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

Example 1 with CurrentDensityClampStimulus

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

the class XmlReader method getElectricalStimulus.

/**
 * This method process Electrical Stimulus, also called Clamps.
 * Creation date: (6/6/2002 4:46:18 PM)
 * @return cbit.vcell.mapping.ElectricalStimulus
 * @param param org.jdom.Element
 */
private ElectricalStimulus getElectricalStimulus(Element param, SimulationContext currentSimulationContext) throws XmlParseException {
    ElectricalStimulus clampStimulus = null;
    // get name
    // String name = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // get Electrode
    Electrode electrode = getElectrode(param.getChild(XMLTags.ElectrodeTag, vcNamespace), currentSimulationContext);
    if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.VoltageClampTag)) {
        // is a voltage clamp
        clampStimulus = new VoltageClampStimulus(electrode, "voltClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag) || param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.CurrentDensityClampTag_oldName)) {
        // is a current density clamp
        clampStimulus = new CurrentDensityClampStimulus(electrode, "currDensityClampElectrode", new Expression(0.0), currentSimulationContext);
    } else if (param.getAttributeValue(XMLTags.TypeAttrTag).equalsIgnoreCase(XMLTags.TotalCurrentClampTag)) {
        // is a "total" current clamp
        clampStimulus = new TotalCurrentClampStimulus(electrode, "totalCurrClampElectrode", new Expression(0.0), currentSimulationContext);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        clampStimulus.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in the electrical stimulus.
        VariableHash varHash = new VariableHash();
        Model model = currentSimulationContext.getModel();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    Domain domain = null;
                    varHash.addVariable(new Function(paramName, paramExp, domain));
                } else {
                    if (model.getReservedSymbolByName(paramName) != null) {
                        varHash.removeVariable(paramName);
                        Domain domain = null;
                        varHash.addVariable(new Function(paramName, paramExp, domain));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies:", e);
            }
            LocalParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                if (role.equals(XMLTags.ParamRoleTotalCurrentTag)) {
                    if (clampStimulus instanceof TotalCurrentClampStimulus) {
                        tempParam = ((TotalCurrentClampStimulus) clampStimulus).getCurrentParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRoleTotalCurrentDensityTag) || role.equals(XMLTags.ParamRoleTotalCurrentDensityOldNameTag)) {
                    if (clampStimulus instanceof CurrentDensityClampStimulus) {
                        tempParam = ((CurrentDensityClampStimulus) clampStimulus).getCurrentDensityParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                } else if (role.equals(XMLTags.ParamRolePotentialDifferenceTag)) {
                    if (clampStimulus instanceof VoltageClampStimulus) {
                        tempParam = ((VoltageClampStimulus) clampStimulus).getVoltageParameter();
                    } else {
                        varHash.removeVariable(paramName);
                        continue;
                    }
                }
            } else {
                continue;
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in electricalstimulus");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                LocalParameter multNameParam = clampStimulus.getLocalParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    clampStimulus.renameParameter(paramName, tempName);
                    multNameParam = clampStimulus.getLocalParameter(tempName);
                }
                clampStimulus.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            clampStimulus.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = clampStimulus.getLocalParameter(paramFunction.getName());
                if (tempParam == null) {
                    clampStimulus.addUserDefinedParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        clampStimulus.setParameterValue(tempParam, paramFunction.getExpression());
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for simContext : " + currentSimulationContext.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for simContext : " + currentSimulationContext.getName(), e);
    } finally {
        clampStimulus.reading(false);
    }
    return clampStimulus;
}

Example 2 with CurrentDensityClampStimulus

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of an Electrode.
 * Creation date: (6/6/2002 2:32:56 PM)
 * @return Element
 * @param param cbit.vcell.mapping.Electrode
 */
private Element getXML(ElectricalStimulus param) {
    String electricalStimulusType = null;
    if (param instanceof VoltageClampStimulus) {
        // process a VoltageClampStimulus object
        electricalStimulusType = XMLTags.VoltageClampTag;
    } else if (param instanceof CurrentDensityClampStimulus) {
        // Process a CurrentClampStimulus
        electricalStimulusType = XMLTags.CurrentDensityClampTag;
    } else if (param instanceof TotalCurrentClampStimulus) {
        // Process a CurrentClampStimulus
        electricalStimulusType = XMLTags.TotalCurrentClampTag;
    }
    Element electricalStimulus = new Element(XMLTags.ClampTag);
    // Need to add electrode ??
    Element electrode = getXML(param.getElectrode());
    electricalStimulus.addContent(electrode);
    // Add attributes
    electricalStimulus.setAttribute(XMLTags.TypeAttrTag, electricalStimulusType);
    // Add Kinetics Parameters
    LocalParameter[] parameters = param.getLocalParameters();
    for (int i = 0; i < parameters.length; i++) {
        LocalParameter parm = parameters[i];
        Element tempparameter = new Element(XMLTags.ParameterTag);
        // Get parameter attributes
        tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
        tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, ((ElectricalStimulusParameterType) parm.getRole()).roleDescription);
        VCUnitDefinition unit = parm.getUnitDefinition();
        if (unit != null) {
            tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
        }
        tempparameter.addContent(mangleExpression(parm.getExpression()));
        // Add the parameter to the general electricalstimulus object
        electricalStimulus.addContent(tempparameter);
    }
    return electricalStimulus;
}

