Examples with ChannelDisplayInfo qupath.lib.display.ChannelDisplayInfo used on opensource projects

Example 6 with ChannelDisplayInfo

use of qupath.lib.display.ChannelDisplayInfo in project qupath by qupath.

the class BrightnessContrastCommand method handleSliderChange.

void handleSliderChange() {
    if (slidersUpdating)
        return;
    ChannelDisplayInfo infoVisible = getCurrentInfo();
    if (infoVisible == null)
        return;
    double minValue = sliderMin.getValue();
    double maxValue = sliderMax.getValue();
    imageDisplay.setMinMaxDisplay(infoVisible, (float) minValue, (float) maxValue);
    // Avoid displaying -0... which looks weird
    if (Math.abs(Math.round(minValue * 100)) == 0)
        minValue = 0;
    if (Math.abs(Math.round(maxValue * 100)) == 0)
        maxValue = 0;
    // viewer.updateThumbnail();
    viewer.repaintEntireImage();
// histogramPanel.setVerticalLines(new double[]{infoVisible.getMinDisplay(), infoVisible.getMaxDisplay()}, ColorToolsFX.TRANSLUCENT_BLACK_FX);
}

Example 7 with ChannelDisplayInfo

use of qupath.lib.display.ChannelDisplayInfo in project qupath by qupath.

the class BrightnessContrastCommand method updateHistogram.

private void updateHistogram() {
    if (table == null || !isInitialized())
        return;
    ChannelDisplayInfo infoSelected = getCurrentInfo();
    Histogram histogram = (imageDisplay == null || infoSelected == null) ? null : imageDisplay.getHistogram(infoSelected);
    // histogram = histogramMap.get(infoSelected);
    if (histogram == null) {
        histogramPanel.getHistogramData().clear();
    } else {
        // Any animation is slightly nicer if we can modify the current data, rather than creating a new one
        if (histogramPanel.getHistogramData().size() == 1) {
            Color color = infoSelected.getColor() == null ? ColorToolsFX.TRANSLUCENT_BLACK_FX : ColorToolsFX.getCachedColor(infoSelected.getColor());
            histogramPanel.getHistogramData().get(0).setHistogram(histogram, color);
        } else {
            HistogramData histogramData = HistogramPanelFX.createHistogramData(histogram, true, infoSelected.getColor());
            histogramData.setNormalizeCounts(true);
            histogramPanel.getHistogramData().setAll(histogramData);
        }
    }
    NumberAxis xAxis = (NumberAxis) histogramPanel.getChart().getXAxis();
    if (infoSelected != null && infoSelected.getMaxAllowed() == 255 && infoSelected.getMinAllowed() == 0) {
        xAxis.setAutoRanging(false);
        xAxis.setLowerBound(0);
        xAxis.setUpperBound(255);
    } else if (infoSelected != null) {
        xAxis.setAutoRanging(false);
        xAxis.setLowerBound(infoSelected.getMinAllowed());
        xAxis.setUpperBound(infoSelected.getMaxAllowed());
    // xAxis.setAutoRanging(true);
    }
    if (infoSelected != null)
        xAxis.setTickUnit(infoSelected.getMaxAllowed() - infoSelected.getMinAllowed());
    // Don't use the first of last count if it's an outlier
    NumberAxis yAxis = (NumberAxis) histogramPanel.getChart().getYAxis();
    if (infoSelected != null && histogram != null) {
        long maxCount = 0L;
        for (int i = 1; i < histogram.nBins() - 1; i++) maxCount = Math.max(maxCount, histogram.getCountsForBin(i));
        if (maxCount == 0)
            maxCount = histogram.getMaxCount();
        yAxis.setAutoRanging(false);
        yAxis.setLowerBound(0);
        yAxis.setUpperBound((double) maxCount / histogram.getCountSum());
    }
    histogramPanel.getChart().getXAxis().setTickLabelsVisible(true);
    histogramPanel.getChart().getXAxis().setLabel("Pixel value");
    histogramPanel.getChart().getYAxis().setTickLabelsVisible(true);
    // histogramPanel.getChart().getYAxis().setLabel("Frequency");
    GridPane pane = new GridPane();
    pane.setHgap(4);
    pane.setVgap(2);
    int r = 0;
    if (histogram != null) {
        pane.add(new Label("Min"), 0, r);
        pane.add(new Label(df.format(histogram.getMinValue())), 1, r);
        r++;
        pane.add(new Label("Max"), 0, r);
        pane.add(new Label(df.format(histogram.getMaxValue())), 1, r);
        r++;
        pane.add(new Label("Mean"), 0, r);
        pane.add(new Label(df.format(histogram.getMeanValue())), 1, r);
        r++;
        pane.add(new Label("Std.dev"), 0, r);
        pane.add(new Label(df.format(histogram.getStdDev())), 1, r);
        r++;
    }
    chartTooltip.setGraphic(pane);
    if (r == 0)
        Tooltip.uninstall(histogramPanel.getChart(), chartTooltip);
    else
        Tooltip.install(histogramPanel.getChart(), chartTooltip);
}

Example 8 with ChannelDisplayInfo

use of qupath.lib.display.ChannelDisplayInfo in project qupath by qupath.

the class BrightnessContrastCommand method toggleTableSelectedChannels.

