Video compression with example files throwing errors

[Abhishek935]

Hi, I am testing tierspy using your example files. I have Python 3.6 and Mac Mojave. I keep getting the following error. Please help.

Capture_Ch1_18062015_140908 Assigning trajectories. Total time = 0:00:04, fps = 306.8; Frame 1000 of 1208
ERROR:
AttributeError: 'DataFrame' object has no attribute 'ix'
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 216, got 192
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning:numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
Traceback (most recent call last):
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 108, in
ProcessWorker(**args, cmd_original = subprocess.list2cmdline(sys.argv))
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 38, in init
self.execAllPoints()
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py", line 66, in execAllPoints
cmd_original = self.cmd_original)
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/trackProvenance.py", line 28, in execThisPoint
func(**argkws)
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/traj_join/joinBlobsTrajectories.py", line 390, in joinBlobsTrajectories
joinGapsTrajectories(trajectories_file, min_track_size, max_frames_gap, area_ratio_lim)
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/traj_join/joinBlobsTrajectories.py", line 254, in joinGapsTrajectories
area_ratio_lim=area_ratio_lim
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/traj_join/joinBlobsTrajectories.py", line 364, in joinGapsTrajectoriesDF
relations_dict, valid_indexes = _findNextTraj(plate_worms, area_ratio_lim, min_track_size, max_frames_gap)
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/analysis/traj_join/joinBlobsTrajectories.py", line 303, in _findNextTraj
first_rows = df.ix[tracks_data['frame_number']['argmin'].values]
File "/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/pandas/core/generic.py", line 5273, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
'/Users/abhishek/anaconda3/envs/tierpsy/bin/python' '/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/processing/ProcessWorker.py' '/Users/abhishek/Downloads/example_data/multiworm/Capture_Ch1_18062015_140908.mov' --masks_dir '/Users/abhishek/Tmp/MaskedVideos/' --results_dir '/Users/abhishek/Tmp/Results/' --json_file '/Users/abhishek/anaconda3/envs/tierpsy/lib/python3.6/site-packages/tierpsy/extras/param_files/MULTIWORM_OPENWORM.json' --analysis_checkpoints 'TRAJ_JOIN' 'SKE_INIT' 'BLOB_FEATS' 'SKE_CREATE' 'SKE_FILT' 'SKE_ORIENT' 'INT_PROFILE' 'INT_SKE_ORIENT' 'FEAT_CREATE'

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Tasks: 1 finished, 0 remaining. Total_time 0:00:10.

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[ver228]

It seems the error is due to a deprecation error. The version 1.0 of pandas deprecated some expressions (https://stackoverflow.com/questions/59991397/attributeerror-dataframe-object-has-no-attribute-ix). The error should corrected in the current HEAD version in our repo. However, it is not yet uploaded to conda-forge.

In the meanwhile, I recommend you to downgrade pandas to conda install pandas=0.25. This should solve the problem.