use of uk.ac.sussex.gdsc.smlm.ij.gui.PeakResultTableModel in project GDSC-SMLM by aherbert.
the class ImageJ3DResultsViewer method menuActionPerformed.
private void menuActionPerformed(ActionEvent event) {
final Object src = event.getSource();
ContentAction action = null;
// Adapted from univ.resetView()
if (src == resetRotation) {
univ.fireTransformationStarted();
// rotate so that y shows downwards
final Transform3D t = new Transform3D();
final AxisAngle4d aa = new AxisAngle4d(1, 0, 0, Math.PI);
t.set(aa);
univ.getRotationTG().setTransform(t);
univ.fireTransformationUpdated();
univ.fireTransformationFinished();
return;
}
if (src == resetTranslation) {
univ.fireTransformationStarted();
final Transform3D t = new Transform3D();
univ.getTranslateTG().setTransform(t);
univ.recalculateGlobalMinMax();
univ.getViewPlatformTransformer().centerAt(univ.getGlobalCenterPoint());
univ.fireTransformationUpdated();
univ.fireTransformationFinished();
return;
}
if (src == resetZoom) {
univ.fireTransformationStarted();
final Transform3D t = new Transform3D();
univ.getZoomTG().setTransform(t);
final Point3d max = new Point3d();
final Point3d min = new Point3d();
univ.getGlobalMaxPoint(max);
univ.getGlobalMinPoint(min);
final float range = (float) (max.x - min.x);
final double d = (range) / Math.tan(Math.PI / 8);
univ.getViewPlatformTransformer().zoomTo(d);
univ.fireTransformationUpdated();
univ.fireTransformationFinished();
return;
}
if (src == updateSettings) {
final ImageJ3DResultsViewerSettings.Builder settings = SettingsManager.readImageJ3DResultsViewerSettings(0).toBuilder();
final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
final ResultsSettings.Builder s = ResultsSettings.newBuilder();
ResultsTableSettings localResultsTableSettings = resultsTableSettings.get();
s.setResultsTableSettings(localResultsTableSettings);
gd.addMessage("Click on the image to view localisation data.\nCtrl/Alt key must be pressed.");
final TextField[] tf = new TextField[1];
gd.addStringField("Highlight_colour", settings.getHighlightColour(), new OptionListener<String>() {
@Override
public boolean collectOptions(String value) {
createHighlightColour(value);
int red;
int green;
int blue;
final Color3f color = highlightColor.get();
if (color == null) {
red = blue = 0;
green = 255;
} else {
red = (int) (color.x * 255);
green = (int) (color.y * 255);
blue = (int) (color.z * 255);
}
final ExtendedGenericDialog egd = new ExtendedGenericDialog("Highlight colour", null);
egd.addSlider("Red", 0, 255, red);
egd.addSlider("Green", 0, 255, green);
egd.addSlider("Blue", 0, 255, blue);
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
red = (int) egd.getNextNumber();
green = (int) egd.getNextNumber();
blue = (int) egd.getNextNumber();
final Color c = new Color(red, green, blue);
final String cvalue = c.getRed() + "," + c.getGreen() + "," + c.getBlue();
tf[0].setText(cvalue);
return true;
}
@Override
public boolean collectOptions() {
return false;
}
});
tf[0] = gd.getLastTextField();
gd.addCheckbox("Add_to_selection", settings.getAddToSelection());
ResultsManager.addTableResultsOptions(gd, s, ResultsManager.FLAG_NO_SECTION_HEADER);
gd.addMessage("Allow the 'Find Eye Point' command to save to settings");
gd.addCheckbox("Save_eye_point", settings.getSaveEyePoint());
// Same as CropResults
gd.addChoice("Crop_name_option", CropResults.NAME_OPTIONS, settings.getNameOption(), new OptionListener<Integer>() {
@Override
public boolean collectOptions(Integer value) {
settings.setNameOption(value);
final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
if (settings.getNameOption() == CropResults.NAME_OPTION_NAME) {
return false;
} else if (settings.getNameOption() == CropResults.NAME_OPTION_SUFFIX) {
final String name = (TextUtils.isNullOrEmpty(settings.getNameSuffix())) ? " Cropped" : settings.getNameSuffix();
egd.addStringField("Name_suffix", name, MathUtils.clip(20, 60, name.length()));
} else if (settings.getNameOption() == CropResults.NAME_OPTION_SEQUENCE) {
final String name = settings.getNameSuffix();
egd.addStringField("Name_suffix", name, MathUtils.clip(20, 60, name.length()));
int counter = settings.getNameCounter();
if (counter < 1) {
counter = 1;
}
egd.addNumericField("Name_counter", counter, 0);
} else {
throw new IllegalStateException("Unknown name option: " + settings.getNameOption());
}
egd.showDialog(true, gd);
if (egd.wasCanceled()) {
