restore opencv-python to a hard dependency (#155)

* restore `opencv-python` to a hard dependency

* add change log entry

.github/workflows/ci.yml

@@ -38,7 +38,6 @@ jobs:
           python-version: '3.11'
         - macos: test-xdist
           python-version: '3.11'
-        - linux: test-opencv-xdist
         - linux: test-cov-xdist
           coverage: 'codecov'
   test_downstream:

CHANGES.rst

@@ -22,6 +22,8 @@ Other
 
 - update minimum version of ``numpy`` to ``1.20`` and add minimum dependency testing to CI [#153]
 
+- restore ``opencv-python`` to a hard dependency [#155]
+
 1.3.4 (2023-02-13)
 ==================
 

pyproject.toml

@@ -15,6 +15,7 @@ dependencies = [
     'astropy >=5.0.4',
     'scipy >=1.6.0',
     'numpy >=1.20',
+    'opencv-python >=4.6.0.66',
 ]
 dynamic = ['version']
 
@@ -35,9 +36,6 @@ test = [
     'pytest-doctestplus',
     'pytest-openfiles >=0.5.0',
 ]
-opencv = [
-    'opencv-python >=4.6.0.66',
-]
 
 [project.urls]
 'repository' = 'https://github.com/spacetelescope/stcal'

src/stcal/jump/jump.py

@@ -3,19 +3,11 @@
 import time
 
 import numpy as np
+import cv2 as cv
 
 from . import constants
 from . import twopoint_difference as twopt
 
-ELLIPSE_PACKAGE = None
-try:
-    import cv2 as cv
-
-    ELLIPSE_PACKAGE = 'opencv-python'
-except (ImportError, ModuleNotFoundError):
-    ELLIPSE_PACKAGE_WARNING = '`opencv-python` must be installed (`pip install stcal[opencv]`) ' \
-                              'in order to use ellipses'
-
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
 
@@ -400,10 +392,7 @@ def extend_snowballs(plane, snowballs, sat_flag, jump_flag, expansion=1.5):
         center = (round(ceny), round(cenx))
         extend_radius = round(jump_radius * expansion)
         color = (0, 0, 4)
-        if ELLIPSE_PACKAGE == 'opencv-python':
-            image = cv.circle(image, center, extend_radius, color, -1)
-        else:
-            raise ModuleNotFoundError(ELLIPSE_PACKAGE_WARNING)
+        image = cv.circle(image, center, extend_radius, color, -1)
         jump_circle = image[:, :, 2]
         saty, satx = np.where(sat_pix == 2)
         jump_circle[saty, satx] = 0
@@ -435,10 +424,7 @@ def extend_ellipses(plane, ellipses, sat_flag, jump_flag, expansion=1.1):
         center = (round(ceny), round(cenx))
         axes = (round(axis1 / 2), round(axis2 / 2))
         color = (0, 0, 4)
-        if ELLIPSE_PACKAGE == 'opencv-python':
-            image = cv.ellipse(image, center, axes, alpha, 0, 360, color, -1)
-        else:
-            raise ModuleNotFoundError(ELLIPSE_PACKAGE_WARNING)
+        image = cv.ellipse(image, center, axes, alpha, 0, 360, color, -1)
         jump_ellipse = image[:, :, 2]
         saty, satx = np.where(sat_pix == 2)
         jump_ellipse[saty, satx] = 0
@@ -450,27 +436,21 @@ def find_circles(dqplane, bitmask, min_area):
     # Using an input DQ plane this routine will find the groups of pixels with at least the minimum
     # area and return a list of the minimum enclosing circle parameters.
     pixels = np.bitwise_and(dqplane, bitmask)
-    if ELLIPSE_PACKAGE == 'opencv-python':
-        contours, hierarchy = cv.findContours(pixels, cv.RETR_EXTERNAL, cv.CHAIN_APPROX_SIMPLE)
-        bigcontours = [con for con in contours if cv.contourArea(con) >= min_area]
-        circles = [cv.minEnclosingCircle(con) for con in bigcontours]
-    else:
-        raise ModuleNotFoundError(ELLIPSE_PACKAGE_WARNING)
+    contours, hierarchy = cv.findContours(pixels, cv.RETR_EXTERNAL, cv.CHAIN_APPROX_SIMPLE)
+    bigcontours = [con for con in contours if cv.contourArea(con) >= min_area]
+    circles = [cv.minEnclosingCircle(con) for con in bigcontours]
     return circles
 
