Java tutorial
/* *------------------------------------------------------------------------------ * 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; import java.awt.BorderLayout; import java.awt.Color; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; import java.util.Vector; import java.util.Map.Entry; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JFileChooser; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import javax.swing.table.DefaultTableModel; import org.apache.commons.collections.CollectionUtils; import org.jhotdraw.draw.Figure; import org.openmicroscopy.shoola.agents.measurement.IconManager; import org.openmicroscopy.shoola.agents.measurement.MeasurementAgent; 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.AnnotationDescription; import org.openmicroscopy.shoola.agents.measurement.util.model.AnalysisStatsWrapper.StatsType; import org.openmicroscopy.shoola.env.config.Registry; import omero.log.Logger; import org.openmicroscopy.shoola.env.rnd.roi.ROIShapeStats; import org.openmicroscopy.shoola.env.ui.UserNotifier; import org.openmicroscopy.shoola.util.file.ExcelWriter; import org.openmicroscopy.shoola.util.image.geom.Factory; 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.MeasurementAttributes; import org.openmicroscopy.shoola.util.roi.model.util.Coord3D; import org.openmicroscopy.shoola.util.ui.UIUtilities; import org.openmicroscopy.shoola.util.ui.filechooser.FileChooser; import omero.gateway.model.ChannelData; /** * Displays the intensity results. * * @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 * @since OME3.0 */ class IntensityResultsView extends JPanel implements ActionListener, TabPaneInterface { /** Index to identify tab */ public final static int INDEX = MeasurementViewerUI.INTENSITYRESULTVIEW_INDEX; /** The add button name. */ private final static String ADD_NAME = "Add"; /** Tooltip for the add button. */ private final static String ADD_DESCRIPTION = "Add Intensities for " + "the selected ROIs to results table."; /** The addAll button name. */ private final static String ADDALL_NAME = "Add Selected"; /** Tooltip for the add button. */ private final static String ADDALL_DESCRIPTION = "Add Intensities for " + "all the shapes of the selected ROIs to results table."; /** The remove button name. */ private final static String REMOVE_NAME = "Remove"; /** Tooltip for the remove button. */ private final static String REMOVE_DESCRIPTION = "Remove Results in " + "selected row from table."; /** The remove button name. */ private final static String REMOVE_ALL_NAME = "Remove All"; /** Tooltip for the remove button. */ private final static String REMOVE_ALL_DESCRIPTION = "Remove all the Results from table."; /** The save button name. */ private final static String SAVE_NAME = "Export to Excel..."; /** Tooltip for the save button. */ private final static String SAVE_DESCRIPTION = "Save Intensities " + "to Excel File."; /** Reference to the view. */ private MeasurementViewerUI view; /** The results table. */ private JTable results; /** The results model for the results table. */ private ResultsTableModel resultsModel; /** The remove button. */ private JButton removeButton; /** The save button. */ private JButton saveButton; /** The add button. */ private JButton addButton; /** The addAll button. */ private JButton addAllButton; /** The add button. */ private JButton removeAllButton; /** 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 Results View"; /** Action command id indicating to remove the selected rows. */ private static final int REMOVE = 0; /** Action command id indicating to add new row. */ private static final int ADD = 1; /** Action command id indicating to add new row. */ private static final int ADDALL = 4; /** Action command id indicating to remove all the rows. */ private static final int REMOVE_ALL = 2; /** Action command id indicating to save the results. */ private static final int SAVE = 3; /** Reference to the model. */ private MeasurementViewerModel model; /** The map of <ROIShape, ROIStats> .