def test_compare_lazy_and_nonlazy(self):
y, x = np.mgrid[75:83:9j, 85:95:11j]
s = mdtd.generate_4d_data(
probe_size_x=11,
probe_size_y=9,
ring_x=None,
image_size_x=160,
image_size_y=140,
disk_x=x,
disk_y=y,
disk_r=40,
disk_I=20,
blur=True,
blur_sigma=1,
downscale=False,
)
s_lazy = LazyDiffraction2D(
da.from_array(s.data, chunks=(1, 1, 140, 160)))
s_com = s.center_of_mass()
s_lazy_com = s_lazy.center_of_mass()
np.testing.assert_equal(s_com.data, s_lazy_com.data)
com_nav_extent = s_com.axes_manager.navigation_extent
lazy_com_nav_extent = s_lazy_com.axes_manager.navigation_extent
assert com_nav_extent == lazy_com_nav_extent
com_sig_extent = s_com.axes_manager.signal_extent
lazy_com_sig_extent = s_lazy_com.axes_manager.signal_extent
assert com_sig_extent == lazy_com_sig_extent
def test_correct_disk_x_y_and_radius_random(self):
x, y, px, py = 56, 48, 4, 5
x, y = randint(45, 55, size=(py, px)), randint(45, 55, size=(py, px))
r = randint(20, 40, size=(py, px))
s = mdtd.generate_4d_data(
probe_size_x=px,
probe_size_y=py,
image_size_x=120,
image_size_y=100,
disk_x=x,
disk_y=y,
disk_r=5,
disk_I=20,
ring_x=x,
ring_y=y,
ring_r=r,
ring_I=5,
blur=True,
downscale=False,
)
dask_array = da.from_array(s.data, chunks=(4, 4, 50, 50))
s = LazyDiffraction2D(dask_array)
s_com = s.center_of_mass()
s_r = s.radial_average(centre_x=s_com.inav[0].data,
centre_y=s_com.inav[1].data)
s_r = s_r.isig[15:] # Do not include the disk
r -= 15 # Need to shift the radius, due to not including the disk
assert (s_r.data.argmax(axis=-1) == r).all()
def test_nav_1(self):
data_shape = (5, 40, 40)
array0 = da.ones(shape=data_shape, chunks=(5, 5, 5))
s0 = LazyDiffraction2D(array0)
s0_r = s0.radial_average()
assert s0_r.axes_manager.navigation_shape == data_shape[:1]
assert (s0_r.data[:, :-1] == 1).all()
def test_simple(self):
array0 = da.ones(shape=(10, 10, 40, 40), chunks=(5, 5, 5, 5))
s0 = LazyDiffraction2D(array0)
s0_r = s0.radial_average()
assert (s0_r.data[:, :, :-1] == 1).all()
data_shape = 2, 2, 11, 11
array1 = np.zeros(data_shape)
array1[:, :, 5, 5] = 1
dask_array = da.from_array(array1, chunks=(1, 1, 1, 1))
s1 = LazyDiffraction2D(dask_array)
s1.axes_manager.signal_axes[0].offset = -5
s1.axes_manager.signal_axes[1].offset = -5
s1_r = s1.radial_average()
assert np.all(s1_r.data[:, :, 0] == 1)
assert np.all(s1_r.data[:, :, 1:] == 0)
def get_hot_pixel_signal(lazy=False):
"""Get Diffraction2D signal with a disk in the middle.
Has 4 pixels with value equal to 50000, to simulate hot pixels.
