Examples with MathExecutable cbit.vcell.solvers.MathExecutable used on opensource projects

Example 6 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class NFSimSolver method main.

public static void main(String[] args) {
    String baseName = "SimID_";
    String workingDir = "C:\\Users\\jmasison\\.vcell\\simdata\\user\\sub\\";
    String executable = "C:\\Users\\jmasison\\workspace\\VCell_trunk\\localsolvers\\win64\\NFsim_x64.exe";
    String blankDelimiters = " \t";
    String debugfile = "C:\\Users\\jmasison\\.vcell\\simdata\\user\\sub\\debug.txt";
    int seed = 1807259453;
    int steps = 100;
    // unit system is in sec
    double duration = 0.1;
    Map<Integer, Double> timestepMap = new HashMap<>();
    BufferedReader br = null;
    PrintWriter writer = null;
    try {
        writer = new PrintWriter(debugfile, "UTF-8");
        for (int i = 1; i < steps + 1; i++) {
            // print				writer.println("\t\t\t\tentering i loop");
            // C:\\TEMP\\eee\\SimID_000.nfsimInput
            String input = workingDir + baseName + "000" + ".nfsimInput";
            String output = workingDir + baseName + i + ".gdat";
            String species = workingDir + baseName + i + ".species";
            double interval = duration / steps;
            // we start at timepoint 0
            double dur = interval * (i - 1);
            String sdur = "" + dur;
            if (sdur.length() > 6) {
                sdur = sdur.substring(0, 6);
            }
            // average length of patterns at this timepoint, over many simulations
            double averageOfAverage = 0;
            int numSimulations = 50;
            for (int ii = 0; ii < numSimulations; ii++) {
                // print					writer.println("\t\t\t\t\tentering ii loop");
                // calculate a new seed for this simulation (same start seeds will be used for each time point)
                int curSeed = seed + ii * 538297;
                // String command = executable + " -seed " + curSeed + " -vcell -xml " + input + " -o " + output + " -sim " + sdur + " -ss " + species + " -oSteps 1" + " -notf -cb";
                // Process p = Runtime.getRuntime().exec(command);
                // p.waitFor();
                String curspecies = species + "_sim_" + ii;
                String[] commands = new String[] { executable, "-seed", Integer.toString(curSeed), "-vcell", "-xml", input, "-o", output, "-sim", sdur, "-ss", curspecies, "-oSteps", "1", "-notf", "-cb" };
                MathExecutable mathExe = new MathExecutable(commands, new File(workingDir));
                try {
                    mathExe.start();
                } catch (ExecutableException e) {
                    e.printStackTrace();
                    System.out.println("exe failed, exitValue=" + mathExe.getExitValue() + ", \nstderr=" + mathExe.getStderrString() + ", \nstdout=" + mathExe.getStdoutString());
                }
                // command = "cmd.exe /c del " + workingDir + "*.gdat";
                // p = Runtime.getRuntime().exec(command);
                // p.waitFor();
                // delete the intermediate .gdat files
                // MathExecutable mathExeDel = new MathExecutable(new String[] {"cmd.exe", "/c", "del", workingDir, "*.gdat"}, new File(workingDir));
                // try {
                // mathExeDel.start();
                // } catch (ExecutableException e) {
                // e.printStackTrace();
                // }
                Map<Integer, Integer> occurencesMap = new HashMap<>();
                br = new BufferedReader(new FileReader(curspecies));
                // ex: A(s!1,t!2).B(u!1).B(u!2)  5
                String line;
                while ((line = br.readLine()) != null) {
                    if (line.startsWith("#")) {
                        continue;
                    }
                    // how many molecules in the above pattern => 3
                    int numMolecules = 1;
                    // how many instances of this pattern => 5
                    int number;
                    StringTokenizer nextLine = new StringTokenizer(line, blankDelimiters);
                    // A(s!1,t!2).B(u!1).B(u!2)
                    String pattern = nextLine.nextToken();
                    for (int j = 0; j < pattern.length(); j++) {
                        if (pattern.charAt(j) == '.') {
                            // numMolecules equals the number of 'dot' characters in string + 1
                            numMolecules++;
                        }
                    }
                    // 5
                    String s = nextLine.nextToken();
                    number = Integer.parseInt(s);
                    if (occurencesMap.containsKey(numMolecules)) {
                        int currentNumber = occurencesMap.get(numMolecules);
                        currentNumber += number;
                        occurencesMap.put(numMolecules, currentNumber);
                    } else {
                        occurencesMap.put(numMolecules, number);
                    }
                }
                double up = 0;
                double down = 0;
                for (Map.Entry<Integer, Integer> entry : occurencesMap.entrySet()) {
                    Integer key = entry.getKey();
                    if (key == 1) {
                        continue;
                    }
                    Integer value = entry.getValue();
                    up += key * value;
                    down += value;
                // print						writer.println(curspecies+"_"+i+" : "+ up + ", " + down);
                }
                double average;
                if (down > 0) {
                    average = up / down;
                } else {
                    average = 0;
                }
                // print					writer.println("average: "+average);; writer.println();
                averageOfAverage += average;
                // print					writer.println("Avergae_of_average_for_sim_"+ii+"_time_"+i+" : "+average);; writer.println();
                br.close();
            // if uncimmented make sure to use mathexecutable
            // command = "cmd.exe /c del " + workingDir + "*.species";
            // p = Runtime.getRuntime().exec(command);
            // p.waitFor();
            }
            averageOfAverage = averageOfAverage / numSimulations;
            // print				writer.println("Final_average_for_time_"+i+" : "+averageOfAverage); writer.println();
            // save average for time step (i) to map
            timestepMap.put(i, averageOfAverage);
        }
        // exited both loops
        // print		writer.println();
        writer.println("Time\tAverageCLusterSize");
        for (int j = 1; j < steps + 1; j++) {
            writer.println((j - 1) + "\t" + timestepMap.get(j));
        }
        writer.println();
        writer.println("Done");
        writer.close();
        System.out.println("\n\n\n\nDone\n\n");
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        try {
            if (br != null) {
                br.close();
            }
        } catch (IOException ex) {
            ex.printStackTrace();
        }
    }
}

Example 7 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class NFSimSolver method initialize.

/**
 * This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("NFSimSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    String inputFilename = getInputFilename();
    if (lg.isTraceEnabled())
        lg.trace("NFSimSolver.initialize() inputFilename = " + getInputFilename());
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    try (PrintWriter pw = new PrintWriter(inputFilename)) {
        NFSimFileWriter stFileWriter = new NFSimFileWriter(pw, simTask, bMessaging);
        stFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    }
    PrintWriter lg = null;
    String logFilename = getLogFilename();
    String outputFilename = getOutputFilename();
    try {
        lg = new PrintWriter(logFilename);
        String shortOutputFilename = outputFilename.substring(1 + outputFilename.lastIndexOf("\\"));
        lg.println(NFSIM_DATA_IDENTIFIER + " " + shortOutputFilename);
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate log file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        if (lg != null) {
            lg.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
// setMathExecutable(new
// cbit.vcell.solvers.MathExecutable(executableName + " gibson " +
// getBaseName() + ".stochInput" + " " + getBaseName() + ".stoch"));
}