Example 3 with CurrentDensityClampStimulus

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

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 4 with CurrentDensityClampStimulus

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

the class ITextWriter method writeMembraneMapping.

protected void writeMembraneMapping(Section simContextSection, SimulationContext simContext) throws DocumentException {
    GeometryContext geoContext = simContext.getGeometryContext();
    if (geoContext == null) {
        return;
    }
    Section memMapSection = null;
    Table memMapTable = null;
    StructureMapping[] structMappings = geoContext.getStructureMappings();
    for (int i = 0; i < structMappings.length; i++) {
        MembraneMapping memMapping = null;
        if (structMappings[i] instanceof FeatureMapping) {
            continue;
        } else {
            memMapping = (MembraneMapping) structMappings[i];
        }
        String structName = memMapping.getStructure().getName();
        String initVoltage = "";
        Expression tempExp = memMapping.getInitialVoltageParameter().getExpression();
        VCUnitDefinition tempUnit = memMapping.getInitialVoltageParameter().getUnitDefinition();
        if (tempExp != null) {
            initVoltage = tempExp.infix();
            if (tempUnit != null) {
                initVoltage += "   " + tempUnit.getSymbolUnicode();
            }
        }
        String spCap = "";
        tempExp = memMapping.getSpecificCapacitanceParameter().getExpression();
        tempUnit = memMapping.getSpecificCapacitanceParameter().getUnitDefinition();
        if (tempExp != null) {
            spCap = tempExp.infix();
            if (tempUnit != null) {
                spCap += "   " + tempUnit.getSymbolUnicode();
            }
        }
        if (memMapTable == null) {
            memMapTable = getTable(4, 100, 1, 3, 3);
            memMapTable.addCell(createCell("Electrical Mapping - Membrane Potential", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
            memMapTable.addCell(createHeaderCell("Membrane", getBold(), 1));
            memMapTable.addCell(createHeaderCell("Calculate V (T/F)", getBold(), 1));
            memMapTable.addCell(createHeaderCell("V initial", getBold(), 1));
            memMapTable.addCell(createHeaderCell("Specific Capacitance", getBold(), 1));
            memMapTable.endHeaders();
        }
        memMapTable.addCell(createCell(structName, getFont()));
        memMapTable.addCell(createCell((memMapping.getCalculateVoltage() ? " T " : " F "), getFont()));
        memMapTable.addCell(createCell(initVoltage, getFont()));
        memMapTable.addCell(createCell(spCap, getFont()));
    }
    if (memMapTable != null) {
        memMapSection = simContextSection.addSection("Membrane Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        memMapSection.add(memMapTable);
    }
    int[] widths = { 1, 1, 1, 5, 8 };
    Table electTable = null;
    ElectricalStimulus[] electricalStimuli = simContext.getElectricalStimuli();
    for (int j = 0; j < electricalStimuli.length; j++) {
        if (j == 0) {
            electTable = getTable(5, 100, 1, 3, 3);
            electTable.addCell(createCell("Electrical Mapping - Electrical Stimulus", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            electTable.addCell(createHeaderCell("Stimulus Name", getBold(), 1));
            electTable.addCell(createHeaderCell("Current Name", getBold(), 1));
            electTable.addCell(createHeaderCell("Clamp Type", getBold(), 1));
            electTable.addCell(createHeaderCell("Voltage/Current Density", getBold(), 1));
            electTable.addCell(createHeaderCell("Clamp Device", getBold(), 1));
            electTable.endHeaders();
        }
        String stimName = electricalStimuli[j].getName();
        String currName = "";
        String clampType = "", expStr = "";
        Expression tempExp = null;
        VCUnitDefinition tempUnit = null;
        if (electricalStimuli[j] instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus stimulus = (CurrentDensityClampStimulus) electricalStimuli[j];
            LocalParameter currentDensityParameter = stimulus.getCurrentDensityParameter();
            tempExp = currentDensityParameter.getExpression();
            tempUnit = currentDensityParameter.getUnitDefinition();
            clampType = "Current Density (deprecated)";
        } else if (electricalStimuli[j] instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus stimulus = (TotalCurrentClampStimulus) electricalStimuli[j];
            LocalParameter totalCurrentParameter = stimulus.getCurrentParameter();
            tempExp = totalCurrentParameter.getExpression();
            tempUnit = totalCurrentParameter.getUnitDefinition();
            clampType = "Current";
        } else if (electricalStimuli[j] instanceof VoltageClampStimulus) {
            VoltageClampStimulus stimulus = (VoltageClampStimulus) electricalStimuli[j];
            Parameter voltageParameter = stimulus.getVoltageParameter();
            tempExp = voltageParameter.getExpression();
            tempUnit = voltageParameter.getUnitDefinition();
            clampType = "Voltage";
        }
        if (tempExp != null) {
            expStr = tempExp.infix();
            if (tempUnit != null) {
                expStr += "   " + tempUnit.getSymbolUnicode();
            }
        }
        electTable.addCell(createCell(stimName, getFont()));
        electTable.addCell(createCell(currName, getFont()));
        electTable.addCell(createCell(clampType, getFont()));
        electTable.addCell(createCell(expStr, getFont()));
        // add electrode info
        Electrode electrode = electricalStimuli[j].getElectrode();
        if (electrode == null) {
            electTable.addCell(createCell("N/A", getFont()));
        } else {
            Coordinate c = electrode.getPosition();
            String location = c.getX() + ", " + c.getY() + ", " + c.getZ();
            String featureName = electrode.getFeature().getName();
            electTable.addCell(createCell("(" + location + ") in " + featureName, getFont()));
        }
    }
    if (electTable != null) {
        if (memMapSection == null) {
            memMapSection = simContextSection.addSection("Membrane Mapping For " + simContext.getName(), 1);
        }
        electTable.setWidths(widths);
        memMapSection.add(electTable);
    }
    // add temperature
    Table tempTable = getTable(1, 75, 1, 3, 3);
    tempTable.setAlignment(Table.ALIGN_LEFT);
    tempTable.addCell(createCell("Temperature: " + simContext.getTemperatureKelvin() + " K", getFont()));
    if (memMapSection != null) {
        memMapSection.add(tempTable);
    }
}

