def test_load_dm(self):
filename = os.path.join(tomotools_path, "tests",
"test_data", "HAADF.dm3")
stack = tomotools.load(filename)
assert stack.axes_manager[0].name == 'Tilt'
assert stack.axes_manager[0].offset == -90.0
assert stack.axes_manager.signal_shape == (64, 64)
assert stack.axes_manager.navigation_shape == (91,)
def test_load_hspy(self):
filename = os.path.join(tomotools_path, "tests",
"test_data", "HAADF.mrc")
stack = tomotools.load(filename)
assert type(stack) is TomoStack
assert stack.axes_manager.signal_shape == (256, 256)
assert stack.axes_manager.navigation_shape == (77,)
assert stack.__repr__()[0:10] == '<TomoStack'
def test_register_ecc(self):
filename = os.path.join(my_path, "test_data", "HAADF.mrc")
stack = tomotools.load(filename)
reg = stack.inav[0:20].stack_register('ECC')
assert type(reg) is tomotools.TomoStack
assert reg.axes_manager.signal_shape == \
stack.inav[0:20].axes_manager.signal_shape
assert reg.axes_manager.navigation_shape == \
stack.inav[0:20].axes_manager.navigation_shape
def get_needle_data(aligned=False):
"""
Retrieve experimental tilt series of needle-shaped specimen.
Returns
----------
needle : TomoStack object
TomoStack containing the simulated catalyst tilt series
"""
if aligned:
filename = os.path.join(tomotools_path, "tests", "test_data",
"HAADF_Aligned.hdf5")
needle =\
tomotools.load(filename)
else:
filename = os.path.join(tomotools_path, "tests", "test_data",
"HAADF.mrc")
needle =\
tomotools.load(filename)
return needle
def get_catalyst_tilt_series(misalign=False,
minshift=-5,
maxshift=5,
tiltshift=0,
tiltrotate=0,
xonly=False,
noise=False,
noise_factor=0.2):
"""
Retrieve model catalyst tilt series.
Arguments
----------
misalign : bool
If True, apply random shifts to each projection to simulated drift
minshift : float
Lower bound for random shifts
maxshift : float
Upper bound for random shifts
tiltshift : float
Number of pixels by which to shift entire tilt series. Simulates
offset tilt axis.
rotate : float
Angle by which to rotate entire tilt series. Simulates non-vertical
tilt axis.
xonly : bool
If True, shifts are only applied along the X-axis
noise : bool
If True, add Gaussian noise to the stack
noise_factor : float
Percentage noise to be added. Must be between 0 and 1.
Returns
----------
catalyst : TomoStack object
TomoStack containing the simulated catalyst tilt series
"""
filename = os.path.join(tomotools_path, "tests", "test_data",
"Catalyst3DModel_TiltSeries180.hdf5")
catalyst =\
tomotools.load(filename)
if misalign:
catalyst = misalign_stack(catalyst,
min_shift=minshift,
max_shift=maxshift,
tilt_shift=tiltshift,
tilt_rotate=tiltrotate,
x_only=xonly)
if noise:
catalyst = add_gaussian_noise(catalyst, noise_factor)
return catalyst
def test_signal_to_stack_with_tiltsignal(self):
filename = os.path.join(tomotools_path, "tests",
"test_data", "HAADF.mrc")
tilt_signal = tomotools.load(filename)
tilt_signal.set_tilts(-76, 2)
signal = hs.signals.Signal2D(np.random.random([77, 100, 100]))
stack = tomotools.io.signal_to_tomo_stack(signal,
tilt_signal=tilt_signal)
assert stack.axes_manager[0].name == 'Tilt'
assert stack.axes_manager.signal_shape == (100, 100)
assert stack.axes_manager.navigation_shape == (77,)
assert stack.axes_manager[0].axis.all() == \
tilt_signal.axes_manager[0].axis.all()
def test_load_unknown(self):
filename = os.path.join(tomotools_path, "tests",
"test_data", "HAADF.NONE")
with pytest.raises(ValueError):
tomotools.load(filename)