def normalize(img_or_stack, *args, **kwargs):
try:
img = imgify(img_or_stack)
return normalize_image(img, *args, **kwargs)
except FileNotFoundError:
stack = stackify(img_or_stack)
return normalize_stack(stack, *args, **kwargs)
def cutout_stack(stack, mask_outer=0.2):
stack = stackify(stack)
_, h0, w0 = len(stack), stack[0].data.shape[0], stack[0].data.shape[1]
dy, dx = (int(mask_outer * h0), int(mask_outer * w0))
if mask_outer == 0:
data = np.array([img.data for img in stack])
else:
data = np.array([img.data[dy:-dy, dx:-dx] for img in stack])
return LEEMStack(data)
def stack2vectors(stack, mask_outer=0.2):
stack = stackify(stack)
_, h0, w0 = len(stack), stack[0].data.shape[0], stack[0].data.shape[1]
dy, dx = (int(mask_outer * h0), int(mask_outer * w0))
h, w = (h0 - 2 * dy, w0 - 2 * dx)
if mask_outer == 0:
data = np.array([img.data.flatten() for img in stack]).T
else:
data = np.array([img.data[dy:-dy, dx:-dx].flatten()
for img in stack]).T
return data, h, w
def get_max_variance_idx(stack):
stack = stackify(stack)
max_var = 0
max_index = 0
for i, img in enumerate(stack):
var = np.var((img.data.flatten() - np.amin(img.data)) /
(np.amax(img.data) - np.amin(img.data)))
if var > max_var:
max_var = var
max_index = i
return max_index
def __init__(self, stack, profile, BZ_pix, d, gamma=None, Vi=0):
self.stack = stackify(stack)
self.profile = profile
if gamma is None:
gamma = profile.position
self.gamma = np.array(gamma)
self.k_BZ = 2 * np.pi / d
self.k_res = self.k_BZ / BZ_pix
self.Vi = Vi
self.data = None
def calculate_dose(stack, pressurefield="pressure1", approx=1):
"""Maybe get rid of approx?."""
stack = stackify(stack)
pressure = getattr(stack, pressurefield)[::approx]
rel_time = stack.rel_time[::approx]
approx_dose = np.cumsum(pressure * np.gradient(rel_time)) * 1e6
# scale up to original length:
long_dose = np.repeat(approx_dose, approx)
cutoff = len(long_dose) - len(stack)
if cutoff < 0:
raise ValueError("Error calculating dose")
return long_dose[cutoff // 2:len(stack) + cutoff // 2]
def normalize_stack(stack, mcp, dark_counts=100):
stack = stackify(stack)
mcp = imgify(mcp)
if not isinstance(dark_counts, (int, float, complex)):
dark_counts = imgify(dark_counts)
stack_normed = stack.copy()
for i, img in enumerate(progress_bar(stack, "Normalizing...")):
stack_normed[i] = normalize_image(img, mcp, dark_counts=dark_counts)
# is this monkey-patching necessary?:
stack_normed.mcp = mcp
stack_normed.dark_counts = dark_counts
return stack_normed
def get_rsm(stack, cut, xy0, kpara_per_pix):
stack = stackify(stack)
res_y, res_x = len(stack), np.rint(cut.length).astype(int)
z = np.zeros((res_y, res_x))
kx = np.zeros((res_y + 1, res_x + 1))
kx[:, :] = kpara_per_pix * cut.length * np.linspace(-0.5, 0.5, res_x + 1)
ky = np.zeros((res_y + 1, res_x + 1))
kpara = get_kpara(cut, xy0, kpara_per_pix, length=res_x + 1)
dE = np.mean(np.diff(stack.energy))
for i, img in enumerate(progress_bar(stack, "Calculating RSM...")):
ky[i, :] = get_kperp(stack.energy[i] - dE / 2, kpara)
z[i, :] = np.log(cut(img.data, length=res_x))
ky[-1, :] = get_kperp(stack.energy[-1] + dE / 2, kpara)
return kx, ky, z
def align(stack, **kwargs):
"""
Use these keyword arguments:
algorithm={"ecc"}
roi: defines a ROI, which can be any shape (circle, rectangle...).
Defaults to 15% rectangular cutoff
for ecc:
trafo={"translation","rigid","affine"} (default=translation)
max_iter=int maximum iterations, default: 500
eps=number threshold to reach, default: 1e-4
avg=int alignment ist averaged by matching with avg Number of previous images,
default: 1
"""
stack = stackify(stack)
alignment = find_alignment_matrices(stack, **kwargs)
stack = apply_alignment_matrices(stack, alignment)
stack.alignment = alignment
return stack, alignment
def rsm(stack, start, end, xy0, kpara_per_pix=7.67e7):
stack = stackify(stack)
cut = RSMCut(start=start, end=end)
kx, ky, z = get_rsm(stack, cut, xy0=xy0, kpara_per_pix=kpara_per_pix)
return kx, ky, z
def test_stackify(stack, stack_fname):
assert isinstance(utility.stackify(stack), base.LEEMStack)
assert isinstance(utility.stackify(stack_fname), base.LEEMStack)