seabirdfilehandler 0.4.2__py3-none-any.whl → 0.5.0__py3-none-any.whl

seabirdfilehandler/datatablefiles.py

@@ -1,930 +0,0 @@
-from pathlib import Path
-from typing import Union, Tuple
-from datetime import datetime, time, timedelta
-import re
-import pandas as pd
-import numpy as np
-import logging
-import warnings
-from seabirdfilehandler.parameter import Parameters
-from seabirdfilehandler.validation_modules import CnvValidationList
-from seabirdfilehandler.seabirdfiles import SeaBirdFile
-from seabirdfilehandler.dataframe_meta_accessor import (
-    SeriesMetaAccessor,
-    DataFrameMetaAccessor,
-)
-
-logger = logging.getLogger(__name__)
-
-
-class DataTableFile(SeaBirdFile):
-    """Collection of methods for the SeaBird files that feature some kind of
-    data table that is represented in a pandas dataframe.
-
-    Parameters
-    ----------
-
-    Returns
-    -------
-
-    """
-
-    def __init__(self, path_to_file):
-        super().__init__(path_to_file)
-        self.original_df: pd.DataFrame
-        self.df: pd.DataFrame
-
-    def define_output_path(
-        self,
-        file_path: Path | str | None = None,
-        file_name: str | None = None,
-        file_type: str = ".csv",
-    ) -> Path:
-        """Creates a Path object holding the desired output path.
-
-        Parameters
-        ----------
-        file_path : Path :
-            directory the file sits in (Default value = self.file_dir)
-        file_name : str :
-            the original file name (Default value = self.file_name)
-        file_type : str :
-            the output file type (Default = '.csv')
-        Returns
-        -------
-        a Path object consisting of the full path of the new file
-
-        """
-        file_path = self.file_dir if file_path is None else file_path
-        file_name = self.file_name if file_name is None else file_name
-        if file_type[0] != ".":
-            file_type = "." + file_type
-        return Path(file_path).joinpath(file_name).with_suffix(file_type)
-
-    def to_csv(
-        self,
-        selected_columns: list | None = None,
-        with_header: bool = True,
-        output_file_path: Path | str | None = None,
-        output_file_name: str | None = None,
-    ):
-        """Writes a csv from the current dataframe. Takes a list of columns to
-        use, a boolean for writing the header and the output file parameters.
-
-        Parameters
-        ----------
-        selected_columns : list :
-            a list of columns to include in the csv
-            (Default value = self.df.columns)
-        with_header : boolean :
-            indicating whether the header shall appear in the output
-             (Default value = True)
-        output_file_path : Path :
-            file directory (Default value = None)
-        output_file_name : str :
-            original file name (Default value = None)
-
-        Returns
-        -------
-
-        """
-        selected_columns = (
-            self.df.columns if selected_columns is None else selected_columns
-        )
-        df = self.df[selected_columns].reset_index(drop=True)
-        new_file_path = self.define_output_path(
-            output_file_path, output_file_name
-        )
-        if with_header:
-            with open(new_file_path, "w") as file:
-                for line in self.header:
-                    file.write(line)
-            df.to_csv(new_file_path, index=False, mode="a")
-        else:
-            df.to_csv(new_file_path, index=False, mode="w")
-        logger.info(f"Wrote file {self.path_to_file} to {new_file_path}.")
-
-    def selecting_columns(
-        self,
-        list_of_columns: list | str,
-        df: pd.DataFrame | None = None,
-    ):
-        """Alters the dataframe to only hold the given columns.
-
-        Parameters
-        ----------
-        list_of_columns: list or str : a collection of columns
-        df : pandas.Dataframe :
-            Dataframe (Default value = None)
-
-        Returns
-        -------
-
-        """
-        df = self.df if df is None else df
-        # ensure that the input is a list, so that isin() can do its job
-        if isinstance(list_of_columns, str):
-            list_of_columns = [list_of_columns]
-        if isinstance(df, pd.DataFrame):
-            self.df = df[list_of_columns].reset_index(drop=True)
-
-
-class BottleFile(DataTableFile):
-    """Class that represents a SeaBird Bottle File. Organizes the files table
-    information into a pandas dataframe. This allows the usage of this
-    powerful library for statistics, visualization, data manipulation, export,
-    etc.
