Examples with QuPathViewer qupath.lib.gui.viewer.QuPathViewer used on opensource projects

Example 11 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class ToolBarComponent method promptToUpdateMagnification.

void promptToUpdateMagnification() {
    QuPathViewer viewer = qupath.getViewer();
    if (viewer == null || !viewer.hasServer())
        return;
    double fullMagnification = viewer.getServer().getMetadata().getMagnification();
    boolean hasMagnification = !Double.isNaN(fullMagnification);
    if (hasMagnification) {
        double defaultValue = Math.rint(viewer.getMagnification() * 1000) / 1000;
        Double value = Dialogs.showInputDialog("Set magnification", "Enter magnification", defaultValue);
        if (value == null)
            return;
        if (Double.isFinite(value) && value > 0)
            viewer.setMagnification(value.doubleValue());
        else
            Dialogs.showErrorMessage("Set downsample factor", "Invalid magnification " + value + ". \nPlease use a value greater than 0.");
    } else {
        double defaultValue = Math.rint(viewer.getDownsampleFactor() * 1000) / 1000;
        Double value = Dialogs.showInputDialog("Set downsample factor", "Enter downsample factor", defaultValue);
        if (value == null)
            return;
        if (Double.isFinite(value) && value > 0)
            viewer.setDownsampleFactor(value.doubleValue());
        else
            Dialogs.showErrorMessage("Set downsample factor", "Invalid downsample " + value + ". \nPlease use a value greater than 0.");
    }
}

Example 12 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class OMEPyramidWriterCommand method run.

