/** * Returns the rois if any stored in the ROI manager. * @return See above. */ public static Roi[] readFromRoiManager() { RoiManager manager = RoiManager.getInstance(); if (manager == null) return null; return manager.getRoisAsArray(); }
/** * Returns the rois if any stored in the ROI manager. * @return See above. */ public static Roi[] readFromRoiManager() { RoiManager manager = RoiManager.getInstance(); if (manager == null) return null; return manager.getRoisAsArray(); }
/** This is a macro-callable version of getSelectedIndexes(). * Example: indexes=split(call("ij.plugin.frame.RoiManager.getIndexesAsString")); */ public static String getIndexesAsString() { RoiManager rm = RoiManager.getInstance(); if (rm==null) return ""; String str = Arrays.toString(rm.getSelectedIndexes()); str = str.replaceAll(",",""); return str.substring(1,str.length()-1); }
/** This is a macro-callable version of getSelectedIndexes(). * Example: indexes=split(call("ij.plugin.frame.RoiManager.getIndexesAsString")); */ public static String getIndexesAsString() { RoiManager rm = RoiManager.getInstance(); if (rm==null) return ""; String str = Arrays.toString(rm.getSelectedIndexes()); str = str.replaceAll(",",""); return str.substring(1,str.length()-1); }
/** Obsolete */ public void setShowAllROIs(boolean showAllROIs) { RoiManager rm = RoiManager.getInstance(); if (rm!=null) rm.runCommand(showAllROIs?"show all":"show none"); }
/** Obsolete */ public void setShowAllROIs(boolean showAllROIs) { RoiManager rm = RoiManager.getInstance(); if (rm!=null) rm.runCommand(showAllROIs?"show all":"show none"); }
/** Returns a reference to the ROI Manager window or to the macro batch mode RoiManager, or null if neither exists. */ public static RoiManager getInstance2() { RoiManager rm = getInstance(); if (rm==null && IJ.isMacro()) rm = Interpreter.getBatchModeRoiManager(); return rm; }
/** Returns a reference to the ROI Manager window or to the macro batch mode RoiManager, or null if neither exists. */ public static RoiManager getInstance2() { RoiManager rm = getInstance(); if (rm==null && IJ.isMacro()) rm = Interpreter.getBatchModeRoiManager(); return rm; }
void hide() { ImagePlus imp = IJ.getImage(); imp.setHideOverlay(true); RoiManager rm = RoiManager.getInstance(); if (rm!=null) rm.runCommand("show none"); }
void hide() { ImagePlus imp = IJ.getImage(); imp.setHideOverlay(true); RoiManager rm = RoiManager.getInstance(); if (rm!=null) rm.runCommand("show none"); }
/** * A method to fill the masks array with data based on the ROI manager. */ protected boolean createMasksFromRoiManager(final int width, final int height) { final RoiManager roiManager = RoiManager.getInstance(); if (roiManager == null) { IJ.error("Could not get ROI Manager instance."); return false; } final Roi[] selectedRois = roiManager.getSelectedRoisAsArray(); // create the ROIs createMasksAndRois(selectedRois, width, height); return true; }
public boolean roiManagerSelect(Roi roi, boolean delete) { RoiManager rm=RoiManager.getInstance(); if (rm==null) return false; int index = rm.getRoiIndex(roi); if (index<0) return false; if (delete) { rm.select(imp, index); rm.runCommand("delete"); } else rm.selectAndMakeVisible(imp, index); return true; }
protected void exportToROIManager(ImagePlus image) { Roi[] rois = map.get(image); if (rois == null) return; int currentSlice = image.getCurrentSlice(); RoiManager manager = RoiManager.getInstance(); if (manager == null) manager = new RoiManager(); for (int i = 0; i < rois.length; i++) if (rois[i] != null) { image.setSliceWithoutUpdate(i + 1); manager.add(image, rois[i], i + 1); } image.setSlice(currentSlice); }
public boolean roiManagerSelect(Roi roi, boolean delete) { RoiManager rm=RoiManager.getInstance(); if (rm==null) return false; int index = rm.getRoiIndex(roi); if (index<0) return false; if (delete) { rm.select(imp, index); rm.runCommand("delete"); } else rm.selectAndMakeVisible(imp, index); return true; }
@Override protected void exportToROIManager(ImagePlus image) { Roi[] rois = map.get(image); if (rois == null) return; int currentSlice = image.getCurrentSlice(); RoiManager manager = RoiManager.getInstance(); if (manager == null) manager = new RoiManager(); for (int i = 0; i < rois.length; i++) if (specifiedByUser(rois[i])) { image.setSliceWithoutUpdate(i + 1); manager.add(image, rois[i], i + 1); } image.setSlice(currentSlice); }
static Roi checkForROIs(Dataset dataset) throws NoLineException { // TODO : dataset should be used here ImagePlus imp = ij.WindowManager.getCurrentImage(); Roi roi = null; if (imp != null) { roi = imp.getRoi(); } if (roi == null) { // Look in ROI manager, if open RoiManager rm = RoiManager.getInstance(); if (rm != null) roi = rm.getRoi(0); } if (roi == null) { throw new NoLineException("Please define a line in order to build the kymograph."); } if (!"Straight Line".equals(roi.getTypeAsString()) && !"Polyline".equals(roi .getTypeAsString())) { throw new NoLineException("Please use the Straight Line or Segmented Line selection tool."); } return roi; }
void show() { ImagePlus imp = IJ.getImage(); imp.setHideOverlay(false); if (imp.getOverlay()==null) { RoiManager rm = RoiManager.getInstance(); if (rm!=null && rm.getCount()>1) { if (!IJ.isMacro()) rm.toFront(); rm.runCommand("show all with labels"); } } }
void show() { ImagePlus imp = IJ.getImage(); imp.setHideOverlay(false); if (imp.getOverlay()==null) { RoiManager rm = RoiManager.getInstance(); if (rm!=null && rm.getCount()>1) { if (!IJ.isMacro()) rm.toFront(); rm.runCommand("show all with labels"); } } }
protected void importFromROIManager() { ImagePlus image = WindowManager.getCurrentImage(); if (image == null) return; Roi[] rois = getRois(image); RoiManager manager = RoiManager.getInstance(); if (manager == null) return; List labels = manager.getList(); @SuppressWarnings("unchecked") Hashtable<String, Roi> table = (Hashtable<String, Roi>)manager.getROIs(); for (int i = 0; i < labels.getItemCount(); i++) { String label = labels.getItem(i); int index = manager.getSliceNumber(label) - 1; if (index >= 0 && index < rois.length) rois[index] = table.get(label); } setRoi(image, rois[image.getCurrentSlice() - 1]); }
@Override public void process(final Module module) { // assign singleton RoiManager to single RoiManager input final ModuleItem<RoiManager> roiManagerInput = moduleService.getSingleInput( module, RoiManager.class); if (roiManagerInput != null) { RoiManager roiManager; if (roiManagerInput.isRequired()) { roiManager = RoiManager.getRoiManager(); } else { roiManager = RoiManager.getInstance(); } if (roiManager == null) return; module.setInput(roiManagerInput.getName(), roiManager); module.resolveInput(roiManagerInput.getName()); } } }