plt.plot(np.asarray(shifts).reshape((j+1)*shift.shape[0],shift.shape[1]))
#%% apply shifts to another channel, you need to reload the original movie other channel (mov_other_channel)
if False:
# here reload the original imaging channel from movie
totalShifts=np.sum(np.asarray(shifts),axis=0)[:,0:2].tolist()
mov_other_channel.applyShifstToMovie(totalShifts)
#%% if you want to apply the shifts only ones to reduce the smoothing
if False:
totalShifts=np.sum(np.asarray(shifts),axis=0)[:,0:2].tolist()
m=XMovie(filename, frameRate=frameRate);
m.applyShifstToMovie(totalShifts)
#%% plot movie median
minBrightness=0;
maxBrightness=20;
medMov=np.median(m.mov,axis=0)
plt.imshow(medMov,cmap=plt.cm.Greys_r,vmin=minBrightness,vmax=maxBrightness)
#%% save motion corrected movie inpython format along with the results. This takes some time now but will save a lot later...
np.savez(filename_mc,mov=m.mov,frameRate=frameRate,templates=templates,shifts=shifts,max_shift=max_shift)
#%% RELOAD MOTION CORRECTED MOVIE
m=XMovie(mat=np.load(filename_mc)['mov'], frameRate=frameRate);
max_shift=np.load(filename_mc)['max_shift']
