Java tutorial
/* * org.openmicroscopy.shoola.agents.measurement.view.IntensityView * *------------------------------------------------------------------------------ * Copyright (C) 2006-2014 University of Dundee. All rights reserved. * * * This program 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. * This program 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 this program; if not, write to the Free Software Foundation, Inc., * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. * *------------------------------------------------------------------------------ */ package org.openmicroscopy.shoola.agents.measurement.view; //Java imports import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Point; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; import java.util.Map.Entry; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.DefaultComboBoxModel; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JSlider; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; //Third-party libraries import org.apache.commons.collections.CollectionUtils; import org.jhotdraw.draw.Figure; //Application-internal dependencies import org.openmicroscopy.shoola.agents.measurement.IconManager; import org.openmicroscopy.shoola.agents.measurement.MeasurementAgent; import org.openmicroscopy.shoola.util.file.ExcelWriter; import org.openmicroscopy.shoola.util.image.geom.Factory; import org.openmicroscopy.shoola.util.roi.figures.MeasureBezierFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasureEllipseFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasureLineConnectionFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasureLineFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasurePointFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasureRectangleFigure; import org.openmicroscopy.shoola.util.roi.figures.MeasureTextFigure; import org.openmicroscopy.shoola.util.roi.figures.ROIFigure; import org.openmicroscopy.shoola.util.roi.model.ROIShape; import org.openmicroscopy.shoola.util.roi.model.annotation.AnnotationKeys; import org.openmicroscopy.shoola.util.roi.model.annotation.MeasurementAttributes; import org.openmicroscopy.shoola.util.roi.model.util.Coord3D; import org.openmicroscopy.shoola.util.ui.ColorListRenderer; import org.openmicroscopy.shoola.util.ui.UIUtilities; import org.openmicroscopy.shoola.util.ui.filechooser.FileChooser; import org.openmicroscopy.shoola.util.ui.slider.OneKnobSlider; import org.openmicroscopy.shoola.agents.measurement.util.ChannelSummaryModel; import org.openmicroscopy.shoola.agents.measurement.util.ChannelSummaryTable; import org.openmicroscopy.shoola.agents.measurement.util.TabPaneInterface; import org.openmicroscopy.shoola.agents.measurement.util.model.AnalysisStatsWrapper; import org.openmicroscopy.shoola.agents.measurement.util.model.AnalysisStatsWrapper.StatsType; import org.openmicroscopy.shoola.env.config.Registry; import org.openmicroscopy.shoola.env.log.Logger; import org.openmicroscopy.shoola.env.ui.UserNotifier; import pojos.ChannelData; /** * Displays statistics computed on the pixels intensity value of a given * ROI shape. * * @author Jean-Marie Burel * <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a> * @author Donald MacDonald * <a href="mailto:donald@lifesci.dundee.ac.uk">donald@lifesci.dundee.ac.uk</a> * @version 3.0 * <small> * (<b>Internal version:</b> $Revision: $Date: $) * </small> * @since OME3.0 */ class IntensityView extends JPanel implements ActionListener, TabPaneInterface, ChangeListener, PropertyChangeListener { /** Index to identify tab */ public final static int INDEX = MeasurementViewerUI.INTENSITY_INDEX; /** Width of the text field components. */ public final static int TEXT_WIDTH = 100; /** Height of the text field components. */ public final static int TEXT_HEIGHT = 26; /** Width of label components. */ public final static int LABEL_WIDTH = 60; /** Height of label components. */ public final static int LABEL_HEIGHT = 26; /** The initial size of the intensity table dialog. */ private Dimension intensityTableSize = new Dimension(300, 300); /** The default preview of the sheet displaying the channel's name.*/ private static final String CHANNEL_SHEET = "Channel name "; /** The state of the Intensity View. */ static enum State { /** Analysing data. */ ANALYSING, /** Ready to analyse. */ READY } /** * Intensity view state, if Analysing we should not all the user to * change combobox or save. */ private State state = State.READY; /** The name of the panel. */ private static final String NAME = "Intensity View"; /** The save button action command. */ private static final int SAVE_ACTION = 0; /** The show table action button. */ private static final int SHOW_TABLE_ACTION = 1; /** The channel selection action command. */ private static final int CHANNEL_SELECTION = 2; /** Reference to the model. */ private MeasurementViewerModel model; /** Reference to the view. */ private MeasurementViewerUI view; /** * SelectChannelsForm the form to select the channels to output to the * file. */ private ChannelSelectionForm channelsSelectionForm; /** The map of <ROIShape, ROIStats> .