diff --git a/skimage/morphology/__init__.py b/skimage/morphology/__init__.py index a313f4ca..7d294911 100644 --- a/skimage/morphology/__init__.py +++ b/skimage/morphology/__init__.py @@ -6,6 +6,7 @@ from .selem import (square, rectangle, diamond, disk, cube, octahedron, ball, octagon, star) from .watershed import watershed from ._skeletonize import skeletonize, medial_axis +from .skel import compute_thin_image as compute_thin_image from .convex_hull import convex_hull_image, convex_hull_object from .greyreconstruct import reconstruction from .misc import remove_small_objects, remove_small_holes diff --git a/skimage/morphology/data/3/pngs/1.png b/skimage/morphology/tests/data/3/pngs/1.png similarity index 100% rename from skimage/morphology/data/3/pngs/1.png rename to skimage/morphology/tests/data/3/pngs/1.png diff --git a/skimage/morphology/data/3/pngs/2.png b/skimage/morphology/tests/data/3/pngs/2.png similarity index 100% rename from skimage/morphology/data/3/pngs/2.png rename to skimage/morphology/tests/data/3/pngs/2.png diff --git a/skimage/morphology/data/3/pngs/3.png b/skimage/morphology/tests/data/3/pngs/3.png similarity index 100% rename from skimage/morphology/data/3/pngs/3.png rename to skimage/morphology/tests/data/3/pngs/3.png diff --git a/skimage/morphology/data/3/pngs/5.png b/skimage/morphology/tests/data/3/pngs/5.png similarity index 100% rename from skimage/morphology/data/3/pngs/5.png rename to skimage/morphology/tests/data/3/pngs/5.png diff --git a/skimage/morphology/data/3/pngs/6.png b/skimage/morphology/tests/data/3/pngs/6.png similarity index 100% rename from skimage/morphology/data/3/pngs/6.png rename to skimage/morphology/tests/data/3/pngs/6.png diff --git a/skimage/morphology/data/3/pngs/7.png b/skimage/morphology/tests/data/3/pngs/7.png similarity index 100% rename from skimage/morphology/data/3/pngs/7.png rename to skimage/morphology/tests/data/3/pngs/7.png diff --git a/skimage/morphology/data/3/stack.tif b/skimage/morphology/tests/data/3/stack.tif similarity index 100% rename from skimage/morphology/data/3/stack.tif rename to skimage/morphology/tests/data/3/stack.tif diff --git a/skimage/morphology/data/3/stack_fiji.tif b/skimage/morphology/tests/data/3/stack_fiji.tif similarity index 100% rename from skimage/morphology/data/3/stack_fiji.tif rename to skimage/morphology/tests/data/3/stack_fiji.tif diff --git a/skimage/morphology/data/4/1_fiji.png b/skimage/morphology/tests/data/4/1_fiji.png similarity index 100% rename from skimage/morphology/data/4/1_fiji.png rename to skimage/morphology/tests/data/4/1_fiji.png diff --git a/skimage/morphology/data/4/pngs/1.png b/skimage/morphology/tests/data/4/pngs/1.png similarity index 100% rename from skimage/morphology/data/4/pngs/1.png rename to skimage/morphology/tests/data/4/pngs/1.png diff --git a/skimage/morphology/data/4/pngs/2.png b/skimage/morphology/tests/data/4/pngs/2.png similarity index 100% rename from skimage/morphology/data/4/pngs/2.png rename to skimage/morphology/tests/data/4/pngs/2.png diff --git a/skimage/morphology/data/4/pngs/3.png b/skimage/morphology/tests/data/4/pngs/3.png similarity index 100% rename from skimage/morphology/data/4/pngs/3.png rename to skimage/morphology/tests/data/4/pngs/3.png diff --git a/skimage/morphology/data/4/pngs/4.png b/skimage/morphology/tests/data/4/pngs/4.png similarity index 100% rename from skimage/morphology/data/4/pngs/4.png rename to skimage/morphology/tests/data/4/pngs/4.png diff --git a/skimage/morphology/data/4/pngs/5.png b/skimage/morphology/tests/data/4/pngs/5.png similarity index 100% rename from skimage/morphology/data/4/pngs/5.png rename to skimage/morphology/tests/data/4/pngs/5.png diff --git a/skimage/morphology/data/4/pngs/6.png b/skimage/morphology/tests/data/4/pngs/6.png similarity index 100% rename from skimage/morphology/data/4/pngs/6.png rename to skimage/morphology/tests/data/4/pngs/6.png diff --git a/skimage/morphology/data/4/stack.tif b/skimage/morphology/tests/data/4/stack.tif similarity index 100% rename from skimage/morphology/data/4/stack.tif rename to skimage/morphology/tests/data/4/stack.tif diff --git a/skimage/morphology/data/4/stack_fiji.tif b/skimage/morphology/tests/data/4/stack_fiji.tif similarity index 100% rename from skimage/morphology/data/4/stack_fiji.tif rename to skimage/morphology/tests/data/4/stack_fiji.tif diff --git a/skimage/morphology/data/cross.png