Merge pull request #201 from herrmannlab/make_pylibjpeg-libjpeg_optional

Make pylibjpeg-libjpeg optional

Author: CPBridge

.github/workflows/run_unit_tests.yml

@@ -16,6 +16,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.7", "3.8", "3.9", "3.10"]
+        dependencies: [".", "'.[libjpeg]'"]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,7 +28,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install -r requirements_test.txt
-        pip install .
+        pip install ${{ matrix.dependencies }}
     - name: Lint with flake8
       run: |
         flake8 --exclude='bin,build,.eggs,src/highdicom/_*'

docs/installation.rst

@@ -8,7 +8,7 @@ Installation guide
 Requirements
 ------------
 
-* `Python <https://www.python.org/>`_ (version 3.5 or higher)
+* `Python <https://www.python.org/>`_ (version 3.6 or higher)
 * Python package manager `pip <https://pip.pypa.io/en/stable/>`_
 
 .. _installation:
@@ -22,7 +22,22 @@ Pre-build package available at PyPi:
 
     pip install highdicom
 
-Source code available at Github:
+The library relies on the underlying ``pydicom`` package for decoding of pixel
+data, which internally delegates the task to either the ``pillow`` or the
+``pylibjpeg`` packages. Since ``pillow`` is a dependency of *highdicom* and
+will automatically be installed, some transfer syntax can thus be readily
+decoded and encoded (baseline JPEG, JPEG-2000, JPEG-LS). Support for additional
+transfer syntaxes (e.g., lossless JPEG) requires installation of the
+``pylibjpeg`` package as well as the ``pylibjpeg-libjpeg`` and
+``pylibjpeg-openjpeg`` packages. Since ``pylibjpeg-libjpeg`` is licensed under
+a copyleft GPL v3 license, it is not installed by default when you install
+*highdicom*. To install the ``pylibjpeg`` packages along with *highdicom*, use
+
+.. code-block:: none
+
+    pip install highdicom[libjpeg]
+
+Install directly from source code (available on Github):
 
 .. code-block:: none
 

setup.py

@@ -55,8 +55,12 @@ def get_version():
         'numpy>=1.19',
         'pillow>=8.3',
         'pillow-jpls>=1.0',
-        'pylibjpeg>=1.4',
-        'pylibjpeg-libjpeg>=1.3',
-        'pylibjpeg-openjpeg>=1.2',
     ],
+    extras_requires={
+        'libjpeg': [
+            'pylibjpeg>=1.4',
+            'pylibjpeg-libjpeg>=1.3',
+            'pylibjpeg-openjpeg>=1.2'
+        ],
+    },
 )

tests/test_frame.py

@@ -215,6 +215,7 @@ def test_jpeg2000_monochrome(self):
         np.testing.assert_array_equal(frame, decoded_frame)
 
     def test_jpegls_rgb(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 8
         frame = np.ones((16, 32, 3), dtype=np.dtype(f'uint{bits_allocated}'))
         frame *= 255
@@ -244,6 +245,7 @@ def test_jpegls_rgb(self):
         np.testing.assert_array_equal(frame, decoded_frame)
 
     def test_jpegls_monochrome(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 16
         frame = np.zeros((16, 32), dtype=np.dtype(f'uint{bits_allocated}'))
         compressed_frame = encode_frame(

tests/test_pm.py

@@ -584,6 +584,7 @@ def test_multi_frame_sm_image_ushort_encapsulated_jpeg2000(self):
         assert np.array_equal(pmap.pixel_array, pixel_array)
 
     def test_multi_frame_sm_image_ushort_encapsulated_jpegls(self):
+        pytest.importorskip("libjpeg")
         pixel_array = np.random.randint(
             low=0,
             high=2**8,

tests/test_sc.py

@@ -428,6 +428,7 @@ def test_rgb_jpeg2000(self):
         )
 
     def test_monochrome_jpegls(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 16
         photometric_interpretation = 'MONOCHROME2'
         coordinate_system = 'PATIENT'
@@ -455,6 +456,7 @@ def test_monochrome_jpegls(self):
         )
 
     def test_rgb_jpegls(self):
+        pytest.importorskip("libjpeg")
         bits_allocated = 8
         photometric_interpretation = 'YBR_FULL'
         coordinate_system = 'PATIENT'