Examples with Cell us.hebi.matlab.mat.types.Cell used on opensource projects

Example 1 with Cell

use of us.hebi.matlab.mat.types.Cell in project GDSC-SMLM by aherbert.

the class TraceExporter method exportVbSpt.

@SuppressWarnings("resource")
private void exportVbSpt(MemoryPeakResults results) {
    // vbSPT file format:
    // https://sourceforge.net/projects/vbspt/
    // Matlab matrix file (.mat) containing at least one variable that is a cell
    // array where each element, representing a trajectory, is a matrix
    // where the rows define the coordinates in one, two or three dimensions
    // in subsequent timesteps. The number of dimensions to be used for the
    // analysis will be set by the runinputfile.
    // The units are arbitrary but vbSPT starting estimates must be in the same
    // units. Either nm or μm are recommended.
    // 3 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. z coordinate (μm)
    // 
    // Note: An extra column is added containing the frame. This allows results to
    // be uniquely identified using frame,x,y,z
    // Count the IDs. Each new result ID will increment the count.
    final FrameCounter idCounter = new FrameCounter(results.getFirst().getId() - 1);
    results.forEach((PeakResultProcedure) result -> {
        if (idCounter.advance(result.getId())) {
            idCounter.increment();
        }
    });
    // Create the cell array as 1xN
    final Cell out = Mat5.newCell(1, idCounter.getCount());
    // This will reset the counter to zero and ensure the current frame does not match
    // in the event of a single track
    idCounter.advanceAndReset(idCounter.currentFrame() + 1);
    final boolean is3d = results.is3D();
    // Write the tracks
    final LocalList<double[]> list = new LocalList<>();
    results.forEach(DistanceUnit.UM, (XyzrResultProcedure) (x, y, z, result) -> {
        if (idCounter.advance(result.getId())) {
            addTrack(out, idCounter.getCount() - 1, list, is3d);
            idCounter.increment();
            list.clear();
        }
        list.add(new double[] { x, y, z, result.getFrame() });
    });
    addTrack(out, idCounter.getCount() - 1, list, is3d);
    try (MatFile matFile = Mat5.newMatFile()) {
        matFile.addArray("tracks", out);
        Mat5.writeToFile(matFile, Paths.get(settings.directory, results.getName() + ".mat").toFile());
    } catch (final IOException ex) {
        handleException(ex);
    }
}

Example 2 with Cell

use of us.hebi.matlab.mat.types.Cell in project GDSC-SMLM by aherbert.

the class TraceExporterTest method canReadWriteMatCellFile.

@SuppressWarnings("resource")
@Test
void canReadWriteMatCellFile() throws IOException {
    // Create a cell: cell(1,2)
    final int crows = 1;
    final int ccols = 2;
    final Cell cell = Mat5.newCell(crows, ccols);
    // Write a matrix to two cells
    final int rows1 = 2;
    final int cols1 = 3;
    final Matrix m1 = Mat5.newMatrix(rows1, cols1);
    for (int i = 0, size = rows1 * cols1; i < size; i++) {
        m1.setDouble(i, i + 1);
    }
    final int rows2 = 4;
    final int cols2 = 3;
    final Matrix m2 = Mat5.newMatrix(rows2, cols2);
    for (int i = 0, size = rows2 * cols2; i < size; i++) {
        m2.setDouble(i, i + 10);
    }
    // zero-indexed not 1-indexed as per matlab
    cell.set(0, 0, m1);
    cell.set(0, 1, m2);
    final File file = File.createTempFile("double", ".mat");
    file.deleteOnExit();
    final String name = "tracks";
    final MatFile matFile = Mat5.newMatFile().addArray(name, cell);
    Mat5.writeToFile(matFile, file);
    try (Source source = Sources.openFile(file)) {
        final MatFile mat = Mat5.newReader(source).readMat();
        final Cell in = mat.getCell(name);
        Assertions.assertEquals(crows, in.getNumRows());
        Assertions.assertEquals(ccols, in.getNumCols());
        final Matrix m1b = in.getMatrix(0, 0);
        for (int i = 0, size = rows1 * cols1; i < size; i++) {
            Assertions.assertEquals(i + 1, m1b.getDouble(i));
        }
        final Matrix m2b = in.getMatrix(0, 1);
        for (int i = 0, size = rows2 * cols2; i < size; i++) {
            Assertions.assertEquals(i + 10, m2b.getDouble(i));
        }
    }
}