Example
-------
>>> s = pxm.dummy_data.get_hot_pixel_signal()
Lazy signal
>>> s_lazy = pxm.dummy_data.get_hot_pixel_signal(lazy=True)
"""
data = mdtd.MakeTestData(size_x=128, size_y=128, default=False, blur=True)
data.add_disk(64, 64, r=30, intensity=10000)
s = data.signal
s.change_dtype("int64")
s.data += gaussian_filter(s.data, sigma=50)
s.data[76, 4] = 50000
s.data[12, 102] = 50000
s.data[32, 10] = 50000
s.data[120, 61] = 50000
if lazy:
s = LazyDiffraction2D(s)
s.data = da.from_array(s.data, chunks=(64, 64))
else:
s = Diffraction2D(s)
return s
def test_5d_data_compute(self):
dask_array = da.random.random((2, 3, 4, 10, 15),
chunks=(1, 1, 1, 10, 15))
s = LazyDiffraction2D(dask_array)
s.compute()
assert s.__class__ == Diffraction2D
assert dask_array.shape == s.data.shape
def test_lazy(self):
y, x = np.mgrid[75:83:9j, 85:95:11j]
s = mdtd.generate_4d_data(
probe_size_x=11,
probe_size_y=9,
ring_x=None,
image_size_x=160,
image_size_y=140,
disk_x=x,
disk_y=y,
disk_r=40,
disk_I=20,
blur=True,
blur_sigma=1,
downscale=False,
)
s_lazy = LazyDiffraction2D(
da.from_array(s.data, chunks=(1, 1, 140, 160)))
s_lazy_com = s_lazy.center_of_mass()
np.testing.assert_allclose(s_lazy_com.inav[0].data, x)
np.testing.assert_allclose(s_lazy_com.inav[1].data, y)
s_lazy_1d = s_lazy.inav[0]
s_lazy_1d_com = s_lazy_1d.center_of_mass()
np.testing.assert_allclose(s_lazy_1d_com.inav[0].data, x[:, 0])
np.testing.assert_allclose(s_lazy_1d_com.inav[1].data, y[:, 0])
s_lazy_0d = s_lazy.inav[0, 0]
s_lazy_0d_com = s_lazy_0d.center_of_mass()
np.testing.assert_allclose(s_lazy_0d_com.inav[0].data, x[0, 0])
np.testing.assert_allclose(s_lazy_0d_com.inav[1].data, y[0, 0])
def test_disk_radius(self):
s = LazyDiffraction2D(
da.random.randint(100, size=(5, 5, 30, 30), chunks=(1, 1, 10, 10)))
s_template0 = s.template_match_disk(disk_r=2, lazy_result=False)
s_template1 = s.template_match_disk(disk_r=4, lazy_result=False)
assert s.data.shape == s_template0.data.shape
assert s.data.shape == s_template1.data.shape
assert not (s_template0.data == s_template1.data).all()
def test_big_value(self):
data_shape = (5, 40, 40)
big_value = 50000000
array0 = np.ones(shape=data_shape) * big_value
dask_array = da.from_array(array0, chunks=(2, 10, 10))
s0 = LazyDiffraction2D(dask_array)
s0_r = s0.radial_average()
assert s0_r.axes_manager.navigation_shape == data_shape[:1]
assert (s0_r.data[:, :-1] == big_value).all()
def test_rotate_diffraction_keep_shape(self):
shape = (7, 5, 4, 15)
s = Diffraction2D(np.zeros(shape))
s_rot = s.rotate_diffraction(angle=45)
assert s.axes_manager.shape == s_rot.axes_manager.shape
s_lazy = LazyDiffraction2D(da.zeros(shape, chunks=(1, 1, 1, 1)))
s_rot_lazy = s_lazy.rotate_diffraction(angle=45)
assert s_lazy.axes_manager.shape == s_rot_lazy.axes_manager.shape
def test_lazy(self):
data = np.zeros((10, 10, 30, 30))
x, y = 20, 10
data[:, :, y, x] += 1
data = da.from_array(data, chunks=(5, 5, 5, 5))
s = LazyDiffraction2D(data)
shift_x, shift_y = 4, 3
s_shift = s.shift_diffraction(shift_x=shift_x, shift_y=shift_y)
s_shift.compute()
assert s_shift.data[0, 0, y - shift_y, x - shift_x] == 1
s_shift.data[:, :, y - shift_y, x - shift_x] = 0
assert s_shift.data.sum() == 0
def test_2d_data_compute(self):
dask_array = da.random.random((100, 150), chunks=(50, 50))
s = LazyDiffraction2D(dask_array)
scale0, scale1, metadata_string = 0.5, 1.5, "test"
s.axes_manager[0].scale = scale0
s.axes_manager[1].scale = scale1
s.metadata.Test = metadata_string
s.compute()
assert s.__class__ == Diffraction2D
assert not hasattr(s.data, "compute")
assert s.axes_manager[0].scale == scale0
assert s.axes_manager[1].scale == scale1
assert s.metadata.Test == metadata_string
assert dask_array.shape == s.data.shape
def test_lazy_result(self):
data = da.ones((10, 10, 20, 20), chunks=(10, 10, 10, 10))
s_lazy = LazyDiffraction2D(data)
s_lazy_com = s_lazy.center_of_mass(lazy_result=True)
assert s_lazy_com._lazy
