Add function to convert ijrois to labelimage

2d_spots_in_fibers.py

@@ -36,7 +36,7 @@ from net.imglib2.roi import Regions
 from net.imglib2.roi.labeling import LabelRegions
 from net.imglib2.algorithm.labeling import ConnectedComponents
 # BIOP imports
-from ch.epfl.biop.ij2command import Labels2Rois
+from ch.epfl.biop.ij2command import Labels2Rois, Rois2Labels
 # python imports
 import os
 
@@ -707,6 +707,33 @@ def save_labelimage_as_ijroiset(label_imp, filename, suffix, target):
     rm.reset()
 
 
+def load_rois_from_zip(path):
+    """Load ROIs from the given zip file and add them to the RoiManager.
+
+    Parameters
+    ----------
+    path : string
+        Path to the ROI zip file.
+    """
+    rm = RoiManager.getInstance()
+    if not rm:
+        rm = RoiManager()
+    rm.reset()
+
+    rm.runCommand("Open", path)
+
+
+def convert_rois_to_labelimage(imp):
+    rm = RoiManager.getInstance()
+    if not rm:
+        rm = RoiManager()
+
+    label_imp = command.run( Rois2Labels , False , 'imp' , imp , 'rm', rm).get().getOutput("label_imp")
+    rm.reset() # TODO: should be optional but can be default
+
+    return label_imp
+
+
 def close_images(list_of_imps):
     """Close given ImagePlus images