*/ private Map ROIStats; /** Table for summary of measurement values. */ private ChannelSummaryTable channelSummaryTable; /** Model for summary of measurement values. */ private ChannelSummaryModel channelSummaryModel; /** The channel selected in the Combo box. */ private int selectedChannel = -1; /** The name of the channel selected in the Combo box. */ private String selectedChannelName; /** Select to choose the channel to show values for . */ private JComboBox channelSelection; /** The save button. */ private JButton saveButton; /** The slider controlling the movement of the analysis through Z. */ private OneKnobSlider zSlider; /** The slider controlling the movement of the analysis through T. */ private OneKnobSlider tSlider; /** List of the channel names. */ private Map<Integer, String> channelName = new TreeMap<Integer, String>(); /** List of the channel colours. */ private Map<Integer, Color> channelColour = new TreeMap<Integer, Color>(); /** Map of the channel sums, for each selected channel. */ private Map<Integer, Double> channelSum = new TreeMap<Integer, Double>(); /** Map of the channel minimum, for each selected channel. */ private Map<Integer, Double> channelMin = new TreeMap<Integer, Double>(); /** Map of the channel Max, for each selected channel. */ private Map<Integer, Double> channelMax = new TreeMap<Integer, Double>(); /** Map of the channel Mean, for each selected channel. */ private Map<Integer, Double> channelMean = new TreeMap<Integer, Double>(); /** Map of the channel std. dev., for each selected channel. */ private Map<Integer, Double> channelStdDev = new TreeMap<Integer, Double>(); /** Map of the channel name to channel number .*/ private Map<String, Integer> nameMap = new LinkedHashMap<String, Integer>(); /** The map of the shape stats to coord. */ private TreeMap<Coord3D, Map<StatsType, Map>> shapeStatsList; /** Map of the pixel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Map<Point, Double>>> pixelStats; /** Map of the minimum channel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Double>> minStats; /** Map of the max channel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Double>> maxStats; /** Map of the mean channel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Double>> meanStats; /** Map of the std dev channel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Double>> stdDevStats; /** Map of the sum channel intensity values to coordinates. */ private TreeMap<Coord3D, Map<Integer, Double>> sumStats; /** Map of the coordinates to a shape. */ private TreeMap<Coord3D, ROIShape> shapeMap; /** The current coordinates of the ROI being depicted in the slider. */ private Coord3D coord; /** Button for the calling of the intensity table. */ private JButton showIntensityTable; /** Current ROIShape. */ private ROIShape shape; /** Dialog showing the intensity values for the selected channel. */ private IntensityValuesDialog intensityDialog; /** Table Model. */ private IntensityModel tableModel; /** Indicates the selected plane.*/ private void formatPlane() { if (!zSlider.isVisible() && !tSlider.isVisible()) { view.setPlaneStatus(""); return; } StringBuffer buffer = new StringBuffer(); if (zSlider.isVisible()) buffer.append("Z=" + zSlider.getValue() + " "); if (tSlider.isVisible()) buffer.append("T=" + tSlider.getValue()); view.setPlaneStatus(buffer.toString()); } /** The slider has changed value and the mouse button released. */ private void handleSliderReleased() { if (zSlider == null || tSlider == null || coord == null || state != State.READY) return; Coord3D thisCoord = new Coord3D(zSlider.getValue() - 1, tSlider.getValue() - 1); if (coord.equals(thisCoord)) return; if (!pixelStats.containsKey(thisCoord)) return; Object[] nameColour = (Object[]) channelSelection.getSelectedItem(); String string = (String) nameColour[1]; if (!nameMap.containsKey(string)) { state = State.READY; return; } selectedChannelName = string; int channel = nameMap.get(string); if (channel == -1) return; if (!pixelStats.get(thisCoord).containsKey(channel)) return; state = State.ANALYSING; populateData(thisCoord, channel); formatPlane(); //repaint(); if (shape != null) view.selectFigure(shape.getFigure()); state = State.READY; } /** Initializes the table model.