Examples with FRAPStudy cbit.vcell.microscopy.FRAPStudy used on opensource projects

Example 36 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPStudyPanel method refreshROIs.

protected void refreshROIs() throws Exception {
    try {
        // check if all the data for generating spatial model are ready.
        FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
        if (fStudy == null) {
            throw new Exception("No FrapStudy is defined");
        }
        if (fStudy.getFrapData() == null) {
            throw new Exception("No FrapData is defined");
        }
        if (fStudy.getFrapData().getImageDataset() == null) {
            throw new Exception("No ImageDataSet is defined");
        }
        fStudy.refreshDependentROIs();
    } catch (Exception e) {
        throw e;
    }
}

Example 37 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPStudyPanel method refreshPDEDisplay.

protected void refreshPDEDisplay(DisplayChoice choice) throws Exception {
    Simulation sim = null;
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
        return;
    }
    sim = fStudy.getBioModel().getSimulations()[0];
    FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
    for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
        fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
    }
    PDEDataViewer flourViewer = getFlourDataViewer();
    PDEDataManager dataManager = null;
    if (choice == DisplayChoice.EXTTIMEDATA) {
        flourViewer.setSimulation(null);
        flourViewer.setPdeDataContext(null);
        flourViewer.setDataIdentifierFilter(new DataIdentifierFilter() {

            private String ALL_DATAIDENTIFIERS = "All";

            private String EXP_NORM_FLUOR = "Exp. Norm. Fluor";

            private String SIM_NORM_FLUOR = "Sim. Norm. Fluor";

            private String DEFAULT_VIEW = "Default View (more...)";

            private String[] filterSetNames = new String[] { ALL_DATAIDENTIFIERS, EXP_NORM_FLUOR, SIM_NORM_FLUOR, DEFAULT_VIEW };

            public boolean accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier dataidentifier) {
                if (filterSetName.equals(ALL_DATAIDENTIFIERS)) {
                    return true;
                } else if (filterSetName.equals(EXP_NORM_FLUOR)) {
                    return dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1;
                } else if (filterSetName.equals(SIM_NORM_FLUOR)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_COMBINED) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_IMMOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_MOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) != -1));
                    return a;
                } else if (filterSetName.equals(DEFAULT_VIEW)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1) || (dataidentifier.getName().indexOf(NORM_SIM_VAR) != -1));
                    return a;
                }
                throw new IllegalArgumentException("DataIdentifierFilter: Unknown filterSetName " + filterSetName);
            }

            public String getDefaultFilterName() {
                return DEFAULT_VIEW;
            }

            public String[] getFilterSetNames() {
                return filterSetNames;
            }

            public boolean isAcceptAll(String filterSetName) {
                return filterSetName.equals(ALL_DATAIDENTIFIERS);
            }

            @Override
            public void setPostProcessingMode(boolean bPostProcessingMode) {
            // TODO Auto-generated method stub
            }

            @Override
            public boolean isPostProcessingMode() {
                // TODO Auto-generated method stub
                return false;
            }

