Examples with DataProcessingOutputDataValuesOP cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP used on opensource projects

Example 1 with DataProcessingOutputDataValuesOP

use of cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP in project vcell by virtualcell.

the class SimulationData method getSimDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
public synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    try {
        if (isPostProcessing(outputContext, varName)) {
            PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastDataProcessingOutputInfoTime);
            DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varName, TimePointHelper.createSingleTimeTimePointHelper(extractClosestPostProcessTime(time)), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null);
            DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
            return new SimDataBlock(pdeDataInfo, dataProcessingOutputDataValues.getDataValues()[0], /*1 time only*/
            VariableType.POSTPROCESSING);
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    File pdeFile = getPDEDataFile(time);
    if (pdeFile == null) {
        return null;
    }
    DataSet dataSet = getPDEDataSet(pdeFile, time);
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    long lastModified = getLastModified(pdeFile, zipFile);
    DataSetIdentifier dsi = getDataSetIdentifier(varName);
    if (dsi == null) {
        throw new DataAccessException("data not found for variable " + varName);
    }
    final String varNameInDataSet = dsi.getQualifiedName();
    double[] data = dataSet.getData(varNameInDataSet, zipFile, time, amplistorHelper.solverDataType);
    int varTypeInt = dataSet.getVariableTypeInteger(varNameInDataSet);
    VariableType variableType = null;
    try {
        variableType = VariableType.getVariableTypeFromInteger(varTypeInt);
    } catch (IllegalArgumentException e) {
        e.printStackTrace(System.out);
        System.out.println("invalid varTypeInt = " + varTypeInt + " for variable " + varName + " at time " + time);
        try {
            variableType = SimulationData.getVariableTypeFromLength(getMesh(), data.length);
        } catch (MathException ex) {
            ex.printStackTrace(System.out);
            throw new DataAccessException(ex.getMessage());
        }
    }
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastModified);
    if (data != null) {
        return new SimDataBlock(pdeDataInfo, data, variableType);
    } else {
        return null;
    }
}

Example 2 with DataProcessingOutputDataValuesOP

use of cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP in project vcell by virtualcell.

the class SimulationData method getSimDataTimeSeries0.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
synchronized double[][][] getSimDataTimeSeries0(OutputContext outputContext, String[] varNames, int[][] indexes, boolean[] wantsThisTime, DataSetControllerImpl.SpatialStatsInfo spatialStatsInfo, DataSetControllerImpl.ProgressListener progressListener) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    int resultsCounter = 0;
    for (int i = 0; i < wantsThisTime.length; i += 1) {
        if (wantsThisTime[i]) {
            resultsCounter += 1;
        }
    }
    // min,max,mean,wmean
    final int NUM_STATS = 4;
    // Create results buffer
    // [timePoints][varNames][dataIndexes]
    double[][][] results = new double[resultsCounter][][];
    for (int i = 0; i < results.length; i += 1) {
        results[i] = new double[varNames.length][];
        for (int j = 0; j < results[i].length; j += 1) {
            if (spatialStatsInfo != null) {
                // min,max.mean,wmean
                results[i][j] = new double[NUM_STATS];
            } else {
                results[i][j] = new double[indexes[j].length];
            }
        }
    }
    try {
        if (varNames.length > 0 && isPostProcessing(outputContext, varNames[0])) {
            double[] specificTimePoints = new double[results.length];
            int counter = 0;
            for (int i = 0; i < dataProcessingOutputInfo.getVariableTimePoints().length; i++) {
                if (wantsThisTime[i]) {
                    specificTimePoints[counter] = dataProcessingOutputInfo.getVariableTimePoints()[i];
                    counter++;
                }
            }
            // PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(),vcDataId.getID(),varName,time,lastDataProcessingOutputInfoTime);
            for (int i = 0; i < varNames.length; i++) {
                DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varNames[i], TimePointHelper.createSpecificTimePointHelper(specificTimePoints), DataIndexHelper.createSpecificDataIndexHelper(indexes[i]), outputContext, null);
                DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
                for (int j = 0; j < specificTimePoints.length; j++) {
                    results[j][i] = dataProcessingOutputDataValues.getDataValues()[j];
                }
            }
            return results;
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    String[] varNamesInDataSet = new String[varNames.length];
    for (int i = 0; i < varNamesInDataSet.length; i++) {
        varNamesInDataSet[i] = getDataSetIdentifier(varNames[i]).getQualifiedName();
    }
    // Setup parameters for SimDataReader
    double[] tempDataTimes = dataTimes.clone();
    String[] tempZipFileNames = null;
    if (bZipFormat2) {
        tempZipFileNames = new String[tempDataTimes.length];
    }
    String[] tempSimDataFileNames = new String[tempDataTimes.length];
    for (int i = 0; i < tempDataTimes.length; i += 1) {
        if (bZipFormat2 || bZipFormat1) {
            if (bZipFormat2) {
                tempZipFileNames[i] = getPDEDataZipFile(tempDataTimes[i]).getAbsolutePath();
            }
            tempSimDataFileNames[i] = dataFilenames[i];
        } else {
            // userDirectory.getAbsolutePath()+"\\"+dataFilenames[i];//getPDEDataFile(dataTimes[i]).getAbsolutePath();
            tempSimDataFileNames[i] = amplistorHelper.getFile(dataFilenames[i]).getName();
        }
    }
    SimDataReader sdr = null;
    double[][] singleTimePointResultsBuffer = new double[varNamesInDataSet.length][];
    for (int i = 0; i < singleTimePointResultsBuffer.length; i += 1) {
        singleTimePointResultsBuffer[i] = new double[indexes[i].length];
    }
    // In case sim files have been updated since "wantsThisTime" was calculated
    if (wantsThisTime.length < tempDataTimes.length) {
        double[] tempTempDataTimes = new double[wantsThisTime.length];
        System.arraycopy(tempDataTimes, 0, tempTempDataTimes, 0, wantsThisTime.length);
        tempDataTimes = tempTempDataTimes;
        String[] tempTempZipFileNames = new String[wantsThisTime.length];
        System.arraycopy(tempZipFileNames, 0, tempTempZipFileNames, 0, wantsThisTime.length);
        tempZipFileNames = tempTempZipFileNames;
        String[] tempTempSimDataFileNames = new String[wantsThisTime.length];
        System.arraycopy(tempSimDataFileNames, 0, tempTempSimDataFileNames, 0, wantsThisTime.length);
        tempSimDataFileNames = tempTempSimDataFileNames;
    }
    try {
        sdr = new SimDataReader(wantsThisTime, tempDataTimes, tempZipFileNames, tempSimDataFileNames, varNamesInDataSet, indexes, isChombo());
        int counter = 0;
        int progressCounter = 0;
        while (sdr.hasMoreData()) {
            sdr.getNextDataAtCurrentTime(singleTimePointResultsBuffer);
            // Copy data to timeSeries format
            if (wantsThisTime[counter]) {
                for (int i = 0; i < varNamesInDataSet.length; i += 1) {
                    if (spatialStatsInfo != null) {
                        results[progressCounter][i] = calcSpaceStats(singleTimePointResultsBuffer[i], i, spatialStatsInfo);
                    } else {
                        for (int j = 0; j < indexes[i].length; j += 1) {
                            results[progressCounter][i][j] = singleTimePointResultsBuffer[i][j];
                        }
                    }
                }
                progressCounter += 1;
                if (progressListener != null) {
                    progressListener.updateProgress(100.0 * (double) progressCounter / (double) resultsCounter);
                }
            }
            counter += 1;
        }
        return results;
    } catch (DataAccessException e) {
        throw e;
    } catch (IOException e) {
        throw e;
    } catch (Throwable e) {
        throw new DataAccessException(e.getMessage(), e);
    } finally {
        if (sdr != null) {
            sdr.close();
        }
    }
}

