Skip to content

Commit

Permalink
Fix docs for arguments to tile_and_correct() and tile_and_correct_3d()
Browse files Browse the repository at this point in the history
  • Loading branch information
@pgunn
pgunn committed Dec 10, 2024
1 parent 4d94b6e commit d31d8c8
Showing 1 changed file with 32 additions and 27 deletions.
59 changes: 32 additions & 27 deletions caiman/motion_correction.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,13 +129,13 @@ def __init__(self, fname, min_mov=None, dview=None, max_shifts=(6, 6), niter_rig
max_deviation_rigid:int
maximum deviation allowed for patch with respect to rigid shift
shifts_opencv: Bool
shifts_opencv: bool
apply shifts fast way (but smoothing results)
nonneg_movie: boolean
nonneg_movie: bool
make the SAVED movie and template mostly nonnegative by removing min_mov from movie
use_cuda : boolean (DEPRECATED)
use_cuda : bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
border_nan : bool or string, optional
Expand Down Expand Up @@ -317,7 +317,7 @@ def motion_correct_pwrigid(self, save_movie:bool=True, template:np.ndarray=None,
template: ndarray 2D (or 3D)
if known, one can pass a template to register the frames to
show_template: boolean
show_template: bool
whether to show the updated template at each iteration
Important Fields:
Expand Down Expand Up @@ -1552,7 +1552,7 @@ def register_translation(src_image, target_image, upsample_factor=1,
will be FFT'd to compute the correlation, while "fourier" data will
bypass FFT of input data. Case insensitive.
use_cuda : boolean (DEPRECATED)
use_cuda : bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
Returns:
Expand Down Expand Up @@ -2012,29 +2012,34 @@ def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=N
max_shifts: tuple
max shifts in x and y
newstrides:tuple
strides between patches along each dimension when upsampling the vector fields
newoverlaps:tuple
amount of pixel overlapping between patches along each dimension when upsampling the vector fields
newstrides:tuple
strides between patches along each dimension when upsampling the vector fields
upsample_factor_grid: int
if newshapes or newstrides are not specified this is inferred upsampling by a constant factor the cvector field
upsample_factor_fft: int
resolution of fractional shifts
show_movie: boolean whether to visualize the original and corrected frame during motion correction
show_movie: bool
whether to visualize the original and corrected frame during motion correction
max_deviation_rigid: int
maximum deviation in shifts of each patch from the rigid shift (should not be large)
add_to_movie: if movie is too negative the correction might have some issues. In this case it is good to add values so that it is non negative most of the times
add_to_movie: int
if movie is too negative the correction might have some issues. In this case it is good to add values so that it is non negative most of the times
filt_sig_size: tuple
shifts_opencv: bool
FIXME: (UNDOCUMENTED)
gSig_filt: tuple
standard deviation and size of gaussian filter to center filter data in case of one photon imaging data
use_cuda : boolean (DEPRECATED)
use_cuda: bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
border_nan : bool or string, optional
Expand All @@ -2052,7 +2057,6 @@ def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=N
template = template.astype(np.float64).copy()

if gSig_filt is not None:

img_orig = img.copy()
img = high_pass_filter_space(img_orig, gSig_filt)

Expand All @@ -2064,7 +2068,6 @@ def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=N
img, template, upsample_factor=upsample_factor_fft, max_shifts=max_shifts, use_cuda=use_cuda)

if max_deviation_rigid == 0:

if shifts_opencv:
if gSig_filt is not None:
img = img_orig
Expand All @@ -2073,10 +2076,9 @@ def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=N
img, (-rigid_shts[0], -rigid_shts[1]), border_nan=border_nan)

else:

if gSig_filt is not None:
raise Exception(
'The use of FFT and filtering options have not been tested. Set opencv=True')
'The use of FFT and filtering options have not been tested. Set shifts_opencv=True or do not provide gSig_filt')

new_img = apply_shifts_dft(
sfr_freq, (-rigid_shts[0], -rigid_shts[1]), diffphase, border_nan=border_nan)
Expand Down Expand Up @@ -2173,7 +2175,7 @@ def tile_and_correct(img, template, strides, overlaps, max_shifts, newoverlaps=N

if gSig_filt is not None:
raise Exception(
'The use of FFT and filtering options have not been tested. Set opencv=True')
'The use of FFT and filtering options have not been tested. Set shifts_opencv=True')

imgs = [apply_shifts_dft(im, (
sh[0], sh[1]), dffphs, is_freq=False, border_nan=border_nan) for im, sh, dffphs in zip(
Expand Down Expand Up @@ -2272,17 +2274,21 @@ def tile_and_correct_3d(img:np.ndarray, template:np.ndarray, strides:tuple, over
upsample_factor_fft: int
resolution of fractional shifts
show_movie: boolean whether to visualize the original and corrected frame during motion correction
show_movie: bool
whether to visualize the original and corrected frame during motion correction
max_deviation_rigid: int
maximum deviation in shifts of each patch from the rigid shift (should not be large)
add_to_movie: if movie is too negative the correction might have some issues. In this case it is good to add values so that it is non negative most of the times
filt_sig_size: tuple
shifts_opencv: bool
FIXME: (UNDOCUMENTED)
gSig_filt: tuple
standard deviation and size of gaussian filter to center filter data in case of one photon imaging data
use_cuda : boolean (DEPRECATED)
use_cuda : bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
border_nan : bool or string, optional
Expand All @@ -2299,7 +2305,6 @@ def tile_and_correct_3d(img:np.ndarray, template:np.ndarray, strides:tuple, over
template = template.astype(np.float64).copy()

if gSig_filt is not None:

img_orig = img.copy()
img = high_pass_filter_space(img_orig, gSig_filt)

Expand Down Expand Up @@ -2668,16 +2673,16 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
template: ndarray
if a good approximation of the template to register is available, it can be used
shifts_opencv: boolean
shifts_opencv: bool
toggle the shifts applied with opencv, if yes faster but induces some smoothing
save_movie_rigid: boolean
save_movie_rigid: bool
toggle save movie
subidx: slice
Indices to slice
use_cuda : boolean (DEPRECATED)
use_cuda : bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
indices: tuple(slice), default: (slice(None), slice(None))
Expand Down Expand Up @@ -2825,13 +2830,13 @@ def motion_correct_batch_pwrigid(fname, max_shifts, strides, overlaps, add_to_mo
template: ndarray
if a good approximation of the template to register is available, it can be used
shifts_opencv: boolean
shifts_opencv: bool
toggle the shifts applied with opencv, if yes faster but induces some smoothing
save_movie_rigid: boolean
save_movie_rigid: bool
toggle save movie
use_cuda : boolean (DEPRECATED)
use_cuda : bool (DEPRECATED)
cuda is no longer supported for motion correction; this kwarg will be removed in a future version of Caiman
indices: tuple(slice), default: (slice(None), slice(None))
Expand Down

0 comments on commit d31d8c8

Please sign in to comment.