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

Example 16 with FRAPStudy

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

the class EstParams_ReacBindingDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    FRAPModel[] frapModels = fStudy.getModels();
    Parameter[] params = null;
    // get parameters to display in reaction binding panel
    if (frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getModelParameters() != null) {
        params = frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getModelParameters();
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentSimResults(frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getData());
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentRawSimTimePoints(frapModels[FRAPModel.IDX_MODEL_DIFF_BINDING].getTimepoints());
    } else {
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentSimResults(null);
        ((EstParams_ReacBindingPanel) getPanelComponent()).setCurrentRawSimTimePoints(null);
        if (frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null) {
            params = FRAPModel.createReacBindingParametersFromDiffusionParameters(frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters());
        } else // no parameters are available
        {
            try {
                params = FRAPModel.getInitialParameters(fStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_BINDING], fStudy.getStartingIndexForRecovery());
            } catch (Exception ex) {
                ex.printStackTrace(System.out);
                DialogUtils.showErrorDialog((getPanelComponent()), "Error getting parameters for diffusion plus binding model." + ex.getMessage());
            }
        }
    }
    ((EstParams_ReacBindingPanel) getPanelComponent()).setReacBindingParams(params);
    try {
        ((EstParams_ReacBindingPanel) getPanelComponent()).setData(fStudy.getFrapData(), params, fStudy.getFrapData().getImageDataset().getImageTimeStamps(), fStudy.getStartingIndexForRecovery(), fStudy.getSelectedROIsForErrorCalculation());
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        DialogUtils.showErrorDialog((getPanelComponent()), "Error plotting data for diffusion plus binding model." + ex.getMessage());
    }
}

Example 17 with FRAPStudy

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

the class EstParams_ReacBindingPanel method activateReacDiffEstPanel.

public void activateReacDiffEstPanel() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    // check if we can do auto estimation on reaction binding papameters
    Parameter[] params = null;
    if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null && fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null) {
        params = fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters();
    } else {
        DialogUtils.showErrorDialog(EstParams_ReacBindingPanel.this, "Parameters from 'Diffusion with One Diffusing Component' model " + "is needed for automated estimation of reaction binding parameters.\n" + "Please include the above-mentioned model using 'Choose Model Types' wizard.");
        return;
    }
    if (estGuidePanel == null) {
        estGuidePanel = new FRAPReacDiffEstimationGuidePanel();
    }
    // set initial parameters from diffusion with one diffusing component
    estGuidePanel.setPrimaryParameters(params);
    int choice2 = DialogUtils.showComponentOKCancelDialog(EstParams_ReacBindingPanel.this, estGuidePanel, "FRAP Parameter Estimation Guide");
    if (choice2 == JOptionPane.OK_OPTION) {
        if (estGuidePanel.getParamTable() != null) {
            int rowLen = estGuidePanel.getParamTable().getRowCount();
            for (int i = 0; i < rowLen; i++) {
                String name = ((String) estGuidePanel.getParamTable().getValueAt(i, EstimatedParameterTableModel.COLUMN_NAME));
                double val = ((Double) estGuidePanel.getParamTable().getValueAt(i, EstimatedParameterTableModel.COLUMN_VALUE)).doubleValue();
                if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_FreePartDiffRate])) {
                    reactionDiffusionPanel.setFreeDiffRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_FreePartConc])) {
                    reactionDiffusionPanel.setFreeFraction(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_BWMRate])) {
                    reactionDiffusionPanel.setBleachMonitorRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ComplexConc])) {
                    reactionDiffusionPanel.setComplexFraction(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ReacPseudoOnRate])) {
                    reactionDiffusionPanel.setOnRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_ReacOffRate])) {
                    reactionDiffusionPanel.setOffRate(val + "");
                } else if (name.equals(FRAPReacDiffEstimationGuidePanel.paramNames[FRAPReacDiffEstimationGuidePanel.IDX_Immobile])) {
                    reactionDiffusionPanel.setImmobileFraction(val + "");
                }
            }
        // multisourcePlotPane.setDataSources(null);
        }
    }
}

Example 18 with FRAPStudy

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

the class EstParams_ReacBindingPanel method plotDerivedSimulationResults.