Example 5 with CurrentDensityClampStimulus

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

the class ElectricalStimulusPanel method newStimulus.

/**
 * Comment
 */
private void newStimulus() {
    try {
        SimulationContext simContext = getSimulationContext();
        if (simContext == null) {
            return;
        }
        // 
        // When the voltage and current clamp radio buttons is deselected within the same simulation context (application),
        // display a warning saying that the present clamp settings will be lost (not applicable when the 'no clamp'
        // radiobutton is deselected.
        // 
        ElectricalStimulus currElectricalStimulus = null;
        if (simContext.getElectricalStimuli() != null && simContext.getElectricalStimuli().length > 0) {
            currElectricalStimulus = simContext.getElectricalStimuli()[0];
        }
        // 
        // ignore selection if already selected
        // warn upon deselect if about to loose edits
        // 
        Clamp selectedClamp = (Clamp) clampComboBox.getSelectedItem();
        if (currElectricalStimulus instanceof VoltageClampStimulus) {
            if (selectedClamp == Clamp.Voltage_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present voltage clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Voltage Clamp
                clampComboBox.setSelectedItem(Clamp.Voltage_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof TotalCurrentClampStimulus) {
            if (selectedClamp == Clamp.Total_Current_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Total_Current_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof CurrentDensityClampStimulus) {
            if (selectedClamp == Clamp.Current_Density_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Current_Density_Clamp);
                return;
            }
        }
        if (currElectricalStimulus == null && selectedClamp == Clamp.No_Clamp) {
            return;
        }
        StructureTopology structTopology = getSimulationContext().getModel().getStructureTopology();
        Structure[] structures = getSimulationContext().getModel().getStructures();
        ArrayList<Feature> features = new ArrayList<Feature>();
        for (Structure structure : structures) {
            if (structure instanceof Feature) {
                features.add((Feature) structure);
            }
        }
        if (features.size() < 2) {
            PopupGenerator.showErrorDialog(this, "error: electrodes must be placed in distinct volumetric structures, found " + features.size() + " volumetric structures in model");
            return;
        }
        Feature groundFeature = features.get(0);
        Feature clampedFeature = features.get(1);
        // 
        if (selectedClamp == Clamp.Total_Current_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof TotalCurrentClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                TotalCurrentClampStimulus ccStimulus = new TotalCurrentClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.Current_Density_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof CurrentDensityClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                CurrentDensityClampStimulus ccStimulus = new CurrentDensityClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.No_Clamp) {
            if (simContext.getElectricalStimuli().length > 0) {
                simContext.setElectricalStimuli(new ElectricalStimulus[0]);
            }
        }
        // 
        if (selectedClamp == Clamp.Voltage_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof VoltageClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                VoltageClampStimulus vcStimulus = new VoltageClampStimulus(probeElectrode, "vcElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { vcStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        PopupGenerator.showErrorDialog(this, "Error setting electrical stimulus: " + e.getMessage());
    }
}