PKG add scikit-image package (pyodide#866)

Co-authored-by: Chigozie Nri <[email protected]>

packages/cloudpickle/meta.yaml

@@ -0,0 +1,9 @@
+package:
+  name: cloudpickle
+  version: 1.5.0
+source:
+  sha256: 820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82
+  url: https://files.pythonhosted.org/packages/2b/42/1a742ae7a85e8e15a60696b0519f71db8ee04839fef6007c3859184fbe71/cloudpickle-1.5.0.tar.gz
+test:
+  imports:
+  - cloudpickle

packages/cloudpickle/test_cloudpickle.py

@@ -0,0 +1,21 @@
+def test_cloudpickle(selenium):
+    selenium.load_package("cloudpickle")
+    selenium.run(
+        r"""
+import cloudpickle
+squared = lambda x: x ** 2
+pickled_lambda = cloudpickle.dumps(squared)
+
+import pickle
+new_squared = pickle.loads(pickled_lambda)
+assert new_squared(2) == 4
+
+CONSTANT = 42
+def my_function(data: int) -> int:
+    return data + CONSTANT
+
+pickled_function = cloudpickle.dumps(my_function)
+depickled_function = pickle.loads(pickled_function)
+assert depickled_function(43) == 85
+"""
+    )

packages/pywavelets/meta.yaml

@@ -0,0 +1,16 @@
+package:
+  name: pywavelets
+  version: 1.1.1
+source:
+  sha256: 1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9
+  url: https://files.pythonhosted.org/packages/17/6b/ef989cfb3acff2ea966c5f28a7443ccaec2ee136675dfa0366db2635f78a/PyWavelets-1.1.1.tar.gz
+  patches:
+    - patches/fft.patch
+requirements:
+  run:
+   - numpy
+   - matplotlib
+   - scipy
+test:
+  imports:
+  - pywt

packages/pywavelets/patches/fft.patch

@@ -0,0 +1,13 @@
+This patch can be removed once scipy is updated to >= 0.18
+AttributeError is raised by the absence of next_fast_len
+--- PyWavelets-1.1.1/pywt/_cwt.py.old	2020-12-16 08:19:13.000000000 +0100
++++ PyWavelets-1.1.1/pywt/_cwt.py	2020-12-16 08:20:23.000000000 +0100
+@@ -20,7 +20,7 @@
+         import scipy.fftpack
+         fftmodule = scipy.fftpack
+         next_fast_len = fftmodule.next_fast_len
+-    except ImportError:
++    except (AttributeError, ImportError):
+         fftmodule = np.fft
+
+         # provide a fallback so scipy is an optional requirement

packages/pywavelets/test_pywt.py

@@ -0,0 +1,19 @@
+def test_pywt(selenium):
+    selenium.load_package("pywavelets")
+    selenium.run(
+        r"""
+import pywt
+import numpy as np
+
+def checkit(a,v):
+  assert (np.rint(a) == v).all()
+
+x = [3, 7, 1, 1, -2, 5, 4, 6]
+cA, cD = pywt.dwt(x, 'db2')
+w = pywt.Wavelet('sym3')
+checkit(pywt.idwt(cA, cD, 'db2'),x)
+cA, cD = pywt.dwt(x, wavelet=w, mode='periodization')
+checkit(pywt.idwt(cA, cD, 'sym3', 'symmetric'),[1,1,-2,5])
+checkit(pywt.idwt(cA, cD, 'sym3', 'periodization'),x)
+"""
+    )

packages/scikit-image/meta.yaml

@@ -0,0 +1,21 @@
+package:
+  name: scikit-image
+  version: 0.15.0
+source:
+  patches:
+  - patches/no-openmp.patch
+  - patches/unwrap.patch
+  - patches/preferred_plugins.patch
+  sha256: df111e654b47e5ea456c50553debe4c5ddd97258894c7ad3b7f2f9f10798e053
+  url: https://files.pythonhosted.org/packages/e0/46/ca035f5d7d3414124a3a5ef22cd2e75c0c5149042a668375f1d44eb69f8f/scikit-image-0.15.0.tar.gz
+requirements:
+  run:
+    - numpy
+    - scipy
+    - matplotlib
+    - networkx
+    - pillow
+    - pywavelets
+test:
+  imports:
+  - skimage

packages/scikit-image/patches/no-openmp.patch

@@ -0,0 +1,11 @@
+This patch is integrated upstream in scikit-image 0.18.0
+--- a/setup.py	2019-04-01 22:30:11.000000000 +0000
++++ b/setup.py	2020-12-16 06:21:52.600722138 +0000
+@@ -67,6 +67,7 @@
+ class ConditionalOpenMP(build_ext):
+
+     def can_compile_link(self):
++        return False
+
+         cc = self.compiler
+         fname = 'test.c'

packages/scikit-image/patches/preferred_plugins.patch

@@ -0,0 +1,11 @@
+--- a/skimage/io/manage_plugins.py  2019-03-19 07:17:05.000000000 +0100
++++ b/skimage/io/manage_plugins.py	2020-12-16 12:03:52.000000000 +0100
+@@ -41,7 +41,7 @@
+ # the following preferences.
+ preferred_plugins = {
+     # Default plugins for all types (overridden by specific types below).
+-    'all': ['imageio', 'pil', 'matplotlib', 'qt'],
++    'all': ['pil', 'matplotlib'],
+     'imshow': ['matplotlib'],
+     'imshow_collection': ['matplotlib']
+ }

packages/scikit-image/patches/unwrap.patch

@@ -0,0 +1,115 @@
+This patch is integrated in scikit-image v0.18.0
+diff --git a/skimage/restoration/_unwrap_2d.pyx b/skimage/restoration/_unwrap_2d.pyx
+index ad0dfa2280..8e2d6ee3ae 100644
+--- a/skimage/restoration/_unwrap_2d.pyx
++++ b/skimage/restoration/_unwrap_2d.pyx
+@@ -3,13 +3,17 @@
+ # cython: nonecheck=False
+ # cython: wraparound=False
+
+-cdef extern from *:
+-    void unwrap2D(double* wrapped_image,
+-                  double* unwrapped_image,
+-                  unsigned char* input_mask,
+-                  int image_width, int image_height,
+-                  int wrap_around_x, int wrap_around_y,
+-                  char use_seed, unsigned int seed) nogil
++
++cdef extern from "unwrap_2d_ljmu.h":
++    void unwrap2D(
++            double *wrapped_image,
++            double *UnwrappedImage,
++            unsigned char *input_mask,
++            int image_width, int image_height,
++            int wrap_around_x, int wrap_around_y,
++            char use_seed, unsigned int seed
++            ) nogil
++
+
+ def unwrap_2d(double[:, ::1] image,
+               unsigned char[:, ::1] mask,
+diff --git a/skimage/restoration/_unwrap_3d.pyx b/skimage/restoration/_unwrap_3d.pyx
+index eac50e70fb..2c9bbfbb1d 100644
+--- a/skimage/restoration/_unwrap_3d.pyx
++++ b/skimage/restoration/_unwrap_3d.pyx
+@@ -3,13 +3,18 @@
+ # cython: nonecheck=False
+ # cython: wraparound=False
+
+-cdef extern from *:
+-  void unwrap3D(double* wrapped_volume,
+-                double* unwrapped_volume,
+-                unsigned char* input_mask,
+-                int image_width, int image_height, int volume_depth,
+-                int wrap_around_x, int wrap_around_y, int wrap_around_z,
+-                char use_seed, unsigned int seed) nogil
++
++cdef extern from "unwrap_3d_ljmu.h":
++    void unwrap3D(
++            double *wrapped_volume,
++            double *unwrapped_volume,
++            unsigned char *input_mask,
++            int volume_width, int volume_height, int volume_depth,
++            int wrap_around_x, int wrap_around_y, int wrap_around_z,
++            char use_seed, unsigned int seed
++            ) nogil
++
++
+
+ def unwrap_3d(double[:, :, ::1] image,
+               unsigned char[:, :, ::1] mask,
+diff --git a/skimage/restoration/unwrap_2d_ljmu.c b/skimage/restoration/unwrap_2d_ljmu.c
+index 690a8d7741..ac60a7d98e 100644
+--- a/skimage/restoration/unwrap_2d_ljmu.c
++++ b/skimage/restoration/unwrap_2d_ljmu.c
+@@ -39,6 +39,7 @@
+ #define NOMASK 0
+ #define MASK 1
+
++
+ typedef struct {
+   double mod;
+   int x_connectivity;
+diff --git a/skimage/restoration/unwrap_2d_ljmu.h b/skimage/restoration/unwrap_2d_ljmu.h
+new file mode 100644
+index 0000000000..9b26d808ff
+--- /dev/null
++++ b/skimage/restoration/unwrap_2d_ljmu.h
+@@ -0,0 +1,9 @@
++void unwrap2D(
++        double *wrapped_image,
++        double *UnwrappedImage,
++        unsigned char *input_mask,
++        int image_width, int image_height,
++        int wrap_around_x, int wrap_around_y,
++        char use_seed, unsigned int seed
++        );
++
+diff --git a/skimage/restoration/unwrap_3d_ljmu.c b/skimage/restoration/unwrap_3d_ljmu.c
+index fdd9847ae8..301414cb5e 100644
+--- a/skimage/restoration/unwrap_3d_ljmu.c
++++ b/skimage/restoration/unwrap_3d_ljmu.c
+@@ -40,6 +40,8 @@
+ #define NOMASK 0
+ #define MASK 1
+
++
++
+ typedef struct {
+   double mod;
+   int x_connectivity;
+diff --git a/skimage/restoration/unwrap_3d_ljmu.h b/skimage/restoration/unwrap_3d_ljmu.h
+new file mode 100644
+index 0000000000..8038639073
+--- /dev/null
++++ b/skimage/restoration/unwrap_3d_ljmu.h
+@@ -0,0 +1,9 @@
++void unwrap3D(
++        double *wrapped_volume,
++        double *unwrapped_volume,
++        unsigned char *input_mask,
++        int volume_width, int volume_height, int volume_depth,
++        int wrap_around_x, int wrap_around_y, int wrap_around_z,
++        char use_seed, unsigned int seed
++        );
++

packages/scikit-image/test_skimage.py

@@ -0,0 +1,47 @@
+def test_skimage(selenium):
+    selenium.load_package("scikit-image")
+    selenium.run(
+        r"""
+import numpy as np
+
+from skimage import data
+from skimage import color
+from skimage.util import view_as_blocks
+
+# get astronaut from skimage.data in grayscale
+l = color.rgb2gray(data.astronaut())
+assert l.size == 262144
+assert l.shape == (512,512)
+
+# size of blocks
+block_shape = (4, 4)
+
+# see astronaut as a matrix of blocks (of shape block_shape)
+view = view_as_blocks(l, block_shape)
+assert view.shape == (128, 128, 4, 4)
+
+from skimage.filters import threshold_otsu
+
+to=threshold_otsu(l)
+assert to.hex() == '0x1.8e00000000000p-2'
+
+from skimage.data import astronaut
+from skimage.color import rgb2gray
+from skimage.filters import sobel
+from skimage.segmentation import felzenszwalb, slic, quickshift, watershed
+from skimage.segmentation import mark_boundaries
+from skimage.util import img_as_float
+
+img = img_as_float(astronaut()[::2, ::2])
+
+segments_fz = felzenszwalb(img, scale=100, sigma=0.5, min_size=50)
+segments_slic = slic(img, n_segments=250, compactness=10, sigma=1)
+segments_quick = quickshift(img, kernel_size=3, max_dist=6, ratio=0.5)
+gradient = sobel(rgb2gray(img))
+segments_watershed = watershed(gradient, markers=250, compactness=0.001)
+
+assert len(np.unique(segments_fz)) == 194
+assert len(np.unique(segments_slic)) == 190
+assert len(np.unique(segments_quick)) == 695
+    """
+    )