edu.ucsf.valelab.saim.data.IntensityData.java Source code

Introduction

Here is the source code for edu.ucsf.valelab.saim.data.IntensityData.java

Source

///////////////////////////////////////////////////////////////////////////////
//FILE:          IntensityData.java
//PROJECT:       SAIM
//-----------------------------------------------------------------------------
//
// AUTHOR:       Nico Stuurman
//
// COPYRIGHT:    University of California, San Francisco 2015
//
// LICENSE:      This file is distributed under the BSD license.
//               License text is included with the source distribution.
//
//               This file 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.
//
//               IN NO EVENT SHALL THE COPYRIGHT OWNER OR
//               CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
//               INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES.

package edu.ucsf.valelab.saim.data;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.apache.commons.math3.fitting.WeightedObservedPoint;
import org.jfree.data.xy.XYSeries;

/**
 * Utility to isolate our own data storage mechanism from that of outside 
 * libraries
 * Use this to hold data, and expand output functions as needed
 * @author nico
 */
public class IntensityData {
    private final List<IntensityDataItem> data_;

    public IntensityData() {
        data_ = new ArrayList<IntensityDataItem>();
    }

    public void add(double angle, double intensity, boolean isRadians) {
        IntensityDataItem item = new IntensityDataItem(angle, intensity, isRadians);
        data_.add(item);
    }

    public void add(double angleDegrees, double angleRadians, double intensity) {
        IntensityDataItem item = new IntensityDataItem(angleDegrees, angleRadians, intensity);
        data_.add(item);
    }

    public int size() {
        return data_.size();
    }

    public void clear() {
        data_.clear();
    }

    public double avg() {
        double sum = 0.0;
        for (IntensityDataItem item : data_) {
            sum += item.getIntensity();
        }
        return (sum / (double) data_.size());
    }

    /**
     * Output as needed by apache commons Math library for fitting
     * Currently assigns the weight 1.0 to all points
     * @return list of weightedObservedPoints for fitting
     */
    public ArrayList<WeightedObservedPoint> getWeightedObservedPoints() {
        ArrayList<WeightedObservedPoint> points = new ArrayList<WeightedObservedPoint>();
        for (IntensityDataItem item : data_) {
            points.add(new WeightedObservedPoint(1.0, item.getAngleRadians(), item.getIntensity()));
        }
        return points;
    }

    /**
     * Returns data in a form usable by the JFreeChart library
     * @param name of the data series in JFreeChart
     * @return JFreeChart XYSeries
     */
    public XYSeries getXYSeries(String name) {
        XYSeries series = new XYSeries(name, false, false);
        for (IntensityDataItem item : data_) {
            series.add(item.getAngleDegree(), item.getIntensity());
        }
        return series;
    }

    /**
     * Provide access to a read-only version so that the user can iterate 
     * easily over the data without risking modifications
     * @return read-only version of the data
     */
    public List<IntensityDataItem> getDataList() {
        return Collections.unmodifiableList(data_);
    }
}