Example usage for org.apache.commons.math3.analysis.interpolation SplineInterpolator SplineInterpolator

List of usage examples for org.apache.commons.math3.analysis.interpolation SplineInterpolator SplineInterpolator

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Introduction

In this page you can find the example usage for org.apache.commons.math3.analysis.interpolation SplineInterpolator SplineInterpolator.

Prototype

SplineInterpolator

Source Link

Usage

From source file:uk.ac.diamond.scisoft.ncd.calibration.NCDAbsoluteCalibration.java

public void setAbsoluteData(List<Amount<ScatteringVector>> lstAbsQ, Dataset absI, Unit<ScatteringVector> unit) {
    absQ = new DoubleDataset(lstAbsQ.size());
    for (int idx = 0; idx < lstAbsQ.size(); idx++) {
        Amount<ScatteringVector> vec = lstAbsQ.get(idx);
        absQ.set(vec.doubleValue(unit), idx);

    }// w w  w  . j  ava 2s . c om
    this.absI = absI.clone();

    UnivariateInterpolator interpolator = new SplineInterpolator();
    absInterpolate = interpolator.interpolate((double[]) absQ.getBuffer(), (double[]) absI.getBuffer());
}

From source file:uk.ac.diamond.scisoft.ncd.core.DegreeOfOrientation.java

public Object[] process(Serializable buffer, Serializable axis, final int[] dimensions) {

    double[] parentaxis = (double[]) ConvertUtils.convert(axis, double[].class);
    float[] parentdata = (float[]) ConvertUtils.convert(buffer, float[].class);

    int size = dimensions[dimensions.length - 1];
    double[] myaxis = new double[size];
    double[] mydata = new double[size];
    double[] cos2data = new double[size];
    double[] sin2data = new double[size];
    double[] sincosdata = new double[size];

    for (int i = 0; i < parentaxis.length; i++) {
        myaxis[i] = Math.toRadians(parentaxis[i]);
        mydata[i] = parentdata[i];/*w w w.  ja v a2 s.  co  m*/
        float cos2alpha = (float) Math.cos(2.0 * myaxis[i]);
        float sin2alpha = (float) Math.sin(2.0 * myaxis[i]);
        cos2data[i] = (1.0f + cos2alpha) * parentdata[i] / 2.0;
        sin2data[i] = (1.0f - cos2alpha) * parentdata[i] / 2.0;
        sincosdata[i] = sin2alpha * parentdata[i] / 2.0;
    }

    UnivariateInterpolator interpolator = new SplineInterpolator();
    UnivariateFunction function = interpolator.interpolate(myaxis, mydata);
    UnivariateFunction cos2Function = interpolator.interpolate(myaxis, cos2data);
    UnivariateFunction sin2Function = interpolator.interpolate(myaxis, sin2data);
    UnivariateFunction sincosFunction = interpolator.interpolate(myaxis, sincosdata);

    UnivariateIntegrator integrator = new IterativeLegendreGaussIntegrator(15,
            BaseAbstractUnivariateIntegrator.DEFAULT_RELATIVE_ACCURACY,
            BaseAbstractUnivariateIntegrator.DEFAULT_ABSOLUTE_ACCURACY);

    try {
        float cos2mean = (float) integrator.integrate(INTEGRATION_POINTS, cos2Function, myaxis[0],
                myaxis[myaxis.length - 1]);
        float sin2mean = (float) integrator.integrate(INTEGRATION_POINTS, sin2Function, myaxis[0],
                myaxis[myaxis.length - 1]);
        float sincosmean = (float) integrator.integrate(INTEGRATION_POINTS, sincosFunction, myaxis[0],
                myaxis[myaxis.length - 1]);
        float norm = (float) integrator.integrate(INTEGRATION_POINTS, function, myaxis[0],
                myaxis[myaxis.length - 1]);

        cos2mean /= norm;
        sin2mean /= norm;
        sincosmean /= norm;

        float result = (float) Math.sqrt(Math.pow(cos2mean - sin2mean, 2) - 4.0 * sincosmean * sincosmean);
        double angle = MathUtils.normalizeAngle(Math.atan2(2.0 * sincosmean, cos2mean - sin2mean) / 2.0,
                Math.PI);

