Examples with DataProcessingOutputInfo cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo used on opensource projects

Example 1 with DataProcessingOutputInfo

use of cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo in project vcell by virtualcell.

the class PDEDataViewerPostProcess method dispatchPostProcessUpdate.

private void dispatchPostProcessUpdate(ClientPDEDataContext newClientPDEDataContext) {
    ArrayList<AsynchClientTask> allTasks = new ArrayList<>();
    final String SPATIAL_ERROR_KEY = "SPATIAL_ERROR_KEY";
    AsynchClientTask postProcessInfoTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (postProcessPDEDataViewer != null) {
                // already initialized
                return;
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setMessage("Getting Simulation status...");
            }
            SimulationStatus simStatus = PDEDataViewerPostProcess.this.getDataViewerManager().getRequestManager().getServerSimulationStatus(PDEDataViewerPostProcess.this.getSimulation().getSimulationInfo());
            if (simStatus == null) {
                hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, no simulation status");
                return;
            } else if (!simStatus.isCompleted()) {
                // sim still busy, no postprocessing data
                hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, waiting for completed simulation: " + simStatus.toString());
                return;
            }
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setMessage("Getting Post Process Info...");
            }
            // Get PostProcess Image state variables info
            DataProcessingOutputInfoOP dataProcessingOutputInfoOP = new DataProcessingOutputInfoOP(PDEDataViewerPostProcess.this.getParentPdeDataContext().getVCDataIdentifier(), false, null);
            DataProcessingOutputInfo dataProcessingOutputInfo = (DataProcessingOutputInfo) PDEDataViewerPostProcess.this.getParentPdeDataContext().doDataOperation(dataProcessingOutputInfoOP);
            boolean bFoundImageStateVariables = false;
            if (dataProcessingOutputInfo != null && dataProcessingOutputInfo.getVariableNames() != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        bFoundImageStateVariables = true;
                        break;
                    }
                }
            }
            if (!bFoundImageStateVariables) {
                hashTable.put(SPATIAL_ERROR_KEY, "No spatial PostProcessing variables found. (see Application->Protocols->Microscope Measurement)");
            }
        }
    };
    AsynchClientTask addPanelTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (postProcessPDEDataViewer != null) {
                return;
            }
            if (hashTable.get(SPATIAL_ERROR_KEY) != null) {
                if (PDEDataViewerPostProcess.this.getComponentCount() == 0) {
                    PDEDataViewerPostProcess.this.add(new JLabel((String) hashTable.get(SPATIAL_ERROR_KEY)), BorderLayout.CENTER);
                } else {
                    ((JLabel) PDEDataViewerPostProcess.this.getComponent(0)).setText((String) hashTable.get(SPATIAL_ERROR_KEY));
                }
                throw UserCancelException.CANCEL_GENERIC;
            }
            postProcessPDEDataViewer = new PDEDataViewer();
            parentDataJobListenerHolder.addDataJobListener(postProcessPDEDataViewer);
            PDEDataViewerPostProcess.this.postProcessPDEDataViewer.setPostProcessingPanelVisible(false);
            PDEDataViewerPostProcess.this.add(PDEDataViewerPostProcess.this.postProcessPDEDataViewer, BorderLayout.CENTER);
            postProcessPDEDataViewer.setDataViewerManager(getDataViewerManager());
            postProcessPDEDataViewer.setSimulationModelInfo(getSimulationModelInfo());
            postProcessPDEDataViewer.setSimulation(getSimulation());
        }
    };
    allTasks.addAll(Arrays.asList(PDEDataViewerPostProcess.this.getUpdateTasks()));
    // AsynchClientTask refreshTask = new AsynchClientTask("refreshPostProcess",AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
    // @Override
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // ((ArrayList<AsynchClientTask>)hashTable.get(ClientTaskDispatcher.INTERMEDIATE_TASKS)).addAll(Arrays.asList(PDEDataViewerPostProcess.this.postProcessPDEDataViewer.getRefreshTasks()));
    // }
    // };
    // allTasks.add(refreshTask);
    allTasks.add(0, addPanelTask);
    allTasks.add(0, postProcessInfoTask);
    ClientTaskDispatcher.dispatch(this, new Hashtable<>(), allTasks.toArray(new AsynchClientTask[0]), false, false, false, null, true);
}

Example 2 with DataProcessingOutputInfo

use of cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo in project vcell by virtualcell.

the class PDEDataViewerPostProcess method createPostProcessPDEDataContext.

public static PostProcessDataPDEDataContext createPostProcessPDEDataContext(final ClientPDEDataContext parentPDEDataContext) throws Exception {
    final DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputInfoOP(parentPDEDataContext.getVCDataIdentifier(), false, parentPDEDataContext.getDataManager().getOutputContext()));
    if (dataProcessingOutputInfo == null) {
        return null;
    }
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return new DataSetController() {

