ChromatogramPlotWindowController.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 3 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. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.plots.chromatogram;

import java.awt.BasicStroke;
import java.awt.Font;
import java.awt.Stroke;
import java.awt.geom.Ellipse2D;
import java.io.File;
import java.net.URL;
import java.text.DecimalFormat;

import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.block.BlockBorder;
import org.jfree.chart.labels.XYItemLabelGenerator;
import org.jfree.chart.plot.DatasetRenderingOrder;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYItemRenderer;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.chart.title.LegendTitle;
import org.jfree.chart.title.TextTitle;
import org.jfree.data.RangeType;
import org.jfree.ui.RectangleInsets;

import com.sun.javafx.tk.Toolkit;

import io.github.msdk.datamodel.chromatograms.Chromatogram;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.modules.plots.chromatogram.datasets.ChromatogramDataSet;
import io.github.mzmine.util.JavaFXUtil;
import io.github.mzmine.util.jfreechart.ChartNodeJFreeChart;
import io.github.mzmine.util.jfreechart.IntelligentItemLabelGenerator;
import io.github.mzmine.util.jfreechart.JFreeChartUtils;
import io.github.mzmine.util.jfreechart.JFreeChartUtils.ImgFileType;
import io.github.mzmine.util.jfreechart.ManualZoomDialog;
import javafx.application.Platform;
import javafx.beans.property.BooleanProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.collections.FXCollections;
import javafx.collections.ListChangeListener.Change;
import javafx.collections.ObservableList;
import javafx.event.Event;
import javafx.fxml.FXML;
import javafx.fxml.FXMLLoader;
import javafx.scene.Cursor;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuItem;
import javafx.scene.layout.BorderPane;
import javafx.scene.paint.Color;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.Window;

/**
 * Chromatogram plot window
 */
public class ChromatogramPlotWindowController {

  private final ObservableList<ChromatogramPlotDataSet> datasets =
      FXCollections.observableArrayList();
  private int numberOfDataSets = 0;

  // Colors
  private static final Color gridColor = Color.rgb(220, 220, 220, 0.5);
  private static final Color crossHairColor = Color.GRAY;

  private static final Color labelsColor = Color.BLACK;
  private static final Color backgroundColor = Color.WHITE;
  private static final Color[] plotColors = {Color.rgb(0, 0, 192), // blue
      Color.rgb(192, 0, 0), // red
      Color.rgb(0, 192, 0), // green
      Color.MAGENTA, Color.CYAN, Color.ORANGE};

  private static final Font titleFont = new Font("SansSerif", Font.BOLD, 12);

  private static final String LAYERS_DIALOG_FXML = "ChromatogramLayersDialog.fxml";

  private final BooleanProperty itemLabelsVisible =
      new SimpleBooleanProperty(this, "itemLabelsVisible", true);
  private final BooleanProperty legendVisible =
      new SimpleBooleanProperty(this, "legendVisible", true);

  private File lastSaveDirectory;

  private TextTitle chartTitle, chartSubTitle;

  @FXML
  private BorderPane chartPane;

  @FXML
  private ChartNodeJFreeChart chartNode;

  @FXML
  private MenuItem showSpectrumMenuItem;

  @FXML
  private Menu removeDatasetMenu;

  @FXML
  public void initialize() {

    final JFreeChart chart = chartNode.getChart();
    final XYPlot plot = chart.getXYPlot();

    // Do not set colors and strokes dynamically. They are instead provided
    // by the dataset and configured in configureRenderer()
    plot.setDrawingSupplier(null);
    plot.setDomainGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setRangeGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));
    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    plot.setDomainCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
    plot.setRangeCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);

    // chart properties
    chart.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));

    // legend properties
    LegendTitle legend = chart.getLegend();
    // legend.setItemFont(legendFont);
    legend.setFrame(BlockBorder.NONE);

    // set the X axis (retention time) properties
    NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
    xAxis.setLabel("Retention time (min)");
    xAxis.setUpperMargin(0.03);
    xAxis.setLowerMargin(0.03);
    xAxis.setRangeType(RangeType.POSITIVE);
    xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));

    // set the Y axis (intensity) properties
    NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
    yAxis.setLabel("Intensity");
    yAxis.setRangeType(RangeType.POSITIVE);
    yAxis.setAutoRangeIncludesZero(true);

    // set the fixed number formats, because otherwise JFreeChart sometimes
    // shows exponent, sometimes it doesn't
    DecimalFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    xAxis.setNumberFormatOverride(mzFormat);
    DecimalFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    yAxis.setNumberFormatOverride(intensityFormat);

    chartTitle = chartNode.getChart().getTitle();
    chartTitle.setMargin(5, 0, 0, 0);
    chartTitle.setFont(titleFont);
    chartTitle.setText("Chromatogram");

    chartNode.setCursor(Cursor.CROSSHAIR);

    // Remove the dataset if it is removed from the list
    datasets.addListener((Change<? extends ChromatogramPlotDataSet> c) -> {
      while (c.next()) {
        if (c.wasRemoved()) {
          for (ChromatogramPlotDataSet ds : c.getRemoved()) {
            int index = plot.indexOf(ds);
            plot.setDataset(index, null);
          }
        }
      }
    });

    itemLabelsVisible.addListener((prop, oldVal, newVal) -> {
      for (ChromatogramPlotDataSet dataset : datasets) {
        int datasetIndex = plot.indexOf(dataset);
        XYItemRenderer renderer = plot.getRenderer(datasetIndex);
        renderer.setBaseItemLabelsVisible(newVal);
      }
    });

    legendVisible.addListener((prop, oldVal, newVal) -> {
      legend.setVisible(newVal);
    });
  }

  void addChromatogram(Chromatogram chromatogram, String title) {

    if (!Platform.isFxApplicationThread()) {
      throw new IllegalStateException(
          "Not on FX application thread; currentThread = " + Thread.currentThread().getName());
    }

    final int datasetIndex = numberOfDataSets;
    numberOfDataSets++;

