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When I tried to import a measurements .csv I got a ParserError: Error tokenizing data. C error: Expected 20 fields in line 3, saw 23 from ~\mambaforge\envs\devbio-napari-env\lib\site-packages\pandas\_libs\parsers.pyx:
Cause
pandas is unable to read .csv files that use semicolon as seperator. When importing the file with pd.read_csv() the exact same error occurs, and will succesfully import when given the additional parameter sep = ";" or sep = None (auto detect). Note that semicolon seperated .csv files usually use comma as decimal seperator, which requires decimal="," (no auto detect available), otherwise decimal numbers will be interpreted as strings.
→ So its not a problem of devbio-napari, but pandas and the different .csv and number formats.
Workaround
After replacing the seperators to match pandas default (comma and dot) the import of the csv file into napari worked.
Hi @haesleinhuepf,
the file originates from regionprops export to .csv and was then edited in excel (additional column "custom"). The original unchanged csv could be imported, while the excel edited file caused the error.
Excel uses the system standard number format (german in my case), which lead to the semi-colon seperated csv file with decimal comma numbers which pandas cannot handle on default. After changing the system standard or excel setting to comma seperated csv with decimal dot numbers the import into napari worked.
Problem
When I tried to import a measurements .csv I got a
ParserError: Error tokenizing data. C error: Expected 20 fields in line 3, saw 23
from~\mambaforge\envs\devbio-napari-env\lib\site-packages\pandas\_libs\parsers.pyx
:Cause
pandas is unable to read .csv files that use semicolon as seperator. When importing the file with
pd.read_csv()
the exact same error occurs, and will succesfully import when given the additional parametersep = ";"
orsep = None
(auto detect). Note that semicolon seperated .csv files usually use comma as decimal seperator, which requiresdecimal=","
(no auto detect available), otherwise decimal numbers will be interpreted as strings.→ So its not a problem of devbio-napari, but pandas and the different .csv and number formats.
Workaround
After replacing the seperators to match pandas default (comma and dot) the import of the csv file into napari worked.
Also see
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