Examples with Variable org.flyte.api.v1.Variable used on opensource projects

Example 6 with Variable

use of org.flyte.api.v1.Variable in project vcell by virtualcell.

the class NetCDFReader method getEndTime.

/**
 * Get ending time. 0 dimenstion
 * @return double, ending time.
 */
public double getEndTime() throws IOException {
    Variable v = ncfile.findVariable("TEnd");
    Double val = 0.0;
    try {
        val = v.readScalarDouble();
    } catch (IOException ioe) {
        ioe.printStackTrace(System.err);
        throw new IOException("Cannot get proper ending time from the model.");
    }
    return val;
}

Example 7 with Variable

use of org.flyte.api.v1.Variable in project vcell by virtualcell.

the class NetCDFReader method getCellGrowthTimeSD.

/**
 * Get cell growth time SD, which is the standard deviation of the time between cell divisions.
 * @return double, standard deviation of cell growth time.
 */
public double getCellGrowthTimeSD() throws IOException {
    Variable v = ncfile.findVariable("CellGrowthTimeSD");
    Double val = 0.0;
    try {
        val = v.readScalarDouble();
    } catch (IOException ioe) {
        ioe.printStackTrace(System.err);
        throw new IOException("Cannot get proper standard deviation of the time between cell divisions from the model.");
    }
    return val;
}

Example 8 with Variable

use of org.flyte.api.v1.Variable in project vcell by virtualcell.

the class NetCDFReader method getNumModels_Variable.

/**
 * Get Number of Models.
 * @return int. number of models.
 */
public int getNumModels_Variable() throws IOException {
    Variable v = ncfile.findVariable("NumModels");
    int val = 0;
    try {
        val = v.readScalarInt();
    } catch (IOException ioe) {
        ioe.printStackTrace(System.err);
        throw new IOException("Cannot get proper variable of number of models from the file.");
    }
    return val;
}

Example 9 with Variable

use of org.flyte.api.v1.Variable in project vcell by virtualcell.

the class NetCDFReader method getCellGrowthTime.

/**
 * Get cell growth time, which is the average amount of time between cell divisions.
 * @return double, cell growth time.
 */
public double getCellGrowthTime() throws IOException {
    Variable v = ncfile.findVariable("CellGrowthTime");
    Double val = 0.0;
    try {
        val = v.readScalarDouble();
    } catch (IOException ioe) {
        ioe.printStackTrace(System.err);
        throw new IOException("Cannot get proper cell growth time from the model.");
    }
    return val;
}

Example 10 with Variable

use of org.flyte.api.v1.Variable in project vcell by virtualcell.

the class NetCDFReader method getSpeciesNames_val.

/**
 * Get the real string of species' names. The species' names are stored
 * in a 2 dimentional structure. First dimension is the number of speceis
 * and the second dimension is the allowed string length of the names(default=25).
 * @return String[], the list of the species' names in the model.
 */
public String[] getSpeciesNames_val() throws IOException {
    if ((this != null) && (getSpeciesNames() != null)) {
        Variable snames = getSpeciesNames();
        int[] shape = snames.getShape();
        String[] result = new String[shape[0]];
        ArrayChar.D2 data = null;
        try {
            data = (ArrayChar.D2) snames.read();
        } catch (Exception e) {
            e.printStackTrace(System.err);
            throw new IOException("Can not read species' names from the model.");
        }
        for (int i = 0; i < shape[0]; i++) {
            char[] name = new char[shape[1]];
            for (int j = 0; j < shape[1]; j++) {
                name[j] = data.get(i, j);
            }
            result[i] = new String(name).trim();
        }
        // }
        return result;
    }
    return null;
}