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

Example 16 with MembraneMapping

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

the class StructureMappingTableModel method isCellEditable.

/**
 * Insert the method's description here.
 * Creation date: (2/24/01 12:27:46 AM)
 * @return boolean
 * @param rowIndex int
 * @param columnIndex int
 */
public boolean isCellEditable(int rowIndex, int columnIndex) {
    if (getGeometryContext() == null) {
        return false;
    }
    StructureMapping sm = getGeometryContext().getStructureMapping(rowIndex);
    if (bNonSpatial) {
        if (columnIndex == NONSPATIAL_COLUMN_SIZE) {
            // feature size are editable
            return true;
        }
        return false;
    } else {
        // 
        if (columnIndex == SPATIAL_COLUMN_SUBDOMAIN) {
            return ((sm instanceof FeatureMapping) || (sm instanceof MembraneMapping));
        }
        if (columnIndex == SPATIAL_COLUMN_SIZERATIO) {
            GeometryClass gc = sm.getGeometryClass();
            StructureMapping[] structureMappings = getGeometryContext().getStructureMappings(gc);
            boolean bDimensionless = sm.getUnitSizeParameter() != null && sm.getUnitSizeParameter().getUnitDefinition() != null && sm.getUnitSizeParameter().getUnitDefinition().isEquivalent(getGeometryContext().getModel().getUnitSystem().getInstance_DIMENSIONLESS());
            return (structureMappings != null && structureMappings.length > 1) || !bDimensionless;
        }
        // some boundary conditions are editable
        if ((columnIndex >= SPATIAL_COLUMN_X_MINUS) && (columnIndex <= SPATIAL_COLUMN_Z_PLUS)) {
            if (sm.getGeometryClass() instanceof SurfaceClass) {
                return false;
            }
            return true;
        }
    }
    return false;
}

Example 17 with MembraneMapping

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

the class ElectricalMembraneMappingTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    MembraneMapping membraneMapping = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_CALCULATE_POTENTIAL:
            {
                boolean bCalculatePotential = ((Boolean) aValue).booleanValue();
                membraneMapping.setCalculateVoltage(bCalculatePotential);
                fireTableRowsUpdated(rowIndex, rowIndex);
                break;
            }
        case COLUMN_INITIAL_POTENTIAL:
            {
                Expression newExpression = null;
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        newExpression = new Expression(newExpressionString);
                    }
                    membraneMapping.getInitialVoltageParameter().setExpression(newExpression);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
        case COLUMN_SPECIFIC_CAPACITANCE:
            {
                Expression newExpression = null;
                try {
                    if (aValue instanceof String) {
                        String newExpressionString = (String) aValue;
                        newExpression = new Expression(newExpressionString);
                    } else if (aValue instanceof ScopedExpression) {
                        // newExpression = ((ScopedExpression)aValue).getExpression();
                        throw new RuntimeException("unexpected value type ScopedExpression");
                    }
                    membraneMapping.getSpecificCapacitanceParameter().setExpression(newExpression);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            }
    }
}

Example 18 with MembraneMapping

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

the class ElectricalMembraneMappingTableModel method setGeometryContext.

/**
 * Sets the geometryContext property (cbit.vcell.mapping.GeometryContext) value.
 * @param geometryContext The new value for the property.
 * @see #getGeometryContext
 */
public void setGeometryContext(GeometryContext geometryContext) {
    GeometryContext oldValue = fieldGeometryContext;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        StructureMapping[] oldStructureMappings = oldValue.getStructureMappings();
        for (int i = 0; i < oldStructureMappings.length; i++) {
            if (oldStructureMappings[i] instanceof MembraneMapping) {
                oldStructureMappings[i].removePropertyChangeListener(this);
            }
        }
    }
    fieldGeometryContext = geometryContext;
    if (geometryContext != null) {
        geometryContext.addPropertyChangeListener(this);
        StructureMapping[] newStructureMappings = geometryContext.getStructureMappings();
        for (int i = 0; i < newStructureMappings.length; i++) {
            if (newStructureMappings[i] instanceof MembraneMapping) {
                newStructureMappings[i].addPropertyChangeListener(this);
            }
        }
    }
    refreshData();
}

Example 19 with MembraneMapping

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

the class CurrentClampElectricalDevice method initializeParameters.

private void initializeParameters() throws ExpressionException {
    ElectricalDevice.ElectricalDeviceParameter[] parameters = new ElectricalDevice.ElectricalDeviceParameter[3];
    // 
    // set the transmembrane current (total current, if necessary derive it from the current density).
    // 
    ElectricalDeviceParameter transMembraneCurrent = null;
    ModelUnitSystem modelUnitSystem = mathMapping.getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition currentUnit = modelUnitSystem.getCurrentUnit();
    if (currentClampStimulus instanceof TotalCurrentClampStimulus) {
        TotalCurrentClampStimulus stimulus = (TotalCurrentClampStimulus) currentClampStimulus;
        LocalParameter currentParameter = stimulus.getCurrentParameter();
        transMembraneCurrent = new ElectricalDeviceParameter(DefaultNames[ROLE_TransmembraneCurrent], new Expression(currentParameter.getExpression()), ROLE_TransmembraneCurrent, currentUnit);
    } else if (currentClampStimulus instanceof CurrentDensityClampStimulus) {
        CurrentDensityClampStimulus stimulus = (CurrentDensityClampStimulus) currentClampStimulus;
        LocalParameter currentDensityParameter = stimulus.getCurrentDensityParameter();
        // 
        // here we have to determine the expression for current (from current density).
        // 
        Feature feature1 = currentClampStimulus.getElectrode().getFeature();
        Feature feature2 = mathMapping.getSimulationContext().getGroundElectrode().getFeature();
        Membrane membrane = null;
        StructureTopology structTopology = mathMapping.getSimulationContext().getModel().getStructureTopology();
        if (structTopology.getParentStructure(feature1) != null && structTopology.getOutsideFeature((Membrane) structTopology.getParentStructure(feature1)) == feature2) {
            membrane = ((Membrane) structTopology.getParentStructure(feature1));
        } else if (structTopology.getParentStructure(feature2) != null && structTopology.getOutsideFeature((Membrane) structTopology.getParentStructure(feature2)) == feature1) {
            membrane = ((Membrane) structTopology.getParentStructure(feature2));
        }
        if (membrane == null) {
            throw new RuntimeException("current clamp based on current density crosses multiple membranes, unable to " + "determine single membrane to convert current density into current in Application '" + mathMapping.getSimulationContext().getName() + "'.");
        }
        MembraneMapping membraneMapping = (MembraneMapping) mathMapping.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
        StructureMappingParameter sizeParameter = membraneMapping.getSizeParameter();
        Expression area = null;
        if (mathMapping.getSimulationContext().getGeometry().getDimension() == 0 && (sizeParameter.getExpression() == null || sizeParameter.getExpression().isZero())) {
            area = membraneMapping.getNullSizeParameterValue();
        } else {
            area = new Expression(sizeParameter, mathMapping.getNameScope());
        }
        transMembraneCurrent = new ElectricalDeviceParameter(DefaultNames[ROLE_TransmembraneCurrent], Expression.mult(new Expression(currentDensityParameter.getExpression()), area), ROLE_TransmembraneCurrent, currentUnit);
    } else {
        throw new RuntimeException("unexpected current clamp stimulus type : " + currentClampStimulus.getClass().getName());
    }
    ElectricalDeviceParameter totalCurrent = new ElectricalDeviceParameter(DefaultNames[ROLE_TotalCurrent], new Expression(transMembraneCurrent, getNameScope()), ROLE_TotalCurrent, currentUnit);
    ElectricalDeviceParameter voltage = new ElectricalDeviceParameter(DefaultNames[ROLE_Voltage], null, ROLE_Voltage, modelUnitSystem.getVoltageUnit());
    parameters[0] = totalCurrent;
    parameters[1] = transMembraneCurrent;
    parameters[2] = voltage;
    // 
    // add any user-defined parameters
    // 
    LocalParameter[] stimulusParameters = currentClampStimulus.getLocalParameters();
    for (int i = 0; stimulusParameters != null && i < stimulusParameters.length; i++) {
        if (stimulusParameters[i].getRole() == ElectricalStimulus.ElectricalStimulusParameterType.UserDefined) {
            ElectricalDeviceParameter newParam = new ElectricalDeviceParameter(stimulusParameters[i].getName(), new Expression(stimulusParameters[i].getExpression()), ROLE_UserDefined, stimulusParameters[i].getUnitDefinition());
            parameters = (ElectricalDeviceParameter[]) BeanUtils.addElement(parameters, newParam);
        }
    }
    setParameters(parameters);
}

