Merge branch 'master' into dev

caiman/base/movies.py

@@ -1174,7 +1174,7 @@ def load(file_name,fr=30,start_time=0,meta_data=None,subindices=None,shape=None,
                         except:
                             logging.warning('Your tif file is saved a single page file. Performance will be affected')
                             input_arr = tffl.asarray()
-                            input_arr = input_arr[subindices[0]]
+                            input_arr = input_arr[subindices]
 
                 else:
                     input_arr = tffl.asarray()

caiman/motion_correction.py

@@ -256,7 +256,7 @@ def motion_correct_rigid(self, template=None, save_movie=False):
             self.shifts_rig: shifts in x and y per frame
         """
         logging.debug('Entering Rigid Motion Correction')
-        logging.debug(-self.min_mov) # XXX why the minus?
+        logging.debug(-self.min_mov)  # XXX why the minus?
         self.total_template_rig = template
         self.templates_rig = []
         self.fname_tot_rig = []
@@ -2200,7 +2200,7 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
     """
     corrected_slicer = slice(subidx.start, subidx.stop, subidx.step * 10)
     m = cm.load(fname, subindices=corrected_slicer)
-
+    
     if m.shape[0] < 300:
         m = cm.load(fname, subindices=corrected_slicer)
     elif m.shape[0] < 500:
@@ -2209,14 +2209,20 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
     else:
         corrected_slicer = slice(subidx.start, subidx.stop, subidx.step * 30)
         m = cm.load(fname, subindices=corrected_slicer)
-
+
+    if len(m.shape) < 3:
+        m = cm.load(fname)
+        m = m[corrected_slicer]
+        logging.warning("Your original file was saved as a single page " +
+                        "file. Consider saving it in multiple smaller files" +
+                        "with size smaller than 4GB (if it is a .tif file)")
     if template is None:
         if gSig_filt is not None:
             m = cm.movie(
                 np.array([high_pass_filter_space(m_, gSig_filt) for m_ in m]))
 
         template = cm.motion_correction.bin_median(
-            m.motion_correct(max_shifts[0], max_shifts[1], template=None)[0])
+            m.motion_correct(max_shifts[1], max_shifts[0], template=None)[0])
 
     new_templ = template
     if add_to_movie is None:
@@ -2462,7 +2468,11 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
             T = len(tf.pages)
             if T == 1:  # Fiji-generated TIF
                 is_fiji = True
-                T, d1, d2 = tf[0].shape
+                try:
+                    T, d1, d2 = tf[0].shape
+                except:
+                    T, d1, d2 = tf.asarray().shape
+                    tf.close()
             else:
                 d1, d2 = tf.pages[0].shape