def test_recon_fbp(self):
stack = ds.get_needle_data(True)
slices = stack.isig[:, 120:121].deepcopy()
rec = slices.reconstruct('FBP')
assert type(stack) is tomotools.base.TomoStack
assert type(rec) is tomotools.base.TomoStack
assert rec.data.shape[1] == slices.data.shape[2]
def test_image_filter_none(self):
stack = ds.get_needle_data()
filt = stack.inav[0:10].filter(method=None)
assert filt.axes_manager.navigation_shape == \
stack.inav[0:10].axes_manager.navigation_shape
assert filt.axes_manager.signal_shape == \
stack.inav[0:10].axes_manager.signal_shape
def test_align_to_other(self):
stack = ds.get_needle_data()
stack2 = stack.deepcopy()
reg = stack.stack_register('PC')
reg2 = reg.align_other(stack2)
diff = reg.data - reg2.data
assert diff.sum() == 0.0
def test_stack_normalize(self):
stack = ds.get_needle_data()
norm = stack.normalize()
assert norm.axes_manager.navigation_shape == \
stack.axes_manager.navigation_shape
assert norm.axes_manager.signal_shape == \
stack.axes_manager.signal_shape
assert norm.data.min() == 0.0
def test_tilt_align_com(self):
stack = ds.get_needle_data()
stack.axes_manager[0].offset = -76
stack.axes_manager[0].scale = 2
reg = stack.stack_register('PC')
ali = reg.tilt_align(method='CoM', locs=[64, 128, 192])
tilt_axis = ali.metadata.Tomography.tiltaxis
assert abs(-2.7 - tilt_axis) < 1.0
def test_register_ecc(self):
stack = ds.get_needle_data()
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 test_tilt_align_maximage(self):
stack = ds.get_needle_data()
stack.axes_manager[0].offset = -76
stack.axes_manager[0].scale = 2
reg = stack.stack_register('PC')
ali = reg.tilt_align(method='MaxImage')
tilt_axis = ali.metadata.Tomography.tiltaxis
assert abs(-2.3 - tilt_axis) < 1.0
def test_sirt_error(self):
stack = ds.get_needle_data(True)
rec_stack, error = stack.recon_error(128, iterations=50,
constrain=True, cuda=False)
assert error.data.shape[0] == rec_stack.data.shape[0]
assert rec_stack.data.shape[1:] ==\
(stack.data.shape[2], stack.data.shape[2])
assert (1 - (3.8709e12 / error.data[0])) < 0.001
assert (1 - (2.8624e12 / error.data[1])) < 0.001
def test_set_tilts(self):
stack = ds.get_needle_data()
stack.set_tilts(-50, 5)
assert stack.axes_manager[0].name == "Tilt"
assert stack.axes_manager[0].scale == 5
assert stack.axes_manager[0].units == "degrees"
assert stack.axes_manager[0].offset == -50
assert stack.axes_manager[0].axis.all() == \
np.arange(-50, stack.data.shape[0] * 5 + -50, 5).all()
def test_recon_sirt(self):
stack = ds.get_needle_data(True)
slices = stack.isig[:, 120:121].deepcopy()
rec = slices.reconstruct('SIRT',
constrain=True,
iterations=2,
thresh=0)
assert type(stack) is tomotools.base.TomoStack
assert type(rec) is tomotools.base.TomoStack
assert rec.data.shape[1] == slices.data.shape[2]
def test_register_com(self):
stack = ds.get_needle_data()
stack.metadata.Tomography.tilts = \
stack.metadata.Tomography.tilts[0:20]
reg = stack.inav[0:20].stack_register('COM')
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 test_astra_sirt_2d_data(self):
stack = ds.get_needle_data(True)
angles = stack.axes_manager[0].axis
slices = stack.isig[:, 120].deepcopy().data
rec = recon.astra_sirt(slices, angles,
thickness=None, iterations=2,
constrain=True, thresh=0, cuda=False)
assert rec.shape == (1, slices.shape[1], slices.shape[1])
assert rec.shape[0] == 1
assert type(rec) is numpy.ndarray
def test_astra_project_2d_data(self):
stack = ds.get_needle_data(True)
angles = stack.axes_manager[0].axis
slices = stack.isig[:, 120].deepcopy().data
rec = recon.astra_sirt(slices, angles,
thickness=None, iterations=1,
constrain=True, thresh=0, cuda=False)
sino = recon.astra_project(rec, angles)
assert sino.shape == (len(angles), rec.shape[0], rec.shape[2])
assert sino.shape[1] == 1
assert type(sino) is numpy.ndarray
def test_stack_stats(self):
stack = ds.get_needle_data()
stdout = sys.stdout
sys.stdout = io.StringIO()
stack.stats()
out = sys.stdout.getvalue()
sys.stdout = stdout
out = out.split('\n')
assert out[0] == 'Mean: %.1f' % stack.data.mean()
assert out[1] == 'Std: %.2f' % stack.data.std()
assert out[2] == 'Max: %.1f' % stack.data.max()
assert out[3] == 'Min: %.1f' % stack.data.min()
def test_tilt_align_unknown_method(self):
stack = ds.get_needle_data()
with pytest.raises(ValueError):
stack.tilt_align(method='WRONG')
def test_correlation_check(self):
stack = ds.get_needle_data()
fig = stack.test_correlation()
assert type(fig) is matplotlib.figure.Figure
assert len(fig.axes) == 3
def test_test_align_with_thickness(self):
stack = ds.get_needle_data(True)
stack.test_align(thickness=200)
fig = matplotlib.pylab.gcf()
assert len(fig.axes) == 3
def test_register_unknown_method(self):
stack = ds.get_needle_data()
with pytest.raises(ValueError):
stack.inav[0:20].stack_register('WRONG')
def test_get_aligned_experimental_data(self):
stack = ds.get_needle_data(aligned=True)
assert type(stack) is tomotools.TomoStack
def test_get_experimental_data(self):
stack = ds.get_needle_data()
assert type(stack) is tomotools.TomoStack
def test_test_align_with_angle(self):
stack = ds.get_needle_data(True)
stack.test_align(angle=3.0)
fig = matplotlib.pylab.gcf()
assert len(fig.axes) == 3
def test_align_to_other_no_alignment(self):
stack = ds.get_needle_data()
stack2 = stack.deepcopy()
reg = stack.deepcopy()
with pytest.raises(ValueError):
reg.align_other(stack2)
def test_stack_invert(self):
stack = ds.get_needle_data()
invert = stack.invert()
hist, bins = np.histogram(stack.data)
hist_inv, bins_inv = np.histogram(invert.data)
assert hist[0] > hist_inv[0]
def test_image_filter_wrong_name(self):
stack = ds.get_needle_data()
with pytest.raises(ValueError):
stack.inav[0:10].filter(method='WRONG')
def test_align_to_other_with_crop(self):
stack = ds.get_needle_data()
reg = stack.stack_register('PC', crop=True)
reg2 = reg.align_other(stack)
diff = reg.data - reg2.data
assert diff.sum() == 0.0
def test_test_align_no_slices(self):
stack = ds.get_needle_data(True)
stack.test_align()
fig = matplotlib.pylab.gcf()
assert len(fig.axes) == 3