@Override
public void run() {
    if (currentTask != null && !currentTask.isDone()) {
        if (!Dialogs.showConfirmDialog("OME Pyramid writer", "Do you want to stop the current export?"))
            // TODO: Delete exporting file?
            return;
        else {
            currentTask.cancel(true);
        }
    }
    QuPathViewer viewer = qupath.getViewer();
    int zPos = viewer.getZPosition();
    int tPos = viewer.getTPosition();
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (imageData == null) {
        Dialogs.showNoImageError("OME Pyramid writer");
        return;
    }
    ImageServer<BufferedImage> server = imageData.getServer();
    // Region
    PathObject selected = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ImageRegion region = null;
    int width, height;
    if (selected == null || !selected.hasROI() || !selected.getROI().isArea()) {
        width = server.getWidth();
        height = server.getHeight();
    } else {
        region = ImageRegion.createInstance(selected.getROI());
        width = region.getWidth();
        height = region.getHeight();
    }
    // Set compression - with a sanity check for validity, defaulting to another comparable method if necessary
    CompressionType compression = getDefaultPyramidCompression();
    List<String> compatibleCompression = Arrays.stream(CompressionType.values()).filter(c -> c.supportsImage(server)).map(c -> c.toFriendlyString()).collect(Collectors.toList());
    if (!compatibleCompression.contains(compression.toFriendlyString()))
        compression = CompressionType.DEFAULT;
    var params = new ParameterList().addChoiceParameter("compression", "Compression type", compression.toFriendlyString(), compatibleCompression).addIntParameter("scaledDownsample", "Pyramidal downsample", scaledDownsample.get(), "", 1, 8, "Amount to downsample each consecutive pyramidal level; use 1 to indicate the image should not be pyramidal").addIntParameter("tileSize", "Tile size", getDefaultTileSize(), "px", "Tile size for export (should be between 128 and 8192)").addBooleanParameter("parallelize", "Parallelize export", parallelizeTiling.get(), "Export image tiles in parallel - " + "this should be faster, best keep it on unless you encounter export problems").addBooleanParameter("allZ", "All z-slices", allZ.get(), "Include all z-slices in the stack").addBooleanParameter("allT", "All timepoints", allT.get(), "Include all timepoints in the time-series");
    boolean singleTile = server.getTileRequestManager().getTileRequests(RegionRequest.createInstance(server)).size() == 1;
    params.setHiddenParameters(server.nZSlices() == 1, "allZ");
    params.setHiddenParameters(server.nTimepoints() == 1, "allT");
    params.setHiddenParameters(singleTile, "tileSize", "parallelize");
    if (!Dialogs.showParameterDialog("Export OME-TIFF", params))
        return;
    compression = CompressionType.fromFriendlyString((String) params.getChoiceParameterValue("compression"));
    defaultPyramidCompression.set(compression);
    int downsampleScale = params.getIntParameterValue("scaledDownsample");
    scaledDownsample.set(downsampleScale);
    int tileSize = params.getIntParameterValue("tileSize");
    boolean parallelize = params.getBooleanParameterValue("parallelize");
    if (!singleTile) {
        tileSize = GeneralTools.clipValue(tileSize, 128, 8192);
        defaultTileSize.set(tileSize);
        parallelizeTiling.set(parallelize);
    }
    boolean doAllZ = false;
    boolean doAllT = false;
    if (server.nZSlices() > 1) {
        doAllZ = params.getBooleanParameterValue("allZ");
        allZ.set(doAllZ);
    }
    if (server.nTimepoints() > 1) {
        doAllT = params.getBooleanParameterValue("allT");
        allT.set(doAllT);
    }
    OMEPyramidWriter.Builder builder = new OMEPyramidWriter.Builder(server);
    if (region != null) {
        builder = builder.region(region);
    } else {
        if (server.nZSlices() > 1 && !doAllZ)
            builder.zSlice(zPos);
        if (server.nTimepoints() > 1 && !doAllT)
            builder.timePoint(tPos);
    }
    builder.compression(compression);
    if (downsampleScale <= 1 || Math.max(width, height) / server.getDownsampleForResolution(0) < minSizeForTiling.get())
        builder.downsamples(server.getDownsampleForResolution(0));
    else
        builder.scaledDownsampling(server.getDownsampleForResolution(0), downsampleScale);
    // Set tile size; if we just have one tile, use the image width & height
    if (singleTile)
        builder = builder.tileSize(width, height);
    else
        builder = builder.tileSize(tileSize).parallelize(parallelize);
    if (server.nZSlices() > 1 && doAllZ)
        builder.allZSlices();
    if (server.nTimepoints() > 1 && doAllT)
        builder.allTimePoints();
    // Prompt for file
    File fileOutput = Dialogs.promptToSaveFile("Write pyramid", null, null, "OME TIFF pyramid", ".ome.tif");
    if (fileOutput == null)
        return;
    String name = fileOutput.getName();
    // We can have trouble with only the '.tif' part of the name being included
    if (name.endsWith(".tif") && !name.endsWith(".ome.tif"))
        fileOutput = new File(fileOutput.getParentFile(), name.substring(0, name.length() - 4) + ".ome.tif");
    OMEPyramidSeries writer = builder.build();
    if (pool == null) {
        pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("ome-pyramid-export", false));
    }
    currentTask = pool.submit(new WriterTask(OMEPyramidWriter.createWriter(writer), fileOutput.getAbsolutePath()));
}

Example 13 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class MeasurementMapPane method showMap.

private void showMap() {
    String measurement = listMeasurements.getSelectionModel().getSelectedItem();
    QuPathViewer viewer = qupath.getViewer();
    if (viewer == null || measurement == null)
        return;
    // Reuse mappers if we can
    mapper = mapperMap.get(measurement);
    var colorMapper = selectedColorMap.getValue();
    if (mapper == null) {
        mapper = new MeasurementMapper(colorMapper, measurement, viewer.getHierarchy().getObjects(null, null));
        if (mapper.isValid())
            mapperMap.put(measurement, mapper);
    } else if (colorMapper != null) {
        mapper.setColorMapper(colorMapper);
    }
    if (mapper != null && mapper.isValid()) {
        updatingSliders = true;
        sliderMin.setMin(Math.min(mapper.getDataMinValue(), mapper.getDisplayMinValue()));
        sliderMin.setMax(Math.max(mapper.getDataMaxValue(), mapper.getDisplayMaxValue()));
        sliderMin.setValue(mapper.getDisplayMinValue());
        sliderMin.setBlockIncrement((sliderMin.getMax() - sliderMin.getMin()) / 100);
        sliderMax.setMin(Math.min(mapper.getDataMinValue(), mapper.getDisplayMinValue()));
        sliderMax.setMax(Math.max(mapper.getDataMaxValue(), mapper.getDisplayMaxValue()));
        sliderMax.setValue(mapper.getDisplayMaxValue());
        sliderMax.setBlockIncrement((sliderMax.getMax() - sliderMax.getMin()) / 100);
        updatingSliders = false;
    }
    colorMapKeyImage = createPanelKey(mapper.getColorMapper());
    updateColorMapperKey();
    mapper.setExcludeOutsideRange(cbExcludeOutside.isSelected());
    viewer.forceOverlayUpdate();
    updateMapperBrightnessContrast();
    OverlayOptions overlayOptions = viewer.getOverlayOptions();
    if (overlayOptions != null)
        overlayOptions.setMeasurementMapper(mapper);
}

