deprecation and python3.9 compatibility

Fafa87 · Aug 19, 2023 · e0432aa · e0432aa
1 parent 9e6357c
commit e0432aa
Show file tree

Hide file tree

Showing 71 changed files with 40 additions and 22 deletions.
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["2.7", "3.8"]
+        python-version: ["2.7", "3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v3

diff --git a/cellstar/core/seeder.py b/cellstar/core/seeder.py
@@ -292,7 +292,7 @@ def __init__(self, size=10):
         self._init_grid()
 
     def _init_grid(self):
-        self._grid = np.empty((self._size_x, self._size_y), dtype=np.object)
+        self._grid = np.empty((self._size_x, self._size_y), dtype=object)
         self._grid.fill([])
 
     def _resize(self, to_x, to_y):

diff --git a/cellstar/parameter_fitting/pf_snake.py b/cellstar/parameter_fitting/pf_snake.py
@@ -11,8 +11,8 @@
 
 random.seed(1)  # make it deterministic
 import numpy as np
-import scipy.ndimage.morphology as morph
-import scipy.ndimage.measurements as measure
+import scipy.ndimage as morph
+import scipy.ndimage as measure
 
 from cellstar.utils.calc_util import to_int
 from cellstar.core.seed import Seed

diff --git a/cellstar/utils/calc_util.py b/cellstar/utils/calc_util.py
@@ -61,7 +61,7 @@ def loop_connected_components(mask):
 
     if mask.sum() > 0:
         labeled = sp_image.label(mask)[0]
-        components = sp_image.measurements.find_objects(labeled)
+        components = sp_image.find_objects(labeled)
         c_fin = [(s[0].stop - s[0].start, s[0].stop - 1) for s in components]
         if len(c_fin) > 1 and mask[0] and mask[-1]:
             c_fin[0] = c_fin[0][0] + c_fin[-1][0], c_fin[0][1]

diff --git a/cellstar/utils/image_util.py b/cellstar/utils/image_util.py
@@ -86,18 +86,18 @@ def image_dilate(image, radius):
              contain_pixel(image.shape, (ys[1] + radius, xs[1] + radius))
     ys, xs = (lp[0], hp[0]), (lp[1], hp[1])
     morphology_element = get_circle_kernel(radius)
-    dilated_part = sp.ndimage.morphology.binary_dilation(image[ys[0]:ys[1], xs[0]:xs[1]], morphology_element)
+    dilated_part = sp.ndimage.binary_dilation(image[ys[0]:ys[1], xs[0]:xs[1]], morphology_element)
     image[ys[0]:ys[1], xs[0]:xs[1]] = dilated_part
     return image
 
 
 def image_dilate_with_element(image, n):
-    return sp.ndimage.morphology.grey_dilation(image, size=(n, n))
+    return sp.ndimage.grey_dilation(image, size=(n, n))
 
 
 def image_erode(image, radius):
     morphology_element = get_circle_kernel(radius)
-    return sp.ndimage.morphology.binary_erosion(image, morphology_element)
+    return sp.ndimage.binary_erosion(image, morphology_element)
 
 
 def fill_foreground_holes(mask, kernel_size, minimal_hole_size, min_cluster_area_scaled, mask_min_radius_scaled):
@@ -159,10 +159,10 @@ def fill_holes(mask, kernel_size, minimal_hole_size):
             else:
                 # shrink components and check if they fell apart
                 # close holes
-                components_slice = sp.ndimage.morphology.binary_closing(components_slice, morphology_element)
+                components_slice = sp.ndimage.binary_closing(components_slice, morphology_element)
 
                 # erode holes
-                components_slice = sp.ndimage.morphology.binary_erosion(components_slice, morphology_element)
+                components_slice = sp.ndimage.binary_erosion(components_slice, morphology_element)
 
