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

Example 6 with VCSimulationDataIdentifier

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

the class MathModelWindowManager method simStatusChanged.

/**
 * Insert the method's description here.
 * Creation date: (5/14/2004 11:08:35 AM)
 * @param newMathModel cbit.vcell.mathmodel.MathModel
 */
// private void setMathModel(MathModel newMathModel) {
// resetGeometryListeners((getMathModel() != null?(getMathModel().getMathDescription() != null?getMathModel().getMathDescription().getGeometry():null):null),
// (newMathModel != null?(newMathModel.getMathDescription() != null?newMathModel.getMathDescription().getGeometry():null):null));
// 
// resetMathDescriptionListeners(
// (getMathModel() != null?getMathModel().getMathDescription():null),
// (newMathModel != null?newMathModel.getMathDescription():null));
// if (getMathModel() != null) {
// getMathModel().removePropertyChangeListener(this);
// }
// mathModel = newMathModel;
// if (getMathModel() != null) {
// getMathModel().addPropertyChangeListener(this);
// }
// }
// private void resetMathDescriptionListeners(MathDescription oldMathDescription,MathDescription newMathDescription){
// if(oldMathDescription != null){
// oldMathDescription.removePropertyChangeListener(this);
// }
// if(newMathDescription != null){
// newMathDescription.addPropertyChangeListener(this);
// }
// }
// /**
// * Insert the method's description here.
// * Creation date: (6/14/2004 10:55:40 PM)
// * @param newDocument cbit.vcell.document.VCDocument
// */
// private void showDataViewerPlotsFrame(final javax.swing.JInternalFrame plotFrame) {
// dataViewerPlotsFramesVector.add(plotFrame);
// showFrame(plotFrame);
// plotFrame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() {
// public void internalFrameClosing(javax.swing.event.InternalFrameEvent e) {
// dataViewerPlotsFramesVector.remove(plotFrame);
// }
// });
// }
// /**
// * Insert the method's description here.
// * Creation date: (6/14/2004 10:55:40 PM)
// * @param newDocument cbit.vcell.document.VCDocument
// */
// public void showDataViewerPlotsFrames(javax.swing.JInternalFrame[] plotFrames) {
// for (int i = 0; i < plotFrames.length; i++){
// showDataViewerPlotsFrame(plotFrames[i]);
// }
// }
/**
 * Insert the method's description here.
 * Creation date: (6/9/2004 3:58:21 PM)
 * @param newJobStatus cbit.vcell.messaging.db.SimulationJobStatus
 * @param progress java.lang.Double
 * @param timePoint java.lang.Double
 */
public void simStatusChanged(SimStatusEvent simStatusEvent) {
    // ** events are only generated from server side job statuses **
    KeyValue simKey = simStatusEvent.getVCSimulationIdentifier().getSimulationKey();
    // do we have the sim?
    Simulation[] sims = getMathModel().getSimulations();
    if (sims == null) {
        // we don't have it
        return;
    }
    Simulation simulation = null;
    for (int i = 0; i < sims.length; i++) {
        if (simKey.equals(sims[i].getKey()) || ((sims[i].getSimulationVersion() != null) && simKey.equals(sims[i].getSimulationVersion().getParentSimulationReference()))) {
            simulation = sims[i];
            break;
        }
    }
    if (simulation == null) {
        // we don't have it
        return;
    }
    // we have it; get current server side status
    SimulationStatus simStatus = getRequestManager().getServerSimulationStatus(simulation.getSimulationInfo());
    // if failed, notify
    if (simStatusEvent.isNewFailureEvent()) {
        String qualifier = "";
        if (simulation.getScanCount() > 1) {
            qualifier += "One job from ";
        }
        PopupGenerator.showErrorDialog(this, qualifier + "Simulation '" + simulation.getName() + "' failed\n" + simStatus.getDetails());
    }
    // update status display
    ClientSimManager simManager = simulationWorkspace.getClientSimManager();
    simManager.updateStatusFromServer(simulation);
    // is there new data?
    if (simStatusEvent.isNewDataEvent()) {
        fireNewData(new DataEvent(this, new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), simStatusEvent.getJobIndex())));
    }
}

Example 7 with VCSimulationDataIdentifier

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

the class ExportServiceImpl method fireExportCompleted.