        Object[] output = new Object[] { new float[] { result }, new float[] { (float) Math.toDegrees(angle) },
                new float[] { (float) (result * Math.cos(angle)), (float) (result * Math.sin(angle)) }, };

        return output;

    } catch (TooManyEvaluationsException e) {
        return new Object[] { new float[] { Float.NaN }, new double[] { Double.NaN } };
    } catch (MaxCountExceededException e) {
        return new Object[] { new float[] { Float.NaN }, new double[] { Double.NaN } };
    }
}

From source file:uk.ac.diamond.scisoft.ncd.core.SaxsInvariant.java

public Object[] process(Serializable buffer, Serializable errors, Serializable axis, final int[] dimensions) {

    double[] parentaxis = (double[]) ConvertUtils.convert(axis, double[].class);
    float[] parentdata = (float[]) ConvertUtils.convert(buffer, float[].class);
    double[] parenterrors = (double[]) ConvertUtils.convert(errors, double[].class);

    int shift = (parentaxis[0] > 0 ? 1 : 0);
    int size = dimensions[dimensions.length - 1] + shift;
    double[] myaxis = new double[size];
    double[] mydata = new double[size];
    double[] myerrors = new double[size];

    if (shift > 0) {
        myaxis[0] = 0.0;//from  w  ww .  j a v a2 s . c  om
        mydata[0] = 0.0;
        myerrors[0] = 0.0;
    }

    for (int i = 0; i < parentaxis.length; i++) {
        myaxis[i + shift] = parentaxis[i];
        mydata[i + shift] = parentdata[i] * parentaxis[i] * parentaxis[i];
        myerrors[i + shift] = parenterrors[i] * Math.pow(parentaxis[i], 4);
    }

    UnivariateInterpolator interpolator = new SplineInterpolator();
    UnivariateFunction function = interpolator.interpolate(myaxis, mydata);

    UnivariateIntegrator integrator = new IterativeLegendreGaussIntegrator(15,
            BaseAbstractUnivariateIntegrator.DEFAULT_RELATIVE_ACCURACY,
            BaseAbstractUnivariateIntegrator.DEFAULT_ABSOLUTE_ACCURACY);

    try {
        float result = (float) integrator.integrate(INTEGRATION_POINTS, function, 0.0,
                myaxis[myaxis.length - 1]);

        IDataset data = new FloatDataset(parentdata, dimensions);
        IDataset qaxis = new DoubleDataset(parentaxis, dimensions);
        PorodPlotData porodPlotData = (PorodPlotData) SaxsAnalysisPlotType.POROD_PLOT.getSaxsPlotDataObject();
        SimpleRegression regression = porodPlotData.getPorodPlotParameters(data.squeeze(), qaxis.squeeze());
        Amount<Dimensionless> c4 = porodPlotData.getC4(regression);

        result += (float) (c4.getEstimatedValue() / myaxis[myaxis.length - 1]);

        double error = 0.0;
        for (int i = 0; i < myaxis.length; i++) {
            int idx1 = Math.max(0, i - 1);
            int idx2 = Math.min(myaxis.length - 1, i + 1);
            error += Math.pow((myaxis[idx2] - myaxis[idx1]), 2) * myerrors[i] / 4.0;
        }
        error += Math.pow(c4.getAbsoluteError() / myaxis[myaxis.length - 1], 2);

        return new Object[] { new float[] { result }, new double[] { error } };
    } catch (TooManyEvaluationsException e) {
        return new Object[] { new float[] { Float.NaN }, new double[] { Double.NaN } };
    } catch (MaxCountExceededException e) {
        return new Object[] { new float[] { Float.NaN }, new double[] { Double.NaN } };
    }
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLAddTimeCourseData.java