Example 3 with DataProcessingOutputDataValuesOP

use of cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP in project vcell by virtualcell.

the class RunFakeSimOp method runRefSimulation.

public ImageTimeSeries<UShortImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, double max_intensity, double bleachBlackoutStartTime, double bleachBlackoutStopTime, boolean hasNoise, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner()), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) localWorkspace.getDataSetControllerImpl().doDataOperation(new DataProcessingOutputDataValuesOP(vcDataIdentifier, SimulationContext.FLUOR_DATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null));
    ArrayList<SourceDataInfo> sourceDataInfoArr = dataProcessingOutputDataValues.createSourceDataInfos(new ISize(mesh.getSizeX(), mesh.getSizeY(), 1), origin, extent);
    // find scale factor to scale up the data to avoid losing precision when casting double to short
    double maxDataValue = 0;
    for (int i = 0; i < dataTimes.length; i++) {
        if (sourceDataInfoArr.get(i).getMinMax() != null) {
            maxDataValue = Math.max(maxDataValue, sourceDataInfoArr.get(i).getMinMax().getMax());
        } else {
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            for (int j = 0; j < doubleData.length; j++) {
                maxDataValue = Math.max(maxDataValue, doubleData[j]);
            }
        }
    }
    double scale = max_intensity / maxDataValue;
    ArrayList<UShortImage> outputImages = new ArrayList<UShortImage>();
    ArrayList<Double> outputTimes = new ArrayList<Double>();
    for (int i = 0; i < dataTimes.length; i++) {
        if (dataTimes[i] < bleachBlackoutStartTime || dataTimes[i] > bleachBlackoutStopTime) {
            // saving each time step 2D double array to a UShortImage
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            short[] shortData = new short[isize.getX() * isize.getY()];
            for (int j = 0; j < shortData.length; j++) {
                double dData = doubleData[j] * scale;
                if (dData < 0 || dData > 65535.0) {
                    throw new RuntimeException("scaled pixel out of range of unsigned 16 bit integer, original simulated value = " + doubleData[j] + ", scale = " + scale + ", scaled value = " + dData);
                }
                short sData = (short) (0x0000ffff & ((int) dData));
                if (hasNoise && dData > 0.0) {
                    if (dData > 20) {
                        shortData[j] = (short) (0x0000ffff & (int) RandomVariable.normal(dData, Math.sqrt(dData)));
                    } else {
                        shortData[j] = (short) (0x0000ffff & RandomVariable.poisson(dData));
                    }
                } else {
                    shortData[j] = sData;
                }
            }
            outputTimes.add(dataTimes[i]);
            outputImages.add(new UShortImage(shortData, sourceDataInfoArr.get(i).getOrigin(), sourceDataInfoArr.get(i).getExtent(), sourceDataInfoArr.get(i).getXSize(), sourceDataInfoArr.get(i).getYSize(), 1));
            if (progressListener != null) {
                int progress = (int) (((i + 1) * 1.0 / dataTimes.length) * 100);
                progressListener.setProgress(progress);
            }
        }
    }
    double[] outputTimesArray = new double[outputTimes.size()];
    for (int i = 0; i < outputTimes.size(); i++) {
        outputTimesArray[i] = outputTimes.get(i);
    }
    ImageTimeSeries<UShortImage> fakeFluorTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, outputImages.toArray(new UShortImage[0]), outputTimesArray, 1);
    return fakeFluorTimeSeries;
}