feat: dump and load functionality for pandas dataframes containing Obs

objects added.

pyerrors/input/__init__.py

@@ -10,4 +10,5 @@ from . import hadrons
 from . import json
 from . import misc
 from . import openQCD
+from . import pandas
 from . import sfcf

pyerrors/input/pandas.py

@@ -0,0 +1,72 @@
+import warnings
+import gzip
+import pandas as pd
+from ..obs import Obs
+from .json import create_json_string, import_json_string
+
+
+def dump_df(df, fname, gz=True):
+    """Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.
+
+    Before making use of pandas to_csv functionality Obs objects are serialized via the standardized
+    json format of pyerrors.
+
+    Parameters
+    ----------
+    df : pandas.DataFrame
+        Dataframe to be dumped to a file.
+    fname : str
+        Filename of the output file.
+    gz : bool
+        If True, the output is a gzipped csv file. If False, the output is a csv file.
+    """
+
+    out = df.copy()
+    for column in out:
+        if isinstance(out[column][0], Obs):
+            out[column] = out[column].transform(lambda x: create_json_string(x, indent=0))
+
+    if not fname.endswith('.csv'):
+        fname += '.csv'
+
+    out.to_csv(fname)
+    if gz is True:
+        with open(fname, 'rb') as f_in, gzip.open(fname + ".gz", 'wb') as f_out:
+            f_out.writelines(f_in)
+
+
+def load_df(fname, auto_gamma=False, gz=True):
+    """Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.
+
+    Parameters
+    ----------
+    fname : str
+        Filename of the input file.
+    auto_gamma : bool
+        If True applies the gamma_method to all imported Obs objects with the default parameters for
+        the error analysis. Default False.
+    gz : bool
+        If True, assumes that data is gzipped. If False, assumes JSON file.
+    """
+
+    if not fname.endswith('.csv') and not fname.endswith('.gz'):
+        fname += '.csv'
+
+    if gz is True:
+        if not fname.endswith('.gz'):
+            fname += '.gz'
+        with gzip.open(fname) as f:
+            re_import = pd.read_csv(f)
+    else:
+        if fname.endswith('.gz'):
+            warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
+        re_import = pd.read_csv(fname)
+
+    for column in re_import.select_dtypes(include="object"):
+        if isinstance(re_import[column][0], str):
+            if re_import[column][0][:20] == '{"program":"pyerrors':
+                re_import[column] = re_import[column].transform(lambda x: import_json_string(x, verbose=False))
+                if auto_gamma is True:
+                    re_import[column].apply(Obs.gamma_method)
+
+    return re_import