Examples with View org.scijava.java3d.View used on opensource projects

Example 1 with View

use of org.scijava.java3d.View in project TrakEM2 by trakem2.

the class Display3DGUI method newPanelColors.

private static final JPanel newPanelColors(final Image3DUniverse univ) {
    final JPanel p = new JPanel();
    p.setBackground(Color.white);
    final GridBagLayout gb = new GridBagLayout();
    final GridBagConstraints c = new GridBagConstraints();
    c.anchor = GridBagConstraints.NORTHWEST;
    c.fill = GridBagConstraints.HORIZONTAL;
    p.setLayout(gb);
    final String[] labels = new String[] { "Red", "Green", "Blue" };
    final JScrollBar[] sliders = new JScrollBar[3];
    final JTextField[] typers = new JTextField[3];
    for (int i = 0; i < 3; ++i) {
        final JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL, 255, 1, 0, 256);
        sliders[i] = slider;
        final JTextField typer = new IntegerField(255, 3);
        typers[i] = typer;
        final int k = i;
        slider.addAdjustmentListener(new AdjustmentListener() {

            @Override
            public void adjustmentValueChanged(final AdjustmentEvent e) {
                final Content content = univ.getSelected();
                if (null == content) {
                    Utils.log("Nothing selected!");
                    return;
                }
                Color3f color = content.getColor();
                // default to yellow
                if (null == color)
                    color = new Color3f(1, 1, 0);
                final float[] co = new float[3];
                color.get(co);
                co[k] = e.getValue() / 255.0f;
                content.setColor(new Color3f(co));
                typer.setText(Integer.toString(e.getValue()));
            }
        });
        typer.addKeyListener(new SliderTyperLink(univ, slider, typer));
        final JLabel l = new JLabel(labels[i]);
        // Layout
        c.gridx = 0;
        c.gridy = i;
        gb.setConstraints(l, c);
        p.add(l);
        c.gridx = 1;
        c.weightx = 1;
        c.fill = GridBagConstraints.HORIZONTAL;
        gb.setConstraints(slider, c);
        p.add(slider);
        c.gridx = 2;
        c.weightx = 0;
        c.fill = GridBagConstraints.NONE;
        gb.setConstraints(typer, c);
        p.add(typer);
    }
    // Alpha slider
    c.gridx = 0;
    c.gridy += 1;
    final JLabel aL = new JLabel("Alpha:");
    gb.setConstraints(aL, c);
    p.add(aL);
    c.gridx = 1;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.weightx = 1;
    final JScrollBar alphaSlider = new JScrollBar(JScrollBar.HORIZONTAL, 255, 1, 0, 256);
    gb.setConstraints(alphaSlider, c);
    p.add(alphaSlider);
    c.gridx = 2;
    c.fill = GridBagConstraints.NONE;
    c.weightx = 0;
    final JTextField alphaTyper = new IntegerField(255, 3);
    gb.setConstraints(alphaTyper, c);
    p.add(alphaTyper);
    alphaSlider.addAdjustmentListener(new AdjustmentListener() {

        @Override
        public void adjustmentValueChanged(final AdjustmentEvent e) {
            final Content content = univ.getSelected();
            if (null == content) {
                Utils.log("Nothing selected!");
                return;
            }
            final float alpha = e.getValue() / 255.0f;
            content.setTransparency(1 - alpha);
            alphaTyper.setText(Integer.toString(e.getValue()));
        }
    });
    alphaTyper.addKeyListener(new SliderTyperLink(univ, alphaSlider, alphaTyper));
    // Button to colorize randomly
    c.gridx = 0;
    c.gridy += 1;
    c.gridwidth = 3;
    c.weightx = 1;
    c.insets = new Insets(15, 4, 4, 4);
    final JButton r = new JButton("Assign random colors to all");
    r.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(final ActionEvent e) {
            randomizeColors(univ);
        }
    });
    gb.setConstraints(r, c);
    p.add(r);
    addTitledLineBorder(p, "Colors");
    univ.addUniverseListener(new UniverseListener() {

        @Override
        public void universeClosed() {
        }

        @Override
        public void transformationUpdated(final View arg0) {
        }

        @Override
        public void transformationStarted(final View arg0) {
        }

        @Override
        public void transformationFinished(final View arg0) {
        }

        @Override
        public void contentSelected(final Content arg0) {
            if (null == arg0) {
                return;
            }
            Color3f color = arg0.getColor();
            // default to yellow
            if (null == color)
                color = new Color3f(1, 1, 0);
            final float[] co = new float[3];
            color.get(co);
            for (int i = 0; i < 3; ++i) {
                // Disallow the slider from firing an event when its value is adjusted
                sliders[i].setValueIsAdjusting(true);
                final int val = (int) (co[i] * 255);
                typers[i].setText(Integer.toString(val));
                sliders[i].setValue(val);
            }
            // After all are set, re-enable, which triggers events (the color will be set three times...)
            for (int i = 0; i < 3; ++i) {
                sliders[i].setValueIsAdjusting(false);
            }
            // Alpha slider:
            alphaSlider.setValueIsAdjusting(true);
            final int alpha = (int) ((1 - arg0.getTransparency()) * 255);
            alphaTyper.setText(Integer.toString(alpha));
            alphaSlider.setValue(alpha);
            alphaSlider.setValueIsAdjusting(false);
        }

