def test_field(self, bohren=False, cartesian=False):
p = self.method.particle
p.a_p = 1.
p.n_p = 1.4
p.r_p = [64, 64, 100]
c = coordinates([128, 128])
self.method.coordinates = c
field = self.method.field(bohren=bohren, cartesian=cartesian)
self.assertEqual(field.shape[1], c.shape[1])
def test_hologram(self):
p = self.method.particle
p.a_p = 1.
p.n_p = 1.4
p.r_p = [64, 64, 100]
c = coordinates([128, 128])
self.method.coordinates = c
hologram = self.method.hologram()
self.assertEqual(hologram.shape[0], c.shape[1])
def setUp(self):
data = cv2.imread(TEST_IMAGE, 0).astype(float)
data /= np.mean(data)
coords = coordinates(data.shape)
model = LMHologram(wavelength=0.447, magnification=0.048, n_m=1.34)
self.data = data
self.coords = coords
self.feature = Feature(data=data,
coordinates=coords,
model=model,
percentpix=0.1)
model.particle.r_p = [data.shape[0] // 2, data.shape[1] // 2, 330]
model.particle.a_p = 1.1
model.particle.n_p = 1.4
def setUp(self):
img = cv2.imread(TEST_IMAGE, 0).astype(float)
img /= np.mean(img)
img = img[::4, ::4]
self.shape = img.shape
self.data = img.ravel()
self.coordinates = 4. * coordinates(self.shape)
model = LMHologram(coordinates=self.coordinates)
model.instrument.wavelength = 0.447
model.instrument.magnification = 0.048
model.instrument.n_m = 1.34
model.particle.r_p = [self.shape[0] // 2, self.shape[1] // 2, 330]
model.particle.a_p = 1.1
model.particle.n_p = 1.4
self.optimizer = Optimizer(model=model)
def test_compare_methods(self):
'''check that numpy and cupy pipelines yield consistent results'''
shape = [128, 128]
c = coordinates(shape)
self.method.coordinates = c
self.nmethod.coordinates = c
p = self.method.particle
p.a_p = 1.
p.n_p = 1.4
p.r_p = [64, 64, 100]
self.nmethod.particle = p
field = self.method.field()
nfield = self.nmethod.field()
inten = np.sum(np.abs(field), axis=0).reshape(shape)
ninten = np.sum(np.abs(nfield), axis=0).reshape(shape)
self.assertTrue(np.allclose(inten, ninten))
def test_coordinates(self, corner=None):
shape = [128, 128]
c = coordinates(shape, corner=corner)
self.assertEqual(c.shape[1], np.prod(shape))
def test_normal(self):
c = coordinates(self.shape, flatten=False)
self.assertEqual(c.ndim, 3)
def test_flatten(self):
c = coordinates(self.shape)
self.assertEqual(c.ndim, 2)
def setUp(self):
self.shape = [128, 128]
self.coordinates = coordinates(self.shape)
self.mask = Mask(self.coordinates)
def test_coordinates(self):
c = coordinates(self.shape)
self.method.coordinates = c
self.assertEqual(self.method.coordinates.shape[1], c.shape[1])
def test_coordinates_2d(self):
c = coordinates(self.shape)
self.method.coordinates = c
self.assertEqual(self.method.coordinates.shape[0], 3)
self.assertTrue(np.allclose(self.method.coordinates[0:2, :], c))