                // DataIdentifier[] dataIdentifiers;
                @Override
                public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
                    throw new DataAccessException("Not implemented");
                }

                @Override
                public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getTimeSeriesValues(timeSeriesJobSpec);
                    DataOperation.DataProcessingOutputTimeSeriesOP dataProcessingOutputTimeSeriesOP = new DataOperation.DataProcessingOutputTimeSeriesOP(vcdataID, timeSeriesJobSpec, outputContext, getDataSetTimes(vcdataID));
                    DataOperationResults.DataProcessingOutputTimeSeriesValues dataopDataProcessingOutputTimeSeriesValues = (DataOperationResults.DataProcessingOutputTimeSeriesValues) parentPDEDataContext.doDataOperation(dataProcessingOutputTimeSeriesOP);
                    return dataopDataProcessingOutputTimeSeriesValues.getTimeSeriesJobResults();
                }

                @Override
                public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getSimDataBlock(varName, time);
                    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputValues = (DataOperationResults.DataProcessingOutputDataValues) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputDataValuesOP(vcdataID, varName, TimePointHelper.createSingleTimeTimePointHelper(time), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null));
                    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdataID.getOwner(), vcdataID.getID(), varName, time, Long.MIN_VALUE);
                    SimDataBlock simDataBlock = new SimDataBlock(pdeDataInfo, dataProcessingOutputValues.getDataValues()[0], VariableType.POSTPROCESSING);
                    return simDataBlock;
                }

                @Override
                public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return false;
                }

                @Override
                public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // throw new DataAccessException("PostProcessData mesh not available at this level");
                    return null;
                }

                @Override
                public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
                    throw new DataAccessException("Remote getLineScan method should not be called for PostProcess");
                }

                @Override
                public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    return outputContext.getOutputFunctions();
                }

                @Override
                public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    return dataProcessingOutputInfo.getVariableTimePoints();
                }

                @Override
                public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataIdentifiers();
                    ArrayList<DataIdentifier> postProcessDataIDs = new ArrayList<DataIdentifier>();
                    if (outputContext != null && outputContext.getOutputFunctions() != null) {
                        for (int i = 0; i < outputContext.getOutputFunctions().length; i++) {
                            if (outputContext.getOutputFunctions()[i].isPostProcessFunction()) {
                                postProcessDataIDs.add(new DataIdentifier(outputContext.getOutputFunctions()[i].getName(), VariableType.POSTPROCESSING, null, false, outputContext.getOutputFunctions()[i].getDisplayName()));
                            }
                        }
                    }
                    // get 'state' variables
                    for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                        if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(PostProcessDataType.image)) {
                            DataIdentifier dataIdentifier = new DataIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null, false, dataProcessingOutputInfo.getVariableNames()[i]);
                            postProcessDataIDs.add(dataIdentifier);
                        }
                    }
                    if (postProcessDataIDs.size() > 0) {
                        return postProcessDataIDs.toArray(new DataIdentifier[0]);
                    }
                    return null;
                }

                @Override
                public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return parentPDEDataContext.doDataOperation(dataOperation);
                }

                @Override
                public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @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) {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }
            };
        }
    };
    VCDataManager postProcessVCDataManager = new VCDataManager(dataSetControllerProvider);
    PDEDataManager postProcessPDEDataManager = new PDEDataManager(((ClientPDEDataContext) parentPDEDataContext).getDataManager().getOutputContext(), postProcessVCDataManager, parentPDEDataContext.getVCDataIdentifier());
    PostProcessDataPDEDataContext postProcessDataPDEDataContext = new PostProcessDataPDEDataContext(postProcessPDEDataManager);
    return postProcessDataPDEDataContext;
}

Example 3 with DataProcessingOutputInfo

use of cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo in project vcell by virtualcell.

the class LoadFRAPData_PostProcessingDataDescriptor method preNextProcess.

