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Add 'interp_shifts_precisely' motion parameter
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@ethanbb
ethanbb committed Jan 6, 2025
1 parent 5c50e9f commit 2c214b4
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Showing 2 changed files with 21 additions and 12 deletions.
29 changes: 17 additions & 12 deletions caiman/motion_correction.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def __init__(self, fname, min_mov=None, dview=None, max_shifts=(6, 6), niter_rig
strides=(96, 96), overlaps=(32, 32), splits_els=14, num_splits_to_process_els=None,
upsample_factor_grid=4, max_deviation_rigid=3, shifts_opencv=True, nonneg_movie=True, gSig_filt=None,
use_cuda=False, border_nan=True, pw_rigid=False, num_frames_split=80, var_name_hdf5='mov', is3D=False,
indices=(slice(None), slice(None))):
indices=(slice(None), slice(None)), interp_shifts_precisely=False):
"""
Constructor class for motion correction operations
Expand Down Expand Up @@ -198,6 +198,7 @@ def __init__(self, fname, min_mov=None, dview=None, max_shifts=(6, 6), niter_rig
self.var_name_hdf5 = var_name_hdf5
self.is3D = bool(is3D)
self.indices = indices
self.interp_shifts_precisely = interp_shifts_precisely
if self.use_cuda:
logger.warn("cuda is no longer supported; this kwarg will be removed in a future version of caiman")

Expand Down Expand Up @@ -301,7 +302,8 @@ def motion_correct_rigid(self, template=None, save_movie=False) -> None:
border_nan=self.border_nan,
var_name_hdf5=self.var_name_hdf5,
is3D=self.is3D,
indices=self.indices)
indices=self.indices,
interp_shifts_precisely=self.interp_shifts_precisely)
if template is None:
self.total_template_rig = _total_template_rig

Expand Down Expand Up @@ -362,7 +364,7 @@ def motion_correct_pwrigid(self, save_movie:bool=True, template:np.ndarray=None,
num_splits_to_process=None, num_iter=num_iter, template=self.total_template_els,
shifts_opencv=self.shifts_opencv, save_movie=save_movie, nonneg_movie=self.nonneg_movie, gSig_filt=self.gSig_filt,
use_cuda=self.use_cuda, border_nan=self.border_nan, var_name_hdf5=self.var_name_hdf5, is3D=self.is3D,
indices=self.indices)
indices=self.indices, interp_shifts_precisely=self.interp_shifts_precisely)
if not self.is3D:
if show_template:
plt.imshow(new_template_els)
Expand Down Expand Up @@ -2718,7 +2720,8 @@ def compute_metrics_motion_correction(fname, final_size_x, final_size_y, swap_di
def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_splits_to_process=None, num_iter=1,
template=None, shifts_opencv=False, save_movie_rigid=False, add_to_movie=None,
nonneg_movie=False, gSig_filt=None, subidx=slice(None, None, 1), use_cuda=False,
border_nan=True, var_name_hdf5='mov', is3D=False, indices=(slice(None), slice(None))):
border_nan=True, var_name_hdf5='mov', is3D=False, indices=(slice(None), slice(None)),
interp_shifts_precisely=False):
"""
Function that perform memory efficient hyper parallelized rigid motion corrections while also saving a memory mappable file
Expand Down Expand Up @@ -2838,7 +2841,7 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
dview=dview, save_movie=save_movie, base_name=base_name, subidx = subidx,
num_splits=num_splits_to_process, shifts_opencv=shifts_opencv, nonneg_movie=nonneg_movie, gSig_filt=gSig_filt,
use_cuda=use_cuda, border_nan=border_nan, var_name_hdf5=var_name_hdf5, is3D=is3D,
indices=indices)
indices=indices, interp_shifts_precisely=interp_shifts_precisely)
if is3D:
new_templ = np.nanmedian(np.stack([r[-1] for r in res_rig]), 0)
else:
Expand All @@ -2861,7 +2864,7 @@ def motion_correct_batch_pwrigid(fname, max_shifts, strides, overlaps, add_to_mo
splits=56, num_splits_to_process=None, num_iter=1,
template=None, shifts_opencv=False, save_movie=False, nonneg_movie=False, gSig_filt=None,
use_cuda=False, border_nan=True, var_name_hdf5='mov', is3D=False,
indices=(slice(None), slice(None))):
indices=(slice(None), slice(None)), interp_shifts_precisely=False):
"""
Function that perform memory efficient hyper parallelized rigid motion corrections while also saving a memory mappable file
Expand Down Expand Up @@ -2966,7 +2969,7 @@ def motion_correct_batch_pwrigid(fname, max_shifts, strides, overlaps, add_to_mo
base_name=base_name, num_splits=num_splits_to_process,
shifts_opencv=shifts_opencv, nonneg_movie=nonneg_movie, gSig_filt=gSig_filt,
use_cuda=use_cuda, border_nan=border_nan, var_name_hdf5=var_name_hdf5, is3D=is3D,
indices=indices)
indices=indices, interp_shifts_precisely=interp_shifts_precisely)
if is3D:
new_templ = np.nanmedian(np.stack([r[-1] for r in res_el]), 0)
else:
Expand Down Expand Up @@ -3021,7 +3024,7 @@ def tile_and_correct_wrapper(params):
img_name, out_fname, idxs, shape_mov, template, strides, overlaps, max_shifts,\
add_to_movie, max_deviation_rigid, upsample_factor_grid, newoverlaps, newstrides, \
shifts_opencv, nonneg_movie, gSig_filt, is_fiji, use_cuda, border_nan, var_name_hdf5, \
is3D, indices = params
is3D, indices, interp_shifts_precisely = params