            @Override
            public ArrayList<DataIdentifier> accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier[] dataidentifiers) {
                if (filterSetName.equals(DEFAULT_VIEW)) {
                    ArrayList<DataIdentifier> dataIds = new ArrayList<>();
                    if (dataidentifiers != null) {
                        for (int i = 0; i < dataidentifiers.length; i++) {
                            dataIds.add(dataidentifiers[i]);
                        }
                    }
                    return dataIds;
                }
                throw new RuntimeException("Not Implemented for FRAP");
            }
        });
        ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
        ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
        // add sim
        int jobIndex = 0;
        SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
        // add function to display normalized fluorence data
        Norm_Exp_Fluor = new Expression(Norm_Exp_Fluor_Str);
        SimulationSymbolTable simSymbolTable = simJob.getSimulationSymbolTable();
        if (// one diffusing component
        simSymbolTable.getVariable(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) == null) {
            Norm_Sim = new Expression(Norm_Sim_One_Diff_Str);
        } else // two diffusing components
        {
            Norm_Sim = new Expression(Norm_Sim_Two_Diff_Str);
        }
        AnnotatedFunction[] func = { new AnnotatedFunction(NORM_FLUOR_VAR, Norm_Exp_Fluor, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED), new AnnotatedFunction(NORM_SIM_VAR, Norm_Sim, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED) };
        VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
        VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
        outputContext = new OutputContext(func);
        dataManager = new PDEDataManager(outputContext, getLocalWorkspace().getVCDataManager(), vcDataId);
        ClientPDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
        pdeDataContext.refreshIdentifiers();
        flourViewer.setSimulation(sim);
        flourViewer.setPdeDataContext(pdeDataContext);
        SimulationModelInfo simModelInfo = new SimulationWorkspaceModelInfo(fStudy.getBioModel().getSimulationContext(sim), sim.getName());
        flourViewer.setSimulationModelInfo(simModelInfo);
        getLocalWorkspace().getDataSetControllerImpl().addDataJobListener(flourViewer);
        ((VirtualFrapWindowManager) flourViewer.getDataViewerManager()).setLocalWorkSpace(getLocalWorkspace());
        // do now show post data processing for VFRAP
        flourViewer.setPostProcessingPanelVisible(false);
        flourViewer.repaint();
    }
}

Example 38 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPStudyPanel method showMovie.

private void showMovie() {
    AsynchClientTask createMovieTask = new AsynchClientTask("Buffering movie data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy == null) {
                return;
            }
            if (fStudy.getMovieURLString() != null && fStudy.getMovieFileString() != null) {
                hashTable.put("FrapStudy", fStudy);
                return;
            }
            // create export specs
            Simulation sim = null;
            if (fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
                return;
            } else {
                sim = fStudy.getBioModel().getSimulations()[0];
            }
            FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
            FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
            for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
                fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
            }
            ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
            ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
            // add sim
            int jobIndex = 0;
            SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
            VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
            VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
            PDEDataManager dataManager = new PDEDataManager(null, getLocalWorkspace().getVCDataManager(), vcDataId);
            PDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
            ExportFormat format = ExportFormat.QUICKTIME;
            String[] variableNames = new String[] { NORM_FLUOR_VAR, NORM_SIM_VAR };
            VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
            // int endTimeIndex = (int)Math.round(sim.getSolverTaskDescription().getTimeBounds().getEndingTime()/((UniformOutputTimeSpec)sim.getSolverTaskDescription().getOutputTimeSpec()).getOutputTimeStep());
            int endTimeIndex = getFRAPSimDataViewerPanel().getOriginalDataViewer().getPdeDataContext().getTimePoints().length - 1;
            TimeSpecs timeSpecs = new TimeSpecs(0, endTimeIndex, pdeDataContext.getTimePoints(), ExportConstants.TIME_RANGE);
            int geoMode = ExportConstants.GEOMETRY_SLICE;
            GeometrySpecs geometrySpecs = new GeometrySpecs(null, Coordinate.Z_AXIS, 0, geoMode);
            // 10s
            double duration = 10000;
            DisplayPreferences pref1 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences pref2 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences[] displayPref = new DisplayPreferences[] { pref1, pref2 };
            int imageScale = 1;
            int membraneScale = 1;
            int scaleMode = ImagePaneModel.MESH_MODE;
            // the default setting in MediaSettingsPanel.
            int volVarMemOutlineThickness = 1;
            MovieSpecs mSpec = new MovieSpecs(duration, true, displayPref, ExportFormat.QUICKTIME, ExportConstants.NO_MIRRORING, volVarMemOutlineThickness, imageScale, membraneScale, scaleMode, FormatSpecificSpecs.CODEC_JPEG, 1.0f, /*lossless*/
            false, FormatSpecificSpecs.PARTICLE_NONE);
            // mSpec.setViewZoom(1);
            ExportSpecs exSpecs = new ExportSpecs(vcDataId, format, variableSpecs, timeSpecs, geometrySpecs, mSpec, fStudy.getName(), null);
            // pass the request
            ExportEvent exportEvt = ((VirtualFrapWindowManager) getFlourDataViewer().getDataViewerManager()).startExportMovie(exSpecs, outputContext, this.getClientTaskStatusSupport());
            hashTable.put("ExportEvt", exportEvt);
            hashTable.put("FrapStudy", fStudy);
        }
    };
    AsynchClientTask showMovieTask = new AsynchClientTask("Showing movie ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExportEvent exportEvt = (ExportEvent) hashTable.get("ExportEvt");
            FRAPStudy fStudy = (FRAPStudy) hashTable.get("FrapStudy");
            // show movie if successfully exported
            if (exportEvt != null) {
                final String fileURLString = System.getProperty(PropertyLoader.exportBaseURLProperty) + exportEvt.getJobID() + ".mov";
                final String fileString = System.getProperty(PropertyLoader.exportBaseDirInternalProperty) + exportEvt.getJobID() + ".mov";
                fStudy.setMovieURLString(fileURLString);
                fStudy.setMovieFileString(fileString);
            }
            showMovieInDialog(fStudy.getMovieURLString(), fStudy.getMovieFileString());
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { createMovieTask, showMovieTask }, true, true, null, true);
}

