Enforce ruff/bugbear rule B904

B904 Within an `except` clause, raise exceptions with `raise ... from err` or
     `raise ... from None` to distinguish them from errors in exception handling

bin/create_iods_modules.py

@@ -102,8 +102,8 @@ def _create_modules(directory):
     # https://github.com/innolitics/dicom-standard/tree/master/standard
     try:
         directory = sys.argv[1]
-    except IndexError:
-        raise ValueError('Path to directory must be provided.')
+    except IndexError as e:
+        raise ValueError('Path to directory must be provided.') from e
     if not os.path.exists(directory):
         raise OSError('Path does not exist: "{}"'.format(directory))
     if not os.path.isdir(directory):

src/highdicom/_module_utils.py

@@ -92,8 +92,8 @@ def check_required_attributes(
         for p in base_path:
             try:
                 tree = tree['attributes'][p]
-            except KeyError:
-                raise AttributeError(f"Invalid base path: {base_path}.")
+            except KeyError as e:
+                raise AttributeError(f"Invalid base path: {base_path}.") from e
 
     # Define recursive function
     def check(

src/highdicom/ann/content.py

@@ -111,7 +111,7 @@ def get_values(self, number_of_annotations: int) -> np.ndarray:
                 f'annotation indices: {error}. This may either be due to '
                 'incorrect encoding of the measurements or due to incorrectly '
                 'specified "number_of_annotations".'
-            )
+            ) from error
         return values
 
     @classmethod
@@ -339,11 +339,11 @@ def __init__(
 
         try:
             coordinates = np.concatenate(graphic_data, axis=0)
-        except ValueError:
+        except ValueError as e:
             raise ValueError(
                 'Items of argument "graphic_data" must be arrays with the '
                 'same dimensions.'
-            )
+            ) from e
 
         if coordinates.dtype.kind in ('u', 'i'):
             coordinates = coordinates.astype(np.float32)
@@ -420,8 +420,8 @@ def __init__(
                 )
                 try:
                     measured_values = item.get_values(self.NumberOfAnnotations)
-                except IndexError:
-                    raise ValueError(error_message)
+                except IndexError as e:
+                    raise ValueError(error_message) from e
                 if len(measured_values) != self.NumberOfAnnotations:
                     # This should not occur, but safety first.
                     raise ValueError(error_message)

src/highdicom/color.py

@@ -87,8 +87,8 @@ def __init__(self, icc_profile: bytes):
         """
         try:
             self._icc_transform = self._build_icc_transform(icc_profile)
-        except OSError:
-            raise ValueError('Could not read ICC Profile.')
+        except OSError as e:
+            raise ValueError('Could not read ICC Profile.') from e
 
     def transform_frame(self, array: np.ndarray) -> np.ndarray:
         """Transforms a frame by applying the ICC profile.
@@ -138,8 +138,10 @@ def _build_icc_transform(icc_profile: bytes) -> ImageCmsTransform:
         profile: bytes
         try:
             profile = ImageCmsProfile(BytesIO(icc_profile))
-        except OSError:
-            raise ValueError('Cannot read ICC Profile in image metadata.')
+        except OSError as e:
+            raise ValueError(
+                'Cannot read ICC Profile in image metadata.'
+            ) from e
         name = getProfileName(profile).strip()
         description = getProfileDescription(profile).strip()
         logger.debug(f'found ICC Profile "{name}": "{description}"')

src/highdicom/io.py

@@ -313,12 +313,14 @@ def open(self) -> None:
         if self._fp is None:
             try:
                 self._fp = DicomFile(str(self._filename), mode='rb')
-            except FileNotFoundError:
-                raise FileNotFoundError(f'File not found: "{self._filename}"')
-            except Exception:
+            except FileNotFoundError as e:
+                raise FileNotFoundError(
+                    f'File not found: "{self._filename}"'
+                ) from e
+            except Exception as e:
                 raise OSError(
                     f'Could not open file for reading: "{self._filename}"'
-                )
+                ) from e
         is_little_endian, is_implicit_VR = self._check_file_format(self._fp)
         self._fp.is_little_endian = is_little_endian
         self._fp.is_implicit_VR = is_implicit_VR
@@ -378,7 +380,9 @@ def _read_metadata(self) -> None:
         try:
             metadata = dcmread(self._fp, stop_before_pixels=True)
         except Exception as err:
-            raise OSError(f'DICOM metadata cannot be read from file: "{err}"')
+            raise OSError(
+                f'DICOM metadata cannot be read from file: "{err}"'
+            ) from err
 
         # Cache Transfer Syntax UID, since we need it to decode frame items
         self._transfer_syntax_uid = UID(metadata.file_meta.TransferSyntaxUID)
@@ -392,10 +396,10 @@ def _read_metadata(self) -> None:
         # Determine whether dataset contains a Pixel Data element
         try:
             tag = TupleTag(self._fp.read_tag())
-        except EOFError:
+        except EOFError as e:
             raise ValueError(
                 'Dataset does not represent an image information entity.'
-            )
+            ) from e
         if int(tag) not in _PIXEL_DATA_TAGS:
             raise ValueError(
                 'Dataset does not represent an image information entity.'
@@ -413,7 +417,9 @@ def _read_metadata(self) -> None:
             try:
                 self._basic_offset_table = _get_bot(self._fp, number_of_frames)
             except Exception as err:
-                raise OSError(f'Failed to build Basic Offset Table: "{err}"')
+                raise OSError(
+                    f'Failed to build Basic Offset Table: "{err}"'
+                ) from err
             self._first_frame_offset = self._fp.tell()
         else:
             if self._fp.is_implicit_VR:

src/highdicom/ko/sop.py

@@ -177,11 +177,11 @@ def resolve_reference(self, sop_instance_uid: str) -> Tuple[str, str, str]:
         """
         try:
             return self._reference_lut[sop_instance_uid]
-        except KeyError:
+        except KeyError as e:
             raise ValueError(
                 'Could not find any evidence for SOP Instance UID '
                 f'"{sop_instance_uid}" in KOS document.'
-            )
+            ) from e
 