if isinstance(img_name, tuple):
Expand All @@ -3047,7 +3050,8 @@ def tile_and_correct_wrapper(params):
upsample_factor_fft=10, show_movie=False,
max_deviation_rigid=max_deviation_rigid,
shifts_opencv=shifts_opencv, gSig_filt=gSig_filt,
use_cuda=use_cuda, border_nan=border_nan)
use_cuda=use_cuda, border_nan=border_nan,
interp_shifts_precisely=interp_shifts_precisely)
shift_info.append([total_shift, start_step, xyz_grid])

else:
Expand All @@ -3058,7 +3062,8 @@ def tile_and_correct_wrapper(params):
upsample_factor_fft=10, show_movie=False,
max_deviation_rigid=max_deviation_rigid,
shifts_opencv=shifts_opencv, gSig_filt=gSig_filt,
use_cuda=use_cuda, border_nan=border_nan)
use_cuda=use_cuda, border_nan=border_nan,
interp_shifts_precisely=interp_shifts_precisely)
shift_info.append([total_shift, start_step, xy_grid])

if out_fname is not None:
Expand All @@ -3079,7 +3084,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
upsample_factor_grid=4, order='F', dview=None, save_movie=True,
base_name=None, subidx = None, num_splits=None, shifts_opencv=False, nonneg_movie=False, gSig_filt=None,
use_cuda=False, border_nan=True, var_name_hdf5='mov', is3D=False,
indices=(slice(None), slice(None))):
indices=(slice(None), slice(None)), interp_shifts_precisely=False):
"""
"""
Expand Down Expand Up @@ -3134,7 +3139,7 @@ def motion_correction_piecewise(fname, splits, strides, overlaps, add_to_movie=0
pars.append([fname, fname_tot, idx, shape_mov, template, strides, overlaps, max_shifts, np.array(
add_to_movie, dtype=np.float32), max_deviation_rigid, upsample_factor_grid,
newoverlaps, newstrides, shifts_opencv, nonneg_movie, gSig_filt, is_fiji,
use_cuda, border_nan, var_name_hdf5, is3D, indices])
use_cuda, border_nan, var_name_hdf5, is3D, indices, interp_shifts_precisely])

if dview is not None:
logger.info('** Starting parallel motion correction **')
Expand Down
4 changes: 4 additions & 0 deletions caiman/source_extraction/cnmf/params.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -558,6 +558,9 @@ def __init__(self, fnames=None, dims=None, dxy=(1, 1),
gSig_filt: int or None, default: None
size of kernel for high pass spatial filtering in 1p data. If None no spatial filtering is performed
interp_shifts_precisely: bool, default: False
use patch locations to interpolate shifts rather than just upscaling to size of image (for pw_rigid only)
is3D: bool, default: False
flag for 3D recordings for motion correction
Expand Down Expand Up @@ -858,6 +861,7 @@ def __init__(self, fnames=None, dims=None, dxy=(1, 1),
self.motion = {
'border_nan': 'copy', # flag for allowing NaN in the boundaries
'gSig_filt': None, # size of kernel for high pass spatial filtering in 1p data
'interp_shifts_precisely': False, # interpolate shifts based on patch locations instead of reizing
'is3D': False, # flag for 3D recordings for motion correction
'max_deviation_rigid': 3, # maximum deviation between rigid and non-rigid
'max_shifts': (6, 6), # maximum shifts per dimension (in pixels)
Expand Down

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