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Pandas: ValueError: cannot convert float NaN to integer

I get ValueError: cannot convert float NaN to integer for following:

df = pandas.read_csv('zoom11.csv')
df[['x']] = df[['x']].astype(int)
  • The “x” is a column in the csv file, I cannot spot any float NaN in the file, and I don’t understand the error or why I am getting it.
  • When I read the column as String, then it has values like -1,0,1,…2000, all look very nice int numbers to me.
  • When I read the column as float, then this can be loaded. Then it shows values as -1.0,0.0 etc, still there are no any NaN-s
  • I tried with error_bad_lines = False and dtype parameter in read_csv to no avail. It just cancels loading with same exception.
  • The file is not small (10+ M rows), so cannot inspect it manually, when I extract a small header part, then there is no error, but it happens with full file. So it is something in the file, but cannot detect what.
  • Logically the csv should not have missing values, but even if there is some garbage then I would be ok to skip the rows. Or at least identify them, but I do not see way to scan through file and report conversion errors.

Update: Using the hints in comments/answers I got my data clean with this:

# x contained NaN
df = df[~df['x'].isnull()]

# Y contained some other garbage, so null check was not enough
df = df[df['y'].str.isnumeric()]

# final conversion now worked
df[['x']] = df[['x']].astype(int)
df[['y']] = df[['y']].astype(int)

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Answer

For identifying NaN values use boolean indexing:

print(df[df['x'].isnull()])

Then for removing all non-numeric values use to_numeric with parameter errors='coerce' – to replace non-numeric values to NaNs:

df['x'] = pd.to_numeric(df['x'], errors='coerce')

And for remove all rows with NaNs in column x use dropna:

df = df.dropna(subset=['x'])

Last convert values to ints:

df['x'] = df['x'].astype(int)
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