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

Introduction

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

Prototype

LinearInterpolator

Source Link

Usage

From source file:uk.ac.diamond.scisoft.analysis.fitting.functions.SmoothGoldEdgeFunction.java

@Override
public void setData(IDataset x, IDataset data) {
    this.xds = DatasetUtils.convertToDataset(x);
    this.yds = DatasetUtils.convertToDataset(data);
    try {//from  w  ww . ja va 2s .  c  o  m
        // Smooth the data by the real ammount for the smoothed section of the process
        this.smoothed = ApachePolynomial.getPolynomialSmoothed(xds, yds, (int) Math.round(getParameterValue(0)),
                3);
        // Fit a polyline to this to allow for easy interpolation
        IDataset arg2 = DatasetUtils.cast(smoothed, Dataset.FLOAT64);
        this.polySplineFunction = new LinearInterpolator().interpolate(new DoubleDataset(xds).getData(),
                ((DoubleDataset) arg2).getData());

        lowerFit = new SimpleRegression();
        double lowerProp = xds.getShape()[0] * getParameterValue(1);
        for (int i = 0; i < lowerProp; i++) {
            lowerFit.addData(xds.getDouble(i), yds.getDouble(i));
        }
        lowerFit.regress();

        upperFit = new SimpleRegression();
        double upperProp = xds.getShape()[0] * (1.0 - getParameterValue(1));
        for (int i = xds.getShape()[0] - 1; i > upperProp; i--) {
            upperFit.addData(xds.getDouble(i), yds.getDouble(i));
        }
        upperFit.regress();

    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

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

/**
 * Main command line call./*  w ww.j  a  v  a 2 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());
    }
}

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