Examples with ExtendedGenericDialog uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog used on opensource projects

Example 31 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog 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 32 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createMesh.

@SuppressWarnings("unused")
private static CustomMesh createMesh(final ImageJ3DResultsViewerSettingsOrBuilder settings, LocalList<Point3f> points, final Point3f[] sphereSize, float transparency, float[] alpha) {
    // Coordinates + color
    int stride = 3 + 3;
    if (alpha != null) {
        // add color alpha
        stride++;
    }
    // Support drawing as points ...
    if (settings.getRendering() == 0) {
        final long arraySize = (long) points.size() * stride;
        if (arraySize > CustomContentHelper.MAX_ARRAY_SIZE) {
            final double capacity = (double) arraySize / CustomContentHelper.MAX_ARRAY_SIZE;
            // @formatter:off
            IJ.error(TITLE, TextUtils.wrap(String.format("The results will generate data of %d values. " + "This is amount of data is not supported (%.2fx capacity). " + "Please choose a different dataset with fewer points.", arraySize, capacity), 80));
            // @formatter:on
            return null;
        }
        CustomPointMesh mesh;
        if (alpha != null) {
            final TransparentItemPointMesh mesh2 = new TransparentItemPointMesh(points, null, transparency);
            mesh = mesh2;
            mesh2.setItemAlpha(alpha);
        } else {
            mesh = new ItemPointMesh(points, null, transparency);
        }
        mesh.setPointSize(sphereSize[0].x);
        return mesh;
    }
    final Rendering r = Rendering.forNumber(settings.getRendering());
    // Repeated mesh creation is much faster as the normals are cached.
    // There does not appear to be a difference in the speed the image responds
    // to user interaction between indexed or standard triangles.
    // Currently the RepeatedIndexedTriangleMesh computes the normals a different way to
    // the super class to preserve the orientation of the normals. So if the coordinates
    // are modified through the mesh then the appearance will change. For now just use
    // the RepeatedTriangleMesh.
    // TODO - check this. It may not be true if the shading mode is flat...
    // Also the IndexedTriangleMesh has one normal per vertex and this causes a colour fall-off
    // on the triangle plane towards the edges. The TriangleMesh colours the entire surface
    // of each triangle the same which looks 'normal'.
    final List<Point3f> point = Shape3DHelper.createLocalisationObject(r);
    // + normals
    stride += 3;
    final int singlePointSize = point.size();
    final long size = (long) points.size() * singlePointSize;
    final long arraySize = size * stride;
    if (arraySize > CustomContentHelper.MAX_ARRAY_SIZE) {
        final double capacity = (double) arraySize / CustomContentHelper.MAX_ARRAY_SIZE;
        // @formatter:off
        IJ.error(TITLE, TextUtils.wrap(String.format("The results will generate data of %d values. " + "This is amount of data is not supported (%.2fx capacity). " + "Please choose a different rendering model with fewer vertices.", arraySize, capacity), 80));
        // @formatter:on
        return null;
    }
    if (size > 10000000L) {
        final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
        egd.addMessage("The results will generate a large mesh of " + size + " vertices.\nThis may take a long time to render and may run out of memory.");
        egd.setOKLabel("Continue");
        egd.showDialog();
        if (egd.wasCanceled()) {
            return null;
        }
    }
    IJ.showStatus("Creating 3D mesh ...");
    final double creaseAngle = (r.isHighResolution()) ? 44 : 0;
    // Used for debugging construction time
    final ImageJTrackProgress progress = null;
    if (alpha != null) {
        final TransparentItemTriangleMesh mesh = new TransparentItemTriangleMesh(point.toArray(new Point3f[singlePointSize]), points.toArray(new Point3f[0]), sphereSize, null, transparency, creaseAngle, progress);
        mesh.setItemAlpha(alpha);
        return mesh;
    }
    return new ItemTriangleMesh(point.toArray(new Point3f[singlePointSize]), points.toArray(new Point3f[0]), sphereSize, null, transparency, creaseAngle, progress);
}

Example 33 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class GaussianFit method showDialog.

