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TypeError: acf() got an unexpected keyword argument 'unbiased'
I faced this issue when I tried to use extract_features function from this package.This seemed to be an old, but I still could not figure out the solution for this problem. I've tried to downgrade my statsmodel to 0.12.1, but it turns out it gave me another error saying my pandas package had a compatibility issue as "ImportError: cannot import name 'Int64Index' from 'pandas'". Does anyone have a solution on how to use this package?
Hi @YWU99u - which version of tsfresh, python and statsmodel are you using? Unfortunately, I can not reproduce this issue.
I got the similar error, and I found the message showed file feature_extraction/feature_calculators.py different from current main branch.
Package versions: python 3.7 tsfresh 0.20.1 statsmodels 0.13.2
Error message:
Traceback (most recent call last):
File "/opt/conda/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/opt/conda/lib/python3.7/site-packages/tsfresh/utilities/distribution.py", line 43, in _function_with_partly_reduce
results = list(itertools. chain. from_iterable(results))
File "/opt/conda/lib/python3.7/site-packages/tsfresh/utilities/distribution.py", line 42, in
Hi @XudongWang97! Thanks for sharing those details. The respective file was changes approximately 2 years ago to not contain the "unbiased" parameter anymore, so I am confused why this shows up in version 0.20.1 (3 months ago) again. Are you sure you are using this version and not maybe an older one (just want to double check). How did you install tsfresh? Via pip or conda?
Thank you @nils-braun I install tsfresh by pip. Now I create a new py3.9 environment and it works. It's strange that I cannot reproduce the error in the old py3.7 one. Some dependency issue?
Thanks for looking into this. If you have some time, could you check the package versions in both environments (e.g. with pip freeze) and see if there are significant differences? Thank you!
Hi,
I'm experiencing the same troubles in two different operative systems (Mac OS X and Windows). This is the error message:
<<
Feature Extraction: 0%| | 0/1 [00:03<?, ?it/s]
---------------------------------------------------------------------------
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/utilities/distribution.py", line 43, in _function_with_partly_reduce
results = list(itertools.chain.from_iterable(results))
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/utilities/distribution.py", line 42, in <genexpr>
results = (map_function(chunk, **kwargs) for chunk in chunk_list)
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py", line 337, in _do_extraction_on_chunk
return list(_f())
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py", line 317, in _f
result = func(x, param=parameter_list)
File "/Users/andrea/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/feature_calculators.py", line 404, in agg_autocorrelation
a = acf(x, unbiased=True, fft=n > THRESHOLD_TO_USE_FFT, nlags=max_maxlag)[1:]
TypeError: acf() got an unexpected keyword argument 'unbiased'
"""
The above exception was the direct cause of the following exception:
TypeError Traceback (most recent call last)
Cell In[4], line 18
15 df_for_extraction.columns = ['x', 'y', 'id']
17 #features extraction
---> 18 extracted_features=extract_features(df_for_extraction, column_id="id", column_sort="x", show_warnings=None)
20 #NaN values removal
21 impute(extracted_features)
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py:152, in extract_features(timeseries_container, default_fc_parameters, kind_to_fc_parameters, column_id, column_sort, column_kind, column_value, chunksize, n_jobs, show_warnings, disable_progressbar, impute_function, profile, profiling_filename, profiling_sorting, distributor, pivot)
149 else:
150 warnings.simplefilter("default")
--> 152 result = _do_extraction(df=timeseries_container,
153 column_id=column_id, column_value=column_value,
154 column_kind=column_kind,
155 column_sort=column_sort,
156 n_jobs=n_jobs, chunk_size=chunksize,
157 disable_progressbar=disable_progressbar,
158 show_warnings=show_warnings,
159 default_fc_parameters=default_fc_parameters,
160 kind_to_fc_parameters=kind_to_fc_parameters,
161 distributor=distributor,
162 pivot=pivot)
164 # Impute the result if requested
165 if impute_function is not None:
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py:255, in _do_extraction(df, column_id, column_value, column_kind, column_sort, default_fc_parameters, kind_to_fc_parameters, n_jobs, chunk_size, disable_progressbar, show_warnings, distributor, pivot)
249 raise ValueError("the passed distributor is not an DistributorBaseClass object")
251 kwargs = dict(default_fc_parameters=default_fc_parameters,
252 kind_to_fc_parameters=kind_to_fc_parameters,
253 show_warnings=show_warnings)
--> 255 result = distributor.map_reduce(_do_extraction_on_chunk, data=data,
256 chunk_size=chunk_size,
257 function_kwargs=kwargs)
259 if not pivot:
260 return result
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/utilities/distribution.py:213, in IterableDistributorBaseClass.map_reduce(self, map_function, data, function_kwargs, chunk_size, data_length)
210 else:
211 result = self.distribute(_function_with_partly_reduce, chunk_generator, map_kwargs),
--> 213 result = list(itertools.chain.from_iterable(result))
215 self.close()
217 return result
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tqdm/std.py:1178, in tqdm.__iter__(self)
1175 time = self._time
1177 try:
-> 1178 for obj in iterable:
1179 yield obj
1180 # Update and possibly print the progressbar.
1181 # Note: does not call self.update(1) for speed optimisation.
