Examples with TimeSeriesJobSpec org.vcell.util.document.TimeSeriesJobSpec used on opensource projects

Example 6 with TimeSeriesJobSpec

use of org.vcell.util.document.TimeSeriesJobSpec in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method showTimePlot.

public void showTimePlot() {
    if ((plotChangeTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, plotChangeTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            showTimePlot();
        }
    }, "PdeTimePlotMultipleVariablesPanel update...")) != null) {
        return;
    }
    VariableType varType = multiTimePlotHelper.getVariableType();
    Object[] selectedValues = variableJList.getSelectedValues();
    DataIdentifier[] selectedDataIdentifiers = new DataIdentifier[selectedValues.length];
    System.arraycopy(selectedValues, 0, selectedDataIdentifiers, 0, selectedValues.length);
    if (selectedDataIdentifiers.length > 1) {
        for (DataIdentifier selectedDataIdentifier : selectedDataIdentifiers) {
            if (!selectedDataIdentifier.getVariableType().getVariableDomain().equals(varType.getVariableDomain())) {
                PopupGenerator.showErrorDialog(this, "Please choose VOLUME variables or MEMBRANE variables only");
                variableJList.clearSelection();
                variableJList.setSelectedValue(multiTimePlotHelper.getPdeDatacontext().getVariableName(), true);
                return;
            }
        }
    }
    try {
        final int numSelectedVariables = selectedDataIdentifiers.length;
        final int numSelectedSpatialPoints = pointVector.size();
        int[][] indices = new int[numSelectedVariables][numSelectedSpatialPoints];
        // 
        for (int i = 0; i < numSelectedSpatialPoints; i++) {
            for (int v = 0; v < numSelectedVariables; v++) {
                if (selectedDataIdentifiers[v].getVariableType().equals(varType)) {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                } else {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector2.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector2.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                }
            }
        }
        final String[] selectedVarNames = new String[numSelectedVariables];
        for (int i = 0; i < selectedVarNames.length; i++) {
            selectedVarNames[i] = selectedDataIdentifiers[i].getName();
        }
        final double[] timePoints = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
        TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(selectedVarNames, indices, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(PDEDataViewer.StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
        AsynchClientTask task2 = new AsynchClientTask("showing time plot", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
                int plotCount = numSelectedVariables * numSelectedSpatialPoints;
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
                String[] plotNames = new String[plotCount];
                double[][] plotDatas = new double[1 + plotCount][];
                plotDatas[0] = timePoints;
                int plotIndex = 0;
                for (int v = 0; v < numSelectedVariables; v++) {
                    String varName = selectedVarNames[v];
                    double[][] data = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
                    for (int i = 1; i < data.length; i++) {
                        symbolTableEntries[plotIndex] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
                        plotNames[plotIndex] = varName + " at P[" + (i - 1) + "]";
                        plotDatas[plotIndex + 1] = data[i];
                        plotIndex++;
                    }
                }
                Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
                plotPane.setPlot2D(plot2D);
            }
        };
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2 }, false, true, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 7 with TimeSeriesJobSpec

use of org.vcell.util.document.TimeSeriesJobSpec in project vcell by virtualcell.

the class ASCIIExporter method getPointsTimeSeries.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @throws IOException
 */
private FileDataContainerID getPointsTimeSeries(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variableName, GeometrySpecs geometrySpecs, double[] allTimes, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    org.vcell.util.document.TimeSeriesJobSpec timeSeriesJobSpec = new org.vcell.util.document.TimeSeriesJobSpec(new String[] { variableName }, new int[][] { geometrySpecs.getPointIndexes() }, null, allTimes[beginIndex], 1, allTimes[endIndex], VCDataJobID.createVCDataJobID(user, false));
    org.vcell.util.document.TSJobResultsNoStats timeSeriesJobResults = (org.vcell.util.document.TSJobResultsNoStats) dataServerImpl.getTimeSeriesValues(outputContext, user, vcdID, timeSeriesJobSpec);
    // variableValues[0] is time array
    // variableValues[1] is values for 1st spatial point.
    // variableValues[2] is values for 2nd spatial point.
    // variableValues[n] (n>=1) is values for nth spatial point.
    // the length of variableValues should always be 1 + pointIndexes.length
    // the length of variableValues[n] is allTimes.length
    final double[][] variableValues = timeSeriesJobResults.getTimesAndValuesForVariable(variableName);
    // 
    // put data in csv format
    // 
    SpatialSelection[] pointSpatialSelections = geometrySpecs.getPointSpatialSelections();
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    // FileDataContainer container = fileDataContainerManager.getFileDataContainer(fileDataContainerID);
    // buffer.append(
    // "\"Time Series for variable '" + variableName + "'\" over the range " + allTimes[beginIndex] + " to " + allTimes[endIndex] + "\n");
    fileDataContainerManager.append(fileDataContainerID, "\"variable ('" + variableName + "') times (" + allTimes[beginIndex] + " " + allTimes[endIndex] + ") " + /*+getSpatialSelectionDescription(curve)*/
    "\"\n");
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Coordinates\n");
        fileDataContainerManager.append(fileDataContainerID, "Time,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int k = 0; k < pointSpatialSelections.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + getSpatialSelectionDescription(pointSpatialSelections[k]));
            for (int i = beginIndex; i <= endIndex; i++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        fileDataContainerManager.append(fileDataContainerID, ",Time\n");
        fileDataContainerManager.append(fileDataContainerID, "Coordinates,");
        for (int k = 0; k < pointSpatialSelections.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + getSpatialSelectionDescription(pointSpatialSelections[k]));
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            for (int k = 0; k < pointSpatialSelections.length; k++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    return fileDataContainerID;
}