*/ private void initTableModel() { Double summaryData[][] = new Double[1][1]; List<String> rowNames = new ArrayList<String>(); List<String> columnNames = new ArrayList<String>(); rowNames.add(""); columnNames.add(""); channelSummaryModel = new ChannelSummaryModel(rowNames, columnNames, summaryData); } /** Initializes the component composing the display. */ private void initComponents() { Double data[][] = new Double[1][1]; tableModel = new IntensityModel(data); initTableModel(); channelSummaryTable = new ChannelSummaryTable(channelSummaryModel); showIntensityTable = new JButton("Intensity Values"); showIntensityTable.setEnabled(false); showIntensityTable.addActionListener(this); showIntensityTable.setActionCommand("" + SHOW_TABLE_ACTION); channelSelection = new JComboBox(); channelSelection.setEnabled(false); channelSelection.setVisible(false); channelSelection.addActionListener(this); channelSelection.setActionCommand("" + CHANNEL_SELECTION); saveButton = new JButton("Export to Excel"); saveButton.addActionListener(this); saveButton.setActionCommand("" + SAVE_ACTION); saveButton.setEnabled(false); state = State.READY; zSlider = new OneKnobSlider(); zSlider.setOrientation(JSlider.VERTICAL); zSlider.setPaintTicks(false); zSlider.setPaintLabels(false); zSlider.setMajorTickSpacing(1); zSlider.setShowArrows(true); zSlider.setVisible(false); zSlider.setEndLabel("Z"); zSlider.setShowEndLabel(true); tSlider = new OneKnobSlider(); tSlider.setPaintTicks(false); tSlider.setPaintLabels(false); tSlider.setMajorTickSpacing(1); tSlider.setSnapToTicks(true); tSlider.setShowArrows(true); tSlider.setVisible(false); tSlider.setEndLabel("T"); tSlider.setShowEndLabel(true); zSlider.addPropertyChangeListener(this); tSlider.addPropertyChangeListener(this); zSlider.addChangeListener(this); tSlider.addChangeListener(this); } /** Builds and lays out the UI. */ private void buildGUI() { JPanel scrollPanel = new JPanel(); JPanel containerPanel = new JPanel(); containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.X_AXIS)); JPanel tPanel = tablePanel(); containerPanel.add(zSlider); containerPanel.add(tPanel); JPanel cPanel = new JPanel(); cPanel.setLayout(new BoxLayout(cPanel, BoxLayout.Y_AXIS)); cPanel.add(containerPanel); cPanel.add(tSlider); JPanel buttonPanel = createButtonPanel(); scrollPanel.setLayout(new BoxLayout(scrollPanel, BoxLayout.X_AXIS)); scrollPanel.add(cPanel); scrollPanel.add(buttonPanel); scrollPanel.add(Box.createGlue()); this.setLayout(new BorderLayout()); this.add(scrollPanel, BorderLayout.CENTER); intensityDialog = new IntensityValuesDialog(view, tableModel, channelSelection); } /** * Create the button panel to the right of the summary table. * @return see above. */ private JPanel createButtonPanel() { JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); panel.add(Box.createRigidArea(new Dimension(0, 10))); panel.add(Box.createRigidArea(new Dimension(0, 10))); JPanel intensityPanel = UIUtilities.buildComponentPanel(showIntensityTable); UIUtilities.setDefaultSize(intensityPanel, new Dimension(175, 32)); panel.add(intensityPanel); panel.add(Box.createRigidArea(new Dimension(0, 10))); JPanel savePanel = UIUtilities.buildComponentPanel(saveButton); UIUtilities.setDefaultSize(savePanel, new Dimension(175, 32)); panel.add(savePanel); panel.add(Box.createVerticalGlue()); return panel; } /** * Create the table panel which holds all the intensities for the selected * channel in the table. * @return See Above. */ private JPanel tablePanel() { JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS)); JScrollPane scrollPane = new JScrollPane(channelSummaryTable); scrollPane.setVerticalScrollBar(scrollPane.createVerticalScrollBar()); scrollPane.setHorizontalScrollBar(scrollPane.createHorizontalScrollBar()); panel.add(scrollPane); return panel; } /** Clears the maps just in case the data is not being reassigned. */ private void clearMaps() { if (shapeStatsList != null) shapeStatsList.clear(); shapeStatsList = null; if (pixelStats != null) pixelStats.clear(); pixelStats = null; if (shapeMap != null) shapeMap.clear(); shapeMap = null; if (maxStats != null) maxStats.clear(); maxStats = null; if (meanStats != null) meanStats.clear(); meanStats = null; if (minStats != null) minStats.clear(); minStats = null; if (sumStats != null) sumStats.clear(); sumStats = null; if (stdDevStats != null) stdDevStats.clear(); stdDevStats = null; } /** Clears the combo box. */ private void clearAllValues() { channelSelection.removeAllItems(); } /** Creates the combobox holding the channel list. */ private void createComboBox() { Object[][] channelCols = new Object[channelName.size()][2]; List<ChannelData> metadata = model.getMetadata(); Iterator<ChannelData> i = metadata.iterator(); ChannelData channelData; int channel; int index = 0; while (i.hasNext()) { channelData = i.next(); channel = channelData.getIndex(); if (channelName.containsKey(channel)) { channelCols[index] = new Object[] { channelColour.get(channel), channelName.get(channel) }; index++; } } //if (channelCols.length == 0) //return; channelSelection.setModel(new DefaultComboBoxModel(channelCols)); channelSelection.setRenderer(new ColorListRenderer()); if (selectedChannelName != null) if (nameMap.containsKey(selectedChannelName)) selectedChannel = nameMap.get(selectedChannelName); else selectedChannel = 0; else selectedChannel = 0; if (selectedChannel >= channelSelection.getItemCount() || selectedChannel < 0) return; channelSelection.setSelectedIndex(selectedChannel); channelSelection.setEnabled(true); } /** * Populates the table and fields with the data. * * @param coord the coordinate of the shape being analysed. * @param channel the channel to be analysed. */ private void populateData(Coord3D coord, int channel) { channelSummaryTable.setVisible(true); interpretResults(coord, channel); populateChannelSummaryTable(coord); } /** * Populates the pixels value per channel. * * @param channel The selected channel. */ private void populateChannel() { Object[] nameColour = (Object[]) channelSelection.getSelectedItem(); String string = (String) nameColour[1]; if (!nameMap.containsKey(string)) return; selectedChannelName = string; int channel = nameMap.get(string); if (channel < 0) return; Map<Point, Double> pixels = pixelStats.get(coord).get(channel); if (pixels == null) return; Iterator<Point> pixelIterator = pixels.keySet().iterator(); double minX, maxX, minY, maxY; if (!pixelIterator.hasNext()) return; Point point = pixelIterator.next(); minX = (point.getX()); maxX = (point.getX()); minY = (point.getY()); maxY = (point.getY()); while (pixelIterator.hasNext()) { point = pixelIterator.next(); minX = Math.min(minX, point.getX()); maxX = Math.max(maxX, point.getX()); minY = Math.min(minY, point.getY()); maxY = Math.max(maxY, point.getY()); } int sizeX, sizeY; sizeX = (int) (maxX - minX) + 1; sizeY = (int) ((maxY - minY) + 1); Double[][] data = new Double[sizeX][sizeY]; Iterator<Entry<Point, Double>> i = pixels.entrySet().iterator(); int x, y; Double value; Entry<Point, Double> entry; while (i.hasNext()) { entry = i.next(); point = entry.getKey(); x = (int) (point.getX() - minX); y = (int) (point.getY() - minY); if (x >= sizeX || y >= sizeY) continue; if (pixels.containsKey(point)) value = entry.getValue(); else value = new Double(0); data[x][y] = value; } tableModel = new IntensityModel(data); intensityDialog.setModel(tableModel); } /** * Populate the summary table with the list of values for the ROI at * coord. * @param coord see above. */ private void populateChannelSummaryTable(Coord3D coord) { List<String> statNames = new ArrayList<String>(); List<String> channelNames = new ArrayList<String>(); ROIFigure fig = shape.getFigure(); int count = 0; statNames.add("Min"); statNames.add("Max"); statNames.add("Sum"); statNames.add("Mean"); statNames.add("Std Dev."); statNames.add("NumPixels"); if (areaFigure(fig)) addAreaStats(statNames); else if (lineFigure(fig)) addLineStats(statNames); else if (pointFigure(fig)) addPointStats(statNames); Iterator<Integer> channelIterator = channelName.keySet().iterator(); while (channelIterator.hasNext()) channelNames.add(channelName.get(channelIterator.next())); Double data[][] = new Double[channelName.size()][statNames.size()]; channelIterator = channelName.keySet().iterator(); int channel; count = 0; while (channelIterator.hasNext()) { channel = channelIterator.next(); populateSummaryColumn(fig, data, channel, count); count++; } channelSummaryModel = new ChannelSummaryModel(statNames, channelNames, data); channelSummaryTable.setModel(channelSummaryModel); } /** * Populates the data for use in the summary table for the figure fig, * and for channel. * * @param fig see above. * @param data see above. * @param channel see above. * @param count the column the data is being placed in. */ private void populateSummaryColumn(ROIFigure fig, Double data[][], int channel, int count) { data[count][0] = channelMin.get(channel); data[count][1] = channelMax.get(channel); data[count][2] = channelSum.get(channel); data[count][3] = channelMean.get(channel); data[count][4] = channelStdDev.get(channel); data[count][5] = (double) fig.getSize(); if (areaFigure(fig)) addValuesForAreaFigure(fig, data, channel, count); else if (lineFigure(fig)) addValuesForLineFigure(fig, data, channel, count); else if (pointFigure(fig)) addValuesForPointFigure(fig, data, channel, count); } /** * Add stats in the column for area figures. * @param fig the figure where the stats come from. * @param data the data being populated. * @param count the column in the table being populated. */ private void addValuesForAreaFigure(ROIFigure fig, Double data[][], int channel, int count) { data[count][6] = AnnotationKeys.AREA.get(fig.getROIShape()); data[count][7] = fig.getBounds().getX(); data[count][8] = fig.getBounds().getY(); data[count][9] = AnnotationKeys.WIDTH.get(fig.getROIShape()); data[count][10] = AnnotationKeys.HEIGHT.get(fig.getROIShape()); data[count][11] = AnnotationKeys.CENTREX.get(fig.getROIShape()); data[count][12] = AnnotationKeys.CENTREY.get(fig.getROIShape()); } /** * Add