Remove RoiManager import, get from script parameter instead.

2d_spots_in_fibers.py

@@ -18,7 +18,6 @@ from fiji.plugin.trackmate.action import LabelImgExporter
 # ij imports
 from ij import IJ
 from ij.plugin import ImageCalculator
-from ij.plugin.frame import RoiManager
 from ij.measure import ResultsTable
 from ij.measure import Measurements as M
 from ij.plugin.filter import Analyzer
@@ -386,7 +385,7 @@ def save_results_table(results_table, filename, suffix, target):
     results_table.save(savepath)
 
 
-def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
+def save_labelimage_as_ijroiset(label_imp, rm, filename, suffix, target):
     """Save all labels i a label Images as IJ-ROIset to target location.
       Only 2D, requires PTBIOP update site.
 
@@ -401,10 +400,6 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
     target : str
         the target directory in which to save the table
     """
-    rm = RoiManager.getInstance()
-    if not rm:
-        rm = RoiManager()
-    rm.reset()
     command.run( Labels2Rois , False , 'imp' , label_imp , 'rm', rm).get()
     savename = filename + "_" + str(suffix) + ".zip"
     savepath = os.path.join(target, savename)
@@ -412,19 +407,16 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
     rm.reset()
 
 
-def load_rois_from_zip(path):
+def load_rois_from_zip(path, rm):
     """Load ROIs from the given zip file and add them to the RoiManager.
 
     Parameters
     ----------
     path : string
         Path to the ROI zip file.
+    rm : RoiManager
+        The ROI Manager.
     """
-    rm = RoiManager.getInstance()
-    if not rm:
-        rm = RoiManager()
-    rm.reset()
-
     rm.runCommand("Open", path)