seabirdfilehandler 0.5.1__tar.gz → 0.5.2__tar.gz

{seabirdfilehandler-0.5.1 → seabirdfilehandler-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: seabirdfilehandler
-Version: 0.5.1
+Version: 0.5.2
 Summary: Library of parsers to interact with SeaBird CTD files.
 Keywords: CTD,parser,seabird,data
 Author: Emil Michels

{seabirdfilehandler-0.5.1 → seabirdfilehandler-0.5.2}/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 = "0.5.1"
+version = "0.5.2"
 
 [tool.poetry]
 

{seabirdfilehandler-0.5.1 → seabirdfilehandler-0.5.2}/src/seabirdfilehandler/__init__.py

@@ -5,3 +5,4 @@ from .cnvfile import *
 from .xmlfiles import *
 from .validation_modules import *
 from .file_collection import *
+from .geomar_ctd_file_parser import *

seabirdfilehandler-0.5.2/src/seabirdfilehandler/geomar_ctd_file_parser.py

@@ -0,0 +1,80 @@
+from pathlib import Path
+import pandas as pd
+
+
+class GEOMARCTDFile:
+    """
+    A parser to read .ctd files created by the GEOMAR processing software.
+
+    Goes through the file line by line and sorts the individual lines in
+    corresponding lists. That way, data and different types of metadata are
+    structured on a basic level.
+    In general, this parser is meant to stick close to the way the Seabird-
+    Parsers are written.
+    """
+
+    def __init__(
+        self,
+        path_to_file: Path | str,
+        only_header: bool = False,
+        create_dataframe: bool = True,
+    ):
+        self.path_to_file = Path(path_to_file)
+        self.only_header = only_header
+        self.raw_input = []
+        self.metadata = {}
+        self.history = []
+        self.comment = []
+        self.data_header = []
+        self.raw_data = []
+        self.read_file()
+        if create_dataframe:
+            self.create_dataframe()
+
+    def __str__(self) -> str:
+        return "/n".join(self.raw_data)
+
+    def __repr__(self) -> str:
+        return str(self.path_to_file.absolute())
+
+    def __eq__(self, other) -> bool:
+        return self.raw_data == other.raw_data
+
+    def read_file(self):
+        with open(self.path_to_file, "r") as file:
+            past_header = False
+            for line in file:
+                self.raw_input.append(line)
+                if line.startswith("History"):
+                    self.history.append(
+                        line.removeprefix("History  = # GEOMAR").strip()
+                    )
+                elif line.startswith("Comment"):
+                    self.comment.append(
+                        line.removeprefix("Comment  =").strip()
+                    )
+                elif line.startswith("Columns"):
+                    self.data_header = [
+                        column.removeprefix("Columns  =").strip()
+                        for column in line.split(":")
+                    ]
+                    past_header = True
+                    if self.only_header:
+                        break
+                else:
+                    if not past_header:
+                        try:
+                            key, value = line.split("=")
+                        except ValueError:
+                            key = line
+                            value = ""
+                        self.metadata[key.strip()] = value.strip()
+                    else:
+                        self.raw_data.append(line)
+
+    def create_dataframe(self):
+        self.df = pd.DataFrame(
+            [row.split() for row in self.raw_data],
+            dtype=float,
+            columns=self.data_header,
+        )