error in anipose filter command if turn [filter] parameter for 'True'

[AthiemoneZero]

Hi, I try to leverage Viterbi filter algorithm that was embeded in this package by add some parameters in config.toml file as below:

[filter] enabled = true type = "viterbi" score_threshold = 0.6 medfilt = 17 offset_threshold = 15 spline = true multiprocess = true

but when I typed down filter command in terminal, this issue happended:

Filtering tracked points... C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-ske leton\2024-01-13\pose-2d-filtered\867_1_seg1-vid01-camA.h5 0it [00:02, ?it/s] multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "C:\Users\Admin\anaconda3\envs\DLC\lib\multiprocess ing\pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\an ipose-master\anipose\filter_pose.py", line 121, in viterbi _path_wrapper pts_new, scs_new = viterbi_path(pts, scs, max_offset, thres_dist) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\an ipose-master\anipose\filter_pose.py", line 47, in viterbi_ path return __callback(*args, **kwargs) File "C:\Users\Admin\anaconda3\envs\DLC\lib\site-packages\click\decorators.py", line 84, in new_f unc return ctx.invoke(f, obj, *args, **kwargs) File "C:\Users\Admin\anaconda3\envs\DLC\lib\site-packages\click\core.py", line 760, in invoke return __callback(*args, **kwargs) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\anipose.py", line 14 9, in filter filter_pose_all(config) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\common.py", line 168 , in fun return process_all(config, process_session, **args) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\common.py", line 153 , in process_all output[past_folders] = process_session(config, path, **args) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\filter_pose.py", lin e 387, in process_session points, scores = filter_fun(config, all_points, metadata['bodyparts']) File "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\filter_pose.py", lin e 175, in filter_pose_viterbi for jix, pts_new, scs_new in tqdm(results, ncols=70): File "C:\Users\Admin\anaconda3\envs\DLC\lib\site-packages\tqdm\std.py", line 1182, in __iter__ for obj in iterable: File "C:\Users\Admin\anaconda3\envs\DLC\lib\multiprocessing\pool.py", line 873, in next raise value ValueError: data must be finite, check for nan or inf values

[wyclearnpy]

I encountered the same problem as you, have you solved it?

[AthiemoneZero]

I encountered the same problem as you, have you solved it?

Hi, I found this problem would disappear when you have a well labeled video set. I guess this might somehow be due to some low-likelihood points causing NA value in pose-2d files. Details about what algorithm here to cause this and if fine-tuning for filter parameters could avoid it are still confusing. Looking forward to better answering

[wyclearnpy]

Okay, I understand, I'll try again. Thank you for your reply.

[AthiemoneZero]

Okay, I understand, I'll try again. Thank you for your reply.

Hi, I just confirmed my previous assumption,

I found I failed to filter only one .h5 file from all 3 in pose-2d folder. The error looks like this:

(DLC) C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre>anipose filter
Filtering tracked points...
C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre\20231224_setB_validatio
n\pose-2d-filtered\2024-01-02-vid01-camA.h5
3it [00:03,  1.19s/it]
C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre\20231224_setB_validatio
n\pose-2d-filtered\2024-01-02-vid01-camB.h5
1it [00:02,  2.43s/it]
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "C:\Users\Admin\anaconda3\envs\DLC\lib\multiprocessing\pool.py", line 125, in worker  
    result = (True, func(*args, **kwds))
  File "c:\users\admin\desktop\cxc\dlc_projects\anipose\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 "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\filter_pose.py
", line 47, in viterbi_path
    points_nans = remove_dups(points, thres=5)
  File "c:\users\admin\desktop\cxc\dlc_projects\anipose\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
"""

Overall, my filter section looks like below:

[filter]
enabled = true
type = "viterbi" # or "autoencoder"
score_threshold = 0.0 # Score below which labels are determined erroneous
multiprocess = true #
# https://github.com/lambdaloop/anipose/issues/57

And everything works ok. So this error seems come from bad value in raw pose-2d file. I havent evaluated side-effect caused by lower score_threshold but I am working on this. Hope good news!

[caikangjia]

Okay, I understand, I'll try again. Thank you for your reply.

Hi, I just confirmed my previous assumption,

I found I failed to filter only one .h5 file from all 3 in pose-2d folder. The error looks like this:

(DLC) C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre>anipose filter
Filtering tracked points...
C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre\20231224_setB_validatio
n\pose-2d-filtered\2024-01-02-vid01-camA.h5
3it [00:03,  1.19s/it]
C:\Users\Admin\Desktop\CXC\DLC_projects\anipose\TreDet-world_coor_pre\20231224_setB_validatio
n\pose-2d-filtered\2024-01-02-vid01-camB.h5
1it [00:02,  2.43s/it]
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "C:\Users\Admin\anaconda3\envs\DLC\lib\multiprocessing\pool.py", line 125, in worker  
    result = (True, func(*args, **kwds))
  File "c:\users\admin\desktop\cxc\dlc_projects\anipose\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 "c:\users\admin\desktop\cxc\dlc_projects\anipose\anipose-master\anipose\filter_pose.py
", line 47, in viterbi_path
    points_nans = remove_dups(points, thres=5)
  File "c:\users\admin\desktop\cxc\dlc_projects\anipose\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
"""

Overall, my filter section looks like below:

[filter]
enabled = true
type = "viterbi" # or "autoencoder"
score_threshold = 0.0 # Score below which labels are determined erroneous
multiprocess = true #
# https://github.com/lambdaloop/anipose/issues/57

And everything works ok. So this error seems come from bad value in raw pose-2d file. I havent evaluated side-effect caused by lower score_threshold but I am working on this. Hope good news!

A quick update on this one: Downgrade the SciPy version to 1.9/1.10 may solve the issue. This "Value Error" only happens with SciPy 1.11 or later versions