seabirdfilehandler 0.5.2__tar.gz → 0.5.3__tar.gz

{seabirdfilehandler-0.5.2 → seabirdfilehandler-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: seabirdfilehandler
-Version: 0.5.2
+Version: 0.5.3
 Summary: Library of parsers to interact with SeaBird CTD files.
 Keywords: CTD,parser,seabird,data
 Author: Emil Michels
@@ -20,9 +20,33 @@ Project-URL: Homepage, https://git.io-warnemuende.de/CTD-Software/SeabirdFileHan
 Project-URL: Repository, https://git.io-warnemuende.de/CTD-Software/SeabirdFileHandler
 Description-Content-Type: text/markdown
 
+# Intro
+
 This is a library for handling the different SeaBird file types. Each file is
 meant to be represented by one object that stores all of its information in a
 structured way. Through the grouping of different data types, more complex
-calculations, visualisations and output forms will be possible inside of those
+calculations, visualisations and output forms are possible inside of those
 objects.
 
+By being able to parse edited data and metadata back to the original file
+format, this package can be used to process data using custom ideas, while
+staying compatible to the original SeaBird software packages. This way, one can
+create new workflows that interchangeably use old and new processing modules.
+One implementation of this idea is the [ctd-processing python package](https://ctd-software.pages.io-warnemuende.de/processing/), also developed at the IOW.
+
+The structured metadata does provide the possibility to leverage the vast
+amounts of information stored inside the extensive metadata header. Sensor data
+and processing information are readily available in intuitive dictionaries.
+
+## Development roadmap
+
+### misc improvements
+
+- refactor processing module handling
+- extend individual parameter information
+- handle duplicate input columns
+
+### visualisation
+
+- write an intuitive visualisation module
+

seabirdfilehandler-0.5.3/README.md

@@ -0,0 +1,29 @@
+# Intro
+
+This is a library for handling the different SeaBird file types. Each file is
+meant to be represented by one object that stores all of its information in a
+structured way. Through the grouping of different data types, more complex
+calculations, visualisations and output forms are possible inside of those
+objects.
+
+By being able to parse edited data and metadata back to the original file
+format, this package can be used to process data using custom ideas, while
+staying compatible to the original SeaBird software packages. This way, one can
+create new workflows that interchangeably use old and new processing modules.
+One implementation of this idea is the [ctd-processing python package](https://ctd-software.pages.io-warnemuende.de/processing/), also developed at the IOW.
+
+The structured metadata does provide the possibility to leverage the vast
+amounts of information stored inside the extensive metadata header. Sensor data
+and processing information are readily available in intuitive dictionaries.
+
+## Development roadmap
+
+### misc improvements
+
+- refactor processing module handling
+- extend individual parameter information
+- handle duplicate input columns
+
+### visualisation
+
+- write an intuitive visualisation module

{seabirdfilehandler-0.5.2 → seabirdfilehandler-0.5.3}/pyproject.toml

@@ -19,7 +19,7 @@ classifiers = [
 urls.homepage = "https://git.io-warnemuende.de/CTD-Software/SeabirdFileHandler"
 urls.repository = "https://git.io-warnemuende.de/CTD-Software/SeabirdFileHandler"
 dynamic = []
-version = "0.5.2"
+version = "0.5.3"
 
 [tool.poetry]
 
@@ -43,6 +43,7 @@ pyment = ">=0.3.3"
 pylint = ">=3.0.2"
 pre-commit = ">=3.6.2"
 tomlkit = ">=0.13.2"
+myst-parser = "^4.0.1"
 
 [tool.pytest.ini_options]
 pythonpath = [".", "src", "src/seabirdfilehandler"]

{seabirdfilehandler-0.5.2 → seabirdfilehandler-0.5.3}/src/seabirdfilehandler/cnvfile.py

@@ -19,21 +19,26 @@ class CnvFile(DataFile):
     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.
+    To achieve that, the metadata header is organized by the parent-class,
+    DataFile, while the data table is extracted by this class. The data
+    representation can be a numpy array or pandas dataframe. The handling of
+    the data is mostly done inside parameters, a representation of the
+    individual measurement parameter data and metadata.
+
+    This class is also able to parse the edited data and metadata back to the
+    original .cnv file format, allowing for custom data processing using this
+    representation, while still being able to use Sea-Birds original software
+    on that output. It also allows to stay comparable with other parsers or
+    methods in general.
 
