Examples with HistogramData qupath.lib.gui.charts.HistogramPanelFX.HistogramData used on opensource projects

Example 1 with HistogramData

use of qupath.lib.gui.charts.HistogramPanelFX.HistogramData in project qupath by qupath.

the class HistogramDisplay method setHistogram.

void setHistogram(final PathTableData<?> model, final String columnName) {
    if (model != null && model.getMeasurementNames().contains(columnName)) {
        double[] values = model.getDoubleValues(columnName);
        int nBins = params.getIntParameterValue("nBins");
        if (nBins < 2)
            nBins = 2;
        else if (nBins > 1000)
            nBins = 1000;
        // We can have values in the 'wrong' order to facilitate comparison...
        Arrays.sort(values);
        // Check if we've actually changed anything - if not, then abort
        if (nBins == currentBins && currentValues != null && Arrays.equals(currentValues, values))
            return;
        Histogram histogram = new Histogram(values, nBins);
        // histogram.setNormalizeCounts(params.getBooleanParameterValue("normalizeCounts"));
        HistogramData histogramData = HistogramPanelFX.createHistogramData(histogram, false, (Integer) null);
        histogramData.setNormalizeCounts(params.getBooleanParameterValue("normalizeCounts"));
        panelHistogram.getHistogramData().setAll(histogramData);
        AreaChart<Number, Number> chart = panelHistogram.getChart();
        chart.setVerticalGridLinesVisible(true);
        chart.setHorizontalGridLinesVisible(true);
        chart.setLegendVisible(false);
        // Can't stop them being orange...
        chart.setCreateSymbols(false);
        chart.getXAxis().setLabel("Values");
        chart.getYAxis().setLabel("Counts");
        chart.getYAxis().setTickLabelsVisible(true);
        chart.getYAxis().setTickMarkVisible(true);
        chart.getXAxis().setTickLabelsVisible(true);
        chart.getXAxis().setTickMarkVisible(true);
        chart.setAnimated(params.getBooleanParameterValue("animate"));
        updateTable(histogram);
        currentColumn = columnName;
        currentBins = nBins;
        currentValues = values;
        this.model = model;
    } else
        panelHistogram.getHistogramData().clear();
}

Example 2 with HistogramData

use of qupath.lib.gui.charts.HistogramPanelFX.HistogramData in project qupath by qupath.

the class HistogramDisplay method parameterChanged.

@Override
public void parameterChanged(ParameterList parameterList, String key, boolean isAdjusting) {
    if ("normalizeCounts".equals(key)) {
        boolean doNormalize = params.getBooleanParameterValue("normalizeCounts");
        // This is rather clumsy (compared to just updating the histogram data),
        // but the reason is that the animations are poor when the data is updated in-place
        List<HistogramData> list = new ArrayList<>();
        for (HistogramData histogramData : panelHistogram.getHistogramData()) {
            histogramData.setNormalizeCounts(doNormalize);
            list.add(new HistogramData(histogramData.getHistogram(), false, histogramData.getStroke()));
        // histogramData.update();
        }
        panelHistogram.getHistogramData().setAll(list);
        return;
    } else if ("drawGrid".equals(key)) {
        panelHistogram.getChart().setHorizontalGridLinesVisible(params.getBooleanParameterValue("drawGrid"));
        panelHistogram.getChart().setVerticalGridLinesVisible(params.getBooleanParameterValue("drawGrid"));
        return;
    } else if ("drawAxes".equals(key)) {
        panelHistogram.setShowTickLabels(params.getBooleanParameterValue("drawAxes"));
        return;
    } else if ("nBins".equals(key)) {
        setHistogram(model, comboName.getSelectionModel().getSelectedItem());
        return;
    } else if ("animate".equals(key)) {
        panelHistogram.getChart().setAnimated(params.getBooleanParameterValue("animate"));
    }
}

Example 3 with HistogramData

use of qupath.lib.gui.charts.HistogramPanelFX.HistogramData 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);
}