apply_shifts_movie on 4D movie returns error 'too many values to unpack'

[zylittlep]

Hi all,
when I tried to use apply_shifts_movie to a 4D movie (time x volumetric imaging), regardless of hdf5/tiff format, I got the ValueError saying 'too many values to unpack'. (It worked fine on 3D movie) How should I modify my code to get out of this? Thank you.

[j-friedrich]

Did you set the parameter is3D to True as in the demo?
Running mc.apply_shifts_movie(fname) after executing the cells in the motion correction section works just fine.

[zylittlep]

Yes, I did.
mc_opts_dict = dict(
strides = (96, 96, 4), # 96,96 create a new patch every x pixels for pw-rigid correction
overlaps = (32, 32, 2), # overlap between pathes (size of patch strides+overlaps)
max_shifts = (32, 32, 12), # maximum allowed rigid shift in pixels (view the movie to get a sense of motion)
max_deviation_rigid = 8, # 5maximum deviation allowed for patch with respect to rigid shifts
pw_rigid = True, # flag for performing rigid or piecewise rigid motion correction
is3D=True,
niter_rig= 2, # maximum number of iterations rigid motion correction, in general is 1. 0
splits_rig = 20, # for parallelization split the movies in num_splits chuncks across time
splits_els = 20,
border_nan = 'copy', # replicate values along the boundary (if True, fill in with NaN)
nonneg_movie = False,
upsample_factor_grid = 4,
)

[zylittlep]

figured out why it didn't work in my case. It works when fname is only a string, but not a list. The version I use is 1.8.9.