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

Example 1 with Electrode

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

the class ElectrodePanel method setelectrode1.

/**
 * Set the electrode1 to a new value.
 * @param newValue cbit.vcell.mapping.Electrode
 */
private void setelectrode1(Electrode newValue) {
    if (ivjelectrode1 != newValue) {
        try {
            Electrode oldValue = getelectrode1();
            /* Stop listening for events from the current object */
            if (ivjelectrode1 != null) {
                ivjelectrode1.removePropertyChangeListener(ivjEventHandler);
            }
            ivjelectrode1 = newValue;
            /* Listen for events from the new object */
            if (ivjelectrode1 != null) {
                ivjelectrode1.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            connEtoM5(ivjelectrode1);
            firePropertyChange("electrode", oldValue, newValue);
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
    ;
}

Example 2 with Electrode

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

the class ElectrodePanel method setElectrode.

/**
 * Sets the electrode property (cbit.vcell.mapping.Electrode) value.
 * @param electrode The new value for the property.
 * @see #getElectrode
 */
public void setElectrode(Electrode electrode) {
    Electrode oldValue = fieldElectrode;
    fieldElectrode = electrode;
    firePropertyChange("electrode", oldValue, electrode);
}

Example 3 with Electrode

use of cbit.vcell.mapping.Electrode 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 4 with Electrode

use of cbit.vcell.mapping.Electrode 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 5 with Electrode

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

the class PotentialMapping 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
 */
private static Graph getCircuitGraph(SimulationContext simContext, MathMapping_4_8 mathMapping_4_8) 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_4_8);
            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_4_8);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    StructureTopology structTopology = simContext.getModel().getStructureTopology();
    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);
            // if (!membraneMapping.getResolved()){
            Feature insideFeature = structTopology.getInsideFeature(membrane);
            Feature outsideFeature = structTopology.getOutsideFeature(membrane);
            if (insideFeature != null && outsideFeature != null) {
                Node insideNode = graph.getNode(insideFeature.getName());
                Node outsideNode = graph.getNode(outsideFeature.getName());
                // double capacitance = getTotalMembraneCapacitance(simContext,membrane).evaluateConstant();
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping_4_8);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping_4_8);
                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_4_8);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}