"""Module containing CSV io support."""
from __future__ import annotations
import numpy as np
import pandas as pd
from glotaran.io import ProjectIoInterface
from glotaran.io import register_project_io
from glotaran.parameter import Parameters
from glotaran.parameter.parameter import OPTION_NAMES_DESERIALIZED
from glotaran.utils.io import safe_dataframe_fillna
from glotaran.utils.io import safe_dataframe_replace
[docs]
@register_project_io(["csv"])
class CsvProjectIo(ProjectIoInterface):
"""Plugin for CSV data io."""
[docs]
def load_parameters(self, file_name: str, sep: str = ",") -> Parameters:
"""Load parameters from CSV file.
Parameters
----------
file_name : str
Name of file to be loaded.
sep: str
Other separators can be used optionally., by default ','
Returns
-------
:class:`Parameters
"""
df = pd.read_csv(file_name, skipinitialspace=True, na_values=["None", "none"], sep=sep)
df.columns = [column.lower() for column in df.columns]
df.rename(columns=OPTION_NAMES_DESERIALIZED, inplace=True)
safe_dataframe_fillna(df, "minimum", -np.inf)
safe_dataframe_fillna(df, "maximum", np.inf)
return Parameters.from_dataframe(df, source=file_name)
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def save_parameters(
self,
parameters: Parameters,
file_name: str,
*,
sep: str = ",",
as_optimized: bool = True,
replace_infinfinity: bool = True,
) -> None:
"""Save a :class:`Parameters` to a CSV file.
Parameters
----------
parameters : Parameters
Parameters to be saved to file.
file_name : str
File to write the parameters to.
sep: str
Other separators can be used optionally., by default ','
as_optimized : bool
Weather to include properties which are the result of optimization.
replace_infinfinity : bool
Weather to replace infinity values with empty strings.
"""
df = parameters.to_dataframe()
if replace_infinfinity is True:
safe_dataframe_replace(df, "minimum", -np.inf, "")
safe_dataframe_replace(df, "maximum", np.inf, "")
df.to_csv(file_name, na_rep="None", index=False, sep=sep)