Examples with ExplicitOutputTimeSpec cbit.vcell.solver.ExplicitOutputTimeSpec used on opensource projects

Example 1 with ExplicitOutputTimeSpec

use of cbit.vcell.solver.ExplicitOutputTimeSpec in project vcell by virtualcell.

the class ParameterEstimationTaskSimulatorIDA method getRowColumnRestultSetByBestEstimations.

public RowColumnResultSet getRowColumnRestultSetByBestEstimations(ParameterEstimationTask parameterEstimationTask, String[] paramNames, double[] paramValues) throws Exception {
    // create a temp simulation based on math description
    KeyValue key = new KeyValue("" + Math.abs(new Random().nextLong()));
    SimulationVersion dummyVersion = new SimulationVersion(key, "name", new User("temp", new KeyValue("1")), null, null, null, null, null, null, null);
    Simulation simulation = new Simulation(dummyVersion, parameterEstimationTask.getSimulationContext().getMathDescription());
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    double[] times = refData.getDataByColumn(0);
    double endTime = times[times.length - 1];
    ExplicitOutputTimeSpec exTimeSpec = new ExplicitOutputTimeSpec(times);
    // set simulation ending time and output interval
    simulation.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
    simulation.getSolverTaskDescription().setOutputTimeSpec(exTimeSpec);
    // set parameters as math overrides
    MathOverrides mathOverrides = simulation.getMathOverrides();
    for (int i = 0; i < paramNames.length; i++) {
        mathOverrides.putConstant(new Constant(paramNames[i], new Expression(paramValues[i])));
    }
    SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    IDASolverStandalone idaSolver = new IDASolverStandalone(simTask, ResourceUtil.getLocalSimDir("temp"), false);
    // startSolver();
    idaSolver.runSolver();
    Thread.sleep(1000);
    long startTimeMS = System.currentTimeMillis();
    while (idaSolver.getSolverStatus().isRunning() && System.currentTimeMillis() < (startTimeMS + 10000L)) {
        Thread.sleep(500);
    }
    ODESolverResultSet resultset = idaSolver.getODESolverResultSet();
    return resultset;
}

Example 2 with ExplicitOutputTimeSpec

use of cbit.vcell.solver.ExplicitOutputTimeSpec in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This methos returns a XML representation of a ErrorTolerance.
 * Creation date: (3/3/2001 12:02:33 AM)
 * @return Element
 * @param param cbit.vcell.solver.ErrorTolerance
 */
private Element getXML(OutputTimeSpec param) {
    Element outputOptions = new Element(XMLTags.OutputOptionsTag);
    // Add Atributes
    if (param.isDefault()) {
        DefaultOutputTimeSpec dots = (DefaultOutputTimeSpec) param;
        outputOptions.setAttribute(XMLTags.KeepEveryAttrTag, String.valueOf(dots.getKeepEvery()));
        outputOptions.setAttribute(XMLTags.KeepAtMostAttrTag, String.valueOf(dots.getKeepAtMost()));
    } else if (param.isExplicit()) {
        ExplicitOutputTimeSpec eots = (ExplicitOutputTimeSpec) param;
        outputOptions.setAttribute(XMLTags.OutputTimesAttrTag, eots.toCommaSeperatedOneLineOfString());
    } else if (param.isUniform()) {
        UniformOutputTimeSpec uots = (UniformOutputTimeSpec) param;
        outputOptions.setAttribute(XMLTags.OutputTimeStepAttrTag, String.valueOf(uots.getOutputTimeStep()));
    }
    return outputOptions;
}

Example 3 with ExplicitOutputTimeSpec

use of cbit.vcell.solver.ExplicitOutputTimeSpec in project vcell by virtualcell.

the class OutputOptionsPanel method checkExplicitOutputTimes.

private boolean checkExplicitOutputTimes(ExplicitOutputTimeSpec ots) {
    boolean bValid = true;
    double startingTime = solverTaskDescription.getTimeBounds().getStartingTime();
    double endingTime = solverTaskDescription.getTimeBounds().getEndingTime();
    double[] times = ((ExplicitOutputTimeSpec) ots).getOutputTimes();
    if (times[0] < startingTime || times[times.length - 1] > endingTime) {
        bValid = false;
        String ret = PopupGenerator.showWarningDialog(OutputOptionsPanel.this, "Output times should be within [" + startingTime + "," + endingTime + "].\n\nChange ENDING TIME to " + times[times.length - 1] + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
        if (ret.equals(UserMessage.OPTION_YES)) {
            try {
                solverTaskDescription.setTimeBounds(new TimeBounds(startingTime, times[times.length - 1]));
                bValid = true;
            } catch (PropertyVetoException e) {
                e.printStackTrace(System.out);
                DialogUtils.showErrorDialog(OutputOptionsPanel.this, e.getMessage());
            }
        }
    }
    if (bValid) {
        getOutputTimesTextField().setBorder(UIManager.getBorder("TextField.border"));
    } else {
        getOutputTimesTextField().setBorder(GuiConstants.ProblematicTextFieldBorder);
        javax.swing.SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                getOutputTimesTextField().requestFocus();
            }
        });
    }
    return bValid;
}

Example 4 with ExplicitOutputTimeSpec

use of cbit.vcell.solver.ExplicitOutputTimeSpec in project vcell by virtualcell.

the class OutputOptionsPanel method refresh.

