Examples with VtuVarInfo org.vcell.vis.io.VtuVarInfo used on opensource projects

Example 6 with VtuVarInfo

use of org.vcell.vis.io.VtuVarInfo in project vcell by virtualcell.

the class DisplayTimeSeriesOp method getDataSetControllerProvider.

private DataSetControllerProvider getDataSetControllerProvider(final ImageTimeSeries<? extends Image> imageTimeSeries, final PDEDataViewer pdeDataViewer) 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 {
            pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_START, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
            if (!timeSeriesJobSpec.isCalcSpaceStats() && !timeSeriesJobSpec.isCalcTimeStats()) {
                int[][] indices = timeSeriesJobSpec.getIndices();
                double[] timeStamps = imageTimeSeries.getImageTimeStamps();
                // [var][dataindex+1][timeindex]
                double[][][] dataValues = new double[1][indices[0].length + 1][timeStamps.length];
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    // index 0 is time
                    dataValues[0][0][timeIndex] = timeStamps[timeIndex];
                }
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    float[] pixelValues = imageTimeSeries.getAllImages()[timeIndex].getFloatPixels();
                    for (int samplePointIndex = 0; samplePointIndex < indices[0].length; samplePointIndex++) {
                        int pixelIndex = indices[0][samplePointIndex];
                        dataValues[0][samplePointIndex + 1][timeIndex] = pixelValues[pixelIndex];
                    }
                }
                TSJobResultsNoStats timeSeriesJobResults = new TSJobResultsNoStats(new String[] { "var" }, indices, timeStamps, dataValues);
                pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_COMPLETE, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
                return timeSeriesJobResults;
            }
            return null;
        }

        @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;
        }
    };
    return dataSetControllerProvider;
}

Example 7 with VtuVarInfo

use of org.vcell.vis.io.VtuVarInfo in project vcell by virtualcell.

the class VCellProxyHandler method getDataSetFileOfVariableAtTimeIndex.

@Override
public String getDataSetFileOfVariableAtTimeIndex(SimulationDataSetRef simulationDataSetRef, VariableInfo var, int timeIndex) throws ThriftDataAccessException {
    try {
        if (var.isMeshVar) {
            return getEmptyMeshFile(simulationDataSetRef, var.domainName, timeIndex).getAbsolutePath();
        }
        File meshFileForVariableAndTime = getPopulatedMeshFileLocation(simulationDataSetRef, var, timeIndex);
        if (meshFileForVariableAndTime.exists()) {
            return meshFileForVariableAndTime.getAbsolutePath();
        }
        // 
        // get data from server for this variable, domain, time
        // 
        VtkManager vtkManager = vcellClientDataService.getVtkManager(simulationDataSetRef);
        VariableDomain variableDomainType = VariableDomain.VARIABLEDOMAIN_UNKNOWN;
        if (var.variableDomainType == DomainType.MEMBRANE) {
            variableDomainType = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
        } else if (var.variableDomainType == DomainType.VOLUME) {
            variableDomainType = VariableDomain.VARIABLEDOMAIN_VOLUME;
        }
        org.vcell.vis.io.VtuVarInfo.DataType dataType = org.vcell.vis.io.VtuVarInfo.DataType.CellData;
        if (var.isSetDataType() && var.dataType == DataType.CELLDATA) {
            dataType = org.vcell.vis.io.VtuVarInfo.DataType.CellData;
        } else if (var.isSetDataType() && var.dataType == DataType.POINTDATA) {
            dataType = org.vcell.vis.io.VtuVarInfo.DataType.PointData;
        }
        VtuVarInfo vtuVarInfo = new VtuVarInfo(var.getVariableVtuName(), var.getVariableDisplayName(), var.getDomainName(), variableDomainType, var.getExpressionString(), dataType, var.isMeshVar);
        List<Double> times = getTimePoints(simulationDataSetRef);
        double time = (double) times.get(timeIndex);
        double[] data = vtkManager.getVtuMeshData(vtuVarInfo, time);
        // 
        // get empty mesh file for this domain (getEmptyMeshFile() will ensure that the file exists or create it).
        // 
        File emptyMeshFile = getEmptyMeshFile(simulationDataSetRef, var.getDomainName(), timeIndex);
        if (var.getDataType() == DataType.CELLDATA) {
            VisMeshUtils.writeCellDataToVtu(emptyMeshFile, var.getVariableVtuName(), data, meshFileForVariableAndTime);
        } else if (var.getDataType() == DataType.POINTDATA) {
            VisMeshUtils.writePointDataToVtu(emptyMeshFile, var.getVariableVtuName(), data, meshFileForVariableAndTime);
        }
        return meshFileForVariableAndTime.getAbsolutePath();
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve data file for variable " + var.getVariableVtuName() + " at time index " + timeIndex);
    }
}

