TST: skel3d: redo 3D test images

Remove ad-hoc images from morphology/tests/data folder.
Add a FIJI generated image to skimage/data.

The image was generated via
>>> img = binary_blobs(32, 0.05, n_dim=3, seed=1234)
>>> img = img.astype(np.uint8)*255
>>> img = img[:-2, ...]

then saved as a sequence of png frames, read into FIJI as an image sequence,
and skeletonized via Plugins -> Skeletonize (2D/3D).
This commit is contained in:
Evgeni Burovski
2016-02-05 12:43:29 +00:00
parent d832739300
commit dc702a83ee
21 changed files with 8 additions and 23 deletions
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@@ -11,7 +11,7 @@ import scipy.ndimage as ndi
import skimage
from skimage import io, draw, data_dir
#from skimage import draw
from skimage.data import binary_blobs
from skimage.util import img_as_ubyte
from skimage.morphology import skeletonize_3d
@@ -162,30 +162,15 @@ def test_two_hole_image():
assert_equal(res, img_f)
# trivial 3D images
def test_simple_3d():
for fname in ['3/stack', '4/stack']:
yield check_skel_3d, fname
# 'slow' test: Bat Cochlea from FIJI collections.
def test_large():
for fname in ['bat/bat-cochlea-volume']:
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_3d(fname):
img = io.imread(os.path.join(get_data_path(), fname + '.tif'))
img_f = io.imread(os.path.join(get_data_path(), fname + '_fiji.tif'))
def test_3d_vs_fiji():
# generate an image with blobs and compate its skeleton to
# the skeleton generated by FIJI
img = binary_blobs(32, 0.05, n_dim=3, seed=1234)
img = img[:-2, ...]
img = img.astype(np.uint8)*255
img_s = skeletonize_3d(img)
img_f = io.imread(os.path.join(data_dir, "_blobs_3d_fiji_skeleton.tif"))
assert_equal(img_s, img_f)