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fix prairie_view_loader.py write_single_bigtiff to use uint16 #126

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fix prairie_view_loader.py write_single_bigtiff to use uint16 #126

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6f6b576
Merge pull request #1 from MathiasMahn/claude/platform-independent-pa…
MathiasMahn Feb 9, 2026
eddaac3
Merge pull request #2 from datajoint/main
MathiasMahn Feb 9, 2026
07070ec
Refactor motion correction grid computation logic
MathiasMahn Feb 9, 2026
db9eb15
pw_rigid grid calculation only when flag == true
MathiasMahn Feb 9, 2026
cec3887
moved the patch grid computation in caiman_loader under if pw_rigid =…
MathiasMahn Feb 9, 2026
9f84dfa
Remove dataset requirement for coord_shifts_rig
MathiasMahn Feb 10, 2026
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67 changes: 35 additions & 32 deletions element_interface/caiman_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -558,42 +558,42 @@ def _save_mc(
# Load the first frame of the movie
mc_image = np.reshape(Yr[: np.product(dims), :1], [1] + list(dims), order="F")

# Compute mc.coord_shifts_els
grid = []
if is3D:
for _, _, _, x, y, z, _ in cm.motion_correction.sliding_window_3d(
mc_image[0, :, :, :], mc.overlaps, mc.strides
):
grid.append(
[
x,
x + mc.overlaps[0] + mc.strides[0],
y,
y + mc.overlaps[1] + mc.strides[1],
z,
z + mc.overlaps[2] + mc.strides[2],
]
)
else:
for _, _, x, y, _ in cm.motion_correction.sliding_window(
mc_image[0, :, :], mc.overlaps, mc.strides
):
grid.append(
[
x,
x + mc.overlaps[0] + mc.strides[0],
y,
y + mc.overlaps[1] + mc.strides[1],
]
)

# Open hdf5 file and create 'motion_correction' group
caiman_fp = pathlib.Path(caiman_fp)
h5f = h5py.File(caiman_fp.as_posix(), "r+" if caiman_fp.exists() else "w")
h5g = h5f.require_group("motion_correction")

# Write motion correction shifts and motion corrected summary images to hdf5 file
if mc.pw_rigid:
# Compute mc.coord_shifts_els
grid = []
if is3D:
for _, _, _, x, y, z, _ in cm.motion_correction.sliding_window_3d(
mc_image[0, :, :, :], mc.overlaps, mc.strides
):
grid.append(
[
x,
x + mc.overlaps[0] + mc.strides[0],
y,
y + mc.overlaps[1] + mc.strides[1],
z,
z + mc.overlaps[2] + mc.strides[2],
]
)
else:
for _, _, x, y, _ in cm.motion_correction.sliding_window(
mc_image[0, :, :], mc.overlaps, mc.strides
):
grid.append(
[
x,
x + mc.overlaps[0] + mc.strides[0],
y,
y + mc.overlaps[1] + mc.strides[1],
]
)

h5g.require_dataset(
"x_shifts_els",
shape=np.shape(mc.x_shifts_els),
Expand Down Expand Up @@ -632,9 +632,12 @@ def _save_mc(
data=mc.shifts_rig,
dtype=mc.shifts_rig[0][0].dtype,
)
h5g.require_dataset(
"coord_shifts_rig", shape=np.shape(grid), data=grid, dtype=type(grid[0][0])
)

# Not needed for global single rigid shift - there is no grid!!!
# h5g.require_dataset(
# "coord_shifts_rig", shape=np.shape(grid), data=grid, dtype=type(grid[0][0])
# )

reference_image = (
np.tile(mc.total_template_rig, (1, 1, dims[-1]))
if is3D
Expand Down