dedispurse

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import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.h5.H5File;
import ncsa.hdf.object.Dataset;
import ncsa.hdf.object.Group;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;

import javax.swing.*;
import javax.swing.filechooser.FileNameExtensionFilter;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Arrays;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;

public class AdvancedHDF5Plot {

    private static final double DISPERSION_CONSTANT = 4.148808e3;
    private static boolean verbose = false;
    private static double dm = 350; // Default DM value
    private static double clipTo = 1.5; // Default clip value
    private static boolean useSimulator = false; // Use simulator flag

    public static void main(String[] args) {
        SwingUtilities.invokeLater(() -> createAndShowGUI());
    }

    private static void createAndShowGUI() {
        JFrame frame = new JFrame("Advanced HDF5 Data Analyzer");
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.setLayout(new BorderLayout());

        // Control Panel
        JPanel controlPanel = new JPanel();
        controlPanel.setLayout(new GridLayout(4, 2));

        // Observation ID
        JLabel obsIdLabel = new JLabel("Observation ID:");
        JTextField obsIdField = new JTextField("obs1");
        controlPanel.add(obsIdLabel);
        controlPanel.add(obsIdField);

        // DM Value
        JLabel dmLabel = new JLabel("DM Value:");
        JTextField dmField = new JTextField(Double.toString(dm));
        controlPanel.add(dmLabel);
        controlPanel.add(dmField);

        // Clip Value
        JLabel clipLabel = new JLabel("Clip Value:");
        JTextField clipField = new JTextField(Double.toString(clipTo));
        controlPanel.add(clipLabel);
        controlPanel.add(clipField);

        // Simulator Checkbox
        JCheckBox simulatorCheckBox = new JCheckBox("Use Simulator");
        controlPanel.add(simulatorCheckBox);

        // File Chooser Button
        JButton fileChooserButton = new JButton("Choose HDF5 File");
        controlPanel.add(fileChooserButton);

        // Plot Button
        JButton plotButton = new JButton("Generate Plots");
        controlPanel.add(plotButton);

        frame.add(controlPanel, BorderLayout.NORTH);

        // Chart Panels
        JPanel chartPanel = new JPanel();
        chartPanel.setLayout(new GridLayout(2, 1));
        frame.add(chartPanel, BorderLayout.CENTER);

        // File Chooser
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileFilter(new FileNameExtensionFilter("HDF5 Files", "hdf5"));

        fileChooserButton.addActionListener(e -> {
            int returnValue = fileChooser.showOpenDialog(frame);
            if (returnValue == JFileChooser.APPROVE_OPTION) {
                String filename = fileChooser.getSelectedFile().getPath();
                obsIdField.setText(filename);
            }
        });

        plotButton.addActionListener(e -> {
            String observationId = obsIdField.getText();
            String filename = fileChooser.getSelectedFile().getPath();
            dm = Double.parseDouble(dmField.getText());
            clipTo = Double.parseDouble(clipField.getText());
            useSimulator = simulatorCheckBox.isSelected();
            generateAndDisplayPlots(observationId, filename, chartPanel);
        });

        frame.pack();
        frame.setVisible(true);
    }

    private static void generateAndDisplayPlots(String observationId, String filename, JPanel chartPanel) {
        try {
            double[] freq;
            double[] time;
            double[][] wf;

            if (useSimulator) {
                // Simulate data
                freq = simulateFrequencies(100);
                time = simulateTime(1000);
                wf = new double[time.length][freq.length];
                simulateWaterfallData(wf, time, freq);
            } else {
                // Load data from HDF5 file
                H5File file = new H5File(filename, FileFormat.READ);
                file.open();

                Group observation = (Group) file.get("Observation1");
                displayHDF5Structure(observation, "");

                freq = (double[]) ((Dataset) observation.getMember("Tuning1/freq")).getData();
                time = (double[]) ((Dataset) observation.getMember("time")).getData();

                wf = new double[time.length][freq.length];
                simulateWaterfallData(wf, time, freq);

                file.close();
            }

            double[] delay = calculateDispersionDelay(freq, dm);
            double[][] dedispersedWf = applyIncoherentDedispersion(wf, freq, time, delay);

            SwingUtilities.invokeLater(() -> {
                chartPanel.removeAll();
                chartPanel.add(new ChartPanel(createFreqSpectChart(observationId, freq, time, dedispersedWf)));
                chartPanel.add(new ChartPanel(createDMSpectChart(observationId, freq, time, dedispersedWf)));
                chartPanel.revalidate();
                chartPanel.repaint();
            });

        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static void displayHDF5Structure(Group group, String indent) {
        try {
            for (Object memberObj : group.getMemberList()) {
                if (memberObj instanceof Dataset) {
                    Dataset dataset = (Dataset) memberObj;
                    System.out.println(indent + dataset.getFullName() + ": " + Arrays.toString(dataset.getDims()) + " " + dataset.getDatatype().getDescription());
                } else if (memberObj instanceof Group) {
                    Group subgroup = (Group) memberObj;
                    System.out.println(indent + subgroup.getFullName() + ": Group");
                    displayHDF5Structure(subgroup, indent + "  ");
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static double[] simulateFrequencies(int size) {
        double[] freq = new double[size];
        for (int i = 0; i < size; i++) {
            freq[i] = 1000 + i * 10; // Simulated frequencies from 1000 to 2000 Hz
        }
        return freq;
    }

    private static double[] simulateTime(int size) {
        double[] time = new double[size];
        for (int i = 0; i < size; i++) {
            time[i] = i * 0.01; // Simulated time from 0 to 10 seconds
        }
        return time;
    }

    private static void simulateWaterfallData(double[][] wf, double[] time, double[] freq) {
        ExecutorService executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
        for (int i = 0; i < time.length; i++) {
            final int idx = i;
            executor.submit(() -> {
                for (int j = 0; j < freq.length; j++) {
                    wf[idx][j] = Math.sin(time[idx] + freq[j]);
                }
            });
        }
        executor.shutdown();
        try {
            executor.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }

    private static JFreeChart createFreqSpectChart(String observationId, double[] freq, double[] time, double[][] wf) {
        XYSeriesCollection dataset = new XYSeriesCollection();
        for (int i = 0; i < freq.length; i++) {
            XYSeries series = new XYSeries("Frequency " + freq[i]);
            for (int j = 0; j < time.length; j++) {
                series.add(time[j], wf[j][i]);
            }
            dataset.addSeries(series);
        }

        JFreeChart chart = ChartFactory.createXYLineChart(
                "Frequency Spectrogram: " + observationId,
                "Time",
                "Intensity",
                dataset,
                PlotOrientation.VERTICAL,
                true, true, false);

        customizeChart(chart);
        return chart;
    }

    private static JFreeChart createDMSpectChart(String observationId, double[] freq, double[] time, double[][] wf) {
        XYSeriesCollection dataset = new XYSeriesCollection();
        for (int i = 0; i < time.length; i++) {
            XYSeries series = new XYSeries("Time " + time[i]);
            for (int j = 0; j < freq.length; j++) {
                series.add(freq[j], wf[i][j]);
            }
            dataset.addSeries(series);
        }

        JFreeChart chart = ChartFactory.createXYLineChart(
                "DM Spectrogram: " + observationId,
                "Frequency",
                "Intensity",
                dataset,
                PlotOrientation.VERTICAL,
                true, true, false);

        customizeChart(chart);
        return chart;
    }

    private static void
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