Examples with ODESolverResultSet cbit.vcell.solver.ode.ODESolverResultSet used on opensource projects

Example 51 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class ODEDataInterfaceImpl method extractColumnMin.

@Override
public double[] extractColumnMin(String columnName) throws ExpressionException, ObjectNotFoundException {
    FileFormat hdf5FileFormat = null;
    File to = null;
    try {
        ODESolverResultSet osrs = getOdeSolverResultSet();
        if (osrs instanceof ODESimData) {
            byte[] hdf5FileBytes = ((ODESimData) getOdeSolverResultSet()).getHdf5FileBytes();
            if (hdf5FileBytes != null) {
                to = File.createTempFile("odeStats_" + simulationModelInfo.getSimulationName(), ".hdf5");
                Files.write(hdf5FileBytes, to);
                FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
                if (fileFormat == null) {
                    throw new Exception("Cannot find HDF5 FileFormat.");
                }
                // open the file with read-only access
                hdf5FileFormat = fileFormat.createInstance(to.getAbsolutePath(), FileFormat.READ);
                // open the file and retrieve the file structure
                hdf5FileFormat.open();
                Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) hdf5FileFormat.getRootNode()).getUserObject();
                List<HObject> postProcessMembers = ((Group) root).getMemberList();
                for (HObject nextHObject : postProcessMembers) {
                    System.out.println(nextHObject.getName() + "   " + nextHObject.getClass().getName());
                    H5ScalarDS h5ScalarDS = (H5ScalarDS) nextHObject;
                    h5ScalarDS.init();
                    try {
                        long[] dims = h5ScalarDS.getDims();
                        System.out.println("---" + nextHObject.getName() + " " + nextHObject.getClass().getName() + " Dimensions=" + Arrays.toString(dims));
                        Object obj = h5ScalarDS.read();
                        if (dims.length == 2) {
                            double[] columns = new double[(int) dims[1]];
                            for (int row = 0; row < dims[0]; row++) {
                                System.arraycopy(obj, row * columns.length, columns, 0, columns.length);
                                System.out.println(Arrays.toString(columns));
                            }
                            return null;
                        // return columns;
                        } else {
                            return null;
                        }
                    } catch (Exception e) {
                        return null;
                    }
                }
            }
        }
    } catch (Exception e) {
    } finally {
        if (hdf5FileFormat != null) {
            try {
                hdf5FileFormat.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
        if (to != null) {
            try {
                to.delete();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    return null;
}