                 # don't invade masked pixels
                 components_slice &= np.logical_not(new_mask[slice])

diff --git a/requirements.txt b/requirements.txt
diff --git a/requirements_py27.txt b/requirements_py27.txt
@@ -0,0 +1,6 @@
+numpy==1.16.6
+scipy==1.2.3
+pillow==6.2.2
+matplotlib==2.2.5
+imageio==2.6.1
+pathlib
diff --git a/requirements_py38.txt b/requirements_py38.txt
@@ -0,0 +1,6 @@
+numpy==1.17.5
+scipy==1.5.3
+pillow==6.2.2
+matplotlib==2.2.5
+imageio==2.6.1
+pathlib
diff --git a/requirements_py39.txt b/requirements_py39.txt
@@ -0,0 +1,6 @@
+numpy==1.23.1
+scipy==1.9.0
+pillow==9.2.0
+matplotlib==3.2.2
+imageio==2.21.1
+pathlib
diff --git a/setup.py b/setup.py
@@ -4,9 +4,16 @@
 if sys.version_info[0] == 2:
     numpy_version = "numpy>=1.16"
     scipy_version = "scipy>=1.2.3"
+    pillow_version = "pillow<=6.2.2"
+    matplotlib_version = "matplotlib<=2.2.5"
+    imageio_version = "imageio<=2.6.1"
 else:
     numpy_version = "numpy>=1.17,<=1.23.5"
     scipy_version = "scipy>=1.5.3"
+    pillow_version = "pillow<=9.2"
+    matplotlib_version = "matplotlib>=3.2.2"
+    imageio_version = "imageio>=2.21.1"
+
 
