Examples with Mat5 us.hebi.matlab.mat.format.Mat5 used on opensource projects

Example 1 with Mat5

use of us.hebi.matlab.mat.format.Mat5 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 Mat5

use of us.hebi.matlab.mat.format.Mat5 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);
    }
}