stats in the column for line figures. * @param fig the figure where the stats come from. * @param data the data being populated. * @param channel the channel where the stats come from/. * @param count the column in the table being populated. */ private void addValuesForLineFigure(ROIFigure fig, Double data[][], int channel, int count) { data[count][6] = AnnotationKeys.STARTPOINTX.get(shape); data[count][7] = AnnotationKeys.STARTPOINTY.get(shape); data[count][8] = AnnotationKeys.ENDPOINTX.get(shape); data[count][9] = AnnotationKeys.ENDPOINTY.get(shape); data[count][10] = AnnotationKeys.CENTREX.get(shape); data[count][11] = AnnotationKeys.CENTREY.get(shape); } /** * Add stats in the column for point figures. * @param fig the figure where the stats come from. * @param data the data being populated. * @param channel the channel where the stats come from/. * @param count the column in the table being populated. */ private void addValuesForPointFigure(ROIFigure fig, Double data[][], int channel, int count) { data[count][6] = AnnotationKeys.CENTREX.get(shape); data[count][7] = AnnotationKeys.CENTREY.get(shape); } /** * Sets the rows describing the stats being displayed in the summary table. * @param statNames The list of stats being displayed in the summary table. */ private void addAreaStats(List<String> statNames) { statNames.add("Area"); statNames.add("X Coord"); statNames.add("Y Coord"); statNames.add("Width"); statNames.add("Height"); statNames.add("X Centre"); statNames.add("Y Centre"); } /** * Sets the rows describing the stats being displayed in the summary table. * * @param statNames The list of stats being displayed in the summary table. */ private void addLineStats(List<String> statNames) { statNames.add("X1 Coord"); statNames.add("Y1 Coord"); statNames.add("X2 Coord"); statNames.add("Y2 Coord"); statNames.add("X Centre"); statNames.add("Y Centre"); } /** * Sets the rows describing the stats being displayed in the summary table. * * @param statNames The list of stats being displayed in the summary table. */ private void addPointStats(List<String> statNames) { statNames.add("X Centre"); statNames.add("Y Centre"); } /** * Called by the display analysis results method to build the results into * datastructures used by the intensityView. * @param coord * @param channel */ private void interpretResults(Coord3D coord, int channel) { channelMin = minStats.get(coord); channelMax = maxStats.get(coord); channelMean = meanStats.get(coord); channelStdDev = stdDevStats.get(coord); channelSum = sumStats.get(coord); shape = shapeMap.get(coord); /* Map<Point, Double> pixels = pixelStats.get(coord).get(channel); if (pixels == null) return; Iterator<Point> pixelIterator = pixels.keySet().iterator(); double minX, maxX, minY, maxY; if (!pixelIterator.hasNext()) return; Point point = pixelIterator.next(); minX = (point.getX()); maxX = (point.getX()); minY = (point.getY()); maxY = (point.getY()); while (pixelIterator.hasNext()) { point = pixelIterator.next(); minX = Math.min(minX, point.getX()); maxX = Math.max(maxX, point.getX()); minY = Math.min(minY, point.getY()); maxY = Math.max(maxY, point.getY()); } int sizeX, sizeY; sizeX = (int) (maxX-minX)+1; sizeY = (int) ((maxY-minY)+1); Double[][] data = new Double[sizeX][sizeY]; Iterator<Entry<Point, Double>> i = pixels.entrySet().iterator(); int x, y; Double value; Entry<Point, Double> entry; while (i.hasNext()) { entry = i.next(); point = entry.getKey(); x = (int) (point.getX()-minX); y = (int) (point.getY()-minY); if (x >= sizeX || y >= sizeY) continue; if (pixels.containsKey(point)) value = entry.getValue(); else value = new Double(0); data[x][y] = value; } tableModel = new IntensityModel(data); intensityDialog.setModel(tableModel); */ } /** * Returns <code>true</code> if the passed figure is an area figure, * <code>false</code> otherwise. * * @param fig The param. * @return See above. */ private boolean areaFigure(ROIFigure fig) { if (fig instanceof MeasureEllipseFigure || fig instanceof MeasureRectangleFigure) return true; if (fig instanceof MeasureBezierFigure) { MeasureBezierFigure bFig = (MeasureBezierFigure) fig; if (bFig.isClosed()) return true; } return false; } /** * Returns <code>true</code> if the passed figure is a line figure, * <code>false</code> otherwise. * * @param fig The param. * @return See above. */ private boolean lineFigure(ROIFigure fig) { if (fig instanceof MeasureLineFigure || fig instanceof MeasureLineConnectionFigure) return true; if (fig instanceof MeasureBezierFigure) { MeasureBezierFigure bFig = (MeasureBezierFigure) fig; if (!bFig.isClosed()) return true; } return false; } /** * Returns <code>true</code> if the passed figure is a Point figure, * <code>false</code> otherwise. * * @param fig The param. * @return See above. */ private boolean pointFigure(ROIFigure fig) { return (fig instanceof MeasurePointFigure); } /** Save