Skip to content

Commit

Permalink
Fix: skip rigid/non-rigid motion correction - shifts not in suite2p o…
Browse files Browse the repository at this point in the history 
…utput
  • Loading branch information
@kushalbakshi
kushalbakshi committed Apr 30, 2024
1 parent b51c500 commit 62cd1fe
Showing 1 changed file with 82 additions and 76 deletions.
158 changes: 82 additions & 76 deletions element_calcium_imaging/imaging_no_curation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -828,93 +828,99 @@ def make(self, key):
rigid_correction, nonrigid_correction, nonrigid_blocks = {}, {}, {}
summary_images = []
for idx, (plane, s2p) in enumerate(suite2p_dataset.planes.items()):
# -- rigid motion correction --
if idx == 0:
rigid_correction = {
**key,
"y_shifts": s2p.ops["yoff"],
"x_shifts": s2p.ops["xoff"],
"z_shifts": np.full_like(s2p.ops["xoff"], 0),
"y_std": np.nanstd(s2p.ops["yoff"]),
"x_std": np.nanstd(s2p.ops["xoff"]),
"z_std": np.nan,
"outlier_frames": s2p.ops["badframes"],
}
else:
rigid_correction["y_shifts"] = np.vstack(
[rigid_correction["y_shifts"], s2p.ops["yoff"]]
)
rigid_correction["y_std"] = np.nanstd(
rigid_correction["y_shifts"].flatten()
)
rigid_correction["x_shifts"] = np.vstack(
[rigid_correction["x_shifts"], s2p.ops["xoff"]]
)
rigid_correction["x_std"] = np.nanstd(
rigid_correction["x_shifts"].flatten()
)
rigid_correction["outlier_frames"] = np.logical_or(
rigid_correction["outlier_frames"], s2p.ops["badframes"]
if not all(k in s2p.ops for k in ["xblock", "yblock", "nblocks"]):
logger.warning(
f"Unable to load/ingest non-rigid motion correction for plane {plane}."
"Non-rigid motion correction data is not saved by Suite2p for versions above 0.10.*."
)
# -- non-rigid motion correction --
if s2p.ops["nonrigid"]:
else:
# -- rigid motion correction --
if idx == 0:
nonrigid_correction = {
rigid_correction = {
**key,
"block_height": s2p.ops["block_size"][0],
"block_width": s2p.ops["block_size"][1],
"block_depth": 1,
"block_count_y": s2p.ops["nblocks"][0],
"block_count_x": s2p.ops["nblocks"][1],
"block_count_z": len(suite2p_dataset.planes),
"y_shifts": s2p.ops["yoff"],
"x_shifts": s2p.ops["xoff"],
"z_shifts": np.full_like(s2p.ops["xoff"], 0),
"y_std": np.nanstd(s2p.ops["yoff"]),
"x_std": np.nanstd(s2p.ops["xoff"]),
"z_std": np.nan,
"outlier_frames": s2p.ops["badframes"],
}
else:
nonrigid_correction["outlier_frames"] = np.logical_or(
nonrigid_correction["outlier_frames"],
s2p.ops["badframes"],
rigid_correction["y_shifts"] = np.vstack(
[rigid_correction["y_shifts"], s2p.ops["yoff"]]
)
for b_id, (b_y, b_x, bshift_y, bshift_x) in enumerate(
zip(
s2p.ops["xblock"],
s2p.ops["yblock"],
s2p.ops["yoff1"].T,
s2p.ops["xoff1"].T,
rigid_correction["y_std"] = np.nanstd(
rigid_correction["y_shifts"].flatten()
)
):
if b_id in nonrigid_blocks:
nonrigid_blocks[b_id]["y_shifts"] = np.vstack(
[nonrigid_blocks[b_id]["y_shifts"], bshift_y]
)
nonrigid_blocks[b_id]["y_std"] = np.nanstd(
nonrigid_blocks[b_id]["y_shifts"].flatten()
)
nonrigid_blocks[b_id]["x_shifts"] = np.vstack(
[nonrigid_blocks[b_id]["x_shifts"], bshift_x]
rigid_correction["x_shifts"] = np.vstack(
[rigid_correction["x_shifts"], s2p.ops["xoff"]]
)
rigid_correction["x_std"] = np.nanstd(
rigid_correction["x_shifts"].flatten()
)
rigid_correction["outlier_frames"] = np.logical_or(
rigid_correction["outlier_frames"], s2p.ops["badframes"]
)
# -- non-rigid motion correction --
if s2p.ops["nonrigid"]:
if idx == 0:
nonrigid_correction = {
**key,
"block_height": s2p.ops["block_size"][0],
"block_width": s2p.ops["block_size"][1],
"block_depth": 1,
"block_count_y": s2p.ops["nblocks"][0],
"block_count_x": s2p.ops["nblocks"][1],
"block_count_z": len(suite2p_dataset.planes),
"outlier_frames": s2p.ops["badframes"],
}
else:
nonrigid_correction["outlier_frames"] = np.logical_or(
nonrigid_correction["outlier_frames"],
s2p.ops["badframes"],
)
nonrigid_blocks[b_id]["x_std"] = np.nanstd(
nonrigid_blocks[b_id]["x_shifts"].flatten()
for b_id, (b_y, b_x, bshift_y, bshift_x) in enumerate(
zip(
s2p.ops["xblock"],
s2p.ops["yblock"],
s2p.ops["yoff1"].T,
s2p.ops["xoff1"].T,
)
else:
nonrigid_blocks[b_id] = {
**key,
"block_id": b_id,
"block_y": b_y,
"block_x": b_x,
"block_z": np.full_like(b_x, plane),
"y_shifts": bshift_y,
"x_shifts": bshift_x,
"z_shifts": np.full(
(
len(suite2p_dataset.planes),
len(bshift_x),
):
if b_id in nonrigid_blocks:
nonrigid_blocks[b_id]["y_shifts"] = np.vstack(
[nonrigid_blocks[b_id]["y_shifts"], bshift_y]
)
nonrigid_blocks[b_id]["y_std"] = np.nanstd(
nonrigid_blocks[b_id]["y_shifts"].flatten()
)
nonrigid_blocks[b_id]["x_shifts"] = np.vstack(
[nonrigid_blocks[b_id]["x_shifts"], bshift_x]
)
nonrigid_blocks[b_id]["x_std"] = np.nanstd(
nonrigid_blocks[b_id]["x_shifts"].flatten()
)
else:
nonrigid_blocks[b_id] = {
**key,
"block_id": b_id,
"block_y": b_y,
"block_x": b_x,
"block_z": np.full_like(b_x, plane),
"y_shifts": bshift_y,
"x_shifts": bshift_x,
"z_shifts": np.full(
(
len(suite2p_dataset.planes),
len(bshift_x),
),
0,
),
0,
),
"y_std": np.nanstd(bshift_y),
"x_std": np.nanstd(bshift_x),
"z_std": np.nan,
}
"y_std": np.nanstd(bshift_y),
"x_std": np.nanstd(bshift_x),
"z_std": np.nan,
}

# -- summary images --
motion_correction_key = (
Expand Down

0 comments on commit 62cd1fe

Please sign in to comment.