Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 6 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ClientSimManager method runSmoldynParticleView.

public void runSmoldynParticleView(final Simulation originalSimulation) {
    SimulationOwner simulationOwner = simWorkspace.getSimulationOwner();
    Collection<AsynchClientTask> tasks;
    if (simulationOwner instanceof SimulationContext) {
        tasks = ClientRequestManager.updateMath(documentWindowManager.getComponent(), (SimulationContext) simulationOwner, false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    } else {
        tasks = new ArrayList<>();
    }
    AsynchClientTask pv = new AsynchClientTask("starting particle view", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File[] exes = SolverUtilities.getExes(SolverDescription.Smoldyn);
            assert exes.length == 1 : "one and only one smoldyn solver expected";
            File smoldynExe = exes[0];
            Simulation simulation = new TempSimulation(originalSimulation, false);
            SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
            File inputFile = new File(ResourceUtil.getLocalSimDir(User.tempUser.getName()), simTask.getSimulationJobID() + SimDataConstants.SMOLDYN_INPUT_FILE_EXTENSION);
            inputFile.deleteOnExit();
            PrintWriter pw = new PrintWriter(inputFile);
            SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
            smf.write();
            pw.close();
            String[] cmd = new String[] { smoldynExe.getAbsolutePath(), inputFile.getAbsolutePath() };
            StringBuilder commandLine = new StringBuilder();
            for (int i = 0; i < cmd.length; i++) {
                if (i > 0) {
                    commandLine.append(" ");
                }
                commandLine.append(TokenMangler.getEscapedPathName(cmd[i]));
            }
            System.out.println(commandLine);
            char[] charArrayOut = new char[10000];
            char[] charArrayErr = new char[10000];
            ProcessBuilder processBuilder = new ProcessBuilder(cmd);
            final Process process = processBuilder.start();
            getClientTaskStatusSupport().addProgressDialogListener(new ProgressDialogListener() {

                public void cancelButton_actionPerformed(EventObject newEvent) {
                    process.destroy();
                }
            });
            InputStream errorStream = process.getErrorStream();
            InputStreamReader errisr = new InputStreamReader(errorStream);
            InputStream outputStream = process.getInputStream();
            InputStreamReader outisr = new InputStreamReader(outputStream);
            StringBuilder sb = new StringBuilder();
            boolean running = true;
            while (running) {
                try {
                    process.exitValue();
                    running = false;
                } catch (IllegalThreadStateException e) {
                // process didn't exit yet, do nothing
                }
                if (outputStream.available() > 0) {
                    outisr.read(charArrayOut, 0, charArrayOut.length);
                }
                if (errorStream.available() > 0) {
                    errisr.read(charArrayErr, 0, charArrayErr.length);
                    sb.append(new String(charArrayErr));
                }
            }
            if (sb.length() > 0) {
                throw new RuntimeException(sb.toString());
            }
        }
    };
    tasks.add(pv);
    ClientTaskDispatcher.dispatchColl(documentWindowManager.getComponent(), new Hashtable<String, Object>(), tasks, false, true, null);
}

Example 7 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class VFrapXmlHelper method ReplaceVFrapNamesWithSymbolNames.

// 
// replace vFrap default names in field function arguments with data symbol names -----
// 
public static void ReplaceVFrapNamesWithSymbolNames(BioModel bioModel) throws ExpressionException {
    SimulationContext simContext = bioModel.getSimulationContexts()[0];
    SpeciesContextSpec[] scsArray = simContext.getReactionContext().getSpeciesContextSpecs();
    for (SpeciesContextSpec scs : scsArray) {
        // vFrap('a','c',0.0,'volume')
        Expression exp = scs.getInitialConditionParameter().getExpression();
        FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(exp);
        if (fieldFunctionArgs != null && fieldFunctionArgs.length > 0) {
            for (FieldFunctionArguments args : fieldFunctionArgs) {
                for (DataSymbol ds : simContext.getDataContext().getDataSymbols()) {
                    if (ds instanceof FieldDataSymbol) {
                        FieldDataSymbol fieldDataSymbol = (FieldDataSymbol) ds;
                        // String extDataIdentName = fieldDataSymbol.getExternalDataIdentifier().getName();	// name of field data
                        // String argsFieldName = args.getFieldName();				// roiData
                        // fieldDataSymbol.getFieldDataVarTime() == args.getTime().evaluateConstant()
                        // name of data symbol  ex: postbleach_first_ccccF
                        String dataSymbolName = fieldDataSymbol.getName();
                        // name in expression as it comes from vFrap   ex: postbleach_first
                        String argsVariableName = args.getVariableName();
                        if (dataSymbolName.startsWith(argsVariableName)) {
                            // vcField('roiData','postbleach_first',0.0,'Volume')
                            String oldExpression = args.infix();
                            exp.substituteInPlace(new Expression(oldExpression), new Expression(dataSymbolName));
                            exp.bindExpression(simContext);
                        }
                    }
                }
            }
        }
    }
}

Example 8 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class BioModelWindowManager method updateApplicationHash.

