Fix subidx to enable computing the NoRMCorre template frame from subset of movie frames

caiman/base/movies.py

@@ -1604,6 +1604,22 @@ def rgb2gray(rgb):
         elif extension == '.sima':
             raise Exception("movies.py:load(): FATAL: sima support was removed in 1.9.8")
 
+        elif extension == '.isxd':
+            import isx
+            mov = isx.Movie.read(file_name)
+            T = mov.timing.num_samples
+            dims = mov.spacing.num_pixels
+            fr = 1e6 / mov.timing.period.to_usecs()
+
+            idx_frames = np.arange(T)
+            if subindices is not None:
+                idx_frames = idx_frames[subindices]
+                T = len(idx_frames)
+
+            input_arr = np.zeros([T] + list(dims), dtype=outtype)
+            for idx in range(T):
+                input_arr[idx, :, :] = mov.get_frame_data(idx)
+
         else:
             raise Exception('Unknown file type')
     else:

caiman/motion_correction.py

@@ -2101,6 +2101,7 @@ def high_pass_filter_space(img_orig, gSig_filt=None, freq=None, order=None):
             return cm.movie(np.array([cv2.idft(cv2.dft(img, flags=cv2.DFT_COMPLEX_OUTPUT) * 
                             H[..., None])[..., 0] for img in img_orig]) / (rows*cols))
 
+
 def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=None, newstrides=None, upsample_factor_grid=4,
                      upsample_factor_fft=10, show_movie=False, max_deviation_rigid=2, add_to_movie=0, shifts_opencv=False, gSig_filt=None,
                      use_cuda=False, border_nan=True):