def test_init_with_lists_calling_scale_and_detrend():
t = Topography(np.array([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1]]),
physical_sizes=(1, 1))
# the following commands should be possible without errors
st = t.scale(1)
st.detrend(detrend_mode='center')
def test_attribute_error():
X = np.arange(3).reshape(1, 3)
Y = np.arange(4).reshape(4, 1)
h = X + Y
t = Topography(h, (8, 6))
# nonsense attributes return attribute error
with pytest.raises(AttributeError):
t.ababababababababa
#
# only scaled topographies have coeff
#
with pytest.raises(AttributeError):
t.coeff
st = t.scale(1)
assert st.height_scale_factor == 1
#
# only detrended topographies have detrend_mode
#
with pytest.raises(AttributeError):
st.detrend_mode
dm = st.detrend(detrend_mode='height').detrend_mode
assert dm == 'height'
#
# this all should also work after pickling
#
t2 = pickle.loads(pickle.dumps(t))
with pytest.raises(AttributeError):
t2.height_scale_factor
st2 = t2.scale(1)
assert st2.height_scale_factor == 1
with pytest.raises(AttributeError):
st2.detrend_mode
dm2 = st2.detrend(detrend_mode='height').detrend_mode
assert dm2 == 'height'
#
# this all should also work after scaled+pickled
#
t3 = pickle.loads(pickle.dumps(st))
with pytest.raises(AttributeError):
t3.detrend_mode
dm3 = t3.detrend(detrend_mode='height').detrend_mode
assert dm3 == 'height'
def topography(self, channel_index=None, physical_sizes=None,
height_scale_factor=None, info={}, periodic=False,
subdomain_locations=None, nb_subdomain_grid_pts=None):
if channel_index is None:
channel_index = self._default_channel_index
if subdomain_locations is not None or \
nb_subdomain_grid_pts is not None:
raise RuntimeError(
'This reader does not support MPI parallelization.')
close_file = False
if not hasattr(self._fobj, 'read'):
fobj = open(self._fobj, 'rb')
close_file = True
else:
fobj = self._fobj
channel = self._channels[channel_index]
sx, sy = self._check_physical_sizes(physical_sizes,
channel.physical_sizes)
nx, ny = channel.nb_grid_pts
offset = self._offsets[channel_index]
dtype = np.dtype('<i2')
###################################
fobj.seek(offset)
rawdata = fobj.read(nx * ny * dtype.itemsize)
unscaleddata = np.frombuffer(rawdata, count=nx * ny,
dtype=dtype).reshape(nx, ny)
# internal information from file
_info = dict(unit=channel.info["unit"], data_source=channel.name)
_info.update(info)
if 'acquisition_time' in channel.info:
_info['acquisition_time'] = channel.info['acquisition_time']
# the orientation of the heights is modified in order to match
# the image of gwyddion when plotted with imshow(t.heights().T)
# or pcolormesh(t.heights().T) for origin in lower left and
# with inverted y axis (cartesian coordinate system)
surface = Topography(np.fliplr(unscaleddata.T), (sx, sy), info=_info,
periodic=periodic)
if height_scale_factor is None:
height_scale_factor = channel.info["height_scale_factor"]
surface = surface.scale(height_scale_factor)
if close_file:
fobj.close()
return surface