-
-    Parameters
-    ----------
-
-    Returns
-    -------
-
-    """
-
-    def __init__(self, path_to_file):
-        super().__init__(path_to_file)
-        self.original_df = self.create_dataframe()
-        self.df = self.original_df
-        self.setting_dataframe_dtypes()
-        self.adding_timestamp_column()
-
-    def create_dataframe(self):
-        """Creates a dataframe out of the btl file. Manages the double data
-        header correctly.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-
-        """
-        # TODO: this needs to be broken down into smaller pieces...
-        top_names, bottom_names = self.reading_data_header()
-        # creating statistics column to store the row type information:
-        # 4 rows per bottle, average, standard deviation, max value, min value
-        top_names.append("Statistic")
-        # TODO: sexier way to construct dataframe than opening the file a
-        # second time
-        # # df = pd.DataFrame(self.data, index=None, columns=top_names)
-        df: pd.DataFrame = pd.read_fwf(
-            self.path_to_file,
-            index_col=False,
-            skiprows=len(self.header) + 2,
-            header=None,
-            names=top_names,
-        )
-
-        # handling the double row header
-        rowtypes = df[df.columns[-1]].unique()
-
-        # TODO: can this be made a little pretier?
-        def separate_double_header_row(df, column, length):
-            """
-
-            Parameters
-            ----------
-            df :
-            column :
-            length :
-
-            Returns
-            -------
-
-            """
-            column_idx = df.columns.get_loc(column)
-            old_column = df.iloc[::length, column_idx].reset_index(drop=True)
-            new_column = df.iloc[1::length, column_idx].reset_index(drop=True)
-            old_column_expanded = pd.Series(
-                np.repeat(old_column, length)
-            ).reset_index(drop=True)
-            new_column_expanded = pd.Series(
-                np.repeat(new_column, length)
-            ).reset_index(drop=True)
-            df[column] = old_column_expanded
-            df.insert(
-                column_idx + 1, bottom_names[column_idx], new_column_expanded
-            )
-            return df
-
-        df = separate_double_header_row(df, "Date", len(rowtypes))
-        df = separate_double_header_row(df, top_names[0], len(rowtypes))
-        # remove brackets around statistics values
-        df["Statistic"] = df["Statistic"].str.strip("()")
-        df = df.rename(mapper={"Btl_ID": "Bottle_ID"}, axis=1)
-        return df
-
-    def adding_timestamp_column(self):
-        """Creates a timestamp column that holds both, Date and Time
-        information.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-
-        """
-        # constructing timestamp column
-        timestamp = []
-        for datepoint, timepoint in zip(self.df.Date, self.df.Time):
-            timestamp.append(
-                datetime.combine(datepoint, time.fromisoformat(str(timepoint)))
-            )
-        self.df.insert(2, "Timestamp", timestamp)
-        self.df.Timestamp = pd.to_datetime(self.df.Timestamp)
-
-    def setting_dataframe_dtypes(self):
-        """Sets the types for the column values in the dataframe."""
-        # setting dtypes
-        # TODO: extending this to the other columns!
-        self.df.Date = pd.to_datetime(self.df.Date)
-        self.df.Bottle_ID = self.df.Bottle_ID.astype(int)
-
-    def selecting_rows(
-        self, df=None, statistic_of_interest: Union[list, str] = ["avg"]
-    ):
-        """Creates a dataframe with the given row identifier, using the
-        statistics column. A single string or a list of strings can be
-        processed.
