# pyerrors.input.pandas API documentation

# pyerrors.input.pandas

View Source

      1import warnings
      2import gzip
      3import sqlite3
      4import pandas as pd
      5from ..obs import Obs
      6from ..correlators import Corr
      7from .json import create_json_string, import_json_string
      8
      9
     10def to_sql(df, table_name, db, if_exists='fail', gz=True, **kwargs):
     11    """Write DataFrame including Obs or Corr valued columns to sqlite database.
     12
     13    Parameters
     14    ----------
     15    df : pandas.DataFrame
     16        Dataframe to be written to the database.
     17    table_name : str
     18        Name of the table in the database.
     19    db : str
     20        Path to the sqlite database.
     21    if exists : str
     22        How to behave if table already exists. Options 'fail', 'replace', 'append'.
     23    gz : bool
     24        If True the json strings are gzipped.
     25
     26    Returns
     27    -------
     28    None
     29    """
     30    se_df = _serialize_df(df, gz=gz)
     31    con = sqlite3.connect(db)
     32    se_df.to_sql(table_name, con, if_exists=if_exists, index=False, **kwargs)
     33    con.close()
     34
     35
     36def read_sql(sql, db, auto_gamma=False, **kwargs):
     37    """Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.
     38
     39    Parameters
     40    ----------
     41    sql : str
     42        SQL query to be executed.
     43    db : str
     44        Path to the sqlite database.
     45    auto_gamma : bool
     46        If True applies the gamma_method to all imported Obs objects with the default parameters for
     47        the error analysis. Default False.
     48
     49    Returns
     50    -------
     51    data : pandas.DataFrame
     52        Dataframe with the content of the sqlite database.
     53    """
     54    con = sqlite3.connect(db)
     55    extract_df = pd.read_sql(sql, con, **kwargs)
     56    con.close()
     57    return _deserialize_df(extract_df, auto_gamma=auto_gamma)
     58
     59
     60def dump_df(df, fname, gz=True):
     61    """Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.
     62
     63    Before making use of pandas to_csv functionality Obs objects are serialized via the standardized
     64    json format of pyerrors.
     65
     66    Parameters
     67    ----------
     68    df : pandas.DataFrame
     69        Dataframe to be dumped to a file.
     70    fname : str
     71        Filename of the output file.
     72    gz : bool
     73        If True, the output is a gzipped csv file. If False, the output is a csv file.
     74
     75    Returns
     76    -------
     77    None
     78    """
     79    out = _serialize_df(df, gz=False)
     80
     81    if not fname.endswith('.csv'):
     82        fname += '.csv'
     83
     84    if gz is True:
     85        if not fname.endswith('.gz'):
     86            fname += '.gz'
     87        out.to_csv(fname, index=False, compression='gzip')
     88    else:
     89        out.to_csv(fname, index=False)
     90
     91
     92def load_df(fname, auto_gamma=False, gz=True):
     93    """Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.
     94
     95    Parameters
     96    ----------
     97    fname : str
     98        Filename of the input file.
     99    auto_gamma : bool
    100        If True applies the gamma_method to all imported Obs objects with the default parameters for
    101        the error analysis. Default False.
    102    gz : bool
    103        If True, assumes that data is gzipped. If False, assumes JSON file.
    104
    105    Returns
    106    -------
    107    data : pandas.DataFrame
    108        Dataframe with the content of the sqlite database.
    109    """
    110    if not fname.endswith('.csv') and not fname.endswith('.gz'):
    111        fname += '.csv'
    112
    113    if gz is True:
    114        if not fname.endswith('.gz'):
    115            fname += '.gz'
    116        with gzip.open(fname) as f:
    117            re_import = pd.read_csv(f)
    118    else:
    119        if fname.endswith('.gz'):
    120            warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
    121        re_import = pd.read_csv(fname)
    122
    123    return _deserialize_df(re_import, auto_gamma=auto_gamma)
    124
    125
    126def _serialize_df(df, gz=False):
    127    """Serializes all Obs or Corr valued columns into json strings according to the pyerrors json specification.
    128
    129    Parameters
    130    ----------
    131    df : pandas.DataFrame
    132        DataFrame to be serilized.
    133    gz: bool
    134        gzip the json string representation. Default False.
    135    """
    136    out = df.copy()
    137    for column in out:
    138        if isinstance(out[column][0], (Obs, Corr)):
    139            out[column] = out[column].transform(lambda x: create_json_string(x, indent=0))
    140            if gz is True:
    141                out[column] = out[column].transform(lambda x: gzip.compress(x.encode('utf-8')))
    142    return out
    143
    144
    145def _deserialize_df(df, auto_gamma=False):
    146    """Deserializes all pyerrors json strings into Obs or Corr objects according to the pyerrors json specification.
    147
    148    Parameters
    149    ----------
    150    df : pandas.DataFrame
    151        DataFrame to be deserilized.
    152    auto_gamma : bool
    153        If True applies the gamma_method to all imported Obs objects with the default parameters for
    154        the error analysis. Default False.
    155
    156    Notes:
    157    ------
    158    In case any column of the DataFrame is gzipped it is gunzipped in the process.
    159    """
    160    for column in df.select_dtypes(include="object"):
    161        if isinstance(df[column][0], bytes):
    162            if df[column][0].startswith(b"\x1f\x8b\x08\x00"):
    163                df[column] = df[column].transform(lambda x: gzip.decompress(x).decode('utf-8'))
    164        if isinstance(df[column][0], str):
    165            if '"program":' in df[column][0][:20]:
    166                df[column] = df[column].transform(lambda x: import_json_string(x, verbose=False))
    167                if auto_gamma is True:
    168                    df[column].apply(lambda x: x.gamma_method())
    169    return df

