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

Example 66 with SubVolume

use of cbit.vcell.geometry.SubVolume 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 67 with SubVolume

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

the class Xmlproducer method getXML.

private Element getXML(SurfaceClass param) {
    Element surfaceClassElement = new Element(XMLTags.SurfaceClassTag);
    // add atributes
    surfaceClassElement.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    SubVolume[] subvolArr = param.getAdjacentSubvolumes().toArray(new SubVolume[0]);
    Arrays.sort(subvolArr, new Comparator<SubVolume>() {

        public int compare(SubVolume o1, SubVolume o2) {
            return o1.getName().compareTo(o2.getName());
        }
    });
    if (subvolArr.length > 0) {
        surfaceClassElement.setAttribute(XMLTags.SubVolume1RefAttrTag, subvolArr[0].getName());
    }
    if (subvolArr.length > 1) {
        surfaceClassElement.setAttribute(XMLTags.SubVolume2RefAttrTag, subvolArr[1].getName());
    }
    // If keyFlag is on print the Keyvalue
    if (param.getKey() != null && this.printKeysFlag) {
        surfaceClassElement.setAttribute(XMLTags.KeyValueAttrTag, param.getKey().toString());
    }
    return surfaceClassElement;
}

Example 68 with SubVolume

use of cbit.vcell.geometry.SubVolume 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 69 with SubVolume

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

the class GeometrySubVolumePanel method moveSubvolumeFront.

/**
 * connEtoM6:  (FrontButton.action.actionPerformed(java.awt.event.ActionEvent) --> Geometry.bringForward(Lcbit.vcell.geometry.AnalyticSubVolume;)V)
 * @param arg1 java.awt.event.ActionEvent
 */
private void moveSubvolumeFront() {
    try {
        if ((getSelectedSubVolume() != null)) {
            AsynchClientTask task1 = new AsynchClientTask("moving to front", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                @Override
                public void run(Hashtable<String, Object> hashTable) throws Exception {
                    SubVolume selectedSubVolume = getSelectedSubVolume();
                    if (selectedSubVolume instanceof CSGObject) {
                        getGeometrySpec().bringForward((CSGObject) selectedSubVolume);
                    } else if (selectedSubVolume instanceof AnalyticSubVolume) {
                        getGeometrySpec().bringForward((AnalyticSubVolume) selectedSubVolume);
                    }
                    getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT());
                }
            };
            ClientTaskDispatcher.dispatch(GeometrySubVolumePanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1 }, false);
        }
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 70 with SubVolume

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

the class GeometrySubVolumePanel method refreshButtons.

/**
 * This method was created in VisualAge.
 */
private void refreshButtons() {
    boolean bHasGeometry = getGeometry() != null;
    boolean bHasGeomSpec = (bHasGeometry ? getGeometry().getGeometrySpec() != null : false);
    boolean bImageBased = (bHasGeomSpec ? getGeometry().getGeometrySpec().getImage() != null : false);
    addShapeButton.setEnabled(!bImageBased);
    SubVolume selectedSubVolume = getSelectedSubVolume();
    if (!bHasGeomSpec || getGeometry().getDimension() == 0) {
        getFrontButton().setEnabled(false);
        getBackButton().setEnabled(false);
        getDeleteButton().setEnabled(false);
        addShapeButton.setEnabled(false);
    } else if (selectedSubVolume == null) {
        getFrontButton().setEnabled(false);
        getBackButton().setEnabled(false);
        getDeleteButton().setEnabled(false);
    } else {
        GeometrySpec geometrySpec = getGeometry().getGeometrySpec();
        int numAnalyticOrCSGSubVolumes = geometrySpec.getNumAnalyticOrCSGSubVolumes();
        if (numAnalyticOrCSGSubVolumes > 1) {
            getFrontButton().setEnabled(geometrySpec.getSubVolumeIndex(selectedSubVolume) > 0);
            getBackButton().setEnabled(geometrySpec.getSubVolumeIndex(selectedSubVolume) < (numAnalyticOrCSGSubVolumes - 1));
        } else {
            getFrontButton().setEnabled(false);
            getBackButton().setEnabled(false);
        }
        if (selectedSubVolume instanceof ImageSubVolume || (!bImageBased && (geometrySpec.getNumSubVolumes() <= 1))) {
            getDeleteButton().setEnabled(false);
        } else {
            getDeleteButton().setEnabled(true);
        }
    }
}