Examples with GeometryClass cbit.vcell.geometry.GeometryClass used on opensource projects

Example 36 with GeometryClass

use of cbit.vcell.geometry.GeometryClass in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a MembraneMapping.
 * Creation date: (3/1/2001 8:48:14 PM)
 * @return Element
 * @param param cbit.vcell.mapping.MembraneMapping
 */
private Element getXML(MembraneMapping param) {
    // Allow 'null' subvolumes
    // if (param.getSubVolume() == null) {
    // return null;
    // }
    Element membrane = new Element(XMLTags.MembraneMappingTag);
    // Add atributes
    membrane.setAttribute(XMLTags.MembraneAttrTag, mangle(param.getMembrane().getName()));
    // SurfaceToVolumeRatio if it exsits, amended Sept. 27th, 2007
    if (param.getSurfaceToVolumeParameter().getExpression() != null) {
        membrane.setAttribute(XMLTags.SurfaceToVolumeRatioTag, mangleExpression(param.getSurfaceToVolumeParameter().getExpression()));
    }
    // VolumeFraction if it exsits, amended Sept. 27th, 2007
    if (param.getVolumeFractionParameter().getExpression() != null) {
        membrane.setAttribute(XMLTags.VolumeFractionTag, mangleExpression(param.getVolumeFractionParameter().getExpression()));
    }
    // Add size
    if (param.getSizeParameter().getExpression() != null) {
        membrane.setAttribute(XMLTags.SizeTag, mangleExpression(param.getSizeParameter().getExpression()));
    }
    // Add area/unit_area and area/unit_vol if they exist
    if (param.getAreaPerUnitAreaParameter().getExpression() != null) {
        membrane.setAttribute(XMLTags.AreaPerUnitAreaTag, mangleExpression(param.getAreaPerUnitAreaParameter().getExpression()));
    }
    if (param.getAreaPerUnitVolumeParameter().getExpression() != null) {
        membrane.setAttribute(XMLTags.AreaPerUnitVolumeTag, mangleExpression(param.getAreaPerUnitVolumeParameter().getExpression()));
    }
    // Add the electrical properties
    membrane.setAttribute(XMLTags.CalculateVoltageTag, String.valueOf(param.getCalculateVoltage()));
    membrane.setAttribute(XMLTags.SpecificCapacitanceTag, mangleExpression(param.getSpecificCapacitanceParameter().getExpression()));
    membrane.setAttribute(XMLTags.InitialVoltageTag, mangleExpression(param.getInitialVoltageParameter().getExpression()));
    GeometryClass geometryClass = param.getGeometryClass();
    if (geometryClass != null) {
        membrane.setAttribute(XMLTags.GeometryClassAttrTag, mangle(geometryClass.getName()));
    }
    return membrane;
}

Example 37 with GeometryClass

use of cbit.vcell.geometry.GeometryClass in project vcell by virtualcell.

the class XmlReader method getMembraneMapping.