     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
+    only_header: bool :
+        Whether to stop reading the file after the metadata header.
+    create_dataframe: bool :
+        Whether to create a pandas DataFrame from the data table.
     absolute_time_calculation: bool:
         whether to use a real timestamp instead of the second count
     event_log_column: bool:

{seabirdfilehandler-0.5.2 → seabirdfilehandler-0.5.3}/src/seabirdfilehandler/datafiles.py

@@ -18,15 +18,21 @@ logger = logging.getLogger(__name__)
 
 
 class DataFile:
-    """Collection of methods for the SeaBird files that feature some kind of
-    data table that is represented in a pandas dataframe.
+    """
+    The base class for all Sea-Bird data files, which are .cnv, .btl, and .bl .
+    One instance of this class, or its children, represents one data text file.
+    The different information bits of such a file are structured into individual
+    lists or dictionaries. The data table will be loaded as numpy array and
+    can be converted to a pandas DataFrame. Datatype-specific behavior is
+    implemented in the subclasses.
+
 
     Parameters
     ----------
-
-    Returns
-    -------
-
+    path_to_file: Path | str :
+        The file to the data file.
+    only_header: bool :
+        Whether to stop reading the file after the metadata header.
     """
 
     def __init__(
@@ -66,16 +72,10 @@ class DataFile:
         return self.file_data == other.file_data
 
     def read_file(self):
-        """Reads and structures all the different information present in the
+        """
+        Reads and structures all the different information present in the
         file. Lists and Dictionaries are the data structures of choice. Uses
         basic prefix checking to distinguish different header information.
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-
         """
         past_sensors = False
         with self.path_to_file.open("r", encoding="latin-1") as file:
@@ -109,14 +109,18 @@ class DataFile:
     def sensor_xml_to_flattened_dict(
         self, sensor_data: str
     ) -> list[dict] | dict:
-        """Reads the pure xml sensor input and creates a multilevel dictionary,
+        """
+        Reads the pure xml sensor input and creates a multilevel dictionary,
         dropping the first two dictionaries, as they are single entry only
 
         Parameters
         ----------
+        sensor_data: str:
+            The raw xml sensor data.
 
         Returns
         -------
+        A list of sensor information, which is a structured dict.
 
         """
         full_sensor_dict = xmltodict.parse(sensor_data, process_comments=True)
@@ -153,8 +157,9 @@ class DataFile:
             return tidied_sensor_list
 
     def structure_metadata(self, metadata_list: list) -> dict:
-        """Creates a dictionary to store the metadata that is added by using
-        werums dship API.
+        """
+        Creates a dictionary to store custom metadata, of which Sea-Bird allows
+        12 lines in each file.
 
         Parameters
         ----------
@@ -181,7 +186,8 @@ class DataFile:
         file_name: str | None = None,
         file_type: str = ".csv",
     ) -> Path:
-        """Creates a Path object holding the desired output path.
+        """
+        Creates a Path object holding the desired output path.
 
         Parameters
         ----------
@@ -209,14 +215,13 @@ class DataFile:
         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.
+        """
+        Writes a csv from the given data.
 
         Parameters
         ----------
-        selected_columns : list :
-            a list of columns to include in the csv
-            (Default value = self.df.columns)
+        data: pd.DataFrame | np.ndarray :
+            The source data to use.
         with_header : boolean :
             indicating whether the header shall appear in the output
              (Default value = True)
@@ -246,7 +251,8 @@ class DataFile:
         list_of_columns: list | str,
         df: pd.DataFrame,
     ):
-        """Alters the dataframe to only hold the given columns.
+        """
+        Alters the dataframe to only hold the given columns.
 
         Parameters
         ----------

{seabirdfilehandler-0.5.2 → seabirdfilehandler-0.5.3}/src/seabirdfilehandler/parameter.py

@@ -18,10 +18,10 @@ class Parameters(UserDict):
 
     Parameters
     ----------
-    data: list:
-        The raw data as extraced by SeaBirdFile
-    metadata: list,
-        The raw metadata as extraced by SeaBirdFile
+    data: list
+        The raw data as extraced by DataFile
+    metadata: list
+        The raw metadata as extraced by DataFile
 
     Returns
     -------
@@ -42,6 +42,9 @@ class Parameters(UserDict):
         )
         self.data = self.create_parameter_instances()
 
+    def get_parameter_names(self) -> list[str]:
+        return [parameter["name"] for parameter in self.metadata.values()]
+
     def get_parameter_list(self) -> list[Parameter]:
         """ """
         return list(self.data.values())

seabirdfilehandler-0.5.2/README.md

@@ -1,5 +0,0 @@
-This is a library for handling the different SeaBird file types. Each file is
-meant to be represented by one object that stores all of its information in a
-structured way. Through the grouping of different data types, more complex
-calculations, visualisations and output forms will be possible inside of those
-objects.