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

Example 41 with FRAPStudy

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

the class FRAPBatchRunWorkspace method refreshStatisticsData.

public void refreshStatisticsData() {
    int studySize = getFrapStudies().size();
    // get parameters array (column-name and column-details should be excluded)
    // parameterVals[0] primaryDiffRates, parameterVals[1] primaryMobiles,parameterVals[2]bwmRates
    // parameterVals[3] secDiffRates,parameterVals[4] secMobiles,parameterVals[5] bs_concentration
    // parameterVals[6] reaction on rate, parameterVals[7] reacton off rate, parameterVals[8] immobile
    double[][] parameterVals = new double[BatchRunResultsParamTableModel.NUM_COLUMNS - 2][studySize];
    for (int i = 0; i < (BatchRunResultsParamTableModel.NUM_COLUMNS - 2); i++) {
        // fill all elements with 1e8 first
        Arrays.fill(parameterVals[i], FRAPOptimizationUtils.largeNumber);
    }
    for (int i = 0; i < studySize; i++) {
        FRAPStudy fStudy = getFrapStudies().get(i);
        if (selectedModel == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
            FRAPModel fModel = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT];
            parameterVals[0][i] = fModel.getModelParameters()[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess();
            parameterVals[1][i] = fModel.getModelParameters()[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess();
            parameterVals[2][i] = fModel.getModelParameters()[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess();
            // immobile fraction
            parameterVals[8][i] = Math.max(0, (1 - parameterVals[1][i]));
        } else if (selectedModel == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
            FRAPModel fModel = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS];
            parameterVals[0][i] = fModel.getModelParameters()[FRAPModel.INDEX_PRIMARY_DIFF_RATE].getInitialGuess();
            parameterVals[1][i] = fModel.getModelParameters()[FRAPModel.INDEX_PRIMARY_FRACTION].getInitialGuess();
            parameterVals[2][i] = fModel.getModelParameters()[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess();
            parameterVals[3][i] = fModel.getModelParameters()[FRAPModel.INDEX_SECONDARY_DIFF_RATE].getInitialGuess();
            parameterVals[4][i] = fModel.getModelParameters()[FRAPModel.INDEX_SECONDARY_FRACTION].getInitialGuess();
            // immobile fraction
            parameterVals[8][i] = Math.max(0, (1 - parameterVals[1][i] - parameterVals[4][i]));
        } else if (selectedModel == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
            FRAPModel fModel = fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE];
            parameterVals[2][i] = fModel.getModelParameters()[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess();
            parameterVals[5][i] = fModel.getModelParameters()[FRAPModel.INDEX_BINDING_SITE_CONCENTRATION].getInitialGuess();
            parameterVals[7][i] = fModel.getModelParameters()[FRAPModel.INDEX_OFF_RATE].getInitialGuess();
        }
    }
    double[][] oldStatData = statisticsData;
    // stores statistics for each parameters . (column-name and column-details should be excluded)
    statisticsData = new double[BatchRunResultsStatTableModel.NUM_STATISTICS][BatchRunResultsParamTableModel.NUM_COLUMNS - 2];
    for (int i = 0; i < BatchRunResultsStatTableModel.NUM_STATISTICS; i++) {
        // fill all elements with 1e8 first
        Arrays.fill(statisticsData[i], FRAPOptimizationUtils.largeNumber);
    }
    for (int i = 0; i < BatchRunResultsParamTableModel.NUM_COLUMNS - 2; i++) {
        // statistics for parameters exist(which is not saved as 1e8)
        if (parameterVals[i][0] != FRAPOptimizationUtils.largeNumber) {
            DescriptiveStatistics stat = DescriptiveStatistics.CreateBasicStatistics(parameterVals[i]);
            statisticsData[BatchRunResultsStatTableModel.ROW_IDX_AVERAGE][i] = stat.getMean();
            statisticsData[BatchRunResultsStatTableModel.ROW_IDX_STD][i] = stat.getStandardDeviation();
            statisticsData[BatchRunResultsStatTableModel.ROW_IDX_MEDIAN][i] = stat.getMedian();
            statisticsData[BatchRunResultsStatTableModel.ROW_IDX_MIN][i] = stat.getMin();
            statisticsData[BatchRunResultsStatTableModel.ROW_IDX_MAX][i] = stat.getMax();
        }
    }
    updateAverageParameters();
    firePropertyChange(PROPERTY_CHANGE_BATCHRUN_UPDATE_STATISTICS, oldStatData, statisticsData);
}

Example 42 with FRAPStudy

use of cbit.vcell.microscopy.FRAPStudy 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 43 with FRAPStudy

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

the class FRAPBatchRunWorkspace method setSelectedROIForReactionOffRate.

// If users select reaction off rate model for batch run, the only ROI applied must be bleached ROI
public void setSelectedROIForReactionOffRate() {
    ArrayList<FRAPStudy> frapStudies = this.getFrapStudies();
    boolean[] selectedROIs = FRAPStudy.createSelectedROIsForReactionOffRateModel();
    for (FRAPStudy fStudy : frapStudies) {
        fStudy.setSelectedROIsForErrorCalculation(selectedROIs);
    }
}

Example 44 with FRAPStudy

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

the class FRAPBatchRunWorkspace method clearWorkingSingleWorkspace.

public void clearWorkingSingleWorkspace() {
    FRAPStudy newFrapStudy = new FRAPStudy();
    getWorkingSingleWorkspace().setFrapStudy(newFrapStudy, true, true);
    String oldString = "Before clear all";
    String newString = "After clear all";
    firePropertyChange(PROPERTY_CHANGE_BATCHRUN_DISPLAY_IMG, oldString, newString);
}

Example 45 with FRAPStudy

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

the class BatchRunDetailsPanel method updateViewTreeForNewBatchRunFile.

public void updateViewTreeForNewBatchRunFile(FRAPBatchRunWorkspace batchRunWorkspace) {
    frapBatchRunViewTree.clearAll();
    ArrayList<FRAPStudy> fStudyList = batchRunWorkspace.getFrapStudies();
    DefaultMutableTreeNode firstDocNode = null;
    for (int i = 0; i < fStudyList.size(); i++) {
        // update tree
        if (i == 0) {
            firstDocNode = frapBatchRunViewTree.addBatchRunDocNode(new File(fStudyList.get(i).getXmlFilename()));
        } else {
            frapBatchRunViewTree.addBatchRunDocNode(new File(fStudyList.get(i).getXmlFilename()));
        }
    }
    if (batchRunWorkspace.isBatchRunResultsAvailable()) {
        updateResultsInfo(false);
    }
    // set fist doc selected when opening a new Batch Run file
    frapBatchRunViewTree.setSelectionPath(new TreePath(firstDocNode.getPath()));
}