use of cbit.vcell.simdata.OutputContext in project vcell by virtualcell.
the class SimulationServiceImpl method getData.
public List<Double> getData(SimulationInfo simInfo, VariableInfo varInfo, int timeIndex) throws ThriftDataAccessException, TException {
SimulationServiceContext simServiceContext = sims.get(simInfo.id);
if (simServiceContext == null) {
throw new RuntimeException("simulation results not found");
}
DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
try {
double[] times = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
SimDataBlock simDataBlock = datasetController.getSimDataBlock(outputContext, simServiceContext.vcDataIdentifier, varInfo.getVariableVtuName(), times[timeIndex]);
double[] dataArray = simDataBlock.getData();
ArrayList<Double> dataList = new ArrayList<Double>();
for (double d : dataArray) {
dataList.add(d);
}
return dataList;
} catch (Exception e) {
e.printStackTrace();
throw new ThriftDataAccessException("failed to retrieve data for variable " + varInfo.getVariableVtuName() + ": " + e.getMessage());
}
}
use of cbit.vcell.simdata.OutputContext in project vcell by virtualcell.
the class SimulationServiceImpl method getVariableList.
public List<VariableInfo> getVariableList(SimulationInfo simInfo) throws ThriftDataAccessException, TException {
SimulationServiceContext simServiceContext = sims.get(simInfo.id);
if (simServiceContext == null) {
throw new ThriftDataAccessException("simulation results not found");
}
try {
DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
final DataIdentifier[] dataIdentifiers;
try {
dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
} catch (IOException | DataAccessException e) {
e.printStackTrace();
throw new RuntimeException("failed to retrieve variable information: " + e.getMessage(), e);
}
ArrayList<VariableInfo> varInfos = new ArrayList<VariableInfo>();
for (DataIdentifier dataIdentifier : dataIdentifiers) {
final DomainType domainType;
if (dataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
domainType = DomainType.VOLUME;
} else if (dataIdentifier.getVariableType().equals(VariableType.MEMBRANE)) {
domainType = DomainType.MEMBRANE;
} else {
continue;
}
String domainName = "";
if (dataIdentifier.getDomain() != null) {
domainName = dataIdentifier.getDomain().getName();
}
VariableInfo varInfo = new VariableInfo(dataIdentifier.getName(), dataIdentifier.getDisplayName(), domainName, domainType);
varInfos.add(varInfo);
}
return varInfos;
} catch (Exception e) {
e.printStackTrace();
throw new ThriftDataAccessException("failed to retrieve variable list: " + e.getMessage());
}
}
use of cbit.vcell.simdata.OutputContext in project vcell by virtualcell.
the class SimulationServiceImpl method getDataSetController.
private static DataSetControllerImpl getDataSetController(SimulationServiceContext simServiceContext) {
try {
OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
Cachetable cacheTable = new Cachetable(10000);
DataSetControllerImpl datasetController = new DataSetControllerImpl(cacheTable, simServiceContext.localSimDataDir.getParentFile(), null);
simServiceContext.times = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
simServiceContext.dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
return datasetController;
} catch (IOException | DataAccessException e1) {
e1.printStackTrace();
throw new RuntimeException("failed to read dataset: " + e1.getMessage());
}
}
use of cbit.vcell.simdata.OutputContext 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);
}
use of cbit.vcell.simdata.OutputContext in project vcell by virtualcell.
the class NagiosVCellCheck method checkVCell.
private static String checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int warningTimeout, int criticalTimeout) throws Exception {
long startTime = System.currentTimeMillis();
SimulationStatusPersistent lastSimStatus = null;
if (rmiHostName == null || rmiPort == -1) {
throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
}
String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
VCellBootstrap vcellBootstrap = null;
try {
vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
} catch (Exception e) {
throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
}
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
if (vcellNagiosPassword == null) {
throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
}
VCellConnection vcellConnection = vcellBootstrap.getVCellConnection(new UserLoginInfo("vcellNagios", new DigestedPassword(vcellNagiosPassword)));
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
KeyValue bioModelKey = null;
final String testModelName = "Solver Suite 5.1 (BETA only ode)";
for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
if (bioModelInfo.getVersion().getName().equals(testModelName)) {
bioModelKey = bioModelInfo.getVersion().getVersionKey();
break;
}
}
BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
bioModel.refreshDependencies();
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
final String testSimContextName = "non-spatial ODE";
SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
final String testSimName = "Copy of combined ida/cvode";
Simulation simulation = simulationContext.getSimulation(testSimName);
if (simulation == null) {
throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
}
VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
// SimDataBlock simDataBlock = vcellConnection.getDataSetController().getSimDataBlock(outputContext, vcSimulationDataIdentifier, "RanC_cyt",times[times.length-1]);
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
KeyValue copy1Key = null;
KeyValue copy2Key = null;
try {
if (simulationContext.getSimulations().length != 1) {
throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
}
SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
if (!simulationStatus.isCompleted()) {
throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
}
String copyModelName = testModelName + "_" + rmiHostName + "_" + rmiPort;
for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
if (bioModelInfo.getVersion().getName().equals(copyModelName)) {
throw new UnexpectedTestStateException("Messy test environment, not expecting " + copyModelName + " to exist at this point");
}
}
BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
copy1Key = copyBioModel.getVersion().getVersionKey();
copyBioModel.refreshDependencies();
Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
final String copyTestSimName = "test";
copySim.setName(copyTestSimName);
copyBioModel.refreshDependencies();
copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
copy2Key = copyBioModel.getVersion().getVersionKey();
copyBioModel.refreshDependencies();
Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
if (simulationStatus != null && !simulationStatus.isNeverRan()) {
throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
}
VCSimulationIdentifier newSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
vcellConnection.getSimulationController().startSimulation(newSimID, 1);
lastSimStatus = simulationStatus;
MessageEvent[] messageEvents = null;
while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
Thread.sleep(200);
if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
vcellConnection.getSimulationController().stopSimulation(newSimID);
vcellConnection.getMessageEvents();
break;
}
simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
lastSimStatus = simulationStatus;
}
messageEvents = vcellConnection.getMessageEvents();
}
} finally {
try {
if (copy1Key != null) {
vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (copy2Key != null) {
vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
}
}
}
long endTime = System.currentTimeMillis();
if (criticalTimeout != -1 && ((endTime - startTime) / 1000) > criticalTimeout) {
throw new Exception(checkLevel.toString() + " test exceeded criticalTimeout=" + criticalTimeout + " seconds lastSimStatus=" + lastSimStatus);
}
if (warningTimeout != -1 && ((endTime - startTime) / 1000) > warningTimeout) {
throw new WarningTestConditionException(checkLevel.toString() + " test exceeded warningTimeout=" + warningTimeout + " seconds lastSimStatus=" + lastSimStatus);
}
return vcellBootstrap.getVCellSoftwareVersion();
}
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