added typing information to module parameters

sensospot_data/parameters.py

@@ -3,8 +3,9 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-from pathlib import Path
-from collections import namedtuple
+import pathlib
+from typing import Any, Dict, Union, Optional
+from xml.etree.ElementTree import Element as ElementType
 
 import numpy
 import pandas
@@ -12,11 +13,12 @@ from defusedxml import ElementTree
 
 from . import columns
 
+PathLike = Union[str, pathlib.Path]
 
 
-def _search_measurement_params_file(folder):
+def _search_params_file(folder: PathLike) -> Optional[PathLike]:
     """searches for a exposure settings file in a folder"""
-    folder_path = Path(folder)
+    folder_path = pathlib.Path(folder)
     params_folder = folder_path / "Parameters"
     if not params_folder.is_dir():
         return None
@@ -27,7 +29,7 @@ def _search_measurement_params_file(folder):
         return None
 
 
-def _get_channel_data(channel_node):
+def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
     # child.tag == "ChannelConfig1"
     exposure_id = int(channel_node.tag[-1])
     # channel_description == "[Cy3|Cy5] Green"
@@ -42,24 +44,26 @@ def _get_channel_data(channel_node):
     }
 
 
-def _parse_measurement_params(params_file):
+def _parse_measurement_params(params_file: PathLike) -> pandas.DataFrame:
     """parses the cannel informations from a settings file"""
-    file_path = Path(params_file)
+    file_path = pathlib.Path(params_file)
     with file_path.open("r") as file_handle:
         tree = ElementTree.parse(file_handle)
         data = [_get_channel_data(child) for child in tree.find("Channels")]
     return pandas.DataFrame(data)
 
 
-def get_measurement_params(folder):
+def get_measurement_params(folder: PathLike) -> Optional[pandas.DataFrame]:
     """returns measurement parameters"""
-    params_file = _search_measurement_params_file(folder)
+    params_file = _search_params_file(folder)
     if params_file is not None:
         return _parse_measurement_params(params_file)
     return None
 
 
-def add_optional_measurement_parameters(data_frame, folder):
+def add_measurement_parameters(
+    data_frame: pandas.DataFrame, folder: PathLike
+) -> pandas.DataFrame:
     """adds measurement params to the data frame, if they could be parsed"""
     params = get_measurement_params(folder)
     if params is not None:
@@ -67,7 +71,7 @@ def add_optional_measurement_parameters(data_frame, folder):
         data_exposures = data_frame[columns.EXPOSURE_ID].unique()
         if set(data_exposures) == set(params_exposures):
             return data_frame.merge(params, how="left", on=columns.EXPOSURE_ID)
-    
+
     # only executing if the parameters were not merged to the data frame
     data_frame[columns.PARAMETERS_CHANNEL] = numpy.nan
     data_frame[columns.PARAMETERS_TIME] = numpy.nan

sensospot_data/parser.py

@@ -10,8 +10,7 @@ from collections import namedtuple
 import pandas
 
 from . import columns
-from .parameters import add_optional_measurement_parameters
-
+from .parameters import add_measurement_parameters
 
 REGEX_WELL = re.compile(
     r"""
@@ -146,7 +145,7 @@ def parse_folder(folder, quiet=False):
         data_frame = parse_multiple_files(file_list)
     except ValueError:
         raise ValueError(f"No sensospot data found in folder '{folder}'")
-    data_frame = add_optional_measurement_parameters(data_frame, folder_path)
+    data_frame = add_measurement_parameters(data_frame, folder_path)
     if quiet:
         return data_frame
     return _sanity_check(data_frame)

tests/test_parameters.py

@@ -1,54 +1,51 @@
 import pandas
+
 from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS
 
 
-def test_search_measurement_params_file_ok(example_dir):
-    from sensospot_data.parameters import _search_measurement_params_file
+def test_search_params_file_ok(example_dir):
+    from sensospot_data.parameters import _search_params_file
 
-    result = _search_measurement_params_file(
-        example_dir / EXAMPLE_DIR_WITH_PARAMS
-    )
+    result = _search_params_file(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
     assert result.suffix == ".svexp"
 
 
-def test_search_measurement_params_file_no_parameters_folder(example_dir):
-    from sensospot_data.parameters import _search_measurement_params_file
+def test_search_params_file_no_parameters_folder(example_dir):
+    from sensospot_data.parameters import _search_params_file
 
