeatureExtractor extends GridFeatureExtractor {

    /**
     * 
     */
    private static final long serialVersionUID = -7493565581383426078L;
    ArrayList<Object> knownExtractors;

    boolean[] selection;

    public Instances getInstances() {
        return instances;
    }

    protected Attribute generateClassAttribute() {
        Attribute classAttribute = null;
        if (classValues == null) {
            classAttribute = new Attribute("Class");
        } else {
            classAttribute = new Attribute(className, classValues);
        }
        classAttribute = new Attribute(className);
        return classAttribute;
    }

    @Override
    public void prepareForSerialization() {
        super.prepareForSerialization();
        if (knownExtractors != null) {
            for (int i = 0; i < knownExtractors.size(); i++) {
                GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
                gridFex.prepareForSerialization();
            }
        }
    }

    @Override
    public void setLabelGrid(Grid2D labelGrid) {
        super.setLabelGrid(labelGrid);
        if (knownExtractors != null) {
            for (int i = 0; i < knownExtractors.size(); i++) {
                if (selection[i]) {
                    GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
                    gridFex.setLabelGrid(labelGrid);
                }
            }
        }
    }

    @Override
    public void setDataGrid(Grid2D dataGrid) {
        super.setDataGrid(dataGrid);
        if (knownExtractors != null) {
            for (int i = 0; i < knownExtractors.size(); i++) {
                if (selection[i]) {
                    GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
                    gridFex.setDataGrid(dataGrid);
                    ;
                }
            }
        }
    }

    public void configure() throws Exception {

        knownExtractors = CONRAD.getInstancesFromConrad(GridFeatureExtractor.class);
        selection = new boolean[knownExtractors.size()];

        GenericDialog gDialog = new GenericDialog("Feature Configuration");
        gDialog.addMessage("Select features:");

        for (int i = 0; i < knownExtractors.size(); i++) {
            GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
            if (!(gridFex instanceof MetaFeatureExtractor)) {
                gDialog.addCheckbox(gridFex.toString(), true);
            }
        }

        gDialog.showDialog();

        for (int i = 0; i < knownExtractors.size(); i++) {
            GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
            if (!(gridFex instanceof MetaFeatureExtractor)) {
                selection[i] = gDialog.getNextBoolean();
                if (selection[i]) {
                    gridFex.labelGrid = this.labelGrid;
                    gridFex.dataGrid = this.dataGrid;
                    gridFex.configure();
                    this.attribs = combineAttribs(this.attribs, gridFex.attribs);
                }
            } else {
                selection[i] = false;
            }
        }

        Attribute classAttribute = generateClassAttribute();
        attribs.add(classAttribute);

        // leeres set von feature vectoren
        instances = new Instances(className, attribs, 0);
        instances.setClass(classAttribute);
        configured = true;
    }

    @Override
    public double[] extractFeatureAtIndex(int x, int y) {

        double[] vector = new double[attribs.size()];
        int currentCount = 0;

        for (int i = 0; i < selection.length; i++) {
            if (selection[i]) {
                GridFeatureExtractor gridFex = (GridFeatureExtractor) knownExtractors.get(i);
                double[] localFeatureVector = gridFex.extractFeatureAtIndex(x, y);
                for (int j = 0; j < localFeatureVector.length - 1; j++) {
                    vector[j + currentCount] = localFeatureVector[j];
                }
                currentCount += localFeatureVector.length - 1;
            }
        }

        vector[vector.length - 1] = this.labelGrid.getAtIndex(x, y);
        return vector;

    }

    public static ArrayList<Attribute> combineAttribs(ArrayList<Attribute> a, ArrayList<Attribute> b) {

        if (a == null) {
            a = new ArrayList<Attribute>(0);
        }
        for (int i = 0; i < b.size() - 1; i++) {
            a.add(b.get(i));
        }
        return a;
    }

    @Override
    public String getName() {
        return "Meta Features (any combination of features)";
    }

}