sc.fiji.kappa.gui.CurvesExporter.java Source code

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Here is the source code for sc.fiji.kappa.gui.CurvesExporter.java

Source

/*-
 * #%L
 * A Fiji plugin for Curvature Analysis.
 * %%
 * Copyright (C) 2016 - 2017 Gary Brouhard
 * %%
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 * #L%
 */
package sc.fiji.kappa.gui;

import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;

import javax.swing.JFileChooser;
import javax.swing.filechooser.FileNameExtensionFilter;

import org.apache.commons.io.FilenameUtils;

import com.opencsv.CSVWriter;

import sc.fiji.kappa.curve.BezierGroup;
import sc.fiji.kappa.curve.Curve;

public class CurvesExporter {

    private KappaFrame frame;

    public CurvesExporter(KappaFrame frame) {
        this.frame = frame;
    }

    public void export() throws IOException {
        export(true);
    }

    public void export(boolean exportAveragePerCurve) throws IOException {

        JFileChooser kappaExport = new JFileChooser();

        String dirPath = frame.getImageStack().getOriginalFileInfo().directory;
        if (dirPath != null) {
            String kappaPath = FilenameUtils.removeExtension(frame.getImageStack().getOriginalFileInfo().fileName);
            kappaPath += ".csv";
            File fullPath = new File(dirPath, kappaPath);
            kappaExport.setSelectedFile(fullPath);
        }

        kappaExport.setFileFilter(new FileNameExtensionFilter("CSV File", "csv"));
        kappaExport.setDialogTitle("Export Curve Data");

        // Handles export button action.
        int returnVal = kappaExport.showSaveDialog(frame);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            File file = kappaExport.getSelectedFile();
            exportToFile(file, exportAveragePerCurve);
        }
    }

    public void exportToFile(String file, boolean exportAveragePerCurve) throws IOException {
        exportToFile(new File(file), exportAveragePerCurve);
    }

    public void exportToFile(File file, boolean exportAveragePerCurve) throws IOException {

        BezierGroup curves = frame.getCurves();

        // Appends a .csv
        if (!file.getPath().toLowerCase().endsWith(".csv")) {
            file = new File(file.getPath() + ".csv");
        }

        CSVWriter writer = new CSVWriter(new FileWriter(file.getAbsoluteFile()));

        // Write headers
        List<String> headers = new ArrayList<>();
        headers.add("Curve Name");

        headers.add("Curve Length (um)");
        headers.add("Average Curvature (um-1)");
        headers.add("Curvature Std (um-1)");

        headers.add("X-Coordinate (um)");
        headers.add("Y-Coordinate (um)");
        headers.add("Point Curvature (um-1)");

        headers.add("Red Intensity");
        headers.add("Green Intensity");
        headers.add("Blue Intensity");
        writer.writeNext(headers.stream().toArray(String[]::new));

        // Not used anymore
        int w = frame.getCurrImage().getWidth();
        int h = frame.getCurrImage().getHeight();
        double[][] averaged = new double[w][h];

        StringWriter out = new StringWriter();
        PrintWriter printWriter = new PrintWriter(out);

        for (Curve c : curves) {
            c.printValues(printWriter, averaged, !exportAveragePerCurve);
            writer.flush();
            String[] lines = out.toString().split("\n");

            for (String line : lines) {
                writer.writeNext(line.split(","));
            }
        }

        // close the writer
        writer.close();
    }

}