-
-        Parameters
-        ----------
-        df : pandas.Dataframe :
-            the files Pandas representation (Default value = self.df)
-        statistic_of_interest: list or str :
-            collection of values of the 'statistics' column in self.df
-             (Default value = ['avg'])
-
-        Returns
-        -------
-
-        """
-        df = self.df if df is None else df
-        # ensure that the input is a list, so that isin() can do its job
-        if isinstance(statistic_of_interest, str):
-            statistic_of_interest = [statistic_of_interest]
-        self.df = df.loc[df["Statistic"].isin(statistic_of_interest)]
-
-    def reading_data_header(self):
-        """Identifies and separatly collects the rows that specify the data
-        tables headers.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-
-        """
-        n = 11  # fix column width of a seabird btl file
-        top_line = self.data[0]
-        second_line = self.data[1]
-        top_names = [
-            top_line[i : i + n].split()[0]
-            for i in range(0, len(top_line) - n, n)
-        ]
-        bottom_names = [
-            second_line[i : i + n].split()[0] for i in range(0, 2 * n, n)
-        ]
-        return top_names, bottom_names
-
-    def add_station_and_event_column(self):
-        event_list = [self.metadata["Station"] for _ in self.data]
-        self.df.insert(0, "Event", pd.Series(event_list))
-
-    def add_position_columns(self):
-        latitude_list = [self.metadata["GPS_Lat"] for _ in self.data]
-        self.df.insert(1, "Latitude", pd.Series(latitude_list))
-        longitude_list = [self.metadata["GPS_Lon"] for _ in self.data]
-        self.df.insert(2, "Longitude", pd.Series(longitude_list))
-
-
-class CnvFile(DataTableFile):
-    """
-    A representation of a cnv-file as used by SeaBird.
-
-    This class intends to fully extract and organize the different types of
-    data and metadata present inside of such a file. Downstream libraries shall
-    be able to use this representation for all applications concerning cnv
-    files, like data processing, transformation or visualization.
-
-    To achieve that, the metadata header is organized by the grandparent-class,
-    SeaBirdFile, while the data table is extracted by this class. The data
-    representation of choice is a pandas Dataframe. Inside this class, there
-    are methods to parse cnv data into dataframes, do the reverse of writing a
-    dataframe into cnv compliant form and to manipulate the dataframe in
-    various ways.
-
-    Parameters
-    ----------
-    path_to_file: Path | str:
-        the path to the file
-    full_data_header: bool:
-        whether to use the full data column descriptions for the dataframe
-    long_header_names: bool:
-        whether to use long header names in the dateframe
-    absolute_time_calculation: bool:
-        whether to use a real timestamp instead of the second count
-    event_log_column: bool:
-        whether to add a station and device event column from DSHIP
-    coordinate_columns: bool:
-        whether to add longitude and latitude from the extra metadata header
-
-    """
-
-    def __init__(
-        self,
-        path_to_file: Path | str,
-        create_dataframe: bool = True,
-        absolute_time_calculation: bool = False,
-        event_log_column: bool = False,
-        coordinate_columns: bool = False,
-        data_table_info_level: str = "shortname",
-    ):
-        super().__init__(path_to_file)
-        self.validation_modules = self.obtaining_validation_modules()
-        self.start_time = self.reading_start_time()
-        if create_dataframe:
-            warnings.warn(
-                "The default of constructing a pandas Dataframe will soon be replaced by using the Parameters class that works on numpy arrays.",
-                DeprecationWarning,
-                stacklevel=2,  # Ensures the warning points to the caller's line
-            )
-            self.data_header_meta_info, self.duplicate_columns = (
-                self.reading_data_header(self.data_table_description)
-            )
-            self.original_df = self.create_dataframe(data_table_info_level)
-            self.df = self.original_df
-            if absolute_time_calculation:
-                self.absolute_time_calculation()
-            if event_log_column:
-                self.add_station_and_event_column()
-            if coordinate_columns:
-                self.add_position_columns()
-        else:
-            self.parameters = Parameters(
-                self.data, self.data_table_description
-            )
-
-    def reading_data_header(
-        self, header_info: list = []
-    ) -> Tuple[dict[str, dict], list[int]]:
-        """Reads the tables header data from the header.
