Examples with Domain cbit.vcell.math.Variable.Domain used on opensource projects

Example 51 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class CellQuanVCTranslator method addRateFunction.

private Function addRateFunction(Element varRef, String compName, String mangledName) {
    Element role;
    String stoich = null, roleAtt = null;
    // can only imply the delta function if the stoichiometry attribute is present also
    // not sure if there can be more than one, if not, could just pass in the 'role' element itself.
    @SuppressWarnings("unchecked") Iterator<Element> i = varRef.getChildren(CELLMLTags.ROLE, sNamespace).iterator();
    while (i.hasNext()) {
        role = i.next();
        stoich = role.getAttributeValue(CELLMLTags.stoichiometry, sAttNamespace);
        roleAtt = role.getAttributeValue(CELLMLTags.role, sAttNamespace);
        if (stoich != null)
            break;
    }
    if (stoich != null) {
        // Can only imply the function if a variable_ref with a role of "rate" exists
        JDOMTreeWalker reactionWalker = new JDOMTreeWalker((Element) varRef.getParent(), new ElementFilter(CELLMLTags.ROLE));
        Element rateRole = reactionWalker.getMatchingElement(CELLMLTags.role, sAttNamespace, CELLMLTags.rateRole);
        if (rateRole != null) {
            String rateVarName = ((Element) rateRole.getParent()).getAttributeValue(CELLMLTags.variable, sAttNamespace);
            StringBuffer formula = new StringBuffer("(");
            if (roleAtt.equals(CELLMLTags.productRole))
                formula.append("-(");
            formula.append(stoich + "*" + nm.getMangledName(compName, rateVarName));
            if (roleAtt.equals(CELLMLTags.productRole))
                formula.append(")");
            formula.append(")");
            try {
                Domain domain = null;
                return new Function(mangledName, new Expression(formula.toString()), domain);
            // fnsVector.add(function);
            // mathDescription.addVariable(function);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Error adding function (" + mangledName + ") to mathDexcription : " + e.getMessage());
            }
        }
    }
    return null;
}

Example 52 with Domain

use of cbit.vcell.math.Variable.Domain 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 53 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method retriveVariableNames.

private void retriveVariableNames() throws Exception {
    // read variables only when I have never read the file since variables don't change
    if (dataSetIdentifierList.size() > 0) {
        return;
    }
    File tempFile = getTempSimHdf5File(0.0);
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat meshFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
    meshFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group solGroup = (Group) rootGroup.getMemberList().get(0);
    List<Attribute> solAttrList = solGroup.getMetadata();
    String[] varNames = null;
    int[] varTypes = null;
    for (Attribute attr : solAttrList) {
        String attrName = attr.getName();
        Object value = attr.getValue();
        if (attrName.equals(SOLUTION_ATTR_VARIABLES)) {
            varNames = (String[]) value;
        } else if (attrName.equals(SOLUTION_ATTR_VARIABLE_TYPES)) {
            varTypes = (int[]) value;
        }
    }
    for (int i = 0; i < varNames.length; i++) {
        VariableType varType = VariableType.getVariableTypeFromInteger(varTypes[i]);
        Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
        String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
        dataSetIdentifierList.add(new DataSetIdentifier(varName, varType, domain));
    }
}

Example 54 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class DisplayTimeSeries method displayImageTimeSeries.

public static void displayImageTimeSeries(final ImageTimeSeries<Image> imageTimeSeries, String title, WindowListener windowListener) throws ImageException, IOException {
    ISize size = imageTimeSeries.getISize();
    int dimension = (size.getZ() > 0) ? (3) : (2);
    Extent extent = imageTimeSeries.getExtent();
    Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
    // don't care ... no surfaces
    double filterCutoffFrequency = 0.5;
    VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
    RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
    final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
    final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
    final DataSetController dataSetController = new DataSetController() {

        @Override
        public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
            double timePoint = time;
            double[] timePoints = getDataSetTimes(vcdataID);
            int index = -1;
            for (int i = 0; i < timePoints.length; i++) {
                if (timePoint == timePoints[i]) {
                    index = i;
                    break;
                }
            }
            double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
            PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
            VariableType varType = VariableType.VOLUME;
            return new SimDataBlock(pdeDataInfo, data, varType);
        }

        @Override
        public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return false;
        }

        @Override
        public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return mesh;
        }

        @Override
        public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return new AnnotatedFunction[0];
        }

        @Override
        public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return imageTimeSeries.getImageTimeStamps();
        }

        @Override
        public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return new DataIdentifier[] { dataIdentifier };
        }

        @Override
        public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }
    };
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return dataSetController;
        }
    };
    VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
    OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public User getOwner() {
            return new User("nouser", null);
        }

        public KeyValue getDataKey() {
            return null;
        }

        public String getID() {
            return "mydata";
        }
    };
    PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
    ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
    PDEDataViewer pdeDataViewer = new PDEDataViewer();
    JFrame jframe = new JFrame();
    jframe.setTitle(title);
    jframe.getContentPane().add(pdeDataViewer);
    jframe.setSize(1000, 600);
    jframe.setVisible(true);
    if (windowListener != null) {
        jframe.addWindowListener(windowListener);
    }
    pdeDataViewer.setPdeDataContext(myPdeDataContext);
}