def to_sql(df, table_name, db, if_exists='fail', gz=True, **kwargs): View Source

    11def to_sql(df, table_name, db, if_exists='fail', gz=True, **kwargs):
    12    """Write DataFrame including Obs or Corr valued columns to sqlite database.
    13
    14    Parameters
    15    ----------
    16    df : pandas.DataFrame
    17        Dataframe to be written to the database.
    18    table_name : str
    19        Name of the table in the database.
    20    db : str
    21        Path to the sqlite database.
    22    if exists : str
    23        How to behave if table already exists. Options 'fail', 'replace', 'append'.
    24    gz : bool
    25        If True the json strings are gzipped.
    26
    27    Returns
    28    -------
    29    None
    30    """
    31    se_df = _serialize_df(df, gz=gz)
    32    con = sqlite3.connect(db)
    33    se_df.to_sql(table_name, con, if_exists=if_exists, index=False, **kwargs)
    34    con.close()

Write DataFrame including Obs or Corr valued columns to sqlite database.

###### Parameters

- df (pandas.DataFrame): Dataframe to be written to the database.
- table_name (str): Name of the table in the database.
- db (str): Path to the sqlite database.
- if exists (str): How to behave if table already exists. Options 'fail', 'replace', 'append'.
- gz (bool): If True the json strings are gzipped.

###### Returns

- None

def read_sql(sql, db, auto_gamma=False, **kwargs): View Source

    37def read_sql(sql, db, auto_gamma=False, **kwargs):
    38    """Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.
    39
    40    Parameters
    41    ----------
    42    sql : str
    43        SQL query to be executed.
    44    db : str
    45        Path to the sqlite database.
    46    auto_gamma : bool
    47        If True applies the gamma_method to all imported Obs objects with the default parameters for
    48        the error analysis. Default False.
    49
    50    Returns
    51    -------
    52    data : pandas.DataFrame
    53        Dataframe with the content of the sqlite database.
    54    """
    55    con = sqlite3.connect(db)
    56    extract_df = pd.read_sql(sql, con, **kwargs)
    57    con.close()
    58    return _deserialize_df(extract_df, auto_gamma=auto_gamma)

Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.

###### Parameters

- sql (str): SQL query to be executed.
- db (str): Path to the sqlite database.
- auto_gamma (bool): If True applies the gamma_method to all imported Obs objects with the default parameters for the error analysis. Default False.

###### Returns

- data (pandas.DataFrame): Dataframe with the content of the sqlite database.

def dump_df(df, fname, gz=True): View Source

    61def dump_df(df, fname, gz=True):
    62    """Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.
    63
    64    Before making use of pandas to_csv functionality Obs objects are serialized via the standardized
    65    json format of pyerrors.
    66
    67    Parameters
    68    ----------
    69    df : pandas.DataFrame
    70        Dataframe to be dumped to a file.
    71    fname : str
    72        Filename of the output file.
    73    gz : bool
    74        If True, the output is a gzipped csv file. If False, the output is a csv file.
    75
    76    Returns
    77    -------
    78    None
    79    """
    80    out = _serialize_df(df, gz=False)
    81
    82    if not fname.endswith('.csv'):
    83        fname += '.csv'
    84
    85    if gz is True:
    86        if not fname.endswith('.gz'):
    87            fname += '.gz'
    88        out.to_csv(fname, index=False, compression='gzip')
    89    else:
    90        out.to_csv(fname, index=False)

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.

###### Returns

- None

def load_df(fname, auto_gamma=False, gz=True): View Source

     93def load_df(fname, auto_gamma=False, gz=True):
     94    """Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.
     95
     96    Parameters
     97    ----------
     98    fname : str
     99        Filename of the input file.
    100    auto_gamma : bool
    101        If True applies the gamma_method to all imported Obs objects with the default parameters for
    102        the error analysis. Default False.
    103    gz : bool
    104        If True, assumes that data is gzipped. If False, assumes JSON file.
    105
    106    Returns
    107    -------
    108    data : pandas.DataFrame
    109        Dataframe with the content of the sqlite database.
    110    """
    111    if not fname.endswith('.csv') and not fname.endswith('.gz'):
    112        fname += '.csv'
    113
    114    if gz is True:
    115        if not fname.endswith('.gz'):
    116            fname += '.gz'
    117        with gzip.open(fname) as f:
    118            re_import = pd.read_csv(f)
    119    else:
    120        if fname.endswith('.gz'):
    121            warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
    122        re_import = pd.read_csv(fname)
    123
    124    return _deserialize_df(re_import, auto_gamma=auto_gamma)

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.

###### Returns

- data (pandas.DataFrame): Dataframe with the content of the sqlite database.