-
-        Parameters
-        ----------
-        header_info: list:
-            the header values from the file
-
-        Returns
-        -------
-        a list of dictionaries, that organize the table header information
-
-        """
-        if header_info is []:
-            header_info = self.data_table_description
-        table_header = {}
-        duplicate_columns = []
-        for line in header_info:
-            if line.startswith("name"):
-                header_meta_info = {}
-                # get basic shortname and the full, non-differentiated info
-                shortname = longinfo = line_info = line.split("=")[1].strip()
-                try:
-                    shortname, longinfo = line_info.split(":")
-                except IndexError:
-                    pass
-                finally:
-                    shortname = shortname.strip()
-                    if shortname in list(table_header.keys()):
-                        try:
-                            duplicate_columns.append(
-                                int(line.split("=")[0].strip().split()[1])
-                            )
-                        except IndexError as error:
-                            logger.error(
-                                f"Could not resolve duplicate column: {
-                                    shortname
-                                }, {error}"
-                            )
-                    else:
-                        header_meta_info["shortname"] = shortname
-                        header_meta_info["longinfo"] = longinfo.strip()
-                        metainfo = self._extract_data_header_meta_info(
-                            longinfo.strip()
-                        )
-                        header_meta_info = {**header_meta_info, **metainfo}
-                        table_header[shortname.strip()] = header_meta_info
-        return table_header, duplicate_columns
-
-    def _extract_data_header_meta_info(self, line: str) -> dict:
-        """Extracts the individual information bits inside of the header lines
-
-        Parameters
-        ----------
-        line: str:
-            one header line, trimmed by the 'name =' prefix and the shortname
-
-        Returns
-        -------
-        a dictionary with the information stored
-
-        """
-        regex_string = r"(?:(?P<name0>.+),\s(?P<metainfo0>.+)\s\[(?P<unit0>.+)\]|(?P<name2>.+)\s\[(?P<unit2>.+)\]|(?P<name3>.+),\s(?P<metainfo2>.[^\s]+)|(?P<name4>.+))"
-        regex_check = re.search(regex_string, line, flags=re.IGNORECASE)
-        if regex_check:
-            regex_info = dict(regex_check.groupdict())
-            regex_info = {
-                key[:-1]: value
-                for key, value in regex_info.items()
-                if value is not None
-            }
-            if len(regex_info) > 2:
-                # check for second sensors and adjust their names
-                if regex_info["metainfo"][-1] == "2":
-                    regex_info["name"] = regex_info["name"] + " 2"
-                    regex_info["metainfo"] = regex_info["metainfo"][:-1]
-                    if len(regex_info["metainfo"]) == 0:
-                        regex_info.pop("metainfo")
-            if regex_info["name"] == "flag":
-                regex_info["metainfo"] = regex_info["name"]
-                regex_info["unit"] = regex_info["name"]
-            return regex_info
-        return {}
-
-    def create_dataframe(
-        self,
-        header_info_detail_level: str = "shortname",
-    ) -> pd.DataFrame:
-        """Creates a pandas dataframe by splitting each dataline every 11
-        characters, as SeaBird defines its tables this way.
-
-        Parameters
-        ----------
-        uns_full_header_names: bool:
-            whether to use all header information as dataframe header
-        uns_long_header_names: bool:
-            whether to use header longnames as dataframe header
-
-        Returns
-        -------
-        a pandas.Dataframe that represents the data values inside the cnv file
-
-        """
-        n = 11
-        row_list = []
-        for line in self.data:
-            row_list.append(
-                [
-                    line[i : i + n].split()[0]
-                    for i in range(0, len(line) - n, n)
-                ]
-            )
-        df = pd.DataFrame(row_list, dtype=float)
-        header_names = [
-            metainfo[header_info_detail_level]
-            for metainfo in list(self.data_header_meta_info.values())
-        ]
-        # remove duplicate columns
-        df.drop(labels=self.duplicate_columns, axis=1, inplace=True)
-        self.duplicate_columns = []
-        try:
-            df.columns = header_names
-        except ValueError as error:
-            logger.error(
-                f"Could not set dataframe header for {self.file_name}: {error}"
-            )
-            logger.error(header_names)
-        else:
-            df.meta.metadata = self.data_header_meta_info
-            # df.meta.propagate_metadata_to_series()
-        return df
-
-    def rename_dataframe_header(
-        self,
-        df: pd.DataFrame | None = None,
-        header_detail_level: str = "shortname",
-    ) -> list:
-        df = self.df if df is None else df
-        df.meta.rename(header_detail_level)
-        return [column for column in df.columns]
-
-    def reading_start_time(
-        self,
-        time_source: str = "System UTC",
-    ) -> datetime | None:
-        """
-        Extracts the Cast start time from the metadata header.
