Examples with FRAPBatchRunWorkspace cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace used on opensource projects

Example 1 with FRAPBatchRunWorkspace

use of cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace in project vcell by virtualcell.

the class VirtualFrapBatchRunFrame method open.

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

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VirtualFrapBatchRunFrame.updateStatus("Loading " + inFile.getAbsolutePath() + "...");
        }
    };
    totalTasks.add(preOpenTask);
    // load frap batch run file
    totalTasks.add(batchRunWorkspace.getLoadBatchRunFileTask(inFile));
    // load each single vfrap file
    totalTasks.add(batchRunWorkspace.getLoadSingleFilesTask(localWorkspace));
    // after loading task
    AsynchClientTask updateUIAfterLoadingTask = new AsynchClientTask("Updating User Interface ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPBatchRunWorkspace tempBatchRunWorkspace = (FRAPBatchRunWorkspace) hashTable.get(FRAPBatchRunWorkspace.BATCH_RUN_WORKSPACE_KEY);
            // if loaded successfully, update the batchrunworkspace with the temporary one.
            batchRunWorkspace.update(tempBatchRunWorkspace);
            // update tree
            getBatchRunDetailsPanel().updateViewTreeForNewBatchRunFile(batchRunWorkspace);
            // update ui
            VirtualFrapLoader.mf.setBatchRunFrameTitle(batchRunWorkspace.getBatchRunXmlFileName());
            VirtualFrapBatchRunFrame.updateStatus("Loaded " + tempBatchRunWorkspace.getBatchRunXmlFileName());
        }
    };
    totalTasks.add(updateUIAfterLoadingTask);
    return totalTasks.toArray(new AsynchClientTask[totalTasks.size()]);
}

Example 2 with FRAPBatchRunWorkspace

use of cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace in project vcell by virtualcell.

the class EstParams_OneDiffComponentPanel method loadBatchRunParameters.

public void loadBatchRunParameters(File inFile) {
    String xmlString;
    try {
        xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
        BatchRunXmlReader batchRunXmlReader = new BatchRunXmlReader();
        FRAPBatchRunWorkspace tempBatchRunWorkspace = batchRunXmlReader.getBatchRunWorkspace(XmlUtil.stringToXML(xmlString, null).getRootElement());
        Parameter[] parameters = tempBatchRunWorkspace.getAverageParameters();
        if (parameters != null && parameters.length > 0 && parameters.length == FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF) {
            String paramMsg = "Replace the current parameters with the following parameter values: \n\n";
            for (int i = 0; i < parameters.length; i++) {
                paramMsg = paramMsg + parameters[i].getName() + ": " + parameters[i].getInitialGuess() + "\n";
            }
            String choice = DialogUtils.showWarningDialog(this, paramMsg, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
            if (choice == UserMessage.OPTION_OK) {
                getPureDiffusionPanel().setParameterValues(parameters[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess(), parameters[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess(), parameters[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess());
            }
        } else {
            throw new Exception("Parameters are null or number of applied parameters don't match the number (3) of parameters for diffusion with one diffusing component.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage());
    }
}

Example 3 with FRAPBatchRunWorkspace

use of cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace in project vcell by virtualcell.

the class EstParams_TwoDiffComponentPanel method loadBatchRunParameters.

public void loadBatchRunParameters(File inFile) {
    String xmlString;
    try {
        xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
        BatchRunXmlReader batchRunXmlReader = new BatchRunXmlReader();
        FRAPBatchRunWorkspace tempBatchRunWorkspace = batchRunXmlReader.getBatchRunWorkspace(XmlUtil.stringToXML(xmlString, null).getRootElement());
        Parameter[] parameters = tempBatchRunWorkspace.getAverageParameters();
        if (parameters != null && parameters.length > 0 && parameters.length == FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF) {
            String paramMsg = "Replace the current parameters with the following parameter values, \n";
            for (int i = 0; i < parameters.length; i++) {
                paramMsg = paramMsg + parameters[i].getName() + ": " + parameters[i].getInitialGuess() + "\n";
            }
            String choice = DialogUtils.showWarningDialog(this, paramMsg, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
            if (choice == UserMessage.OPTION_OK) {
                frapWorkspace.getWorkingFrapStudy();
                getPureDiffusionPanel().setParameterValues(parameters[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess(), parameters[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess(), parameters[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess(), parameters[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess(), parameters[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess());
            }
        } else {
            throw new Exception("Parameters are null or number of applied parameters don't match the number (5) of parameters for diffusion with two diffusing components.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage());
    }
}

Example 4 with FRAPBatchRunWorkspace

use of cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace in project vcell by virtualcell.

the class BatchRunDetailsPanel method setBatchRunWorkspace.

public void setBatchRunWorkspace(FRAPBatchRunWorkspace batchRunWorkspace) {
    FRAPBatchRunWorkspace oldBatchRunWorkspace = this.batchRunWorkspace;
    if (oldBatchRunWorkspace != null) {
        oldBatchRunWorkspace.removePropertyChangeListener(this);
    }
    batchRunWorkspace.addPropertyChangeListener(this);
    this.batchRunWorkspace = batchRunWorkspace;
}

Example 5 with FRAPBatchRunWorkspace

use of cbit.vcell.microscopy.batchrun.FRAPBatchRunWorkspace in project vcell by virtualcell.

the class VirtualFrapLoader method loadVFRAP.