public ArrayList<AsynchClientTask> preNextProcess() {
    final String LOADING_MESSAGE = "Loading variable data " + postProcessingDataPanel.getSelectedVariableName() + "...";
    AsynchClientTask updateUIBeforeLoadTask = new AsynchClientTask("Updating status message...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (postProcessingDataPanel.getSelectedVariableName() == null || postProcessingDataPanel.getSelectedDataManager() == null) {
                throw new RuntimeException("Post Processing Data variable not selected");
            }
            VirtualFrapMainFrame.updateStatus(LOADING_MESSAGE);
        }
    };
    AsynchClientTask loadTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String selectedVariableName = postProcessingDataPanel.getSelectedVariableName();
            int selectedSlice = postProcessingDataPanel.getSelectedSlice();
            DataProcessingOutputInfo dataProcessingOutputInfo = postProcessingDataPanel.getSelectedDataProcessingOutputInfo();
            PDEDataManager pdeDataManager = postProcessingDataPanel.getSelectedDataManager();
            DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) pdeDataManager.doDataOperation(new DataOperation.DataProcessingOutputDataValuesOP(pdeDataManager.getVCDataIdentifier(), selectedVariableName, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(selectedSlice), null, null));
            ArrayList<SourceDataInfo> sdiArr = dataProcessingOutputDataValues.createSourceDataInfos(dataProcessingOutputInfo.getVariableISize(selectedVariableName), dataProcessingOutputInfo.getVariableOrigin(selectedVariableName), dataProcessingOutputInfo.getVariableExtent(selectedVariableName));
            FRAPStudy newFRAPStudy = FRAPWorkspace.loadFRAPDataFromDataProcessingOutput(sdiArr, dataProcessingOutputInfo.getVariableTimePoints(), 0, /*data already sliced*/
            65535.0, this.getClientTaskStatusSupport());
            isFileLoaded = true;
            hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
        }
    };
    AsynchClientTask afterLoadingSwingTask = new AsynchClientTask("Setting FrapWorkspace FrapStudy...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy newFRAPStudy = (FRAPStudy) hashTable.get(FRAPStudyPanel.NEW_FRAPSTUDY_KEY);
            // setFrapStudy fires property change, so we have to put it in Swing thread.
            getFrapWorkspace().setFrapStudy(newFRAPStudy, true);
            VirtualFrapLoader.mf.setMainFrameTitle("");
            VirtualFrapMainFrame.updateProgress(0);
            if (isFileLoaded) {
                VirtualFrapMainFrame.updateStatus("Loaded " + postProcessingDataPanel.getSelectedVariableName());
            } else {
                VirtualFrapMainFrame.updateStatus("Failed loading " + postProcessingDataPanel.getSelectedVariableName() + ".");
            }
        }
    };
    ArrayList<AsynchClientTask> tasks = new ArrayList<AsynchClientTask>();
    tasks.add(updateUIBeforeLoadTask);
    tasks.add(loadTask);
    tasks.add(afterLoadingSwingTask);
    return tasks;
}

Example 4 with DataProcessingOutputInfo

use of cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo in project vcell by virtualcell.

the class RasterExporter method exportPDEData.

private NrrdInfo[] exportPDEData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, VariableSpecs variableSpecs, TimeSpecs timeSpecs2, GeometrySpecs geometrySpecs, RasterSpecs rasterSpecs, FileDataContainerManager fileDataContainerManager) throws RemoteException, DataAccessException, IOException {
    CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    DataProcessingOutputInfo dataProcessingOutputInfo = null;
    // check if any of export variables are PostProcess and if so try to get PostProcessOutputInfo
    exportServiceImpl.fireExportProgress(jobID, vcdID, "Check PostProcess", 0.0);
    DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    for (int i = 0; i < dataIdentifiers.length; i++) {
        for (int j = 0; j < variableSpecs.getVariableNames().length; j++) {
            if (variableSpecs.getVariableNames()[j].equals(dataIdentifiers[i].getName()) && VariableType.POSTPROCESSING.equals(dataIdentifiers[i].getVariableType())) {
                try {
                    // we need PostProcessOutputInfo
                    exportServiceImpl.fireExportProgress(jobID, vcdID, "Read PostProcess", 0.0);
                    dataProcessingOutputInfo = (DataProcessingOutputInfo) dataServerImpl.doDataOperation(user, new DataOperation.DataProcessingOutputInfoOP(vcdID, false, outputContext));
                    break;
                } catch (Exception e) {
                    throw new DataAccessException("Export variable '" + variableSpecs.getVariableNames()[j] + "' is PostProcessing type.  Error reading PostProcessing data: " + e.getClass().getName() + " " + e.getMessage());
                }
            }
        }
    }
    long lastUpdateTime = 0;
    switch(rasterSpecs.getFormat()) {
        case NRRD_SINGLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NrrdInfo nrrdInfo = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                            }
                            nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { nrrdInfo };
                        }
                    case GEOMETRY_SLICE:
                        {
                            NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglslice", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                            }
                            sliceNrrdInfo = NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { sliceNrrdInfo };
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_TIME:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NRRDHelper nrrdHelper = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timefull", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo nrrdInfo = nrrdHelper.createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timeslice", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_VARIABLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NRRDHelper nrrdhelHelper = new NRRDHelper(variableSpecs.getVariableNames()[i], mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                                NrrdInfo nrrdInfo = nrrdhelHelper.createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        default:
            {
                throw new DataAccessException("Multiple NRRD file export not yet supported");
            }
    }
}