/**
 * Insert the method's description here.
 * Creation date: (6/1/2004 2:33:41 AM)
 */
private void updateApplicationHash(boolean reset) {
    SimulationContext[] scs = getBioModel().getSimulationContexts();
    Enumeration<SimulationContext> en = getApplicationsHash().keys();
    while (en.hasMoreElements()) {
        SimulationContext sc = (SimulationContext) en.nextElement();
        ApplicationComponents appComponents = getApplicationsHash().get(sc);
        if (!getBioModel().contains(sc)) {
            if (reset) {
                // find one with the same name, if available
                SimulationContext found = null;
                if (scs != null) {
                    for (int i = 0; i < scs.length; i++) {
                        if (scs[i].getName().equals(sc.getName())) {
                            found = scs[i];
                            break;
                        }
                    }
                }
                if (found != null) {
                    // update hash
                    getApplicationsHash().remove(sc);
                    getApplicationsHash().put(found, appComponents);
                    appComponents.resetSimulationContext(found);
                    // check simulation data windows
                    updateSimulationDataViewers(appComponents, found);
                    // rewire listener
                    sc.removePropertyChangeListener(this);
                    found.removePropertyChangeListener(this);
                    found.addPropertyChangeListener(this);
                } else {
                    // we didn't find one, so remove from hash and close all of its windows
                    remove(appComponents, sc);
                }
            } else {
                // shouldn't have it
                remove(appComponents, sc);
            }
        }
    }
}

Example 9 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ClientRequestManager method createRuleBasedBioModelFromApplication.

public void createRuleBasedBioModelFromApplication(final BioModelWindowManager requester, final String name, final SimulationContext simContext) {
    if (simContext == null) {
        PopupGenerator.showErrorDialog(requester, "Selected Application is null, cannot generate corresponding bio model");
        return;
    }
    AsynchClientTask task1 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback dummyCallback = new MathMappingCallback() {

                public void setProgressFraction(float percentDone) {
                }

                public void setMessage(String message) {
                }

                public boolean isInterrupted() {
                    return false;
                }
            };
            MathMapping transformedMathMapping = simContext.createNewMathMapping(dummyCallback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
            // simContext.setMathDescription(transformedMathMapping.getMathDescription());
            BioModel newBioModel = new BioModel(null);
            SimulationContext transformedSimContext = transformedMathMapping.getTransformation().transformedSimContext;
            Model model = transformedSimContext.getModel();
            // for(ReactionStep rs : model.getReactionSteps()) {
            // model.removeReactionStep(rs);
            // }
            newBioModel.setModel(model);
            hashTable.put("newBioModel", newBioModel);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Creating BioModel from BioModel Application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            BioModel newBioModel = (BioModel) hashTable.get("newBioModel");
            DocumentWindowManager windowManager = createDocumentWindowManager(newBioModel);
            getMdiManager().createNewDocumentWindow(windowManager);
        }
    };
    ClientTaskDispatcher.dispatch(requester.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
}

Example 10 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class OutputFunctionsListTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    OutputFunctionContext fc = getOutputFunctionContext();
    SimulationOwner so = null;
    if (fc != null) {
        so = fc.getSimulationOwner();
    }
    if (evt.getSource() == fc && evt.getPropertyName().equals(OutputFunctionContext.PROPERTY_OUTPUT_FUNCTIONS)) {
        setData(outputFunctionContext.getOutputFunctionsList());
    }
    if (evt.getSource() instanceof SimulationContext && evt.getSource() == so && evt.getPropertyName().equals(Model.PROPERTY_NAME_MODEL_ENTITY_NAME)) {
        SimulationContext simulationContext = (SimulationContext) so;
        if (fc.getOutputFunctionsList() == null || fc.getOutputFunctionsList().isEmpty()) {
            return;
        }
        Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
        // 
        // WARNING: this should NOT be used under any circumstance for batch renaming
        // MathDescription, MathMapping, expressions are NOT thread safe
        // 
        AsynchClientTask task0 = new AsynchClientTask("Renaming Functions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                MathMappingCallback callback = new MathMappingCallback() {

                    @Override
                    public void setProgressFraction(float fractionDone) {
                    }

                    @Override
                    public void setMessage(String message) {
                    }

                    @Override
                    public boolean isInterrupted() {
                        return false;
                    }
                };
                MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
                MathDescription mathDesc = null;
                try {
                    mathDesc = mathMapping.getMathDescription(callback);
                } catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
                    e1.printStackTrace();
                }
                String oldName = (String) evt.getOldValue();
                String newName = (String) evt.getNewValue();
                ArrayList<AnnotatedFunction> afList = fc.getOutputFunctionsList();
                List<Expression> changedExpressions = new ArrayList<>();
                for (AnnotatedFunction af : afList) {
                    if (af == null) {
                        continue;
                    }
                    Expression exp = af.getExpression();
                    if (exp == null || exp.getSymbols() == null || exp.getSymbols().length == 0) {
                        continue;
                    }
                    String errMsg = "Failed to rename symbol '" + oldName + "' with '" + newName + "' in the Expression of Function '" + af.getName() + "'.";
                    for (String symbol : exp.getSymbols()) {
                        if (symbol.contentEquals(oldName)) {
                            try {
                                exp.substituteInPlace(new Expression(oldName), new Expression(newName));
                                changedExpressions.add(exp);
                            } catch (ExpressionException e) {
                                e.printStackTrace();
                                throw new RuntimeException(errMsg);
                            }
                        }
                    }
                }
                if (changedExpressions.size() > 0) {
                    try {
                        simulationContext.setMathDescription(mathDesc);
                        for (Expression exp : changedExpressions) {
                            exp.bindExpression(outputFunctionContext);
                        }
                    } catch (ExpressionException | PropertyVetoException e) {
                        e.printStackTrace();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(ownerTable, hashTable, new AsynchClientTask[] { task0 }, false);
    }
    if (evt.getPropertyName().equals(GeometryOwner.PROPERTY_NAME_GEOMETRY)) {
        Geometry oldGeometry = (Geometry) evt.getOldValue();
        Geometry newGeometry = (Geometry) evt.getNewValue();
        // changing from ode to pde
        if (oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            fireTableStructureChanged();
            setData(getOutputFunctionContext().getOutputFunctionsList());
        }
    }
}