Unpickling dictionary that holds pandas dataframes throws AttributeError: 'Dataframe' object has no attribute '_data'

Question

I have a class that performs analyses and attaches the results, which are pandas dataframes, as object attributes:

>>> print(test.image.locate_DF)
              y          x       mass  ...    raw_mass        ep  frame
0     60.177142  59.788709  33.433414  ...  242.080256       NaN      0
1     60.651991  59.773904  33.724308  ...  242.355784       NaN      1
2     60.790437  60.190234  31.117164  ...  236.276671       NaN      2
3     60.771933  60.048123  33.558372  ...  240.981395       NaN      3
4     60.251282  59.775139  31.881009  ...  239.239022       NaN      4
...         ...        ...        ...  ...         ...       ...    ...
7212  68.186380  76.477449  18.122817  ...  176.523091       NaN   9410
7213  68.764444  76.574091  17.486454  ...  173.448306       NaN   9415
7214  68.191152  76.473477  17.402975  ...  172.848119  0.868326   9429
7215  67.034103  76.025885  17.010951  ...  170.928067 -0.600854   9431
7216  68.583276  75.309592  17.852992  ...  178.271558       NaN   9432

Subsequently, I save all the important object attributes in a dictionary, and pickle it for later use:

def save_parameters(self, filepath):
        
        param_dict = {}

    try:
            self.image.locate_DF
        except AttributeError:
            pass
        else:
            param_dict['optical_locate_DF'] = self.image.locate_DF

    with open(filepath, 'wb') as handle:
            pickle.dump(param_dict, handle, 5)

When trying to load that pickled file, I have no problem at all, the dataframe loads perfectly:

>>> test.save_parameters('test.pickle')
>>> with open('test.pickle', 'rb') as handle:
...     result = pickle.load(handle)
...
>>> print(result.keys())
dict_keys(['optical_path', 'optical_feature_diameter', 'optical_feature_minmass', 'optical_locate_DF', 'electrical_path', 'electrical_raw_data', 'electrical_processed_data', 'electrical_mean_voltage'])
>>> print(result['optical_locate_DF'])
              y          x       mass  ...    raw_mass        ep  frame
0     60.177142  59.788709  33.433414  ...  242.080256       NaN      0
1     60.651991  59.773904  33.724308  ...  242.355784       NaN      1
2     60.790437  60.190234  31.117164  ...  236.276671       NaN      2
3     60.771933  60.048123  33.558372  ...  240.981395       NaN      3
4     60.251282  59.775139  31.881009  ...  239.239022       NaN      4
...         ...        ...        ...  ...         ...       ...    ...
7212  68.186380  76.477449  18.122817  ...  176.523091       NaN   9410
7213  68.764444  76.574091  17.486454  ...  173.448306       NaN   9415
7214  68.191152  76.473477  17.402975  ...  172.848119  0.868326   9429
7215  67.034103  76.025885  17.010951  ...  170.928067 -0.600854   9431
7216  68.583276  75.309592  17.852992  ...  178.271558       NaN   9432

[7217 rows x 9 columns]

However, after running my analysis on a bunch of these files on a hpc, and then trying to open that same pickled file (it's named differently now but it's the same file as shown above, with the same analysis performed on it), I get thrown an attribute error by pandas. It states that the dataframe has no '_data' attribute. The dictionary has the same keys and the keys that are not a dataframe are printed without any issues:

>>> resultfile = '../results/diam_15_minmass_17_dist_50_mem_5000_tracklength_500/R9_DNA_50mV_001.pickle'
>>> with open(resultfile, 'rb') as handle:
...     result = pickle.load(handle)
...
>>> print(result.keys())
dict_keys(['optical_path', 'optical_feature_diameter', 'optical_feature_minmass', 'optical_locate_DF', 'optical_tracking_distance', 'optical_tracking_memory', 'optical_tracking_DF', 'optical_kinetics_DF', 'electrical_path', 'electrical_raw_data', 'electrical_processed_data', 'electrical_mean_voltage'])
>>> print(result['optical_locate_DF'])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/core/frame.py", line 680, in __repr__
    self.to_string(
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/core/frame.py", line 801, in to_string
    formatter = fmt.DataFrameFormatter(
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/io/formats/format.py", line 593, in __init__
    self.max_rows_displayed = min(max_rows or len(self.frame), len(self.frame))
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/core/frame.py", line 1041, in __len__
    return len(self.index)
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/core/generic.py", line 5270, in __getattr__
    return object.__getattribute__(self, name)
  File "pandas/_libs/properties.pyx", line 63, in pandas._libs.properties.AxisProperty.__get__
  File "/Users/stevenvanuytsel/miniconda3/envs/simultaneous_measurements/lib/python3.8/site-packages/pandas/core/generic.py", line 5270, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute '_data'

I've looked into the pickle manual, and through a bunch of SO questions, but I can't seem to find out what is going wrong here. Does anyone have an idea how to fix this, and also whether I can still access that data?

Answer 1

I had the same problem. I generated a Pandas dataframe in an environment with Pandas 1.1.1 and saved it to a pickle file.

with open('file.pkl', 'wb') as f:
    pickle.dump(data_frame_object, f)

After unpickling it in another session and printing the dataframe I got the same error. Some testing in different environments showed the following pattern:

• environment with Pandas >= 1.1.0: works
• environment with Pandas == 1.0.5: error message as above
• environment with Pandas == 1.0.3: Kernel crashes

I got the same error using the HDF5 format so it seems to be a compatibility issue with the dataframe and different Pandas versions.

Updating Pandas to 1.1.1 in the affected environments solved the issue for me.

Answer 2

After a long and painful process of cross-checking module versions, I found out that this error was caused due to an update in the pandas version. My mac still ran pandas 1.0.5, whereas the hpc runs pandas 1.1.0. Apparently, there is a mismatch between the two (unsure whether it's just after pickling or also for other file formats used to save).

Answer 3

Maybe the problem has been solved.
Emmm, but I still want to add some comments.

I save the pkl file on the server, but when I load it on my MAC, it crashed, showing 'Dataframe' object has no attribute '_data'

Finally, I found that pandas on my Mac is 1.0.5 but 1.1.5 on the server. When I updated it to the latest, it just worked.