/**
 * Comment
 */
private void refresh() {
    if (solverTaskDescription == null) {
        return;
    }
    // enables the panel where the output interval is set if the solver is IDA
    // Otherwise, that panel is disabled.
    getUniformOutputRadioButton().setEnabled(false);
    BeanUtils.enableComponents(getUniformOutputPanel(), false);
    if (solverTaskDescription.getSolverDescription().equals(SolverDescription.Smoldyn)) {
        getDefaultOutputPanel().setVisible(false);
        getDefaultOutputRadioButton().setVisible(false);
    } else if (solverTaskDescription.getSolverDescription().isChomboSolver()) {
        getDefaultOutputPanel().setVisible(false);
        getDefaultOutputRadioButton().setVisible(false);
        getUniformOutputPanel().setVisible(false);
        getUniformOutputRadioButton().setVisible(false);
    } else {
        getDefaultOutputPanel().setVisible(true);
        getDefaultOutputRadioButton().setVisible(true);
        getDefaultOutputRadioButton().setEnabled(false);
        getUniformOutputPanel().setVisible(true);
        getUniformOutputRadioButton().setVisible(true);
        BeanUtils.enableComponents(getDefaultOutputPanel(), false);
    }
    if (solverTaskDescription.getSimulation().getMathDescription().getGeometry().getDimension() > 0 || solverTaskDescription.getSimulation().getMathDescription().isNonSpatialStoch()) {
        getExplicitOutputPanel().setVisible(false);
        getExplicitOutputRadioButton().setVisible(false);
    } else {
        getExplicitOutputPanel().setVisible(true);
        getExplicitOutputRadioButton().setVisible(true);
        getExplicitOutputRadioButton().setEnabled(false);
        BeanUtils.enableComponents(getExplicitOutputPanel(), false);
    }
    if (solverTaskDescription == null || solverTaskDescription.getSolverDescription() == null) {
        // Also, disable its radiobutton and fields.
        return;
    }
    SolverDescription solverDesc = solverTaskDescription.getSolverDescription();
    // Amended June 2009, no output option for stochastic gibson multiple trials
    if (solverTaskDescription.getStochOpt() != null && solverTaskDescription.getStochOpt().getNumOfTrials() > 1 && solverTaskDescription.getSolverDescription().equals(SolverDescription.StochGibson)) {
        return;
    }
    OutputTimeSpec ots = solverTaskDescription.getOutputTimeSpec();
    if (ots.isDefault()) {
        // if solver is not IDA, if the output Time step radio button had been set,
        // change the setting to the 'keep every' radio button and flush the contents of the output timestep text field.
        // Also, disable its radiobutton and fields.
        getDefaultOutputRadioButton().setSelected(true);
        getKeepEveryTextField().setText(((DefaultOutputTimeSpec) ots).getKeepEvery() + "");
        if (solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver()) {
            getKeepAtMostTextField().setText("");
        } else {
            getKeepAtMostTextField().setText(((DefaultOutputTimeSpec) ots).getKeepAtMost() + "");
        }
        getOutputTimeStepTextField().setText("");
        getOutputTimesTextField().setText("");
    } else if (ots.isUniform()) {
        getUniformOutputRadioButton().setSelected(true);
        getKeepEveryTextField().setText("");
        getKeepAtMostTextField().setText("");
        getOutputTimeStepTextField().setText(((UniformOutputTimeSpec) ots).getOutputTimeStep() + "");
        getOutputTimesTextField().setText("");
    } else if (ots.isExplicit()) {
        getExplicitOutputRadioButton().setSelected(true);
        getKeepEveryTextField().setText("");
        getKeepAtMostTextField().setText("");
        getOutputTimeStepTextField().setText("");
        getOutputTimesTextField().setText(((ExplicitOutputTimeSpec) ots).toCommaSeperatedOneLineOfString() + "");
        getOutputTimesTextField().setCaretPosition(0);
    }
    DefaultOutputTimeSpec dots = new DefaultOutputTimeSpec();
    UniformOutputTimeSpec uots = new UniformOutputTimeSpec(0.05);
    ExplicitOutputTimeSpec eots = new ExplicitOutputTimeSpec(new double[] { 0.1 });
    if (solverDesc.supports(dots)) {
        if (!solverDesc.isSemiImplicitPdeSolver() || ots.isDefault()) {
            getDefaultOutputRadioButton().setEnabled(true);
            if (getDefaultOutputRadioButton().isSelected() || ots.isDefault()) {
                BeanUtils.enableComponents(getDefaultOutputPanel(), true);
            }
        }
    }
    if (solverDesc.supports(uots)) {
        getUniformOutputRadioButton().setEnabled(true);
        if (getUniformOutputRadioButton().isSelected() || ots.isUniform()) {
            BeanUtils.enableComponents(getUniformOutputPanel(), true);
        }
    }
    if (solverDesc.supports(eots)) {
        getExplicitOutputRadioButton().setEnabled(true);
        if (getExplicitOutputRadioButton().isSelected() || ots.isExplicit()) {
            BeanUtils.enableComponents(getExplicitOutputPanel(), true);
        }
    }
    if (solverDesc.isSemiImplicitPdeSolver()) {
        getKeepAtMostTextField().setText("");
        getKeepAtMostTextField().setEnabled(false);
    }
}

