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

Example 1 with MicroscopyXmlReader

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

the class 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 {
                VirtualFrapBatchRunFrame.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 (// .log (vcell log file)
                inFile.getName().endsWith(SimDataConstants.LOGFILE_EXTENSION)) {
                    DataIdentifier[] dataIdentifiers = FrapDataUtils.getDataIdentiferListFromVCellSimulationData(inFile, 0);
                    String[][] rowData = new String[dataIdentifiers.length][1];
                    for (int i = 0; i < dataIdentifiers.length; i++) {
                        if (dataIdentifiers[i].getVariableType().equals(VariableType.VOLUME)) {
                            rowData[i][0] = dataIdentifiers[i].getName();
                        }
                    }
                    int[] selectedIndexArr = DialogUtils.showComponentOKCancelTableList(SingleFileDescriptor.this.getPanelComponent(), "Select Volume Variable", new String[] { "Volume Variable Name" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                    if (selectedIndexArr != null && selectedIndexArr.length > 0) {
                        // newFRAPStudy = getFrapWorkspace().loadFRAPDataFromVcellLogFile(inFile, dataIdentifiers[selectedIndexArr[0]].getName(), this.getClientTaskStatusSupport());
                        isFileLoaded = true;
                    } else {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                } else if (// .vfrap
                inFile.getName().endsWith(VirtualFrapLoader.VFRAP_EXTENSION)) {
                    String xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
                    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                    newFRAPStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), this.getClientTaskStatusSupport());
                    newFRAPStudy.setXmlFilename(inFile.getAbsolutePath());
                    if (!FRAPWorkspace.areExternalDataOK(localWorkspace, newFRAPStudy.getFrapDataExternalDataInfo(), newFRAPStudy.getRoiExternalDataInfo())) {
                        newFRAPStudy.setFrapDataExternalDataInfo(null);
                        newFRAPStudy.setRoiExternalDataInfo(null);
                    }
                } else // .lsm or other image formatss
                {
                    newFRAPStudy = FRAPWorkspace.loadFRAPDataFromImageFile(inFile, this.getClientTaskStatusSupport());
                    isFileLoaded = true;
                }
                // otherwise, popup a dialog saying the result will be invalid.
                if (!batchRunWorkspace.isBatchRunResultsAvailable()) {
                    hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                } else if ((batchRunWorkspace.isBatchRunResultsAvailable() && inFile.getName().endsWith(VirtualFrapLoader.VFRAP_EXTENSION)) && ((newFRAPStudy.getFrapModel(batchRunWorkspace.getSelectedModel()) != null) && (newFRAPStudy.getFrapModel(batchRunWorkspace.getSelectedModel()).getModelParameters() != null))) {
                    // put newfrapstudy into hashtable to be used for next task
                    hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                } else {
                    String continueStr = "Remove results and continue";
                    String cancelStr = "Cancel loading data";
                    String msg = "Loading a new data file,\n or a vfrap file with no model data,\n or a vfrap file with different selected model type, \n will INVALID the existing resuls.";
                    String choice = DialogUtils.showWarningDialog(singleFilePanel, msg, new String[] { continueStr, cancelStr }, continueStr);
                    if (choice == continueStr) {
                        hashTable.put(CLEAR_RESULT_KEY, new Boolean(true));
                        hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                    } else // cancel
                    {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                }
            }
        };
        AsynchClientTask afterLoadingSwingTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // check to see if results need to be cleared
                Boolean needClear = (Boolean) hashTable.get(CLEAR_RESULT_KEY);
                if (needClear != null && needClear.booleanValue()) {
                    double[][] oldAnalysisData = batchRunWorkspace.getAnalysisMSESummaryData();
                    double[][] newAnalysisData = null;
                    batchRunWorkspace.firePropertyChange(FRAPBatchRunWorkspace.PROPERTY_CHANGE_BATCHRUN_CLEAR_RESULTS, oldAnalysisData, newAnalysisData);
                }
                FRAPStudy newFRAPStudy = (FRAPStudy) hashTable.get(FRAPStudyPanel.NEW_FRAPSTUDY_KEY);
                // setFrapStudy fires property change, so we have to put it in Swing thread.
                getBatchRunWorkspace().getWorkingSingleWorkspace().setFrapStudy(newFRAPStudy, true);
                VirtualFrapBatchRunFrame.updateProgress(0);
                if (isFileLoaded) {
                    VirtualFrapBatchRunFrame.updateStatus("Loaded " + fileStr);
                } else {
                    VirtualFrapBatchRunFrame.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 2 with MicroscopyXmlReader

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

the class FRAPBatchRunWorkspace method getLoadSingleFilesTask.