// the function is called when activate in VCell or as standalone.
public static void loadVFRAP(final String[] args, final boolean bStandalone, final DocumentWindowManager documentWindowManager) {
    try {
        File wd = null;
        if (args == null || args.length == 0) {
            wd = ResourceUtil.getUserHomeDir();
        } else {
            wd = new File(args[0]);
        }
        final File workingDirectory = wd;
        SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
                FRAPSingleWorkspace frapWorkspace = new FRAPSingleWorkspace();
                FRAPBatchRunWorkspace batchRunWorkspace = new FRAPBatchRunWorkspace();
                // Check swing availability
                String vers = System.getProperty("java.version");
                if (vers.compareTo("1.1.2") < 0) {
                    System.out.println("!!!WARNING: Swing must be run with a 1.1.2 or higher version JVM!!!");
                }
                /* Set Look and Feel */
                try {
                    UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName());
                } catch (Exception e) {
                    throw new RuntimeException(e.getMessage(), e);
                }
                // set up file choosers
                openVFRAPFileChooser = new LWFileChooser();
                openVFRAPFileChooser.setDialogTitle("Open Virtual FRAP document (.vfrap)");
                openVFRAPFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                openVFRAPFileChooser.addChoosableFileFilter(filter_vfrap);
                openVFRAPFileChooser.setAcceptAllFileFilterUsed(false);
                openVFRAPBatchRunChooser = new LWFileChooser();
                openVFRAPBatchRunChooser.setDialogTitle("Open Virtual FRAP batchrun document (.vfbatch)");
                openVFRAPBatchRunChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                openVFRAPBatchRunChooser.addChoosableFileFilter(filter_vfbatch);
                openVFRAPBatchRunChooser.setAcceptAllFileFilterUsed(false);
                loadFRAPImageFileChooser = new LWFileChooser();
                loadFRAPImageFileChooser.setDialogTitle("Load FRAP image file");
                loadFRAPImageFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                loadFRAPImageFileChooser.addChoosableFileFilter(filter_tif);
                loadFRAPImageFileChooser.addChoosableFileFilter(filter_lsm);
                addDataFileChooser_batchRun = new LWFileChooser();
                addDataFileChooser_batchRun.setDialogTitle("Add a Virtual FRAP docmument or FRAP image file to batchrun");
                addDataFileChooser_batchRun.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                addDataFileChooser_batchRun.addChoosableFileFilter(filter_vfrap);
                addDataFileChooser_batchRun.addChoosableFileFilter(filter_tif);
                addDataFileChooser_batchRun.addChoosableFileFilter(filter_lsm);
                saveFileChooser = new LWFileChooser();
                saveFileChooser.setDialogTitle("Save Virtual FRAP document (.vfrap)");
                saveFileChooser.addChoosableFileFilter(filter_vfrap);
                saveFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                saveAsMatFileChooser = new LWFileChooser();
                saveAsMatFileChooser.setDialogTitle("Save image data to matlab file (.mat)");
                saveAsMatFileChooser.addChoosableFileFilter(filter_mat);
                saveAsMatFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                saveFileChooser_batchRun = new LWFileChooser();
                saveFileChooser_batchRun.setDialogTitle("Save Virtual FRAP batchrun document (.vfbatch)");
                saveFileChooser_batchRun.addChoosableFileFilter(filter_vfbatch);
                saveFileChooser_batchRun.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                saveFileChooser_batchRunSaveSingleFileAs = new LWFileChooser();
                saveFileChooser_batchRunSaveSingleFileAs.addChoosableFileFilter(filter_vfrap);
                saveFileChooser_batchRunSaveSingleFileAs.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                multiOpenFileChooser = new LWFileChooser();
                multiOpenFileChooser.setDialogTitle("Open FRAP image series");
                multiOpenFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                multiOpenFileChooser.addChoosableFileFilter(filter_tif);
                multiOpenFileChooser.setMultiSelectionEnabled(true);
                saveMovieFileChooser = new LWFileChooser();
                saveMovieFileChooser.setDialogTitle("Save to quick time movie (.mov)");
                saveMovieFileChooser.addChoosableFileFilter(filter_qt);
                saveMovieFileChooser.setAcceptAllFileFilterUsed(false);
                saveMovieFileChooser.setCurrentDirectory(new File(localWorkspace.getDefaultWorkspaceDirectory()));
                if (mf == null) {
                    mf = new VirtualFrapMainFrame(localWorkspace, frapWorkspace, batchRunWorkspace, bStandalone, documentWindowManager);
                }
                // System.out.println(mf.getLocation().x + "---"+mf.getLocation().y);
                mf.setMainFrameTitle("");
                mf.setVisible(true);
                // initialize FRAPStudy
                FRAPStudy fStudy = new FRAPStudy();
                frapWorkspace.setFrapStudy(fStudy, true);
                try {
                    Thread.sleep(30);
                } catch (InterruptedException e) {
                }
            }
        });
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}