update linter config and resolve lint and pylint errors

pyproject.toml

@@ -139,7 +139,9 @@ extend-select = [
 ignore = [
   "PLR09",    # Too many <...>
   "PLR2004",  # Magic value used in comparison
-  "ISC001",   # Conflicts with formatter
+  "ISC001",   # Conflicts with formatter,
+  "EM101",    # Exception must not use a string literal, assign to variable first
+  "EM102",    # Exception must not use an f-string literal, assign to variable first
 ]
 isort.required-imports = ["from __future__ import annotations"]
 # Uncomment if using a _compat.typing backport
@@ -162,4 +164,5 @@ messages_control.disable = [
   "missing-module-docstring",
   "missing-function-docstring",
   "wrong-import-position",
+  "C0103",                        # Attribute name doesn't conform to snake_case naming style
 ]

src/pydcmqi/segimage.py

@@ -17,9 +17,9 @@
 
 
 def get_min_max_values(image: sitk.Image) -> tuple[float, float]:
-    filter = sitk.MinimumMaximumImageFilter()
-    filter.Execute(image)
-    return filter.GetMinimum(), filter.GetMaximum()
+    sitk_filter = sitk.MinimumMaximumImageFilter()
+    sitk_filter.Execute(image)
+    return sitk_filter.GetMinimum(), sitk_filter.GetMaximum()
 
 
 def _path(path: str | Path) -> Path:
@@ -122,7 +122,24 @@ class SegmentData:
     """
 
     def __init__(self) -> None:
-        self._data: SegmentDict = {}
+        self._data: SegmentDict = {
+            "labelID": 0,
+            "SegmentLabel": "",
+            "SegmentDescription": "",
+            "SegmentAlgorithmName": "",
+            "SegmentAlgorithmType": "",
+            "recommendedDisplayRGBValue": [0, 0, 0],
+            "SegmentedPropertyCategoryCodeSequence": {
+                "CodeMeaning": "",
+                "CodeValue": "",
+                "CodingSchemeDesignator": "",
+            },
+            "SegmentedPropertyTypeCodeSequence": {
+                "CodeMeaning": "",
+                "CodeValue": "",
+                "CodingSchemeDesignator": "",
+            },
+        }
 
     def setConfigData(self, config: dict) -> None:
         self._data = config.copy()
@@ -319,6 +336,10 @@ def hasAnatomicRegionModifier(self) -> bool:
 
 
 class Segment:
+    """
+    A class to store and manipulate the data for a segmentation or region of interest.
+    """
+
     def __init__(self) -> None:
         self.path: Path | None = None
         self.data = SegmentData()
@@ -426,6 +447,10 @@ def saveAsBinary(self, path: str | Path) -> None:
 
 
 class SegImageData:
+    """
+    A class to store and manipulate the data for a segmentation or region of interest.
+    """
+
     def __init__(self) -> None:
         self._data: SegImageDict = {}
 
@@ -511,6 +536,10 @@ def asdict(self) -> SegImageDict:
 
 
 class SegImageFiles:
+    """
+    A class to store and manipulate the file paths for a segmentation or region of interest.
+    """
+
     def __init__(self) -> None:
         self._dicomseg: Path | None = None
         self._config: Path | None = None
@@ -525,6 +554,10 @@ def config(self) -> Path | None:
 
 
 class SegImage:
+    """
+    A class to store and manipulate the data for a segmentation or region of interest.
+    """
+
     verbose: bool = False
 
     @classmethod
@@ -563,7 +596,7 @@ def load(
         dicomseg_file: Path | str,
         output_dir: Path | str | None = None,
     ) -> bool:
-        print(f"Converting file: {dicomseg_file} into {output_dir}.")
+        # print(f"Converting file: {dicomseg_file} into {output_dir}.") # TODO: use logging
 
         # we create a temporary output directory if none is provided in the specified tmp dir
         if output_dir is None:
@@ -594,7 +627,7 @@ def load(
         self._import(output_dir)
 
         # update file paths
-        self.files._dicomseg = dicomseg_file
+        self.files._dicomseg = dicomseg_file  # pylint: disable=W0212
 
     def _import(
         self, output_dir: Path, disable_file_sanity_checks: bool = False
@@ -610,7 +643,7 @@ def _import(
         config_file = output_dir / "pydcmqi-meta.json"
 
         # load the config file
-        with Path.open(config_file) as f:
+        with Path.open(config_file, encoding="utf-8") as f:
             self._config = json.load(f)
 
         # load data
@@ -635,7 +668,7 @@ def _import(
         self.loaded = True
 
         # store file paths
-        self.files._config = config_file
+        self.files._config = config_file  # pylint: disable=W0212
 
     def write(
         self,
@@ -678,11 +711,11 @@ def write(
 
         # store in the output directory
         # but for now just print
-        print(json.dumps(config, indent=2))
+        # print(json.dumps(config, indent=2)) # TODO: use logging
 
         # store in _debug_test_meta.json
         meta_tmp_file = Path(self.tmp_dir) / "_debug_test_meta.json"
-        with Path.open(meta_tmp_file, "w") as f:
+        with Path.open(meta_tmp_file, "w", encoding="utf-8") as f:
             json.dump(config, f, indent=2)
 
         # export config file if requested

src/pydcmqi/types.py

@@ -4,12 +4,20 @@
 
 
 class TripletDict(TypedDict):
+    """
+    A dictionary defining the keys for any generic triplet.
+    """
+
     CodeMeaning: str
     CodeValue: str
     CodingSchemeDesignator: str
 
 
 class SegmentDict(TypedDict):
+    """
+    A dictionary defining the keys for a single segment within a segmentation image.
+    """
+
     labelID: int
     SegmentLabel: str
     SegmentDescription: str
@@ -21,6 +29,10 @@ class SegmentDict(TypedDict):
 
 
 class SegImageDict(TypedDict):
+    """
+    A dictionary defining the keys for a segmentation image.
+    """
+
     BodyPartExamined: str
     ClinicalTrialCoordinatingCenterName: str
     ClinicalTrialSeriesID: str

tests/test_segimage.py

@@ -168,7 +168,10 @@ def test_tmp_dir(self):
         assert isinstance(segimg4.tmp_dir, Path)
 
         # specifying a tmp_dir with e.g. a numeric type will raise an ValueError
-        with pytest.raises(ValueError):
+        with pytest.raises(
+            ValueError,
+            match="Invalid tmp_dir, must be either None for default, a Path or a string.",
+        ):
             _ = SegImage(tmp_dir=1)