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feat: pandas DataFrame serialization and deserialization can now also

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deal with gzipped json columns. Tests added.
This commit is contained in:
Fabian Joswig 2022-07-04 14:19:30 +01:00
parent a133030114
commit cc9f47c686
2 changed files with 23 additions and 3 deletions
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17
pyerrors/input/pandas.py
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@ -22,7 +22,7 @@ def dump_df(df, fname, gz=True):
If True, the output is a gzipped csv file. If False, the output is a csv file.
"""
out = serialize_df(df)
out = serialize_df(df, gz=False)
if not fname.endswith('.csv'):
fname += '.csv'
@ -62,21 +62,25 @@ def load_df(fname, auto_gamma=False, gz=True):
warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
re_import = pd.read_csv(fname)
return deserialize_df(re_import, auto_gamma)
return deserialize_df(re_import, auto_gamma=auto_gamma)
def serialize_df(df):
def serialize_df(df, gz=False):
"""Serializes all Obs or Corr valued columns into json strings according to the pyerrors json specification.
Parameters
----------
df : pandas.DataFrame
DataFrame to be serilized.
gz: bool
gzip the json string represenation. Default False.
"""
out = df.copy()
for column in out:
if isinstance(out[column][0], (Obs, Corr)):
out[column] = out[column].transform(lambda x: create_json_string(x, indent=0))
if gz is True:
out[column] = out[column].transform(lambda x: gzip.compress(x.encode('utf-8')))
return out
@ -90,8 +94,15 @@ def deserialize_df(df, auto_gamma=False):
auto_gamma : bool
If True applies the gamma_method to all imported Obs objects with the default parameters for
the error analysis. Default False.
Notes:
------
In case any column of the DataFrame is gzipped it is gunzipped in the process.
"""
for column in df.select_dtypes(include="object"):
if isinstance(df[column][0], bytes):
if df[column][0].startswith(b"\x1f\x8b\x08\x00"):
df[column] = df[column].transform(lambda x: gzip.decompress(x).decode('utf-8'))
if isinstance(df[column][0], str):
if df[column][0][:20] == '{"program":"pyerrors':
df[column] = df[column].transform(lambda x: import_json_string(x, verbose=False))