/**
 * Request that channels currently selected (highlighted) in the table have their
 * selected status inverted.  This allows multiple channels to be turned on/off
 * in one step.
 *
 * @see #setTableSelectedChannels(boolean)
 */
private void toggleTableSelectedChannels() {
    if (!isInitialized())
        return;
    Set<ChannelDisplayInfo> selected = new HashSet<>(imageDisplay.selectedChannels());
    for (ChannelDisplayInfo info : table.getSelectionModel().getSelectedItems()) {
        imageDisplay.setChannelSelected(info, !selected.contains(info));
    }
    table.refresh();
    if (viewer != null) {
        // viewer.updateThumbnail();
        viewer.repaintEntireImage();
    }
}

Example 9 with ChannelDisplayInfo

use of qupath.lib.display.ChannelDisplayInfo in project qupath by qupath.

the class BrightnessContrastCommand method updateSliders.

private void updateSliders() {
    if (!isInitialized())
        return;
    ChannelDisplayInfo infoVisible = getCurrentInfo();
    if (infoVisible == null) {
        sliderMin.setDisable(true);
        sliderMax.setDisable(true);
        return;
    }
    float range = infoVisible.getMaxAllowed() - infoVisible.getMinAllowed();
    int n = (int) range;
    boolean is8Bit = range == 255 && infoVisible.getMinAllowed() == 0 && infoVisible.getMaxAllowed() == 255;
    if (is8Bit)
        n = 256;
    else if (n <= 20)
        n = (int) (range / .001);
    else if (n <= 200)
        n = (int) (range / .01);
    slidersUpdating = true;
    double maxDisplay = Math.max(infoVisible.getMaxDisplay(), infoVisible.getMinDisplay());
    double minDisplay = Math.min(infoVisible.getMaxDisplay(), infoVisible.getMinDisplay());
    double minSlider = Math.min(infoVisible.getMinAllowed(), minDisplay);
    double maxSlider = Math.max(infoVisible.getMaxAllowed(), maxDisplay);
    sliderMin.setMin(minSlider);
    sliderMin.setMax(maxSlider);
    sliderMin.setValue(infoVisible.getMinDisplay());
    sliderMax.setMin(minSlider);
    sliderMax.setMax(maxSlider);
    sliderMax.setValue(infoVisible.getMaxDisplay());
    if (is8Bit) {
        sliderMin.setMajorTickUnit(1);
        sliderMax.setMajorTickUnit(1);
        sliderMin.setMinorTickCount(n);
        sliderMax.setMinorTickCount(n);
    } else {
        sliderMin.setMajorTickUnit(1);
        sliderMax.setMajorTickUnit(1);
        sliderMin.setMinorTickCount(n);
        sliderMax.setMinorTickCount(n);
    }
    slidersUpdating = false;
    sliderMin.setDisable(false);
    sliderMax.setDisable(false);
    chartWrapper.getThresholds().clear();
    Color color = Color.rgb(0, 0, 0, 0.2);
    chartWrapper.addThreshold(sliderMin.valueProperty(), color);
    chartWrapper.addThreshold(sliderMax.valueProperty(), color);
    chartWrapper.setIsInteractive(true);
// chartWrapper.getThresholds().setAll(sliderMin.valueProperty(), sliderMax.valueProperty());
// histogramPanel.setVerticalLines(new double[]{infoVisible.getMinDisplay(), infoVisible.getMaxDisplay()}, ColorToolsFX.TRANSLUCENT_BLACK_FX);
}

Example 10 with ChannelDisplayInfo

use of qupath.lib.display.ChannelDisplayInfo in project qupath by qupath.

the class ChannelDisplayTransformServer method readBufferedImage.

@Override
public BufferedImage readBufferedImage(final RegionRequest request) throws IOException {
    // Transform the pixels, if required
    BufferedImage img = getWrappedServer().readBufferedImage(request);
    int width = img.getWidth();
    int height = img.getHeight();
    WritableRaster raster = null;
    float[] pxFloat = null;
    int b = 0;
    for (ChannelDisplayInfo channel : channels) {
        if (channel instanceof SingleChannelDisplayInfo) {
            if (raster == null) {
                SampleModel model = new BandedSampleModel(DataBuffer.TYPE_FLOAT, width, height, nChannels());
                raster = Raster.createWritableRaster(model, null);
            }
            if (raster.getTransferType() == DataBuffer.TYPE_FLOAT) {
                pxFloat = ((SingleChannelDisplayInfo) channel).getValues(img, 0, 0, width, height, pxFloat);
                raster.setSamples(0, 0, width, height, b, pxFloat);
                b++;
            } else {
                logger.error("Unable to apply color transform " + channel.getName() + " - incompatible with previously-applied transforms");
            }
        } else if (channels.size() == 1) {
            int[] rgb = channel.getRGB(img, null, false);
            img.setRGB(0, 0, width, height, rgb, 0, width);
            return img;
        } else {
            logger.error("Cannot apply requested color transforms! Must either be a single RGB transform, or one or more single-channel transforms");
        }
    }
    if (colorModel == null)
        colorModel = ColorModelFactory.createColorModel(PixelType.FLOAT32, channels.size(), false, channels.stream().mapToInt(c -> {
            Integer color = c.getColor();
            if (color == null)
                color = ColorTools.packRGB(255, 255, 255);
            return color;
        }).toArray());
    return new BufferedImage(colorModel, raster, false, null);
}