Example 8 with VtuVarInfo

use of org.vcell.vis.io.VtuVarInfo in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(MovingBoundarySimFiles movingBoundaryFiles, OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException {
    try {
        DataIdentifier[] dataIdentifiers = getDataIdentifiers(outputContext, vcdataID);
        if (dataIdentifiers == null) {
            return null;
        }
        ArrayList<VtuVarInfo> vtuVarInfos = new ArrayList<VtuVarInfo>();
        for (DataIdentifier di : dataIdentifiers) {
            String name = di.getName();
            String displayName = di.getDisplayName();
            if (di.getDomain() != null) {
                System.err.println("DataSetControllerImpl.getVtuVarInfos(movingboundary): need to support proper domain names now");
            }
            String domainName = MovingBoundaryReader.getFakeInsideDomainName();
            VariableDomain variableDomain = null;
            VariableType variableType = di.getVariableType();
            if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
            } else if (variableType.equals(VariableType.MEMBRANE) || variableType.equals(VariableType.MEMBRANE_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
            } else if (variableType.equals(VariableType.POINT_VARIABLE)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_POINT;
            } else if (variableType.equals(VariableType.CONTOUR) || variableType.equals(VariableType.CONTOUR_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_CONTOUR;
            } else if (variableType.equals(VariableType.NONSPATIAL)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_UNKNOWN;
            } else if (variableType.equals(VariableType.POSTPROCESSING)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_POSTPROCESSING;
            } else {
                System.err.print("skipping var " + di + ", unsupported data type");
            }
            String functionExpression = null;
            boolean bMeshVariable = false;
            if (name.toUpperCase().contains("SIZE")) {
                System.err.println("Skipping Moving Boundary variable '" + name + "' because it is a size ... change later");
                continue;
            }
            vtuVarInfos.add(new VtuVarInfo(name, displayName, domainName, variableDomain, functionExpression, DataType.CellData, bMeshVariable));
        }
        return vtuVarInfos.toArray(new VtuVarInfo[0]);
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK variable list: " + e.getMessage(), e);
    }
}

Example 9 with VtuVarInfo

use of org.vcell.vis.io.VtuVarInfo in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(ChomboFiles chomboFiles, OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException {
    try {
        ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
        VtuVarInfo[] vtuVarInfos = chomboVTKFileWriter.getVtuVarInfos(chomboFiles, outputContext, getVCData(vcdataID));
        return vtuVarInfos;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK variable list: " + e.getMessage(), e);
    }
}

Example 10 with VtuVarInfo

use of org.vcell.vis.io.VtuVarInfo in project vcell by virtualcell.

the class ChomboVtkFileWriter method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(ChomboFiles chomboFiles, OutputContext outputContext, VCData vcData) throws DataAccessException, IOException {
    // 
    // read the time=0 chombo dataset into memory to get the var names (probably a more efficient way of doing this).
    // 
    ChomboDataset chomboDataset;
    try {
        int timeIndex = 0;
        chomboDataset = ChomboFileReader.readDataset(chomboFiles, chomboFiles.getTimeIndices().get(timeIndex));
    } catch (Exception e) {
        throw new DataAccessException("failed to read chombo dataset: " + e.getMessage(), e);
    }
    DataIdentifier[] dataIdentifiers = vcData.getVarAndFunctionDataIdentifiers(outputContext);
    for (DataIdentifier di : dataIdentifiers) {
        System.out.println(((di.getDomain() != null) ? di.getDomain().getName() : "none") + "::" + di.getName() + "-" + di.getVariableType());
    }
    // 
    // for each ChomboDomain get list of built-in (mesh) variables, component (regular) volume variables, and Membrane Variables (still tied to the volume).
    // 
    ArrayList<VtuVarInfo> varInfos = new ArrayList<VtuVarInfo>();
    for (ChomboCombinedVolumeMembraneDomain chomboCombinedVolumeMembraneDomain : chomboDataset.getCombinedVolumeMembraneDomains()) {
        ChomboMeshData chomboMeshData = chomboCombinedVolumeMembraneDomain.getChomboMeshData();
        // 
        // process Volume variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String volumeDomainName = chomboCombinedVolumeMembraneDomain.getVolumeDomainName();
            VariableDomain volVariableDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
            for (String builtinVarName : chomboMeshData.getVolumeBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String componentVarName : chomboMeshData.getVisibleVolumeDataNames()) {
                String varName = componentVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_VOLUME && (dataID.getDomain() == null || dataID.getDomain().getName().equals(volumeDomainName))) {
                    String displayName = "(" + volumeDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
        // 
        // process membrane variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String memDomainName = chomboCombinedVolumeMembraneDomain.getMembraneDomainName();
            VariableDomain memVariableDomain = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
            for (ChomboMembraneVarData membraneVarData : chomboMeshData.getMembraneVarData()) {
                String varName = membraneVarData.getName();
                String displayName = "(" + membraneVarData.getDomainName() + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String builtinVarName : chomboMeshData.getMembraneBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + memDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_MEMBRANE && (dataID.getDomain() == null || dataID.getDomain().getName().equals(memDomainName))) {
                    String displayName = "(" + memDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
    }
    return varInfos.toArray(new VtuVarInfo[0]);
}