Merge pull request #1365 from jni/future

Add skimage.future package

bento.info

@@ -33,7 +33,8 @@ UseBackends: Waf
 Library:
     Packages:
         skimage, skimage.color, skimage.data, skimage.draw, skimage.exposure,
-        skimage.feature, skimage.filters, skimage.graph, skimage.io,
+        skimage.feature, skimage.filters, skimage.future, skimage.future.graph,
+        skimage.graph, skimage.io,
         skimage.io._plugins, skimage.measure, skimage.morphology,
         skimage.scripts, skimage.restoration, skimage.segmentation,
         skimage.transform, skimage.util
@@ -151,9 +152,9 @@ Library:
     Extension: skimage.feature._hessian_det_appx
         Sources:
             skimage/exposure/_hessian_det_appx.pyx
-    Extension: skimage.graph._ncut_cy
+    Extension: skimage.future.graph._ncut_cy
         Sources:
-            skimage/graph/_ncut_cy.pyx
+            skimage/future/graph/_ncut_cy.pyx
     Extension: skimage.external.tifffile._tifffile
         Sources:
             skimage/external/tifffile/_tifffile.c

doc/examples/plot_ncut.py

@@ -12,7 +12,8 @@ References
        Pattern Analysis and Machine Intelligence,
        IEEE Transactions on, vol. 22, no. 8, pp. 888-905, August 2000.
 """
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 from matplotlib import pyplot as plt
 
 

doc/examples/plot_rag.py

@@ -14,7 +14,7 @@ The example below also shows how to use a custom function to select the larger
 weight instead.
 
 """
-from skimage.graph import rag
+from skimage.future.graph import rag
 import networkx as nx
 from matplotlib import pyplot as plt
 import numpy as np

doc/examples/plot_rag_draw.py

@@ -6,7 +6,8 @@ Drawing Region Adjacency Graphs (RAGs)
 This example constructs a Region Adjacency Graph (RAG) and draws it with
 the `rag_draw` method.
 """
-from skimage import graph, data, segmentation
+from skimage import data, segmentation
+from skimage.future import graph
 from matplotlib import pyplot as plt, colors
 
 

doc/examples/plot_rag_mean_color.py

@@ -9,7 +9,8 @@ difference in mean color. We then join regions with similar mean color.
 
 """
 
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 from matplotlib import pyplot as plt
 
 

doc/examples/plot_rag_merge.py

@@ -10,7 +10,8 @@ until no highly similar region pairs remain.
 
 """
 
-from skimage import graph, data, io, segmentation, color
+from skimage import data, io, segmentation, color
+from skimage.future import graph
 import numpy as np
 
 

skimage/future/__init__.py

@@ -0,0 +1,10 @@
+"""Functionality with an experimental API. Although you can count on the
+functions in this package being around in the future, the API may change with
+any version update **and will not follow the skimage two-version deprecation
+path**. Therefore, use the functions herein with care, and do not use them in
+production code that will depend on updated skimage versions.
+"""
+
+from . import graph
+
+__all__ = ['graph']

skimage/future/graph/__init__.py

@@ -0,0 +1,12 @@
+from .graph_cut import cut_threshold, cut_normalized
+from .rag import rag_mean_color, RAG, draw_rag
+from .graph_merge import merge_hierarchical
+ncut = cut_normalized
+
+__all__ = ['rag_mean_color',
+           'cut_threshold',
+           'cut_normalized',
+           'ncut',
+           'draw_rag',
+           'merge_hierarchical',
+           'RAG']

skimage/future/graph/graph_cut.py

@@ -37,7 +37,8 @@ def cut_threshold(labels, rag, thresh, in_place=True):
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img)
     >>> rag = graph.rag_mean_color(img, labels)
@@ -107,7 +108,8 @@ def cut_normalized(labels, rag, thresh=0.001, num_cuts=10, in_place=True,
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img, compactness=30, n_segments=400)
     >>> rag = graph.rag_mean_color(img, labels, mode='similarity')

skimage/future/graph/rag.py

@@ -14,7 +14,7 @@ import numpy as np
 from scipy.ndimage import filters
 from scipy import ndimage as nd
 import math
-from .. import draw, measure, segmentation, util, color
+from ... import draw, measure, segmentation, util, color
 try:
     from matplotlib import colors
     from matplotlib import cm
@@ -251,7 +251,8 @@ def rag_mean_color(image, labels, connectivity=2, mode='distance',
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.astronaut()
     >>> labels = segmentation.slic(img)
     >>> rag = graph.rag_mean_color(img, labels)
@@ -364,7 +365,8 @@ def draw_rag(labels, rag, img, border_color=None, node_color='#ffff00',
 
     Examples
     --------
-    >>> from skimage import data, graph, segmentation
+    >>> from skimage import data, segmentation
+    >>> from skimage.future import graph
     >>> img = data.coffee()
     >>> labels = segmentation.slic(img)
     >>> g =  graph.rag_mean_color(img, labels)

skimage/future/graph/setup.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+from skimage._build import cython
+import os.path
+
+base_path = os.path.abspath(os.path.dirname(__file__))
+
+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
+
+    config = Configuration('graph', parent_package, top_path)
+    config.add_data_dir('tests')
+
+    # This function tries to create C files from the given .pyx files.  If
+    # it fails, try to build with pre-generated .c files.
+    cython(['_ncut_cy.pyx'], working_path=base_path)
+    config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
+                         include_dirs=[get_numpy_include_dirs()])
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(maintainer='scikit-image Developers',
+          maintainer_email='scikit-image@googlegroups.com',
+          description='Graph-based Image-processing Algorithms',
+          url='https://github.com/scikit-image/scikit-image',
+          license='Modified BSD',
+          **(configuration(top_path='').todict())
+          )

skimage/future/graph/tests/test_rag.py

@@ -1,5 +1,5 @@
 import numpy as np
-from skimage import graph
+from skimage.future import graph
 from skimage._shared.version_requirements import is_installed
 from numpy.testing.decorators import skipif
 from skimage import segmentation

skimage/future/setup.py

@@ -0,0 +1,12 @@
+
+def configuration(parent_package='skimage', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('future', parent_package, top_path)
+    config.add_subpackage('graph')
+    return config
+
+if __name__ == "__main__":
+    from numpy.distutils.core import setup
+
+    config = configuration(top_path='').todict()
+    setup(**config)

skimage/graph/__init__.py

@@ -1,9 +1,5 @@
 from .spath import shortest_path
 from .mcp import MCP, MCP_Geometric, MCP_Connect, MCP_Flexible, route_through_array
-from .graph_cut import cut_threshold, cut_normalized
-from .rag import rag_mean_color, RAG, draw_rag
-from .graph_merge import merge_hierarchical
-ncut = cut_normalized
 
 
 __all__ = ['shortest_path',

skimage/graph/setup.py

@@ -17,7 +17,6 @@ def configuration(parent_package='', top_path=None):
     cython(['_spath.pyx'], working_path=base_path)
     cython(['_mcp.pyx'], working_path=base_path)
     cython(['heap.pyx'], working_path=base_path)
-    cython(['_ncut_cy.pyx'], working_path=base_path)
 
     config.add_extension('_spath', sources=['_spath.c'],
                          include_dirs=[get_numpy_include_dirs()])
@@ -25,8 +24,6 @@ def configuration(parent_package='', top_path=None):
                          include_dirs=[get_numpy_include_dirs()])
     config.add_extension('heap', sources=['heap.c'],
                          include_dirs=[get_numpy_include_dirs()])
-    config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
-                         include_dirs=[get_numpy_include_dirs()])
     return config
 
 if __name__ == '__main__':

skimage/setup.py

@@ -14,6 +14,7 @@ def configuration(parent_package='', top_path=None):
     config.add_subpackage('feature')
     config.add_subpackage('restoration')
     config.add_subpackage('filters')
+    config.add_subpackage('future')
     config.add_subpackage('graph')
     config.add_subpackage('io')
     config.add_subpackage('measure')