-        """
-        for line in self.sbe9_data:
-            if line.startswith(time_source):
-                start_time = line.split("=")[1]
-                start_time = datetime.strptime(
-                    start_time, " %b %d %Y %H:%M:%S "
-                )
-                return start_time
-        return None
-
-    def absolute_time_calculation(self) -> bool:
-        """
-        Replaces the basic cnv time representation of counting relative to the
-        casts start point, by real UTC timestamps.
-        This operation will act directly on the dataframe.
-
-        """
-        time_parameter = None
-        for parameter in self.df.columns:
-            if parameter.lower().startswith("time"):
-                time_parameter = parameter
-        if time_parameter and self.start_time:
-            self.df.meta.add_column(
-                name="datetime",
-                data=[
-                    timedelta(days=float(time)) + self.start_time
-                    if time_parameter == "timeJ"
-                    else timedelta(seconds=float(time)) + self.start_time
-                    for time in self.df[time_parameter]
-                ],
-            )
-            return True
-        return False
-
-    def add_start_time(self) -> bool:
-        """
-        Adds the Cast start time to the dataframe.
-        Necessary for joins on the time.
-        """
-        if self.start_time:
-            self.df.meta.add_column(
-                name="start_time",
-                data=pd.Series([self.start_time for _ in self.data]),
-            )
-            return True
-        return False
-
-    def obtaining_validation_modules(self) -> CnvValidationList:
-        """
-        Collects the individual validation modules and their respective
-        information, usually present in key-value pairs.
-        """
-        validation_modules = self.processing_info
-        return CnvValidationList(validation_modules)
-
-    def df2cnv(
-        self,
-        header_names: list | None = None,
-        header_detail_level: str | None = None,
-    ) -> list:
-        """
-        Parses a pandas dataframe into a list that represents the lines inside
-        of a cnv data table.
-
-        Parameters
-        ----------
-        header_names: list:
-            a list of dataframe columns that will be parsed
-
-        Returns
-        -------
-        a list of lines in the cnv data table format
-
-        """
-        if not header_detail_level:
-            header_detail_level = self.df.meta.header_detail
-        if not header_names:
-            header_names = [
-                header[header_detail_level]
-                for header in list(self.data_header_meta_info.values())
-            ]
-        df = self.df.drop(
-            labels=[
-                column
-                for column in list(self.df.meta.metadata.keys())
-                if column not in header_names
-            ],
-            axis=1,
-            errors="ignore",
-        )
-        cnv_out = []
-        for _, row in df.iterrows():
-            cnv_like_row = "".join(
-                (lambda column: f"{str(column):>11}")(value) for value in row
-            )
-            cnv_out.append(cnv_like_row + "\n")
-        return cnv_out
-
-    def array2cnv(self) -> list:
-        result = []
-        for row in self.parameters.full_data_array:
-            formatted_row = "".join(f"{elem:11}" for elem in row)
-            result.append(formatted_row + "\n")
-        return result
-
-    def to_cnv(
-        self,
-        file_name: Path | str | None = None,
-        use_dataframe: bool = True,
-        header_list: list | None = None,
-    ):
-        """
-        Writes the values inside of this instance as a new cnv file to disc.