/**
 * This method retuns a MembraneMapping object from a XML representation.
 * Creation date: (5/7/2001 4:12:03 PM)
 * @return cbit.vcell.mapping.MembraneMapping
 * @param param org.jdom.Element
 */
private MembraneMapping getMembraneMapping(Element param, SimulationContext simulationContext) throws XmlParseException {
    // Retrieve attributes
    String membranename = unMangle(param.getAttributeValue(XMLTags.MembraneAttrTag));
    Membrane membraneref = (Membrane) simulationContext.getModel().getStructure(membranename);
    if (membraneref == null) {
        throw new XmlParseException("The Membrane " + membranename + " could not be resolved!");
    }
    // *** Create new Membrane Mapping ****
    MembraneMapping memmap = new MembraneMapping(membraneref, simulationContext, simulationContext.getModel().getUnitSystem());
    // Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007
    if (param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag) != null) {
        String ratio = unMangle(param.getAttributeValue(XMLTags.SurfaceToVolumeRatioTag));
        try {
            memmap.getSurfaceToVolumeParameter().setExpression(unMangleExpression(ratio));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the SurfacetoVolumeRatio Expression " + ratio + " to a membraneMapping!", e);
        }
    }
    // Set VolumeFraction when it exists, amended Sept. 27th, 2007
    if (param.getAttributeValue(XMLTags.VolumeFractionTag) != null) {
        String fraction = unMangle(param.getAttributeValue(XMLTags.VolumeFractionTag));
        try {
            memmap.getVolumeFractionParameter().setExpression(unMangleExpression(fraction));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the VolumeFraction Expression " + fraction + " to a membraneMapping!", e);
        }
    }
    // Set Area/unit_area if it exists, amended Sept. 27th, 2007
    if (param.getAttributeValue(XMLTags.AreaPerUnitAreaTag) != null) {
        String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitAreaTag));
        try {
            memmap.getAreaPerUnitAreaParameter().setExpression(unMangleExpression(ratio));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitArea Expression " + ratio + " to a membraneMapping!", e);
        }
    }
    // Set SurfacetoVolumeRatio when it exists, amended Sept. 27th, 2007
    if (param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag) != null) {
        String ratio = unMangle(param.getAttributeValue(XMLTags.AreaPerUnitVolumeTag));
        try {
            memmap.getAreaPerUnitVolumeParameter().setExpression(unMangleExpression(ratio));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the AreaPerUnitVolume Expression " + ratio + " to a membraneMapping!", e);
        }
    }
    // Set Size
    if (param.getAttributeValue(XMLTags.SizeTag) != null) {
        String size = unMangle(param.getAttributeValue(XMLTags.SizeTag));
        try {
            memmap.getSizeParameter().setExpression(unMangleExpression(size));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("An expressionException was fired when setting the size Expression " + size + " to a membraneMapping!", e);
        }
    } else {
        try {
            memmap.getSizeParameter().setExpression(null);
        } catch (Exception e) {
            e.printStackTrace();
            throw new RuntimeException("unexpected exception while setting structure size", e);
        }
    }
    // ** Set electrical properties **
    // set specific capacitance
    double specificCap = Double.parseDouble(param.getAttributeValue(XMLTags.SpecificCapacitanceTag));
    try {
        memmap.getSpecificCapacitanceParameter().setExpression(new Expression(specificCap));
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException(e);
    }
    // set flag calculate voltage
    boolean calculateVolt = (Boolean.valueOf(param.getAttributeValue(XMLTags.CalculateVoltageTag))).booleanValue();
    memmap.setCalculateVoltage(calculateVolt);
    // set initial Voltage
    String initialVoltString = param.getAttributeValue(XMLTags.InitialVoltageTag);
    try {
        Expression initialExpr = unMangleExpression(initialVoltString);
        memmap.getInitialVoltageParameter().setExpression(initialExpr);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException(e);
    }
    String geometryClassName = param.getAttributeValue(XMLTags.GeometryClassAttrTag);
    if (geometryClassName != null) {
        geometryClassName = unMangle(geometryClassName);
    }
    // Retrieve subvolumeref, allow subvolumes to be 'null'
    if (geometryClassName != null) {
        GeometryClass[] geometryClasses = simulationContext.getGeometry().getGeometryClasses();
        for (int i = 0; i < geometryClasses.length; i++) {
            if (geometryClasses[i].getName().equals(geometryClassName)) {
                try {
                    memmap.setGeometryClass(geometryClasses[i]);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                    throw new XmlParseException("A propertyVetoException was fired when trying to set the subvolume or surface " + geometryClassName + " to a MembraneMapping!", e);
                }
            }
        }
    }
    return memmap;
}

