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

Example 1 with DefaultOutputTimeSpec

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

the class ODETimePlotMultipleScansPanel method updateScanParamChoices.

/**
 * Insert the method's description here.
 * Creation date: (10/18/2005 12:44:06 AM)
 */
private void updateScanParamChoices() {
    AsynchClientTask task1 = new AsynchClientTask("get ode results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            int[] jobIndexes = scanChoiceTable.getSelectedRows();
            VCSimulationIdentifier vcSimulationIdentifier = simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
            int plotCount = jobIndexes.length * variableNames.length;
            SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
            double[][] dataValues = new double[plotCount + 1][];
            PlotData[] plotDatas = new PlotData[plotCount];
            String[] plotNames = new String[plotCount];
            int plotIndex = 0;
            dataValues[0] = null;
            for (int ji = 0; ji < jobIndexes.length; ji++) {
                int jobIndex = jobIndexes[ji];
                final VCDataIdentifier vcdid = new VCSimulationDataIdentifier(vcSimulationIdentifier, jobIndex);
                ODEDataManager odeDatamanager = ((ODEDataManager) dataManager).createNewODEDataManager(vcdid);
                ODESolverResultSet odeSolverResultSet = odeDatamanager.getODESolverResultSet();
                if (ji == 0) {
                    plotPane.setStepViewVisible(simulation.getSolverTaskDescription().getSolverDescription().isNonSpatialStochasticSolver(), odeSolverResultSet.isMultiTrialData());
                    hashTable.put("bMultiTrial", new Boolean(odeSolverResultSet.isMultiTrialData()));
                }
                double[] tdata = null;
                if (!odeSolverResultSet.isMultiTrialData()) {
                    int tcol = odeSolverResultSet.findColumn(ReservedVariable.TIME.getName());
                    tdata = odeSolverResultSet.extractColumn(tcol);
                    if (dataValues[0] == null) {
                        dataValues[0] = tdata;
                    }
                }
                for (int v = 0; v < variableNames.length; v++) {
                    String varname = variableNames[v];
                    int varcol = odeSolverResultSet.findColumn(varname);
                    double[] vdata = odeSolverResultSet.extractColumn(varcol);
                    if (!odeSolverResultSet.isMultiTrialData()) {
                        dataValues[plotIndex + 1] = vdata;
                        // plotNames[plotIndex] = varname + " -- " + JOB_PLOT_NAME + " " + jobIndex;
                        plotDatas[plotIndex] = new PlotData(tdata, vdata);
                    // symbolTableEntries[plotIndex] = simulation.getMathDescription().getVariable(varname);
                    } else {
                        Point2D[] histogram = ODESolverPlotSpecificationPanel.generateHistogram(vdata);
                        double[] x = new double[histogram.length];
                        double[] y = new double[histogram.length];
                        for (int j = 0; j < histogram.length; j++) {
                            x[j] = histogram[j].getX();
                            y[j] = histogram[j].getY();
                        }
                        plotDatas[plotIndex] = new PlotData(x, y);
                    }
                    plotNames[plotIndex] = varname + " -- " + JOB_PLOT_NAME + " " + jobIndex;
                    symbolTableEntries[plotIndex] = simulation.getMathDescription().getVariable(varname);
                    plotIndex++;
                }
            }
            hashTable.put("dataValues", dataValues);
            hashTable.put("plotDatas", plotDatas);
            hashTable.put("plotNames", plotNames);
            hashTable.put("symbolTableEntries", symbolTableEntries);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            double[][] dataValues = (double[][]) hashTable.get("dataValues");
            PlotData[] plotDatas = (PlotData[]) hashTable.get("plotDatas");
            String[] plotNames = (String[]) hashTable.get("plotNames");
            SymbolTableEntry[] symbolTableEntries = (SymbolTableEntry[]) hashTable.get("symbolTableEntries");
            if (plotDatas == null || plotDatas.length == 0 || (plotDatas.length == 1 && plotDatas[0] == null) || plotNames == null) {
                plotPane.setPlot2D(null);
                return;
            }
            Plot2D plot2D = null;
            if (hashTable.get("bMultiTrial") instanceof Boolean && (Boolean) hashTable.get("bMultiTrial")) {
                plot2D = new Plot2D(symbolTableEntries, null, plotNames, plotDatas, new String[] { "Probability Distribution of Species", "Number of Particles", "" });
            } else if (simulation.getSolverTaskDescription().getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
                plot2D = new Plot2D(symbolTableEntries, null, plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
            } else {
                plot2D = new SingleXPlot2D(symbolTableEntries, null, ReservedVariable.TIME.getName(), plotNames, dataValues);
            }
            plotPane.setPlot2D(plot2D);
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 2 with DefaultOutputTimeSpec

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

the class RbmNetworkGenerator method runNFSim.

public static void runNFSim(PrintWriter writer, RbmModelContainer rbmModelContainer, SimulationContext sc, NetworkGenerationRequirements networkGenerationRequirements) {
    // ex: simulate_nf({t_end=>100,n_steps=>50});
    writer.print("simulate_nf({");
    if (sc.getBioModel() == null || sc.getSimulations() == null || sc.getSimulations().length == 0) {
        writer.print("t_end=>100,n_steps=>50");
        writer.println("})");
        return;
    }
    // we just pick whatever the first simulation has, it'll get too complicated to offer the user a list of simulations and ask him to choose
    SolverTaskDescription solverTaskDescription = sc.getSimulations(0).getSolverTaskDescription();
    TimeBounds tb = solverTaskDescription.getTimeBounds();
    double dtime = tb.getEndingTime() - tb.getStartingTime();
    if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec uots = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
        double interval = uots.getOutputTimeStep();
        int steps = (int) Math.round(dtime / interval);
        writer.print("t_end=>" + dtime + ",n_steps=>" + steps);
    } else if (solverTaskDescription.getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
        // currently unsupported, but some old simulations have it
        writer.print("t_end=>" + dtime + ",n_steps=>50");
    } else {
        writer.print("t_end=>100,n_steps=>50");
    }
    writer.println("})");
}

Example 3 with DefaultOutputTimeSpec

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

the class XmlReader method getOutputTimeSpec.

/**
 * This method returns a TimeStep object from a XML Element.
 * Creation date: (5/22/2001 11:45:33 AM)
 * @return cbit.vcell.solver.TimeStep
 * @param param org.jdom.Element
 */
private OutputTimeSpec getOutputTimeSpec(Element param) {
    if (param != null) {
        // get attributes
        if (param.getAttributeValue(XMLTags.KeepEveryAttrTag) != null) {
            int keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryAttrTag));
            int keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostAttrTag));
            return new DefaultOutputTimeSpec(keepEvery, keepAtMost);
        } else if (param.getAttributeValue(XMLTags.OutputTimeStepAttrTag) != null) {
            double outputStep = Double.parseDouble(param.getAttributeValue(XMLTags.OutputTimeStepAttrTag));
            return new UniformOutputTimeSpec(outputStep);
        } else if (param.getAttributeValue(XMLTags.OutputTimesAttrTag) != null) {
            String line = param.getAttributeValue(XMLTags.OutputTimesAttrTag);
            return ExplicitOutputTimeSpec.fromString(line);
        }
    }
    return null;
}

Example 4 with DefaultOutputTimeSpec

use of cbit.vcell.solver.DefaultOutputTimeSpec 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 5 with DefaultOutputTimeSpec

use of cbit.vcell.solver.DefaultOutputTimeSpec 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);
    }
}