def test_s(self):
"""Test the s() function."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
CL = ru.centerline(x, y)
sss = CL.s()
# make assertions
assert np.all(sss == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
def test_long_sine_CLinfs():
"""Long sine wave into CL and using infs function."""
xs = np.linspace(0, 10000, 10001)
ys = 20 * (np.sin(xs / 1000) + 50)
CL = ru.centerline(xs, ys)
CL.infs(40)
# make assertion
assert CL.infs_os[-1] == 10000
def test_ds(self):
"""Test the ds() function."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
CL = ru.centerline(x, y)
dss = CL.ds()
# make assertions
assert np.all(dss == [1., 1., 1., 1., 1., 1., 1., 1., 1., 1.])
def test_init(self):
"""Init the class."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
CL = ru.centerline(x, y)
# make assertions
assert np.all(CL.xo == x)
assert np.all(CL.yo == y)
def test_C(self):
"""Test the C() function."""
x = [0, 1, 2, 3, 4, 5, 4, 3, 2, 1, 0]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
CL = ru.centerline(x, y)
Cs = CL.C()
# make assertions
assert pytest.approx(Cs == np.array(
[-0., 0., 0., 0., 0., 1.57079633, 1.57079633, 0., 0., 0., 0.]))
def test_sine_csmooth():
"""Use a sine wave to compute curvature."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
CL.window_C = 11
# smooth the centerline
Cs = CL.Csmooth()
# check that the smoothed shape is what we expect
assert Cs.shape == (101, )
def test_get_xy(self):
"""Test get xy function."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
CL = ru.centerline(x, y)
x, y, vers = CL._centerline__get_x_and_y()
# make assertions
assert np.all(x == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
assert np.all(y == [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
assert vers == 'original'
def test_init_attr(self):
"""Init with attribute list."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
attribs = {}
attribs['width'] = np.ones((11, )) * 10
CL = ru.centerline(x, y, attribs)
# make assertions
assert np.all(CL.xo == x)
assert np.all(CL.yo == y)
assert np.all(CL.width == np.ones((11, )) * 10)
def test_init_const_attr(self):
"""Init with constant attribute."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
attribs = {}
attribs['width'] = 10.
CL = ru.centerline(x, y, attribs)
# make assertions
assert np.all(CL.xo == x)
assert np.all(CL.yo == y)
assert CL.width == 10.0
def test_csmooth_nowindow():
"""csmooth() without providing a window."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
# set up capture string
capturedOutput = io.StringIO()
sys.stdout = capturedOutput
# smooth the centerline
Cs = CL.Csmooth()
# grab output
sys.stdout = sys.__stdout__
# assert output
assert capturedOutput.getvalue()[:-1] == 'Must provide a smoothing window.'
def test_zs_noinflection():
"""zs_plot without inflection points."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
# set up capture string
capturedOutput = io.StringIO()
sys.stdout = capturedOutput
# call plot
CL.zs_plot()
# grab output
sys.stdout = sys.__stdout__
# assert output
assert capturedOutput.getvalue(
)[:-1] == 'Must compute inflection points first.'
def test_get_xy_sm(self):
"""Test get xy function with xs."""
x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
xs = [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
ys = [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11]
attribs = {}
attribs['xs'] = xs
attribs['ys'] = ys
CL = ru.centerline(x, y, attribs=attribs)
x, y, vers = CL._centerline__get_x_and_y()
# make assertions
assert np.all(x == [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20])
assert np.all(y == [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11])
assert vers == 'smooth'
def test_zs_nomigrates():
"""zs_plot without migration rates."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
CL.infs_os = [1]
CL.ints = [2]
# set up capture string
capturedOutput = io.StringIO()
sys.stdout = capturedOutput
# call plot
CL.zs_plot()
# grab output
sys.stdout = sys.__stdout__
# assert output
assert capturedOutput.getvalue(
)[:-1] == 'Must compute migration rates first.'
def test_sine_plot():
"""Use sine wave to test plotting of CenterLine."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
CL.plot()
plt.savefig(
os.path.join(
basepath,
os.path.normpath('tests/results/synthetic_cycles/sinewave.png')))
plt.close()
# assert file exists now
assert os.path.isfile(
os.path.join(
basepath,
os.path.normpath(
'tests/results/synthetic_cycles/sinewave.png'))) == True
def test_plot_withattrs():
"""Testing CenterLine plotting with various attributes."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
CL = ru.centerline(xs, ys)
CL.infs_os = [0]
CL.ints_all = [1]
CL.ints = [2]
CL.plot()
plt.savefig(
os.path.join(
basepath,
os.path.normpath(
'tests/results/synthetic_cycles/sinewaveattrs.png')))
plt.close()
# assert file exists now
assert os.path.isfile(
os.path.join(
basepath,
os.path.normpath(
'tests/results/synthetic_cycles/sinewaveattrs.png'))) == True
def test_sine_curvature():
"""Use a sine wave to compute curvature."""
xs = np.linspace(0, 100, 101)
ys = np.sin(xs) + 5
C, Areturn, sdist = ru.curvars(xs, ys)
# make some simple assertions about shape of outputs
assert C.shape == (100, )
assert Areturn.shape == (100, )
assert sdist.shape == (100, )
# now define this as a centerline
CL = ru.centerline(xs, ys)
# smooth the centerline
CL.window_cl = 10
CL.smooth(n=2)
# make some assertions about the smoothing
assert CL.xs.shape == (101, )
assert CL.ys.shape == (101, )
assert np.sum(CL.xs != xs) > 0
assert np.sum(CL.ys != ys) > 0
# resample the centerline to 50 points
CL.resample(50)
# assert resampled dimensions are as expected
assert CL.xrs.shape == (50, )
assert CL.yrs.shape == (50, )