def test_get_rgb_image_rois(self):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
# Get channels by ROIs
rois1 = [
vbse_gen.roi_from_grid(i) for i in np.ndindex(vbse_gen.grid_shape)
][:3]
vbse_rgb_img1 = vbse_gen.get_rgb_image(r=rois1[0],
g=rois1[1],
b=rois1[2])
# Get channels from grid tile indices
rois2 = [(0, 0), (0, 1), (0, 2)]
vbse_rgb_img2 = vbse_gen.get_rgb_image(r=rois2[0],
g=rois2[1],
b=rois2[2])
assert isinstance(vbse_rgb_img1, VirtualBSEImage)
assert vbse_rgb_img1.data.dtype == np.dtype([("R", "u1"), ("G", "u1"),
("B", "u1")])
vbse_rgb_img1.change_dtype(np.uint8)
vbse_rgb_img2.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img1.data, vbse_rgb_img2.data)
def test_get_rgb_1d(self):
s = EBSD(np.random.random(9 * 3600).reshape((9, 60, 60)))
vbse_gen = VirtualBSEGenerator(s)
with pytest.raises(ValueError,
match="The signal dimension cannot be "):
_ = vbse_gen.get_rgb_image(r=(0, 0), g=(0, 1), b=(0, 2))
def test_get_rgb_alpha_signal(self):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
vbse_img = s.get_virtual_bse_intensity(roi=RectangularROI(0, 0, 10, 10))
vbse_rgb_img1 = vbse_gen.get_rgb_image(
r=(0, 1), g=(0, 2), b=(0, 3), alpha=vbse_img
)
vbse_rgb_img2 = vbse_gen.get_rgb_image(
r=(0, 1), g=(0, 2), b=(0, 3), alpha=vbse_img.data,
)
vbse_rgb_img1.change_dtype(np.uint8)
vbse_rgb_img2.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img1.data, vbse_rgb_img2.data)
def test_get_rgb_multiple_rois_per_channel(self, r, g, b,
desired_mean_intensity):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
vbse_rgb_img1 = vbse_gen.get_rgb_image(r=r, g=g, b=b)
vbse_rgb_img1.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img1.data.mean(), desired_mean_intensity)
roi_r = vbse_gen.roi_from_grid(r)
roi_g = vbse_gen.roi_from_grid(g)
roi_b = vbse_gen.roi_from_grid(b)
vbse_rgb_img2 = vbse_gen.get_rgb_image(r=roi_r, g=roi_g, b=roi_b)
vbse_rgb_img2.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img1.data, vbse_rgb_img2.data)
def test_get_rgb_image_lazy(self):
s = load(KIKUCHIPY_FILE, lazy=True)
vbse_gen = VirtualBSEGenerator(s)
assert isinstance(vbse_gen.signal, LazyEBSD)
vbse_rgb_img = vbse_gen.get_rgb_image(r=(0, 0), g=(0, 1), b=(0, 2))
assert isinstance(vbse_rgb_img.data, np.ndarray)
def test_get_rgb_image_dtype(self):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
vbse_rgb_img = vbse_gen.get_rgb_image(r=(0, 0),
g=(0, 1),
b=(0, 2),
dtype_out=np.uint16)
assert vbse_rgb_img.data.dtype == np.dtype([("R", "u2"), ("G", "u2"),
("B", "u2")])
def test_get_rgb_image_contrast_stretching(self, percentile,
desired_mean_intensity):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
vbse_rgb_img = vbse_gen.get_rgb_image(r=(0, 0),
g=(0, 1),
b=(0, 2),
percentiles=percentile)
vbse_rgb_img.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img.data.mean(), desired_mean_intensity)
def test_get_rgb_alpha(self, alpha_add, desired_mean_intensity):
s = load(KIKUCHIPY_FILE)
vbse_gen = VirtualBSEGenerator(s)
alpha = np.arange(9).reshape((3, 3))
alpha[0] += alpha_add
vbse_rgb_img = vbse_gen.get_rgb_image(
r=(0, 0), g=(0, 1), b=(0, 2), alpha=alpha
)
vbse_rgb_img.change_dtype(np.uint8)
assert np.allclose(vbse_rgb_img.data.mean(), desired_mean_intensity)
def test_normalize_rgb_raises(self, dummy_signal):
vbse_gen = VirtualBSEGenerator(dummy_signal)
vbse_gen.grid_shape = (3, 3)
rgb = vbse_gen.get_rgb_image(r=(0, 0), g=(0, 1), b=(1, 0))
with pytest.raises(NotImplementedError):
rgb.normalize_intensity()