Merge pull request #70 from lagru/update-to-0-19

WIP: Update notebooks for EuroSciPy 2022

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/3_morphological_operations.ipynb

@@ -86,7 +86,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "skdemo.imshow_all(image, morphology.erosion(image, sq), shape=(1, 2))"
+    "skdemo.imshow_all(image, morphology.erosion(image, sq))"
    ]
   },
   {

lectures/4_segmentation.ipynb

@@ -338,7 +338,7 @@
     "indices = draw.circle_perimeter(100, 220, 25)\n",
     "\n",
     "astronaut_labels[indices] = 1\n",
-    "astronaut_labels[points[:, 1].astype(np.int), points[:, 0].astype(np.int)] = 2\n",
+    "astronaut_labels[points[:, 1].astype(int), points[:, 0].astype(int)] = 2\n",
     "\n",
     "image_show(astronaut_labels);"
    ]

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/skdemo/_skdemo.py

@@ -42,30 +42,39 @@ def imshow_rgb_shifted(rgb_image, shift=100, ax=None):
     ax.set_axis_off()
 
 
-def imshow_all(*images, **kwargs):
+def imshow_all(
+    *images, limits='image', titles=None, shape=None, size=5, **kwargs
+):
     """ Plot a series of images side-by-side.
 
     Convert all images to float so that images have a common intensity range.
 
     Parameters
     ----------
-    limits : str
+    images : tuple
+        The images to plot.
+    limits : 'image' or 'dtype', optional
         Control the intensity limits. By default, 'image' is used set the
         min/max intensities to the min/max of all images. Setting `limits` to
         'dtype' can also be used if you want to preserve the image exposure.
     titles : list of str
         Titles for subplots. If the length of titles is less than the number
         of images, empty strings are appended.
+    shape : tuple, optional
+        A two-element tuple that defines the shape of the subfigure grid as
+        (rows, columns). If not given, all `ìmages` are shown in a single row.
+    size : int, optional
+        Width and height of each subplot in inches.
     kwargs : dict
         Additional keyword-arguments passed to `imshow`.
     """
     images = [img_as_float(img) for img in images]
 
-    titles = kwargs.pop('titles', [])
+    if titles is None:
+        titles = []
     if len(titles) != len(images):
         titles = list(titles) + [''] * (len(images) - len(titles))
 
-    limits = kwargs.pop('limits', 'image')
     if limits == 'image':
         kwargs.setdefault('vmin', min(img.min() for img in images))
         kwargs.setdefault('vmax', max(img.max() for img in images))
@@ -74,13 +83,13 @@ def imshow_all(*images, **kwargs):
         kwargs.setdefault('vmin', vmin)
         kwargs.setdefault('vmax', vmax)
 
-    nrows, ncols = kwargs.get('shape', (1, len(images)))
+    if shape is None:
+        shape = (1, len(images))
+    nrows, ncols = shape
 
-    size = nrows * kwargs.pop('size', 5)
-    width = size * len(images)
-    if nrows > 1:
-        width /= nrows * 1.33
-    fig, axes = plt.subplots(nrows=nrows, ncols=ncols, figsize=(width, size))
+    height = nrows * size
+    width = ncols * size
+    fig, axes = plt.subplots(nrows=nrows, ncols=ncols, figsize=(width, height))
     for ax, img, label in zip(axes.ravel(), images, titles):
         ax.imshow(img, **kwargs)
         ax.set_title(label)

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",

lectures/solutions/1_image_filters.ipynb

@@ -2526,7 +2526,7 @@
     "* [Rank filters example](http://scikit-image.org/docs/dev/auto_examples/applications/plot_rank_filters.html)\n",
     "* [Restoration API](http://scikit-image.org/docs/stable/api/skimage.restoration.html)\n",
     "\n",
-    "Take a look at this [neat feature](https://github.com/scikit-image/scikit-image/pull/2647) merged last year:\n",
+    "Take a look at this [neat feature](https://github.com/scikit-image/scikit-image/pull/2647):\n",
     "\n",
     "![cycle spinning](../images/cycle_spin.png)"
    ]

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