-    result = _search_measurement_params_file(
-        example_dir / EXAMPLE_DIR_WO_PARAMS
-    )
+    result = _search_params_file(example_dir / EXAMPLE_DIR_WO_PARAMS)
 
     assert result is None
 
 
 def test_ssearch_measurement_params_file_parameters_file(tmpdir):
-    from sensospot_data.parameters import _search_measurement_params_file
+    from sensospot_data.parameters import _search_params_file
 
     params_dir = tmpdir / "Parameters"
     params_dir.mkdir()
 
-    result = _search_measurement_params_file(tmpdir)
+    result = _search_params_file(tmpdir)
 
     assert result is None
 
 
 def test_parse_channel_info(example_dir):
     from sensospot_data.parameters import (
+        _search_params_file,
         _parse_measurement_params,
-        _search_measurement_params_file,
     )
 
-    params = _search_measurement_params_file(
-        example_dir / EXAMPLE_DIR_WITH_PARAMS
-    )
+    params = _search_params_file(example_dir / EXAMPLE_DIR_WITH_PARAMS)
     result = _parse_measurement_params(params)
 
-    expected = pandas.DataFrame({
-        "Exposure.Id": [1,2,3],
-        "Parameters.Channel": ["green", "red", "red"],
-        "Parameters.Time" : [100.0, 150.0, 15.0]
-    })
+    expected = pandas.DataFrame(
+        {
+            "Exposure.Id": [1, 2, 3],
+            "Parameters.Channel": ["green", "red", "red"],
+            "Parameters.Time": [100.0, 150.0, 15.0],
+        }
+    )
 
     assert result.equals(expected)
 
@@ -58,12 +55,14 @@ def test_get_measurement_params_file_found(example_dir):
 
     result = get_measurement_params(example_dir / EXAMPLE_DIR_WITH_PARAMS)
 
-    expected = pandas.DataFrame({
-        "Exposure.Id": [1,2,3],
-        "Parameters.Channel": ["green", "red", "red"],
-        "Parameters.Time" : [100.0, 150.0, 15.0]
-    })
-    
+    expected = pandas.DataFrame(
+        {
+            "Exposure.Id": [1, 2, 3],
+            "Parameters.Channel": ["green", "red", "red"],
+            "Parameters.Time": [100.0, 150.0, 15.0],
+        }
+    )
+
     assert result.equals(expected)
 
 
@@ -75,13 +74,11 @@ def test_get_measurement_params_file_not_found(example_dir):
     assert result is None
 
 
-def test_add_optional_measurement_parameters_with_params_file(
-    exposure_df, example_dir
-):
-    from sensospot_data.parameters import add_optional_measurement_parameters
+def test_add_measurement_parameters_with_params_file(exposure_df, example_dir):
+    from sensospot_data.parameters import add_measurement_parameters
 
     folder = example_dir / EXAMPLE_DIR_WITH_PARAMS
-    exposure_df = add_optional_measurement_parameters(exposure_df, folder)
+    exposure_df = add_measurement_parameters(exposure_df, folder)
 
     expected = [(1, "green", 100), (2, "red", 150), (3, "red", 15)]
     for exposure_id, channel, time in expected:
@@ -91,18 +88,16 @@ def test_add_optional_measurement_parameters_with_params_file(
         assert example_row["Parameters.Time"] == time
 
 
-def test_add_optional_measurement_parameters_without_params_file(
+def test_add_measurement_parameters_without_params_file(
     exposure_df, example_dir
 ):
-    from sensospot_data.parameters import add_optional_measurement_parameters
+    from sensospot_data.parameters import add_measurement_parameters
 
     folder = example_dir / EXAMPLE_DIR_WO_PARAMS
-    exposure_df = add_optional_measurement_parameters(exposure_df, folder)
+    exposure_df = add_measurement_parameters(exposure_df, folder)
 
     for exposure_id in range(1, 4):
         mask = exposure_df["Exposure.Id"] == exposure_id
         one_exposure_data_frame = exposure_df.loc[mask]
         assert one_exposure_data_frame["Parameters.Channel"].hasnans
         assert one_exposure_data_frame["Parameters.Time"].hasnans
-
-