 
 def find_ellipses(dqplane, bitmask, min_area):
     # Using an input DQ plane this routine will find the groups of pixels with at least the minimum
     # area and return a list of the minimum enclosing ellipse parameters.
     pixels = np.bitwise_and(dqplane, bitmask)
-    if ELLIPSE_PACKAGE == 'opencv-python':
-        contours, hierarchy = cv.findContours(pixels, cv.RETR_EXTERNAL, cv.CHAIN_APPROX_SIMPLE)
-        bigcontours = [con for con in contours if cv.contourArea(con) > min_area]
-        # minAreaRect is used becuase fitEllipse requires 5 points and it is possible to have a contour
-        # with just 4 points.
-        ellipses = [cv.minAreaRect(con) for con in bigcontours]
-    else:
-        raise ModuleNotFoundError(ELLIPSE_PACKAGE_WARNING)
+    contours, hierarchy = cv.findContours(pixels, cv.RETR_EXTERNAL, cv.CHAIN_APPROX_SIMPLE)
+    bigcontours = [con for con in contours if cv.contourArea(con) > min_area]
+    # minAreaRect is used becuase fitEllipse requires 5 points and it is possible to have a contour
+    # with just 4 points.
+    ellipses = [cv.minAreaRect(con) for con in bigcontours]
     return ellipses
 
 

tests/test_jump.py

@@ -6,14 +6,6 @@
 
 DQFLAGS = {'JUMP_DET': 4, 'SATURATED': 2, 'DO_NOT_USE': 1}
 
-try:
-    import cv2 as cv # noqa: F401
-
-    OPENCV_INSTALLED = True
-except ImportError:
-    OPENCV_INSTALLED = False
-
-
 @pytest.fixture(scope='function')
 def setup_cube():
     def _cube(ngroups, readnoise=10):
@@ -31,7 +23,6 @@ def _cube(ngroups, readnoise=10):
     return _cube
 
 
-@pytest.mark.xfail(not OPENCV_INSTALLED, reason="`opencv-python` not installed")
 def test_find_simple_circle():
     plane = np.zeros(shape=(5, 5), dtype=np.uint8)
     plane[2, 2] = DQFLAGS['JUMP_DET']
@@ -43,7 +34,6 @@ def test_find_simple_circle():
     assert circle[0][1] == pytest.approx(1.0, 1e-3)
 
 
-@pytest.mark.xfail(not OPENCV_INSTALLED, reason="`opencv-python` not installed")
 def test_find_simple_ellipse():
     plane = np.zeros(shape=(5, 5), dtype=np.uint8)
     plane[2, 2] = DQFLAGS['JUMP_DET']

tox.ini

@@ -44,7 +44,6 @@ commands =
 [testenv]
 description =
     run tests
-    opencv: requiring opencv-python
     jwst: of JWST pipeline
     romancal: of Romancal pipeline
     oldestdeps: with the oldest supported version of key dependencies
@@ -53,7 +52,6 @@ description =
     xdist: using parallel processing
 extras =
     test
-    opencv: opencv
 deps =
     xdist: pytest-xdist
     jwst: jwst[test] @ git+https://github.com/spacetelescope/jwst.git
@@ -78,7 +76,6 @@ commands =
     jwst: --pyargs jwst --ignore-glob=timeconversion --ignore-glob=associations --ignore-glob=*/scripts/* \
     romancal: --pyargs romancal \
     cov: --cov=. --cov-config=pyproject.toml --cov-report=term-missing --cov-report=xml \
-    opencv: -- tests/test_jump.py \
     {posargs}
 
 [testenv:build-docs]