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Take indices into account when applying piecewise shifts #1538

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Take indices into account when applying piecewise shifts #1538

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24 changes: 18 additions & 6 deletions caiman/motion_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -456,24 +456,36 @@ def apply_shifts_movie(self, fname, rigid_shifts: Optional[bool] = None, save_me
sh[0], sh[1]), 0, is_freq=False, border_nan=self.border_nan) for img, sh in zip(
Y, self.shifts_rig)]
else:
# take potential upsampling into account when recreating patch grid
dims = Y.shape[1:]
patch_centers = get_patch_centers(dims, overlaps=self.overlaps, strides=self.strides,
shifts_opencv=self.shifts_opencv, upsample_factor_grid=self.upsample_factor_grid)
# take indices and potential upsampling into account when recreating patch grid
dims = Y[0][self.indices].shape
patch_centers_orig = get_patch_centers(
dims, overlaps=self.overlaps, strides=self.strides,
shifts_opencv=self.shifts_opencv, upsample_factor_grid=self.upsample_factor_grid)

# if only a portion of the original image was used, offset/multiply patch centers to now apply to the whole movie
patch_centers = tuple([
list(dim_inds.start + dim_inds.step * np.array(dim_centers_orig))
for dim_inds, dim_centers_orig in zip(self.indices, patch_centers_orig)
])

# force shifts_interpolate if there was any cropping - easier than making a special-case path that
# resizes the shifts and extrapolates to the border but doesn't fully take patch centers into account
shifts_interpolate = True if any(dim_inds != slice(None) for dim_inds in self.indices) else self.shifts_interpolate

if self.is3D:
# x_shifts_els and y_shifts_els are switched intentionally
m_reg = [
apply_pw_shifts_remap_3d(img, shifts_y=-x_shifts, shifts_x=-y_shifts, shifts_z=-z_shifts,
patch_centers=patch_centers, border_nan=self.border_nan,
shifts_interpolate=self.shifts_interpolate)
shifts_interpolate=shifts_interpolate)
for img, x_shifts, y_shifts, z_shifts in zip(Y, self.x_shifts_els, self.y_shifts_els, self.z_shifts_els)
]

else:
# x_shifts_els and y_shifts_els are switched intentionally
m_reg = [
apply_pw_shifts_remap_2d(img, shifts_y=-x_shifts, shifts_x=-y_shifts, patch_centers=patch_centers,
border_nan=self.border_nan, shifts_interpolate=self.shifts_interpolate)
border_nan=self.border_nan, shifts_interpolate=shifts_interpolate)
for img, x_shifts, y_shifts in zip(Y, self.x_shifts_els, self.y_shifts_els)
]

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