the results to an Excel File. */ private void saveResults() { channelsSelectionForm = new ChannelSelectionForm(channelName); FileChooser chooser = view.createSaveToExcelChooser(); chooser.addComponentToControls(channelsSelectionForm); if (chooser.showDialog() != JFileChooser.APPROVE_OPTION) return; File file = chooser.getFormattedSelectedFile(); List<Integer> channels = channelsSelectionForm.getUserSelection(); if (channels == null || channels.size() == 0) { UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier(); un.notifyInfo("Save Results", " Please select at least a channel."); view.setStatus("No Channel selected to output."); return; } ExcelWriter writer = null; try { writer = new ExcelWriter(file.getAbsolutePath()); writer.openFile(); writer.createSheet("Channel Summary"); Iterator<Coord3D> coordMapIterator = shapeMap.keySet().iterator(); Coord3D currentCoord; int n = channels.size(); Integer channel; if (channelSummarySelected(channels)) outputSummary(writer, shapeMap); BufferedImage originalImage = model.getRenderedImage(); if (originalImage != null) { BufferedImage image = Factory.copyBufferedImage(originalImage); // Add the ROI for the current plane to the image. //TODO: Need to check that. model.setAttributes(MeasurementAttributes.SHOWID, true); model.getDrawingView().print(image.getGraphics()); model.setAttributes(MeasurementAttributes.SHOWID, false); try { writer.addImageToWorkbook("ThumbnailImage", image); } catch (Exception e) { Logger logger = MeasurementAgent.getRegistry().getLogger(); logger.error(this, "Cannot write Image: " + e.toString()); } int col = writer.getMaxColumn(0); writer.writeImage(0, col + 1, 256, 256, "ThumbnailImage"); } String name; String sheet; if (channelSummarySelected(channels) && channels.size() != 1) while (coordMapIterator.hasNext()) { currentCoord = coordMapIterator.next(); for (int i = 0; i < n; i++) { channel = channels.get(i); if (channel == ChannelSelectionForm.SUMMARYVALUE) continue; if (!nameMap.containsKey(channelName.get(channel))) continue; int rowIndex = 0; name = channelName.get(channel); sheet = CHANNEL_SHEET + name; //First check if the sheet already exists. if (writer.setCurrentSheet(sheet) == null) writer.createSheet(sheet); writeHeader(writer, rowIndex, currentCoord); channel = nameMap.get(name); writeData(writer, rowIndex, currentCoord, channel.intValue()); } } writer.close(); } catch (Exception e) { Logger logger = MeasurementAgent.getRegistry().getLogger(); logger.error(this, "Cannot save ROI results: " + e.toString()); UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier(); String message = "An error occurred while trying to" + " save the data.\nPlease try again."; if (e instanceof NumberFormatException) { message = "We only support the British/American style of " + "representing numbers,\nusing a decimal point rather " + "than a comma."; } un.notifyInfo("Save Results", message); //delete the file file.delete(); try { writer.close(); } catch (Exception e2) { //ignore: cannot close the writer. } return; } Registry reg = MeasurementAgent.getRegistry(); UserNotifier un = reg.getUserNotifier(); un.notifyInfo("Save ROI results", "The ROI results have been " + "successfully saved."); } /** * Create summary table with horizontal columns. * * @param writer The Excel writer. * @param rowIndex The selected row. */ private void printSummaryHeader(ExcelWriter writer, int rowIndex) { writer.writeElement(rowIndex, 0, "channel"); writer.writeElement(rowIndex, 1, "zsection"); writer.writeElement(rowIndex, 2, "time"); for (int y = 0; y < channelSummaryTable.getRowCount(); y++) writer.writeElement(rowIndex, 3 + y, channelSummaryTable.getValueAt(y, 0)); } /** * Outputs the summary information from the shape map. * * @param writer The Excel writer. * @param shapeMap see above. * @throws IOException */ private void outputSummary(ExcelWriter writer, TreeMap<Coord3D, ROIShape> shapeMap) { int rowIndex = 0; printSummaryHeader(writer, rowIndex); rowIndex++; Coord3D start = shapeMap.firstKey(); Coord3D end = shapeMap.lastKey(); Coord3D coord; List<Integer> channels = new ArrayList<Integer>(channelName.keySet()); Set<Coord3D> keys; Iterator<Coord3D> i; for (Integer c : channels) { keys = shapeMap.keySet(); i = keys.iterator(); while (i.hasNext()) { coord = (Coord3D) i.next(); populateData(coord, c); outputSummaryRow(writer, rowIndex, c, coord.getZSection(), coord.getTimePoint()); rowIndex++; } } } /** * Adds the any remaining fields (min, max, mean, stdDev) to the file being * saved. * * @param writer The Excel writer. * @param rowIndex The selected row. * @param channel The channel to output. * @param z z-section to output. * @param t timepoint to output. */ private void outputSummaryRow(ExcelWriter writer, int rowIndex, Integer channel, int z, int t) { String name = channelName.get(channel); writer.writeElement(rowIndex, 