I encountered the following problem when performing the anipose filter step. It was still running successfully a month ago

[wyclearnpy]

(DEEPLABCUT) D:\A_3DFishPose>anipose filter
Filtering tracked points...
D:\A_3DFishPose\2024.2.29\pose-2d-filtered\koipose0_camA.h5
0it [00:01, ?it/s]
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "E:\anaconda3\envs\DEEPLABCUT\lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "d:\anipose-master\anipose\filter_pose.py", line 121, in viterbi_path_wrapper
pts_new, scs_new = viterbi_path(pts, scs, max_offset, thres_dist)
File "d:\anipose-master\anipose\filter_pose.py", line 47, in viterbi_path
points_nans = remove_dups(points, thres=5)
File "d:\anipose-master\anipose\filter_pose.py", line 29, in remove_dups
tree = cKDTree(pts_ix.reshape(-1, 3))
File "_ckdtree.pyx", line 561, in scipy.spatial._ckdtree.cKDTree.init
ValueError: data must be finite, check for nan or inf values
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "\?\E:\anaconda3\envs\DEEPLABCUT\Scripts\anipose-script.py", line 33, in
sys.exit(load_entry_point('anipose', 'console_scripts', 'anipose')())
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1157, in call
return self.main(*args, **kwargs)
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\decorators.py", line 92, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "d:\anipose-master\anipose\anipose.py", line 149, in filter
filter_pose_all(config)
File "d:\anipose-master\anipose\common.py", line 168, in fun
return process_all(config, process_session, **args)
File "d:\anipose-master\anipose\common.py", line 153, in process_all
output[past_folders] = process_session(config, path, **args)
File "d:\anipose-master\anipose\filter_pose.py", line 387, in process_session
points, scores = filter_fun(config, all_points, metadata['bodyparts'])
File "d:\anipose-master\anipose\filter_pose.py", line 175, in filter_pose_viterbi
for jix, pts_new, scs_new in tqdm(results, ncols=70):
File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\tqdm\std.py", line 1182, in iter
for obj in iterable:
File "E:\anaconda3\envs\DEEPLABCUT\lib\multiprocessing\pool.py", line 870, in next
raise value
ValueError: data must be finite, check for nan or inf values

[caikangjia]

(DEEPLABCUT) D:\A_3DFishPose>anipose filter Filtering tracked points... D:\A_3DFishPose\2024.2.29\pose-2d-filtered\koipose0_camA.h5 0it [00:01, ?it/s] multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "E:\anaconda3\envs\DEEPLABCUT\lib\multiprocessing\pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "d:\anipose-master\anipose\filter_pose.py", line 121, in viterbi_path_wrapper pts_new, scs_new = viterbi_path(pts, scs, max_offset, thres_dist) File "d:\anipose-master\anipose\filter_pose.py", line 47, in viterbi_path points_nans = remove_dups(points, thres=5) File "d:\anipose-master\anipose\filter_pose.py", line 29, in remove_dups tree = cKDTree(pts_ix.reshape(-1, 3)) File "_ckdtree.pyx", line 561, in scipy.spatial._ckdtree.cKDTree.init ValueError: data must be finite, check for nan or inf values """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "?\E:\anaconda3\envs\DEEPLABCUT\Scripts\anipose-script.py", line 33, in sys.exit(load_entry_point('anipose', 'console_scripts', 'anipose')()) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1157, in call return self.main(*args, **kwargs) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\decorators.py", line 92, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) File "d:\anipose-master\anipose\anipose.py", line 149, in filter filter_pose_all(config) File "d:\anipose-master\anipose\common.py", line 168, in fun return process_all(config, process_session, **args) File "d:\anipose-master\anipose\common.py", line 153, in process_all output[past_folders] = process_session(config, path, **args) File "d:\anipose-master\anipose\filter_pose.py", line 387, in process_session points, scores = filter_fun(config, all_points, metadata['bodyparts']) File "d:\anipose-master\anipose\filter_pose.py", line 175, in filter_pose_viterbi for jix, pts_new, scs_new in tqdm(results, ncols=70): File "E:\anaconda3\envs\DEEPLABCUT\lib\site-packages\tqdm\std.py", line 1182, in iter for obj in iterable: File "E:\anaconda3\envs\DEEPLABCUT\lib\multiprocessing\pool.py", line 870, in next raise value ValueError: data must be finite, check for nan or inf values

Hi, I found the problem. The SciPy 1.11+ caused this issue. Downgrade to SciPy 1.10/1.9 will have the filter running.