Examples with ColorMaps qupath.lib.color.ColorMaps used on opensource projects

Example 1 with ColorMaps

use of qupath.lib.color.ColorMaps in project qupath by qupath.

the class ViewTrackerAnalysisCommand method run.

@Override
public void run() {
    if (dialog == null) {
        dialog = new Stage();
        dialog.sizeToScene();
        dialog.initOwner(qupath.getStage());
        dialog.setTitle("Recording analysis");
        currentFrame.set(tracker.getFrame(0));
        int nCols = nCols(tracker);
        for (int i = 0; i < nCols; i++) {
            final int col = i;
            final String columnName = getColumnName(tracker, col);
            TableColumn<ViewRecordingFrame, Object> column = new TableColumn<>(columnName);
            column.setCellValueFactory(new Callback<CellDataFeatures<ViewRecordingFrame, Object>, ObservableValue<Object>>() {

                @Override
                public ObservableValue<Object> call(CellDataFeatures<ViewRecordingFrame, Object> frame) {
                    return new SimpleObjectProperty<>(getColumnValue(frame.getValue(), columnName));
                }
            });
            table.getColumns().add(column);
        }
        table.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
        table.getSelectionModel().selectedItemProperty().addListener((v, o, frame) -> {
            if (frame != null)
                currentFrame.set(frame);
        });
        refreshTracker();
        playback.getCurrentFrame().addListener((v, o, frame) -> currentFrame.set(frame));
        currentFrame.addListener((v, o, frame) -> {
            if (frame == null)
                return;
            // Set viewer for frame
            ViewTrackerPlayback.setViewerForFrame(viewer, frame);
            // Set slide overview for frame
            slideOverview.setVisibleShape(frame);
            zSlider.setValue(frame.getZ());
            tSlider.setValue(frame.getT());
            timeSlider.setValue(frame.getTimestamp());
            slideOverview.paintCanvas(o.getZ() != frame.getZ() || o.getT() != frame.getT(), false);
        });
        mainPane = new SplitPane();
        mainPane.setDividerPositions(1.0);
        BorderPane tablePane = new BorderPane();
        tablePane.setCenter(table);
        // ----------------------------------------------------------------------//
        // ----------------- SLIDE OVERVIEW (TOP LEFT)------------------//
        // ----------------------------------------------------------------------//
        int z = server.getMetadata().getSizeZ();
        int t = server.getMetadata().getSizeT();
        tSlider = new Slider(0, t - 1, 0);
        tSlider.setBlockIncrement(1);
        tSlider.setValue(viewer.getTPosition());
        tSlider.valueProperty().addListener((v, o, n) -> {
            tSlider.setValue(n.intValue());
            viewer.setTPosition(n.intValue());
            slideOverview.paintCanvas();
        });
        zSlider = new Slider(0, z - 1, 0);
        zSlider.setBlockIncrement(1);
        zSlider.setMinorTickCount(0);
        zSlider.setMajorTickUnit(1);
        zSlider.setShowTickMarks(true);
        zSlider.setValue(viewer.getZPosition());
        zSlider.valueProperty().addListener((v, o, n) -> {
            zSlider.setValue(n.intValue());
            viewer.setZPosition(n.intValue());
            slideOverview.paintCanvas();
        });
        zSlider.setOrientation(Orientation.VERTICAL);
        var timeSliderLength = tracker.getLastTime() - tracker.getStartTime();
        timeSlider = new Slider(0L, timeSliderLength, 0L);
        timeSlider.setMinWidth(250.0);
        if (timeSliderLength > 0) {
            timeSlider.setMajorTickUnit(timeSliderLength / 4);
            timeSlider.setMinorTickCount(0);
            timeSlider.setShowTickMarks(true);
        }
        timeSlider.valueProperty().addListener((v, o, n) -> {
            var frame = tracker.getFrameForTime(n.longValue());
            currentFrame.set(frame);
            if (table.getSelectionModel().getSelectedItem() != frame)
                table.getSelectionModel().select(frame);
        });
        timeSlider.setOnMouseClicked(e -> {
            playback.doStopPlayback();
        });
        long startTime = tracker.getStartTime();
        long endTime = tracker.getLastTime();
        Label timepointLabel = new Label();
