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Fix subidx to enable computing the NoRMCorre template frame from subset of movie frames #1133

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Fix subidx to enable computing the NoRMCorre template frame from subset of movie frames #1133

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8662025
fix subidx to compute motion correction template from a movie slice
ludovicbellier Apr 26, 2023
eb35738
Merge pull request #1 from inscopix/subidx
ludovicbellier Apr 28, 2023
4aebaae
Update README.md
EricThomson Jun 30, 2023
17cd8e2
Merge pull request #1125 from EricThomson/main
EricThomson Jun 30, 2023
24f5efc
Merge branch 'flatironinstitute:main' into master
ludovicbellier Jul 6, 2023
164f496
refocus PR on subidx
ludovicbellier Jul 7, 2023
a08a067
Merge branch 'dev' into master
ludovicbellier Jul 7, 2023
88d1b48
isxd reading ability
ludovicbellier Oct 11, 2023
e4eea82
Revert "isxd reading ability"
ludovicbellier Oct 11, 2023
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14 changes: 9 additions & 5 deletions caiman/motion_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ 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)), subidx=slice(None, None, 1)):
"""
Constructor class for motion correction operations

Expand Down Expand Up @@ -206,6 +206,7 @@ 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.subidx = subidx
if self.use_cuda and not HAS_CUDA:
logging.debug("pycuda is unavailable. Falling back to default FFT.")

Expand Down Expand Up @@ -310,7 +311,8 @@ 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,
subidx=self.subidx)
if template is None:
self.total_template_rig = _total_template_rig

Expand Down Expand Up @@ -2816,7 +2818,9 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl
Exception 'The movie contains nans. Nans are not allowed!'

"""

if subidx.start is not None:
print(f"Computing template from frames {subidx}.")

dims, T = cm.source_extraction.cnmf.utilities.get_file_size(fname, var_name_hdf5=var_name_hdf5)
Ts = np.arange(T)[subidx].shape[0]
step = Ts // 10 if is3D else Ts // 50
Expand Down Expand Up @@ -2878,10 +2882,10 @@ def motion_correct_batch_rigid(fname, max_shifts, dview=None, splits=56, num_spl

fname_tot_rig, res_rig = motion_correction_piecewise(fname, splits, strides=None, overlaps=None,
add_to_movie=add_to_movie, template=old_templ, max_shifts=max_shifts, max_deviation_rigid=0,
dview=dview, save_movie=save_movie, base_name=base_name, subidx = subidx,
dview=dview, save_movie=save_movie, 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, subidx=None)
if is3D:
new_templ = np.nanmedian(np.stack([r[-1] for r in res_rig]), 0)
else:
Expand Down