use of ij3d.Content in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method createImage3DUniverse.
/**
* Creates the image 3D universe with a unique name.
*
* @param title the title
* @param titleList the title list (of titles to ignore)
* @return the image 3D universe
*/
private Image3DUniverse createImage3DUniverse(String title, List<String> titleList) {
// Get a unique name by appending numbers to the end
String title2 = title;
int counter = 2;
while (titleList.contains(title2)) {
title2 = title + " " + (counter++);
}
final Image3DUniverse universe = new Image3DUniverse();
universe.addUniverseListener(new LocalUniverseListener());
universe.setShowBoundingBoxUponSelection(false);
universe.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
// Capture a canvas mouse click/region and identify the coordinates.
final ImageCanvas3D canvas = (ImageCanvas3D) universe.getCanvas();
final BranchGroup scene = universe.getScene();
final MouseListener mouseListener = new MouseAdapter() {
@Override
public void mouseClicked(final MouseEvent event) {
if (!consumeEvent(event)) {
return;
}
// Consume the event
event.consume();
// This finds the vertex indices of the rendered object.
final Pair<Content, IntersectionInfo> pair = getPickedContent(canvas, scene, event.getX(), event.getY());
if (pair == null) {
// Do the same as the mouseClicked in Image3DUniverse
universe.select(null);
return;
}
// Only process content added from localisations
final Content c = pair.getKey();
if (!(c.getUserData() instanceof ResultsMetaData)) {
// Do the same as the mouseClicked in Image3DUniverse
universe.select(c);
return;
}
final ResultsMetaData data = (ResultsMetaData) c.getUserData();
final MemoryPeakResults results = data.results;
// Look up the localisation from the clicked vertex
final ContentInstant content = c.getCurrent();
int index = -1;
if (content.getContent() instanceof CustomMeshNode) {
final CustomMeshNode node = (CustomMeshNode) content.getContent();
final CustomMesh mesh = node.getMesh();
int vertexCount;
final GeometryArray ga = (GeometryArray) mesh.getGeometry();
// Default to the number of vertices
vertexCount = ga.getValidVertexCount();
final int countPerLocalisation = vertexCount / results.size();
// Determine the localisation
final int vertexIndex = pair.getValue().getVertexIndices()[0];
index = vertexIndex / countPerLocalisation;
} else if (content.getContent() instanceof ItemGroupNode) {
// All shapes have the index as the user data
final Object o = pair.getValue().getGeometry().getUserData();
if (o instanceof Integer) {
index = (Integer) pair.getValue().getGeometry().getUserData();
}
}
if (index == -1) {
return;
}
final PeakResult result = results.get(index);
if (event.getClickCount() > 1) {
// Centre on the localisation
final Point3d coordinate = new Point3d();
coordinate.set(data.points.get(index));
// Handle the local transform of the content ...
final Transform3D vWorldToLocal = getVworldToLocal(content);
vWorldToLocal.transform(coordinate);
universe.centerAt(coordinate);
} else if (event.isShiftDown()) {
// Ctrl+Shift held down to remove selected
data.removeFromSelectionModel(result);
} else {
// Ctrl held down to set selection
data.addToSelectionModel(result);
}
}
private boolean consumeEvent(final MouseEvent event) {
if (event.isConsumed() || event.getButton() != MouseEvent.BUTTON1 || !(event.isControlDown())) {
return false;
}
if (event.getClickCount() == 1) {
return true;
}
return (event.getClickCount() == 2);
}
};
// 0 = ImageCanvas3D
// 1 = DefaultUniverse
// 2 = Image3DUniverse
final MouseListener[] l = canvas.getMouseListeners();
for (int i = 0; i < l.length; i++) {
if (l[i].getClass().getName().contains("Image3DUniverse")) {
// We want to be before the Image3DUniverse to allow consuming the click event.
// Only allow the click event.
// This disables the right-click pop-up menu.
// It doesn't have anything of use for localisations anyway.
canvas.removeMouseListener(l[i]);
canvas.addMouseListener(mouseListener);
canvas.addMouseListener(new MouseListenerWrapper(l[i], MouseListenerWrapper.MOUSE_CLICKED));
}
}
// 0 = ImageCanvas3D
// 1 = DefaultUniverse
// 2 = Image3DUniverse
// 3 = EventCatcher (from scijava)
final MouseMotionListener[] ml = canvas.getMouseMotionListeners();
for (int i = 0; i < ml.length; i++) {
if (ml[i].getClass().getName().contains("Image3DUniverse")) {
// Ignore this as it just shows the name in the IJ status bar
canvas.removeMouseMotionListener(ml[i]);
}
}
// Finally display the window
universe.show();
final ImageWindow3D window = universe.getWindow();
GUI.center(window);
window.setTitle(title2);
WindowManager.addWindow(window);
window.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent event) {
WindowManager.removeWindow(window);
}
});
// Add a new menu for SMLM functionality
createSmlmMenuBar(universe);
return universe;
}
use of ij3d.Content in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method getTotalTransparentObjects.
private static long getTotalTransparentObjects(Image3DUniverse univ, String ignoreName) {
long size = 0;
for (final Iterator<Content> it = univ.contents(); it.hasNext(); ) {
final Content c = it.next();
if (ignoreName.equals(c.getName())) {
continue;
}
if (!(c.getUserData() instanceof ResultsMetaData)) {
return 0;
}
final ContentInstant content = c.getCurrent();
if (content.getContent() instanceof ItemGroupNode) {
final ItemGroupNode node = (ItemGroupNode) content.getContent();
final ItemGroup g = node.getItemGroup();
if (g instanceof ItemGeometryGroup) {
size += g.size();
}
}
}
return size;
}
use of ij3d.Content in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method run.
@Override
public void run(String arg) {
// For testing
// if (true || Utils.isExtraOptions())
// {
// new ImageJ3DResultsViewerDemo().run(arg);
// return;
// }
SmlmUsageTracker.recordPlugin(this.getClass(), arg);
if (ImageJ3DViewerUtils.JAVA_3D_VERSION == null) {
IJ.error(TITLE, "Java 3D is not available");
return;
}
if (MemoryPeakResults.isMemoryEmpty()) {
IJ.error(TITLE, "There are no fitting results in memory");
return;
}
final ImageJ3DResultsViewerSettings.Builder settings = SettingsManager.readImageJ3DResultsViewerSettings(0).toBuilder();
addToSelection.set(settings.getAddToSelection());
// Get a list of the window titles available. Allow the user to select
// an existing window or a new one.
final String title = TITLE;
final List<Image3DUniverse> univList = new LocalList<>();
final List<String> titleList = new LocalList<>();
titleList.add("New window");
buildWindowList(title, univList, titleList);
final String[] titles = titleList.toArray(new String[0]);
final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
gd.addMessage("Select a dataset to display");
ResultsManager.addInput(gd, settings.getInputOption(), InputSource.MEMORY);
// The behaviour is to allow the settings to store if the user prefers a new window
// or to reuse an existing window. If 'new window' then a new window should always
// be selected. Otherwise open in the same window as last time. If there was no last
// window then the settings will carried over from the last ImageJ session.
final String window = (settings.getNewWindow()) ? "" : lastWindow.get();
gd.addChoice("Window", titles, window);
gd.addSlider("Transparancy", 0, 0.9, settings.getTransparency(), new OptionListener<Double>() {
@Override
public boolean collectOptions(Double value) {
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Transparancy options", null);
egd.addCheckbox("Support_dynamic_transparency", settings.getSupportDynamicTransparency());
egd.addCheckbox("Enable_dynamic_transparency", settings.getEnableDynamicTransparency());
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setSupportDynamicTransparency(egd.getNextBoolean());
settings.setEnableDynamicTransparency(egd.getNextBoolean());
return true;
}
});
gd.addChoice("Colour", LutHelper.getLutNames(), settings.getLut());
gd.addChoice("Rendering", RENDERING, settings.getRendering(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setRendering(value);
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Drawing mode options", null);
final int rendering = settings.getRendering();
if (rendering != 0) {
return false;
}
egd.addNumericField("Pixel_size", settings.getPixelSize(), 2, 6, "px");
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setPixelSize(egd.getNextNumber());
return true;
}
});
gd.addCheckbox("Shaded", settings.getShaded());
gd.addChoice("Size_mode", SIZE_MODE, settings.getSizeMode(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setSizeMode(value);
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Size mode options", null);
final SizeMode mode = SizeMode.forNumber(settings.getSizeMode());
if (mode == SizeMode.FIXED_SIZE) {
egd.addNumericField("Size", settings.getSize(), 2, 6, "nm");
} else {
// Other modes do not require options
return false;
}
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setSize(egd.getNextNumber());
return true;
}
});
gd.addChoice("Sort_mode", SORT_MODE, settings.getSortMode(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setSortMode(value);
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Sort mode options", null);
final SortMode mode = SortMode.forNumber(settings.getSortMode());
if (mode == SortMode.NONE) {
return false;
}
egd.addMessage(TextUtils.wrap("Note: The sort mode is used to correctly render transparent objects. " + "For non-transparent objects faster rendering is achieved with a reverse " + "sort to put close objects at the front.", 80));
egd.addMessage(TextUtils.wrap(mode.getDetails(), 80));
egd.addMessage("Define the direction of the view");
egd.addNumericField("Direction_x", settings.getSortDirectionX(), 3, 10, "");
egd.addNumericField("Direction_y", settings.getSortDirectionY(), 3, 10, "");
egd.addNumericField("Direction_z", settings.getSortDirectionZ(), 3, 10, "");
if (mode == SortMode.PERSPECTIVE) {
egd.addMessage("Define the view eye position");
egd.addNumericField("Eye_x", settings.getSortEyeX(), 3, 10, "nm");
egd.addNumericField("Eye_y", settings.getSortEyeY(), 3, 10, "nm");
egd.addNumericField("Eye_z", settings.getSortEyeZ(), 3, 10, "nm");
}
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setSortDirectionX(egd.getNextNumber());
settings.setSortDirectionY(egd.getNextNumber());
settings.setSortDirectionZ(egd.getNextNumber());
if (mode == SortMode.PERSPECTIVE) {
settings.setSortEyeX(egd.getNextNumber());
settings.setSortEyeY(egd.getNextNumber());
settings.setSortEyeZ(egd.getNextNumber());
}
return true;
}
});
gd.addChoice("Transparency_mode", TRANSPARENCY_MODE, settings.getTransparencyMode(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setTransparencyMode(value);
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Transparency mode options", null);
final TransparencyMode mode = TransparencyMode.forNumber(settings.getTransparencyMode());
if (mode == TransparencyMode.NONE) {
return false;
}
egd.addSlider("Min_transparancy", 0, 0.95, settings.getMinTransparency());
egd.addSlider("Max_transparancy", 0, 0.95, settings.getMaxTransparency());
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setMinTransparency(egd.getNextNumber());
settings.setMaxTransparency(egd.getNextNumber());
return true;
}
});
addColourMode(settings, gd);
gd.addMessage("2D options");
gd.addChoice("Depth_mode", DEPTH_MODE, settings.getDepthMode(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setDepthMode(value);
return collectOptions(false);
}
@Override
public boolean collectOptions() {
return collectOptions(true);
}
private boolean collectOptions(boolean silent) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Depth mode options", null);
final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
if (mode == DepthMode.NONE) {
return false;
}
egd.addNumericField("Depth_range", settings.getDepthRange(), 2, 6, "nm");
if (mode == DepthMode.DITHER) {
egd.addNumericField("Dither_seed", settings.getDitherSeed(), 0);
}
egd.setSilent(silent);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
settings.setDepthRange(egd.getNextNumber());
if (mode == DepthMode.DITHER) {
settings.setDitherSeed((int) egd.getNextNumber());
}
return true;
}
});
addHelp(gd);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
final String name = ResultsManager.getInputSource(gd);
final int windowChoice = gd.getNextChoiceIndex();
lastWindow.set(titles[windowChoice]);
settings.setInputOption(name);
settings.setTransparency(gd.getNextNumber());
settings.setLut(gd.getNextChoiceIndex());
settings.setRendering(gd.getNextChoiceIndex());
settings.setShaded(gd.getNextBoolean());
settings.setSizeMode(gd.getNextChoiceIndex());
settings.setSortMode(gd.getNextChoiceIndex());
settings.setTransparencyMode(gd.getNextChoiceIndex());
settings.setColourMode(gd.getNextChoiceIndex());
settings.setDepthMode(gd.getNextChoiceIndex());
gd.collectOptions();
if (windowChoice == 0) {
// Store if the user chose a new window when they had a choice of an existing window
if (titleList.size() > 1) {
settings.setNewWindow(true);
// Otherwise they had no choice so leave the preferences as they are.
}
} else {
// This was not a new window
settings.setNewWindow(false);
}
SettingsManager.writeSettings(settings);
MemoryPeakResults results = ResultsManager.loadInputResults(name, false, null, null);
if (MemoryPeakResults.isEmpty(results)) {
IJ.error(TITLE, "No results could be loaded");
return;
}
// Determine if the drawing mode is supported and compute the point size
final Point3f[] sphereSize = createSphereSize(results, settings);
if (sphereSize == null) {
return;
}
// Cache the table settings
resultsTableSettings.set(settings.getResultsTableSettings());
// Create a 3D viewer.
if (windowChoice == 0) {
univ = createImage3DUniverse(title, titleList);
} else {
// Ignore the new window
univ = univList.get(windowChoice - 1);
}
lastWindow.set(univ.getWindow().getTitle());
results = results.copy();
// Commence a digest
final Future<PeakResultsDigest> futureDigest = PeakResultsDigest.digestLater(executorService, results.toArray());
final LocalList<Point3f> points = getPoints(results, settings);
final ResultsMetaData data = new ResultsMetaData(settings.build(), results, points, sphereSize);
sort(data);
final float[] alpha = createAlpha(results, settings, sphereSize);
final float transparency = getTransparency(settings);
final Color3f[] colors = createColour(results, settings);
ContentNode contentNode;
// Build to support true transparency (depends on settings).
// Currently this is not supported for PointArrays as they require colouring
// in the coordinate data.
IJ.showStatus("Creating 3D geometry ...");
if (settings.getSupportDynamicTransparency()) {
final ItemGeometryGroup pointGroup = createItemGroup(settings, sphereSize, points, alpha, transparency, colors);
if (pointGroup == null) {
IJ.showStatus("");
return;
}
if (settings.getEnableDynamicTransparency()) {
final long total = points.size() + getTotalTransparentObjects(univ, name);
activateDynamicTransparency(univ, total, settings.getEnableDynamicTransparency());
} else {
activateDynamicTransparency(univ, 0, settings.getEnableDynamicTransparency());
}
contentNode = new ItemGroupNode(pointGroup);
} else {
final ItemMesh mesh = createItemMesh(settings, points, sphereSize, transparency, alpha);
if (mesh == null) {
IJ.showStatus("");
return;
}
setColour(mesh, colors);
contentNode = new CustomMeshNode(mesh);
}
IJ.showStatus("Creating 3D content ...");
// Use custom content to support adding new switchable nodes
final CustomContent content = new CustomContent(name, !settings.getSupportDynamicTransparency());
final CustomContentInstant contentInstant = (CustomContentInstant) content.getCurrent();
contentInstant.setTransparency((float) settings.getTransparency());
contentInstant.setShaded(settings.getShaded());
contentInstant.showCoordinateSystem(UniverseSettings.showLocalCoordinateSystemsByDefault);
contentInstant.display(contentNode);
createHighlightColour(settings.getHighlightColour());
content.setUserData(data);
// Prevent relative rotation
content.setLocked(true);
// Set up the click selection node
data.createClickSelectionNode(contentInstant);
// Set up the results selection model
data.digest = PeakResultsDigest.waitForDigest(futureDigest, -1);
if (data.digest == null) {
IJ.error(TITLE, "Failed to identify repeat results set");
IJ.showStatus("");
return;
}
Triple<PeakResultTableModel, ListSelectionModel, PeakResultTableModelFrame> triplet = resultsTables.get(data.digest);
if (triplet == null) {
triplet = Triple.of(new PeakResultTableModel(results, false, // Note the settings do not matter until the table is set live
resultsTableSettings.get()), new DefaultListSelectionModel(), null);
triplet.getLeft().setCheckDuplicates(true);
resultsTables.put(data.digest, triplet);
}
// Preserve orientation on the content
final boolean auto = univ.getAutoAdjustView();
final Content oldContent = univ.getContent(name);
if (oldContent == null) {
univ.setAutoAdjustView(true);
} else {
univ.removeContent(name);
univ.setAutoAdjustView(false);
}
IJ.showStatus("Drawing 3D content ... ");
final StopWatch sw = StopWatch.createStarted();
final Future<Content> future = univ.addContentLater(content);
Content added = null;
for (; ; ) {
try {
// Wait for 1 second
for (int i = 0; i < 20; i++) {
Thread.sleep(50);
if (future.isDone()) {
// Only get the result when finished, so avoiding a blocking wait
added = future.get();
break;
}
}
if (added != null) {
break;
}
final long seconds = sw.getTime(TimeUnit.SECONDS);
if (seconds % 20 == 0) {
final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE, null);
egd.addMessage("Current wait time is " + sw.toString());
egd.setOKLabel("Wait");
egd.showDialog();
if (egd.wasCanceled()) {
future.cancel(true);
break;
}
}
IJ.showStatus("Drawing 3D content ... " + seconds);
} catch (final InterruptedException ex) {
Thread.currentThread().interrupt();
} catch (final ExecutionException ex) {
break;
}
}
univ.setAutoAdjustView(auto);
// Initialise the selection model
if (added != null) {
data.addSelectionModel(triplet);
}
IJ.showStatus("");
}
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