@Override
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    final double[] limits = getLimits(imp.getProcessor());
    final double minValue = limits[0];
    final double maxValue = limits[1];
    settings = Settings.load();
    if (settings.background > maxValue) {
        settings.background = (int) maxValue;
    }
    if (settings.background < minValue) {
        settings.background = (int) minValue;
    }
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("gaussian-fit"));
    gd.addMessage("Fit 2D Gaussian to identified maxima");
    gd.addMessage("--- Image smoothing ---\n" + "- Within a 2n+1 box\n");
    gd.addSlider("Smoothing", 0, 4.5, settings.smooth);
    gd.addMessage("--- Maxima identification ---\n" + "- Within a 2n+1 box\n");
    gd.addSlider("Box_size", 1, 15, settings.boxSize);
    gd.addSlider("Background", minValue, maxValue, settings.background);
    gd.addSlider("Min_height", 0, maxValue, settings.peakHeight);
    gd.addSlider("Fraction_above_background", 0, 1.01, settings.fractionAboveBackground);
    gd.addSlider("Min_width", 0, 20, settings.peakWidth);
    gd.addSlider("Top_N", 0, 20, settings.topN);
    gd.addCheckbox("Block_find_algorithm", settings.blockFindAlgorithm);
    gd.addCheckbox("Neighbour_check", settings.neighbourCheck);
    gd.addSlider("Border", 0, 15, settings.border);
    gd.addMessage("--- Gaussian fitting ---");
    gd.addChoice("PSF", getPsfTypeNames(), PsfProtosHelper.getName(getPsfType()));
    gd.addCheckbox("Fit_background", settings.fitBackground);
    gd.addNumericField("Max_iterations", settings.maxIterations, 0);
    gd.addNumericField("Relative_threshold", settings.relativeThreshold, -3);
    gd.addNumericField("Absolute_threshold", settings.absoluteThreshold, -3);
    gd.addCheckbox("Single_fit", settings.singleFit);
    gd.addNumericField("Single_region_size", settings.singleRegionSize, 0);
    gd.addNumericField("Initial_StdDev", settings.initialPeakStdDev, 3);
    gd.addCheckbox("Log_progress", settings.logProgress);
    gd.addCheckbox("Show_deviations", settings.showDeviations);
    gd.addCheckbox("Filter_results", settings.filterResults);
    gd.addCheckbox("Show_fit", settings.showFit);
    gd.addPreviewCheckbox(pfr);
    gd.addDialogListener(this::dialogItemChanged);
    gd.showDialog();
    if (gd.wasCanceled() || !dialogItemChanged(gd, null)) {
        imp.setOverlay(null);
        return DONE;
    }
    return FLAGS;
}

Example 34 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class Fire method showDialog.

private boolean showDialog() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(pluginTitle);
    gd.addMessage("Compute the resolution using Fourier Ring Correlation");
    gd.addHelp(HelpUrls.getUrl("fourier-image-resolution"));
    final boolean single = results2 == null;
    gd.addMessage("Image construction options:");
    gd.addChoice("Image_scale", Settings.scaleItems, settings.imageScaleIndex);
    gd.addChoice("Auto_image_size", Settings.imageSizeItems, settings.imageSizeIndex);
    if (extraOptions) {
        gd.addCheckbox("Use_signal (if present)", settings.useSignal);
    }
    gd.addNumericField("Max_per_bin", settings.maxPerBin, 0);
    gd.addMessage("Fourier options:");
    final String[] fourierMethodNames = SettingsManager.getNames((Object[]) Frc.FourierMethod.values());
    gd.addChoice("Fourier_method", fourierMethodNames, fourierMethodNames[settings.fourierMethodIndex]);
    final String[] samplingMethodNames = SettingsManager.getNames((Object[]) Frc.SamplingMethod.values());
    gd.addChoice("Sampling_method", samplingMethodNames, samplingMethodNames[settings.samplingMethodIndex]);
    gd.addSlider("Sampling_factor", 0.2, 4, settings.perimeterSamplingFactor);
    gd.addMessage("FIRE options:");
    final String[] thresholdMethodNames = SettingsManager.getNames((Object[]) Frc.ThresholdMethod.values());
    gd.addChoice("Threshold_method", thresholdMethodNames, thresholdMethodNames[settings.thresholdMethodIndex]);
    gd.addCheckbox("Show_FRC_curve", settings.showFrcCurve);
    if (single) {
        gd.addMessage("For single datasets:");
        gd.addNumericField("Block_size", settings.blockSize, 0);
        gd.addCheckbox("Random_split", settings.randomSplit);
        gd.addNumericField("Repeats", settings.repeats, 0);
        gd.addCheckbox("Show_FRC_curve_repeats", settings.showFrcCurveRepeats);
        gd.addCheckbox("Show_FRC_time_evolution", settings.showFrcTimeEvolution);
        gd.addCheckbox("Spurious correlation correction", settings.spuriousCorrelationCorrection);
        gd.addNumericField("Q-value", settings.qvalue, 3);
        gd.addNumericField("Precision_Mean", settings.mean, 2, 6, "nm");
        gd.addNumericField("Precision_Sigma", settings.sigma, 2, 6, "nm");
        if (extraOptions) {
            gd.addNumericField("Threads", getLastNThreads(), 0);
        }
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.imageScaleIndex = gd.getNextChoiceIndex();
    settings.imageSizeIndex = gd.getNextChoiceIndex();
    if (extraOptions) {
        myUseSignal = settings.useSignal = gd.getNextBoolean();
    }
    settings.maxPerBin = Math.abs((int) gd.getNextNumber());
    settings.fourierMethodIndex = gd.getNextChoiceIndex();
    fourierMethod = FourierMethod.values()[settings.fourierMethodIndex];
    settings.samplingMethodIndex = gd.getNextChoiceIndex();
    samplingMethod = SamplingMethod.values()[settings.samplingMethodIndex];
    settings.perimeterSamplingFactor = gd.getNextNumber();
    settings.thresholdMethodIndex = gd.getNextChoiceIndex();
    thresholdMethod = Frc.ThresholdMethod.values()[settings.thresholdMethodIndex];
    settings.showFrcCurve = gd.getNextBoolean();
    if (single) {
        settings.blockSize = Math.max(1, (int) gd.getNextNumber());
        settings.randomSplit = gd.getNextBoolean();
        settings.repeats = Math.max(1, (int) gd.getNextNumber());
        settings.showFrcCurveRepeats = gd.getNextBoolean();
        settings.showFrcTimeEvolution = gd.getNextBoolean();
        settings.spuriousCorrelationCorrection = gd.getNextBoolean();
        settings.qvalue = Math.abs(gd.getNextNumber());
        settings.mean = Math.abs(gd.getNextNumber());
        settings.sigma = Math.abs(gd.getNextNumber());
        if (extraOptions) {
            setThreads((int) gd.getNextNumber());
            setLastNThreads(this.numberOfThreads);
        }
    }
    // Check arguments
    try {
        ParameterUtils.isAboveZero("Perimeter sampling factor", settings.perimeterSamplingFactor);
        if (single && settings.spuriousCorrelationCorrection) {
            ParameterUtils.isAboveZero("Q-value", settings.qvalue);
            ParameterUtils.isAboveZero("Precision Mean", settings.mean);
            ParameterUtils.isAboveZero("Precision Sigma", settings.sigma);
            // Set these for use in FIRE computation
            setCorrectionParameters(settings.qvalue, settings.mean, settings.sigma);
        }
    } catch (final IllegalArgumentException ex) {
        IJ.error(pluginTitle, ex.getMessage());
        return false;
    }
    return true;
}