/**
 * Main command line call.//from   www.  j a va2 s .c  o  m
 * 
 * @param args  command line arguments
 * 
 * @throws IOException if an unexpected IO error occurs. Most common errors are reported nicer
 *                     than throwing an exception.
 */
public static void main(String[] args) throws IOException {

    Options options = getCommandLineOptions();

    try {
        CommandLineParser parser = new DefaultParser();
        CommandLine commandLine = parser.parse(options, args);

        // Handle help option
        if (commandLine.hasOption(OPTION_HELP)) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp(PROGRAM_NAME, options);
            return;
        }

        // Everything should be in the options so if there are any any left then we have an 
        // error
        if (commandLine.getArgs().length != 0) {
            String error = "Usage error: unexpected arguments:";
            for (String s : commandLine.getArgList()) {
                error = error + " " + s;
            }
            throw new ParseException(error);
        }

        // One of sbmlOut or csvOut is required
        if (!commandLine.hasOption(OPTION_SBML_OUT) && !commandLine.hasOption(OPTION_CSV_OUT)) {
            throw new ParseException("One of sbmlOut or csvOut arguments is required.");
        }

        // Get the CSV in file
        Reader csvInReader;
        if (commandLine.hasOption(OPTION_CSV_IN)) {
            String fileName = commandLine.getOptionValue(OPTION_CSV_IN);
            csvInReader = new BufferedReader(new FileReader(fileName));
        } else {
            // Read from stdin
            csvInReader = new BufferedReader(new InputStreamReader(System.in));
        }

        // Get SBML in reader
        SBMLDocument doc;
        if (commandLine.hasOption(OPTION_SBML_IN)) {
            File file = new File(commandLine.getOptionValue(OPTION_SBML_IN));
            doc = SBMLReader.read(file);
        } else {
            // Create an empty SBML model
            int level = getIntegerOption(commandLine, OPTION_SBML_LEVEL, DEFAULT_SBML_LEVEL);
            int version = getIntegerOption(commandLine, OPTION_SBML_VERSION, DEFAULT_SBML_VERSION);
            doc = new SBMLDocument(level, version);
            doc.createModel("model");
        }

        // Get SBML out file
        File sbmlOutFile = null;
        if (commandLine.hasOption(OPTION_SBML_OUT)) {
            sbmlOutFile = new File(commandLine.getOptionValue(OPTION_SBML_OUT));
        }

        // CSV file out
        BufferedWriter csvOutWriter = null;
        if (commandLine.hasOption(OPTION_CSV_OUT)) {
            File csvFileOut = new File(commandLine.getOptionValue(OPTION_CSV_OUT));
            csvOutWriter = new BufferedWriter(new FileWriter(csvFileOut));
        }

        // Interpolator
        String interpolatorName = DEFAULT_INTERPOLATOR;
        Interpolator interpolator = null;
        if (commandLine.hasOption(OPTION_INTERPOLATOR)) {
            interpolatorName = commandLine.getOptionValue(OPTION_INTERPOLATOR);
        }
        // Map interpolator to appropriate class instance
        if (interpolatorName.equalsIgnoreCase("cubic")) {
            interpolator = new PolynomialInterpolator(new SplineInterpolator());
        } else if (interpolatorName.equalsIgnoreCase("linear")) {
            interpolator = new PolynomialInterpolator(new LinearInterpolator());
        } else {
            throw new ParseException("Unknown interpolator: " + interpolatorName);
        }

        // Do the work
        process(csvInReader, doc.getModel(), csvOutWriter, getSeparator(commandLine), interpolator);

        csvInReader.close();
        if (csvOutWriter != null)
            csvOutWriter.close();

        // Write the SBML file out
        if (commandLine.hasOption(OPTION_SBML_OUT)) {
            SBMLWriter.write(doc, sbmlOutFile, "SBMLAddTimeCourseData", "1.0");
        }