 with open("README.rst") as f:
     long_description = f.read()
@@ -40,6 +47,7 @@ def run(self):
         "Programming Language :: Python :: 2.7",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Image Recognition",
         "Topic :: Scientific/Engineering"
@@ -51,9 +59,9 @@ def run(self):
     install_requires=[
         numpy_version,
         scipy_version,
-        "pillow<=6.2.2",
-        "matplotlib<=2.2.5",
-        "imageio<=2.6.1",
+        pillow_version,
+        matplotlib_version,
+        imageio_version,
         "pathlib"
     ],
     keywords=["brightfield", "yeast", "segmentation", "adapting"],
@@ -68,5 +76,5 @@ def run(self):
         "pytest"
     ],
     url="https://github.com/Fafa87/cellstar",
-    version="2.0.2"
+    version="2.0.3"
 )
diff --git a/tests/expected/rank_fitting/background.tif b/tests/expected/rank_fitting/background.tif
diff --git a/tests/expected/rank_fitting/brighter.tif b/tests/expected/rank_fitting/brighter.tif
diff --git a/tests/expected/rank_fitting/brighter_original.tif b/tests/expected/rank_fitting/brighter_original.tif
diff --git a/tests/expected/rank_fitting/cell_border_mask.tif b/tests/expected/rank_fitting/cell_border_mask.tif
diff --git a/tests/expected/rank_fitting/cell_content_mask.tif b/tests/expected/rank_fitting/cell_content_mask.tif
diff --git a/tests/expected/rank_fitting/darker.tif b/tests/expected/rank_fitting/darker.tif
diff --git a/tests/expected/rank_fitting/darker_original.tif b/tests/expected/rank_fitting/darker_original.tif
diff --git a/tests/expected/rank_fitting/foreground_mask.tif b/tests/expected/rank_fitting/foreground_mask.tif
diff --git a/tests/expected/rank_fitting/image_back_difference.tif b/tests/expected/rank_fitting/image_back_difference.tif
diff --git a/tests/expected/rank_fitting/image_mask.tif b/tests/expected/rank_fitting/image_mask.tif
diff --git a/tests/expected/rank_fitting/seeds_0.png b/tests/expected/rank_fitting/seeds_0.png
diff --git a/tests/expected/rank_fitting/seeds_1.png b/tests/expected/rank_fitting/seeds_1.png
diff --git a/tests/expected/rank_fitting/seeds_2.png b/tests/expected/rank_fitting/seeds_2.png
diff --git a/tests/expected/rank_fitting/seeds_3.png b/tests/expected/rank_fitting/seeds_3.png
diff --git a/tests/expected/rank_fitting/seeds_4.png b/tests/expected/rank_fitting/seeds_4.png
diff --git a/tests/expected/rank_fitting/seeds_5.png b/tests/expected/rank_fitting/seeds_5.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_0.png b/tests/expected/rank_fitting/snakes_rainbow_0.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_1.png b/tests/expected/rank_fitting/snakes_rainbow_1.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_2.png b/tests/expected/rank_fitting/snakes_rainbow_2.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_3.png b/tests/expected/rank_fitting/snakes_rainbow_3.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_4.png b/tests/expected/rank_fitting/snakes_rainbow_4.png
diff --git a/tests/expected/rank_fitting/snakes_rainbow_5.png b/tests/expected/rank_fitting/snakes_rainbow_5.png
diff --git a/tests/expected/sample_brightfield/background.tif b/tests/expected/sample_brightfield/background.tif
diff --git a/tests/expected/sample_brightfield/brighter.tif b/tests/expected/sample_brightfield/brighter.tif
diff --git a/tests/expected/sample_brightfield/brighter_original.tif b/tests/expected/sample_brightfield/brighter_original.tif
diff --git a/tests/expected/sample_brightfield/cell_border_mask.tif b/tests/expected/sample_brightfield/cell_border_mask.tif
diff --git a/tests/expected/sample_brightfield/cell_content_mask.tif b/tests/expected/sample_brightfield/cell_content_mask.tif
diff --git a/tests/expected/sample_brightfield/darker.tif b/tests/expected/sample_brightfield/darker.tif
diff --git a/tests/expected/sample_brightfield/darker_original.tif b/tests/expected/sample_brightfield/darker_original.tif
diff --git a/tests/expected/sample_brightfield/foreground_mask.tif b/tests/expected/sample_brightfield/foreground_mask.tif
diff --git a/tests/expected/sample_brightfield/image_back_difference.tif b/tests/expected/sample_brightfield/image_back_difference.tif
diff --git a/tests/expected/sample_brightfield/image_mask.tif b/tests/expected/sample_brightfield/image_mask.tif
diff --git a/tests/expected/sample_brightfield/seeds_0.png b/tests/expected/sample_brightfield/seeds_0.png
diff --git a/tests/expected/sample_brightfield/seeds_1.png b/tests/expected/sample_brightfield/seeds_1.png
diff --git a/tests/expected/sample_brightfield/seeds_2.png b/tests/expected/sample_brightfield/seeds_2.png
diff --git a/tests/expected/sample_brightfield/seeds_3.png b/tests/expected/sample_brightfield/seeds_3.png
diff --git a/tests/expected/sample_brightfield/segmented.tif b/tests/expected/sample_brightfield/segmented.tif
diff --git a/tests/expected/sample_brightfield/snakes_rainbow_0.png b/tests/expected/sample_brightfield/snakes_rainbow_0.png
diff --git a/tests/expected/sample_brightfield/snakes_rainbow_1.png b/tests/expected/sample_brightfield/snakes_rainbow_1.png
diff --git a/tests/expected/sample_brightfield/snakes_rainbow_2.png b/tests/expected/sample_brightfield/snakes_rainbow_2.png
diff --git a/tests/expected/sample_brightfield/snakes_rainbow_3.png b/tests/expected/sample_brightfield/snakes_rainbow_3.png
diff --git a/tests/expected/synthetic/background.tif b/tests/expected/synthetic/background.tif
diff --git a/tests/expected/synthetic/brighter.tif b/tests/expected/synthetic/brighter.tif
diff --git a/tests/expected/synthetic/brighter_original.tif b/tests/expected/synthetic/brighter_original.tif
diff --git a/tests/expected/synthetic/cell_border_mask.tif b/tests/expected/synthetic/cell_border_mask.tif
diff --git a/tests/expected/synthetic/cell_content_mask.tif b/tests/expected/synthetic/cell_content_mask.tif
diff --git a/tests/expected/synthetic/darker.tif b/tests/expected/synthetic/darker.tif
diff --git a/tests/expected/synthetic/darker_original.tif b/tests/expected/synthetic/darker_original.tif
diff --git a/tests/expected/synthetic/foreground_mask.tif b/tests/expected/synthetic/foreground_mask.tif
diff --git a/tests/expected/synthetic/image_back_difference.tif b/tests/expected/synthetic/image_back_difference.tif
diff --git a/tests/expected/synthetic/image_mask.tif b/tests/expected/synthetic/image_mask.tif
diff --git a/tests/expected/synthetic_3/background.tif b/tests/expected/synthetic_3/background.tif
diff --git a/tests/expected/synthetic_3/brighter.tif b/tests/expected/synthetic_3/brighter.tif
diff --git a/tests/expected/synthetic_3/brighter_original.tif b/tests/expected/synthetic_3/brighter_original.tif
diff --git a/tests/expected/synthetic_3/cell_border_mask.tif b/tests/expected/synthetic_3/cell_border_mask.tif
diff --git a/tests/expected/synthetic_3/cell_content_mask.tif b/tests/expected/synthetic_3/cell_content_mask.tif
diff --git a/tests/expected/synthetic_3/darker.tif b/tests/expected/synthetic_3/darker.tif
diff --git a/tests/expected/synthetic_3/darker_original.tif b/tests/expected/synthetic_3/darker_original.tif
diff --git a/tests/expected/synthetic_3/foreground_mask.tif b/tests/expected/synthetic_3/foreground_mask.tif
diff --git a/tests/expected/synthetic_3/image_back_difference.tif b/tests/expected/synthetic_3/image_back_difference.tif
diff --git a/tests/expected/synthetic_3/image_mask.tif b/tests/expected/synthetic_3/image_mask.tif