Example 35 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class ImageJ3DResultsViewer method createItemMesh.

private static ItemMesh createItemMesh(final ImageJ3DResultsViewerSettingsOrBuilder settings, LocalList<Point3f> points, final Point3f[] sphereSize, float transparency, float[] alpha) {
    final Rendering rendering = Rendering.forNumber(settings.getRendering());
    final int colorDepth = (alpha != null) ? 4 : 3;
    final Shape3D shape = Shape3DHelper.createShape(rendering, colorDepth);
    final GeometryArray ga = (GeometryArray) shape.getGeometry();
    final Appearance appearance = shape.getAppearance();
    // Estimate the largest array required for the data.
    // The mesh is created by reference using an array for coords, normals and colors.
    final int singlePointVertexSize = ga.getValidVertexCount();
    int singlePointIndexSize = 0;
    final int stride = Math.max(3, colorDepth);
    if (ga instanceof IndexedGeometryArray) {
        // Indexed arrays may have much larger index array than the vertex array
        singlePointIndexSize = ((IndexedGeometryArray) ga).getIndexCount();
    }
    final int singlePointSize = Math.max(singlePointIndexSize, stride * singlePointVertexSize);
    final long arraySize = (long) points.size() * singlePointSize;
    if (arraySize > CustomContentHelper.MAX_ARRAY_SIZE) {
        final double capacity = (double) arraySize / CustomContentHelper.MAX_ARRAY_SIZE;
        // @formatter:off
        IJ.error(TITLE, TextUtils.wrap(String.format("The results will generate data of %d values. " + "This is amount of data is not supported (%.2fx capacity). " + "Please choose a different dataset with fewer points or " + "different rendering model.", arraySize, capacity), 80));
        // @formatter:on
        return null;
    }
    // Support drawing as points ...
    if (settings.getRendering() == 0) {
        final ItemMesh mesh = new ReferenceItemMesh(points.toArray(new Point3f[0]), ga, appearance, null, null, transparency);
        if (alpha != null) {
            mesh.setItemAlpha(alpha);
        }
        mesh.getAppearance().getPointAttributes().setPointSize(sphereSize[0].x);
        return mesh;
    }
    final int triangles = Shape3DHelper.getNumberOfTriangles(rendering);
    final long size = (long) points.size() * triangles;
    if (size > 10000000L) {
        final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
        egd.addMessage("The results will generate a large mesh of " + size + " triangles.\nThis may take a long time to render and may run out of memory.");
        egd.setOKLabel("Continue");
        egd.showDialog();
        if (egd.wasCanceled()) {
            return null;
        }
    }
    IJ.showStatus("Creating 3D mesh ...");
    final ItemMesh mesh = new ReferenceItemMesh(points.toArray(new Point3f[0]), ga, appearance, sphereSize, null, transparency);
    if (alpha != null) {
        mesh.setItemAlpha(alpha);
    }
    return mesh;
}