def stackify(stack, virtual=False):
if isinstance(stack, base.LEEMStack):
return stack
if isinstance(stack, base.LEEMImg):
return base.LEEMStack([stack])
# raise ValueError("LEEMStack expected, but got LEEMImg")
return base.LEEMStack(stack, virtual=virtual)
def test_stack_constructor_nonsense():
with pytest.raises(ValueError):
_ = base.LEEMStack("nonsense")
with pytest.raises(FileNotFoundError):
_ = base.LEEMStack(["nonsense.dat"], nolazy=True)
stack = base.LEEMStack(["nonsense.dat"])
with pytest.raises(FileNotFoundError):
assert stack[0].data
def test_stack_constructor_globbing(stack_folder):
stack1 = base.LEEMStack(stack_folder, virtual=True)
stack2 = base.LEEMStack(stack_folder + "/*.dat", virtual=True)
stack3 = base.LEEMStack(stack_folder + "/", virtual=True)
assert len(stack1) == len(stack2) == len(stack3)
for i in [0, -1]:
assert stack1[i] == stack2[i]
assert stack1[i] == stack3[i]
stack3 = base.LEEMStack(IMG_FNAMES_COMPATIBLE[0])
assert len(stack3) == 1
def test_stack_virtuality(stack_fname):
stack2 = base.LEEMStack(stack_fname, virtual=True)
if not isinstance(stack2.fnames[0], str) or not stack2.fnames[0].endswith(".dat"):
assert not stack2._virtual
return
stack = base.LEEMStack(stack_fname, virtual=False)
assert stack2._images is None
assert len(stack) == len(stack2)
assert stack[0].data.shape == stack2[0].data.shape
assert stack[-1].meta == stack2[-1].meta
def test_stack_set_virtual(stack_fname):
if "tif" in stack_fname:
return
stack = base.LEEMStack(stack_fname, virtual=True)
assert stack._images is None
stack.virtual = False
assert len(stack._images) == len(stack)
def test_stack_normalize(inplace, copy, normed_img):
img = base.LEEMImg(TESTDATA_DIR + "bremen.dat")
if copy:
stack = base.LEEMStack([img.copy(), img.copy()])
else:
stack = base.LEEMStack([img, img])
ref = stack
if inplace:
stack.normalize(mcp=MCP_IMG_FNAME, inplace=inplace, dark_counts=100)
else:
stack = stack.normalize(mcp=MCP_IMG_FNAME,
inplace=inplace,
dark_counts=100)
assert (stack is ref) == inplace
for img, ref_img in zip(stack, ref):
assert (img is ref_img) == inplace
assert_array_equal(img.image, normed_img.image)
def main():
# pylint: disable=unused-variable
import sys
stack = base.LEEMStack("testdata/test_IVLEED_VO2-RuO2")
stack = stack[::4]
# stack = stack[::10]
# rsm_calc = rsm.RSM(
# stack,
# [503, 519],
# profile_start=[105, 303],
# profile_end=[919, 710],
# # kpara_per_pix=3.84e7
# kpara_per_pix=7.67e7
# )
# plt.imshow(np.log(stack[10].data))
# plt.scatter(
# [503, 304, 711, 105, 919],
# [510, 411, 610, 303, 710],
# s=5, color="k"
# )
# plt.show()
# sys.exit()
# for img in stack[:10]:
# plt.plot(np.log(rsm_calc.get_line(img.data)))
# plt.figure()
# kpara = rsm_calc.get_kpara_along_line()
# kperp = rsm_calc.get_kperp_along_line(stack.energy[10], kpara)
# for energy in stack.energy:
# plt.plot(rsm_calc.get_kperp_along_line(energy, kpara))
# plt.plot(kpara)
# plt.figure()
# plt.plot(kperp)
# plt.figure()
cut = rsm.RSMCut(start=[105, 303], end=[919, 710])
kx, ky, z = rsm.get_rsm(
stack, cut,
xy0=[503, 519],
kpara_per_pix=7.67e7
)
plt.pcolormesh(
kx * 1e-10, ky * 1e-10,
z,
shading="flat",
cmap="gray"
)
plot_stack(stack)
plt.show()
def pendry_stack():
loaded = False
try:
stack = base.LEEMStack(TESTDATA_DIR + "pendried_stack.lstk")
loaded = True
except FileNotFoundError:
stack = base.LEEMStack(TESTDATA_DIR +
"test_stack_IV_RuO2_normed_aligned_80-130.tif")
stack.energy = np.linspace(3.0, 50.0, len(stack))
X, _, _ = cluster.stack2vectors(
stack, mask_outer=0.2) # cut away 20% on every side
if loaded:
X = stack.pendry
else:
# cut out a few bad frames
X = np.delete(X, list((range(10))) + [160], axis=1)
energy = np.delete(stack.energy, list((range(10))) + [160])
X = cluster.pendryfy(X, energy)
stack.pendry = X
stack.save(TESTDATA_DIR + "pendried_stack.lstk")
return stack
def test_stack_constructor_nonsense():
with pytest.raises(ValueError):
_ = base.LEEMStack("nonsense")
with pytest.raises(FileNotFoundError):
_ = base.LEEMStack(["nonsense.dat"])
def test_stack_constructor(stack_fname, virtual):
stack = base.LEEMStack(stack_fname, virtual=virtual)
assert isinstance(stack[0], base.LEEMImg)
assert stack[0].image.shape == stack[-1].image.shape
def test_stack_pickling(stack):
stack.save(TESTDATA_DIR + "test_stack.lstk")
stack2 = base.LEEMStack(TESTDATA_DIR + "test_stack.lstk")
assert stack == stack2
def test_stack_constructor_array():
stack = base.LEEMStack(STACK_FNAMES[0])
data = np.stack([img.data for img in stack], axis=0)
stack2 = base.LEEMStack(data)
assert len(stack2) == len(stack)
def test_stack_constructor_lists():
stack = base.LEEMStack(IMG_FNAMES_COMPATIBLE)
stack2 = base.LEEMStack([base.LEEMImg(ifn) for ifn in IMG_FNAMES_COMPATIBLE])
assert stack == stack2
assert stack.path == "NO_PATH"
def test_stack_constructor_globbing():
stack = base.LEEMStack(TESTDATA_DIR + "*.dat")
stack2 = base.LEEMStack(TESTDATA_DIR + "*")
assert len(stack2) >= len(stack)
stack3 = base.LEEMStack(IMG_FNAMES_COMPATIBLE[0])
assert len(stack3) == 1
def main():
# pylint: disable=unused-variable, too-many-locals
import matplotlib.pyplot as plt
n_components = 15
# for n_clusters in range(8, 9):
n_clusters = 8
loaded = False
try:
# raise FileNotFoundError
stack = base.LEEMStack(TESTDATA_DIR + "pendried_stack.lstk")
loaded = True
except FileNotFoundError:
stack = base.LEEMStack(TESTDATA_DIR +
"test_stack_IV_RuO2_normed_aligned_80-130.tif")
stack.energy = np.linspace(3.0, 50.0, len(stack))
stack = stack[10:]
X, h, w = cluster.stack2vectors(
stack, mask_outer=0.2) # cut away 20% on every side
if loaded:
X = stack.pendry
else:
X = cluster.pendryfy(X, stack.energy, smoothing_params={"both": True})
stack.pendry = X
stack.save(TESTDATA_DIR + "pendried_stack.lstk")
trafo, inv_trafo, model = cluster.component_analysis(
X, "pca", n_components=n_components)
W = trafo(X)
comps = cluster.vectors2stack(W, h, w)
# labels, model = cluster.repeat_cluster_analysis(
# W, "pc-kmeans", n_iter=50, init="random",
# n_clusters=n_clusters, metric="euclidean_square"
# )
labels, model = cluster.elbow_cluster_analysis(W,
"pc-kmeans",
start=3,
end=10,
init="random",
n_clusters=n_clusters,
metric="euclidean_square")
fig, ax = plt.subplots()
for Y in cluster.extract_IVs(X, labels):
ax.plot(stack.energy, Y)
fig3, ax3 = plt.subplots()
ax3.imshow(labels.reshape(h, w))
fig4, ax4 = plt.subplots()
cluster.plot_IVs(stack, labels, ax=ax4)
# fig.savefig(f"{n_clusters}_pendry.png")
# fig3.savefig(f"{n_clusters}_clustermap.png")
# fig4.savefig(f"{n_clusters}_IVs.png")
# plt.close(fig)
# plt.close(fig3)
# plt.close(fig4)
plt.show()