Example 20 with MembraneMapping

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

the class ElectricalCircuitGraph method getTotalMembraneCurrent.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 12:56:13 PM)
 * @return cbit.vcell.parser.Expression
 * @param simContext cbit.vcell.mapping.SimulationContext
 * @param membrane cbit.vcell.model.Membrane
 */
private static Expression getTotalMembraneCurrent(SimulationContext simContext, Membrane membrane, AbstractMathMapping mathMapping) throws ExpressionException {
    MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
    if (!membraneMapping.getCalculateVoltage()) {
        return new Expression(0.0);
    }
    // 
    // gather current terms
    // 
    Expression currentExp = new Expression(0.0);
    ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
    StructureMappingParameter sizeParameter = membraneMapping.getSizeParameter();
    Expression area = null;
    if (simContext.getGeometry().getDimension() == 0 && (sizeParameter.getExpression() == null || sizeParameter.getExpression().isZero())) {
        System.out.println("size not set for membrane \"" + membrane.getName() + "\", refer to Structure Mapping in Application \"" + mathMapping.getSimulationContext().getName() + "\"");
        area = membraneMapping.getNullSizeParameterValue();
    } else {
        area = new Expression(sizeParameter, mathMapping.getNameScope());
    }
    for (int i = 0; i < reactionSpecs.length; i++) {
        // 
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        if (reactionSpecs[i].getReactionStep().getKinetics() instanceof DistributedKinetics) {
            ReactionStep rs = reactionSpecs[i].getReactionStep();
            DistributedKinetics distributedKinetics = (DistributedKinetics) rs.getKinetics();
            if (rs.getStructure() == membrane) {
                if (!distributedKinetics.getCurrentDensityParameter().getExpression().isZero()) {
                    // 
                    // change sign convension from inward current to outward current (which is consistent with voltage convension)
                    // 
                    currentExp = Expression.add(currentExp, Expression.negate(Expression.mult(new Expression(distributedKinetics.getCurrentDensityParameter(), mathMapping.getNameScope()), area)));
                }
            }
        } else {
            ReactionStep rs = reactionSpecs[i].getReactionStep();
            LumpedKinetics lumpedKinetics = (LumpedKinetics) rs.getKinetics();
            if (rs.getStructure() == membrane) {
                if (!lumpedKinetics.getLumpedCurrentParameter().getExpression().isZero()) {
                    // 
                    if (!(membraneMapping.getGeometryClass() instanceof CompartmentSubVolume)) {
                        throw new RuntimeException("math generation for total currents within spatial electrophysiology not yet implemented");
                    }
                    Expression lumpedCurrentSymbolExp = new Expression(lumpedKinetics.getLumpedCurrentParameter(), mathMapping.getNameScope());
                    currentExp = Expression.add(currentExp, Expression.negate(lumpedCurrentSymbolExp));
                }
            }
        }
    }
    return currentExp.flatten();
}