mov = libtiff.TiffFile(current_file)
mov = mov.get_tiff_array()
mov = np.array(mov[:,:,:],dtype='d')
frame1 = len(mov[:,0,0])
nrow = len(mov[0,:,0])
ncol = len(mov[0,0,:])
if count == 0:
if assignmask == 0:
fig1, ax = plt.subplots()
cax = ax.imshow(mov[0,:,:], interpolation='none', cmap='afmhot')
cbar = fig1.colorbar(cax, ax=ax)
print("Choose polygon ROI by clicking multiple points")
print("If finished, press enter")
pts = plt.ginput(0, timeout=0)
pts = np.array(pts)
mask = polygon.mask_polygon(mov,pts)
print("Choose background")
bgpts = plt.ginput(1, timeout=0)
bgpts = np.array(bgpts)
ax.plot(pts[:,0],pts[:,1], 'b-+')
ax.plot([bgpts[:,0]+bgscan,bgpts[:,0]+bgscan,bgpts[:,0]-bgscan,bgpts[:,0]-bgscan,bgpts[:,0]+bgscan],[bgpts[:,1]+bgscan,bgpts[:,1]-bgscan,bgpts[:,1]-bgscan,bgpts[:,1]+bgscan,bgpts[:,1]+bgscan], '-o', color='w')
ax.set_xlim([0,ncol])
ax.set_ylim([nrow,0])
fig1.canvas.draw()
elif assignmask == 1:
fig1, ax = plt.subplots()
cax = ax.imshow(mov[0,:,:], interpolation='none', cmap='afmhot')
cbar = fig1.colorbar(cax, ax=ax)
cax1 = ax.imshow(mask, interpolation='none', cmap='gray', alpha=0.5)
cbar1 = fig1.colorbar(cax1, ax=ax)
if thresholdmask == 0:
