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

Example 21 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy 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 22 with FRAPStudy

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

the class LoadFRAPData_SingleFileDescriptor method preNextProcess.

// load the data before the panel disappears
public ArrayList<AsynchClientTask> preNextProcess() {
    // create AsynchClientTask arraylist
    ArrayList<AsynchClientTask> taskArrayList = new ArrayList<AsynchClientTask>();
    if (singleFilePanel.getFileName().length() > 0) {
        final String fileStr = singleFilePanel.getFileName();
        final String LOADING_MESSAGE = "Loading " + fileStr + "...";
        AsynchClientTask updateUIBeforeLoadTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                VirtualFrapMainFrame.updateStatus(LOADING_MESSAGE);
            }
        };
        AsynchClientTask loadTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FRAPStudy newFRAPStudy = null;
                File inFile = new File(fileStr);
                if (inFile != null) {
                    if (// .log (vcell log file)
                    inFile.getName().endsWith(SimDataConstants.LOGFILE_EXTENSION)) {
                        DataIdentifier[] dataIdentifiers = FrapDataUtils.getDataIdentiferListFromVCellSimulationData(inFile, 0);
                        ArrayList<String> selectedIdentifiers = new ArrayList<String>();
                        for (int i = 0; i < dataIdentifiers.length; i++) {
                            if (dataIdentifiers[i].getVariableType().equals(VariableType.VOLUME)) {
                                selectedIdentifiers.add(dataIdentifiers[i].getName());
                            }
                        }
                        String[][] rowData = new String[selectedIdentifiers.size()][1];
                        for (int i = 0; i < selectedIdentifiers.size(); i++) {
                            rowData[i][0] = selectedIdentifiers.get(i);
                        }
                        int[] selectedIndexArr = DialogUtils.showComponentOKCancelTableList(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), "Select Volume Variable", new String[] { "Volume Variable Name" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                        if (selectedIndexArr != null && selectedIndexArr.length > 0) {
                            scalePanel = getScalePanelForLoadingLogFile();
                            int choice = DialogUtils.showComponentOKCancelDialog(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), scalePanel, "Input image maximum intensity (max: 65535)");
                            if (choice == JOptionPane.OK_OPTION) {
                                Double maxIntensity = null;
                                if (scalePanel.getInputScaleString() != null) {
                                    maxIntensity = new Double(scalePanel.getInputScaleString());
                                }
                                newFRAPStudy = FRAPWorkspace.loadFRAPDataFromVcellLogFile(inFile, selectedIdentifiers.get(selectedIndexArr[0]), null, maxIntensity, true, this.getClientTaskStatusSupport());
                                isFileLoaded = true;
                            } else {
                                throw UserCancelException.CANCEL_GENERIC;
                            }
                        } else {
                            throw UserCancelException.CANCEL_GENERIC;
                        }
                    } else if (inFile.getName().endsWith(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5)) {
                        scalePanel = getScalePanelForLoadingLogFile();
                        int choice = DialogUtils.showComponentOKCancelDialog(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), scalePanel, "Input data maximum value (max: 65535) which is used to avoid losing double precision when casting it to short.");
                        if (choice == JOptionPane.OK_OPTION) {
                            Double maxIntensity = null;
                            if (scalePanel.getInputScaleString() != null) {
                                maxIntensity = new Double(scalePanel.getInputScaleString());
                            }
                            newFRAPStudy = FRAPWorkspace.loadFRAPDataFromHDF5File(inFile, maxIntensity, this.getClientTaskStatusSupport());
                            isFileLoaded = true;
                        } else {
                            throw UserCancelException.CANCEL_GENERIC;
                        }
                    } else // .lsm or other image formatss
                    {
                        newFRAPStudy = FRAPWorkspace.loadFRAPDataFromImageFile(inFile, this.getClientTaskStatusSupport());
                        isFileLoaded = true;
                    }
                } else {
                    throw new RuntimeException("Input file is null.");
                }
                // for all loaded file
                hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
            }
        };
        AsynchClientTask afterLoadingSwingTask = new AsynchClientTask(LOADING_MESSAGE, 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 " + fileStr);
                } else {
                    VirtualFrapMainFrame.updateStatus("Failed loading " + fileStr + ".");
                }
            }
        };
        taskArrayList.add(updateUIBeforeLoadTask);
        taskArrayList.add(loadTask);
        taskArrayList.add(afterLoadingSwingTask);
    } else {
        DialogUtils.showErrorDialog(singleFilePanel, "Load File name is empty. Please input a file name to continue.");
        throw new RuntimeException("Load File name is empty. Please input a file name to continue.");
    }
    return taskArrayList;
}

Example 23 with FRAPStudy

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

the class ChooseModel_ModelTypesDescriptor method preNextProcess.

