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

Example 6 with FRAPStudy

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

the class FRAPDataPanel method plotROI.

protected void plotROI() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getFrapData() == null) {
        return;
    }
    saveROI();
    double[] averageFluor = FRAPDataAnalysis.getAverageROIIntensity(fStudy.getFrapData(), fStudy.getFrapData().getCurrentlyDisplayedROI(), null, null);
    showCurve(new String[] { "f" }, fStudy.getFrapData().getImageDataset().getImageTimeStamps(), new double[][] { averageFluor });
}

Example 7 with FRAPStudy

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

the class FRAPDataPanel method crop.

// There are two FRAPDataPanel instances, one is in MainFrame and antoher is in DefineROIWizard
// The crop function is called in DefineROIWizard, the image change will only be reflected in the
// FRAPDataPanel in DefineROIWizard. The newFrapStudy will only be set to FrapdataPanel in Mainframe
// when FINISH button is pressed.
protected void crop(Rectangle cropRectangle) throws ImageException {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getFrapData() == null) {
        return;
    }
    getOverlayEditorPanelJAI().saveUserChangesToROI();
    FRAPData frapData = fStudy.getFrapData();
    FRAPData newFrapData = frapData.crop(cropRectangle);
    FRAPStudy newFrapStudy = new FRAPStudy();
    newFrapStudy.setFrapData(newFrapData);
    newFrapStudy.setXmlFilename(fStudy.getXmlFilename());
    newFrapStudy.setFrapDataExternalDataInfo(fStudy.getFrapDataExternalDataInfo());
    newFrapStudy.setRoiExternalDataInfo(fStudy.getRoiExternalDataInfo());
    newFrapStudy.setStoredRefData(fStudy.getStoredRefData());
    newFrapStudy.setModels(fStudy.getModels());
    newFrapStudy.setStartingIndexForRecovery(fStudy.getStartingIndexForRecovery());
    getFrapWorkspace().setFrapStudy(newFrapStudy, false);
}

Example 8 with FRAPStudy

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

the class FRAPStudyPanel method clearMovieBuffer.

public void clearMovieBuffer() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy != null) {
        fStudy.setMovieURLString(null);
        fStudy.setMovieFileString(null);
    }
}

Example 9 with FRAPStudy

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

the class FRAPStudyPanel method getEstimateParametersWizard.

