Examples with VCUnitDefinition cbit.vcell.units.VCUnitDefinition used on opensource projects

Example 91 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class XmlReader method getGeometrySurfaceDescription.

private GeometrySurfaceDescription getGeometrySurfaceDescription(Element param, Geometry geom) throws XmlParseException {
    GeometrySurfaceDescription gsd = geom.getGeometrySurfaceDescription();
    String cutoffStr = param.getAttributeValue(XMLTags.CutoffFrequencyAttrTag);
    String xDim = param.getAttributeValue(XMLTags.NumSamplesXAttrTag);
    String yDim = param.getAttributeValue(XMLTags.NumSamplesYAttrTag);
    String zDim = param.getAttributeValue(XMLTags.NumSamplesZAttrTag);
    if (cutoffStr == null || xDim == null || yDim == null || zDim == null) {
        throw new XmlParseException("Attributes for element Surface Description not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
    }
    try {
        ISize isize = new ISize(Integer.parseInt(xDim), Integer.parseInt(yDim), Integer.parseInt(zDim));
        gsd.setVolumeSampleSize(isize);
        gsd.setFilterCutoffFrequency(new Double(cutoffStr));
        // these lists are allowed to be empty.
        ArrayList<Element> memRegions = new ArrayList<Element>(param.getChildren(XMLTags.MembraneRegionTag, vcNamespace));
        ArrayList<Element> volRegions = new ArrayList<Element>(param.getChildren(XMLTags.VolumeRegionTag, vcNamespace));
        ArrayList<GeometricRegion> regions = new ArrayList<GeometricRegion>();
        GeometryUnitSystem geometryUnitSystem = geom.getUnitSystem();
        for (Element temp : volRegions) {
            String regionID = temp.getAttributeValue(XMLTags.RegionIDAttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            String subvolumeRef = temp.getAttributeValue(XMLTags.SubVolumeAttrTag);
            if (regionID == null || name == null || subvolumeRef == null) {
                throw new XmlParseException("Attributes for element Volume Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            SubVolume subvolume = geom.getGeometrySpec().getSubVolume(subvolumeRef);
            if (subvolume == null) {
                throw new XmlParseException("The subvolume " + subvolumeRef + " could not be resolved.");
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            VolumeGeometricRegion vgr = new VolumeGeometricRegion(name, size, unit, subvolume, Integer.parseInt(regionID));
            regions.add(vgr);
        }
        for (Element temp : memRegions) {
            String volRegion_1 = temp.getAttributeValue(XMLTags.VolumeRegion_1AttrTag);
            String volRegion_2 = temp.getAttributeValue(XMLTags.VolumeRegion_2AttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            if (volRegion_1 == null || volRegion_2 == null || name == null) {
                throw new XmlParseException("Attributes for element Membrane Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            VolumeGeometricRegion region1 = getAdjacentVolumeRegion(regions, volRegion_1);
            VolumeGeometricRegion region2 = getAdjacentVolumeRegion(regions, volRegion_2);
            if (region1 == null || region2 == null) {
                throw new XmlParseException("Element Membrane Region refernces invalid volume regions, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            SurfaceGeometricRegion rsl = new SurfaceGeometricRegion(name, size, unit);
            rsl.addAdjacentGeometricRegion(region1);
            region1.addAdjacentGeometricRegion(rsl);
            rsl.addAdjacentGeometricRegion(region2);
            region2.addAdjacentGeometricRegion(rsl);
            regions.add(rsl);
        }
        if (regions.size() > 0) {
            gsd.setGeometricRegions((GeometricRegion[]) regions.toArray(new GeometricRegion[regions.size()]));
        }
    } catch (Exception e) {
        System.err.println("Unable to read geometry surface description from XML, for geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
        e.printStackTrace();
    }
    return gsd;
}

Example 92 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class Xmlproducer method getXML.

