def test_nonuniform(self):
surf = read_xyz(os.path.join(DATADIR, 'example.xyz'))
self.assertFalse(surf.is_uniform)
self.assertEqual(surf.dim, 1)
surf = surf.detrend(detrend_mode='height')
self.assertFalse(surf.is_uniform)
self.assertEqual(surf.dim, 1)
def test_read_1d():
surface = read_xyz(os.path.join(DATADIR, 'example.xyz'))
assert not surface.is_uniform
x, y = surface.positions_and_heights()
assert len(x) > 0
assert len(x) == len(y)
assert not surface.is_uniform
assert surface.dim == 1
assert not surface.is_periodic
def test_read(self):
surface = read_xyz(
os.path.join(DATADIR, 'line_scan_1_minimal_spaces.asc'))
self.assertFalse(surface.is_uniform)
self.assertEqual(surface.dim, 1)
x, y = surface.positions_and_heights()
self.assertGreater(len(x), 0)
self.assertEqual(len(x), len(y))
def test_simple_nonuniform_line_scan(self):
surf = read_xyz(
os.path.join(DATADIR, 'line_scan_1_minimal_spaces.asc'))
self.assertAlmostEqual(surf.physical_sizes, (9.0,))
self.assertFalse(surf.is_uniform)
self.assertFalse('unit' in surf.info)
bw = surf.bandwidth()
self.assertAlmostEqual(bw[0], (8 * 1. + 2 * 0.5 / 10) / 9)
self.assertAlmostEqual(bw[1], 9)
def test_read_2d(filename):
"""
Here the order of points in the input file shouldn't matter.
"""
surface = read_xyz(os.path.join(DATADIR, filename))
assert surface.is_uniform
x, y, z = surface.positions_and_heights()
assert x.shape == (4, 4)
assert y.shape == (4, 4)
assert z.shape == (4, 4)
assert surface.dim == 2
assert not surface.is_periodic
assert_allclose(z, [[1., 1., 1., 1.], [1., 2., 2., 1.], [1., 1., 1., 1.],
[1., 1., 1., 1.]])
def test_nonuniform_unit_conversion(file_format_examples):
surf = read_xyz(os.path.join(file_format_examples, 'example.xyz'),
unit='um')
assert surf.unit == 'um'
surf2 = surf.to_unit('mm')
assert surf2.info['unit'] == 'mm'
assert surf2.unit == 'mm'
np.testing.assert_almost_equal(
tuple(p / 1000 for p in surf.physical_sizes), surf2.physical_sizes)
np.testing.assert_almost_equal(tuple(p / 1000 for p in surf.positions()),
surf2.positions())
np.testing.assert_almost_equal(surf.rms_height_from_profile() / 1000,
surf2.rms_height_from_profile())
np.testing.assert_almost_equal(surf.rms_slope_from_profile(),
surf2.rms_slope_from_profile())
np.testing.assert_almost_equal(surf.rms_curvature_from_profile() * 1000,
surf2.rms_curvature_from_profile())
def test_nonuniform_scaled_topography(file_format_examples):
surf = read_xyz(os.path.join(file_format_examples, 'example.xyz'))
sx, = surf.physical_sizes
for fac in [1.0, 2.0, np.pi]:
surf2 = surf.scale(fac)
np.testing.assert_almost_equal(fac * surf.rms_height_from_profile(),
surf2.rms_height_from_profile())
np.testing.assert_almost_equal(surf.positions(), surf2.positions())
surf2 = surf.scale(fac, 2 * fac)
np.testing.assert_almost_equal(fac * surf.rms_height_from_profile(),
surf2.rms_height_from_profile())
np.testing.assert_almost_equal(2 * fac * surf.positions(),
surf2.positions())
sx2, = surf2.physical_sizes
np.testing.assert_almost_equal(2 * fac * sx, sx2)
x = surf.positions()
x2 = surf2.positions()
np.testing.assert_almost_equal(2 * fac * x, x2)
x2, h2 = surf2.positions_and_heights()
np.testing.assert_almost_equal(2 * fac * x, x2)
def test_detrend(self):
t = read_xyz(os.path.join(DATADIR, 'example.xyz'))
self.assertFalse(t.detrend('center').is_periodic)
self.assertFalse(t.detrend('height').is_periodic)