mirror of
https://github.com/wassname/scikit-image.git
synced 2026-07-27 11:27:08 +08:00
85 lines
2.1 KiB
Python
85 lines
2.1 KiB
Python
from __future__ import division, print_function, absolute_import
|
|
|
|
import numpy as np
|
|
from numpy.testing import assert_equal
|
|
|
|
from skimage import io
|
|
|
|
from skel import compute_thin_image
|
|
|
|
import matplotlib.pyplot as plt
|
|
import matplotlib.ticker as ticker
|
|
|
|
# nose test generators:
|
|
|
|
# 2D images
|
|
def test_simple_2d_images():
|
|
for fname in ("strip", "loop", "cross", "two-hole"):
|
|
yield check_skel, fname
|
|
|
|
# trivial 3D images
|
|
def test_simple_3d():
|
|
for fname in ['3/stack', '4/stack']:
|
|
yield check_skel_3d, fname
|
|
|
|
|
|
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)
|
|
|
|
if viz:
|
|
ax = _viz(img, **dict(marker='s', color='b', s=99, alpha=0.2))
|
|
|
|
# compute
|
|
img1_2d = compute_thin_image(img)
|
|
|
|
if viz:
|
|
ax = _viz(img1_2d, ax, **dict(marker='o', color='r',
|
|
s=80, alpha=0.7, label='us'))
|
|
|
|
# compare to FIJI
|
|
img_f = np.loadtxt('data/' + fname + '_fiji.txt', dtype=np.uint8)
|
|
|
|
if not viz:
|
|
# actually compare images
|
|
assert_equal(img1_2d, img_f)
|
|
else:
|
|
ax = _viz(img_f, ax, **dict(marker='o', color='g', s=45, label='fiji'))
|
|
|
|
ax.legend()
|
|
ax.grid(True)
|
|
|
|
def yformatter(val, pos):
|
|
return int(img.shape[1] - val + 1)
|
|
def xformatter(val, pos):
|
|
return int(val + 1)
|
|
ax.xaxis.set_major_formatter(ticker.FuncFormatter(xformatter))
|
|
ax.yaxis.set_major_formatter(ticker.FuncFormatter(yformatter))
|
|
|
|
plt.show()
|
|
|
|
|
|
def _viz(img, ax=None, **kwds):
|
|
if ax is None:
|
|
import matplotlib.pyplot as plt
|
|
fix, ax = plt.subplots()
|
|
|
|
x, y = np.nonzero(img)
|
|
ax.scatter(y, img.shape[1] - x, **kwds)
|
|
return ax
|
|
|
|
|
|
def check_skel_3d(fname):
|
|
img = io.imread('data/' + fname + '.tif')
|
|
img_f = io.imread('data/' + fname + '_fiji.tif')
|
|
|
|
img_s = compute_thin_image(img)
|
|
assert_equal(img_s, img_f)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
import sys
|
|
if len(sys.argv) < 2:
|
|
sys.exit("Expect an image name from the data/ directory.")
|
|
check_skel(sys.argv[1], True)
|