return false;
}
if (settings.getNameOption() == CropResults.NAME_OPTION_SUFFIX) {
settings.setNameSuffix(egd.getNextString());
} else if (settings.getNameOption() == CropResults.NAME_OPTION_SEQUENCE) {
settings.setNameSuffix(egd.getNextString());
settings.setNameCounter(Math.max(1, (int) egd.getNextNumber()));
}
return true;
}
@Override
public boolean collectOptions() {
return false;
}
});
gd.addCheckbox("Update_existing_tables", localResultsTableSettings.getUpdateExistingTables());
addHelp(gd);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
settings.setHighlightColour(gd.getNextString());
boolean add = gd.getNextBoolean();
addToSelection.set(add);
settings.setAddToSelection(add);
final ResultsTableSettings.Builder resultsTableSettingsBuilder = s.getResultsTableSettingsBuilder();
resultsTableSettingsBuilder.setShowTable(gd.getNextBoolean());
settings.setSaveEyePoint(gd.getNextBoolean());
settings.setNameOption(gd.getNextChoiceIndex());
resultsTableSettingsBuilder.setUpdateExistingTables(gd.getNextBoolean());
createHighlightColour(settings.getHighlightColour());
// Save updated settings
localResultsTableSettings = resultsTableSettingsBuilder.build();
settings.setResultsTableSettings(localResultsTableSettings);
SettingsManager.writeSettings(settings);
// Update the table settings for all the selection models
if (resultsTableSettingsBuilder.getUpdateExistingTables()) {
for (final Triple<PeakResultTableModel, ?, ?> t : resultsTables.values()) {
t.getLeft().setTableSettings(localResultsTableSettings);
}
}
action = new UpdateHighlightColourAction();
}
if (src == toggleDynamicTransparency) {
final long total = getTotalTransparentObjects(univ, "");
final View view = univ.getViewer().getView();
final boolean activate = view.getTransparencySortingPolicy() == View.TRANSPARENCY_SORT_NONE;
activateDynamicTransparency(univ, total, activate);
return;
}
// Actions to perform on content
if (src == changeColour) {
action = new ChangeColourContentAction();
} else if (src == resetAll) {
univ.resetView();
univ.select(null);
action = new ResetViewContentAction(false);
} else if (src == resetSelectedView) {
action = new ResetViewContentAction(true);
} else if (src == findEyePoint) {
action = new FindEyePointContentAction();
} else if (src == sortBackToFront) {
action = new SortContentAction(false);
} else if (src == sortFrontToBack) {
action = new SortContentAction(true);
} else if (src == colourSurface) {
action = new ColourSurfaceContentAction();
} else if (src == toggleTransparent) {
action = new ToggleTransparentAction();
} else if (src == toggleShaded) {
action = new ToggleShadedAction();
} else if (src == changePointSize) {
action = new ChangePointSizeContentAction();
} else if (src == increasePointSize) {
action = UpdatePointSizeContentAction.INCREASE;
} else if (src == decreasePointSize) {
action = UpdatePointSizeContentAction.DECREASE;
} else if (src == cropResults) {
action = new CropResultsAction();
} else if (src == showHelp) {
showHelp();
return;
}
if (action == null) {
return;
}
if (univ.getSelected() != null) {
action.run(univ.getSelected());
} else {
for (final Iterator<Content> it = univ.contents(); it.hasNext(); ) {
if (action.run(it.next()) < 0) {
break;
}
}
}
action.finish();
}
use of uk.ac.sussex.gdsc.smlm.ij.gui.PeakResultTableModel 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("");
}
use of uk.ac.sussex.gdsc.smlm.ij.gui.PeakResultTableModel in project GDSC-SMLM by aherbert.
the class ResultsManager method showInteractiveTable.
/**
* Show interactive table.
*
* @param results the results
* @param resultsTableSettings the results table settings
*/
public static void showInteractiveTable(MemoryPeakResults results, ResultsTableSettings resultsTableSettings) {
final PeakResultTableModel model = new PeakResultTableModel(results, true, resultsTableSettings);
final PeakResultTableModelFrame frame = new PeakResultTableModelFrame(model);
frame.setTitle(results.getName());
frame.setVisible(true);
// Save changes to the interactive table settings
model.addSettingsUpdatedAction(s -> {
// Load the latest settings and save the table options
final ResultsSettings.Builder resultsSettings = SettingsManager.readResultsSettings(0).toBuilder();
resultsSettings.setResultsTableSettings(s);
SettingsManager.writeSettings(resultsSettings.build());
});
}
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