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281 lines
11 KiB
Python
281 lines
11 KiB
Python
import numpy as np
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from numpy.fft import fftshift, ifftshift
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from numpy import fft
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import pytest
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import torch as t
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from cdtools.tools import interactions
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# Have a random probe and a random object and test the two
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# functions for a variety of overlaps
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# Also I want a probe that's just a single pixel
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#
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@pytest.fixture(scope='module')
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def random_probe():
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return np.random.rand(256, 256) * np.exp(2j * np.pi * np.random.rand(256, 256))
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@pytest.fixture(scope='module')
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def random_obj():
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return np.random.rand(900, 900) * np.exp(2j * np.pi * np.random.rand(900, 900))
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@pytest.fixture(scope='module')
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def single_pixel_probe(scope='module'):
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probe = np.zeros((256, 256), dtype=np.complex128)
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probe[128, 128] = 1
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return probe
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def test_translations_to_pixel():
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# First, try the case where everything is ones and simple
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basis = t.Tensor([[0, -1, 0], [-1, 0, 0]]).t()
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translations = t.rand((10, 3))
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output = interactions.translations_to_pixel(basis, translations)
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assert t.allclose(output, -translations[:, :2].flip(1))
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# Next, try a case with a single translation
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translation = t.rand((3))
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output = interactions.translations_to_pixel(basis, translation)
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assert t.allclose(output, -translation[:2].flip(0))
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# Then, try a case with no surface normal but with a real conversion
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basis = t.Tensor([[0, -2, 0], [-1, 0, 0.1]]).t()
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translations = t.rand((10, 3))
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output = interactions.translations_to_pixel(basis, translations)
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basis_vectors_inv = t.pinverse(basis)
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translations[:, 2] = 0 # manually project off z component
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assert t.allclose(output, t.mm(translations, basis_vectors_inv.t()))
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# Finally, try a case with a known surface normal (reflection)
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basis = t.Tensor([[0, -1, 0], [0, 0, 1]]).t()
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surface_normal = t.Tensor([np.sqrt(2), 0, -np.sqrt(2)])
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translations = t.rand((10, 3))
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output = interactions.translations_to_pixel(basis, translations,
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surface_normal=surface_normal)
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exp_translations = t.stack((-translations[:, 1], translations[:, 0]), dim=1)
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assert t.allclose(output, exp_translations)
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def test_pixel_to_translations():
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# First, try the case where everything is ones and simple
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basis = t.Tensor([[0, -1, 0], [-1, 0, 0]]).t()
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translations = t.rand((10, 3))
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translations[:, 2] = 0
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output = interactions.translations_to_pixel(basis, translations)
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roundtrip = interactions.pixel_to_translations(basis, output)
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assert t.allclose(translations, roundtrip)
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# Next, try a case with a single translation
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translation = t.rand((3))
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translation[2] = 0
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output = interactions.translations_to_pixel(basis, translation)
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roundtrip = interactions.pixel_to_translations(basis, output)
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assert t.allclose(translation, roundtrip)
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# Then, try a case with no surface normal but with a real conversion
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basis = t.Tensor([[0, -2, 0], [-1, 0, 0.1]]).t()
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translations = t.rand((10, 3))
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translations[:, 2] = 0 # manually project off z component
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output = interactions.translations_to_pixel(basis, translations)
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roundtrip = interactions.pixel_to_translations(basis, output)
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assert t.allclose(translations, roundtrip)
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# Finally, try a case with a known surface normal (reflection)
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basis = t.Tensor([[0, -1, 0], [0, 0, 1]]).t()
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surface_normal = t.Tensor([np.sqrt(2), 0, -np.sqrt(2)])
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translations = t.rand((10, 3))
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translations[:, 2] = 0 # manually project off z component
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output = interactions.translations_to_pixel(basis, translations,
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surface_normal=surface_normal)
