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

Example 1 with Matrix

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

the class TraceExporterTest method canReadWriteMatFile.

@SuppressWarnings("resource")
@Test
void canReadWriteMatFile() throws IOException {
    // Write a double matrix
    final int rows = 4;
    final int cols = 5;
    final Matrix out = Mat5.newMatrix(rows, cols);
    // row, col
    final int row = 3;
    final int col = 4;
    out.setDouble(row, col, 5.0);
    Assertions.assertEquals(5.0, out.getDouble(row, col));
    // From AbstractArray.getColumnMajorIndex(row, col)
    // Column major index: row + rows * col
    Assertions.assertEquals(5.0, out.getDouble(row + rows * col), "column major index");
    // Fill using index
    for (int i = 0, size = rows * cols; i < size; i++) {
        out.setDouble(i, i + 1);
    }
    final File file = File.createTempFile("double", ".mat");
    file.deleteOnExit();
    final String name = "tracks";
    final MatFile matFile = Mat5.newMatFile().addArray(name, out);
    Mat5.writeToFile(matFile, file);
    try (Source source = Sources.openFile(file)) {
        final MatFile mat = Mat5.newReader(source).readMat();
        final Matrix in = mat.getMatrix(name);
        Assertions.assertEquals(rows, in.getNumRows());
        Assertions.assertEquals(cols, in.getNumCols());
        for (int i = 0, size = rows * cols; i < size; i++) {
            Assertions.assertEquals(i + 1, in.getDouble(i));
        }
    }
}

Example 2 with Matrix

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

the class TraceExporter method addTrack.

/**
 * Adds the track to the cell at the given row index.
 *
 * @param cell the output cell
 * @param index the index
 * @param list the list
 * @param is3d true if the data is 3D, otherwise write 2D data
 */
@SuppressWarnings("resource")
private static void addTrack(Cell cell, int index, LocalList<double[]> list, boolean is3d) {
    if (list.isEmpty()) {
        return;
    }
    // Create the matrix
    final int rows = list.size();
    final Matrix m = Mat5.newMatrix(rows, is3d ? 4 : 3);
    // Set up column offsets
    final int col1 = rows * 1;
    final int col2 = rows * 2;
    final int col3 = rows * 3;
    for (int i = 0; i < rows; i++) {
        final double[] xyz = list.unsafeGet(i);
        m.setDouble(i, xyz[0]);
        m.setDouble(i + col1, xyz[1]);
        if (is3d) {
            m.setDouble(i + col2, xyz[2]);
            m.setDouble(i + col3, xyz[3]);
        } else {
            m.setDouble(i + col2, xyz[3]);
        }
    }
    cell.set(index, m);
}

Example 3 with Matrix

use of us.hebi.matlab.mat.types.Matrix 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 4 with Matrix

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

the class TraceExporter method exportAnaDda.

@SuppressWarnings("resource")
private void exportAnaDda(MemoryPeakResults results) {
    // anaDDA list of tracked localisations file format:
    // https://github.com/HohlbeinLab/anaDDA
    // Matlab matrix file.
    // 5 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. frame number
    // 4. track id
    // 5. frame time (s)
    // Count the number of localisations including start/end frames
    final Counter row = new Counter();
    results.forEach((PeakResultProcedure) result -> {
        row.increment(getLength(result));
    });
    // Create the matrix
    final int rows = row.getCount();
    final Matrix out = Mat5.newMatrix(rows, 5);
    // Set up column offsets
    final int col1 = rows * 1;
    final int col2 = rows * 2;
    final int col3 = rows * 3;
    final int col4 = rows * 4;
    // Frame time in seconds. This is not the frame time point converted to seconds
    // but the exposure duration of the frame.
    final double frameTime = results.getCalibrationReader().getExposureTime() / 1000;
    row.reset();
    results.forEach(DistanceUnit.UM, (XyrResultProcedure) (x, y, result) -> {
        if (result.hasEndFrame()) {
            for (int t = result.getFrame(); t <= result.getEndFrame(); t++) {
                final int index = row.getAndIncrement();
                out.setDouble(index, x);
                out.setDouble(index + col1, y);
                out.setDouble(index + col2, t);
                out.setDouble(index + col3, result.getId());
                out.setDouble(index + col4, frameTime);
            }
        } else {
            // Column major index: row + rows * col
            final int index = row.getAndIncrement();
            out.setDouble(index, x);
            out.setDouble(index + col1, y);
            out.setDouble(index + col2, result.getFrame());
            out.setDouble(index + col3, result.getId());
            out.setDouble(index + col4, frameTime);
        }
    });
    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 5 with Matrix

use of us.hebi.matlab.mat.types.Matrix 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));
        }
    }
}