        timepointLabel.textProperty().bind(Bindings.createStringBinding(() -> "t=" + GeneralTools.formatNumber(tSlider.getValue(), 2), tSlider.valueProperty()));
        Label zSliceLabel = new Label();
        zSliceLabel.textProperty().bind(Bindings.createStringBinding(() -> "z=" + GeneralTools.formatNumber(zSlider.getValue(), 2), zSlider.valueProperty()));
        Label timeLabelLeft = new Label();
        timeLabelLeft.textProperty().bind(Bindings.createStringBinding(() -> ViewTrackerTools.getPrettyTimestamp(startTime, (long) timeSlider.getValue() + startTime), timeSlider.valueProperty()));
        Label timeLabelRight = new Label();
        timeLabelRight.textProperty().bind(Bindings.createStringBinding(() -> "-" + ViewTrackerTools.getPrettyTimestamp((long) timeSlider.getValue() + startTime, endTime), timeSlider.valueProperty()));
        if (t == 1) {
            tSlider.setVisible(false);
            timepointLabel.setVisible(false);
        }
        if (z == 1) {
            zSlider.setVisible(false);
            zSliceLabel.setVisible(false);
        }
        Button btnPlay = new Button();
        btnPlay.setGraphic(iconPlay);
        btnPlay.setOnAction(e -> {
            if (!playback.isPlaying()) {
                // If it's not playing already, start playing
                playback.setFirstFrame(currentFrame.get());
                // Set the right slide overview image plane and visible shape for current frame
                slideOverview.paintCanvas();
                playback.doStartPlayback();
            } else {
                // If already playing, pause the playback where it currently is
                playback.doStopPlayback();
            }
        });
        Button btnStop = new Button();
        btnStop.setGraphic(iconStop);
        btnStop.setOnAction(e -> {
            playback.doStopPlayback();
            timeSlider.setValue(tracker.getFrame(0).getTimestamp());
        });
        // If we have a total of 0 or 1 frame in recording, disable playback
        btnPlay.disableProperty().bind(new SimpleBooleanProperty(tracker.nFrames() <= 1));
        btnStop.disableProperty().bind(new SimpleBooleanProperty(tracker.nFrames() <= 1));
        playback.playingProperty().addListener((v, o, n) -> {
            if (n) {
                btnPlay.setGraphic(iconPause);
                // btnPlay.setText("Pause");
                zSlider.setDisable(true);
                tSlider.setDisable(true);
            } else {
                btnPlay.setGraphic(iconPlay);
                // btnPlay.setText("Play");
                zSlider.setDisable(false);
                tSlider.setDisable(false);
            }
        });
        // --------------------------------------------------------------//
        // ----------- DATA VISUALIZATION PANE ---------------//
        // --------------------------------------------------------------//
        visualizationCheckBox = new CheckBox("Enable data overlay");
        // Label normalizedByLabel = new Label("Normalized by");
        // Bound below in the Binding section
        progressIndicator = new ProgressIndicator();
        progressIndicator.setPrefSize(15, 15);
        // ToggleGroup toggleGroup = new ToggleGroup();
        // timeNormalizedRadio = new RadioButton("Time");
        // timeNormalizedRadio.setSelected(true);
        // timeNormalizedRadio.setToggleGroup(toggleGroup);
        // 
        // downsampleNormalizedRadio = new RadioButton("Downsample");
        // downsampleNormalizedRadio.setToggleGroup(toggleGroup);
        // Create a color mapper ComboBox
        colorMaps = FXCollections.observableArrayList(ColorMaps.getColorMaps().values());
        ComboBox<ColorMap> colorMapCombo = new ComboBox<>(colorMaps);
        colorMapCombo.setMinWidth(350);
        colorMapCanvas = new ColorMapCanvas(10, colorMaps.get(0));
        colorMapCombo.getSelectionModel().selectedItemProperty().addListener((v, o, n) -> colorMapCanvas.setColorMap(n));
        if (colorMapCombo.getSelectionModel().isEmpty() && !colorMapCombo.getItems().isEmpty())
            colorMapCombo.getSelectionModel().selectFirst();
        colorMapCombo.setTooltip(new Tooltip("Select color map"));
        // ------------------ TIME DISPLAYED RANGESLIDER ------------------//
        Label timeDisplayedLeftLabel = new Label();
        Label timeDisplayedRightLabel = new Label();