// get client task for loading each single vfrap files in a batch run
public AsynchClientTask getLoadSingleFilesTask(LocalWorkspace arg_localWorkspace) {
    final LocalWorkspace localWorkspace = arg_localWorkspace;
    AsynchClientTask openSingleFilesTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPBatchRunWorkspace tempBatchRunWorkspace = (FRAPBatchRunWorkspace) hashTable.get(BATCH_RUN_WORKSPACE_KEY);
            if (tempBatchRunWorkspace != null) {
                ArrayList<FRAPStudy> fStudyList = tempBatchRunWorkspace.getFrapStudies();
                int size = fStudyList.size();
                for (int i = 0; i < size; i++) {
                    String fileName = fStudyList.get(i).getXmlFilename();
                    File fStudyFile = new File(fileName);
                    if (// .vfrap
                    fileName.endsWith("." + VirtualFrapLoader.VFRAP_EXTENSION) || fileName.endsWith(".xml")) {
                        this.getClientTaskStatusSupport().setMessage("Loading(.vfrap) " + (i + 1) + " of " + size + " : " + fileName);
                        FRAPStudy newFRAPStudy = null;
                        String xmlString = XmlUtil.getXMLString(fStudyFile.getAbsolutePath());
                        MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                        newFRAPStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), this.getClientTaskStatusSupport());
                        // if((newFRAPStudy.getFrapDataExternalDataInfo() != null || newFRAPStudy.getRoiExternalDataInfo() != null) &&
                        // !FRAPWorkspace.areExternalDataOK(localWorkspace,newFRAPStudy.getFrapDataExternalDataInfo(),newFRAPStudy.getRoiExternalDataInfo()))
                        // {
                        // throw new Exception("External Files of Frap Document " + fStudyFile.getAbsolutePath() + " are corrupted");
                        // }
                        newFRAPStudy.setXmlFilename(fileName);
                        // get dimentsion reduced experimental data
                        newFRAPStudy.getDimensionReducedExpData();
                        // restore the dimension reduced fitting data(2 dimensional array).
                        int selectedModelIdx = tempBatchRunWorkspace.getSelectedModel();
                        FRAPModel frapModel = newFRAPStudy.getFrapModel(selectedModelIdx);
                        // optimization was done but data wasn't save with file, need to restore data
                        if (frapModel != null && frapModel.getModelParameters() != null && frapModel.getModelParameters().length > 0 && frapModel.getData() == null) {
                            if (frapModel.getModelIdentifer().equals(FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_REACTION_OFF_RATE])) {
                                FRAPOptFunctions frapOptFunc = new FRAPOptFunctions(newFRAPStudy);
                                newFRAPStudy.setFrapOptFunc(frapOptFunc);
                                frapModel.setData(frapOptFunc.getFitData(frapModel.getModelParameters()));
                            } else {
                                FRAPOptData optData = new FRAPOptData(newFRAPStudy, frapModel.getModelParameters().length, localWorkspace, newFRAPStudy.getStoredRefData());
                                newFRAPStudy.setFrapOptData(optData);
                                frapModel.setData(optData.getFitData(frapModel.getModelParameters()));
                            }
                        }
                        tempBatchRunWorkspace.getFrapStudies().remove(i);
                        tempBatchRunWorkspace.getFrapStudies().add(i, newFRAPStudy);
                    }
                }
                // save loaded tempBatchRunWorkspace to hashtable
                hashTable.put(BATCH_RUN_WORKSPACE_KEY, tempBatchRunWorkspace);
            }
        }
    };
    return openSingleFilesTask;
}

Example 3 with MicroscopyXmlReader

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

the class BatchRunDisplayPanel method getFRAPDataPanel.