// For events in SimulationContext - XML is very similar to math events
public Element getXML(BioEvent[] bioEvents) throws XmlParseException {
    Element bioEventsElement = new Element(XMLTags.BioEventsTag);
    for (int i = 0; i < bioEvents.length; i++) {
        Element eventElement = new Element(XMLTags.BioEventTag);
        eventElement.setAttribute(XMLTags.NameAttrTag, mangle(bioEvents[i].getName()));
        String triggerType = bioEvents[i].getTriggerType().getXmlName();
        // Add atributes
        eventElement.setAttribute(XMLTags.BioEventTriggerTypeAttrTag, triggerType);
        eventElement.setAttribute(XMLTags.UseValuesFromTriggerTimeAttrTag, Boolean.toString(bioEvents[i].getUseValuesFromTriggerTime()));
        // Add BioEvent Parameters
        LocalParameter[] parameters = bioEvents[i].getEventParameters();
        for (LocalParameter parm : parameters) {
            if (parm.getExpression() != null) {
                Element tempparameter = new Element(XMLTags.ParameterTag);
                // Get parameter attributes
                tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
                tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, bioEvents[i].getParameterType(parm).getRoleXmlName());
                VCUnitDefinition unit = parm.getUnitDefinition();
                if (unit != null) {
                    tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                }
                tempparameter.addContent(mangleExpression(parm.getExpression()));
                // Add the parameter to the general kinetics object
                eventElement.addContent(tempparameter);
            }
        }
        ArrayList<BioEvent.EventAssignment> eventAssignmentsList = bioEvents[i].getEventAssignments();
        if (eventAssignmentsList != null) {
            for (BioEvent.EventAssignment eventAssignment : eventAssignmentsList) {
                Element eventAssignmentElement = new Element(XMLTags.EventAssignmentTag);
                eventAssignmentElement.setAttribute(XMLTags.EventAssignmentVariableAttrTag, eventAssignment.getTarget().getName());
                eventAssignmentElement.addContent(mangleExpression(eventAssignment.getAssignmentExpression()));
                eventElement.addContent(eventAssignmentElement);
            }
        }
        bioEventsElement.addContent(eventElement);
    }
    System.out.println(XmlUtil.xmlToString(bioEventsElement));
    return bioEventsElement;
}

Example 93 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class Xmlproducer method getXML.

public Element getXML(SpatialProcess[] spatialProcesses) throws XmlParseException {
    Element spatialProcessesElement = new Element(XMLTags.SpatialProcessesTag);
    for (SpatialProcess spatialProcess : spatialProcesses) {
        Element spatialProcessElement = new Element(XMLTags.SpatialProcessTag);
        spatialProcessElement.setAttribute(XMLTags.NameAttrTag, mangle(spatialProcess.getName()));
        if (spatialProcess instanceof PointKinematics) {
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_PointKinematics);
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessPointObjectAttrTag, ((PointKinematics) spatialProcess).getPointObject().getName());
        } else if (spatialProcess instanceof PointLocation) {
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_PointLocation);
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessPointObjectAttrTag, ((PointLocation) spatialProcess).getPointObject().getName());
        } else if (spatialProcess instanceof SurfaceKinematics) {
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_SurfaceKinematics);
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessSurfaceObjectAttrTag, ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject().getName());
        } else if (spatialProcess instanceof VolumeKinematics) {
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_VolumeKinematics);
            spatialProcessElement.setAttribute(XMLTags.SpatialProcessVolumeObjectAttrTag, ((VolumeKinematics) spatialProcess).getVolumeRegionObject().getName());
        } else {
            throw new RuntimeException("spatialProcess type " + spatialProcess.getClass().getSimpleName() + " not yet supported for persistence.");
        }
        LocalParameter[] parameters = spatialProcess.getParameters();
        for (LocalParameter parm : parameters) {
            if (parm.getExpression() != null) {
                Element tempparameter = new Element(XMLTags.ParameterTag);
                // Get parameter attributes
                tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
                tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, spatialProcess.getParameterType(parm).getRoleXmlName());
                VCUnitDefinition unit = parm.getUnitDefinition();
                if (unit != null) {
                    tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                }
                tempparameter.addContent(mangleExpression(parm.getExpression()));
                spatialProcessElement.addContent(tempparameter);
            }
        }
        spatialProcessesElement.addContent(spatialProcessElement);
    }
    System.out.println(XmlUtil.xmlToString(spatialProcessesElement));
    return spatialProcessesElement;
}

Example 94 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class XmlReader method getSpatialProcesses.