     @classmethod
     def from_dataset(cls, dataset: Dataset) -> 'KeyObjectSelectionDocument':

src/highdicom/legacy/sop.py

@@ -62,8 +62,10 @@ def _convert_legacy_to_enhanced(
     from highdicom._modules import MODULE_ATTRIBUTE_MAP
     try:
         ref_ds = sf_datasets[0]
-    except IndexError:
-        raise ValueError('No data sets of single-frame legacy images provided.')
+    except IndexError as e:
+        raise ValueError(
+            'No data sets of single-frame legacy images provided.'
+        ) from e
 
     if mf_dataset is None:
         mf_dataset = Dataset()
@@ -455,8 +457,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'MR':
             raise ValueError(
@@ -548,8 +550,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'CT':
             raise ValueError(
@@ -627,8 +629,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'PT':
             raise ValueError(

src/highdicom/pm/sop.py

@@ -456,8 +456,8 @@ def __init__(
             sffg_item.RealWorldValueMappingSequence = real_world_value_mappings
             try:
                 real_world_value_mappings[0]
-            except IndexError:
-                raise TypeError(error_message)
+            except IndexError as e:
+                raise TypeError(error_message) from e
             if not isinstance(
                 real_world_value_mappings[0],
                 RealWorldValueMapping
@@ -479,8 +479,8 @@ def __init__(
             )
             try:
                 real_world_value_mappings[0][0]
-            except IndexError:
-                raise TypeError(error_message)
+            except IndexError as e:
+                raise TypeError(error_message) from e
             if not isinstance(
                 real_world_value_mappings[0][0],
                 RealWorldValueMapping
@@ -700,7 +700,9 @@ def __init__(
                 palette_color_lut_transformation,
                 'PaletteColorLookupTableUID'
             ):
-                self.PaletteColorLookupTableUID = palette_color_lut_transformation.PaletteColorLookupTableUID
+                self.PaletteColorLookupTableUID = (
+                    palette_color_lut_transformation.PaletteColorLookupTableUID
+                )
         else:
             self.PixelPresentation = 'MONOCHROME'
 

src/highdicom/seg/sop.py

@@ -2061,7 +2061,7 @@ def __init__(
                             'Could not determine position of plane '
                             f'#{plane_index} in three dimensional coordinate '
                             f'system based on dimension index values: {error}'
-                        )
+                        ) from error
                 else:
                     dimension_index_values = []
 

src/highdicom/sr/templates.py

@@ -624,11 +624,11 @@ def _get_coded_modality(sop_class_uid: str) -> Code:
     }
     try:
         return sopclass_to_modality_map[sop_class_uid]
-    except KeyError:
+    except KeyError as e:
         raise ValueError(
             'SOP Class UID does not identify a SOP Class '
             'for storage of an image information entity.'
-        )
+        ) from e
 
 
 class Template(ContentSequence):

src/highdicom/sr/utils.py

@@ -138,11 +138,11 @@ def get_coded_name(item: Dataset) -> CodedConcept:
     """
     try:
         name = item.ConceptNameCodeSequence[0]
-    except AttributeError:
+    except AttributeError as e:
         raise AttributeError(
             'Dataset does not contain attribute "ConceptNameCodeSequence" and '
             'thus doesn\'t represent a SR Content Item.'
-        )
+        ) from e
     return CodedConcept.from_dataset(name)
 
 
@@ -162,11 +162,11 @@ def get_coded_value(item: Dataset) -> CodedConcept:
     """
     try:
         value = item.ConceptCodeSequence[0]
-    except AttributeError:
+    except AttributeError as e:
         raise AttributeError(
             'Dataset does not contain attribute "ConceptCodeSequence" and '
             'thus doesn\'t represent a SR Content Item of Value Type CODE.'
-        )
+        ) from e
     return CodedConcept.from_dataset(value)
 
 

src/highdicom/sr/value_types.py

@@ -424,12 +424,12 @@ def index(self, val: ContentItem) -> int:  # type: ignore[override]
         error_message = f'Item "{val.name}" is not in Sequence.'
         try:
             matches = self._lut[val.name]
-        except KeyError:
-            raise ValueError(error_message)
+        except KeyError as e:
+            raise ValueError(error_message) from e
         try:
             index = matches.index(val)
-        except ValueError:
-            raise ValueError(error_message)
+        except ValueError as e:
+            raise ValueError(error_message) from e
         return index
 
     def find(self, name: Union[Code, CodedConcept]) -> 'ContentSequence':
@@ -618,17 +618,17 @@ def _check_dataset(
             )
         try:
             ValueTypeValues(dataset.ValueType)
-        except TypeError:
+        except TypeError as e:
             raise ValueError(
                 f'Item #{index} of sequence is not an SR Content Item '
                 f'because it has unknown Value Type "{dataset.ValueType}":'
                 f'\n{dataset}'
-            )
-        except AttributeError:
+            ) from e
+        except AttributeError as e:
             raise AttributeError(
                 f'Item #{index} of sequence is not an SR Content Item:\n'
                 f'{dataset}'
-            )
+            ) from e
         if not hasattr(dataset, 'RelationshipType') and not is_root and is_sr:
             raise AttributeError(
                 f'Item #{index} of sequence is not a value SR Content Item '