public FRAPDataPanel getFRAPDataPanel() {
    if (frapDataPanel == null) {
        // the frap data panel in the main frame is not editable
        frapDataPanel = new FRAPDataPanel(false);
        // set display mode
        frapDataPanel.adjustComponents(VFrap_OverlayEditorPanelJAI.DISPLAY_WITH_ROIS);
        Hashtable<String, Cursor> cursorsForROIsHash = new Hashtable<String, Cursor>();
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_CELLROI]);
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_BLEACHROI]);
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_BACKGROUNDROI]);
        frapDataPanel.getOverlayEditorPanelJAI().setCursorsForROIs(cursorsForROIsHash);
        VFrap_OverlayEditorPanelJAI.CustomROIImport importVFRAPROI = new VFrap_OverlayEditorPanelJAI.CustomROIImport() {

            public boolean importROI(File inputFile) throws Exception {
                try {
                    if (!VirtualFrapLoader.filter_vfrap.accept(inputFile)) {
                        return false;
                    }
                    String xmlString = XmlUtil.getXMLString(inputFile.getAbsolutePath());
                    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                    FRAPStudy importedFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
                    VirtualFrapMainFrame.updateProgress(0);
                    ROI roi = getBatchRunWorkspace().getWorkingSingleWorkspace().getWorkingFrapStudy().getFrapData().getCurrentlyDisplayedROI();
                    ROI[] importedROIs = importedFrapStudy.getFrapData().getRois();
                    if (importedFrapStudy.getFrapData() != null && importedROIs != null) {
                        if (!importedROIs[0].getISize().compareEqual(roi.getISize())) {
                            throw new Exception("Imported ROI mask size (" + importedROIs[0].getISize().getX() + "," + importedROIs[0].getISize().getY() + "," + importedROIs[0].getISize().getZ() + ")" + " does not match current Frap DataSet size (" + roi.getISize().getX() + "," + roi.getISize().getY() + "," + roi.getISize().getZ() + ")");
                        }
                        for (int i = 0; i < importedROIs.length; i++) {
                            getBatchRunWorkspace().getWorkingSingleWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(importedROIs[i]);
                        }
                    // undoableEditSupport.postEdit(FRAPStudyPanel.CLEAR_UNDOABLE_EDIT);
                    }
                    return true;
                } catch (Exception e1) {
                    throw new Exception("VFRAP ROI Import - " + e1.getMessage());
                }
            }
        };
        frapDataPanel.getOverlayEditorPanelJAI().setCustomROIImport(importVFRAPROI);
    }
    return frapDataPanel;
}

Example 4 with MicroscopyXmlReader

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

the class FRAPStudyPanel method open.

// open .vfrap document
public AsynchClientTask[] open(final File inFile) {
    final String LOADING_MESSAGE = "Loading " + inFile.getAbsolutePath() + "...";
    ArrayList<AsynchClientTask> totalTasks = new ArrayList<AsynchClientTask>();
    // check if save is needed before loading data
    if (getFrapWorkspace().getWorkingFrapStudy().isSaveNeeded()) {
        String choice = DialogUtils.showWarningDialog(FRAPStudyPanel.this, "There are unsaved changes. Save current document before loading new document?", new String[] { SAVE_CONTINUE_MSG, NO_THANKS_MSG }, SAVE_CONTINUE_MSG);
        if (choice.equals(SAVE_CONTINUE_MSG)) {
            AsynchClientTask[] saveTasks = save();
            for (int i = 0; i < saveTasks.length; i++) {
                totalTasks.add(saveTasks[i]);
            }
        }
    }
    AsynchClientTask preOpenTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

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

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy newFRAPStudy = null;
            String newVFRAPFileName = null;
            if (// .vfrap
            inFile.getName().endsWith("." + VirtualFrapLoader.VFRAP_EXTENSION) || inFile.getName().endsWith(".xml")) {
                String xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
                MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                newFRAPStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), this.getClientTaskStatusSupport());
                if (!FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), newFRAPStudy.getFrapDataExternalDataInfo(), newFRAPStudy.getRoiExternalDataInfo())) {
                    newFRAPStudy.setFrapDataExternalDataInfo(null);
                    newFRAPStudy.setRoiExternalDataInfo(null);
                }
                newVFRAPFileName = inFile.getAbsolutePath();
                // for loaded file
                newFRAPStudy.setXmlFilename(newVFRAPFileName);
                hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
            } else {
                throw new Exception("Invalid Virtual Frap file name!");
            }
        }
    };
    totalTasks.add(loadTask);
    AsynchClientTask updateUIAfterLoadingTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = (FRAPStudy) hashTable.get(FRAPStudyPanel.NEW_FRAPSTUDY_KEY);
            getFrapWorkspace().setFrapStudy(fStudy, true);
            String fName = "";
            if (fStudy != null && fStudy.getXmlFilename() != null && fStudy.getXmlFilename().length() > 0) {
                fName = fStudy.getXmlFilename();
                VirtualFrapLoader.mf.setMainFrameTitle(fName);
                VirtualFrapMainFrame.updateStatus("Loaded " + fName);
            } else {
                VirtualFrapMainFrame.updateStatus(LOADING_MESSAGE + " Failed.");
            }
            VirtualFrapMainFrame.updateProgress(0);
            // clear movie buffer
            clearMovieBuffer();
            // clear plot selected indices
            if (diffOneDescriptor != null && diffTwoDescriptor != null) {
                diffOneDescriptor.clearSelectedPlotIndices();
                diffTwoDescriptor.clearSelectedPlotIndices();
            }
        }
    };
    totalTasks.add(updateUIAfterLoadingTask);
    return totalTasks.toArray(new AsynchClientTask[totalTasks.size()]);
}