Example 39 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class BatchRunXmlReader method getBatchRunWorkspace.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @param param org.jdom.Element
 * @return cbit.vcell.biomodel.BioModel
 * @throws XmlParseException
 */
public FRAPBatchRunWorkspace getBatchRunWorkspace(Element param) throws XmlParseException {
    FRAPBatchRunWorkspace tempBatchRunWorkspace = new FRAPBatchRunWorkspace();
    // Element param = root.getChild(MicroscopyXMLTags.FrapBatchRunTag);
    // selected model index
    Element selectedModexIndexElement = param.getChild(MicroscopyXMLTags.BatchRunSelectedModelTypeTag);
    String selectedModexIndexStr = selectedModexIndexElement.getText();
    int selectedModelIndex = (new Integer(selectedModexIndexStr).intValue());
    if (selectedModexIndexStr != null && selectedModexIndexStr.length() > 0) {
        tempBatchRunWorkspace.setSelectedModel(selectedModelIndex);
    }
    // get average model parameters when there is selected model
    Element averageParametersElement = param.getChild(MicroscopyXMLTags.ModelParametersTag);
    Parameter[] params = null;
    if (averageParametersElement != null && averageParametersElement.getAttributes().size() > 0) {
        if (selectedModelIndex == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
            params = new Parameter[FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF];
            double primaryDiffRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.PrimaryRateAttrTag));
            params[FRAPModel.INDEX_PRIMARY_DIFF_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_DIFF_RATE], FRAPModel.REF_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getScale(), primaryDiffRate);
            double primaryFraction = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.PrimaryFractionAttTag));
            params[FRAPModel.INDEX_PRIMARY_FRACTION] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_FRACTION], FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), primaryFraction);
            double bwmRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag));
            params[FRAPModel.INDEX_BLEACH_MONITOR_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE], FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getLowerBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getUpperBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), bwmRate);
        } else if (selectedModelIndex == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
            params = new Parameter[FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF];
            double primaryDiffRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.PrimaryRateAttrTag));
            params[FRAPModel.INDEX_PRIMARY_DIFF_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_DIFF_RATE], FRAPModel.REF_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getScale(), primaryDiffRate);
            double primaryFraction = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.PrimaryFractionAttTag));
            params[FRAPModel.INDEX_PRIMARY_FRACTION] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_PRIMARY_FRACTION], FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), primaryFraction);
            double bwmRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag));
            params[FRAPModel.INDEX_BLEACH_MONITOR_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE], FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getLowerBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getUpperBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), bwmRate);
            double secDiffRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.SecondRateAttrTag));
