Examples with Geometry org.sbml.jsbml.ext.spatial.Geometry used on opensource projects

Example 1 with Geometry

use of org.sbml.jsbml.ext.spatial.Geometry in project vcell by virtualcell.

the class ImportSBMLCommand method run.

@Override
public void run() {
    // Read SBML document
    SBMLDocument document = null;
    try {
        document = SBMLReader.read(file);
    } catch (XMLStreamException | IOException e) {
        e.printStackTrace();
    }
    // Get SBML geometry
    SpatialModelPlugin modelPlugin = (SpatialModelPlugin) document.getModel().getPlugin("spatial");
    Geometry geometry = modelPlugin.getGeometry();
    SampledField sampledField = geometry.getListOfSampledFields().get(0);
    // Parse pixel values to int
    String[] imgStringArray = sampledField.getSamples().split(" ");
    int[] imgArray = new int[imgStringArray.length];
    for (int i = 0; i < imgStringArray.length; i++) {
        imgArray[i] = Integer.parseInt(imgStringArray[i]);
    }
    // Create the image and display
    int width = sampledField.getNumSamples1();
    int height = sampledField.getNumSamples2();
    ArrayImg<UnsignedIntType, IntArray> img = ArrayImgs.unsignedInts(imgArray, width, height);
    displayService.createDisplay(img);
}