        @Override
        public void contentRemoved(final Content arg0) {
        }

        @Override
        public void contentChanged(final Content arg0) {
            if (arg0 == univ.getSelected()) {
                contentSelected(arg0);
            }
        }

        @Override
        public void contentAdded(final Content arg0) {
        }

        @Override
        public void canvasResized() {
        }
    });
    return p;
}

Example 2 with View

use of org.scijava.java3d.View 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();
}

Example 3 with View

use of org.scijava.java3d.View in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method activateDynamicTransparency.

private static void activateDynamicTransparency(Image3DUniverse univ, long size, boolean enable) {
    if (size == 0) {
        IJ.log("No transparent objects");
        enable = false;
    }
    final View view = univ.getViewer().getView();
    final boolean isEnabled = view.getTransparencySortingPolicy() == View.TRANSPARENCY_SORT_GEOMETRY;
    if (enable == isEnabled) {
        return;
    }
    if (enable) {
        if (size > 20000L) {
            final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
            egd.addMessage("The results contain " + size + " transparent objects.\nDynamic transparency may take a long time to render.");
            egd.setOKLabel("Dynamic");
            egd.setCancelLabel("Standard");
            egd.showDialog();
            if (egd.wasCanceled()) {
                return;
            }
        }
        view.setTransparencySortingPolicy(View.TRANSPARENCY_SORT_GEOMETRY);
        IJ.log("Enabled dynamic transparency");
    // Q. I am not sure if this is required if objects are sorted?
    // view.setDepthBufferFreezeTransparent(false)
    } else {
        view.setTransparencySortingPolicy(View.TRANSPARENCY_SORT_NONE);
        IJ.log("Disabled dynamic transparency");
    }
    final JMenuBar menubar = univ.getMenuBar();
    final JMenu menu = menubar.getMenu(menubar.getMenuCount() - 1);
    for (int i = 0; i < menu.getItemCount(); i++) {
        final JMenuItem item = menu.getItem(i);
        if (item == null) {
            continue;
        }
        if (item.getText().equals("Toggle dynamic transparency")) {
            ((JCheckBoxMenuItem) item).setSelected(enable);
        }
    }
}

Example 4 with View

use of org.scijava.java3d.View in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewerDemo method run.

