Examples with MLCell com.jmatio.types.MLCell used on opensource projects

Example 1 with MLCell

use of com.jmatio.types.MLCell in project vcell by virtualcell.

the class FrapDataUtils method saveImageDatasetAsExternalMatlabData.

// export the frap data to matlab file. The matlab file contains timestamps(1*Tn) , mask(numImgX * numImgY),
// ImageDataSet(1*Tn) each cell of (1*Tn) point to a 2d image(numImgX * numImgY)
public static void saveImageDatasetAsExternalMatlabData(FRAPData frapData, LocalWorkspace localWorkspace, String matlabFileName, int startingIndexForRecovery, CartesianMesh cartesianMesh) throws IOException {
    ImageDataset imageDataset = frapData.getImageDataset();
    if (imageDataset.getSizeC() > 1) {
        throw new RuntimeException("FRAPData.saveImageDatasetAsExternalMatlabData(): multiple channels not yet supported");
    }
    int numX = cartesianMesh.getSizeX();
    int numY = cartesianMesh.getSizeY();
    // prepare variable to write into matlab file, listOfVars is the outmost structure to write to Matlab file.
    ArrayList<MLArray> listOfVars = new ArrayList<MLArray>();
    double[] timeArray = imageDataset.getImageTimeStamps();
    ROI cellROI = frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    short[] shortCellMask = cellROI.getPixelsXYZ();
    // add image data set to Matlab cell, each cell points to a numX*numY array
    MLCell imageCell = new MLCell("ImageDataSet", new int[] { timeArray.length, 1 });
    for (int tIndex = 0; tIndex < imageDataset.getSizeT(); tIndex++) {
        // images according to zIndex at specific time points(tIndex)
        short[] originalData = imageDataset.getPixelsZ(0, tIndex);
        double[] doubleImgData = new double[originalData.length];
        for (int i = 0; i < originalData.length; i++) {
            doubleImgData[i] = 0x0000ffff & originalData[i];
        }
        MLDouble mlDoublImgData = new MLDouble("ImageDataAtTime_" + tIndex, doubleImgData, numX);
        imageCell.set(mlDoublImgData, tIndex, 0);
    }
    listOfVars.add(imageCell);
    // create mask in a Matlab 2D double(numX*numY)
    double[] doubleCellMask = new double[shortCellMask.length];
    for (int i = 0; i < shortCellMask.length; i++) {
        doubleCellMask[i] = 0x0000ffff & shortCellMask[i];
    }
    MLDouble cellMask = new MLDouble("CellMask", doubleCellMask, numX);
    listOfVars.add(cellMask);
    // create times in a Matlab 2D double(1*numTimePoints)
    MLDouble times = new MLDouble("ExperimentalTimeStamps", new double[][] { timeArray });
    listOfVars.add(times);
    MatFileWriter writer = new MatFileWriter();
    writer.write(matlabFileName, listOfVars);
}