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/multiprocessing/pool.py:870, in IMapIterator.next(self, timeout)
868 if success:
869 return value
--> 870 raise value
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/multiprocessing/pool.py:125, in worker()
123 job, i, func, args, kwds = task
124 try:
--> 125 result = (True, func(*args, **kwds))
126 except Exception as e:
127 if wrap_exception and func is not _helper_reraises_exception:
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/utilities/distribution.py:43, in _function_with_partly_reduce()
41 kwargs = kwargs or {}
42 results = (map_function(chunk, **kwargs) for chunk in chunk_list)
---> 43 results = list(itertools.chain.from_iterable(results))
44 return results
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/utilities/distribution.py:42, in <genexpr>()
25 """
26 Small helper function to call a function (map_function)
27 on a list of data chunks (chunk_list) and convert the results into
(...)
39 :rtype: list
40 """
41 kwargs = kwargs or {}
---> 42 results = (map_function(chunk, **kwargs) for chunk in chunk_list)
43 results = list(itertools.chain.from_iterable(results))
44 return results
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py:337, in _do_extraction_on_chunk()
334 else:
335 warnings.simplefilter("default")
--> 337 return list(_f())
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/extraction.py:317, in _f()
314 x = data.values
316 if func.fctype == "combiner":
--> 317 result = func(x, param=parameter_list)
318 else:
319 if parameter_list:
File ~/opt/anaconda3/envs/ts_fresh/lib/python3.9/site-packages/tsfresh/feature_extraction/feature_calculators.py:404, in agg_autocorrelation()
402 a = [0] * len(x)
403 else:
--> 404 a = acf(x, unbiased=True, fft=n > THRESHOLD_TO_USE_FFT, nlags=max_maxlag)[1:]
405 return [("f_agg_\"{}\"__maxlag_{}".format(config["f_agg"], config["maxlag"]),
406 getattr(np, config["f_agg"])(a[:int(config["maxlag"])])) for config in param]
TypeError: acf() got an unexpected keyword argument 'unbiased'
I have python 3.9.19 installed but anything works.
I tried to change the python version but still no solution. Can you help me?
The strange things is that the same script works in an old computer with the following configuration: tsfresh: 0.20.2 pandas: 2.0.1 matplotlib: 3.7.1 statamodels: 0.14.1 python: 3.9.16
Hi @kiraminnie - can you check the version of tsfresh you are using? It looks like this is a (rather) old version.
Hi @nils-braun , thank you for your support. I have installed the 0.18.0 version. Do you think this is the problem? I don't understand the right combination of versions for Python, tsfresh, statsmodels. It seems there is a combination of libraries working...
Thank you again for your support.
Yes, tsfresh 0.18.0 is from 2021 (!), so it definitely will not work with any recent packages. I would recommend updating to the newest version (0.20.2). In general, the newest version of a package is usually the best one. If all package authors have their dependencies declared correctly, you do not need to sort out a combination yourself and pip will do it for you.
Thank @nils-braun, I think the problem is that I'm unable to upgrade tsfresh.
I installed many times, all the times using a new environment but the version is always the same: 0.18.0
(WGM_tsfresh) andrea@pcdyn-sl-143 ~ % pip install --upgrade tsfresh
Requirement already satisfied: tsfresh in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (0.20.2)
Requirement already satisfied: requests>=2.9.1 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (2.31.0)
Requirement already satisfied: numpy>=1.15.1 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (1.26.4)
Requirement already satisfied: pandas>=0.25.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (2.2.1)
Requirement already satisfied: scipy>=1.2.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (1.13.0)
Requirement already satisfied: statsmodels>=0.13 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (0.14.1)
Requirement already satisfied: patsy>=0.4.1 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (0.5.6)
Requirement already satisfied: scikit-learn>=0.22.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (1.4.2)
Requirement already satisfied: tqdm>=4.10.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (4.66.2)
Requirement already satisfied: stumpy>=1.7.2 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (1.12.0)
Requirement already satisfied: cloudpickle in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from tsfresh) (3.0.0)
Requirement already satisfied: python-dateutil>=2.8.2 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from pandas>=0.25.0->tsfresh) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from pandas>=0.25.0->tsfresh) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from pandas>=0.25.0->tsfresh) (2024.1)
Requirement already satisfied: six in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from patsy>=0.4.1->tsfresh) (1.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from requests>=2.9.1->tsfresh) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from requests>=2.9.1->tsfresh) (3.6)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from requests>=2.9.1->tsfresh) (2.2.1)
Requirement already satisfied: certifi>=2017.4.17 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from requests>=2.9.1->tsfresh) (2024.2.2)
Requirement already satisfied: joblib>=1.2.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from scikit-learn>=0.22.0->tsfresh) (1.4.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from scikit-learn>=0.22.0->tsfresh) (3.4.0)
Requirement already satisfied: packaging>=21.3 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from statsmodels>=0.13->tsfresh) (24.0)
Requirement already satisfied: numba>=0.55.2 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from stumpy>=1.7.2->tsfresh) (0.59.1)
Requirement already satisfied: llvmlite<0.43,>=0.42.0dev0 in ./opt/anaconda3/envs/WGM_tsfresh/lib/python3.12/site-packages (from numba>=0.55.2->stumpy>=1.7.2->tsfresh) (0.42.0)
(WGM_tsfresh) andrea@pcdyn-sl-143 ~ % conda search tsfresh
Loading channels: done
Name Version Build Channel
tsfresh 0.18.0 pyhd3eb1b0_0 pkgs/main
Hi @nils-braun I've reinstalled Anaconda and now I was able to install the right version of tsfresh, which is working. Thank you very much for your help