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roundtrip = interactions.pixel_to_translations(basis, output,
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surface_normal=surface_normal)
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assert t.allclose(translations, roundtrip)
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def test_project_translations_to_sample():
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# First, try the case where everything is ones and simple
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basis = t.Tensor([[0, -1, 0], [-1, 0, 0]]).t()
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translations = t.rand((10, 3))
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pixels, props = interactions.project_translations_to_sample(basis, translations)
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assert np.allclose(pixels[:, 0].numpy(), -translations[:, 1])
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assert np.allclose(pixels[:, 1].numpy(), -translations[:, 0])
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assert np.allclose(props.numpy(), -translations[:, 2:].numpy())
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# Next, a simple tilt along one axis. This is a 45 degree rotation
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# around the positive y-axis
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# Thus, y-axis translations are unaffected, but x-axis translations
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# induce a motion of 1/sqrt(2) in the j- pixel space, as well as
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# creating a propagation (negative propagation for positive x)
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basis = t.Tensor([[0, -1e-3, 0], [-np.sqrt(2) * 1e-3, 0, np.sqrt(2) * 1e-3]]).t()
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translations = t.rand((10, 3))
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pixels, props = interactions.project_translations_to_sample(basis, translations)
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print(props.numpy())
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print(-translations[:, 2:].numpy() - translations[:, :1].numpy())
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assert np.allclose(pixels[:, 0].numpy(), -translations[:, 1] * 1e3)
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assert np.allclose(pixels[:, 1].numpy(), -translations[:, 0] * 1e3 / np.sqrt(2))
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assert np.allclose(props.numpy(), -translations[:, 2:].numpy() - translations[:, :1].numpy())
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# Finally, we check a non-orthogonal case
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def test_ptycho_2D_round(random_probe, random_obj):
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# Test a stack of images
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translations = np.random.rand(10, 2) * 500
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exit_waves_np = [random_probe * random_obj[tr[0]:tr[0] + random_probe.shape[0],
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tr[1]:tr[1] + random_probe.shape[1]] for
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tr in np.round(translations).astype(int)]
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exit_waves_t = interactions.ptycho_2D_round(t.as_tensor(random_probe),
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t.as_tensor(random_obj),
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t.as_tensor(translations))
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assert np.allclose(exit_waves_t.numpy(), exit_waves_np)
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# Test the single wave case
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exit_wave_t = interactions.ptycho_2D_round(t.as_tensor(random_probe),
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t.as_tensor(random_obj),
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t.as_tensor(translations[0]))
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assert np.allclose(exit_wave_t.numpy(), exit_waves_np[0])
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def test_ptycho_2D_linear(single_pixel_probe, random_obj):
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# For this one, I just want to check one translation, but
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# I need to check both formats
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translations = np.array([[46.7, 53.2]])
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translation = np.array([46.7, 53.2])
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exit_waves_probe = interactions.ptycho_2D_linear(
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t.as_tensor(single_pixel_probe),
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t.as_tensor(random_obj),
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t.as_tensor(translations),
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shift_probe=True)
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exit_wave_probe = interactions.ptycho_2D_linear(
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t.as_tensor(single_pixel_probe),
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t.as_tensor(random_obj),
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t.tensor(translation),
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shift_probe=True)
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# Check that the outputs match
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assert t.allclose(exit_waves_probe[0], exit_wave_probe)
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exit_waves_obj = interactions.ptycho_2D_linear(t.as_tensor(single_pixel_probe), t.as_tensor(random_obj), t.tensor(translations), shift_probe=False)
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exit_wave_obj = interactions.ptycho_2D_linear(
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t.as_tensor(single_pixel_probe),
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t.as_tensor(random_obj),
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t.tensor(translation),
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shift_probe=False)
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# Check that the outputs match
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assert t.allclose(exit_waves_obj[0], exit_wave_obj)
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# For the shifted probe, we should find 4 pixels with intensity
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exit_waves_probe = t.as_tensor(exit_waves_probe)[0]
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probe_shift = np.array([[0.3 * 0.8, 0.3 * 0.2],
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[0.7 * 0.8, 0.7 * 0.2]])
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obj_section = random_obj[128 + 46:128 + 48,
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128 + 53:128 + 55]
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exit_section = exit_waves_probe[128:130, 128:130]
