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