@Override
public void run(String arg) {
    if (ImageJ3DViewerUtils.JAVA_3D_VERSION == null) {
        IJ.error(TITLE, "Java 3D is not available");
        return;
    }
    final boolean renderingTest = true;
    if (renderingTest) {
        // Put all the shapes from rendering on a view and see how they look.
        final Image3DUniverse univ = new Image3DUniverse();
        univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
        univ.show();
        final ImageWindow3D w = univ.getWindow();
        GUI.center(w);
        // Test how many vertices a primitive sphere has
        float x = 0;
        final float y = 0;
        final float space = 2.5f;
        for (final Rendering rendering : Rendering.values()) {
            final Shape3D shape = Shape3DHelper.createShape(rendering, 3);
            final Appearance a = shape.getAppearance();
            final ItemMesh mesh = new ReferenceItemMesh(new Point3f[] { new Point3f(x, y, 0) }, (GeometryArray) shape.getGeometry(), a, null, null, 0f);
            ImageJUtils.log("R=%s %s  Vc=%d  V=%d  T=%d", rendering, shape.getGeometry().getClass().getSimpleName(), mesh.getVerticesCountPerItem(), mesh.getVerticesPerItem(), Shape3DHelper.getNumberOfTriangles(rendering));
            if (rendering == Rendering.POINT) {
                a.getPointAttributes().setPointSize(10);
            }
            univ.addCustomMesh(mesh, x + "," + y);
            x += space;
        }
        return;
    }
    final boolean sphereTest = true;
    if (sphereTest) {
        // Sphere test
        // Put lots of spheres on a view and see how they look.
        // Is it worth supporting an ItemTriangleStripMesh so we can control
        // the sphere better than the icosahedron?
        final Image3DUniverse univ = new Image3DUniverse();
        univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
        univ.show();
        final ImageWindow3D w = univ.getWindow();
        GUI.center(w);
        // Test how many vertices a primitive sphere has
        float x = 0;
        float y = 0;
        final float space = 2.5f;
        Appearance app = null;
        for (int d = 0; d < 4; d++) {
            final List<Point3f> points = customnode.MeshMaker.createIcosahedron(d, 1f);
            final Pair<Point3f[], int[]> p = CustomContentHelper.createIndexedObject(points);
            final int v = points.size();
            final int t = v / 3;
            ImageJUtils.log("Icosahedron divisions = %d, V=%d, T=%d, Vi=%d (%.2f), i=%d", d, v, t, p.getKey().length, v / (double) p.getKey().length, p.getValue().length);
            CustomMesh mesh = new ItemTriangleMesh(points.toArray(new Point3f[0]), new Point3f[] { new Point3f(x, y, 0) }, null, null, 0);
            app = mesh.getAppearance();
            univ.addCustomMesh(mesh, x + "," + y + "," + t);
            final float y2 = y + space;
            mesh = new ItemIndexedTriangleMesh(p.getKey(), p.getValue(), new Point3f[] { new Point3f(x, y2, 0) }, null, null, 0);
            univ.addCustomMesh(mesh, x + "," + y2 + "," + t);
            x += space;
        }
        // Avoid null pointer warnings
        if (app == null) {
            throw new NullPointerException();
        }
        // The T=800 sphere looks about the same as the Icosahedron(div=3) T=1280
        // This may be a better super-high resolution option.
        x = 0;
        y += 2 * space;
        app = (Appearance) app.cloneNodeComponent(true);
        // a.getColoringAttributes().setColor(0, 1, 0);
        app.getMaterial().setDiffuseColor(0, 1, 0);
        for (int d = 4; d < 50; d += 4) {
            // This is a triangle strip array so is more space efficient
            final Sphere s = new Sphere(1, Primitive.GENERATE_NORMALS, d);
            final int t = s.getNumTriangles();
            ImageJUtils.log("Sphere divisions = %d, V=%d, T=%d", d, s.getNumVertices(), t);
            final ItemGeometryGroup g = new ItemGeometryGroup(new Point3f[] { new Point3f(x, y, 0) }, (GeometryArray) s.getShape().getGeometry(), app, null, null, null);
            final String name = x + "," + y + "," + t;
            final CustomContent content = new CustomContent(name, true);
            content.getCurrent().display(new ItemGroupNode(g));
            univ.addContent(content);
            x += space;
        }
        return;
    }
    LocalList<Point3f> pointList;
    float scale;
    if (MemoryPeakResults.isMemoryEmpty()) {
        pointList = new LocalList<>();
        int range;
        // 9 points
        range = 1;
        // range = 49; // 99^3 = 970299 points
        for (int x = -range; x <= range; x++) {
            for (int y = -range; y <= range; y++) {
                for (int z = -range; z <= range; z++) {
                    pointList.add(new Point3f(x, y, z));
                }
            }
        }
        scale = 0.25f;
    } else {
        final ImageJ3DResultsViewerSettings.Builder settings = SettingsManager.readImageJ3DResultsViewerSettings(0).toBuilder();
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Select a dataset to display");
        ResultsManager.addInput(gd, settings.getInputOption(), InputSource.MEMORY);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
        final String name = ResultsManager.getInputSource(gd);
        settings.setInputOption(name);
        SettingsManager.writeSettings(settings);
        final MemoryPeakResults results = ResultsManager.loadInputResults(name, false, null, null);
        if (MemoryPeakResults.isEmpty(results)) {
            IJ.error(TITLE, "No results could be loaded");
            IJ.showStatus("");
            return;
        }
        pointList = ImageJ3DResultsViewer.getPoints(results, settings);
        if (pointList == null) {
            return;
        }
        scale = 10f;
    }
    final Image3DUniverse univ = new Image3DUniverse();
    univ.showAttribute(DefaultUniverse.ATTRIBUTE_SCALEBAR, false);
    univ.show();
    final ImageWindow3D w = univ.getWindow();
    GUI.center(w);
    final View view = univ.getViewer().getView();
    view.setTransparencySortingPolicy(View.TRANSPARENCY_SORT_GEOMETRY);
    // I am not sure if this is required if objects are sorted.
    // view.setDepthBufferFreezeTransparent(false)
    IJ.showStatus("Creating points ...");
    final Point3f[] points = pointList.toArray(new Point3f[0]);
    final Point3f[] sizes = new Point3f[] { new Point3f(scale, scale, scale) };
    final Appearance appearance = new Appearance();
    final TransparencyAttributes ta = new TransparencyAttributes();
    ta.setTransparency(0.5f);
    ta.setTransparencyMode(TransparencyAttributes.FASTEST);
    appearance.setTransparencyAttributes(ta);
    final ItemGeometryGroup pointGroup = new ItemGeometryGroup(points, null, appearance, sizes, null, null);
    // pointGroup = new OrderedItemGeometryGroup(points, null, appearance, sizes, null, null);
    // // This supports transparency sorting
    // BranchGroup bg = new BranchGroup();
    // bg.addChild(pointGroup);
    // bg.compile();
    // univ.getScene().addChild(bg);
    // // This does not since ContentInstant uses an OrderedPath to show:
    // // the content; the object bounding box, coordinate system and point list
    // final Content c = new Content("Test");
    // final ContentInstant content = c.getCurrent();
    // content.display(new PointGroupNode(pointGroup));
    // univ.addContent(c);
    // This does since ItemGeometryNode uses a Group to show the points as individual shapes
    // and the CustomContentInstant uses a group not an ordered group so show all the adornments.
    IJ.showStatus("Displaying points ...");
    final CustomContent c = new CustomContent("Test", false);
    final ContentInstant content = c.getCurrent();
    content.display(new ItemGroupNode(pointGroup));
    univ.addContent(c);
    IJ.showStatus("Done");
}