private void plotDerivedSimulationResults(AnalysisParameters[] anaParams) {
    try {
        if (getCurrentSimResults() == null || getCurrentRawSimTimePoints() == null || allDataHash == null || allDataHash.get(anaParams[0]) == null || (allDataHash.get(anaParams[0])[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE]) == null) {
            multisourcePlotPane.setDataSources(null);
            return;
        }
        String description = null;
        int totalROIlen = FRAPData.VFRAP_ROI_ENUM.values().length;
        boolean[] wantsROITypes = new boolean[totalROIlen];
        System.arraycopy(frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation(), 0, wantsROITypes, 0, totalROIlen);
        ODESolverResultSet simSolverResultSet = new ODESolverResultSet();
        simSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            String currentROIName = FRAPData.VFRAP_ROI_ENUM.values()[j].name();
            String name = (description == null ? /*"sim D="+diffusionRates[diffusionRateIndex]+"::"*/
            "" : description) + currentROIName;
            simSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
        }
        int totalWantedROIlen = 0;
        for (int i = 0; i < wantsROITypes.length; i++) {
            if (wantsROITypes[i]) {
                totalWantedROIlen++;
            }
        }
        FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
        // 
        // populate time
        // 
        double[] shiftedSimTimes = getCurrentRawSimTimePoints();
        int startIndexRecovery = fStudy.getStartingIndexForRecovery();
        for (int j = 0; j < shiftedSimTimes.length; j++) {
            double[] row = new double[totalWantedROIlen + 1];
            row[0] = shiftedSimTimes[j] + fStudy.getFrapData().getImageDataset().getImageTimeStamps()[startIndexRecovery];
            simSolverResultSet.addRow(row);
        }
        // 
        // populate values
        // 
        double[][] currentSimData = getCurrentSimResults();
        // populate sim data
        int columncounter = 0;
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            double[] values = currentSimData[j];
            for (int k = 0; k < values.length; k++) {
                simSolverResultSet.setValue(k, columncounter + 1, values[k]);
            }
            columncounter++;
        }
        // get exp data and generate datasource to display
        // anaParams[0] is the key in allDataHash to get the dataSource[]:exp & sim
        DataSource[] selectedRowDataSourceArr = allDataHash.get(anaParams[0]);
        if (selectedRowDataSourceArr != null) {
            // referenceData is the exp data
            // ReferenceData referenceData = (ReferenceData)selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE].getSource();
            final DataSource expDataSource = /*new DataSource(referenceData,"exp")*/
            selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE];
            // from simulation
            final DataSource simDataSource = new DataSource.DataSourceRowColumnResultSet("sim", simSolverResultSet);
            DataSource[] newDataSourceArr = new DataSource[2];
            newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE] = expDataSource;
            newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_SIMDATASOURCE] = simDataSource;
            // the following paragraph of code is just to get selected color for selected ROIs
            // and make them the same as we show on ChooseModel_RoiForErrorPanel/RoiForErrorPanel
            // double valid ROI colors (not include cell and background)
            int validROISize = FRAPData.VFRAP_ROI_ENUM.values().length - 2;
            Color[] fullColors = ColorUtil.generateAutoColor(validROISize * 2, getBackground(), new Integer(0));
            boolean[] selectedROIs = frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation();
            int selectedROICounter = 0;
            for (int i = 0; i < selectedROIs.length; i++) {
                if (selectedROIs[i]) {
                    selectedROICounter++;
                }
            }
            // double the size, each ROI is a comparison of exp and sim
            Color[] selectedColors = new Color[selectedROICounter * 2];
            int selectedColorIdx = 0;
            for (int i = 0; i < selectedROIs.length; i++) {
                if (selectedROIs[i] && i == 0) {
                    selectedColors[selectedColorIdx] = fullColors[i];
                    selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i + validROISize];
                    selectedColorIdx++;
                }
                if (// skip cell and background ROIs
                selectedROIs[i] && i > 2) {
                    selectedColors[selectedColorIdx] = fullColors[i - 2];
                    selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i - 2 + validROISize];
                    selectedColorIdx++;
                }
            }
            multisourcePlotPane.setDataSources(newDataSourceArr, selectedColors);
            multisourcePlotPane.selectAll();
        }
    } catch (Exception e2) {
        e2.printStackTrace();
        DialogUtils.showErrorDialog(this, "Error graphing Optimizer data " + e2.getMessage());
    }
}

Example 19 with FRAPStudy

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

the class EstParams_ReactionOffRateDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
    Parameter[] params = fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters();
    try {
        if (params == null) {
            params = fStudy.getFrapOptFunc().getBestParamters(fStudy.getFrapData(), null, true);
        }
        ((EstParams_ReactionOffRatePanel) getPanelComponent()).setData(params, fStudy.getFrapData(), /*fStudy.getFrapOptFunc().getOffRateResults(),*/
        fStudy.getStartingIndexForRecovery());
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        DialogUtils.showErrorDialog((getPanelComponent()), "Error getting parameters for reaction dominant off rate model.");
    }
}

Example 20 with FRAPStudy

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

the class LoadFRAPData_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().setFrapStudy(newFRAPStudy, true);
                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;
}