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

Example 1 with MLArray

use of com.jmatio.types.MLArray in project tika by apache.

the class MatParser method parse.

public void parse(InputStream stream, ContentHandler handler, Metadata metadata, ParseContext context) throws IOException, SAXException, TikaException {
    //Set MIME type as Matlab
    metadata.set(Metadata.CONTENT_TYPE, MATLAB_MIME_TYPE);
    TemporaryResources tmp = TikaInputStream.isTikaInputStream(stream) ? null : new TemporaryResources();
    try {
        // Use TIS so we can spool a temp file for parsing.
        TikaInputStream tis = TikaInputStream.get(stream, tmp);
        //Extract information from header file
        //input .mat file
        MatFileReader mfr = new MatFileReader(tis.getFile());
        //.mat header information
        MatFileHeader hdr = mfr.getMatFileHeader();
        // Example header: "MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Sun Mar  2 23:41:57 2014"
        // Break header information into its parts
        String[] parts = hdr.getDescription().split(",");
        if (parts[2].contains("Created")) {
            int lastIndex1 = parts[2].lastIndexOf("Created on:");
            String dateCreated = parts[2].substring(lastIndex1 + "Created on:".length()).trim();
            metadata.set("createdOn", dateCreated);
        }
        if (parts[1].contains("Platform")) {
            int lastIndex2 = parts[1].lastIndexOf("Platform:");
            String platform = parts[1].substring(lastIndex2 + "Platform:".length()).trim();
            metadata.set("platform", platform);
        }
        if (parts[0].contains("MATLAB")) {
            metadata.set("fileType", parts[0]);
        }
        // Get endian indicator from header file
        // Retrieve endian bytes and convert to string
        String endianBytes = new String(hdr.getEndianIndicator(), UTF_8);
        // Convert bytes to characters to string
        String endianCode = String.valueOf(endianBytes.toCharArray());
        metadata.set("endian", endianCode);
        //Text output	
        XHTMLContentHandler xhtml = new XHTMLContentHandler(handler, metadata);
        xhtml.startDocument();
        xhtml.newline();
        //Loop through each variable
        for (Map.Entry<String, MLArray> entry : mfr.getContent().entrySet()) {
            String varName = entry.getKey();
            MLArray varData = entry.getValue();
            xhtml.element("p", varName + ":" + String.valueOf(varData));
            // If the variable is a structure, extract variable info from structure
            if (varData.isStruct()) {
                MLStructure mlStructure = (MLStructure) mfr.getMLArray(varName);
                xhtml.startElement("ul");
                xhtml.newline();
                for (MLArray element : mlStructure.getAllFields()) {
                    xhtml.startElement("li");
                    xhtml.characters(String.valueOf(element));
                    // If there is an embedded structure, extract variable info.
                    if (element.isStruct()) {
                        xhtml.startElement("ul");
                        // Should this actually be a recursive call?
                        xhtml.element("li", element.contentToString());
                        xhtml.endElement("ul");
                    }
                    xhtml.endElement("li");
                }
                xhtml.endElement("ul");
            }
        }
        xhtml.endDocument();
    } catch (IOException e) {
        throw new TikaException("Error parsing Matlab file with MatParser", e);
    } finally {
        if (tmp != null) {
            tmp.dispose();
        }
    }
}

Example 2 with MLArray

use of com.jmatio.types.MLArray 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);
}