0, name); writer.writeElement(rowIndex, 1, "" + (z + 1)); writer.writeElement(rowIndex, 2, "" + (t + 1)); int col; String v; for (int y = 0; y < channelSummaryTable.getRowCount(); y++) { col = getColumn(name); if (col == -1) continue; v = (String) channelSummaryTable.getValueAt(y, col); if (v != null) { if (v.contains(".") && v.contains(",")) { v = v.replace(".", ""); v = v.replace(",", "."); } writer.writeElement(rowIndex, 3 + y, new Double(v)); } } } /** * Returns the column for the name equal to the string. * * @param name see above. * @return see above. */ private int getColumn(String name) { for (int i = 0; i < channelSummaryModel.getColumnCount(); i++) if (channelSummaryModel.getColumnName(i).equals(name)) return i; return -1; } /** * Returns <code>true</code> if the user has selected the summary channel, * <code>false</code> otherwise. * * @param selection see above. * @return see above. */ private boolean channelSummarySelected(List<Integer> selection) { for (Integer value : selection) if (value == ChannelSelectionForm.SUMMARYVALUE) return true; return false; } /** * Writes the header information for the file, image, projects, dataset. * * @param writer The Excel writer. * @param rowIndex The selected row. * @param currentCoord The coord of the shape being written. * @throws IOException Thrown if the data cannot be written. */ private void writeHeader(ExcelWriter writer, int rowIndex, Coord3D currentCoord) { writer.writeElement(rowIndex, 0, "Image "); writer.writeElement(rowIndex, 1, model.getImageName()); rowIndex++; writer.writeElement(rowIndex, 0, "Z "); writer.writeElement(rowIndex, 1, (currentCoord.getZSection() + 1)); rowIndex++; writer.writeElement(rowIndex, 0, "T "); writer.writeElement(rowIndex, 1, (currentCoord.getTimePoint() + 1)); rowIndex++; } /** * Writes the channel intensities and stats to the files. * * @param writer The Excel writer. * @param rowIndex The selected row. * @param coord The specified coordinate. * @param channel The channel to output. */ private void writeData(ExcelWriter writer, int rowIndex, Coord3D coord, int channel) { populateData(coord, channel); writer.writeTableToSheet(rowIndex, 0, tableModel); } /** Shows the intensity results dialog. */ private void showIntensityResults() { populateChannel(); UIUtilities.setLocationRelativeToAndSizeToWindow(this, intensityDialog, intensityTableSize); } /** * Creates a new instance. * * @param view Reference to the View. Mustn't be <code>null</code>. * @param model Reference to the Model. Mustn't be <code>null</code>. */ IntensityView(MeasurementViewerUI view, MeasurementViewerModel model) { if (view == null) throw new IllegalArgumentException("No view."); if (model == null) throw new IllegalArgumentException("No model."); this.view = view; this.model = model; selectedChannelName = ""; initComponents(); buildGUI(); } /** * Returns the name of the component. * * @return See above. */ String getComponentName() { return NAME; } /** * Returns the icon of the component. * * @return See above. */ Icon getComponentIcon() { IconManager icons = IconManager.getInstance(); return icons.getIcon(IconManager.INTENSITYVIEW); } /** Invokes when ROI are removed. */ void onFigureRemoved() { channelSelection.setEnabled(false); showIntensityTable.setEnabled(false); saveButton.setEnabled(false); channelSelection.setVisible(false); channelSummaryTable.setVisible(false); } /** * Get the analysis results from the model and convert to the * necessary array. data types using the ROIStats wrapper then * create the appropriate table data and summary statistics. */ void displayAnalysisResults() { if (state == State.ANALYSING) return; this.ROIStats = model.getAnalysisResults(); if (ROIStats == null || ROIStats.size() == 0) return; state = State.ANALYSING; clearMaps(); shapeStatsList = new TreeMap<Coord3D, Map<StatsType, Map>>(new Coord3D()); pixelStats = new TreeMap<Coord3D, Map<Integer, Map<Point, Double>>>(new Coord3D()); shapeMap = new TreeMap<Coord3D, ROIShape>(new Coord3D()); minStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D()); maxStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D()); meanStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D()); sumStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D()); stdDevStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D()); Entry entry; Iterator j = ROIStats.entrySet().iterator(); channelName = new TreeMap<Integer, String>(); nameMap = new LinkedHashMap<String, Integer>(); int minZ = Integer.MAX_VALUE, maxZ = Integer.MIN_VALUE; int minT = Integer.MAX_VALUE, maxT = Integer.MIN_VALUE; clearAllValues(); Coord3D c3D; Map<StatsType, Map> shapeStats; ChannelData channelData; int channel; Iterator<ChannelData> i; List<ChannelData> metadata = model.getMetadata(); while (j.hasNext()) { entry = (Entry) j.next(); shape = (ROIShape) entry.getKey(); c3D = shape.getCoord3D(); minT = Math.min(minT, c3D.getTimePoint()); maxT = Math.max(maxT, c3D.getTimePoint()); minZ = Math.min(minZ, c3D.getZSection()); maxZ = Math.max(maxZ, c3D.getZSection()); shapeMap.put(c3D, shape); if (shape.getFigure() instanceof MeasureTextFigure) { state = State.READY; return; } shapeStats = AnalysisStatsWrapper.convertStats((Map) entry.getValue()); if (shapeStats != null) { shapeStatsList.put(c3D, shapeStats); minStats.put(c3D, shapeStats.get(StatsType.MIN)); maxStats.put(c3D, shapeStats.get(StatsType.MAX)); meanStats.put(c3D, shapeStats.get(StatsType.MEAN)); sumStats.put(c3D, shapeStats.get(StatsType.SUM)); stdDevStats.put(c3D, shapeStats.get(StatsType.STDDEV)); pixelStats.put(c3D, shapeStats.get(StatsType.PIXEL_PLANEPOINT2D)); } /* really inefficient but hey.... quick hack just now till refactor */ channelName.clear(); nameMap.clear(); channelColour.clear(); i = metadata.iterator(); List<String> names = new ArrayList<String>(); String name; while (i.hasNext()) { channelData = i.next(); channel = channelData.getIndex(); if (model.isChannelActive(channel)) { name = channelData.getChannelLabeling(); if (names.contains(name)) name += " " + channel; channelName.put(channel, name); nameMap.put(channelName.get(channel), channel); channelColour.put(channel, (Color) model.getActiveChannels().get(channel)); } } } if (channelName.size() != channelColour.size() || nameMap.size() == 0) { createComboBox(); channelSelection.setVisible(channelSelection.getItemCount() > 0); List<String> names = channelSummaryModel.getRowNames(); List<String> channelNames = new ArrayList<String>(); Double data[][] = new Double[channelName.size()][names.size()]; channelSummaryModel = new ChannelSummaryModel(names, channelNames, data); channelSummaryTable.setModel(channelSummaryModel); if (intensityDialog != null) intensityDialog.setVisible(false); state = State.READY; showIntensityTable.setEnabled(channelSelection.isVisible()); saveButton.setEnabled(tableModel.getRowCount() > 0); return; } maxZ = maxZ + 1; minZ = minZ + 1; maxT = maxT + 1; minT = minT + 1; createComboBox(); channelSelection.setVisible(channelSelection.getItemCount() > 0); showIntensityTable.setEnabled(channelSelection.isVisible()); Object[] nameColour = (Object[]) channelSelection.getSelectedItem(); String string = (String) nameColour[1]; selectedChannel = nameMap.get(string); zSlider.setMaximum(maxZ); zSlider.setMinimum(minZ); tSlider.setMaximum(maxT); tSlider.setMinimum(minT); zSlider.setVisible((maxZ != minZ)); tSlider.setVisible((maxT != minT)); tSlider.setValue(model.getCurrentView().getTimePoint() + 1); zSlider.setValue(model.getCurrentView().getZSection() + 1); coord = new Coord3D(zSlider.getValue() - 1, tSlider.getValue() - 1); shape = shapeMap.get(coord); populateData(coord, selectedChannel); formatPlane(); saveButton.setEnabled(tableModel.getRowCount() > 0); state = State.READY; } /** Invokes when figures are selected. */ void onFigureSelected() { Set<Figure> selectedFigures = view.getDrawingView().getSelectedFigures(); if (CollectionUtils.isEmpty(selectedFigures)) { boolean row = tableModel.getRowCount() > 1; showIntensityTable.setEnabled(row); channelSelection.setEnabled(row); saveButton.setEnabled(row); } else { boolean size = channelSelection.getModel().getSize() > 0; channelSelection.setEnabled(size); showIntensityTable.setEnabled(size); saveButton.setEnabled(size); } } /** * Indicates any on-going analysis. * * @param analyse Passes <code>true</code> when analyzing, * <code>false</code> otherwise. */ void onAnalysed(boolean analyse) { if (!analyse) { onFigureSelected(); } else { showIntensityTable.setEnabled(false); saveButton.setEnabled(false); } zSlider.setEnabled(!analyse); tSlider.setEnabled(!analyse); } /** * Implemented as specified by the I/F {@link TabPaneInterface} * @see TabPaneInterface#getIndex() */ public int getIndex() { return INDEX; } /** * Reacts to the controls. * @see ActionListener#actionPerformed(ActionEvent) */ public void actionPerformed(ActionEvent e) { if (state == State.ANALYSING) return; int index = Integer.parseInt(e.getActionCommand()); switch (index) { case CHANNEL_SELECTION: populateChannel(); break; case SAVE_ACTION: saveResults(); break; case SHOW_TABLE_ACTION: showIntensityResults(); } } /** * Reacts to slider moves. * @see ChangeListener#stateChanged(ChangeEvent) */ public void stateChanged(ChangeEvent evt) { Object src = evt.getSource(); if (src == zSlider || src == tSlider) { formatPlane(); OneKnobSlider slider = (OneKnobSlider) src; if (!slider.isDragging()) { handleSliderReleased(); } } } /** * Listens to property fired by {@link #zSlider} or {@link #tSlider}. * @see ChangeListener#stateChanged(ChangeEvent) */ public void propertyChange(PropertyChangeEvent evt) { String name = evt.getPropertyName(); if (OneKnobSlider.ONE_KNOB_RELEASED_PROPERTY.equals(name)) { handleSliderReleased(); } } }