Fix optional imports for tests

Author: CPBridge

src/highdicom/frame.py

@@ -3,7 +3,6 @@
 from typing import Optional, Union
 
 import numpy as np
-from openjpeg.utils import encode_array
 from PIL import Image
 from pydicom.dataset import Dataset, FileMetaDataset
 from pydicom.encaps import encapsulate
@@ -313,6 +312,15 @@ def encode_frame(
                         'Array must contain only 0 and 1 for bits_allocated = 1'
                     )
                 array = array.astype(bool)
+
+            try:
+                from openjpeg.utils import encode_array
+            except ModuleNotFoundError:
+                raise ModuleNotFoundError(
+                    "Highdicom requires the pylibjpeg-openjpeg package to compress "
+                    "frames using the JPEG2000Lossless transfer syntax."
+                )
+
             data = encode_array(
                 array,
                 bits_stored=1,

tests/test_frame.py

@@ -25,6 +25,7 @@ def setUp(self):
         )
 
     def test_jpeg_rgb(self):
+        pytest.importorskip("libjpeg")
         filepath = str(self._test_files_dir.joinpath('frame_rgb.jpeg'))
         with open(filepath, 'br') as fp:
             compressed_frame = fp.read()
@@ -70,6 +71,7 @@ def test_jpeg_rgb(self):
         )
 
     def test_jpeg_rgb_empty(self):
+        pytest.importorskip("libjpeg")
         filepath = str(self._test_files_dir.joinpath('frame_rgb_empty.jpeg'))
         with open(filepath, 'br') as fp:
             compressed_frame = fp.read()
@@ -161,6 +163,7 @@ def test_jpeg_monochrome(self):
         assert compressed_frame.endswith(b'\xFF\xD9')
 
     def test_jpeg2000_rgb(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         frame = np.ones((48, 32, 3), dtype=np.dtype(f'uint{bits_allocated}'))
         frame[2:4, 5:30, 0] = 7
@@ -190,6 +193,7 @@ def test_jpeg2000_rgb(self):
         np.testing.assert_allclose(frame, decoded_frame, atol=2)
 
     def test_jpeg2000_monochrome(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         frame = np.zeros((48, 32), dtype=np.dtype(f'uint{bits_allocated}'))
         frame[2:4, 5:30] = 7
@@ -218,6 +222,7 @@ def test_jpeg2000_monochrome(self):
         np.testing.assert_allclose(frame, decoded_frame, atol=2)
 
     def test_jpeg2000lossless_rgb(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         frame = np.ones((48, 32, 3), dtype=np.dtype(f'uint{bits_allocated}'))
         frame *= 255
@@ -247,6 +252,7 @@ def test_jpeg2000lossless_rgb(self):
         np.testing.assert_array_equal(frame, decoded_frame)
 
     def test_jpeg2000lossless_monochrome(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 16
         frame = np.zeros((48, 32), dtype=np.dtype(f'uint{bits_allocated}'))
         compressed_frame = encode_frame(
@@ -274,6 +280,7 @@ def test_jpeg2000lossless_monochrome(self):
         np.testing.assert_array_equal(frame, decoded_frame)
 
     def test_jpeg2000lossless_single_bit(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 1
         frame = np.zeros((48, 32), dtype=np.dtype('uint8'))
         frame[12:45, 3:6] = 1

tests/test_pm.py

@@ -555,6 +555,7 @@ def test_multi_frame_sm_image_ushort_palette_lut(self):
         assert instance.PixelPresentation == 'MONOCHROME'
 
     def test_multi_frame_sm_image_ushort_encapsulated_jpeg2000(self):
+        pytest.importorskip("openjpeg")
         pixel_array = np.random.randint(
             low=0,
             high=2**8,

tests/test_sc.py

@@ -320,6 +320,7 @@ def test_rgb_rle(self):
         )
 
     def test_monochrome_jpeg_baseline(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 8
         photometric_interpretation = 'MONOCHROME2'
         coordinate_system = 'PATIENT'
@@ -349,6 +350,7 @@ def test_monochrome_jpeg_baseline(self):
         )
 
     def test_rgb_jpeg_baseline(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 8
         photometric_interpretation = 'YBR_FULL_422'
         coordinate_system = 'PATIENT'
@@ -376,6 +378,7 @@ def test_rgb_jpeg_baseline(self):
         np.testing.assert_allclose(frame, reread_frame, rtol=1.2)
 
     def test_monochrome_jpeg2000lossless(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         photometric_interpretation = 'MONOCHROME2'
         coordinate_system = 'PATIENT'
@@ -403,6 +406,7 @@ def test_monochrome_jpeg2000lossless(self):
         )
 
     def test_monochrome_jpeg2000(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         photometric_interpretation = 'MONOCHROME2'
         coordinate_system = 'PATIENT'
@@ -431,6 +435,7 @@ def test_monochrome_jpeg2000(self):
         )
 
     def test_rgb_jpeg2000(self):
+        pytest.importorskip("openjpeg")
         bits_allocated = 8
         photometric_interpretation = 'YBR_RCT'
         coordinate_system = 'PATIENT'

tests/test_seg.py

@@ -1641,8 +1641,15 @@ def test_construction_autotile(
 
         transfer_syntax_uids = [
             ExplicitVRLittleEndian,
-            JPEG2000Lossless,
         ]
+        try:
+            import openjpeg  # noqa: F401
+        except ModuleNotFoundError:
+            pass
+        else:
+            transfer_syntax_uids += [
+                JPEG2000Lossless,
+            ]
         if segmentation_type.value == 'FRACTIONAL':
             try:
                 import libjpeg  # noqa: F401
@@ -1749,6 +1756,8 @@ def test_pixel_types_fractional(
         pix_type,
         test_data,
     ):
+        if fractional_transfer_syntax_uid == JPEG2000Lossless:
+            pytest.importorskip("openjpeg")
         if fractional_transfer_syntax_uid == JPEGLSLossless:
             pytest.importorskip("libjpeg")
 
@@ -1907,6 +1916,8 @@ def test_pixel_types_binary(
         pix_type,
         test_data,
     ):
+        if binary_transfer_syntax_uid == JPEG2000Lossless:
+            pytest.importorskip("openjpeg")
         sources, mask = self._tests[test_data]
 
         # Two segments, overlapping