Example 14 with QuPathViewer

use of qupath.lib.gui.viewer.QuPathViewer in project qupath by qupath.

the class RotateImageCommand method createDialog.

Stage createDialog() {
    QuPathViewer viewerTemp = qupath.getViewer();
    if (dialog == null) {
        dialog = new Stage();
        dialog.initOwner(qupath.getStage());
        dialog.initStyle(StageStyle.TRANSPARENT);
        dialog.setTitle("Rotate view");
        StackPane pane = new StackPane();
        pane.setPadding(new Insets(5));
        slider = new CircularSlider();
        slider.setPrefSize(150, 150);
        slider.setValue(viewerTemp == null ? 0 : Math.toDegrees(viewerTemp.getRotation()));
        slider.setTickSpacing(10);
        slider.setShowValue(true);
        slider.setSnapToTicks(false);
        slider.setOnKeyPressed(e -> {
            if (e.getCode() == KeyCode.SHIFT) {
                slider.setSnapToTicks(true);
                slider.setShowTickMarks(true);
            }
        });
        slider.setOnKeyReleased(e -> {
            if (e.getCode() == KeyCode.SHIFT) {
                slider.setSnapToTicks(false);
                slider.setShowTickMarks(false);
            }
        });
        slider.setPadding(new Insets(5, 0, 10, 0));
        slider.setTooltip(new Tooltip("Double-click to manually set the rotation"));
        final DropShadow shadow = new DropShadow();
        shadow.setColor(Color.rgb(0, 0, 0, 0.65));
        slider.setEffect(shadow);
        final Button button = new Button("x");
        button.setTooltip(new Tooltip("Close image rotation slider"));
        button.setOnMouseClicked(e -> dialog.close());
        pane.getChildren().addAll(slider, button);
        final double[] delta = new double[2];
        slider.getTextArea().setOnMousePressed(e -> {
            delta[0] = dialog.getX() - e.getScreenX();
            delta[1] = dialog.getY() - e.getScreenY();
        });
        slider.getTextArea().setOnMouseDragged(e -> {
            dialog.setX(e.getScreenX() + delta[0]);
            dialog.setY(e.getScreenY() + delta[1]);
        });
        StackPane.setAlignment(button, Pos.TOP_RIGHT);
        // Set opacity for the close button
        pane.setStyle("-fx-background-color: transparent; -fx-background-radius: 10;");
        final double outOpacity = .2;
        button.setOpacity(outOpacity);
        FadeTransition fade = new FadeTransition();
        fade.setDuration(Duration.millis(150));
        fade.setNode(button);
        pane.setOnMouseEntered(e -> {
            fade.stop();
            fade.setFromValue(button.getOpacity());
            fade.setToValue(1.);
            fade.play();
        });
        pane.setOnMouseExited(e -> {
            fade.stop();
            fade.setFromValue(button.getOpacity());
            fade.setToValue(outOpacity);
            fade.play();
        });
        final Scene scene = new Scene(pane);
        scene.setFill(Color.TRANSPARENT);
        dialog.setOnHiding(e -> {
            qupath.viewerProperty().removeListener(this);
            dialog = null;
        });
        dialog.setScene(scene);
        dialog.setResizable(true);
    }
    if (viewerTemp != null)
        slider.rotationProperty().bindBidirectional(viewerTemp.rotationProperty());
    return dialog;
}