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

Example 1 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;
}

Example 2 with FRAPStudy

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

the class FRAPBatchRunWorkspace method addFrapStudy.

public void addFrapStudy(FRAPStudy newFrapStudy) {
    File newFile = new File(newFrapStudy.getXmlFilename());
    ArrayList<FRAPStudy> frapStudies = getFrapStudies();
    int size = frapStudies.size();
    int insertIdx = size;
    for (int i = 0; i < size; i++) {
        File xmlFile = new File(frapStudies.get(i).getXmlFilename());
        if (newFile.getName().compareTo(xmlFile.getName()) == 0) {
            if (newFile.getAbsolutePath().compareTo(xmlFile.getAbsolutePath()) < 0) {
                insertIdx = i;
                break;
            }
        } else if (newFile.getName().compareTo(xmlFile.getName()) < 0) {
            insertIdx = i;
            break;
        }
    }
    if (insertIdx == size) {
        frapStudies.add(newFrapStudy);
    } else {
        frapStudies.add(insertIdx, newFrapStudy);
    }
    // enable save button
    VirtualFrapBatchRunFrame.enableSave(frapStudies != null && frapStudies.size() > 0);
}

Example 3 with FRAPStudy

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

the class FRAPBatchRunWorkspace method getSaveSingleFilesTask.

// get client task for saving single vfrap files
public AsynchClientTask getSaveSingleFilesTask() {
    AsynchClientTask saveSingleFileTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            int size = getFrapStudies().size();
            for (int i = 0; i < getFrapStudies().size(); i++) {
                FRAPStudy fStudy = getFrapStudies().get(i);
                File outFile = new File(fStudy.getXmlFilename());
                this.getClientTaskStatusSupport().setMessage("Saving file " + (i + 1) + " of " + size + " :" + outFile.getAbsolutePath() + " ...");
                saveProcedure(outFile, fStudy, this.getClientTaskStatusSupport());
            }
        }
    };
    return saveSingleFileTask;
}

Example 4 with FRAPStudy

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

the class FRAPBatchRunWorkspace method updateDisplayForTreeSelection.

public void updateDisplayForTreeSelection(Object selection) {
    String oldString = null;
    if (// doc
    displaySelection instanceof File) {
        oldString = ((File) displaySelection).getAbsolutePath();
    } else if (// results
    displaySelection instanceof String) {
        oldString = ((String) displaySelection);
    }
    displaySelection = selection;
    if (// doc
    selection instanceof File) {
        String newString = ((File) selection).getAbsolutePath();
        FRAPStudy selectedFrapStudy = getFRAPStudy(newString);
        setWorkingFRAPStudy(selectedFrapStudy);
        firePropertyChange(PROPERTY_CHANGE_BATCHRUN_DISPLAY_IMG, oldString, newString);
    } else if (// results
    selection instanceof String) {
        firePropertyChange(PROPERTY_CHANGE_BATCHRUN_DISPLAY_PARAM, oldString, (selection));
    }
}

Example 5 with FRAPStudy

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

the class MultiFileDescriptor method preNextProcess.

// load the data before the panel disappears
public ArrayList<AsynchClientTask> preNextProcess() {
    // create AsynchClientTask arraylist
    ArrayList<AsynchClientTask> taskArrayList = new ArrayList<AsynchClientTask>();
    final File[] files = multiFilePanel.getSelectedFiles();
    if (files.length > 0) {
        final String filePath = files[0].getParent();
        final String LOADING_MESSAGE = "Loading files from directory " + filePath + "...";
        AsynchClientTask updateUIBeforeLoadTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

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

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FRAPStudy newFRAPStudy = null;
                newFRAPStudy = FRAPWorkspace.loadFRAPDataFromMultipleFiles(files, this.getClientTaskStatusSupport(), multiFilePanel.isTimeSeries(), multiFilePanel.getTimeInterval());
                isFileLoaded = true;
                // for all loaded files
                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().setWorkingFRAPStudy(newFRAPStudy);
                VirtualFrapLoader.mf.setMainFrameTitle("");
                VirtualFrapMainFrame.updateProgress(0);
                if (isFileLoaded) {
                    VirtualFrapMainFrame.updateStatus("Loaded files from " + filePath);
                } else {
                    VirtualFrapMainFrame.updateStatus("Failed loading files from " + filePath + ".");
                }
            }
        };
        taskArrayList.add(updateUIBeforeLoadTask);
        taskArrayList.add(loadTask);
        taskArrayList.add(afterLoadingSwingTask);
    } else {
        DialogUtils.showErrorDialog(multiFilePanel, "No file is selected. Please input one or more file names to continue.");
        throw new RuntimeException("No file is selected. Please input one or more file names to continue.");
    }
    return taskArrayList;
}