public Wizard getEstimateParametersWizard() {
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getSelectedModels().size() == 0) {
        return null;
    } else {
        if (estimateParamWizard == null) {
            estimateParamWizard = new Wizard(JOptionPane.getFrameForComponent(this));
            estimateParamWizard.getDialog().setTitle("Estimate Parameters");
            // initialize the wizard panels
            diffOneDescriptor = new EstParams_OneDiffComponentDescriptor();
            diffOneDescriptor.setFrapWorkspace(getFrapWorkspace());
            diffTwoDescriptor = new EstParams_TwoDiffComponentDescriptor();
            diffTwoDescriptor.setFrapWorkspace(getFrapWorkspace());
            offRateDescriptor = new EstParams_ReactionOffRateDescriptor();
            offRateDescriptor.setFrapWorkspace(getFrapWorkspace());
            compareResultsDescriptor = new EstParams_CompareResultsDescriptor();
            compareResultsDescriptor.setFrapWorkspace(getFrapWorkspace());
        }
        // Dynamicly link the wizard pages according to the selected models.
        // clear all first
        estimateParamWizard.clearAllPanels();
        WizardPanelDescriptor lastDescriptor = null;
        for (int i = 0; i < fStudy.getSelectedModels().size(); i++) {
            int modelType = fStudy.getSelectedModels().get(i).intValue();
            if (modelType == FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT) {
                estimateParamWizard.registerWizardPanel(EstParams_OneDiffComponentDescriptor.IDENTIFIER, diffOneDescriptor);
                diffOneDescriptor.setBackPanelDescriptorID((lastDescriptor == null) ? null : lastDescriptor.getPanelDescriptorIdentifier());
                if (// not the first wizard page
                lastDescriptor != null) {
                    lastDescriptor.setNextPanelDescriptorID(EstParams_OneDiffComponentDescriptor.IDENTIFIER);
                }
                lastDescriptor = diffOneDescriptor;
            } else if (modelType == FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS) {
                estimateParamWizard.registerWizardPanel(EstParams_TwoDiffComponentDescriptor.IDENTIFIER, diffTwoDescriptor);
                diffTwoDescriptor.setBackPanelDescriptorID((lastDescriptor == null) ? null : lastDescriptor.getPanelDescriptorIdentifier());
                if (lastDescriptor != null) {
                    lastDescriptor.setNextPanelDescriptorID(EstParams_TwoDiffComponentDescriptor.IDENTIFIER);
                }
                lastDescriptor = diffTwoDescriptor;
            } else if (modelType == FRAPModel.IDX_MODEL_REACTION_OFF_RATE) {
                estimateParamWizard.registerWizardPanel(EstParams_ReactionOffRateDescriptor.IDENTIFIER, offRateDescriptor);
                offRateDescriptor.setBackPanelDescriptorID((lastDescriptor == null) ? null : lastDescriptor.getPanelDescriptorIdentifier());
                if (lastDescriptor != null) {
                    lastDescriptor.setNextPanelDescriptorID(EstParams_ReactionOffRateDescriptor.IDENTIFIER);
                }
                lastDescriptor = offRateDescriptor;
            }
        }
        // the last one should always be the compare page
        estimateParamWizard.registerWizardPanel(EstParams_CompareResultsDescriptor.IDENTIFIER, compareResultsDescriptor);
        lastDescriptor.setNextPanelDescriptorID(EstParams_CompareResultsDescriptor.IDENTIFIER);
        compareResultsDescriptor.setBackPanelDescriptorID(lastDescriptor.getPanelDescriptorIdentifier());
        // each time when load the wizard, it should start from the first possible page.
        if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null) {
            estimateParamWizard.setCurrentPanel(EstParams_OneDiffComponentDescriptor.IDENTIFIER);
        } else if (fStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] != null) {
            estimateParamWizard.setCurrentPanel(EstParams_TwoDiffComponentDescriptor.IDENTIFIER);
        } else if (fStudy.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] != null) {
            estimateParamWizard.setCurrentPanel(EstParams_ReactionOffRateDescriptor.IDENTIFIER);
        }
        return estimateParamWizard;
    }
}

Example 10 with FRAPStudy

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

the class FRAPStudyPanel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(FRAPSingleWorkspace.PROPERTY_CHANGE_FRAPSTUDY_NEW) || evt.getPropertyName().equals(FRAPSingleWorkspace.PROPERTY_CHANGE_FRAPSTUDY_UPDATE)) {
        if (evt.getNewValue() instanceof FRAPStudy) {
            FRAPStudy fStudy = (FRAPStudy) evt.getNewValue();
            // set status for save button
            VirtualFrapMainFrame.enableSave(!(fStudy == null || fStudy.getFrapData() == null));
            // update analysis stage and results
            updateWorkflowStage(fStudy);
            updateAnalysisResult(fStudy);
            // undoable support
            try {
                undoableEditSupport.postEdit(FRAPStudyPanel.CLEAR_UNDOABLE_EDIT);
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (evt.getPropertyName().equals(FRAPSingleWorkspace.PROPERTY_CHANGE_BEST_MODEL)) {
        clearBestModelData();
        getAnalysisResultsPanel().clearBestModelDisplay();
        if (evt.getNewValue() != null && evt.getNewValue() instanceof Integer) {
            int newBestModelIdx = ((Integer) evt.getNewValue()).intValue();
            (getAnalysisResultsPanel()).setBestModel(newBestModelIdx, getLocalWorkspace());
        } else {
            SwingUtilities.invokeLater(new Runnable() {

                public void run() {
                    getAnalysisResultsPanel().clearResultTable();
                }
            });
        }
    }
}