fix subidx to compute motion correction template from a movie slice

caiman/motion_correction.py

@@ -99,7 +99,7 @@ def __init__(self, fname, min_mov=None, dview=None, max_shifts=(6, 6), niter_rig
                  strides=(96, 96), overlaps=(32, 32), splits_els=14, num_splits_to_process_els=None,
                  upsample_factor_grid=4, max_deviation_rigid=3, shifts_opencv=True, nonneg_movie=True, gSig_filt=None,
                  use_cuda=False, border_nan=True, pw_rigid=False, num_frames_split=80, var_name_hdf5='mov',is3D=False,
-                 indices=(slice(None), slice(None))):
+                 indices=(slice(None), slice(None)), subidx=slice(None, None, 1)):
         """
         Constructor class for motion correction operations
 
@@ -213,6 +213,7 @@ def __init__(self, fname, min_mov=None, dview=None, max_shifts=(6, 6), niter_rig
         self.var_name_hdf5 = var_name_hdf5
         self.is3D = bool(is3D)
         self.indices = indices
+        self.subidx = subidx
         if self.use_cuda and not HAS_CUDA:
             logging.debug("pycuda is unavailable. Falling back to default FFT.")
 
@@ -317,7 +318,8 @@ def motion_correct_rigid(self, template=None, save_movie=False) -> None:
                 border_nan=self.border_nan,
                 var_name_hdf5=self.var_name_hdf5,
                 is3D=self.is3D,
-                indices=self.indices)
+                indices=self.indices,
+                subidx=self.subidx)
             if template is None:
                 self.total_template_rig = _total_template_rig
 
@@ -2830,7 +2832,9 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
         Exception 'The movie contains nans. Nans are not allowed!'
 
     """
-
+    if subidx.start is not None:
+        print(f"Computing template from frames {subidx}.")
+
     dims, T = cm.source_extraction.cnmf.utilities.get_file_size(fname, var_name_hdf5=var_name_hdf5)
     Ts = np.arange(T)[subidx].shape[0]
     step = Ts // 10 if is3D else Ts // 50
@@ -2863,6 +2867,8 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
                 m = m.copy()
             template = caiman.motion_correction.bin_median(
                     m.motion_correct(max_shifts[1], max_shifts[0], template=None)[0])
+    else:
+        template = high_pass_filter_space(template, gSig_filt)
 
     new_templ = template
     if add_to_movie is None:
@@ -2892,10 +2898,10 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
 
         fname_tot_rig, res_rig = motion_correction_piecewise(fname, splits, strides=None, overlaps=None,
                                                              add_to_movie=add_to_movie, template=old_templ, max_shifts=max_shifts, max_deviation_rigid=0,
-                                                             dview=dview, save_movie=save_movie, base_name=base_name, subidx = subidx,
+                                                             dview=dview, save_movie=save_movie, base_name=base_name,
                                                              num_splits=num_splits_to_process, shifts_opencv=shifts_opencv, nonneg_movie=nonneg_movie, gSig_filt=gSig_filt,
                                                              use_cuda=use_cuda, border_nan=border_nan, var_name_hdf5=var_name_hdf5, is3D=is3D,
-                                                             indices=indices)
+                                                             indices=indices, subidx=None)
         if is3D:
             new_templ = np.nanmedian(np.stack([r[-1] for r in res_rig]), 0)           
         else:

environment.yml

@@ -1,7 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- python >=3.10
+- python =3.9
 - bokeh
 - coverage
 - cython