        timeDisplayedSlider = new RangeSlider(0, timeSliderLength, 0, timeSliderLength);
        timeDisplayedSlider.setMinWidth(250.0);
        // Prompt input from user (min time)
        timeDisplayedLeftLabel.setOnMouseClicked(e -> {
            if (e.getButton().equals(MouseButton.PRIMARY) && e.getClickCount() == 2) {
                GridPane gp = new GridPane();
                TextField tf = new TextField();
                SimpleDateFormat format = new SimpleDateFormat("HH:mm:ss");
                try {
                    tf.setTextFormatter(new TextFormatter<>(new DateTimeStringConverter(format), format.parse("00:00:00")));
                } catch (ParseException ex) {
                    logger.error("Error parsing the input time: ", ex.getLocalizedMessage());
                }
                gp.addRow(0, new Label("Enter time"), tf);
                var response = Dialogs.showConfirmDialog("Set min time", gp);
                if (response) {
                    long time = TimeUnit.HOURS.toMillis(Integer.parseInt(tf.getText(0, 2))) + TimeUnit.MINUTES.toMillis(Integer.parseInt(tf.getText(3, 5))) + TimeUnit.SECONDS.toMillis(Integer.parseInt(tf.getText(6, 8)));
                    timeDisplayedSlider.setLowValue(time);
                    updateOverlays();
                }
            }
        });
        // Prompt input from user (max time)
        timeDisplayedRightLabel.setOnMouseClicked(e -> {
            if (e.getButton().equals(MouseButton.PRIMARY) && e.getClickCount() == 2) {
                GridPane gp = new GridPane();
                TextField tf = new TextField();
                SimpleDateFormat format = new SimpleDateFormat("HH:mm:ss");
                try {
                    tf.setTextFormatter(new TextFormatter<>(new DateTimeStringConverter(format), format.parse(ViewTrackerTools.getPrettyTimestamp((long) timeDisplayedSlider.getHighValue()))));
                } catch (ParseException ex) {
                    logger.error("Error parsing the input time: ", ex.getLocalizedMessage());
                }
                gp.addRow(0, new Label("Enter time"), tf);
                var response = Dialogs.showConfirmDialog("Set max time", gp);
                if (response) {
                    long time = ViewTrackerTools.getTimestampFromPrettyString(tf.getText());
                    timeDisplayedSlider.setHighValue(time);
                    updateOverlays();
                }
            }
        });
        timeDisplayedLeftLabel.textProperty().bind(Bindings.createStringBinding(() -> ViewTrackerTools.getPrettyTimestamp(startTime, (long) timeDisplayedSlider.getLowValue() + startTime), timeDisplayedSlider.lowValueProperty()));
        timeDisplayedRightLabel.textProperty().bind(Bindings.createStringBinding(() -> ViewTrackerTools.getPrettyTimestamp(startTime, (long) timeDisplayedSlider.getHighValue() + startTime), timeDisplayedSlider.highValueProperty()));
        // ------------------ DOWNSAMPLE RANGESLIDER ------------------//
        List<Double> allFramesDownsamples = tracker.getAllFrames().stream().map(e -> e.getDownsampleFactor()).collect(Collectors.toList());
        var minDownsample = allFramesDownsamples.stream().min(Comparator.naturalOrder()).get();
        var maxDownsample = allFramesDownsamples.stream().max(Comparator.naturalOrder()).get();
        downsampleSlider = new RangeSlider(minDownsample, maxDownsample, minDownsample, maxDownsample);
        Label downsampleLeftLabel = new Label();
        Label downsampleRightLabel = new Label();
        // Prompt input from user (min downsample)
        downsampleLeftLabel.setOnMouseClicked(e -> {
            if (e.getButton().equals(MouseButton.PRIMARY) && e.getClickCount() == 2) {
                ParameterList params = new ParameterList();
                params.addDoubleParameter("downsampleFilterLow", "Enter downsample", downsampleSlider.getLowValue());
                if (!Dialogs.showParameterDialog("Set min downsample", params))
                    return;
                double downFactor = params.getDoubleParameterValue("downsampleFilterLow");
                downsampleSlider.setLowValue(downFactor);
                updateOverlays();
            }
        });
        // Prompt input from user (max downsample)
        downsampleRightLabel.setOnMouseClicked(e -> {
            if (e.getButton().equals(MouseButton.PRIMARY) && e.getClickCount() == 2) {
                ParameterList params = new ParameterList();
                params.addDoubleParameter("downsampleFilterHigh", "Enter downsample", downsampleSlider.getHighValue());
                if (!Dialogs.showParameterDialog("Set max downsample", params))
                    return;
                double downFactor = params.getDoubleParameterValue("downsampleFilterHigh");
                downsampleSlider.setHighValue(downFactor);
                updateOverlays();
            }
        });
        downsampleLeftLabel.textProperty().bind(Bindings.createStringBinding(() -> GeneralTools.formatNumber(downsampleSlider.getLowValue(), 2), downsampleSlider.lowValueProperty()));
        downsampleRightLabel.textProperty().bind(Bindings.createStringBinding(() -> GeneralTools.formatNumber(downsampleSlider.getHighValue(), 2), downsampleSlider.highValueProperty()));
        // TODO: if using keys to change sliders, nothing will trigger the overlay update
        dataMaps = new ViewTrackerDataMaps(server, tracker);
        timeDisplayedSlider.setOnMouseReleased(v -> updateOverlays());
        downsampleSlider.setOnMouseReleased(v -> updateOverlays());
        colorMapCanvas.colorMapProperty().addListener((v, o, n) -> updateOverlays());
        progressIndicator.visibleProperty().bind(dataMaps.generatingOverlayProperty());
        visualizationCheckBox.selectedProperty().addListener((v, o, n) -> {
            if (n)
                updateOverlays();
            else {
                viewer.getCustomOverlayLayers().clear();
                slideOverview.setOverlay(null);
            }
        });
        // timeNormalizedRadio.selectedProperty().addListener((v, o, n) -> updateOverlays());
        // --------------------------------------------------------------//
        // ---------- PUTTING EVERYTHING TOGETHER ---------//
        // --------------------------------------------------------------//
        GridPane mainLeftPane = new GridPane();
        GridPane slideOverviewPane = new GridPane();
        GridPane dataVisualizationPane = new GridPane();
        mainLeftPane.setPadding(new Insets(5.0, 5.0, 5.0, 15.0));
        slideOverviewPane.setPadding(new Insets(5.0, 5.0, 5.0, 5.0));
        dataVisualizationPane.setPadding(new Insets(5.0, 5.0, 15.0, 5.0));
        mainLeftPane.addRow(0, slideOverviewPane);
        mainLeftPane.addRow(1, dataVisualizationPane);
        GridPane canvasPane = new GridPane();
        GridPane timelinePane = new GridPane();
        GridPane playbackPane = new GridPane();
        // GridPane normalizedByPane = new GridPane();
        GridPane rangeSlidersPane = new GridPane();
        GridPane downsamplePane = new GridPane();
        Separator sep = new Separator();
        slideOverviewPane.setHgap(10);
        slideOverviewPane.setVgap(10);
        dataVisualizationPane.setHgap(10);
        dataVisualizationPane.setVgap(10);
        playbackPane.setHgap(10.0);
        // normalizedByPane.setHgap(10.0);
        rangeSlidersPane.setHgap(10.0);
        rangeSlidersPane.setVgap(10.0);
        downsamplePane.setHgap(10.0);
        // Some 'invisible' elements might shift the canvas to the right, so make sure this doesn't happen
        if (zSlider.isVisible()) {
            canvasPane.addRow(0, new HBox(), timepointLabel, tSlider);
            canvasPane.addRow(1, zSliceLabel, zSlider, slideOverview.getCanvas());
            zSlider.setTooltip(new Tooltip("Slide to change the visible z-slice"));
        } else {
            canvasPane.addRow(0, timepointLabel, tSlider, new HBox());
            canvasPane.addRow(1, new HBox(), slideOverview.getCanvas());
        }
        if (tSlider.isVisible())
            tSlider.setTooltip(new Tooltip("Slide to change the visible timepoint"));
        // normalizedByPane.addRow(0, timeNormalizedRadio, downsampleNormalizedRadio, progressIndicator);
        // normalizedByPane.addRow(0, progressIndicator);
        timelinePane.addRow(0, timeLabelLeft, timeSlider, timeLabelRight);
        playbackPane.addRow(0, btnPlay, btnStop);
        timelinePane.setAlignment(Pos.CENTER);
        playbackPane.setAlignment(Pos.CENTER);
        canvasPane.setAlignment(Pos.CENTER);
        btnPlay.setTooltip(new Tooltip("Play the recording"));
        btnStop.setTooltip(new Tooltip("Rewind the recording"));
