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

Example 6 with GeometryContext

use of cbit.vcell.mapping.GeometryContext 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 7 with GeometryContext

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

the class StructureMappingTableModel 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) {
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_GEOMETRY_CONTEXT)) {
        GeometryContext oldValue = (GeometryContext) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            StructureMapping[] oldStructureMappings = oldValue.getStructureMappings();
            for (int i = 0; i < oldStructureMappings.length; i++) {
                oldStructureMappings[i].removePropertyChangeListener(this);
            }
            SubVolume[] subvols = oldValue.getGeometry().getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subvols.length; i++) {
                subvols[i].removePropertyChangeListener(this);
            }
        }
        GeometryContext newValue = (GeometryContext) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            StructureMapping[] newStructureMappings = newValue.getStructureMappings();
            for (int i = 0; i < newStructureMappings.length; i++) {
                newStructureMappings[i].addPropertyChangeListener(this);
            }
            SubVolume[] subvols = newValue.getGeometry().getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subvols.length; i++) {
                subvols[i].addPropertyChangeListener(this);
            }
        }
        update();
    }
    if (evt.getSource() == getGeometryContext() && evt.getPropertyName().equals(GeometryOwner.PROPERTY_NAME_GEOMETRY)) {
        SubVolume[] subvols = ((Geometry) evt.getOldValue()).getGeometrySpec().getSubVolumes();
        for (int i = 0; i < subvols.length; i++) {
            subvols[i].removePropertyChangeListener(this);
        }
        subvols = ((Geometry) evt.getNewValue()).getGeometrySpec().getSubVolumes();
        for (int i = 0; i < subvols.length; i++) {
            subvols[i].addPropertyChangeListener(this);
        }
        update();
    }
    // subvolume name change
    if (evt.getSource() instanceof SubVolume) {
        update();
    }
    if (evt.getSource() instanceof GeometryContext && evt.getPropertyName().equals(GeometryContext.PROPERTY_STRUCTURE_MAPPINGS)) {
        StructureMapping[] oldStructureMappings = (StructureMapping[]) evt.getOldValue();
        StructureMapping[] newStructureMappings = (StructureMapping[]) evt.getNewValue();
        for (int i = 0; oldStructureMappings != null && i < oldStructureMappings.length; i++) {
            oldStructureMappings[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newStructureMappings != null && i < newStructureMappings.length; i++) {
            newStructureMappings[i].addPropertyChangeListener(this);
        }
        update();
    }
    if (evt.getSource() instanceof StructureMapping) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}

Example 8 with GeometryContext

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

the class StructureMappingTableModel 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;
    fieldGeometryContext = geometryContext;
    firePropertyChange(PROPERTY_GEOMETRY_CONTEXT, oldValue, geometryContext);
}

Example 9 with GeometryContext

use of cbit.vcell.mapping.GeometryContext 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 10 with GeometryContext

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

the class StructureMappingPanel 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;
    fieldGeometryContext = geometryContext;
    firePropertyChange(PROPERTY_GEOMETRY_CONTEXT, oldValue, geometryContext);
}