-
-        Parameters
-        ----------
-        file_name: Path:
-            the new file name to use for writing
-        use_current_df: bool:
-            whether to use the current dataframe as data table
-        use_current_validation_header: bool:
-            whether to use the current processing module list
-        header_list: list:
-            the data columns to use for the export
-
-        """
-        file_name = self.path_to_file if file_name is None else file_name
-        # content construction
-        if use_dataframe:
-            data = self.df2cnv(header_list)
-        else:
-            data = self.array2cnv()
-        self._update_header()
-        self.file_data = [*self.header, *data]
-        # writing content out
-        try:
-            with open(file_name, "w", encoding="latin-1") as file:
-                for line in self.file_data:
-                    file.write(line)
-
-        except IOError as error:
-            logger.error(f"Could not write cnv file: {error}")
-
-    def _update_header(self):
-        """Re-creates the cnv header."""
-        self.data_table_description = self._form_data_table_info()
-        self.header = [
-            *[f"* {data}" for data in self.sbe9_data[:-1]],
-            *[f"** {data}" for data in self.metadata_list],
-            f"* {self.sbe9_data[-1]}",
-            *[f"# {data}" for data in self.data_table_description],
-            *[f"# {data}" for data in self.sensor_data],
-            *[f"# {data}" for data in self.processing_info],
-            "*END*\n",
-        ]
-
-    def _form_data_table_info(self) -> list:
-        """Recreates the data table descriptions, like column names and spans
-        from the structured dictionaries these values were stored in."""
-        new_table_info = []
-        for key, value in self.data_table_stats.items():
-            new_table_info.append(f"{key} = {value}\n")
-        for index, (name, _) in enumerate(self.data_table_names_and_spans):
-            new_table_info.append(f"name {index} = {name}\n")
-        for index, (_, span) in enumerate(self.data_table_names_and_spans):
-            new_table_info.append(f"span {index} = {span}\n")
-        for key, value in self.data_table_misc.items():
-            new_table_info.append(f"{key} = {value}\n")
-        return new_table_info
-
-    def add_processing_metadata(self, addition: str | list):
-        """
-        Adds new processing lines to the list of processing module information
-
-        Parameters
-        ----------
-        addition: str:
-            the new information line
-
-        """
-        # TODO: use CnvprocessingList here
-        if isinstance(addition, str):
-            addition = [addition]
-        for line in addition:
-            self.file_data.append(line)
-            # add the new info line *before* the 'file_type = ascii' line
-            self.processing_info.insert(-1, line)
-
-    def add_station_and_event_column(self) -> bool:
-        """
-        Adds a column with the DSHIP station and device event numbers to the
-        dataframe. These must be present inside the extra metadata header.
-
-        """
-        try:
-            event_list = [self.metadata["Station"] for _ in self.data]
-        except KeyError:
-            return False
-        else:
-            self.df.meta.add_column(
-                name="Event", data=pd.Series(event_list), location=0
-            )
-            return True
-
-    def add_position_columns(self) -> bool:
-        """
-        Adds a column with the longitude and latitude to the dataframe.
-        These must be present inside the extra metadata header.
-
-        """
-        if ("latitude" or "longitude") in [
-            column["shortname"]
-            for column in list(self.df.meta.metadata.values())
-        ]:
-            return True
-        try:
-            latitude_list = [self.metadata["GPS_Lat"] for _ in self.data]
-            longitude_list = [self.metadata["GPS_Lon"] for _ in self.data]
-        except KeyError:
-            return False
-        else:
-            self.df.meta.add_column(
-                name="Latitude", data=pd.Series(latitude_list), location=1
-            )
-            self.df.meta.add_column(
-                name="Longitude", data=pd.Series(longitude_list), location=2
-            )
-            return True
-
-    def add_cast_number(self, number: int | None = None) -> bool:
-        """
-        Adds a column with the cast number to the dataframe.
-
-        Parameters
-        ----------
-        number: int:
-            the cast number of this files cast
-
-        """
-        if ("Cast" in self.metadata.keys()) and (not number):
-            number = int(self.metadata["Cast"])
-        try:
-            self.df.meta.add_column(
-                name="Cast",
-                data=pd.Series([number for _ in self.data]),
-                location=0,
-            )
-        except ValueError:
-            # Cast is already part of the dataframe, so nothing left to do
-            return False
-        else:
-            return True
-
-
-class BottleLogFile(DataTableFile):
-    """Bottle Log file representation, that extracts the three different data
-    types from the file: reset time and the table with bottle IDs and
-    corresponding data ranges.