        int row = 0;
        PaneTools.addGridRow(slideOverviewPane, row++, 0, null, new HBox(), canvasPane);
        PaneTools.addGridRow(slideOverviewPane, row++, 0, null, timeLabelLeft, timeSlider, timeLabelRight);
        PaneTools.addGridRow(slideOverviewPane, row++, 0, "Playback options", new HBox(), playbackPane);
        PaneTools.addGridRow(slideOverviewPane, row++, 0, null, sep, sep, sep, sep);
        row = 0;
        PaneTools.addGridRow(dataVisualizationPane, row++, 0, "Show the amount of time spent in each region of the image", visualizationCheckBox, progressIndicator);
        PaneTools.addGridRow(dataVisualizationPane, row++, 0, "The data will only take into account the values recorded in-between this range", new Label("Time range"), timeDisplayedLeftLabel, timeDisplayedSlider, timeDisplayedRightLabel);
        PaneTools.addGridRow(dataVisualizationPane, row++, 0, "The data will only take into account the values recorded in-between this range", new Label("Downsample range"), downsampleLeftLabel, downsampleSlider, downsampleRightLabel);
        PaneTools.addGridRow(dataVisualizationPane, row++, 0, "Color map", new Label("Color map"), colorMapCombo, colorMapCombo, colorMapCombo);
        PaneTools.addGridRow(dataVisualizationPane, row++, 0, null, colorMapCanvas, colorMapCanvas, colorMapCanvas, colorMapCanvas);
        for (Node child : dataVisualizationPane.getChildren()) {
            if (child == visualizationCheckBox)
                continue;
            if (child == downsampleSlider)
                child.disableProperty().bind(visualizationCheckBox.selectedProperty().not().or(new SimpleBooleanProperty(minDownsample == maxDownsample)));
            else
                // else if (child == downsampleNormalizedRadio)
                // child.disableProperty().bind(visualizationCheckBox.selectedProperty().not().or(new SimpleBooleanProperty(minDownsample == maxDownsample)));
                child.disableProperty().bind(visualizationCheckBox.selectedProperty().not());
        }
        ColumnConstraints col1 = new ColumnConstraints();
        ColumnConstraints col2 = new ColumnConstraints();
        ColumnConstraints col3 = new ColumnConstraints();
        ColumnConstraints col4 = new ColumnConstraints();
        col2.setHgrow(Priority.ALWAYS);
        slideOverviewPane.getColumnConstraints().addAll(col1, col2, col3, col4);
        // --------------------- BOTTOM BUTTON PANE---------------------//
        Button btnExpand = new Button("Show frames");
        Button btnOpen = new Button("Open directory");
        btnOpen.setDisable(tracker.getFile() == null);
        List<Button> buttons = new ArrayList<>();
        btnOpen.setOnAction(e -> GuiTools.browseDirectory(tracker.getFile()));
        btnExpand.setOnAction(e -> {
            if (btnExpand.getText().equals("Show frames")) {
                dialog.setWidth(initialWidth + 700);
                dialog.setResizable(true);
                dialog.setMinWidth(initialWidth + 50);
                dialog.setMinHeight(initialHeight);
                mainLeftPane.setMinWidth(initialWidth);
                mainLeftPane.setMaxWidth(initialWidth);
                mainPane.getItems().add(tablePane);
                mainPane.setDividerPositions(0.0);
                btnExpand.setText("Hide frames");
            } else {
                mainPane.getItems().remove(tablePane);
                btnExpand.setText("Show frames");
                dialog.setWidth(initialWidth + 30);
                dialog.setHeight(initialHeight);
                dialog.setResizable(false);
            }
        });
        buttons.add(btnOpen);
        buttons.add(btnExpand);
        GridPane panelButtons = PaneTools.createColumnGridControls(buttons.toArray(new ButtonBase[0]));
        PaneTools.addGridRow(mainLeftPane, row++, 0, null, panelButtons, panelButtons, panelButtons);
        mainPane.getItems().add(mainLeftPane);
        dialog.setScene(new Scene(mainPane));
    }
    viewer.imageDataProperty().addListener((v, o, n) -> dialog.hide());
    dialog.setOnHiding(e -> {
        viewer.getCustomOverlayLayers().clear();
        playback.doStopPlayback();
        isOpenedProperty.set(false);
    });
    dialog.setResizable(false);
    dialog.show();
    initialWidth = dialog.getWidth();
    initialHeight = dialog.getHeight();
}