BUG: ValueError: Cannot convert non-finite values (NA or inf) to integer only when DF exceed certain size

[ben-arnao]

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• (optional) I have confirmed this bug exists on the master branch of pandas.

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Here is the code in question:

    print(df.shape)
    print(df.memory_usage().sum())
    df.dropna(inplace=True)  # drop rows with not enough lookback (they will be nan)

The line dropna line is what throws the error

So when i run my code with adding 500 features/columns the output is following

(2177432, 503)
4398412768

However when i run the same exact code for 1000 features

(2177432, 1003)
8753276768

I get an error

  File "C:\Users\Ben\PycharmProjects\tradingbot\tradingbot\trainer\sample_maker.py", line 17, in get_signal_features
    df.dropna(inplace=True)  # drop rows with not enough lookback (they will be nan)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\frame.py", line 4751, in dropna
    count = agg_obj.count(axis=agg_axis)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\frame.py", line 7807, in count
    return result.astype("int64")
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\generic.py", line 5698, in astype
    new_data = self._data.astype(dtype=dtype, copy=copy, errors=errors)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\internals\managers.py", line 582, in astype
    return self.apply("astype", dtype=dtype, copy=copy, errors=errors)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\internals\managers.py", line 442, in apply
    applied = getattr(b, f)(**kwargs)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\internals\blocks.py", line 625, in astype
    values = astype_nansafe(vals1d, dtype, copy=True)
  File "C:\Users\Ben\PycharmProjects\tradingbot\venv\lib\site-packages\pandas\core\dtypes\cast.py", line 868, in astype_nansafe
    raise ValueError("Cannot convert non-finite values (NA or inf) to integer")
ValueError: Cannot convert non-finite values (NA or inf) to integer

The version i am running is 1.0.5

[jorisvandenbossche]

@ben-arnao could you provide a reproducible example? (see eg https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)

[ben-arnao]

@jorisvandenbossche

Please see below

import numpy as np
import pandas as pd


def test(lookback, columns):
    df = pd.DataFrame({'value': np.random.random_sample((columns,))})

    df['value'] = df['value'].astype(np.float32)

    for x in range(1, lookback + 1):
        df['_relhist_' + str(x)] = df['value'].shift(periods=x, fill_value=np.nan) / df['value'] - 1
    df.dropna(inplace=True)
    print(df.shape)


test(100, 300000)  # does not throw error

test(1000, 3000000)  # throws error

[ben-arnao]

I think i've been able to narrow it down to the sum() function failing with larger dataframes. In the pandas.core.frame module there is a count(self, axis=0, level=None, numeric_only=False) function around line 7700

The execution enters the block of code where result = notna(frame).sum(axis=axis) is performed.

If we do a few print statements after this bit of code

        print(notna(frame).isnull().values.any())
        print(notna(frame))
        print(notna(frame).sum(axis=axis))

We can see here that we correctly mark cells as True or False, for null/not null.

notna(frame).isnull().values.any() Shows us that for both cases, there is no null values for the null-indicator frame (which is correct).

So the frame that notna(frame) return is valid.

However we can see that when we do sum(axis=axis) This is where the smaller frame has no problems counting the nulls, but for the larger frame, every cell is simply NaN leading me to believe that there is something in the sum() function that fails when operating on larger dataframes.

[ben-arnao]

The issue is this

np.prod((2244367, 1253) returns -1482775445

Obviously this is a numpy issue, as there is some sort of overload going on here. But we can pretty easily deal with the problem for now in pandas by just checking that the mask size is positive since the mask size should never be negative.

In line 1313 of nanops check_below_min_count

non_nulls = np.prod(shape)

We see that this value is incorrectly set negative. Which causes the next line

        if non_nulls < min_count:
            return True

to return true and then set our result to nan

        if check_below_min_count(shape, mask, min_count):
            result = np.nan

If we just add a condition to the above line requires the mask also be positive, this should resolve the issue

[simonjayhawkins]

The issue is this

np.prod((2244367, 1253) returns -1482775445

Obviously this is a numpy issue, as there is some sort of overload going on here. But we can pretty easily deal with the problem for now in pandas by just checking that the mask size is positive since the mask size should never be negative.

or specifying dtype would give the correct answer

>>> np.prod((2244367, 1253), dtype="int64")
2812191851
>>>

see also #34827

[fonnesbeck]

Is there a plan to fix this, or a workaround in the meantime?

[jreback]

community PRs are always welcome @fonnesbeck as pandas is all volunteer and there issue prioritization is not possible in a direct way

[fonnesbeck]

Actually, this may not be an issue with newer versions of NumPy. np.prod does now appear to return int64s, so the failure demonstrated by @simonjayhawkins no longer occurs.

[FactorizeD]

take