-
-    Parameters
-    ----------
-
-    Returns
-    -------
-
-    """
-
-    def __init__(self, path_to_file, create_dataframe=False):
-        super().__init__(path_to_file)
-        self.reset_time = self.obtaining_reset_time()
-        self.origin_cnv = self.raw_file_data[0].strip()
-        self.data = self.data_whitespace_removal()
-
-        if create_dataframe:
-            self.original_df = self.create_dataframe()
-            self.df = self.original_df
-        else:
-            self.data_list = self.create_list()
-
-    def data_whitespace_removal(self) -> list:
-        """Strips the input from whitespace characters, in this case especially
-        newline characters.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        the original data stripped off the whitespaces
-
-        """
-        temp_data = []
-        for line in self.raw_file_data[2:]:
-            temp_data.append(line.strip())
-        return temp_data
-
-    def obtaining_reset_time(self) -> datetime:
-        """Reading reset time with small input check.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        a datetime.datetime object of the device reset time
-
-        """
-
-        regex_check = re.search(
-            r"RESET\s(\w{3}\s\d+\s\d{4}\s\d\d:\d\d:\d\d)",
-            self.raw_file_data[1],
-        )
-        if regex_check:
-            return datetime.strptime(regex_check.group(1), "%b %d %Y %H:%M:%S")
-        else:
-            error_message = """BottleLogFile is not formatted as expected:
-                Reset time could not be extracted."""
-            logger.error(error_message)
-            raise IOError(error_message)
-
-    def create_list(self) -> list:
-        """Creates a list of usable data from the list specified in self.data.
-        the list consists of: an array of ID's representing the bottles, the date and time of the data sample
-        and the lines of the cnv corresponding to the bottles
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        a list representing the bl files table information
-        """
-        content_array = []
-        for i in range(len(self.data)):
-            bottles = [int(x) for x in self.data[i].split(",")[:2]]
-            date = self.convert_date(self.data[i].split(",")[2])
-            lines = tuple([int(x) for x in self.data[i].split(",")[3:]])
-
-            content_array.append([bottles, date, lines])
-
-        return content_array
-
-    def convert_date(self, date: str):
-        """Converts the Dates of the .bl files to an ISO 8601 standard
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        a string with the date in the form of "yymmddThhmmss"
-        """
-        date = date.strip()
-        month_list = [
-            "Jan",
-            "Feb",
-            "Mar",
-            "Apr",
-            "May",
-            "Jun",
-            "Jul",
-            "Aug",
-            "Sep",
-            "Oct",
-            "Nov",
-            "Dec",
-        ]
-
-        month_ind = month_list.index(date.split(" ")[0]) + 1
-        if month_ind < 10:
-            month = "0" + str(month_ind)
-        else:
-            month = str(month_ind)
-        day = date.split(" ")[1]
-        year = (date.split(" ")[2])[2:]
-        time = date.split(" ")[3].replace(":", "")
-        return year + month + day + "T" + time
-
-    def create_dataframe(self) -> pd.DataFrame:
-        """Creates a dataframe from the list specified in self.data.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        a pandas.Dataframe representing the bl files table information
-        """
-        data_lists = []
-        for line in self.data:
-            inner_list = line.split(",")
-            # dropping first column as its the index
-            data_lists.append(inner_list[1:])
-        df = pd.DataFrame(data_lists)
-        df.columns = ["Bottle ID", "Datetime", "start_range", "end_range"]
-        return df
-
-
-class FieldCalibrationFile(DataTableFile):
-    def __init__(self, path_to_file):
-        super().__init__(path_to_file)
-        self.original_df = self.create_dataframe()
-        self.df = self.original_df
-
-    def create_dataframe(self) -> pd.DataFrame:
-        try:
-            return pd.read_csv(self.path_to_file, skiprows=len(self.header))
-        except IOError as error:
-            logger.error(f"Could not read field calibration file: {error}.")
-            return pd.DataFrame()