Example 5 with DataProcessingOutputInfo

use of cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo in project vcell by virtualcell.

the class PDEDataViewer method calcAutoAllTimes.

private void calcAutoAllTimes() throws Exception {
    HashSet<String> stateVarNames = null;
    Variable theVariable = null;
    boolean bStateVar = true;
    boolean isFieldData = getPdeDataContext().getVCDataIdentifier() instanceof ExternalDataIdentifier || getPdeDataContext().getVCDataIdentifier() instanceof MergedDataInfo;
    if (isFieldData) {
        // fielddata
        DataIdentifier[] dataids = getPdeDataContext().getDataIdentifiers();
        stateVarNames = new HashSet<>();
        for (int i = 0; i < dataids.length; i++) {
            if (!dataids[i].isFunction()) {
                stateVarNames.add(dataids[i].getName());
            }
        // System.out.println("name:'"+dataids[i].getName()+"' type:"+dataids[i].getVariableType()+" func:"+dataids[i].isFunction());
        }
        bStateVar = !getPdeDataContext().getDataIdentifier().isFunction();
        if (bStateVar) {
            theVariable = new VolVariable(getPdeDataContext().getDataIdentifier().getName(), getPdeDataContext().getDataIdentifier().getDomain());
        } else {
            AnnotatedFunction[] funcs = getPdeDataContext().getFunctions();
            for (int i = 0; i < funcs.length; i++) {
                if (funcs[i].getName().equals(getPdeDataContext().getDataIdentifier().getName())) {
                    theVariable = funcs[i];
                    break;
                }
            }
        }
    } else {
        stateVarNames = getSimulation().getMathDescription().getStateVariableNames();
        theVariable = getSimulation().getMathDescription().getVariable(getPdeDataContext().getVariableName());
        if (theVariable == null) {
            theVariable = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext().getOutputFunction(getPdeDataContext().getVariableName());
        }
        if (theVariable == null) {
            DataProcessingOutputInfo dataProcessingOutputInfo = DataProcessingResultsPanel.getDataProcessingOutputInfo(getPdeDataContext());
            if (dataProcessingOutputInfo != null && Arrays.asList(dataProcessingOutputInfo.getVariableNames()).contains(getPdeDataContext().getVariableName())) {
                // PostProcess Variable
                return;
            }
        }
        bStateVar = stateVarNames.contains(getPdeDataContext().getVariableName());
    }
    if (theVariable == null) {
        throw new Exception("Unexpected Alltimes... selected variable '" + getPdeDataContext().getVariableName() + "' is not stateVariable or OutputFunction");
    }
    if (getPDEDataContextPanel1().getdisplayAdapterService1().getAllTimes()) {
        // min-max over all timepoints (allTimes)
        if (theVariable.isConstant()) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            double constVal = theVariable.getExpression().evaluateConstant();
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(constVal, constVal));
        } else if (bStateVar) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), new String[] { theVariable.getName() });
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // no postprocessinfo
                return;
            }
            FunctionStatistics functionStatistics = new FunctionStatistics(varStatsArr.get(0).minValuesOverTime, varStatsArr.get(0).maxValuesOverTime);
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
        } else if (theVariable instanceof Function) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
            Function flattened = MathDescription.getFlattenedFunctions(SimulationSymbolTable.createMathSymbolTableFactory(), getSimulation().getMathDescription(), new String[] { theVariable.getName() })[0];
            if (flattened == null) {
                flattened = (Function) theVariable;
            }
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), stateVarNames.toArray(new String[0]));
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // check for no postprocessinfo
                return;
            }
            if (varStatsArr.size() == stateVarNames.size()) {
                if (getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                    getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().updateAll();
                }
                FunctionStatistics functionStatistics = FunctionRangeGenerator.getFunctionStatistics(flattened.getExpression(), varStatsArr.toArray(new VarStatistics[0]), getPdeDataContext().getTimePoints(), getPdeDataContext().getCartesianMesh(), calcInDomainBitSet(), getPdeDataContext().getDataIdentifier().getVariableType());
                getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
            } else {
                throw new Exception("Unexpectede AllTimes... calculated state var stats size != mathdescr state var size");
            }
        } else {
            throw new Exception("Unexpected AllTimes... not constant, stateVar or function");
        }
    } else {
        // min-max at each timepoint (currTime)
        if (!(theVariable instanceof Function)) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
        } else {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
        }
        getPDEDataContextPanel1().setFunctionStatisticsRange(null);
    }
}