*/ private Map<ROIShape, Map<Integer, ROIShapeStats>> ROIStats; /** 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 mins, 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 HashMap<String, Integer>(); /** Map of the min channel intensity values to coord. */ private Map<Coord3D, Map<Integer, Double>> minStats; /** Map of the max channel intensity values to coord. */ private Map<Coord3D, Map<Integer, Double>> maxStats; /** Map of the mean channel intensity values to coord. */ private Map<Coord3D, Map<Integer, Double>> meanStats; /** Map of the std dev channel intensity values to coord. */ private Map<Coord3D, Map<Integer, Double>> stdDevStats; /** Map of the sum channel intensity values to coord. */ private Map<Coord3D, Map<Integer, Double>> sumStats; /** Map of the coordinate to a shape. */ private Map<Coord3D, ROIShape> shapeMap; /** The current coordinate of the ROI being depicted in the slider. */ private Coord3D coord; /** Current ROIShape. */ private ROIShape shape; /** * Wraps an ROI shape such that its string representation shows its ID, * or <q>--</q> if it a client-side shape. This is used for the shape IDs * in the first column of the results model table so that it is easy to * query any row to discover to which ROI shape it pertains. */ private static class ShapeAsID { private final ROIShape shape; private final String id; /** * Construct a new ShapeAsID instance. * @param shape the ROI shape that the instance is to wrap, may not be null */ private ShapeAsID(ROIShape shape) { if (shape == null) throw new IllegalArgumentException(new NullPointerException()); this.shape = shape; /* how the shape ID should display in the results model table */ if (shape.getROI().isClientSide()) this.id = "--"; else this.id = Long.toString(shape.getROIShapeID()); } /* a string suited for the ID column of the results model table */ @Override public String toString() { return this.id; } /** * @return the wrapped ROI shape */ private ROIShape getShape() { return this.shape; } } /** * Implemented as specified by the I/F {@link TabPaneInterface} * @see TabPaneInterface#getIndex() */ public int getIndex() { return INDEX; } /** Initializes the component composing the display. */ private void initComponents() { state = State.READY; removeButton = new JButton(REMOVE_NAME); removeButton.setToolTipText(UIUtilities.formatToolTipText(REMOVE_DESCRIPTION)); removeButton.setActionCommand("" + REMOVE); removeButton.addActionListener(this); saveButton = new JButton(SAVE_NAME); saveButton.setToolTipText(UIUtilities.formatToolTipText(SAVE_DESCRIPTION)); saveButton.setActionCommand("" + SAVE); saveButton.addActionListener(this); setButtonsEnabled(false); addButton = new JButton(ADD_NAME); addButton.setToolTipText(UIUtilities.formatToolTipText(ADD_DESCRIPTION)); addButton.setActionCommand("" + ADD); addButton.addActionListener(this); addAllButton = new JButton(ADDALL_NAME); addAllButton.setToolTipText(UIUtilities.formatToolTipText(ADDALL_DESCRIPTION)); addAllButton.setActionCommand("" + ADDALL); addAllButton.addActionListener(this); removeAllButton = new JButton(REMOVE_ALL_NAME); removeAllButton.setToolTipText(UIUtilities.formatToolTipText(REMOVE_ALL_DESCRIPTION)); removeAllButton.setActionCommand("" + REMOVE_ALL); removeAllButton.addActionListener(this); addAllButton.setEnabled(false); removeAllButton.setEnabled(false); removeButton.setEnabled(false); } /** * Sets the <code>enabled</code> flag of the {@link #saveButton}. * * @param enabled The value to set. */ private void setButtonsEnabled(boolean enabled) { saveButton.setEnabled(enabled); } /** Builds and lays out the UI. */ private void buildGUI() { resultsModel = new ResultsTableModel(); resultsModel.addColumn(AnnotationDescription.ROIID_STRING); resultsModel.addColumn("Z"); resultsModel.addColumn("T"); resultsModel.addColumn("Channel"); resultsModel.addColumn("Text"); resultsModel.addColumn("Min"); resultsModel.addColumn("Max"); resultsModel.addColumn("Sum"); resultsModel.addColumn("Mean"); resultsModel.addColumn("stdDev"); results = new JTable(resultsModel); results.getSelectionModel().addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { onFigureSelected(); } }); JPanel centrePanel = new JPanel(); centrePanel.setLayout(new BorderLayout()); JScrollPane scrollPane = new JScrollPane(results); centrePanel.add(scrollPane, BorderLayout.CENTER); JPanel bottomPanel = new JPanel(); bottomPanel.setLayout(new FlowLayout()); //bottomPanel.add(addButton); bottomPanel.add(addAllButton); bottomPanel.add(removeButton); bottomPanel.add(removeAllButton); bottomPanel.add(saveButton); JPanel containerPanel = new JPanel(); containerPanel.setLayout(new BorderLayout()); containerPanel.add(centrePanel, BorderLayout.CENTER); containerPanel.add(bottomPanel, BorderLayout.SOUTH); setLayout(new BorderLayout()); add(containerPanel, BorderLayout.CENTER); } /** * Returns <code>true</code> if the shape is already displayed for * the specified channel, <code>false</code> otherwise. * * @param shape The shape to add. * @param channelName The name of channel to display. */ private boolean isValueDisplayed(ROIShape shape, String channelName) { long id = shape.getID(); int z = shape.getCoord3D().getZSection(); int t = shape.getCoord3D().getTimePoint(); for (int i = 0; i < resultsModel.getRowCount(); i++) { ROIShape s = ((ShapeAsID) resultsModel.getValueAt(i, 0)).getShape(); if (s.getID() == id && s.getCoord3D().getZSection() == z && s.getCoord3D().getTimePoint() == t) { //check channel String v = (String) resultsModel.getValueAt(i, 3); if (v.equals(channelName)) return true; } } return false; } /** * Populates the table with the data. * * @param shape The analyzed shape. */ private void getResults(ROIShape shape) { Vector<Vector<Object>> rows = new Vector<Vector<Object>>(); final ShapeAsID shapeID = new ShapeAsID(shape); Iterator<String> channelIterator = channelName.values().iterator(); channelMin = minStats.get(coord); channelMax = maxStats.get(coord); channelMean = meanStats.get(coord); channelStdDev = stdDevStats.get(coord); channelSum = sumStats.get(coord); String cName; int channel; Vector<Object> rowData; while (channelIterator.hasNext()) { cName = channelIterator.next(); channel = nameMap.get(cName); if (!isValueDisplayed(shape, cName)) { rowData = new Vector<Object>(); rowData.add(shapeID); rowData.add(shape.getCoord3D().getZSection() + 1); rowData.add(shape.getCoord3D().getTimePoint() + 1); rowData.add(cName); rowData.add(MeasurementAttributes.TEXT.get(shape.getFigure())); rowData.add(channelMin.get(channel)); rowData.add(channelMax.get(channel)); rowData.add(channelSum.get(channel)); rowData.add(channelMean.get(channel)); rowData.add(channelStdDev.get(channel)); rows.add(rowData); } } for (Vector<Object> data : rows) { resultsModel.addRow(data); } results.repaint(); } /** Saves the results of the table to an Excel file. */ private void saveResults() { FileChooser chooser = view.createSaveToExcelChooser(); if (chooser.showDialog() != JFileChooser.APPROVE_OPTION) return; File file = chooser.getFormattedSelectedFile(); ExcelWriter writer = null; try { String filename = file.getAbsolutePath(); writer = new ExcelWriter(filename); writer.openFile(); writer.createSheet("Intensity Results"); writer.writeTableToSheet(0, 0, resultsModel); BufferedImage originalImage = model.getRenderedImage(); 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.setAttributes(MeasurementAttributes.SHOWID, false); try { if (image != null) { model.getDrawingView().print(image.getGraphics()); writer.addImageToWorkbook("ThumbnailImage", image); int col = writer.getMaxColumn(0); writer.writeImage(0, col + 1, 256, 256, "ThumbnailImage"); } } catch (Exception e) { Logger logger = MeasurementAgent.getRegistry().getLogger(); logger.error(this, "Cannot write Image: " + e.toString()); } writer.close(); } catch (IOException e) { Logger logger = MeasurementAgent.getRegistry().getLogger(); logger.error(this, "Cannot save ROI results: " + e.toString()); UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier(); un.notifyInfo("Save Results", "An error occurred while trying to" + " save the data.