    ChromatogramDataSet newDataSet = new ChromatogramDataSet(chromatogram, title);

    datasets.add(newDataSet);

    final XYPlot plot = chartNode.getChart().getXYPlot();

    final Color newColor = plotColors[datasetIndex % plotColors.length];
    newDataSet.setColor(newColor);

    configureRenderer(newDataSet, datasetIndex);

    newDataSet.colorProperty().addListener(e -> {
      Platform.runLater(() -> configureRenderer(newDataSet, datasetIndex));
    });

    newDataSet.lineThicknessProperty().addListener(e -> {
      Platform.runLater(() -> configureRenderer(newDataSet, datasetIndex));
    });
    newDataSet.showDataPointsProperty().addListener(e -> {
      Platform.runLater(() -> configureRenderer(newDataSet, datasetIndex));
    });

    // Once everything is configured, add the dataset to the plot
    plot.setDataset(datasetIndex, newDataSet);
  }

  private void configureRenderer(ChromatogramPlotDataSet dataset, int datasetIndex) {

    final XYPlot plot = chartNode.getChart().getXYPlot();

    XYLineAndShapeRenderer newRenderer = new XYLineAndShapeRenderer();
    final int lineThickness = dataset.getLineThickness();
    newRenderer.setBaseShape(new Ellipse2D.Double(-2 * lineThickness, -2 * lineThickness,
        4 * lineThickness + 1, 4 * lineThickness + 1));
    newRenderer.setBaseShapesFilled(true);
    newRenderer.setBaseShapesVisible(dataset.getShowDataPoints());
    newRenderer.setDrawOutlines(false);

    Stroke baseStroke = new BasicStroke(lineThickness);
    newRenderer.setBaseStroke(baseStroke);

    // Set tooltips for legend
    newRenderer.setLegendItemToolTipGenerator((ds, series) -> {
      if (ds instanceof ChromatogramPlotDataSet) {
        return ((ChromatogramPlotDataSet) ds).getDescription();
      } else
        return null;
    });

    // Set color
    Color baseColor = dataset.getColor();
    newRenderer.setBasePaint(JavaFXUtil.convertColorToAWT(baseColor));

    // Set label generator
    XYItemLabelGenerator intelligentLabelGenerator =
        new IntelligentItemLabelGenerator(chartNode, 100, dataset);
    newRenderer.setBaseItemLabelGenerator(intelligentLabelGenerator);
    newRenderer.setBaseItemLabelPaint(JavaFXUtil.convertColorToAWT(labelsColor));
    newRenderer.setBaseItemLabelsVisible(itemLabelsVisible.get());
    newRenderer.setBaseItemLabelsVisible(true);

    // Set tooltip generator
    newRenderer.setBaseToolTipGenerator(dataset);

    plot.setRenderer(datasetIndex, newRenderer);

  }

  public void handleShowSpectrum(Event e) {

  }

  public void handleNormalizeIntensityScale(Event e) {

  }

  public void handleResetIntensityScale(Event e) {

  }

  public void handleSetupLayers(Event e) {
    try {
      URL layersDialogFXML = getClass().getResource(LAYERS_DIALOG_FXML);
      FXMLLoader loader = new FXMLLoader(layersDialogFXML);
      Stage layersDialog = loader.load();
      ChromatogramLayersDialogController controller = loader.getController();
      controller.configure(datasets, this);
      layersDialog.initModality(Modality.APPLICATION_MODAL);
      layersDialog.show();
    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }

  public void handleContextMenuShowing(Event e) {

  }

  public void handleChartMousePressed(Event e) {

  }

  public void handleChartKeyPressed(Event e) {

  }

  public void handleAddChromatogramFromFile(Event e) {

  }

  public void handleAddChromatogramFromText(Event e) {

  }

  public void handleCopyImage(Event e) {
    JFreeChartUtils.exportToClipboard(chartNode);
  }

  public void handleCopyChromatogram(Event e) {

  }

  public void handleExportJPG(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.JPG);
  }

  public void handleExportPNG(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.PNG);
  }

  public void handleExportPDF(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.PDF);
  }

  public void handleExportSVG(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.SVG);
  }

  public void handleExportEMF(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.EMF);
  }

  public void handleExportEPS(Event event) {
    JFreeChartUtils.showSaveDialog(chartNode, ImgFileType.EPS);
  }

  public void handleExportMzML(Event e) {}

  public void handleExportCSV(Event e) {}

  public void handleExportTXT(Event e) {}

  public void handleManualZoom(Event e) {
    XYPlot plot = chartNode.getChart().getXYPlot();
    Window parent = chartNode.getScene().getWindow();
    ManualZoomDialog dialog = new ManualZoomDialog(parent, plot);
    dialog.show();
  }

  public void handleZoomOut(Event e) {
    XYPlot plot = chartNode.getChart().getXYPlot();
    plot.getDomainAxis().setAutoRange(true);
    plot.getRangeAxis().setAutoRange(true);
  }

  public void handleToggleLabels(Event event) {
    itemLabelsVisible.set(!itemLabelsVisible.get());
  }

  public void handleToggleLegend(Event event) {
    legendVisible.set(!legendVisible.get());
  }

  public void handlePrint(Event event) {
    JFreeChartUtils.printChart(chartNode);
  }

}