Examples with VariableType cbit.vcell.math.VariableType used on opensource projects

Example 51 with VariableType

use of cbit.vcell.math.VariableType 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 52 with VariableType

use of cbit.vcell.math.VariableType in project vcell by virtualcell.

the class OutputFunctionContext method propertyChange.

public void propertyChange(java.beans.PropertyChangeEvent event) {
    if (event.getSource() == simulationOwner && event.getPropertyName().equals("mathDescription")) {
        rebindAll();
    }
    if (event.getPropertyName().equals("geometry")) {
        Geometry oldGeometry = (Geometry) event.getOldValue();
        Geometry newGeometry = (Geometry) event.getNewValue();
        // changing from ode to pde
        if (oldGeometry != null && oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            ArrayList<AnnotatedFunction> newFuncList = new ArrayList<AnnotatedFunction>();
            for (AnnotatedFunction function : outputFunctionsList) {
                try {
                    Expression newexp = new Expression(function.getExpression());
                    // making sure that output function is not direct function of constant.
                    newexp.bindExpression(this);
                    // here use math description as symbol table because we allow
                    // new expression itself to be function of constant.
                    MathDescription mathDescription = getSimulationOwner().getMathDescription();
                    newexp = MathUtilities.substituteFunctions(newexp, mathDescription).flatten();
                    VariableType newFuncType = VariableType.VOLUME;
                    String[] symbols = newexp.getSymbols();
                    if (symbols != null) {
                        // figure out the function type
                        VariableType[] varTypes = new VariableType[symbols.length];
                        for (int i = 0; i < symbols.length; i++) {
                            Variable var = mathDescription.getVariable(symbols[i]);
                            varTypes[i] = VariableType.getVariableType(var);
                        }
                        // check with flattened expression to find out the variable type of the new expression
                        Function flattenedFunction = new Function(function.getName(), newexp, function.getDomain());
                        newFuncType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, true);
                    }
                    AnnotatedFunction newFunc = new AnnotatedFunction(function.getName(), function.getExpression(), function.getDomain(), "", newFuncType, FunctionCategory.OUTPUTFUNCTION);
                    newFuncList.add(newFunc);
                    newFunc.bind(this);
                } catch (ExpressionException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                } catch (InconsistentDomainException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                }
            }
            try {
                setOutputFunctions0(newFuncList);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
                throw new RuntimeException(e.getMessage());
            }
        }
    }
}

Example 53 with VariableType

use of cbit.vcell.math.VariableType in project vcell by virtualcell.

the class ROIDataGenerator method getROIDataGeneratorDescription.

public String getROIDataGeneratorDescription(File userDirectory, SimulationJob simulationJob) throws Exception {
    // DataAccessException, FileNotFoundException, MathException, IOException, DivideByZeroException, ExpressionException
    Simulation simulation = simulationJob.getSimulation();
    StringBuffer sb = new StringBuffer();
    sb.append(ROI_GENERATOR_BEGIN + " " + name + "\n");
    sb.append("VolumePoints " + volumePoints.length + "\n");
    for (int i = 0; i < volumePoints.length; i++) {
        sb.append(volumePoints[i] + " ");
        if ((i + 1) % 20 == 0) {
            sb.append("\n");
        }
    }
    sb.append("\n");
    if (membranePoints != null && membranePoints.length > 0) {
        sb.append("MembranePoints " + membranePoints.length + "\n");
        for (int i = 0; i < membranePoints.length; i++) {
            sb.append(membranePoints[i] + " ");
            if ((i + 1) % 20 == 0) {
                sb.append("\n");
            }
        }
        sb.append("\n");
    }
    sb.append("SampleImage " + numImgRegions + " " + zSlice + " " + fieldDataKey + " " + fieldFuncArguments.infix() + "\n");
    sb.append("StoreEnabled " + bStoreEnabled + "\n");
    // sample image field data file
    FieldDataIdentifierSpec fdis = getSampleImageFieldData(simulation.getVersion().getOwner());
    if (fdis == null) {
        throw new DataAccessException("Can't find sample image in ROI data generator.");
    }
    String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
    DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
    CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
    SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
    VariableType varType = fdis.getFieldFuncArgs().getVariableType();
    VariableType dataVarType = simDataBlock.getVariableType();
    if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
        throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
    }
    double[] origData = simDataBlock.getData();
    String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simulationJob.getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
    File fdatFile = new File(userDirectory, filename);
    DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
    sb.append("SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile + "\n");
    sb.append(ROI_GENERATOR_END);
    return sb.toString();
}

Example 54 with VariableType

use of cbit.vcell.math.VariableType 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);
}