def test_load_no_physical_sizes(comm_self):
nb_grid_pts = (128, 128)
size = (3, 3)
np.random.seed(1)
t = fourier_synthesis(nb_grid_pts, size, 0.8, rms_slope=0.1)
# Topographies always have physical size information, we need to create a
# NetCDF file without any manually
with Dataset('no_physical_sizes.nc', 'w', format='NETCDF3_CLASSIC') as nc:
nc.createDimension('x', nb_grid_pts[0])
nc.createDimension('y', nb_grid_pts[1])
nc.createVariable('heights', 'f8', ('x', 'y'))
nc.variables['heights'] = t.heights()
# Attempt to open full file on each process
# with pytest.raises(ValueError):
# # This raises an error because the physical sizes are not present
# t2 = read_topography('no_physical_sizes.nc')
t2 = read_topography('no_physical_sizes.nc', physical_sizes=size)
assert t.physical_sizes == t2.physical_sizes
assert 'unit' not in t2.info
np.testing.assert_array_almost_equal(t.heights(), t2.heights())
os.remove('no_physical_sizes.nc')
def reentrant_line_scan():
"""Return an reentrant line scan."""
data = """
0 1
1 1
2 1
2 2
3 2
4 2
"""
in_mem_file = io.StringIO(data)
return read_topography(in_mem_file)
def test_save_and_load(comm):
nb_grid_pts = (128, 128)
size = (3, 3)
np.random.seed(1)
t = fourier_synthesis(nb_grid_pts, size, 0.8, rms_slope=0.1, unit='µm')
fft = FFT(nb_grid_pts, communicator=comm, fft="mpi")
fft.create_plan(1)
dt = t.domain_decompose(fft.subdomain_locations,
fft.nb_subdomain_grid_pts,
communicator=comm)
assert t.unit == 'µm'
assert dt.unit == 'µm'
assert t.info['unit'] == 'µm'
assert dt.info['unit'] == 'µm'
if comm.size > 1:
assert dt.is_domain_decomposed
# Save file
dt.to_netcdf('parallel_save_test.nc')
# Attempt to open full file on each MPI process
t2 = read_topography('parallel_save_test.nc')
assert t.physical_sizes == t2.physical_sizes
assert t.unit == t2.unit
assert t.info['unit'] == t2.info['unit']
np.testing.assert_array_almost_equal(t.heights(), t2.heights())
# Attempt to open file in parallel
r = NCReader('parallel_save_test.nc', communicator=comm)
assert r.channels[0].nb_grid_pts == nb_grid_pts
t3 = r.topography(subdomain_locations=fft.subdomain_locations,
nb_subdomain_grid_pts=fft.nb_subdomain_grid_pts)
assert t.physical_sizes == t3.physical_sizes
assert t.unit == t3.unit
assert t.info['unit'] == t3.info['unit']
np.testing.assert_array_almost_equal(dt.heights(), t3.heights())
assert t3.is_periodic
comm.barrier()
if comm.rank == 0:
os.remove('parallel_save_test.nc')
def test_save_and_load_no_unit(comm_self):
nb_grid_pts = (128, 128)
size = (3, 3)
np.random.seed(1)
t = fourier_synthesis(nb_grid_pts, size, 0.8, rms_slope=0.1)
# Save file
t.to_netcdf('no_unit.nc')
t2 = read_topography('no_unit.nc')
assert t.physical_sizes == t2.physical_sizes
assert 'unit' not in t2.info
np.testing.assert_array_almost_equal(t.heights(), t2.heights())
os.remove('no_unit.nc')
def test_save_and_load_line_scan(comm_self):
nb_grid_pts = (128, )
size = (3, )
np.random.seed(1)
t = fourier_synthesis(nb_grid_pts, size, 0.8, rms_slope=0.1)
t.info['unit'] = 'µm'
with tempfile.TemporaryDirectory() as d:
tmpfn = f'{d}/line_scan.nc'
# Save file
t.to_netcdf(tmpfn)
# Read file
t2 = read_topography(tmpfn)
assert t == t2
parser = ArgumentParser(description='Plot a 2D surface map (pressure, gap, '
'etc.).')
parser.add_argument('filename', metavar='FILENAME', help='name of map file')
parser.add_argument('--logscale',
help='log scaling',
action='store_true',
default=False)
parser.add_argument('--fftshift',
help='fft shift',
action='store_true',
default=False)
arguments = parser.parse_args()
###
surface = read_topography(arguments.filename)
###
try:
sx, sy = surface.physical_sizes
except TypeError:
sx, sy = surface.nb_grid_pts
nx, ny = surface.nb_grid_pts
fig = plt.figure()
ax = fig.add_subplot(111, aspect=sx / sy)
Y, X = np.meshgrid((np.arange(ny) + 0.5) * sy / ny,
(np.arange(nx) + 0.5) * sx / nx)
Z = surface[...]
if arguments.fftshift: