def save_roi_set(imp=IJ.getImage()): img_dir, name = get_file_info() roi_dir = make_roi_dir(img_dir, name) roi_path = make_roi_path(roi_dir, name) rm = RoiManager().getInstance() rm.deselect() rm.runCommand("Save", roi_path) rm.runCommand("delete")
def save_roi_set(imp): img_dir, name = get_file_info(imp) roi_path = make_roi_path(img_dir, name) rm = RoiManager().getInstance() rm.deselect() if roi_path is not None: rm.runCommand("Save",roi_path) rm.runCommand("delete")
def save_roi_set(imp=IJ.getImage()): img_dir, name = get_file_info() roi_dir = make_roi_dir(img_dir, name) roi_path = make_roi_path(roi_dir, name) Roi.setColor(Color.blue) rm = RoiManager().getInstance() rm.deselect() rm.runCommand("Save", roi_path) ol = imp.getOverlay() if ol is None: ol = Overlay() for roi in rm.getRoisAsArray(): ol.add(roi) imp.setOverlay(ol) rm.runCommand("delete") ol.setStrokeColor(Color.blue) Roi.setColor(Color.yellow)
rm.reset() rm.runCommand("Open", os.path.join(folder, "selected.zip")) # rename the remaining ROIs so that VSI can deal with them # i is the index within ROI Mgr. i+1 is the number given by VSI Reader # get base name of ROIs # searching the last 5 characters for the hashmark because there are usually 2 in the ROI name oldname = rm.getName(0) hashPos = oldname.find("#",-5) + 1 # print hashPos basename = oldname[0:hashPos] # print "Basename is " + basename nROIs = rm.getCount() for i in range(0, nROIs): roiNum = i + 1 rm.select(i) rm.runCommand("Rename", basename + str(roiNum)) rm.deselect() rm.runCommand("Save", os.path.join(folder, "renamed.zip")) # finally, user should select all the ROIs and click Extract Current Image # and save a copy with the overlay of ROIs # for serial sections, use a large thumbnail to make ROIs. # Re-open the "renamed" file and the 2nd series, activate ROIs on the other series image, adjust positions, RENAME TO SERIES 2 and extract