assert s_lazy_com.axes_manager.signal_shape == (10, 10)
s_lazy_1d = s_lazy.inav[0]
s_lazy_1d_com = s_lazy_1d.center_of_mass(lazy_result=True)
assert s_lazy_1d_com._lazy
assert s_lazy_1d_com.axes_manager.signal_shape == (10, )
s_lazy_0d = s_lazy.inav[0, 0]
s_lazy_0d_com = s_lazy_0d.center_of_mass(lazy_result=True)
assert s_lazy_0d_com._lazy
assert s_lazy_0d_com.axes_manager.signal_shape == ()
def test_correct_radius_random(self):
x, y, px, py = 56, 48, 4, 5
r = np.random.randint(20, 40, size=(py, px))
s = mdtd.generate_4d_data(
probe_size_x=px,
probe_size_y=py,
image_size_x=120,
image_size_y=100,
disk_I=0,
ring_x=x,
ring_y=y,
ring_r=r,
ring_I=5,
blur=True,
downscale=False,
)
dask_array = da.from_array(s.data, chunks=(4, 4, 50, 50))
s = LazyDiffraction2D(dask_array)
s.axes_manager.signal_axes[0].offset = -x
s.axes_manager.signal_axes[1].offset = -y
s_r = s.radial_average()
assert (s_r.data.argmax(axis=-1) == r).all()
def test_correct_radius_simple(self):
x, y, r, px, py = 40, 51, 30, 4, 5
s = mdtd.generate_4d_data(
probe_size_x=px,
probe_size_y=py,
image_size_x=120,
image_size_y=100,
disk_I=0,
ring_x=x,
ring_y=y,
ring_r=r,
ring_I=5,
blur=True,
downscale=False,
)
dask_array = da.from_array(s.data, chunks=(4, 4, 50, 50))
s = LazyDiffraction2D(dask_array)
s.axes_manager.signal_axes[0].offset = -x
s.axes_manager.signal_axes[1].offset = -y
s_r = s.radial_average()
assert s_r.axes_manager.navigation_shape == (px, py)
assert (s_r.data.argmax(axis=-1) == 30).all()
def generate_4d_data(
probe_size_x=10,
probe_size_y=10,
image_size_x=50,
image_size_y=50,
disk_x=25,
disk_y=25,
disk_r=5,
disk_I=20,
ring_x=25,
ring_y=25,
ring_r=20,
ring_I=6,
ring_lw=0,
ring_e_x=None,
ring_e_y=25,
ring_e_semi_len0=15,
ring_e_semi_len1=15,
ring_e_r=0,
ring_e_I=6,
ring_e_lw=1,
blur=True,
blur_sigma=1,
downscale=True,
add_noise=False,
noise_amplitude=1,
lazy=False,
lazy_chunks=None,
show_progressbar=True,
):
"""Generate a test dataset containing a disk and diffraction ring.
Useful for checking that radial average algorithms are working
properly.
The centre, intensity and radius position of the ring and disk can vary
as a function of probe position, through the disk_x, disk_y, disk_r,
disk_I, ring_x, ring_y, ring_r and ring_I arguments.
In addition, the line width of the ring can be varied with ring_lw.
There is also an elliptical ring, which can be added separately
to the circular ring. This elliptical ring uses the ring_e_*
arguments. It is disabled by default.
The ring can be deactivated by setting ring_x=None.
The disk can be deactivated by setting disk_x=None.
The elliptical ring can be deactivated by setting ring_e_x=None.
Parameters
----------
probe_size_x, probe_size_y : int, default 10
Size of the navigation dimension.
image_size_x, image_size_y : int, default 50
Size of the signal dimension.
disk_x, disk_y : int or NumPy 2D-array, default 20
Centre position of the disk. Either integer or NumPy 2-D array.
See examples on how to make them the correct size.
To deactivate the disk, set disk_x=None.
disk_r : int or NumPy 2D-array, default 5
Radius of the disk. Either integer or NumPy 2-D array.
See examples on how to make it the correct size.
disk_I : int or NumPy 2D-array, default 20
Intensity of the disk, for each of the pixels.
So if I=30, the each pixel in the disk will have a value of 30.
Note, this value will change if blur=True or downscale=True.
ring_x, ring_y : int or NumPy 2D-array, default 20
Centre position of the ring. Either integer or NumPy 2-D array.
See examples on how to make them the correct size.
To deactivate the ring, set ring_x=None.
ring_r : int or NumPy 2D-array, default 20
Radius of the ring. Either integer or NumPy 2-D array.
See examples on how to make it the correct size.
ring_I : int or NumPy 2D-array, default 6
Intensity of the ring, for each of the pixels.
So if I=5, each pixel in the ring will have a value of 5.
