Examples with ROI cbit.vcell.VirtualMicroscopy.ROI used on opensource projects

Example 41 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class FRAPDataPanel method initialize.

/**
 * This method initializes this
 *
 * @return void
 */
private void initialize() {
    GridBagConstraints gridBagConstraints1 = new GridBagConstraints();
    gridBagConstraints1.gridx = 0;
    gridBagConstraints1.ipadx = 0;
    gridBagConstraints1.ipady = 0;
    gridBagConstraints1.fill = GridBagConstraints.BOTH;
    gridBagConstraints1.weighty = 1.0D;
    gridBagConstraints1.weightx = 1.0D;
    gridBagConstraints1.gridy = 0;
    this.setSize(653, 492);
    this.setLayout(new GridBagLayout());
    this.add(getOverlayEditorPanelJAI(), gridBagConstraints1);
    getOverlayEditorPanelJAI().addPropertyChangeListener(new PropertyChangeListener() {

        public void propertyChange(PropertyChangeEvent evt) {
            if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_TIMEPLOTROI_PROPERTY)) {
                try {
                    plotROI();
                } catch (Exception e) {
                    DialogUtils.showErrorDialog(FRAPDataPanel.this, "Error Time Plot ROI:\n" + e.getMessage());
                }
            } else if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_CURRENTROI_PROPERTY)) {
                try {
                    String roiName = (String) evt.getNewValue();
                    if (roiName != null) {
                        getFrapWorkspace().getWorkingFrapStudy().getFrapData().setCurrentlyDisplayedROI(getFrapWorkspace().getWorkingFrapStudy().getFrapData().getRoi(roiName), false);
                    }
                } catch (Exception e) {
                    DialogUtils.showErrorDialog(FRAPDataPanel.this, "Error Setting Current ROI:\n" + e.getMessage());
                }
            } else if (evt.getPropertyName().equals(VFrap_OverlayEditorPanelJAI.FRAP_DATA_UNDOROI_PROPERTY)) {
                try {
                    ROI undoableROI = (ROI) evt.getNewValue();
                    getFrapWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(undoableROI);
                } catch (Exception e) {
                    PopupGenerator.showErrorDialog(FRAPDataPanel.this, "Error Setting Current ROI:\n" + e.getMessage());
                }
            }
        }
    });
    VFrap_OverlayEditorPanelJAI.CustomROIImport importVFRAPROI = new VFrap_OverlayEditorPanelJAI.CustomROIImport() {

        public boolean importROI(File inputFile) throws Exception {
            try {
                if (!VirtualFrapLoader.filter_vfrap.accept(inputFile)) {
                    return false;
                }
                String xmlString = XmlUtil.getXMLString(inputFile.getAbsolutePath());
                MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                FRAPStudy importedFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
                VirtualFrapMainFrame.updateProgress(0);
                ROI roi = getFrapWorkspace().getWorkingFrapStudy().getFrapData().getCurrentlyDisplayedROI();
                ROI[] importedROIs = importedFrapStudy.getFrapData().getRois();
                if (importedFrapStudy.getFrapData() != null && importedROIs != null) {
                    if (!importedROIs[0].getISize().compareEqual(roi.getISize())) {
                        throw new Exception("Imported ROI mask size (" + importedROIs[0].getISize().getX() + "," + importedROIs[0].getISize().getY() + "," + importedROIs[0].getISize().getZ() + ")" + " does not match current Frap DataSet size (" + roi.getISize().getX() + "," + roi.getISize().getY() + "," + roi.getISize().getZ() + ")");
                    }
                    for (int i = 0; i < importedROIs.length; i++) {
                        getFrapWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(importedROIs[i]);
                    }
                // undoableEditSupport.postEdit(FRAPStudyPanel.CLEAR_UNDOABLE_EDIT);
                }
                return true;
            } catch (Exception e1) {
                throw new Exception("VFRAP ROI Import - " + e1.getMessage());
            }
        }
    };
    getOverlayEditorPanelJAI().setCustomROIImport(importVFRAPROI);
}

Example 42 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class BatchRunDisplayPanel method getFRAPDataPanel.

public FRAPDataPanel getFRAPDataPanel() {
    if (frapDataPanel == null) {
        // the frap data panel in the main frame is not editable
        frapDataPanel = new FRAPDataPanel(false);
        // set display mode
        frapDataPanel.adjustComponents(VFrap_OverlayEditorPanelJAI.DISPLAY_WITH_ROIS);
        Hashtable<String, Cursor> cursorsForROIsHash = new Hashtable<String, Cursor>();
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_CELLROI]);
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_BLEACHROI]);
        cursorsForROIsHash.put(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name(), FRAPStudyPanel.ROI_CURSORS[FRAPStudyPanel.CURSOR_BACKGROUNDROI]);
        frapDataPanel.getOverlayEditorPanelJAI().setCursorsForROIs(cursorsForROIsHash);
        VFrap_OverlayEditorPanelJAI.CustomROIImport importVFRAPROI = new VFrap_OverlayEditorPanelJAI.CustomROIImport() {

            public boolean importROI(File inputFile) throws Exception {
                try {
                    if (!VirtualFrapLoader.filter_vfrap.accept(inputFile)) {
                        return false;
                    }
                    String xmlString = XmlUtil.getXMLString(inputFile.getAbsolutePath());
                    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                    FRAPStudy importedFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
                    VirtualFrapMainFrame.updateProgress(0);
                    ROI roi = getBatchRunWorkspace().getWorkingSingleWorkspace().getWorkingFrapStudy().getFrapData().getCurrentlyDisplayedROI();
                    ROI[] importedROIs = importedFrapStudy.getFrapData().getRois();
                    if (importedFrapStudy.getFrapData() != null && importedROIs != null) {
                        if (!importedROIs[0].getISize().compareEqual(roi.getISize())) {
                            throw new Exception("Imported ROI mask size (" + importedROIs[0].getISize().getX() + "," + importedROIs[0].getISize().getY() + "," + importedROIs[0].getISize().getZ() + ")" + " does not match current Frap DataSet size (" + roi.getISize().getX() + "," + roi.getISize().getY() + "," + roi.getISize().getZ() + ")");
                        }
                        for (int i = 0; i < importedROIs.length; i++) {
                            getBatchRunWorkspace().getWorkingSingleWorkspace().getWorkingFrapStudy().getFrapData().addReplaceRoi(importedROIs[i]);
                        }
                    // undoableEditSupport.postEdit(FRAPStudyPanel.CLEAR_UNDOABLE_EDIT);
                    }
                    return true;
                } catch (Exception e1) {
                    throw new Exception("VFRAP ROI Import - " + e1.getMessage());
                }
            }
        };
        frapDataPanel.getOverlayEditorPanelJAI().setCustomROIImport(importVFRAPROI);
    }
    return frapDataPanel;
}

Example 43 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class DefineROI_RoiForErrorPanel method refreshCheckboxes.

public void refreshCheckboxes() {
    FRAPData frapData = frapWorkspace.getWorkingFrapStudy().getFrapData();
    ROI[] rois = frapData.getRois();
    // disable all the checkboxes first
    setAllCheckboxesEnabled(false);
    setAllCheckboxesSelected(false);
    // disable ROIs with 0 pixel in it
    // or disselect checkboxes according to stored selected ROIS
    boolean[] storedSelectedROIs = frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation();
    for (int i = 0; i < rois.length; i++) {
        if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()).getNonzeroPixelsCount() > 0) {
            roi_bleachedCheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleachedCheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring1CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring1CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring2CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring2CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring3CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring3CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring4CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring4CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring5CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring5CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring6CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring6CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring7CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring7CheckBox.setSelected(true);
            }
        } else if (rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name()) && frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name()).getNonzeroPixelsCount() > 0) {
            roi_bleached_ring8CheckBox.setEnabled(true);
            if (storedSelectedROIs == null || storedSelectedROIs.length < 1 || storedSelectedROIs[i]) {
                roi_bleached_ring8CheckBox.setSelected(true);
            }
        }
    }
}

Example 44 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class DefineROI_RoiForErrorPanel method refreshROIImageForDisplay.

public void refreshROIImageForDisplay() {
    FRAPData frapData = frapWorkspace.getWorkingFrapStudy().getFrapData();
    ROI[] allROIs = getAllROIs();
    Color[] allColors = getAllROIColors();
    ArrayList<ROI> plottedROIs = new ArrayList<ROI>();
    ArrayList<Color> plottedColors = new ArrayList<Color>();
    if (roi_bleachedCheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED]);
    }
    if (roi_bleached_ring1CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING1]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING1]);
    }
    if (roi_bleached_ring2CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING2]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING2]);
    }
    if (roi_bleached_ring3CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING3]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING3]);
    }
    if (roi_bleached_ring4CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING4]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING4]);
    }
    if (roi_bleached_ring5CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING5]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING5]);
    }
    if (roi_bleached_ring6CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING6]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING6]);
    }
    if (roi_bleached_ring7CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING7]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING7]);
    }
    if (roi_bleached_ring8CheckBox.isSelected()) {
        plottedROIs.add(allROIs[IDX_ROI_BLEACHED_RING8]);
        plottedColors.add(allColors[IDX_ROI_BLEACHED_RING8]);
    }
    // show ROI image
    ROI[] plottedROIArray = new ROI[plottedROIs.size()];
    plottedROIArray = plottedROIs.toArray(plottedROIArray);
    Color[] plottedColorArray = new Color[plottedColors.size()];
    plottedColorArray = plottedColors.toArray(plottedColorArray);
    roiImagePanel.refreshROIImage(plottedROIArray, plottedColorArray, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()), Color.white);
}

Example 45 with ROI

use of cbit.vcell.VirtualMicroscopy.ROI in project vcell by virtualcell.

the class VFrap_OverlayEditorPanelJAI method fireUndoableEditROI.

@SuppressWarnings("serial")
private void fireUndoableEditROI(final String editType) {
    if (undoableROI == null) {
        return;
    }
    final ROI originalROI = undoableROI;
    undoableROI = null;
    if (editType != null && undoableEditSupport != null) {
        undoableEditSupport.postEdit(new AbstractUndoableEdit() {

            public boolean canUndo() {
                return true;
            }

            public String getUndoPresentationName() {
                return editType + " " + originalROI.getROIName();
            }

            public void undo() throws CannotUndoException {
                super.undo();
                firePropertyChange(FRAP_DATA_UNDOROI_PROPERTY, null, originalROI);
            }
        });
    } else {
        if (undoableEditSupport != null) {
            undoableEditSupport.postEdit(VFrap_OverlayEditorPanelJAI.CLEAR_UNDOABLE_EDIT);
        }
    }
}