/**
 * Insert the method's description here.
 * Creation date: (4/1/2001 11:20:45 AM)
 * @deprecated
 */
protected ExportEvent fireExportCompleted(long jobID, VCDataIdentifier vcdID, String format, String location, ExportSpecs exportSpecs) {
    User user = null;
    Object object = jobRequestIDs.get(new Long(jobID));
    if (object != null) {
        user = (User) object;
    }
    TimeSpecs timeSpecs = (exportSpecs != null) ? exportSpecs.getTimeSpecs() : (null);
    VariableSpecs varSpecs = (exportSpecs != null) ? exportSpecs.getVariableSpecs() : (null);
    final KeyValue dataKey;
    if (vcdID instanceof VCSimulationDataIdentifier) {
        dataKey = ((VCSimulationDataIdentifier) vcdID).getSimulationKey();
    } else if (vcdID instanceof ExternalDataIdentifier) {
        dataKey = ((ExternalDataIdentifier) vcdID).getSimulationKey();
    } else {
        throw new RuntimeException("unexpected VCDataIdentifier");
    }
    ExportEvent event = new ExportEvent(this, jobID, user, vcdID.getID(), dataKey, ExportEvent.EXPORT_COMPLETE, format, location, null, timeSpecs, varSpecs);
    fireExportEvent(event);
    return event;
}

Example 8 with VCSimulationDataIdentifier

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

the class FiniteVolumeFileWriter method writeFieldData.

/**
 * # Field Data
 * FIELD_DATA_BEGIN
 * #id, name, varname, time filename
 * 0 _VCell_FieldData_0 FRAP_binding_ALPHA rfB 0.1 \\users\\fgao\\SimID_22489731_0_FRAP_binding_ALPHA_rfB_0_1.fdat
 * FIELD_DATA_END
 * @throws FileNotFoundException
 * @throws ExpressionException
 * @throws DataAccessException
 */
private void writeFieldData() throws FileNotFoundException, ExpressionException, DataAccessException {
    FieldDataIdentifierSpec[] fieldDataIDSpecs = simTask.getSimulationJob().getFieldDataIdentifierSpecs();
    if (fieldDataIDSpecs == null || fieldDataIDSpecs.length == 0) {
        return;
    }
    String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
    DataSetControllerImpl dsci = new DataSetControllerImpl(null, workingDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
    printWriter.println("# Field Data");
    printWriter.println("FIELD_DATA_BEGIN");
    printWriter.println("#id, type, new name, name, varname, time, filename");
    FieldFunctionArguments psfFieldFunc = null;
    Variable var = simTask.getSimulationJob().getSimulationSymbolTable().getVariable(Simulation.PSF_FUNCTION_NAME);
    if (var != null) {
        FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(var.getExpression());
        if (ffas == null || ffas.length == 0) {
            throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
        } else {
            Expression newexp = new Expression(ffas[0].infix());
            if (!var.getExpression().compareEqual(newexp)) {
                throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
            }
            psfFieldFunc = ffas[0];
        }
    }
    int index = 0;
    HashSet<FieldDataIdentifierSpec> uniqueFieldDataIDSpecs = new HashSet<FieldDataIdentifierSpec>();
    uniqueFieldDataNSet = new HashSet<FieldDataNumerics>();
    for (int i = 0; i < fieldDataIDSpecs.length; i++) {
        if (!uniqueFieldDataIDSpecs.contains(fieldDataIDSpecs[i])) {
            FieldFunctionArguments ffa = fieldDataIDSpecs[i].getFieldFuncArgs();
            File newResampledFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName((VCSimulationDataIdentifier) simTask.getSimulationJob().getVCDataIdentifier(), fieldDataIDSpecs[i].getFieldFuncArgs()));
            uniqueFieldDataIDSpecs.add(fieldDataIDSpecs[i]);
            VariableType varType = fieldDataIDSpecs[i].getFieldFuncArgs().getVariableType();
            SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fieldDataIDSpecs[i].getExternalDataIdentifier(), fieldDataIDSpecs[i].getFieldFuncArgs().getVariableName(), fieldDataIDSpecs[i].getFieldFuncArgs().getTime().evaluateConstant());
            VariableType dataVarType = simDataBlock.getVariableType();
            if (varType.equals(VariableType.UNKNOWN)) {
                varType = dataVarType;
            } else if (!varType.equals(dataVarType)) {
                throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
            }
            if (psfFieldFunc != null && psfFieldFunc.equals(ffa)) {
                psfFieldIndex = index;
            }
            String fieldDataID = "_VCell_FieldData_" + index;
            printWriter.println(index + " " + varType.getTypeName() + " " + fieldDataID + " " + ffa.getFieldName() + " " + ffa.getVariableName() + " " + ffa.getTime().infix() + " " + newResampledFieldDataFile);
            uniqueFieldDataNSet.add(new FieldDataNumerics(SimulationData.createCanonicalFieldFunctionSyntax(ffa.getFieldName(), ffa.getVariableName(), ffa.getTime().evaluateConstant(), ffa.getVariableType().getTypeName()), fieldDataID));
            index++;
        }
    }
    if (psfFieldIndex >= 0) {
        printWriter.println("PSF_FIELD_DATA_INDEX " + psfFieldIndex);
    }
    printWriter.println("FIELD_DATA_END");
    printWriter.println();
}