Note, this value will change if blur=True or downscale=True.
ring_lw : int or NumPy 2D-array, default 0
Line width of the ring. If ring_lw=1, the line will be 3 pixels wide.
If ring_lw=2, the line will be 5 pixels wide.
ring_e_x, ring_e_y : int or NumPy 2D-array, default 20
Centre position of the elliptical ring. Either integer or
NumPy 2-D array. See examples on how to make them the correct size.
To deactivate the ring, set ring_x=None (which is the default).
ring_e_semi_len0, ring_e_semi_len1 : int or NumPy 2D-array, default 15
Semi lengths of the elliptical ring. Either integer or NumPy 2-D
arrays. See examples on how to make it the correct size.
ring_e_I : int or NumPy 2D-array, default 6
Intensity of the elliptical ring, for each of the pixels.
So if I=5, each pixel in the ring will have a value of 5.
Note, this value will change if blur=True or downscale=True.
ring_e_r : int or NumPy 2D-array, default 0
Rotation of the elliptical ring, in radians.
ring_e_lw : int or NumPy 2D-array, default 0
Line width of the ring. If ring_lw=1, the line will be 3 pixels wide.
If ring_lw=2, the line will be 5 pixels wide.
blur : bool, default True
If True, do a Gaussian blur of the disk.
blur_sigma : int, default 1
Sigma of the Gaussian blurring, if blur is True.
downscale : bool, default True
If True, use upscaling (then downscaling) to anti-alise the disk.
add_noise : bool, default False
Add Gaussian random noise.
noise_amplitude : float, default 1
The amplitude of the noise, if add_noise is True.
lazy : bool, default False
If True, the signal will be lazy
lazy_chunks : tuple, optional
Used if lazy is True, default (10, 10, 10, 10).
Returns
-------
signal : HyperSpy Signal2D
Signal with 2 navigation dimensions and 2 signal dimensions.
Examples
--------
>>> from pyxem.dummy_data import make_diffraction_test_data as mdtd
>>> s = mdtd.generate_4d_data(show_progressbar=False)
>>> s.plot()
Using more arguments
>>> s = mdtd.generate_4d_data(probe_size_x=20, probe_size_y=30,
... image_size_x=50, image_size_y=90,
... disk_x=30, disk_y=70, disk_r=9, disk_I=30,
... ring_x=35, ring_y=65, ring_r=20, ring_I=10,
... blur=False, downscale=False, show_progressbar=False)
Adding some Gaussian random noise
>>> s = mdtd.generate_4d_data(add_noise=True, noise_amplitude=3,
... show_progressbar=False)
Different centre positions for each probe position.
Note the size=(20, 10), and probe_x=10, probe_y=20: size=(y, x).
>>> import numpy as np
>>> disk_x = np.random.randint(5, 35, size=(20, 10))
>>> disk_y = np.random.randint(5, 45, size=(20, 10))
>>> disk_I = np.random.randint(50, 100, size=(20, 10))
>>> ring_x = np.random.randint(5, 35, size=(20, 10))
>>> ring_y = np.random.randint(5, 45, size=(20, 10))
>>> ring_r = np.random.randint(10, 15, size=(20, 10))
>>> ring_I = np.random.randint(1, 30, size=(20, 10))
>>> ring_lw = np.random.randint(1, 5, size=(20, 10))
>>> s = mdtd.generate_4d_data(probe_size_x=10, probe_size_y=20,
... image_size_x=40, image_size_y=50, disk_x=disk_x, disk_y=disk_y,
... disk_I=disk_I, ring_x=ring_x, ring_y=ring_y, ring_r=ring_r,
... ring_I=ring_I, ring_lw=ring_lw, show_progressbar=False)
Do not plot the disk
>>> s = mdtd.generate_4d_data(disk_x=None, show_progressbar=False)
Do not plot the ring
>>> s = mdtd.generate_4d_data(ring_x=None, show_progressbar=False)
Plot only an elliptical ring
>>> from numpy.random import randint, random
>>> s = mdtd.generate_4d_data(
... probe_size_x=10, probe_size_y=10,
... disk_x=None, ring_x=None,
... ring_e_x=randint(20, 30, (10, 10)),
... ring_e_y=randint(20, 30, (10, 10)),