Example 8 with TimeSeriesJobSpec

use of org.vcell.util.document.TimeSeriesJobSpec in project vcell by virtualcell.

the class ASCIIExporter method getCurveTimeSeries.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @throws IOException
 */
private FileDataContainerID getCurveTimeSeries(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variableName, SpatialSelection curve, double[] allTimes, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    int[] pointIndexes = null;
    double[] distances = null;
    int[] crossingMembraneIndexes = null;
    if (curve instanceof SpatialSelectionVolume) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionVolume) curve).getIndexSamples(0.0, 1.0);
        pointIndexes = ssh.getSampledIndexes();
        distances = ssh.getWorldCoordinateLengths();
        crossingMembraneIndexes = ssh.getMembraneIndexesInOut();
    } else if (curve instanceof SpatialSelectionMembrane) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionMembrane) curve).getIndexSamples();
        if (((SpatialSelectionMembrane) curve).getSelectionSource() instanceof SinglePoint) {
            pointIndexes = new int[] { ssh.getSampledIndexes()[0] };
            distances = new double[] { 0 };
        } else {
            pointIndexes = ssh.getSampledIndexes();
            distances = ssh.getWorldCoordinateLengths();
        }
    }
    org.vcell.util.document.TimeSeriesJobSpec timeSeriesJobSpec = new org.vcell.util.document.TimeSeriesJobSpec(new String[] { variableName }, new int[][] { pointIndexes }, new int[][] { crossingMembraneIndexes }, allTimes[beginIndex], 1, allTimes[endIndex], VCDataJobID.createVCDataJobID(user, false));
    org.vcell.util.document.TSJobResultsNoStats timeSeriesJobResults = (org.vcell.util.document.TSJobResultsNoStats) dataServerImpl.getTimeSeriesValues(outputContext, user, vcdID, timeSeriesJobSpec);
    // variableValues[0] is time array
    // variableValues[1] is values for 1st spatial point.
    // variableValues[2] is values for 2nd spatial point.
    // variableValues[n] (n>=1) is values for nth spatial point.
    // the length of variableValues should always be 1 + pointIndexes.length
    // the length of variableValues[n] is allTimes.length
    final double[][] variableValues = timeSeriesJobResults.getTimesAndValuesForVariable(variableName);
    // 
    // put data in csv format
    // 
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    fileDataContainerManager.append(fileDataContainerID, "\"variable ('" + variableName + "') times (" + allTimes[beginIndex] + " " + allTimes[endIndex] + ") " + getSpatialSelectionDescription(curve) + "\"\n");
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Distances\n");
        fileDataContainerManager.append(fileDataContainerID, "Times,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int j = 0; j < distances.length; j++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[j]);
            for (int i = beginIndex; i <= endIndex; i++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        fileDataContainerManager.append(fileDataContainerID, ",Times\n");
        fileDataContainerManager.append(fileDataContainerID, "Distances,");
        for (int i = 0; i < distances.length; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            for (int j = 0; j < distances.length; j++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    return fileDataContainerID;
}

Example 9 with TimeSeriesJobSpec

use of org.vcell.util.document.TimeSeriesJobSpec in project vcell by virtualcell.

the class DataSetControllerImpl method getDataProcessingOutput.