Example 9 with VCSimulationDataIdentifier

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

the class ClientPDEDataContext method setDataManager.

/**
 * Insert the method's description here.
 * Creation date: (10/3/00 5:03:43 PM)
 */
// public abstract void refreshIdentifiers();
/**
 * This method is called from SimResultsViewer.updateScanParamChoices(),
 * which is going to update results view upon a choice of scanned parameters.
 */
public void setDataManager(PDEDataManager newDataManager) throws DataAccessException {
    VCDataIdentifier oldid = dataManager.getVCDataIdentifier();
    VCDataIdentifier newid = newDataManager.getVCDataIdentifier();
    if (oldid instanceof VCSimulationDataIdentifier && newid instanceof VCSimulationDataIdentifier && ((VCSimulationDataIdentifier) oldid).getVcSimID().equals(((VCSimulationDataIdentifier) newid).getVcSimID())) {
        PDEDataManager oldPDataManager = dataManager;
        dataManager = newDataManager;
        DataIdentifier[] dis = getDataManager().getDataIdentifiers();
        double[] times = getDataManager().getDataSetTimes();
        setDataIdentifiers(dis);
        setTimePoints(times);
        externalRefresh();
        setVCDataIdentifier(dataManager.getVCDataIdentifier());
        firePropertyChange(SimDataConstants.PDE_DATA_MANAGER_CHANGED, oldPDataManager, newDataManager);
    } else {
        throw new RuntimeException("DataManager change not allowed: oldID = " + oldid + " newID = " + newid);
    }
}

Example 10 with VCSimulationDataIdentifier

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

the class DataSetControllerImpl method fieldFunctionSubstitution.

