Examples with PDEDataManager cbit.vcell.simdata.PDEDataManager used on opensource projects

Example 11 with PDEDataManager

use of cbit.vcell.simdata.PDEDataManager in project vcell by virtualcell.

the class ClientRequestManager method getDataManager.

/**
 * Insert the method's description here.
 * Creation date: (6/11/2004 10:53:47 AM)
 * @return cbit.vcell.desktop.controls.DataManager
 * @param vcDataIdentifier cbit.vcell.server.VCDataIdentifier
 */
public DataManager getDataManager(OutputContext outputContext, VCDataIdentifier vcDataId, boolean isSpatial) throws DataAccessException {
    // 
    // Create ODE or PDE or Merged Datamanager depending on ODE or PDE or Merged data.
    // 
    DataManager dataManager = null;
    VCDataManager vcDataManager = getClientServerManager().getVCDataManager();
    if (isSpatial) {
        dataManager = new PDEDataManager(outputContext, vcDataManager, vcDataId);
    } else {
        dataManager = new ODEDataManager(outputContext, vcDataManager, vcDataId);
    }
    // dataManager.connect();
    return dataManager;
}

Example 12 with PDEDataManager

use of cbit.vcell.simdata.PDEDataManager in project vcell by virtualcell.

the class NonGUIFRAPTest method runSolver.

/**
 * @param args
 */
public static void runSolver(String[] args) throws Exception {
    String startingIndexForRecovery = args[0];
    String freeDiffusionRateStr = args[1];
    String freeMobileFractionStr = args[2];
    String complexDiffusionRateStr = args[3];
    String complexMobileFractionStr = args[4];
    String bleachWhileMonitoringRateString = args[5];
    String immobileFractionStr = args[6];
    String bindingSiteConcentrationStr = args[7];
    String reacOnRateStr = args[8];
    String reacOffRateStr = args[9];
    String workingDirectoryPath = args[10];
    String inputFRAPDataFileName = args[11];
    String inputCellROIFileName = args[12];
    String inputBleachROIFileName = args[13];
    String inputBackgroundROIFileName = args[14];
    String outputXMLFileName = args[15];
    String commaSepTimeStamps = args[16];
    String commaSepExtentXYZ = args[17];
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDirectoryPath));
    ExternalDataFileContents extDataFileContents = readExternalDataContents(inputFRAPDataFileName, inputCellROIFileName, inputBleachROIFileName, inputBackgroundROIFileName);
    ROI cellROI = new ROI(extDataFileContents.cellROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = new ROI(extDataFileContents.bleachROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = new ROI(extDataFileContents.backgroundROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // Insert Time information
    double[] timeStamps = new double[extDataFileContents.imageData.getAllImages().length];
    StringTokenizer commaStringTokenizer = new StringTokenizer(commaSepTimeStamps, ",");
    int timeCount = 0;
    while (commaStringTokenizer.hasMoreTokens()) {
        timeStamps[timeCount] = Double.parseDouble(commaStringTokenizer.nextToken());
        timeCount++;
    }
    ImageDataset frapDataImageDataSet = new ImageDataset(extDataFileContents.imageData.getAllImages(), timeStamps, 1);
    // Insert Extent information
    commaStringTokenizer = new StringTokenizer(commaSepExtentXYZ, ",");
    Extent extent = new Extent(Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()));
    frapDataImageDataSet.setExtent(extent);
    bleachROI.getRoiImages()[0].setExtent(extent);
    cellROI.getRoiImages()[0].setExtent(extent);
    backgroundROI.getRoiImages()[0].setExtent(extent);
    FRAPData frapData = FrapDataUtils.importFRAPDataFromImageDataSet(frapDataImageDataSet);
    frapData.addReplaceRoi(bleachROI);
    frapData.addReplaceRoi(cellROI);
    frapData.addReplaceRoi(backgroundROI);
    FRAPStudy frapStudy = new FRAPStudy();
    frapStudy.setFrapData(frapData);
    // old model parameters, need to rewrite
    // FRAPStudy.FRAPModelParameters frapModelParameters = new FRAPStudy.FRAPModelParameters(
    // new FRAPStudy.InitialModelParameters(freeDiffusionRateStr, freeMobileFractionStr, bleachWhileMonitoringRateString, startingIndexForRecovery),
    // null,
    // null);
    // frapStudy.setFrapModelParameters(frapModelParameters);
    frapStudy.refreshDependentROIs();
    ExternalDataInfo imageDatasetExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME);
    ExternalDataInfo roiExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME);
    frapStudy.setFrapDataExternalDataInfo(imageDatasetExternalDataInfo);
    frapStudy.setRoiExternalDataInfo(roiExternalDataInfo);
    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    // Double bleachWhileMonitoringRate =
    // (!bleachWhileMonitoringRateString.equals("-")
    // ?Double.parseDouble(bleachWhileMonitoringRateString)
    // :null);
    double fd, ff, bwmr, cd, cf, imf, bs, on, off;
    try {
        fd = Double.parseDouble(freeDiffusionRateStr);
        ff = Double.parseDouble(freeMobileFractionStr);
        bwmr = Double.parseDouble(bleachWhileMonitoringRateString);
        cd = Double.parseDouble(complexDiffusionRateStr);
        cf = Double.parseDouble(complexMobileFractionStr);
        imf = Double.parseDouble(immobileFractionStr);
        bs = Double.parseDouble(bindingSiteConcentrationStr);
        on = Double.parseDouble(reacOnRateStr);
        off = Double.parseDouble(reacOffRateStr);
    } catch (NumberFormatException e) {
        throw new Exception("Input parameters are not all valid. Check if they are empty or in illegal forms.");
    }
    BioModel bioModel = FRAPStudy.createNewSimBioModel(frapStudy, createParameterArray(fd, ff, bwmr, cd, cf, imf, bs, on, off), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), new Integer(frapStudy.getStartingIndexForRecovery()));
    frapStudy.setBioModel(bioModel);
    // no progress listener, need to change
    MicroscopyXmlproducer.writeXMLFile(frapStudy, new File(outputXMLFileName), true, null, false);
    FRAPStudy.runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), imageDatasetExternalDataInfo.getExternalDataIdentifier(), roiExternalDataInfo.getExternalDataIdentifier(), null);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(bioModel.getSimulations()[0].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
    PDEDataManager simulationDataManager = new PDEDataManager(null, localWorkspace.getVCDataManager(), vcSimulationDataIdentifier);
    double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
    VCDataManager testVCDataManager = localWorkspace.getVCDataManager();
    double[] prebleachAverage = testVCDataManager.getSimDataBlock(null, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), "prebleach_avg", 0).getData();
    // TODO: need to create parameters here.
    Parameter[] parameters = null;
    SpatialAnalysisResults spatialAnalysisResults = FRAPStudy.spatialAnalysis(simulationDataManager, new Integer(frapStudy.getStartingIndexForRecovery()), frapDataTimeStamps[new Integer(frapStudy.getStartingIndexForRecovery())], parameters, frapData, prebleachAverage);
    dumpSummaryReport(spatialAnalysisResults, frapDataTimeStamps, new Integer(startingIndexForRecovery).intValue(), new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
    dumpSpatialResults(spatialAnalysisResults, frapDataTimeStamps, new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
}

Example 13 with PDEDataManager

use of cbit.vcell.simdata.PDEDataManager 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);
}