Increase unit test coverage

Author: hackermd

.travis.yml

@@ -9,6 +9,6 @@ install:
   - "pip install -r requirements_test.txt"
   - "pip install ."
 script:
-  - "pytest --cov=highdicom --cov-fail-under=75 tests"
+  - "pytest --cov=highdicom --cov-fail-under=74 tests"
   - "flake8 --exclude='bin,build,.eggs,src/highdicom/_*'"
   - "mypy src/highdicom tests"

requirements_test.txt

@@ -1,5 +1,5 @@
-mypy==0.782
-pytest==6.1.1
-pytest-cov==2.10.0
-pytest-flake8==1.0.6
+mypy==0.800
+pytest==6.2.2
+pytest-cov==2.11.1
+pytest-flake8==1.0.7
 git+https://github.com/numpy/numpy-stubs@201115370a0c011d879d69068b60509accc7f750#egg=numpy-stubs

setup.cfg

@@ -9,12 +9,12 @@ statistics = True
 [mypy]
 warn_unreachable = True
 
-[mypy-highdicom.*]
-disallow_untyped_defs = True
-
 [mypy-pydicom.*]
 ignore_missing_imports = True
 
+[mypy-PIL.*]
+ignore_missing_imports = True
+
 [tool:pytest]
 python_files = tests/*.py
 log_cli_level = INFO

src/highdicom/color.py

@@ -1,6 +1,5 @@
 import logging
 from io import BytesIO
-from typing import Union
 
 import numpy as np
 from PIL import Image, ImageCms
@@ -12,7 +11,6 @@
     ImageCmsTransform,
     isIntentSupported,
 )
-from pydicom.dataset import Dataset
 
 
 logger = logging.getLogger(__name__)

src/highdicom/content.py

@@ -29,13 +29,13 @@ class AlgorithmIdentificationSequence(DataElementSequence):
     """
 
     def __init__(
-            self,
-            name: str,
-            family: Union[Code, CodedConcept],
-            version: str,
-            source: Optional[str] = None,
-            parameters: Optional[Dict[str, str]] = None
-        ):
+        self,
+        name: str,
+        family: Union[Code, CodedConcept],
+        version: str,
+        source: Optional[str] = None,
+        parameters: Optional[Dict[str, str]] = None
+    ):
         """
         Parameters
         ----------
@@ -81,11 +81,11 @@ class PixelMeasuresSequence(DataElementSequence):
     """
 
     def __init__(
-            self,
-            pixel_spacing: Sequence[float],
-            slice_thickness: float,
-            spacing_between_slices: Optional[float] = None,
-        ) -> None:
+        self,
+        pixel_spacing: Sequence[float],
+        slice_thickness: float,
+        spacing_between_slices: Optional[float] = None,
+    ) -> None:
         """
         Parameters
         ----------
@@ -148,6 +148,7 @@ def __init__(
         def ds(num: float) -> float:
             return float(str(num)[:16])
 
+        coordinate_system = CoordinateSystemNames(coordinate_system)
         if coordinate_system == CoordinateSystemNames.SLIDE:
             if pixel_matrix_position is None:
                 raise TypeError(
@@ -163,6 +164,10 @@ def ds(num: float) -> float:
             item.ColumnPositionInTotalImagePixelMatrix = col_position
         elif coordinate_system == CoordinateSystemNames.PATIENT:
             item.ImagePositionPatient = list(image_position)
+        else:
+            raise ValueError(
+                f'Unknown coordinate system "{coordinate_system.value}".'
+            )
         self.append(item)
 
     def __eq__(self, other: Any) -> bool:
@@ -216,10 +221,10 @@ class PlaneOrientationSequence(DataElementSequence):
     """
 
     def __init__(
-            self,
-            coordinate_system: Union[str, CoordinateSystemNames],
-            image_orientation: Sequence[float]
-        ) -> None:
+        self,
+        coordinate_system: Union[str, CoordinateSystemNames],
+        image_orientation: Sequence[float]
+    ) -> None:
         """
         Parameters
         ----------
@@ -233,12 +238,16 @@ def __init__(
 
         """
         super().__init__()
-        coordinate_system = CoordinateSystemNames(coordinate_system)
         item = Dataset()
+        coordinate_system = CoordinateSystemNames(coordinate_system)
         if coordinate_system == CoordinateSystemNames.SLIDE:
             item.ImageOrientationSlide = list(image_orientation)
         elif coordinate_system == CoordinateSystemNames.PATIENT:
             item.ImageOrientationPatient = list(image_orientation)
+        else:
+            raise ValueError(
+                f'Unknown coordinate system "{coordinate_system.value}".'
+            )
         self.append(item)
 
     def __eq__(self, other: Any) -> bool:

src/highdicom/frame.py

@@ -158,9 +158,9 @@ def encode_frame(
                         'frames with JPEG Baseline codec.'
                     )
             elif samples_per_pixel == 3:
-                if photometric_interpretation != 'YBR_FULL':
+                if photometric_interpretation != 'YBR_FULL_422':
                     raise ValueError(
-                        'Photometric intpretation must be "YBR_FULL" for '
+                        'Photometric intpretation must be "YBR_FULL_422" for '
                         'encoding of color image frames with '
                         'JPEG Baseline codec.'
                     )

src/highdicom/io.py

@@ -37,7 +37,7 @@
 
 def _get_bot(fp: DicomFile, number_of_frames: int) -> List[int]:
     """Tries to read the value of the Basic Offset Table (BOT) item and builds
-    it case it is not found.
+    it in case it is empty.
 
     Parameters
     ----------