\nPlease try again."); 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."); } /** Removes the selected results from the table. */ private void removeResults() { int[] rows = results.getSelectedRows(); for (int i = 0; i < rows.length; i++) { resultsModel.removeRow(rows[i] - i); } results.clearSelection(); setButtonsEnabled(results.getRowCount() > 0); } /** * @return the ROI shapes currently in the results table rows, never null */ private Set<ROIShape> getShapesInRows() { final Set<ROIShape> shapes = new HashSet<ROIShape>(); for (int i = 0; i < resultsModel.getRowCount(); i++) shapes.add(((ShapeAsID) resultsModel.getValueAt(i, 0)).getShape()); return shapes; } /** * Check to see if the selected figure contains textFigure * @param selectedFigures see above. * @return see above. */ private boolean validFigures(Set<Figure> selectedFigures) { if (CollectionUtils.isEmpty(selectedFigures)) return false; for (Figure figure : selectedFigures) if (figure instanceof MeasureTextFigure) return false; return true; } /** * Adds the statistics from the selected ROI to the table. */ private void addResults() { Set<Figure> selectedFigures = view.getDrawingView().getSelectedFigures(); if (!validFigures(selectedFigures)) return; if (CollectionUtils.isEmpty(selectedFigures) || state == State.ANALYSING) return; state = State.ANALYSING; List<ROIShape> shapeList = new ArrayList<ROIShape>(); final Set<ROIShape> alreadyInTable = getShapesInRows(); Iterator<Figure> iterator = selectedFigures.iterator(); ROIFigure fig; Map<ROIShape, Map<Integer, ROIShapeStats>> analysisResults = model.getAnalysisResults(); if (analysisResults == null) analysisResults = Collections.emptyMap(); ROIShape shape; while (iterator.hasNext()) { fig = (ROIFigure) iterator.next(); shape = fig.getROIShape(); if (alreadyInTable.contains(shape)) removeShape(shape); final Map<Integer, ROIShapeStats> shapeStatsByChannel = analysisResults.get(shape); if (shapeStatsByChannel == null || shapeStatsByChannel.isEmpty()) /* if empty, they were probably wiped out by AnalysisStatsWrapper.convertStats */ shapeList.add(shape); } if (shapeList.size() > 0) { view.calculateStats(shapeList); onFigureSelected(); } state = State.READY; } /** * Removes the shape from the table. * * @param shapeID The identifier of the shape. */ private void removeShape(ROIShape shape) { List<Integer> indexes = new ArrayList<Integer>(); for (int i = 0; i < resultsModel.getRowCount(); i++) if (((ShapeAsID) resultsModel.getValueAt(i, 0)).getShape().equals(shape)) indexes.add(i); Iterator<Integer> j = indexes.iterator(); while (j.hasNext()) { resultsModel.removeRow(j.next()); } } /** * Sets the enabled flag of the various buttons. * * @param value The value to set. */ private void setControls(boolean value) { addAllButton.setEnabled(value); removeAllButton.setEnabled(value); removeButton.setEnabled(value); saveButton.setEnabled(value); } /** * Adds the statistics from the ROIShapes of the select ROI to the table. */ private void addAllResults() { Set<Figure> selectedFigures = view.getDrawingView().getSelectedFigures(); if (CollectionUtils.isEmpty(selectedFigures) || state == State.ANALYSING) return; state = State.ANALYSING; setControls(false); List<ROIShape> shapeList = new ArrayList<ROIShape>(); final Set<ROIShape> alreadyInTable = getShapesInRows(); Iterator<Figure> i = selectedFigures.iterator(); ROIFigure fig; TreeMap<Coord3D, ROIShape> treeMap; Iterator<Coord3D> j; ROIShape shape; Map<ROIShape, Map<Integer, ROIShapeStats>> analysisResults = model.getAnalysisResults(); if (analysisResults == null) analysisResults = Collections.emptyMap(); while (i.hasNext()) { fig = (ROIFigure) i.next(); if (!