Update deprecated and removed API for skimage 0.19

Renamed circle to disk in v0.17 [1], using footprint in favor of selem
since v0.19 [2], therefore update the minimal requirement.

[1] https://github.com/scikit-image/scikit-image/blob/main/doc/release/release_0.17.rst
[2] https://github.com/scikit-image/scikit-image/releases/tag/v0.19.0

Author: lagru

lectures/00_images_are_arrays.ipynb

@@ -511,13 +511,13 @@
     "green = np.zeros((300, 300))\n",
     "blue = np.zeros((300, 300))\n",
     "\n",
-    "r, c = draw.circle(100, 100, 100)\n",
+    "r, c = draw.disk(center=(100, 100), radius=100)\n",
     "red[r, c] = 1\n",
     "\n",
-    "r, c = draw.circle(100, 200, 100)\n",
+    "r, c = draw.disk(center=(100, 200), radius=100)\n",
     "green[r, c] = 1\n",
     "\n",
-    "r, c = draw.circle(200, 150, 100)\n",
+    "r, c = draw.disk(center=(200, 150), radius=100)\n",
     "blue[r, c] = 1\n",
     "\n",
     "f, axes = plt.subplots(1, 3)\n",

lectures/5_tophat_filters.ipynb

@@ -173,7 +173,7 @@
     }
    ],
    "source": [
-    "image_show(morph.closing(text, selem=morph.rectangle(3,3)))"
+    "image_show(morph.closing(text, footprint=morph.rectangle(3,3)))"
    ]
   },
   {
@@ -218,7 +218,7 @@
     }
    ],
    "source": [
-    "image_show(morph.closing(text, selem=morph.rectangle(31,31)))"
+    "image_show(morph.closing(text, footprint=morph.rectangle(31,31)))"
    ]
   },
   {
@@ -263,7 +263,7 @@
     }
    ],
    "source": [
-    "bth = morph.black_tophat(text, selem=morph.rectangle(31,31))\n",
+    "bth = morph.black_tophat(text, footprint=morph.rectangle(31,31))\n",
     "image_show(bth)"
    ]
   },
@@ -366,7 +366,7 @@
     "elapsed = list()\n",
     "for sz in [3, 11, 31]:\n",
     "   tic=time.perf_counter()\n",
-    "   a = morph.closing(text, selem=morph.rectangle(sz,sz))\n",
+    "   a = morph.closing(text, footprint=morph.rectangle(sz,sz))\n",
     "   elapsed.append(time.perf_counter()-tic)\n",
     "\n",
     "print(elapsed)"
@@ -392,7 +392,7 @@
     "elapsed = list()\n",
     "for sz in [3, 11, 31]:\n",
     "   tic=time.perf_counter()\n",
-    "   a = morph.closing(text, selem=morph.disk(sz))\n",
+    "   a = morph.closing(text, footprint=morph.disk(sz))\n",
     "   elapsed.append(time.perf_counter()-tic)\n",
     "\n",
     "print(elapsed)\n",

lectures/6_watershed_tricks.ipynb

@@ -174,7 +174,7 @@
     "peak_mask = np.zeros_like(smoothed, dtype=bool)\n",
     "peak_mask[tuple(peak_idx.T)] = True\n",
     "# dilate them and label\n",
-    "peak_mask = skimage.morphology.dilation(peak_mask, selem=skimage.morphology.square(11))\n",
+    "peak_mask = skimage.morphology.dilation(peak_mask, footprint=skimage.morphology.square(11))\n",
     "# display\n",
     "peak_overlay = skimage.color.label2rgb(peak_mask, image=smoothed, bg_label=0)\n",
     "a=image_show(peak_overlay)"

lectures/solutions/00_images_are_arrays.ipynb

@@ -133,13 +133,13 @@
     "green = np.zeros((300, 300))\n",
     "blue = np.zeros((300, 300))\n",
     "\n",
-    "r, c = draw.circle(100, 100, 100)\n",
+    "r, c = draw.disk(center=(100, 100), radius=100)\n",
     "red[r, c] = 1\n",
     "\n",
-    "r, c = draw.circle(100, 200, 100)\n",
+    "r, c = draw.disk(center=(100, 200), radius=100)\n",
     "green[r, c] = 1\n",
     "\n",
-    "r, c = draw.circle(200, 150, 100)\n",
+    "r, c = draw.disk(center=(200, 150), radius=100)\n",
     "blue[r, c] = 1\n",
     "\n",
     "f, axes = plt.subplots(1, 3)\n",

requirements.txt

@@ -1,4 +1,4 @@
-scikit-image[data] >= 0.18
+scikit-image[data] >= 0.19
 numpy >= 1.12
 scipy >= 1.0
 matplotlib >= 2.1