Examples with Dataset net.imagej.Dataset used on opensource projects

Example 1 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class DatasetSelectionPanel method addComboBox.

public void addComboBox(Dataset[] datasets, String description) {
    JComboBox<Dataset> comboBox = new JComboBox<>(datasets);
    add(new JLabel(description));
    add(comboBox);
    datasetMap.put(description, comboBox);
}

Example 2 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class PlotROIStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("ROI Mean Intensity", "Time", "Mean Intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (RandomAccessibleInterval<T> data : datasetROIsMap.keySet()) {
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        List<Overlay> overlays = datasetROIsMap.get(data);
        for (int i = 0; i < overlays.size(); i++) {
            Overlay overlay = overlays.get(i);
            RandomAccessibleInterval<T> cropped = crop(data, overlay);
            Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, cropped);
            plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
            legendLabels.append("ROI ");
            legendLabels.append(i + 1);
            legendLabels.append("\n");
        }
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}

Example 3 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class VCellResultService method importCsv.

public Dataset importCsv(File directory) throws FileNotFoundException {
    File[] files = directory.listFiles();
    // TODO: Better handling
    if (files == null)
        return null;
    ArrayList<ArrayList<Float>> timeSeries = new ArrayList<>(files.length);
    Scanner scanner;
    int dataSize = 0;
    for (File file : files) {
        scanner = new Scanner(file);
        scanner.useDelimiter("[,\n]");
        while (scanner.hasNext() && !scanner.hasNextDouble()) {
            scanner.next();
        }
        if (!scanner.hasNextDouble()) {
            scanner.close();
            return null;
        }
        ArrayList<Float> data = new ArrayList<>();
        while (scanner.hasNextDouble()) {
            data.add(scanner.nextFloat());
        }
        scanner.close();
        timeSeries.add(data);
        dataSize = data.size();
    }
    int[] dimensions = { dataSize, timeSeries.size() };
    Img<FloatType> img = new ArrayImgFactory<FloatType>().create(dimensions, new FloatType());
    Cursor<FloatType> cursor = img.localizingCursor();
    while (cursor.hasNext()) {
        cursor.next();
        int xPos = cursor.getIntPosition(0);
        int tPos = cursor.getIntPosition(1);
        Float val = timeSeries.get(tPos).get(xPos);
        cursor.get().set(val);
    }
    Dataset dataset = datasetService.create(img);
    // Drop single dimensions
    @SuppressWarnings("unchecked") ImgPlus<FloatType> imgPlus = (ImgPlus<FloatType>) dataset.getImgPlus();
    FinalInterval interval = Intervals.createMinMax(0, 0, imgPlus.dimension(0) - 1, imgPlus.dimension(1) - 1);
    ImgPlus<FloatType> cropped = ops.transform().crop(imgPlus, interval, true);
    dataset.setImgPlus(cropped);
    System.out.println(dataset.numDimensions());
    dataset.setName(directory.getName());
    return dataset;
}

Example 4 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class CompareController method getMaskFromGeometry.

private RandomAccessibleInterval<BitType> getMaskFromGeometry() {
    DatasetSelectionPanel panel = new DatasetSelectionPanel();
    List<Dataset> geometryList = model.getProject().getGeometry();
    final String description = "Geometry: ";
    panel.addComboBox(geometryList.toArray(new Dataset[geometryList.size()]), description);
    int returnVal = JOptionPane.showConfirmDialog(view, panel, "Select cell geometry", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
    if (returnVal == JOptionPane.OK_OPTION) {
        Dataset geometry = panel.getSelectedDatasetForDescription(description);
        @SuppressWarnings("unchecked") RandomAccessibleInterval<BitType> mask = (RandomAccessibleInterval<BitType>) opService.run("largestRegionSlice", geometry);
        return mask;
    }
    return null;
}

Example 5 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class CompareView method setContent.

@Override
public void setContent(DisplayPanel displayPanel) {
    for (int i = 0; i < panels.size(); i++) {
        if (i >= datasets.size())
            break;
        JPanel panel = panels.get(i);
        if (panel.getComponentCount() == 0) {
            SwingImageDisplayPanel imagePanel = (SwingImageDisplayPanel) displayPanel;
            Dataset dataset = datasets.get(i);
            datasetImagePanelMap.put(dataset, imagePanel.getDisplay());
            panel.add(imagePanel, BorderLayout.CENTER);
            labels.get(i).setText(dataset.getName());
            break;
        }
    }
}