Example 38 with GeometryClass

use of cbit.vcell.geometry.GeometryClass in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a featureMapping object.
 * Creation date: (3/1/2001 8:16:57 PM)
 * @return Element
 * @param param cbit.vcell.mapping.FeatureMapping
 */
private Element getXML(FeatureMapping param) {
    // Allow null subvolumes
    // if (param.getSubVolume()==null) {	//5/92001
    // return null;
    // }
    Element feature = new Element(XMLTags.FeatureMappingTag);
    // Add atributes
    feature.setAttribute(XMLTags.FeatureAttrTag, mangle(param.getFeature().getName()));
    GeometryClass geometryClass = param.getGeometryClass();
    if (geometryClass != null) {
        feature.setAttribute(XMLTags.GeometryClassAttrTag, Xmlproducer.mangle(geometryClass.getName()));
        if (geometryClass instanceof SubVolume) {
            feature.setAttribute(XMLTags.SubVolumeAttrTag, Xmlproducer.mangle(geometryClass.getName()));
        }
    }
    // Add size
    if (param.getSizeParameter().getExpression() != null)
        feature.setAttribute(XMLTags.SizeTag, mangleExpression(param.getSizeParameter().getExpression()));
    // Add volume/unit_Area and volume/unit_vol if they exist
    if (param.getVolumePerUnitAreaParameter().getExpression() != null) {
        feature.setAttribute(XMLTags.VolumePerUnitAreaTag, mangleExpression(param.getVolumePerUnitAreaParameter().getExpression()));
    }
    if (param.getVolumePerUnitVolumeParameter().getExpression() != null) {
        feature.setAttribute(XMLTags.VolumePerUnitVolumeTag, mangleExpression(param.getVolumePerUnitVolumeParameter().getExpression()));
    }
    // write BoundariesyConditions
    Element boundariestypes = new Element(XMLTags.BoundariesTypesTag);
    // Xm
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueXm, param.getBoundaryConditionTypeXm().boundaryTypeStringValue());
    // Xp
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueXp, param.getBoundaryConditionTypeXp().boundaryTypeStringValue());
    // Ym
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueYm, param.getBoundaryConditionTypeYm().boundaryTypeStringValue());
    // Yp
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueYp, param.getBoundaryConditionTypeYp().boundaryTypeStringValue());
    // Zm
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueZm, param.getBoundaryConditionTypeZm().boundaryTypeStringValue());
    // Zp
    boundariestypes.setAttribute(XMLTags.BoundaryAttrValueZp, param.getBoundaryConditionTypeZp().boundaryTypeStringValue());
    // add boundaries to the feature
    feature.addContent(boundariestypes);
    return feature;
}

Example 39 with GeometryClass

use of cbit.vcell.geometry.GeometryClass in project vcell by virtualcell.

the class OutputFunctionsPanel method addFunction.

private void addFunction() throws Exception {
    String funcName = getFunctionNameTextField().getText();
    Expression funcExp = null;
    funcExp = new Expression(getFunctionExpressionTextField().getText());
    Domain domain = null;
    VariableType newFunctionVariableType = null;
    boolean bSpatial = simulationWorkspace.getSimulationOwner().getGeometry().getDimension() > 0;
    if (bSpatial) {
        Object selectedItem = getSubdomainComboBox().getSelectedItem();
        if (selectedItem instanceof GeometryClass) {
            GeometryClass geoClass = (GeometryClass) selectedItem;
            domain = new Domain(geoClass);
            if (selectedItem instanceof SubVolume) {
                newFunctionVariableType = VariableType.VOLUME;
            } else if (selectedItem instanceof SurfaceClass) {
                newFunctionVariableType = VariableType.MEMBRANE;
            }
        } else if (selectedItem instanceof VariableType) {
            newFunctionVariableType = (VariableType) selectedItem;
        } else {
            newFunctionVariableType = VariableType.UNKNOWN;
        }
    } else {
        newFunctionVariableType = VariableType.NONSPATIAL;
    }
    AnnotatedFunction tempFunction = new AnnotatedFunction(funcName, funcExp, domain, null, newFunctionVariableType, FunctionCategory.OUTPUTFUNCTION);
    VariableType vt = outputFunctionContext.computeFunctionTypeWRTExpression(tempFunction, funcExp);
    FunctionCategory category = FunctionCategory.OUTPUTFUNCTION;
    if (vt.equals(VariableType.POSTPROCESSING)) {
        category = FunctionCategory.POSTPROCESSFUNCTION;
    }
    AnnotatedFunction newFunction = new AnnotatedFunction(funcName, funcExp, domain, null, vt, category);
    outputFunctionContext.addOutputFunction(newFunction);
    setSelectedObjects(new Object[] { newFunction });
    enableDeleteFnButton();
}

Example 40 with GeometryClass

use of cbit.vcell.geometry.GeometryClass in project vcell by virtualcell.

the class OutputFunctionsPanel method getSubdomainComboBox.

private JComboBox getSubdomainComboBox() {
    if (subdomainComboBox == null) {
        try {
            subdomainComboBox = new JComboBox();
            subdomainComboBox.setRenderer(new DefaultListCellRenderer() {

                @Override
                public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                    super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                    if (value instanceof GeometryClass) {
                        setText(((GeometryClass) value).getName());
                    } else if (value instanceof VariableType) {
                        setText(((VariableType) value).getTypeName());
                    }
                    return this;
                }
            });
        } catch (java.lang.Throwable e) {
            e.printStackTrace(System.out);
        }
    }
    return subdomainComboBox;
}