private Expression fieldFunctionSubstitution(OutputContext outputContext, final VCDataIdentifier vcdID, Expression functionExpression) throws ExpressionException, DataAccessException, IOException, MathException {
    SimResampleInfoProvider simResampleInfoProvider = null;
    Expression origExpression = new Expression(functionExpression);
    if (vcdID instanceof VCSimulationDataIdentifier) {
        simResampleInfoProvider = ((VCSimulationDataIdentifier) vcdID);
    } else if (vcdID instanceof VCSimulationDataIdentifierOldStyle) {
        simResampleInfoProvider = ((VCSimulationDataIdentifierOldStyle) vcdID);
    } else if (vcdID instanceof ExternalDataIdentifier) {
        simResampleInfoProvider = ((ExternalDataIdentifier) vcdID);
    } else {
        return origExpression;
    }
    FieldFunctionArguments[] fieldfuncArgumentsArr = FieldUtilities.getFieldFunctionArguments(origExpression);
    if (fieldfuncArgumentsArr == null || fieldfuncArgumentsArr.length == 0) {
        return origExpression;
    }
    String[] origSymbols = origExpression.getSymbols();
    Vector<SymbolTableEntry> originalSymbolTablEntrryV = new Vector<SymbolTableEntry>();
    for (int i = 0; origSymbols != null && i < origSymbols.length; i++) {
        if (!originalSymbolTablEntrryV.contains(origExpression.getSymbolBinding(origSymbols[i]))) {
            originalSymbolTablEntrryV.add(origExpression.getSymbolBinding(origSymbols[i]));
        }
    }
    Expression exp = new Expression(origExpression);
    // 
    // Handle Field Data Function field(...)
    // 
    double[][] resampledFieldDatas = null;
    HashMap<String, Integer> substSymbolIndexH = new HashMap<String, Integer>();
    // if(fieldfuncArgumentsArr != null && fieldfuncArgumentsArr.length > 0){
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecArr = getFieldDataIdentifierSpecs(fieldfuncArgumentsArr, simResampleInfoProvider.getOwner());
    // Substitute Field Data Functions for simple symbols for lookup-------
    for (int i = 0; i < fieldfuncArgumentsArr.length; i += 1) {
        for (int j = 0; j < fieldDataIdentifierSpecArr.length; j++) {
            if (fieldfuncArgumentsArr[i].equals(fieldDataIdentifierSpecArr[j].getFieldFuncArgs())) {
                String substFieldName = fieldfuncArgumentsArr[i].getFieldName() + "_" + fieldfuncArgumentsArr[i].getVariableName() + "_" + fieldfuncArgumentsArr[i].getTime().evaluateConstant();
                substFieldName = TokenMangler.fixTokenStrict(substFieldName);
                if (exp.hasSymbol(substFieldName)) {
                    throw new DataAccessException("Substitute Field data name is not unique");
                }
                String fieldFuncString = SimulationData.createCanonicalFieldFunctionSyntax(fieldDataIdentifierSpecArr[j].getExternalDataIdentifier().getName(), fieldfuncArgumentsArr[i].getVariableName(), fieldfuncArgumentsArr[i].getTime().evaluateConstant(), fieldfuncArgumentsArr[i].getVariableType().getTypeName());
                exp.substituteInPlace(new Expression(fieldFuncString), new Expression(substFieldName));
                substSymbolIndexH.put(substFieldName, i);
                break;
            }
        }
    }
    // ----------------------------------------------------------------------
    boolean[] bResample = new boolean[fieldDataIdentifierSpecArr.length];
    Arrays.fill(bResample, true);
    writeFieldFunctionData(outputContext, fieldDataIdentifierSpecArr, bResample, getMesh(simResampleInfoProvider), simResampleInfoProvider, getMesh(simResampleInfoProvider).getNumMembraneElements(), FVSolverStandalone.HESM_KEEP_AND_CONTINUE);
    resampledFieldDatas = new double[fieldfuncArgumentsArr.length][];
    for (int i = 0; i < fieldfuncArgumentsArr.length; i += 1) {
        // File resampledFile =
        // new File(getUserDir(vcsdID.getOwner()),
        // vcsdID.getID()+
        // FieldDataIdentifierSpec.getDefaultFieldDataFileNameForSimulation(fieldfuncArgumentsArr[i])
        // );
        // File resampledFile = new File(getPrimaryUserDir(simResampleInfoProvider.getOwner(), true),
        // SimulationData.createCanonicalResampleFileName(
        // simResampleInfoProvider, fieldfuncArgumentsArr[i]));
        File resampledFile = ((SimulationData) getVCData(simResampleInfoProvider)).getFieldDataFile(simResampleInfoProvider, fieldfuncArgumentsArr[i]);
        resampledFieldDatas[i] = DataSet.fetchSimData(fieldfuncArgumentsArr[i].getVariableName(), resampledFile);
    }
    // }
    // Rebind all the symbols
    String[] dependentIDs = exp.getSymbols();
    VariableSymbolTable varSymbolTable = new VariableSymbolTable();
    for (int i = 0; dependentIDs != null && i < dependentIDs.length; i++) {
        SymbolTableEntry newSymbolTableEntry = null;
        for (int j = 0; j < originalSymbolTablEntrryV.size(); j++) {
            if (originalSymbolTablEntrryV.elementAt(j).getName().equals(dependentIDs[i])) {
                newSymbolTableEntry = originalSymbolTablEntrryV.elementAt(j);
                break;
            }
        }
        if (newSymbolTableEntry == null) {
            if (substSymbolIndexH.containsKey(dependentIDs[i])) {
                int resampledDataIndex = substSymbolIndexH.get(dependentIDs[i]).intValue();
                FieldDataParameterVariable fieldDataParameterVariable = new FieldDataParameterVariable(dependentIDs[i], resampledFieldDatas[resampledDataIndex]);
                newSymbolTableEntry = fieldDataParameterVariable;
            }
        }
        if (newSymbolTableEntry == null) {
            throw new DataAccessException("Field Data Couldn't find substituted expression while evaluating function");
        }
        varSymbolTable.addVar(newSymbolTableEntry);
    }
    exp.bindExpression(varSymbolTable);
    return exp;
}