public static DataOperationResults getDataProcessingOutput(DataOperation dataOperation, File dataProcessingOutputFileHDF5) throws Exception {
    DataOperationResults dataProcessingOutputResults = null;
    FileFormat hdf5FileFormat = null;
    try {
        if (dataProcessingOutputFileHDF5.exists()) {
            // retrieve an instance of H5File
            FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
            if (fileFormat == null) {
                throw new Exception("Cannot find HDF5 FileFormat.");
            }
            // open the file with read-only access
            hdf5FileFormat = fileFormat.open(dataProcessingOutputFileHDF5.getAbsolutePath(), FileFormat.READ);
            hdf5FileFormat.setMaxMembers(Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS);
            // open the file and retrieve the file structure
            hdf5FileFormat.open();
            Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) hdf5FileFormat.getRootNode()).getUserObject();
            if (dataOperation instanceof DataProcessingOutputInfoOP) {
                DataProcessingHelper dataProcessingHelper = new DataProcessingHelper();
                iterateHDF5(root, "", dataProcessingHelper);
                dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputInfo(dataOperation.getVCDataIdentifier(), dataProcessingHelper.getVarNames(), dataProcessingHelper.getVarISizes(), dataProcessingHelper.times, dataProcessingHelper.getVarUnits(), dataProcessingHelper.getPostProcessDataTypes(), dataProcessingHelper.getVarOrigins(), dataProcessingHelper.getVarExtents(), dataProcessingHelper.getVarStatValues());
                // map function names to PostProcess state variable name
                ArrayList<String> postProcessImageVarNames = new ArrayList<String>();
                for (int i = 0; i < ((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getVariableNames().length; i++) {
                    String variableName = ((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getVariableNames()[i];
                    if (((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getPostProcessDataType(variableName).equals(DataOperationResults.DataProcessingOutputInfo.PostProcessDataType.image)) {
                        postProcessImageVarNames.add(variableName);
                    }
                }
                HashMap<String, String> mapFunctionNameToStateVarName = null;
                if (((DataProcessingOutputInfoOP) dataOperation).getOutputContext() != null) {
                    mapFunctionNameToStateVarName = new HashMap<String, String>();
                    for (int i = 0; i < ((DataProcessingOutputInfoOP) dataOperation).getOutputContext().getOutputFunctions().length; i++) {
                        AnnotatedFunction annotatedFunction = ((DataProcessingOutputInfoOP) dataOperation).getOutputContext().getOutputFunctions()[i];
                        if (annotatedFunction.getFunctionType().equals(VariableType.POSTPROCESSING)) {
                            String[] symbols = annotatedFunction.getExpression().flatten().getSymbols();
                            // Find any PostProcess state var that matches a symbol in the function
                            for (int j = 0; j < symbols.length; j++) {
                                if (postProcessImageVarNames.contains(symbols[j])) {
                                    mapFunctionNameToStateVarName.put(annotatedFunction.getName(), symbols[j]);
                                    break;
                                }
                            }
                        }
                    }
                }
                if (mapFunctionNameToStateVarName != null && mapFunctionNameToStateVarName.size() > 0) {
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputInfo(((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults), mapFunctionNameToStateVarName);
                }
            } else {
                OutputContext outputContext = dataOperation.getOutputContext();
                String[] variableNames = null;
                DataIndexHelper dataIndexHelper = null;
                TimePointHelper timePointHelper = null;
                if (dataOperation instanceof DataOperation.DataProcessingOutputDataValuesOP) {
                    variableNames = new String[] { ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getVariableName() };
                    dataIndexHelper = ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getDataIndexHelper();
                    timePointHelper = ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getTimePointHelper();
                } else if (dataOperation instanceof DataOperation.DataProcessingOutputTimeSeriesOP) {
                    variableNames = ((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getTimeSeriesJobSpec().getVariableNames();
                    TimeSeriesJobSpec timeSeriesJobSpec = ((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getTimeSeriesJobSpec();
                    double[] specificTimepoints = extractTimeRange(((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getAllDatasetTimes(), timeSeriesJobSpec.getStartTime(), timeSeriesJobSpec.getEndTime());
                    timePointHelper = TimePointHelper.createSpecificTimePointHelper(specificTimepoints);
                    timeSeriesJobSpec.initIndices();
                    dataIndexHelper = DataIndexHelper.createSpecificDataIndexHelper(timeSeriesJobSpec.getIndices()[0]);
                } else {
