Time series feature extractor error with spectral `can not reindex on an axis with duplicate labels`

[MillerQuintero2001]

Hi, I was applying feature extraction in a time series dataframe, but I found this issue:

import tsfel
cfg = tsfel.get_features_by_domain(["statistical", "temporal", "spectral"])

X_train = tsfel.time_series_features_extractor(cfg, x_train_array, fs=1/86400)
X_test = tsfel.time_series_features_extractor(cfg, x_test_array, fs=1/86400)

But I got this error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[10], line 4
      1 import tsfel
      2 cfg = tsfel.get_features_by_domain(["statistical", "temporal", "spectral"])
----> 4 X_train = tsfel.time_series_features_extractor(cfg, x_train_array, fs=1/86400)
      5 X_test = tsfel.time_series_features_extractor(cfg, x_test_array, fs=1/86400)

File ~/Documentos/Dev/Startup/poc-data-china-energy/.venv/lib/python3.13/site-packages/tsfel/feature_extraction/calc_features.py:390, in time_series_features_extractor(config, timeseries, fs, window_size, overlap, verbose, **kwargs)
    379     features_final = calc_window_features(
    380         config,
    381         timeseries,
   (...)    386         single_window=True,
    387     )
    389 # Assuring the same feature extraction order
--> 390 features_final = features_final.reindex(sorted(features_final.columns), axis=1)
    391 return features_final.reset_index(drop=True)

File ~/Documentos/Dev/Startup/poc-data-china-energy/.venv/lib/python3.13/site-packages/pandas/core/frame.py:6078, in DataFrame.reindex(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)
   5843 def reindex(
   5844     self,
   5845     labels=None,
   (...)   5855     tolerance=None,
   5856 ) -> DataFrame:
   5857     """
   5858     Conform DataFrame to new index with optional filling logic.
   5859 
   (...)   6076     See the :ref:`user guide <basics.reindexing>` for more.
   6077     """
-> 6078     return super().reindex(
   6079         labels=labels,
   6080         index=index,
   6081         columns=columns,
   6082         axis=axis,
   6083         method=method,
   6084         level=level,
   6085         fill_value=fill_value,
   6086         limit=limit,
   6087         tolerance=tolerance,
   6088         copy=copy,
   6089     )

File ~/Documentos/Dev/Startup/poc-data-china-energy/.venv/lib/python3.13/site-packages/pandas/core/generic.py:5476, in NDFrame.reindex(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)
   5473     return self._reindex_multi(axes, fill_value)
   5475 # perform the reindex on the axes
-> 5476 return self._reindex_axes(
   5477     axes, level, limit, tolerance, method, fill_value
   5478 ).__finalize__(self, method="reindex")

File ~/Documentos/Dev/Startup/poc-data-china-energy/.venv/lib/python3.13/site-packages/pandas/core/generic.py:5498, in NDFrame._reindex_axes(self, axes, level, limit, tolerance, method, fill_value)
   5495     continue
   5497 ax = self._get_axis(a)
-> 5498 new_index, indexer = ax.reindex(
   5499     labels, level=level, limit=limit, tolerance=tolerance, method=method
   5500 )
   5502 axis = self._get_axis_number(a)
   5503 obj = obj._reindex_with_indexers(
   5504     {axis: [new_index, indexer]},
   5505     fill_value=fill_value,
   5506     allow_dups=False,
   5507 )

File ~/Documentos/Dev/Startup/poc-data-china-energy/.venv/lib/python3.13/site-packages/pandas/core/indexes/base.py:4253, in Index.reindex(self, target, method, level, limit, tolerance)
   4250     raise ValueError("cannot handle a non-unique multi-index!")
   4251 elif not self.is_unique:
   4252     # GH#42568
-> 4253     raise ValueError("cannot reindex on an axis with duplicate labels")
   4254 else:
   4255     indexer, _ = self.get_indexer_non_unique(target)

ValueError: cannot reindex on an axis with duplicate labels

It seems like internally is creating a columns dataframe that already exists with that name, so, at the moment to apply reindex the error raises.

When I don't specify a fs (use the default that until I know is 100 Hz), this error doesn't raise.

Maybe it can't work with non integer sample frequency.

Steps to recreate

I was using a public dataset, so I don't have problem to give the exact data that I was using.

1. Download .parquet file
2. Read the file in a dataframe (pandas or polars)
3. Use the following code:

# Series to list of numpy arrays
x_train_array = []
for array in x_train[:, 2:].to_numpy():
    x_train_array.append(array)
import tsfel
cfg = tsfel.get_features_by_domain(["statistical", "temporal", "spectral"])

X_train = tsfel.time_series_features_extractor(cfg, x_train_array, fs=1/86400)

I know that the problem is with spectral feature, cause a run an experiment individually with each feature:

Data: https://drive.google.com/file/d/1sTXC_SCIWi-oKoYOC5QxBN9ZlFl_ha7W/view?usp=sharing
Version: tsfel == 0.2.0