... ring_e_semi_len0=randint(10, 20, (10, 10)),
... ring_e_semi_len1=randint(10, 20, (10, 10)),
... ring_e_r=random((10, 10))*np.pi,
... ring_e_lw=randint(1, 3, (10, 10)))
"""
if disk_x is None:
plot_disk = False
else:
plot_disk = True
if not isiterable(disk_x):
disk_x = np.ones((probe_size_y, probe_size_x)) * disk_x
if not isiterable(disk_y):
disk_y = np.ones((probe_size_y, probe_size_x)) * disk_y
if not isiterable(disk_r):
disk_r = np.ones((probe_size_y, probe_size_x)) * disk_r
if not isiterable(disk_I):
disk_I = np.ones((probe_size_y, probe_size_x)) * disk_I
if ring_x is None:
plot_ring = False
else:
plot_ring = True
if not isiterable(ring_x):
ring_x = np.ones((probe_size_y, probe_size_x)) * ring_x
if not isiterable(ring_y):
ring_y = np.ones((probe_size_y, probe_size_x)) * ring_y
if not isiterable(ring_r):
ring_r = np.ones((probe_size_y, probe_size_x)) * ring_r
if not isiterable(ring_I):
ring_I = np.ones((probe_size_y, probe_size_x)) * ring_I
if not isiterable(ring_lw):
ring_lw = np.ones((probe_size_y, probe_size_x)) * ring_lw
if ring_e_x is None:
plot_ring_e = False
else:
plot_ring_e = True
if not isiterable(ring_e_x):
ring_e_x = np.ones((probe_size_y, probe_size_x)) * ring_e_x
if not isiterable(ring_e_y):
ring_e_y = np.ones((probe_size_y, probe_size_x)) * ring_e_y
if not isiterable(ring_e_semi_len0):
ring_e_semi_len0 = np.ones((probe_size_y, probe_size_x)) * ring_e_semi_len0
if not isiterable(ring_e_semi_len1):
ring_e_semi_len1 = np.ones((probe_size_y, probe_size_x)) * ring_e_semi_len1
if not isiterable(ring_e_I):
ring_e_I = np.ones((probe_size_y, probe_size_x)) * ring_e_I
if not isiterable(ring_e_lw):
ring_e_lw = np.ones((probe_size_y, probe_size_x)) * ring_e_lw
if not isiterable(ring_e_r):
ring_e_r = np.ones((probe_size_y, probe_size_x)) * ring_e_r
signal_shape = (probe_size_y, probe_size_x, image_size_y, image_size_x)
s = Diffraction2D(np.zeros(shape=signal_shape))
for i in tqdm(s, desc="Make test data", disable=not show_progressbar):
index = s.axes_manager.indices[::-1]
test_data = MakeTestData(
size_x=image_size_x,
size_y=image_size_y,
default=False,
blur=blur,
blur_sigma=blur_sigma,
downscale=downscale,
)
if plot_disk:
dx, dy, dr = disk_x[index], disk_y[index], disk_r[index]
dI = disk_I[index]
test_data.add_disk(dx, dy, dr, intensity=dI)
if plot_ring:
rx, ry, rr = ring_x[index], ring_y[index], ring_r[index]
rI, rLW = ring_I[index], ring_lw[index]
test_data.add_ring(rx, ry, rr, intensity=rI, lw_pix=rLW)
if plot_ring_e:
rex, rey = ring_e_x[index], ring_e_y[index]
resl0, resl1 = ring_e_semi_len0[index], ring_e_semi_len1[index]
reI, reLW, rer = ring_e_I[index], ring_e_lw[index], ring_e_r[index]
test_data.add_ring_ellipse(
x0=rex,
y0=rey,
semi_len0=resl0,
semi_len1=resl1,
rotation=rer,
intensity=reI,
lw_r=reLW,
)
s.data[index][:] = test_data.signal.data[:]
if add_noise:
s.data[index][:] += (
np.random.random(size=(image_size_y, image_size_x)) * noise_amplitude
)
s.axes_manager.indices = [0] * s.axes_manager.navigation_dimension
if lazy:
if lazy_chunks is None:
lazy_chunks = 10, 10, 10, 10
data_lazy = da.from_array(s.data, lazy_chunks)
s = LazyDiffraction2D(data_lazy)
return s
def test_different_shape(self):
array = da.ones(shape=(7, 9, 30, 40), chunks=(3, 3, 5, 5))
s = LazyDiffraction2D(array)
s_r = s.radial_average()
assert (s_r.data[:, :, :-2] == 1).all()
def test_lazy_input(self):
s = LazyDiffraction2D(
da.random.randint(100, size=(5, 5, 20, 20), chunks=(1, 1, 10, 10)))
s_template = s.template_match_disk()
assert s.data.shape == s_template.data.shape
assert s._lazy is True