(fig instanceof MeasureTextFigure)) { treeMap = fig.getROI().getShapes(); j = treeMap.keySet().iterator(); while (j.hasNext()) { shape = treeMap.get(j.next()); if (!alreadyInTable.contains(shape)) { final Map<Integer, ROIShapeStats> shapeStatsByChannel = analysisResults.get(shape); if (shapeStatsByChannel == null || shapeStatsByChannel.isEmpty()) /* if empty, they were probably wiped out by AnalysisStatsWrapper.convertStats */ shapeList.add(shape); } } } } if (shapeList.isEmpty()) { if (!analysisResults.isEmpty()) { displayAnalysisResults(); } } else { view.calculateStats(shapeList); } } /** * 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>. */ IntensityResultsView(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; 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); } /** * 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() { this.ROIStats = model.getAnalysisResults(); onFigureSelected(); if (ROIStats == null || ROIStats.size() == 0) { state = State.READY; return; } 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 HashMap<String, Integer>(); Map<StatsType, Map> shapeStats; Coord3D c3D; ChannelData channelData; int channel; List<ChannelData> metadata = model.getMetadata(); Iterator<ChannelData> i; while (j.hasNext()) { entry = (Entry) j.next(); shape = (ROIShape) entry.getKey(); //shapeMap.put(shape.getCoord3D(), shape); if (shape.getFigure() instanceof MeasureTextFigure) { state = State.READY; return; } c3D = shape.getCoord3D(); shapeStats = AnalysisStatsWrapper.convertStats((Map) entry.getValue()); if (shapeStats != null) { 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)); } channelName.clear(); nameMap.clear(); channelColour.clear(); i = metadata.iterator(); while (i.hasNext()) { channelData = i.next(); channel = channelData.getIndex(); if (model.isChannelActive(channel)) { channelName.put(channel, channelData.getChannelLabeling()); nameMap.put(channelName.get(channel), channel); channelColour.put(channel, (Color) model.getActiveChannels().get(channel)); } } if (channelName.size() == 0 || nameMap.size() == 0 || channelColour.size() == 0) { state = State.READY; return; } coord = c3D; getResults(shape); } setButtonsEnabled(true); onFigureSelected(); state = State.READY; } /** Invokes when figures are selected. */ void onFigureSelected() { Set<Figure> selectedFigures = view.getDrawingView().getSelectedFigures(); boolean valid = validFigures(selectedFigures); addButton.setEnabled(valid); addAllButton.setEnabled(valid); if (results != null) { int count = results.getRowCount(); int[] rows = results.getSelectedRows(); removeButton.setEnabled(rows != null && rows.length > 0); removeAllButton.setEnabled(count > 0); } else { removeButton.setEnabled(false); removeAllButton.setEnabled(false); } } /** Removes the results from the table. */ void removeAllResults() { int count = results.getRowCount(); for (int i = count - 1; i >= 0; i--) resultsModel.removeRow(i); model.setAnalysisResults(null); setButtonsEnabled(false); onFigureSelected(); } /** * Listens to the controls. * @see ActionListener#actionPerformed(ActionEvent) * */ public void actionPerformed(ActionEvent e) { int index = Integer.parseInt(e.getActionCommand()); switch (index) { case ADD: addResults(); break; case ADDALL: addAllResults(); break; case SAVE: saveResults(); break; case REMOVE: removeResults(); break; case REMOVE_ALL: removeAllResults(); } } /** * The table model for the results table, only overridden to make it read * only. */ class ResultsTableModel extends DefaultTableModel { /** * Overridden to make sure that the cell cannot be edited. * @see DefaultTableModel#isCellEditable(int, int) */ public boolean isCellEditable(int row, int col) { return false; } } }