Example 5 with ExplicitOutputTimeSpec

use of cbit.vcell.solver.ExplicitOutputTimeSpec in project vcell by virtualcell.

the class OutputOptionsPanel method setSolverTaskDescription.

/**
 * set solver description. The contained {@link SolverTaskDescription#getSimulation()}
 * is usually a temporary cloned object with  a null {@link SimulationOwner}  ; therefore
 * we required the {@link UnitInfo} of the actual {@link Simulation} owner as a parameter
 * @param newValue
 * @param unitInfo not null
 */
public final void setSolverTaskDescription(SolverTaskDescription newValue, UnitInfo unitInfo) {
    Objects.requireNonNull(unitInfo);
    SolverTaskDescription oldValue = solverTaskDescription;
    /* Stop listening for events from the current object */
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    /* Listen for events from the new object */
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    chomboOutputOptionsPanel.setSolverTaskDescription(solverTaskDescription);
    firePropertyChange("solverTaskDescription", oldValue, newValue);
    getOutputTimeStepTextField().addFocusListener(ivjEventHandler);
    getDefaultOutputRadioButton().addActionListener(ivjEventHandler);
    getUniformOutputRadioButton().addActionListener(ivjEventHandler);
    getExplicitOutputRadioButton().addActionListener(ivjEventHandler);
    getKeepEveryTextField().addFocusListener(ivjEventHandler);
    getKeepAtMostTextField().addFocusListener(ivjEventHandler);
    getOutputTimesTextField().addFocusListener(ivjEventHandler);
    getOutputTimeStepTextField().setInputVerifier(new InputVerifier() {

        @Override
        public boolean verify(JComponent input) {
            return false;
        }

        @Override
        public boolean shouldYieldFocus(JComponent input) {
            boolean bValid = true;
            try {
                double outputTime = Double.parseDouble(getOutputTimeStepTextField().getText());
                if (solverTaskDescription.getOutputTimeSpec().isUniform() && !solverTaskDescription.getSolverDescription().hasVariableTimestep()) {
                    double timeStep = solverTaskDescription.getTimeStep().getDefaultTimeStep();
                    double suggestedInterval = outputTime;
                    if (outputTime < timeStep) {
                        suggestedInterval = timeStep;
                        bValid = false;
                    } else if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)) {
                        double n = outputTime / timeStep;
                        int intn = (int) Math.round(n);
                        if (intn != n) {
                            bValid = false;
                            suggestedInterval = (intn * timeStep);
                        }
                    }
                    if (!bValid) {
                        String ret = PopupGenerator.showWarningDialog(OutputOptionsPanel.this, "Output Interval", "Output Interval must " + "be integer multiple of time step.\n\nChange Output Interval to " + suggestedInterval + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
                        if (ret.equals(UserMessage.OPTION_YES)) {
                            getOutputTimeStepTextField().setText(suggestedInterval + "");
                            bValid = true;
                        }
                    }
                }
            } catch (NumberFormatException ex) {
                DialogUtils.showErrorDialog(OutputOptionsPanel.this, "Wrong number format " + ex.getMessage().toLowerCase());
                bValid = false;
            }
            if (bValid) {
                getOutputTimeStepTextField().setBorder(UIManager.getBorder("TextField.border"));
            } else {
                getOutputTimeStepTextField().setBorder(GuiConstants.ProblematicTextFieldBorder);
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        getOutputTimeStepTextField().requestFocus();
                    }
                });
            }
            return bValid;
        }
    });
    getOutputTimesTextField().setInputVerifier(new InputVerifier() {

        @Override
        public boolean verify(JComponent input) {
            return false;
        }

        @Override
        public boolean shouldYieldFocus(JComponent input) {
            ExplicitOutputTimeSpec eots = ExplicitOutputTimeSpec.fromString(getOutputTimesTextField().getText());
            return checkExplicitOutputTimes(eots);
        }
    });
    // set time label units
    JLabel timeUnitsLabel = getTimeStepUnitsLabel();
    timeUnitsLabel.setText(unitInfo.getTimeUnitString());
}