Merge pull request #908 from flatironinstitute/MWB_fixes

bug fixes for NWB demo, and pin pynwb momentarily

caiman/source_extraction/cnmf/estimates.py

@@ -1638,9 +1638,9 @@ def save_NWB(self,
             ps.add_column('snr', 'signal to noise ratio')
             ps.add_column('accepted', 'in accepted list')
             ps.add_column('rejected', 'in rejected list')
-            if self.cnn_preds:
+            if self.cnn_preds is not None:
                 ps.add_column('cnn', 'description of CNN')
-            if self.idx_components:
+            if self.idx_components is not None:
                 ps.add_column('keep', 'in idx_components')
 
             # Add ROIs
@@ -1651,9 +1651,9 @@ def save_NWB(self,
                     add_roi_kwargs.update(accepted=i in self.accepted_list)
                 if hasattr(self, 'rejected_list'):
                     add_roi_kwargs.update(rejected=i in self.rejected_list)
-                if self.cnn_preds:
+                if self.cnn_preds is not None:
                     add_roi_kwargs.update(cnn=self.cnn_preds[i])
-                if self.idx_components:
+                if self.idx_components is not None:
                     add_roi_kwargs.update(keep=i in self.idx_components)
 
                 ps.add_roi(**add_roi_kwargs)

demos/general/demo_pipeline_NWB.py

@@ -80,8 +80,6 @@ def main():
              session_id='Session 1',
              var_name_hdf5='TwoPhotonSeries')
 #%% First setup some parameters for data and motion correction
-
-
     # motion correction parameters
     dxy = (2., 2.)  # spatial resolution in x and y in (um per pixel)
     # note the lower than usual spatial resolution here
@@ -109,7 +107,8 @@ def main():
         'overlaps': overlaps,
         'max_deviation_rigid': max_deviation_rigid,
         'border_nan': 'copy',
-        'var_name_hdf5': 'acquisition/TwoPhotonSeries'
+        #'var_name_hdf5': 'acquisition/TwoPhotonSeries'
+        'var_name_hdf5': 'TwoPhotonSeries'
     }
 
     opts = params.CNMFParams(params_dict=mc_dict)

environment.yml

@@ -21,7 +21,7 @@ dependencies:
 - peakutils
 - pims
 - psutil
-- pynwb
+- pynwb==1.4.0
 - pyqtgraph
 - scikit-image
 - scikit-learn