b/skimage/morphology/tests/data/cross.png similarity index 100% rename from skimage/morphology/data/cross.png rename to skimage/morphology/tests/data/cross.png diff --git a/skimage/morphology/data/cross.txt b/skimage/morphology/tests/data/cross.txt similarity index 100% rename from skimage/morphology/data/cross.txt rename to skimage/morphology/tests/data/cross.txt diff --git a/skimage/morphology/data/cross_fiji.txt b/skimage/morphology/tests/data/cross_fiji.txt similarity index 100% rename from skimage/morphology/data/cross_fiji.txt rename to skimage/morphology/tests/data/cross_fiji.txt diff --git a/skimage/morphology/data/loop.png b/skimage/morphology/tests/data/loop.png similarity index 100% rename from skimage/morphology/data/loop.png rename to skimage/morphology/tests/data/loop.png diff --git a/skimage/morphology/data/loop.txt b/skimage/morphology/tests/data/loop.txt similarity index 100% rename from skimage/morphology/data/loop.txt rename to skimage/morphology/tests/data/loop.txt diff --git a/skimage/morphology/data/loop_fiji.txt b/skimage/morphology/tests/data/loop_fiji.txt similarity index 100% rename from skimage/morphology/data/loop_fiji.txt rename to skimage/morphology/tests/data/loop_fiji.txt diff --git a/skimage/morphology/data/strip.png b/skimage/morphology/tests/data/strip.png similarity index 100% rename from skimage/morphology/data/strip.png rename to skimage/morphology/tests/data/strip.png diff --git a/skimage/morphology/data/strip.txt b/skimage/morphology/tests/data/strip.txt similarity index 100% rename from skimage/morphology/data/strip.txt rename to skimage/morphology/tests/data/strip.txt diff --git a/skimage/morphology/data/strip_fiji.txt b/skimage/morphology/tests/data/strip_fiji.txt similarity index 100% rename from skimage/morphology/data/strip_fiji.txt rename to skimage/morphology/tests/data/strip_fiji.txt diff --git a/skimage/morphology/data/two-hole.png b/skimage/morphology/tests/data/two-hole.png similarity index 100% rename from skimage/morphology/data/two-hole.png rename to skimage/morphology/tests/data/two-hole.png diff --git a/skimage/morphology/data/two-hole.txt b/skimage/morphology/tests/data/two-hole.txt similarity index 100% rename from skimage/morphology/data/two-hole.txt rename to skimage/morphology/tests/data/two-hole.txt diff --git a/skimage/morphology/data/two-hole_fiji.txt b/skimage/morphology/tests/data/two-hole_fiji.txt similarity index 100% rename from skimage/morphology/data/two-hole_fiji.txt rename to skimage/morphology/tests/data/two-hole_fiji.txt diff --git a/skimage/morphology/test_simple_2d.py b/skimage/morphology/tests/test_skeletonize_3d.py similarity index 75% rename from skimage/morphology/test_simple_2d.py rename to skimage/morphology/tests/test_skeletonize_3d.py index c4a5cd2b..4bd48af7 100644 --- a/skimage/morphology/test_simple_2d.py +++ b/skimage/morphology/tests/test_skeletonize_3d.py @@ -1,11 +1,14 @@ from __future__ import division, print_function, absolute_import +import os + import numpy as np from numpy.testing import assert_equal +import skimage from skimage import io -from skel import compute_thin_image +from skimage.morphology import compute_thin_image import matplotlib.pyplot as plt import matplotlib.ticker as ticker @@ -23,9 +26,18 @@ def test_simple_3d(): yield check_skel_3d, fname +def get_data_path(): + # XXX this is a bad temp hack + return os.path.join(os.path.split(skimage.__file__)[0], + 'morphology', + 'tests', + 'data') + + def check_skel(fname, viz=False): # compute the thin image and compare the result to that of ImageJ - img = np.loadtxt('data/' + fname + '.txt', dtype=np.uint8) + + img = np.loadtxt(os.path.join(get_data_path(), fname+'.txt'), dtype=np.uint8) if viz: ax = _viz(img, **dict(marker='s', color='b', s=99, alpha=0.2)) @@ -38,7 +50,7 @@ def check_skel(fname, viz=False): s=80, alpha=0.7, label='us')) # compare to FIJI - img_f = np.loadtxt('data/' + fname + '_fiji.txt', dtype=np.uint8) + img_f = np.loadtxt(os.path.join(get_data_path(), fname+'_fiji.txt'), dtype=np.uint8) if not viz: # actually compare images @@ -70,8 +82,8 @@ def _viz(img, ax=None, **kwds): def check_skel_3d(fname): - img = io.imread('data/' + fname + '.tif') - img_f = io.imread('data/' + fname + '_fiji.tif') + img = io.imread(os.path.join(get_data_path(), fname+'.tif')) + img_f = io.imread(os.path.join(get_data_path(), fname+'_fiji.tif')) img_s = compute_thin_image(img) assert_equal(img_s, img_f)