public ArrayList<AsynchClientTask> preNextProcess() {
    ArrayList<AsynchClientTask> tasks = new ArrayList<AsynchClientTask>();
    AsynchClientTask aTask1 = new AsynchClientTask("Saving selected model types...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
            if (fStudy == null) {
                throw new Exception("FRAPStudy is null. Please load data.");
            }
            boolean[] models = modelTypesPanel.getModelTypes();
            // perform checkings...is one selected, is koffRatemodel selected(in this case force to use bleached ROI only)
            if (modelTypesPanel.getNumUserSelectedModelTypes() < 1) {
                throw new Exception("At least one model type has to be selected.");
            }
            // if reaction dominant off rate model is selected, we have to make sure that the bleached ROI should be selected.
            if (models[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] && !fStudy.getSelectedROIsForErrorCalculation()[FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.ordinal()]) {
                String choice = DialogUtils.showWarningDialog(modelTypesPanel, "To evaluate Reaction Dominant Off Rate model, bleached ROI must be selected. \n\nSelecte 'Continue' to have bleached ROI automatically added and proceed. Or,\nSelecte 'Cancel' to stop proceeding.", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
                if (choice.equals(UserMessage.OPTION_CONTINUE)) {
                    fStudy.getSelectedROIsForErrorCalculation()[FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.ordinal()] = true;
                } else {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            // update selected models in FrapStudy
            fStudy.refreshModels(models);
        }
    };
    tasks.add(aTask1);
    return tasks;
}

Example 24 with FRAPStudy

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

the class ChooseModel_ModelTypesDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
    // if there are models selected and saved, load the model types. otherwise, apply default(diffusion with one component is selected).
    if (fStudy.getModels() != null && fStudy.getModels().length > 0 && fStudy.getSelectedModels().size() > 0) {
        modelTypesPanel.clearAllSelected();
        FRAPModel[] models = fStudy.getModels();
        if (models[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null) {
            modelTypesPanel.setDiffOneSelected(true);
        }
        if (models[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] != null) {
            modelTypesPanel.setDiffTwoSelected(true);
        }
        if (models[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] != null) {
            modelTypesPanel.setReactionOffRateSelected(true);
        }
    } else // new frap document
    {
        modelTypesPanel.clearAllSelected();
        modelTypesPanel.setDiffOneSelected(true);
    }
}

Example 25 with FRAPStudy

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

the class BatchRunXmlProducer method getXML.

/**
 * This method returns a XML representation
 * for a frap batch run including
 */
private static Element getXML(FRAPBatchRunWorkspace param) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element batchRunNode = new Element(MicroscopyXMLTags.FrapBatchRunTag);
    // Get selected model index
    Element selectedModelIdxElem = new Element(MicroscopyXMLTags.BatchRunSelectedModelTypeTag);
    selectedModelIdxElem.setText(mangle(param.getSelectedModel() + ""));
    batchRunNode.addContent(selectedModelIdxElem);
    // Get average model parameters
    Element parametersNode = new Element(MicroscopyXMLTags.ModelParametersTag);
    Parameter[] avgParams = param.getAverageParameters();
    if (avgParams != null) {
        if (param.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF) {
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryRateAttrTag, avgParams[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryFractionAttTag, avgParams[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
        } else if (param.getSelectedModel() == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF) {
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryRateAttrTag, avgParams[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.PrimaryFractionAttTag, avgParams[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.SecondRateAttrTag, avgParams[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.SecondFractionAttTag, avgParams[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess() + "");
        } else if (param.getSelectedModel() == FRAPModel.IDX_MODEL_REACTION_OFF_RATE && avgParams.length == FRAPModel.NUM_MODEL_PARAMETERS_REACTION_OFF_RATE) {
            parametersNode.setAttribute(MicroscopyXMLTags.BleachWhileMonitoringTauAttrTag, avgParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.BindingSiteConcentrationAttTag, avgParams[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION].getInitialGuess() + "");
            parametersNode.setAttribute(MicroscopyXMLTags.ReactionOffRateAttTag, avgParams[FRAPModel.INDEX_OFF_RATE].getInitialGuess() + "");
        }
    }
    batchRunNode.addContent(parametersNode);
    // Get frap study file lists
    if (param.getFrapStudies() != null && param.getFrapStudies().size() > 0) {
        Element frapStudyListNode = new Element(MicroscopyXMLTags.FrapStudyListTag);
        frapStudyListNode.setAttribute(MicroscopyXMLTags.NumFrapStudyListAttrTag, Integer.toString(param.getFrapStudies().size()));
        ArrayList<FRAPStudy> frapList = param.getFrapStudies();
        for (int i = 0; i < frapList.size(); i++) {
            if (frapList.get(i).getXmlFilename() != null) {
                Element fileNameNode = new Element(MicroscopyXMLTags.FrapFileNameTag);
                fileNameNode.addContent(frapList.get(i).getXmlFilename());
                frapStudyListNode.addContent(fileNameNode);
            }
        }
        batchRunNode.addContent(frapStudyListNode);
    }
    return batchRunNode;
}