public SpatialProcess[] getSpatialProcesses(SimulationContext simContext, Element spatialProcessesElement) throws XmlParseException {
    Iterator<Element> spatialProcessElementIterator = spatialProcessesElement.getChildren(XMLTags.SpatialProcessTag, vcNamespace).iterator();
    ArrayList<SpatialProcess> spatialProcessList = new ArrayList<SpatialProcess>();
    while (spatialProcessElementIterator.hasNext()) {
        Element spatialProcessElement = (Element) spatialProcessElementIterator.next();
        SpatialProcess spatialProcess = null;
        String name = unMangle(spatialProcessElement.getAttributeValue(XMLTags.NameAttrTag));
        String type = unMangle(spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessTypeAttrTag));
        if (type.equals(XMLTags.SpatialProcessTypeAttrValue_PointKinematics)) {
            PointKinematics pointKinematics = new PointKinematics(name, simContext);
            String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag);
            PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName);
            pointKinematics.setPointObject(pointObject);
            spatialProcess = pointKinematics;
        } else if (type.equals(XMLTags.SpatialProcessTypeAttrValue_PointLocation)) {
            PointLocation pointLocation = new PointLocation(name, simContext);
            String pointObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessPointObjectAttrTag);
            PointObject pointObject = (PointObject) simContext.getSpatialObject(pointObjectName);
            pointLocation.setPointObject(pointObject);
            spatialProcess = pointLocation;
        } else if (type.equals(XMLTags.SpatialProcessTypeAttrValue_SurfaceKinematics)) {
            SurfaceKinematics surfaceKinematics = new SurfaceKinematics(name, simContext);
            String surfaceRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessSurfaceObjectAttrTag);
            SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) simContext.getSpatialObject(surfaceRegionObjectName);
            surfaceKinematics.setSurfaceRegionObject(surfaceRegionObject);
            spatialProcess = surfaceKinematics;
        } else if (type.equals(XMLTags.SpatialProcessTypeAttrValue_VolumeKinematics)) {
            VolumeKinematics volumeKinematics = new VolumeKinematics(name, simContext);
            String volumeRegionObjectName = spatialProcessElement.getAttributeValue(XMLTags.SpatialProcessVolumeObjectAttrTag);
            VolumeRegionObject volumeRegionObject = (VolumeRegionObject) simContext.getSpatialObject(volumeRegionObjectName);
            volumeKinematics.setVolumeRegionObject(volumeRegionObject);
            spatialProcess = volumeKinematics;
        }
        // set parameters
        Iterator<Element> paramElementIter = spatialProcessElement.getChildren(XMLTags.ParameterTag, vcNamespace).iterator();
        ArrayList<LocalParameter> parameters = new ArrayList<LocalParameter>();
        while (paramElementIter.hasNext()) {
            Element paramElement = paramElementIter.next();
            // Get parameter attributes
            String paramName = paramElement.getAttributeValue(XMLTags.NameAttrTag);
            Expression exp = unMangleExpression(paramElement.getText());
            String roleStr = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
            SpatialProcessParameterType parameterType = SpatialProcessParameterType.fromRoleXmlName(roleStr);
            VCUnitDefinition unit = simContext.getModel().getUnitSystem().getInstance_TBD();
            String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
            if (unitSymbol != null) {
                unit = simContext.getModel().getUnitSystem().getInstance(unitSymbol);
            }
            parameters.add(spatialProcess.createNewParameter(paramName, parameterType, exp, unit));
        }
        try {
            spatialProcess.setParameters(parameters.toArray(new LocalParameter[0]));
        } catch (PropertyVetoException | ExpressionBindingException e) {
            e.printStackTrace();
            throw new XmlParseException("failed to read parameters in bioEvent " + name + ": " + e.getMessage(), e);
        }
        spatialProcessList.add(spatialProcess);
    }
    return spatialProcessList.toArray(new SpatialProcess[0]);
}

Example 95 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class XmlReader method getModelParameter.

public ModelParameter getModelParameter(Element paramElement, Model model) {
    // get its attributes : name, role and unit definition
    String glParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag));
    String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    int glParamRole = -1;
    if (role.equals(XMLTags.ParamRoleUserDefinedTag)) {
        glParamRole = Model.ROLE_UserDefined;
    } else {
        throw new RuntimeException("unknown type of model parameter (not user-defined)");
    }
    // 
    // int glParamRole = -1;
    // if (role.equals(XMLTags.ParamRoleUserDefinedTag)) {
    // glParamRole = Model.ROLE_UserDefined;
    // } else	if (role.equals(XMLTags.RoleVariableRateTag)) {
    // glParamRole = Model.ROLE_VariableRate;
    // } else {
    // throw new RuntimeException("unknown type of model parameter (not user-defined or variable rate)");
    // }
    String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
    VCUnitDefinition glParamUnit = null;
    if (unitSymbol != null) {
        glParamUnit = modelUnitSystem.getInstance(unitSymbol);
    }
    // get parameter contents : expression; annotation, if any.
    String glParamExpStr = paramElement.getText();
    Expression glParamExp = unMangleExpression(glParamExpStr);
    String glParamAnnotation = null;
    String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        glParamAnnotation = unMangle(annotationText);
    }
    // create new global parameter
    ModelParameter newGlParam = model.new ModelParameter(glParamName, glParamExp, glParamRole, glParamUnit);
    newGlParam.setModelParameterAnnotation(glParamAnnotation);
    return newGlParam;
}