    } catch (ParseException e) {
        System.err.println("Error: " + e.getLocalizedMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(PROGRAM_NAME, options);
    } catch (FileNotFoundException e) {
        System.err.println("Error: File not found: " + e.getLocalizedMessage());
    } catch (WstxUnexpectedCharException e) {
        System.err.println("Error reading SBML file: " + e.getLocalizedMessage());
    } catch (XMLStreamException e) {
        System.err.println("Error reading SBML file: " + e.getLocalizedMessage());
    } catch (IllegalArgumentException e) {
        System.err.println("Error: " + e.getLocalizedMessage());
    }
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing a NULL model.
 *//*w w  w. j av  a  2s.  c om*/
@Test
public void addParameterArrayVersionNullModel() {

    boolean caughtException = false;
    setSinData();

    try {
        SBMLTimeCourseDataHelper.addParameter(null, "myParam", _times, _values,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("sbmlModel parameter cannot be null", iae.getMessage());
    }

    if (!caughtException)
        fail("Expected IllegalArgumentException");

}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing a NULL parameter name.
 *//*from w w  w .  j a  v a 2  s.c  o  m*/
@Test
public void addParameterArrayVersionNullParameterName() {

    boolean caughtException = false;
    setSinData();
    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");

    try {
        SBMLTimeCourseDataHelper.addParameter(model, null, _times, _values,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("parameterName parameter cannot be null", iae.getMessage());
    }

    if (!caughtException)
        fail("Expected IllegalArgumentException");
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing NULL times.
 *//*from w w w  . j av a 2s.  co m*/
@Test
public void addParameterArrayVersionNullTimes() {

    boolean caughtException = false;
    setSinData();
    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");

    try {
        SBMLTimeCourseDataHelper.addParameter(model, "myParam", null, _values,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("times parameter cannot be null", iae.getMessage());
    }

    if (!caughtException)
        fail("Expected IllegalArgumentException");
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing NULL values.
 *///from  w ww  .ja v  a 2s . com
@Test
public void addParameterArrayVersionNullValues() {

    boolean caughtException = false;
    setSinData();
    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");

    try {
        SBMLTimeCourseDataHelper.addParameter(model, "myParam", _times, null,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("values parameter cannot be null", iae.getMessage());
    }

    if (!caughtException)
        fail("Expected IllegalArgumentException");
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing times and values arrays of 
 * different lengths.//  w ww  . j ava2s .  co m
 */
@Test
public void addParameterArrayVersionDifferentLengthArrays() {
    boolean caughtException = false;
    setSinData();
    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");

    // Make longer values array
    double[] values = new double[_values.length + 1];
    System.arraycopy(_values, 0, values, 0, _values.length);
    values[values.length - 1] = 0.0;

    try {
        SBMLTimeCourseDataHelper.addParameter(model, "myParam", _times, values,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("Number of data points in values parameter differs from times parameter",
                iae.getMessage());
    }

    if (!caughtException)
        fail("Expected IllegalArgumentException");
}

From source file:uk.ac.ed.bio.SynthSys.SBMLDataTools.SBMLTimeCourseDataHelperTest.java

/**
 * Tests that the correct exception is produced when passing too few data points.
 *//*ww w  .  j a  v  a 2  s  .  c  o  m*/
@Test
public void tooFewDataPoints() {
    boolean caughtException = false;

    _times = new double[] { -3.0, -2.0 };
    _values = new double[_times.length];

    for (int i = 0; i < _times.length; ++i) {
        _values[i] = Math.sin(_times[i]);
    }

    SBMLDocument doc = new SBMLDocument(3, 1);
    Model model = doc.createModel("test_model");

    try {
        SBMLTimeCourseDataHelper.addParameter(model, "myParam", _times, _values,
                new PolynomialInterpolator(new SplineInterpolator()));
    } catch (IllegalArgumentException iae) {
        caughtException = true;
        assertEquals("Data in the times and values parameters must contain at least 3 data points",
                iae.getMessage());
    }
    if (!caughtException)
        fail("Expected IllegalArgumentException");
}