Example 5 with MicroscopyXmlReader

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

the class FRAPDataPanel method initialize.

/**
 * This method initializes this
 *
 * @return void
 */
private void initialize() {
    GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
    gridBagConstraints1.gridx = 0;
    gridBagConstraints1.ipadx = 0;
    gridBagConstraints1.ipady = 0;
    gridBagConstraints1.fill = GridBagConstraints.BOTH;
    gridBagConstraints1.weighty = 1.0D;
    gridBagConstraints1.weightx = 1.0D;
    gridBagConstraints1.gridy = 0;
    this.setSize(653, 492);
    this.setLayout(new GridBagLayout());
    this.add(getOverlayEditorPanelJAI(), gridBagConstraints1);
    getOverlayEditorPanelJAI().addPropertyChangeListener(new PropertyChangeListener() {

        public void propertyChange(PropertyChangeEvent evt) {
            if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_TIMEPLOTROI_PROPERTY)) {
                try {
                    plotROI();
                } catch (Exception e) {
                    DialogUtils.showErrorDialog(FRAPDataPanel.this, "Error Time Plot ROI:\n" + e.getMessage());
                }
            } else if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_CURRENTROI_PROPERTY)) {
                try {
                    String roiName = (String) evt.getNewValue();
                    if (roiName != null) {
                        getFrapWorkspace().getWorkingFrapStudy().getFrapData().setCurrentlyDisplayedROI(getFrapWorkspace().getWorkingFrapStudy().getFrapData().getRoi(roiName), false);
                    }
                } catch (Exception e) {
                    DialogUtils.showErrorDialog(FRAPDataPanel.this, "Error Setting Current ROI:\n" + e.getMessage());
                }
            } else if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_UNDOROI_PROPERTY)) {
                try {
                    ROI undoableROI = (ROI) evt.getNewValue();
                    getFrapWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(undoableROI);
                } catch (Exception e) {
                    PopupGenerator.showErrorDialog(FRAPDataPanel.this, "Error Setting Current ROI:\n" + e.getMessage());
                }
            }
        }
    });
    VFrap_OverlayEditorPanelJAI.CustomROIImport importVFRAPROI = new VFrap_OverlayEditorPanelJAI.CustomROIImport() {

        public boolean importROI(File inputFile) throws Exception {
            try {
                if (!VirtualFrapLoader.filter_vfrap.accept(inputFile)) {
                    return false;
                }
                String xmlString = XmlUtil.getXMLString(inputFile.getAbsolutePath());
                MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                FRAPStudy importedFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
                VirtualFrapMainFrame.updateProgress(0);
                ROI roi = getFrapWorkspace().getWorkingFrapStudy().getFrapData().getCurrentlyDisplayedROI();
                ROI[] importedROIs = importedFrapStudy.getFrapData().getRois();
                if (importedFrapStudy.getFrapData() != null && importedROIs != null) {
                    if (!importedROIs[0].getISize().compareEqual(roi.getISize())) {
                        throw new Exception("Imported ROI mask size (" + importedROIs[0].getISize().getX() + "," + importedROIs[0].getISize().getY() + "," + importedROIs[0].getISize().getZ() + ")" + " does not match current Frap DataSet size (" + roi.getISize().getX() + "," + roi.getISize().getY() + "," + roi.getISize().getZ() + ")");
                    }
                    for (int i = 0; i < importedROIs.length; i++) {
                        getFrapWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(importedROIs[i]);
                    }
                // undoableEditSupport.postEdit(FRAPStudyPanel.CLEAR_UNDOABLE_EDIT);
                }
                return true;
            } catch (Exception e1) {
                throw new Exception("VFRAP ROI Import - " + e1.getMessage());
            }
        }
    };
    getOverlayEditorPanelJAI().setCustomROIImport(importVFRAPROI);
}