            params[FRAPModel.INDEX_SECONDARY_DIFF_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_SECONDARY_DIFF_RATE], FRAPModel.REF_SECOND_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_SECOND_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_SECOND_DIFFUSION_RATE_PARAM.getScale(), secDiffRate);
            double secFraction = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.SecondFractionAttTag));
            params[FRAPModel.INDEX_SECONDARY_FRACTION] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_SECONDARY_FRACTION], FRAPModel.REF_SECOND_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_SECOND_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_SECOND_MOBILE_FRACTION_PARAM.getScale(), secFraction);
        } else if (selectedModelIndex == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
            params = new Parameter[FRAPModel.NUM_MODEL_PARAMETERS_REACTION_OFF_RATE];
            double bwmRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag));
            params[FRAPModel.INDEX_BLEACH_MONITOR_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE], FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getLowerBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getUpperBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), bwmRate);
            double fittingParam = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.BindingSiteConcentrationAttTag));
            params[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION], FRAPModel.REF_BS_CONCENTRATION_OR_A.getLowerBound(), FRAPModel.REF_BS_CONCENTRATION_OR_A.getUpperBound(), FRAPModel.REF_BS_CONCENTRATION_OR_A.getScale(), fittingParam);
            double offRate = Double.parseDouble(averageParametersElement.getAttributeValue(MicroscopyXMLTags.ReactionOffRateAttTag));
            params[FRAPModel.INDEX_OFF_RATE] = new Parameter(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_OFF_RATE], FRAPModel.REF_REACTION_OFF_RATE.getLowerBound(), FRAPModel.REF_REACTION_OFF_RATE.getUpperBound(), FRAPModel.REF_REACTION_OFF_RATE.getScale(), offRate);
            params[FRAPModel.INDEX_PRIMARY_DIFF_RATE] = null;
            params[FRAPModel.INDEX_PRIMARY_FRACTION] = null;
            params[FRAPModel.INDEX_SECONDARY_DIFF_RATE] = null;
            params[FRAPModel.INDEX_SECONDARY_FRACTION] = null;
            params[FRAPModel.INDEX_ON_RATE] = null;
        }
        tempBatchRunWorkspace.setAverageParameters(params);
    }
    // get FrapStudy file list
    Element frapStudyListElement = param.getChild(MicroscopyXMLTags.FrapStudyListTag);
    String numFrapStudiesStr = frapStudyListElement.getAttributeValue(MicroscopyXMLTags.NumFrapStudyListAttrTag);
    Integer.parseInt(numFrapStudiesStr);
    // get each individual FRAPStudy
    @SuppressWarnings("unchecked") List<Element> fileNameList = frapStudyListElement.getChildren(MicroscopyXMLTags.FrapFileNameTag);
    for (int i = 0; i < fileNameList.size(); i++) {
        String fileName = fileNameList.get(i).getText();
        // create empty frap study to put in temporay batchrunworkspace
        FRAPStudy fStudy = new FRAPStudy();
        fStudy.setXmlFilename(fileName);
        tempBatchRunWorkspace.addFrapStudy(fStudy);
    }
    return tempBatchRunWorkspace;
}

Example 40 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy in project vcell by virtualcell.

the class FRAPBatchRunWorkspace method refreshMSESummaryData.

public void refreshMSESummaryData() {
    int studySize = getFrapStudies().size();
    analysisMSESummaryData = new double[studySize][FRAPData.VFRAP_ROI_ENUM.values().length - 2 + 1];
    for (int i = 0; i < studySize; i++) {
        FRAPStudy fStudy = getFrapStudies().get(i);
        fStudy.createAnalysisMSESummaryData();
        analysisMSESummaryData[i] = fStudy.getAnalysisMSESummaryData()[getSelectedModel()];
    }
}