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assert np.allclose(probe_shift * obj_section, exit_section)
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# For the shifted obj, we should find one pixel with intensity
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exit_waves_obj = t.as_tensor(exit_waves_obj)[0]
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obj_shift = np.array([[0.3 * 0.8, 0.3 * 0.2],
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[0.7 * 0.8, 0.7 * 0.2]])
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obj_section = random_obj[128 + 46:128 + 48,
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128 + 53:128 + 55]
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exit_pixel = exit_waves_obj[128, 128]
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assert np.isclose(np.sum(obj_shift * obj_section), exit_pixel)
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# Test for a single translation
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def test_ptycho_2D_sinc(single_pixel_probe, random_obj):
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# For this one, I just want to check one translation, but
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# I need to check both formats
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translations = np.array([[46.7, 53.2]])
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translation = np.array([46.7, 53.2])
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exit_waves_probe = interactions.ptycho_2D_sinc(
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t.as_tensor(single_pixel_probe),
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t.as_tensor(random_obj),
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t.as_tensor(translations),
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shift_probe=True)
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exit_wave_probe = interactions.ptycho_2D_sinc(
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t.as_tensor(single_pixel_probe),
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t.as_tensor(random_obj),
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t.as_tensor(translation),
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shift_probe=True)
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# Check that the outputs match
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assert t.allclose(exit_waves_probe[0], exit_wave_probe)
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# Now we explicitly define what the sinc interpolated array should
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# look like
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xs = np.arange(256) - 128
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Ys, Xs = np.meshgrid(xs, xs)
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sinc_probe = np.sinc(Xs) * np.sinc(Ys)
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# Just check that the unshifted probe is correct
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assert np.allclose(single_pixel_probe, sinc_probe)
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sinc_shifted_probe = np.sinc(Xs - 0.7) * np.sinc(Ys - 0.2)
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obj_section = random_obj[46:46 + 256,
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53:53 + 256]
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exit_wave_np = sinc_shifted_probe * obj_section
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exit_wave_torch = exit_wave_probe.numpy()
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# The fidelity isn't great due to the FFT-based approach, so we need
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# a pretty relaxed condition
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assert np.max(np.abs(exit_wave_np - exit_wave_torch)) < 0.005
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def test_RPI_interaction(random_probe, random_obj):
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random_obj1 = random_obj[:79, :68] * 0 + 1
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random_probe1 = random_probe * 0 + 1
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t_random_obj1 = t.as_tensor(random_obj1)
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t_random_probe1 = t.as_tensor(random_probe1)
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t_output1 = interactions.RPI_interaction(t_random_probe1, t_random_obj1)
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obj1_fourier = fftshift(fft.fft2(ifftshift(random_obj1), norm='ortho'))
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obj1_ups = np.zeros(random_probe1.shape[:2]).astype(np.complex128)
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obj1_ups[random_probe1.shape[0] // 2 - 79 // 2:
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-(random_probe1.shape[0] - 79 - (random_probe1.shape[0] // 2 - 79 // 2)),
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(random_probe1.shape[1] - 68) // 2:
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(random_probe1.shape[1] - 68) // 2 + 68] = obj1_fourier
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output1 = random_probe1 * fftshift(fft.ifft2(ifftshift(obj1_ups),
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norm='ortho'))
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output1 = output1 * np.sqrt(output1.shape[-2] * output1.shape[-1] / (random_obj1.shape[-2] * random_obj1.shape[-1]))
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assert np.allclose(t_output1, output1)
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random_obj2 = np.stack([random_obj[:64, :89]] * 3)
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random_probe2 = random_probe[3:, 5:]
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t_random_obj2 = t.as_tensor(random_obj2)
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t_random_probe2 = t.as_tensor(random_probe2)
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t_output2 = interactions.RPI_interaction(t_random_probe2, t_random_obj2)
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obj2_fourier = fftshift(fft.fft2(ifftshift(random_obj2), norm='ortho'))
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obj2_ups = np.zeros((3,) + random_probe2.shape[:2]).astype(np.complex128)
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obj2_ups[:, (random_probe2.shape[0] - 64) // 2:
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(random_probe2.shape[0] - 64) // 2 + 64,
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(random_probe2.shape[1] - 89) // 2:
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(random_probe2.shape[1] - 89) // 2 + 89] = obj2_fourier
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output2 = random_probe2 * fftshift(fft.ifft2(ifftshift(obj2_ups),
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norm='ortho'))
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output2 = output2 * np.sqrt(output2.shape[-2] * output2.shape[-1] / (random_obj2.shape[-2] * random_obj2.shape[-1]))
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assert np.allclose(t_output2, output2)
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