                    throw new Exception("Unknown Dataoperation " + dataOperation.getClass().getName());
                }
                if (variableNames.length != 1) {
                    throw new Exception("Only 1 variable request at a time");
                }
                AnnotatedFunction[] annotatedFunctions = (outputContext == null ? null : outputContext.getOutputFunctions());
                AnnotatedFunction foundFunction = null;
                if (annotatedFunctions != null) {
                    for (int i = 0; i < annotatedFunctions.length; i++) {
                        if (annotatedFunctions[i].getName().equals(variableNames[0])) {
                            foundFunction = annotatedFunctions[i];
                            break;
                        }
                    }
                }
                double[] alltimes = null;
                if (foundFunction != null) {
                    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(dataOperation.getVCDataIdentifier(), false, dataOperation.getOutputContext()), dataProcessingOutputFileHDF5);
                    alltimes = dataProcessingOutputInfo.getVariableTimePoints();
                    FunctionHelper functionHelper = getPostProcessStateVariables(foundFunction, dataProcessingOutputInfo);
                    DataProcessingHelper dataProcessingHelper = new DataProcessingHelper(functionHelper.postProcessStateVars, timePointHelper, dataIndexHelper);
                    iterateHDF5(root, "", dataProcessingHelper);
                    dataProcessingOutputResults = evaluatePostProcessFunction(dataProcessingOutputInfo, functionHelper.postProcessStateVars, dataProcessingHelper.specificDataValues, dataIndexHelper, timePointHelper, functionHelper.flattenedBoundExpression, variableNames[0]);
                } else {
                    DataProcessingHelper dataProcessingHelper = new DataProcessingHelper(new String[] { variableNames[0] }, timePointHelper, dataIndexHelper);
                    iterateHDF5(root, "", dataProcessingHelper);
                    alltimes = dataProcessingHelper.times;
                    if (dataProcessingHelper.specificDataValues == null) {
                        throw new Exception("Couldn't find postprocess data as specified for var=" + variableNames[0]);
                    }
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputDataValues(dataOperation.getVCDataIdentifier(), variableNames[0], timePointHelper, dataIndexHelper, dataProcessingHelper.specificDataValues[0]);
                }
                if (dataOperation instanceof DataOperation.DataProcessingOutputTimeSeriesOP) {
                    TimeSeriesJobResults timeSeriesJobResults = null;
                    DataProcessingOutputTimeSeriesOP dataProcessingOutputTimeSeriesOP = (DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation;
                    // [time][data]
                    double[][] dataValues = ((DataOperationResults.DataProcessingOutputDataValues) dataProcessingOutputResults).getDataValues();
                    double[] desiredTimes = (timePointHelper.isAllTimePoints() ? alltimes : timePointHelper.getTimePoints());
                    double[][][] timeSeriesFormatedValuesArr = new double[variableNames.length][dataIndexHelper.getDataIndexes().length + 1][desiredTimes.length];
                    for (int i = 0; i < timeSeriesFormatedValuesArr.length; i++) {
                        // var
                        for (int j = 0; j < timeSeriesFormatedValuesArr[i].length; j++) {
                            // index
                            if (j == 0) {
                                timeSeriesFormatedValuesArr[i][j] = desiredTimes;
                                continue;
                            }
                            for (int k = 0; k < timeSeriesFormatedValuesArr[i][j].length; k++) {
                                // time
                                // assume 1 variable for now
                                timeSeriesFormatedValuesArr[i][j][k] = dataValues[k][j - 1];
                            }
                        }
                    }
                    if (dataProcessingOutputTimeSeriesOP.getTimeSeriesJobSpec().isCalcSpaceStats()) {
                        SpatialStatsInfo spatialStatsInfo = new SpatialStatsInfo();
                        spatialStatsInfo.bWeightsValid = false;
                        timeSeriesJobResults = calculateStatisticsFromWhole(dataProcessingOutputTimeSeriesOP.getTimeSeriesJobSpec(), timeSeriesFormatedValuesArr, timePointHelper.getTimePoints(), spatialStatsInfo);
                    } else {
                        timeSeriesJobResults = new TSJobResultsNoStats(variableNames, new int[][] { dataIndexHelper.getDataIndexes() }, timePointHelper.getTimePoints(), timeSeriesFormatedValuesArr);
                    }
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputTimeSeriesValues(dataOperation.getVCDataIdentifier(), timeSeriesJobResults);
                }
            }
        } else {
            throw new FileNotFoundException("Data Processing Output file '" + dataProcessingOutputFileHDF5.getPath() + "' not found");
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (hdf5FileFormat != null) {
            try {
                hdf5FileFormat.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return dataProcessingOutputResults;
}

Example 10 with TimeSeriesJobSpec

use of org.vcell.util.document.TimeSeriesJobSpec 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;
}