protected void loadSettings(final String xmlFilename) throws IOException, JDOMException {
final SAXBuilder sax = new SAXBuilder();
final Document doc = sax.build(xmlFilename);
final Element root = doc.getRootElement();
viewer.stateFromXml(root);
setupAssignments.restoreFromXml(root);
manualTransformation.restoreFromXml(root);
bookmarks.restoreFromXml(root);
activeSourcesDialog.update();
viewer.requestRepaint();
}
public static void initBrightness(
final double cumulativeMinCutoff,
final double cumulativeMaxCutoff,
final ViewerPanel viewer,
final SetupAssignments setupAssignments) {
initBrightness(cumulativeMinCutoff, cumulativeMaxCutoff, viewer.getState(), setupAssignments);
}
protected void saveSettings(final String xmlFilename) throws IOException {
final Element root = new Element("Settings");
root.addContent(viewer.stateToXml());
root.addContent(setupAssignments.toXml());
root.addContent(manualTransformation.toXml());
root.addContent(bookmarks.toXml());
final Document doc = new Document(root);
final XMLOutputter xout = new XMLOutputter(Format.getPrettyFormat());
xout.output(doc, new FileWriter(xmlFilename));
}
/**
* @param converterSetups list of {@link ConverterSetup} that control min/max and color of
* sources.
* @param sources list of pairs of source of some type and converter from that type to ARGB.
* @param spimData may be null. The {@link AbstractSpimData} of the dataset (if there is one). If
* it exists, it is used to set up a "Crop" dialog.
* @param numTimepoints the number of timepoints in the dataset.
* @param cache handle to cache. This is used to control io timing.
* @param windowTitle title of the viewer window.
* @param windowWidth width of the viewer window.
* @param windowHeight height of the viewer window.
* @param progressWriter a {@link ProgressWriter} to which BDV may report progress (currently only
* used in the "Record Movie" dialog).
*/
public BigDataViewer(
final ArrayList<ConverterSetup> converterSetups,
final ArrayList<SourceAndConverter<?>> sources,
final AbstractSpimData<?> spimData,
final int numTimepoints,
final Cache cache,
final String windowTitle,
final int windowWidth,
final int windowHeight,
final ProgressWriter progressWriter) {
viewerFrame = new ViewerFrame(windowWidth, windowHeight, sources, numTimepoints, cache);
if (windowTitle != null) viewerFrame.setTitle(windowTitle);
viewer = viewerFrame.getViewerPanel();
for (final ConverterSetup cs : converterSetups)
if (RealARGBColorConverterSetup.class.isInstance(cs))
((RealARGBColorConverterSetup) cs).setViewer(viewer);
manualTransformation = new ManualTransformation(viewer);
manualTransformationEditor =
new ManualTransformationEditor(viewer, viewerFrame.getKeybindings());
bookmarks = new Bookmarks();
bookmarkEditor = new BookmarksEditor(viewer, viewerFrame.getKeybindings(), bookmarks);
setupAssignments = new SetupAssignments(converterSetups, 0, 65535);
if (setupAssignments.getMinMaxGroups().size() > 0) {
final MinMaxGroup group = setupAssignments.getMinMaxGroups().get(0);
for (final ConverterSetup setup : setupAssignments.getConverterSetups())
setupAssignments.moveSetupToGroup(setup, group);
}
brightnessDialog = new BrightnessDialog(viewerFrame, setupAssignments);
cropDialog =
(spimData == null)
? null
: new CropDialog(viewerFrame, viewer, spimData.getSequenceDescription());
movieDialog = new RecordMovieDialog(viewerFrame, viewer, progressWriter);
// this is just to get updates of window size:
viewer.getDisplay().addOverlayRenderer(movieDialog);
activeSourcesDialog =
new VisibilityAndGroupingDialog(viewerFrame, viewer.getVisibilityAndGrouping());
helpDialog = new HelpDialog(viewerFrame);
fileChooser = new JFileChooser();
fileChooser.setFileFilter(
new FileFilter() {
@Override
public String getDescription() {
return "xml files";
}
@Override
public boolean accept(final File f) {
if (f.isDirectory()) return true;
if (f.isFile()) {
final String s = f.getName();
final int i = s.lastIndexOf('.');
if (i > 0 && i < s.length() - 1) {
final String ext = s.substring(i + 1).toLowerCase();
return ext.equals("xml");
}
}
return false;
}
});
final KeyProperties keyProperties = KeyProperties.readPropertyFile();
NavigationActions.installActionBindings(viewerFrame.getKeybindings(), viewer, keyProperties);
BigDataViewerActions.installActionBindings(viewerFrame.getKeybindings(), this, keyProperties);
final JMenuBar menubar = new JMenuBar();
JMenu menu = new JMenu("File");
menubar.add(menu);
final ActionMap actionMap = viewerFrame.getKeybindings().getConcatenatedActionMap();
final JMenuItem miLoadSettings =
new JMenuItem(actionMap.get(BigDataViewerActions.LOAD_SETTINGS));
miLoadSettings.setText("Load settings");
menu.add(miLoadSettings);
final JMenuItem miSaveSettings =
new JMenuItem(actionMap.get(BigDataViewerActions.SAVE_SETTINGS));
miSaveSettings.setText("Save settings");
menu.add(miSaveSettings);
menu = new JMenu("Settings");
menubar.add(menu);
final JMenuItem miBrightness =
new JMenuItem(actionMap.get(BigDataViewerActions.BRIGHTNESS_SETTINGS));
miBrightness.setText("Brightness & Color");
menu.add(miBrightness);
final JMenuItem miVisibility =
new JMenuItem(actionMap.get(BigDataViewerActions.VISIBILITY_AND_GROUPING));
miVisibility.setText("Visibility & Grouping");
menu.add(miVisibility);
menu = new JMenu("Tools");
menubar.add(menu);
if (cropDialog != null) {
final JMenuItem miCrop = new JMenuItem(actionMap.get(BigDataViewerActions.CROP));
miCrop.setText("Crop");
menu.add(miCrop);
}
final JMenuItem miMovie = new JMenuItem(actionMap.get(BigDataViewerActions.RECORD_MOVIE));
miMovie.setText("Record Movie");
menu.add(miMovie);
final JMenuItem miManualTransform =
new JMenuItem(actionMap.get(BigDataViewerActions.MANUAL_TRANSFORM));
miManualTransform.setText("Manual Transform");
menu.add(miManualTransform);
menu = new JMenu("Help");
menubar.add(menu);
final JMenuItem miHelp = new JMenuItem(actionMap.get(BigDataViewerActions.SHOW_HELP));
miHelp.setText("Show Help");
menu.add(miHelp);
viewerFrame.setJMenuBar(menubar);
}
/**
* Set a "good" initial viewer transform. The viewer transform is chosen such that for the first
* source,
*
* <ul>
* <li>the XY plane is aligned with the screen plane,
* <li>the <em>z = dim_z / 2</em> slice is shown,
* <li>centered and scaled such that the full <em>dim_x</em> by <em>dim_y</em> is visible.
* </ul>
*
* This calls {@link #initTransform(int, int, boolean, ViewerState)}, using the size of the
* viewer's display component.
*
* @param viewer the viewer (containing at least one source) to have its transform set.
*/
public static void initTransform(final ViewerPanel viewer) {
final Dimension dim = viewer.getDisplay().getSize();
final ViewerState state = viewer.getState();
final AffineTransform3D viewerTransform = initTransform(dim.width, dim.height, false, state);
viewer.setCurrentViewerTransform(viewerTransform);
}