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

Example 11 with ROI

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

the class DefineROI_SummaryPanel method setLoadInfo.

public void setLoadInfo(final FRAPStudy frapStudy) {
    if (frapStudy != null && frapStudy.getFrapData() != null) {
        // enable components to change values
        BeanUtils.enableComponents(getInfoPanel(), true);
        BeanUtils.enableComponents(getIndexPanel(), true);
        // set info panel
        ImageDataset imgDataset = frapStudy.getFrapData().getImageDataset();
        imgXTextField.setText(NumberUtils.formatNumber(imgDataset.getExtent().getX(), 15));
        imgYTextField.setText(NumberUtils.formatNumber(imgDataset.getExtent().getY(), 15));
        FRAPData fData = frapStudy.getFrapData();
        ROI cellROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
        ROI bleachedROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
        ROI backgroundROI = fData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
        if (cellROI.getNonzeroPixelsCount() < 1) {
            cellROIUndefined.setSelected(true);
            cellROIDefined.setSelected(false);
        } else {
            cellROIUndefined.setSelected(false);
            cellROIDefined.setSelected(true);
        }
        if (bleachedROI.getNonzeroPixelsCount() < 1) {
            bleachROIUndefined.setSelected(true);
            bleachROIDefined.setSelected(false);
        } else {
            bleachROIUndefined.setSelected(false);
            bleachROIDefined.setSelected(true);
        }
        if (backgroundROI.getNonzeroPixelsCount() < 1) {
            bgROIUndefined.setSelected(true);
            bgROIDefined.setSelected(false);
        } else {
            bgROIUndefined.setSelected(false);
            bgROIDefined.setSelected(true);
        }
        // they are not editable
        imgXTextField.setEditable(false);
        imgYTextField.setEditable(false);
        cellROIDefined.setEnabled(false);
        cellROIUndefined.setEnabled(false);
        bleachROIDefined.setEnabled(false);
        bleachROIUndefined.setEnabled(false);
        bgROIDefined.setEnabled(false);
        bgROIUndefined.setEnabled(false);
        // set index panel
        startIndexCombo.removeAllItems();
        double[] timeSteps = frapStudy.getFrapData().getImageDataset().getImageTimeStamps();
        for (int i = 0; i < timeSteps.length; i++) {
            startIndexCombo.addItem(timeSteps[i] + "");
        }
        if (bleachROIDefined.isSelected()) {
            int index = (frapStudy.getStartingIndexForRecovery() == null ? FRAPDataAnalysis.calculateRecoveryIndex(frapStudy.getFrapData()) : frapStudy.getStartingIndexForRecovery());
            startIndexCombo.setSelectedIndex(index);
            startIndexAvaliableLabel.setText(START_IDX_AVAILABLE_STR);
        } else {
            startIndexCombo.setSelectedIndex(0);
            startIndexAvaliableLabel.setText(START_IDX_UNAVAILABLE_STR);
        }
    } else {
        imgXTextField.setText("");
        imgYTextField.setText("");
        cellROIDefined.setSelected(false);
        cellROIUndefined.setSelected(false);
        bleachROIDefined.setSelected(false);
        bleachROIUndefined.setSelected(false);
        bgROIDefined.setSelected(false);
        bgROIUndefined.setSelected(false);
        startIndexCombo.removeAllItems();
        startIndexCombo.addItem("     N/A     ");
        BeanUtils.enableComponents(getInfoPanel(), false);
        BeanUtils.enableComponents(getIndexPanel(), false);
    }
}

Example 12 with ROI

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

the class VFrap_ROIAssistPanel method showComponentOKCancelTableList.

public int[] showComponentOKCancelTableList(final Component requester, String title, String[] columnNames, Object[][] rowData, int listSelectionModel_SelectMode, final RegionInfo[] regionInfoArr, final short[] multiObjectROIPixels) throws UserCancelException {
    DefaultTableModel tableModel = new DefaultTableModel() {

        public boolean isCellEditable(int row, int column) {
            return false;
        }
    };
    tableModel.setDataVector(rowData, columnNames);
    final JTable table = new JTable(tableModel);
    table.setSelectionMode(listSelectionModel_SelectMode);
    JScrollPane scrollPane = new JScrollPane(table);
    table.setPreferredScrollableViewportSize(new Dimension(500, 250));
    table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!e.getValueIsAdjusting()) {
                try {
                    int index = table.getSelectedRow();
                    // System.out.println("list index="+index);
                    RegionInfo keepRegion = regionInfoArr[index];
                    short[] removePixels = multiObjectROIPixels.clone();
                    for (int i = 0; i < removePixels.length; i++) {
                        if (!keepRegion.isIndexInRegion(i)) {
                            removePixels[i] = 0;
                        }
                    }
                    UShortImage ushortImage = new UShortImage(removePixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                    final ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
                    frapData.addReplaceRoi(newCellROI);
                } catch (Exception e2) {
                    e2.printStackTrace();
                    throw new RuntimeException("Error selecting resolved ROI", e2);
                }
            }
        }
    });
    ScopedExpressionTableCellRenderer.formatTableCellSizes(table);
    int result = DialogUtils.showComponentOKCancelDialog(requester, scrollPane, title);
    if (result != JOptionPane.OK_OPTION) {
        throw UserCancelException.CANCEL_GENERIC;
    }
    return table.getSelectedRows();
}

Example 13 with ROI

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

the class VFrap_ROIAssistPanel method processTimepoint.

private void processTimepoint() {
    new Thread(new Runnable() {

        public void run() {
            try {
                boolean bInvert = !frapData.getCurrentlyDisplayedROI().getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name());
                short[] cellMask = null;
                if (bInvert) {
                    cellMask = frapData.getRoi(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name()).getPixelsXYZ();
                }
                short[] shortPixels = new short[lastROISourceDataShort.length];
                for (int i = 0; i < lastROISourceDataShort.length; i++) {
                    shortPixels[i] = (short) (isSet(frapData.getCurrentlyDisplayedROI().getROIName(), lastROISourceDataShort[i], thresholdSlider.getValue(), thresholdSliderIntensityLookup, (cellMask == null ? true : cellMask[i] != 0)) ? 0xFFFF : 0);
                }
                UShortImage ushortImage = new UShortImage(shortPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
                ROI newCellROI = new ROI(ushortImage, frapData.getCurrentlyDisplayedROI().getROIName());
                final ROI forceValidROI = forceROIValid(newCellROI);
                SwingUtilities.invokeAndWait(new Runnable() {

                    public void run() {
                        // }});
                        frapData.addReplaceRoi(forceValidROI);
                    }
                });
            } catch (final Exception e2) {
                lastROISourceDataShort = null;
                e2.printStackTrace();
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        // }});
                        DialogUtils.showErrorDialog(VFrap_ROIAssistPanel.this, "Error setting new ROI. " + e2.getMessage());
                    }
                });
            }
        }
    }).start();
}

Example 14 with ROI

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

the class VFrap_ROIAssistPanel method forceROIValid.

private ROI forceROIValid(ROI validateROI) throws Exception {
    if (validateROI.getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name())) {
        lastRegionInfos = null;
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                // }});
                applyROIButton.setEnabled(true);
                resolveROIButton.setEnabled(false);
                fillVoidsButton.setEnabled(false);
            }
        });
        return validateROI;
    }
    if (validateROI.getNonzeroPixelsCount() < 1) {
        return validateROI;
    }
    // 
    // Remove pixels touching only at corners
    // 
    short[] validatePixels = validateROI.getPixelsXYZ();
    // 
    // Remove noise objects
    // 
    lastRegionInfos = calculateRegionInfos(validatePixels);
    Vector<RegionInfo> roiRegionInfoV = new Vector<RegionInfo>();
    for (int i = 0; i < lastRegionInfos.length; i++) {
        if (lastRegionInfos[i].getPixelValue() == 1) {
            roiRegionInfoV.add(lastRegionInfos[i]);
        }
    // System.out.println(lastRegionInfos[i]);
    }
    // if(validateROI.getROIType().equals(RoiType.ROI_CELL) || validateROI.getROIType().equals(RoiType.ROI_BLEACHED)){
    if (roiRegionInfoV.size() > 1) {
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                applyROIButton.setEnabled(false);
                resolveROIButton.setEnabled(true);
                fillVoidsButton.setEnabled(false);
            }
        });
    } else {
        final boolean hasInternalVoids = fillVoids(validatePixels, true);
        SwingUtilities.invokeAndWait(new Runnable() {

            public void run() {
                // }});
                lastRegionInfos = null;
                applyROIButton.setEnabled(!hasInternalVoids);
                resolveROIButton.setEnabled(false);
                fillVoidsButton.setEnabled(hasInternalVoids);
            }
        });
    }
    UShortImage ushortImage = new UShortImage(validatePixels, validateROI.getRoiImages()[0].getOrigin(), validateROI.getRoiImages()[0].getExtent(), validateROI.getISize().getX(), validateROI.getISize().getY(), validateROI.getISize().getZ());
    ROI newROI = new ROI(ushortImage, validateROI.getROIName());
    if (newROI.compareEqual(validateROI)) {
        return validateROI;
    }
    return newROI;
}

Example 15 with ROI

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

the class VFrap_OverlayEditorPanelJAI method showROIAssist.

public void showROIAssist() {
    // shows up with automatica detected region of interest regardless of whatever is defined, users may lose defined ROI by accidentally clicking the ROI assistant.
    if (getRoiSouceData().getCurrentlyDisplayedROI() != null && getRoiSouceData().getCurrentlyDisplayedROI().getNonzeroPixelsCount() > 0) {
        String choice = DialogUtils.showWarningDialog(this, "Invoking the ROI assistant will override already defined '" + getRoiSouceData().getCurrentlyDisplayedROI().getROIName() + "'. Do you want to continue?", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CANCEL);
        if (choice.equals(UserMessage.OPTION_CANCEL)) {
            return;
        }
    }
    // only check when doing roiAssist for bleached, this is actually used by VFRAP. (VCell has Cell ROI only)
    if (getRoiSouceData().getCurrentlyDisplayedROI().getROIName().equals(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()) && getRoiSouceData().getRoi(VFrap_ROISourceData.VFRAP_ROI_ENUM.ROI_CELL.name()).getNonzeroPixelsCount() < 1) {
        DialogUtils.showInfoDialog(VFrap_OverlayEditorPanelJAI.this, "Cell ROI must be defined before using ROI Assist Tool to create Bleached ROI.");
        return;
    }
    ROI originalROI = null;
    try {
        originalROI = new ROI(roi);
    } catch (Exception ex) {
        ex.printStackTrace();
    // can't happen
    }
    getROIAssistPanel().init(originalROI, getRoiSouceData(), VFrap_OverlayEditorPanelJAI.this);
    setROIAssistVisible(true);
    adjustComponentsForVFRAP(SHOW_RIO_ASSISTANT);
}