use of cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP.DataIndexHelper 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;
}
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