I copied the examples code into a Jupyter Notebook and ran it. The exact code sitting in Jupyter (Python 3) is below:
import os
import logging
import time
import numpy as np
from imageio import imread
import matplotlib
from matplotlib import pyplot as plt
import morphsnakes as ms
# in case you are running on machine without display, e.g. server
if os.environ.get('DISPLAY', '') == '':
logging.warning('No display found. Using non-interactive Agg backend.')
matplotlib.use('Agg')
PATH_IMG_NODULE = 'morphsnakes-master/images/mama07ORI.bmp'
PATH_IMG_STARFISH = 'morphsnakes-master/images/seastar2.png'
PATH_IMG_LAKES = 'morphsnakes-master/images/lakes3.jpg'
PATH_IMG_CAMERA = 'morphsnakes-master/images/camera.png'
PATH_IMG_COINS = 'morphsnakes-master/images/coins.png'
PATH_ARRAY_CONFOCAL = 'morphsnakes-master/images/confocal.npy'
def visual_callback_2d(background, fig=None):
"""
Returns a callback than can be passed as the argument `iter_callback`
of `morphological_geodesic_active_contour` and
`morphological_chan_vese` for visualizing the evolution
of the levelsets. Only works for 2D images.
Parameters
----------
background : (M, N) array
Image to be plotted as the background of the visual evolution.
fig : matplotlib.figure.Figure
Figure where results will be drawn. If not given, a new figure
will be created.
Returns
-------
callback : Python function
A function that receives a levelset and updates the current plot
accordingly. This can be passed as the `iter_callback` argument of
`morphological_geodesic_active_contour` and
`morphological_chan_vese`.
"""
# Prepare the visual environment.
if fig is None:
fig = plt.figure()
fig.clf()
ax1 = fig.add_subplot(1, 2, 1)
ax1.imshow(background, cmap=plt.cm.gray)
ax2 = fig.add_subplot(1, 2, 2)
ax_u = ax2.imshow(np.zeros_like(background), vmin=0, vmax=1)
plt.pause(0.001)
def callback(levelset):
if ax1.collections:
del ax1.collections[0]
ax1.contour(levelset, [0.5], colors='r')
ax_u.set_data(levelset)
fig.canvas.draw()
plt.pause(0.001)
return callback
def visual_callback_3d(fig=None, plot_each=1):
"""
Returns a callback than can be passed as the argument `iter_callback`
of `morphological_geodesic_active_contour` and
`morphological_chan_vese` for visualizing the evolution
of the levelsets. Only works for 3D images.
Parameters
----------
fig : matplotlib.figure.Figure
Figure where results will be drawn. If not given, a new figure
will be created.
plot_each : positive integer
The plot will be updated once every `plot_each` calls to the callback
function.
Returns
-------
callback : Python function
A function that receives a levelset and updates the current plot
accordingly. This can be passed as the `iter_callback` argument of
`morphological_geodesic_active_contour` and
`morphological_chan_vese`.
"""
from mpl_toolkits.mplot3d import Axes3D
# PyMCubes package is required for `visual_callback_3d`
try:
import mcubes
except ImportError:
raise ImportError("PyMCubes is required for 3D `visual_callback_3d`")
# Prepare the visual environment.
if fig is None:
fig = plt.figure()
fig.clf()
ax = fig.add_subplot(111, projection='3d')
plt.pause(0.001)
counter = [-1]
def callback(levelset):
counter[0] += 1
if (counter[0] % plot_each) != 0:
return
if ax.collections:
del ax.collections[0]
coords, triangles = mcubes.marching_cubes(levelset, 0.5)
ax.plot_trisurf(coords[:, 0], coords[:, 1], coords[:, 2],
triangles=triangles)
plt.pause(0.1)
return callback
def rgb2gray(img):
"""Convert a RGB image to gray scale."""
return 0.2989 * img[..., 0] + 0.587 * img[..., 1] + 0.114 * img[..., 2]
def example_nodule():
logging.info('Running: example_nodule (MorphGAC)...')
# Load the image.
img = imread(PATH_IMG_NODULE)[..., 0] / 255.0
# g(I)
gimg = ms.inverse_gaussian_gradient(img, alpha=1000, sigma=5.48)
# Initialization of the level-set.
init_ls = ms.circle_level_set(img.shape, (100, 126), 20)
# Callback for visual plotting
callback = visual_callback_2d(img)
# MorphGAC.
ms.morphological_geodesic_active_contour(gimg, iterations=45,
init_level_set=init_ls,
smoothing=1, threshold=0.31,
balloon=1, iter_callback=callback)
def example_starfish():
logging.info('Running: example_starfish (MorphGAC)...')
# Load the image.
imgcolor = imread(PATH_IMG_STARFISH) / 255.0
img = rgb2gray(imgcolor)
# g(I)
gimg = ms.inverse_gaussian_gradient(img, alpha=1000, sigma=2)
# Initialization of the level-set.
init_ls = ms.circle_level_set(img.shape, (163, 137), 135)
# Callback for visual plotting
callback = visual_callback_2d(imgcolor)
# MorphGAC.
ms.morphological_geodesic_active_contour(gimg, iterations=100,
init_level_set=init_ls,
smoothing=2, threshold=0.3,
balloon=-1, iter_callback=callback)
def example_coins():
logging.info('Running: example_coins (MorphGAC)...')
# Load the image.
img = imread(PATH_IMG_COINS) / 255.0
# g(I)
gimg = ms.inverse_gaussian_gradient(img)
# Manual initialization of the level set
init_ls = np.zeros(img.shape, dtype=np.int8)
init_ls[10:-10, 10:-10] = 1
# Callback for visual plotting
callback = visual_callback_2d(img)
# MorphGAC.
ms.morphological_geodesic_active_contour(gimg, 230, init_ls,
smoothing=1, threshold=0.69,
balloon=-1, iter_callback=callback)
def example_lakes():
logging.info('Running: example_lakes (MorphACWE)...')
# Load the image.
imgcolor = imread(PATH_IMG_LAKES)/255.0
img = rgb2gray(imgcolor)
# MorphACWE does not need g(I)
# Initialization of the level-set.
init_ls = ms.circle_level_set(img.shape, (80, 170), 25)
# Callback for visual plotting
callback = visual_callback_2d(imgcolor)
# Morphological Chan-Vese (or ACWE)
ms.morphological_chan_vese(img, iterations=200,
init_level_set=init_ls,
smoothing=3, lambda1=1, lambda2=1,
iter_callback=callback)
def example_camera():
"""
Example with `morphological_chan_vese` with using the default
initialization of the level-set.
"""
logging.info('Running: example_camera (MorphACWE)...')
# Load the image.
img = imread(PATH_IMG_CAMERA)/255.0
# Callback for visual plotting
callback = visual_callback_2d(img)
# Morphological Chan-Vese (or ACWE)
ms.morphological_chan_vese(img, 35,
smoothing=3, lambda1=1, lambda2=1,
iter_callback=callback)
def example_confocal3d():
logging.info('Running: example_confocal3d (MorphACWE)...')
# Load the image.
img = np.load(PATH_ARRAY_CONFOCAL)
# Initialization of the level-set.
init_ls = ms.circle_level_set(img.shape, (30, 50, 80), 25)
# Callback for visual plotting
callback = visual_callback_3d(plot_each=20)
# Morphological Chan-Vese (or ACWE)
ms.morphological_chan_vese(img, iterations=150,
init_level_set=init_ls,
smoothing=1, lambda1=1, lambda2=2,
iter_callback=callback)
if __name__ == '__main__':
logging.basicConfig(level=logging.DEBUG)
example_nodule()
example_starfish()
example_coins()
example_lakes()
example_camera()
# Uncomment the following line to see a 3D example
# This is skipped by default since mplot3d is VERY slow plotting 3d meshes
# example_confocal3d()
logging.info("Done.")
plt.show()
After running this (and yes, I put the images in the correct place) it produced the following error:
NameError Traceback (most recent call last)
<ipython-input-7-e6b7bfe1611c> in <module>()
263 if __name__ == '__main__':
264 logging.basicConfig(level=logging.DEBUG)
--> 265 example_nodule()
266 example_starfish()
267 example_coins()
<ipython-input-7-e6b7bfe1611c> in example_nodule()
153 init_level_set=init_ls,
154 smoothing=1, threshold=0.31,
--> 155 balloon=1, iter_callback=callback)
156
157
C:\ProgramData\Anaconda3\lib\site-packages\morphsnakes.py in morphological_geodesic_active_contour(gimage, iterations, init_level_set, smoothing, threshold, balloon, iter_callback)
468 u = np.int8(init_level_set > 0)
469
--> 470 iter_callback(u)
471
472 for _ in range(iterations):
<ipython-input-7-e6b7bfe1611c> in callback(levelset)
65 ax_u.set_data(levelset)
66 fig.canvas.draw()
---> 67 plt.pause(0.001)
68
69 return callback
C:\ProgramData\Anaconda3\lib\site-packages\matplotlib\pyplot.py in pause(interval)
292 canvas.start_event_loop(interval)
293 else:
--> 294 time.sleep(interval)
295
296
NameError: name 'time' is not defined
So, of course, first I check C:\ProgramData\Anaconda3\lib\site-packages\matplotlib\pyplot.py because:
So, I discover that yes, the time module is in fact imported in this script. It makes no sense why this error is being thrown. And, it prevents me from testing any of the examples. What can I do to solve it?
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent