Merge branch 'nd2support' of https://github.com/tdincer/suite2p into nd2support

Author: tdincer

suite2p/extraction/extract.py

@@ -132,7 +132,7 @@ def extract_traces_from_masks(ops, cell_masks, neuropil_masks):
     if 'reg_file_chan2' in ops:
         with BinaryRWFile(Ly=ops['Ly'], Lx=ops['Lx'],
                           filename=ops['reg_file_chan2']) as f:    
-            F_chan2, Fneu_chan2 = extract_traces(cell_masks, neuropil_masks, batch_size=batch_size)
+            F_chan2, Fneu_chan2 = extract_traces(f, cell_masks, neuropil_masks, batch_size=batch_size)
     return F, Fneu, F_chan2, Fneu_chan2
 
 def extraction_wrapper(stat, f_reg, f_reg_chan2=None, cell_masks=None, neuropil_masks=None, ops=default_ops()):

suite2p/gui/rungui.py

@@ -481,7 +481,7 @@ def revert_default_ops(self):
     def save_text(self):
         for k in range(len(self.editlist)):
             key = self.keylist[k]
-            self.ops[key] = self.editlist[k].get_text(self.intkeys, self.boolkeys)
+            self.ops[key] = self.editlist[k].get_text(self.intkeys, self.boolkeys, self.stringkeys)
 
     def load_ops(self, name=None):
         print('loading ops')

suite2p/io/nwb.py

@@ -516,8 +516,7 @@ def save_nwb(save_folder):
         # BACKGROUNDS
         # (meanImg, Vcorr and max_proj are REQUIRED)
         bg_strs = ["meanImg", "Vcorr", "max_proj", "meanImg_chan2"]
-        nplanes = ops["nplanes"]
-        for iplane in range(nplanes):
+        for iplane, ops in enumerate(ops1):
             images = Images("Backgrounds_%d" % iplane)
             for bstr in bg_strs:
                 if bstr in ops: