def test_2d_diagonal(self):
array = np.asarray([np.arange(6) for _ in range(6)])
expected = np.array([
0,
0.71428571,
1.42857143,
2.14285714,
2.85714286,
3.57142857,
4.28571429,
5.0,
])
output = gu.linecut(array, indices=[(0, 5), (0, 5)], interp_order=1)
self.assertTrue(np.allclose(output, expected))
def test_3d_diagonal(self):
array = np.asarray([[np.arange(6) for _ in range(6)]
for _ in range(6)])
expected = np.array([
0,
0.55555556,
1.11111111,
1.66666667,
2.22222222,
2.77777778,
3.33333333,
3.88888889,
4.44444444,
5.0,
])
output = gu.linecut(array,
indices=[(0, 5), (0, 5), (0, 5)],
interp_order=1)
self.assertTrue(np.allclose(output, expected))
def on_click(event):
"""
Function to interact with a plot, return the position of clicked pixel.
If flag_pause==1 or if the mouse is out of plot axes, it will not register the click
:param event: mouse click event
"""
global diff_pattern, starting_point, endpoint, distance, fig_diff, ax0, ax1, ax2
global q_text, load_qvalues, vmin, vmax, qx, qy, qz, ax3, plt0, plt1, plt2, cut
global plt0_start, plt1_start, plt2_start, plt0_stop, plt1_stop, plt2_stop
if event.inaxes == ax3: # print the distance value at the mouse position
q_text.remove()
if load_qvalues:
q_text = fig_diff.text(
0.55, 0.43, f"distance = {event.xdata:.3f} (1/A)", size=10
)
else:
q_text = fig_diff.text(0.55, 0.43, f"distance = {event.xdata:.1f}", size=10)
plt.draw()
update_cut = False
else:
if event.button == 1: # left button
if event.inaxes == ax0: # hor=X, ver=Y
starting_point[2], starting_point[1] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
elif event.inaxes == ax1: # hor=X, ver=rocking curve
starting_point[2], starting_point[0] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
elif event.inaxes == ax2: # hor=Y, ver=rocking curve
starting_point[1], starting_point[0] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
else:
update_cut = False
elif event.button == 3: # right button
if event.inaxes == ax0: # hor=X, ver=Y
endpoint[2], endpoint[1] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
elif event.inaxes == ax1: # hor=X, ver=rocking curve
endpoint[2], endpoint[0] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
elif event.inaxes == ax2: # hor=Y, ver=rocking curve
endpoint[1], endpoint[0] = (
int(np.rint(event.xdata)),
int(np.rint(event.ydata)),
)
update_cut = True
else:
update_cut = False
else:
update_cut = False
if update_cut:
q_text.remove()
q_text = fig_diff.text(0.55, 0.25, "", size=10)
print(f"starting_point = {starting_point}, endpoint = {endpoint}")
cut = gu.linecut(
diff_pattern,
indices=list(zip(starting_point, endpoint)),
interp_order=1,
)
if qx.ndim == 1:
d_q = np.sqrt(
(qx[endpoint[0]] - qx[starting_point[0]]) ** 2
+ (qz[endpoint[1]] - qz[starting_point[1]]) ** 2
+ (qy[endpoint[2]] - qy[starting_point[2]]) ** 2
)
else:
d_q = np.sqrt(
(
qx[endpoint[0], endpoint[1], endpoint[2]]
- qx[starting_point[0], starting_point[1], starting_point[2]]
)
** 2
+ (
qz[endpoint[0], endpoint[1], endpoint[2]]
- qz[starting_point[0], starting_point[1], starting_point[2]]
)
** 2
+ (
qy[endpoint[0], endpoint[1], endpoint[2]]
- qy[starting_point[0], starting_point[1], starting_point[2]]
)
** 2
)
distance = np.linspace(0, d_q, num=len(cut))
plt0.remove()
plt1.remove()
plt2.remove()
(plt0,) = ax0.plot(
[starting_point[2], endpoint[2]], [starting_point[1], endpoint[1]], "r-"
) # sum axis 0
(plt1,) = ax1.plot(
[starting_point[2], endpoint[2]], [starting_point[0], endpoint[0]], "r-"
) # sum axis 1
(plt2,) = ax2.plot(
[starting_point[1], endpoint[1]], [starting_point[0], endpoint[0]], "r-"
) # sum axis 2
plt0_start.remove()
plt1_start.remove()
plt2_start.remove()
plt0_stop.remove()
plt1_stop.remove()
plt2_stop.remove()
(plt0_start,) = ax0.plot(
[starting_point[2]], [starting_point[1]], "bo"
) # sum axis 0
(plt0_stop,) = ax0.plot([endpoint[2]], [endpoint[1]], "ro") # sum axis 0
(plt1_start,) = ax1.plot(
[starting_point[2]], [starting_point[0]], "bo"
) # sum axis 1
(plt1_stop,) = ax1.plot([endpoint[2]], [endpoint[0]], "ro") # sum axis 1
(plt2_start,) = ax2.plot(
[starting_point[1]], [starting_point[0]], "bo"
) # sum axis 2
(plt2_stop,) = ax2.plot([endpoint[1]], [endpoint[0]], "ro") # sum axis 2
ax3.cla()
ax3.plot(distance, np.log10(cut), "-or", markersize=3)
if load_qvalues:
ax3.set_xlabel("distance along the linecut (1/A)")
else:
ax3.set_xlabel("distance along the linecut (pixels)")
ax3.set_ylabel("Int (A.U.)")
ax3.axis("auto")
ax3.set_ylim(bottom=-2)
plt.tight_layout()
plt.draw()
raise ValueError("q components should be 1D or 3D arrays")
if load_qvalues:
print(f"COM[qx, qz, qy] = {qxCOM:.3f} 1/A, {qzCOM:.3f} 1/A, {qyCOM:.3f} 1/A")
else:
print(f"COM[qx, qz, qy] = {qxCOM:.3f}, {qzCOM:.3f}, {qyCOM:.3f}")
####################
# interactive plot #
####################
plt.ioff()
starting_point = starting_point or [nz // 2, 0, nx // 2]
endpoint = endpoint or [nz // 2, ny - 1, nx // 2]
cut = gu.linecut(
diff_pattern,
indices=list(zip(starting_point, endpoint)),
interp_order=1,
)
if qx.ndim == 1:
dq = np.sqrt(
(qx[endpoint[0]] - qx[starting_point[0]]) ** 2
+ (qz[endpoint[1]] - qz[starting_point[1]]) ** 2
+ (qy[endpoint[2]] - qy[starting_point[2]]) ** 2
)
else:
dq = np.sqrt(
(
qx[endpoint[0], endpoint[1], endpoint[2]]
- qx[starting_point[0], starting_point[1], starting_point[2]]
)
** 2
def on_click(event):
"""
Function to interact with a plot, return the position of clicked pixel.
If flag_pause==1 or if the mouse is out of plot axes, it will not register the click
:param event: mouse click event
"""
global linecut_prtf, z0, y0, x0, endpoint, distances_q
global fig_prtf, ax0, ax1, ax2, ax3, plt0, plt1, plt2, cut, res_text
if event.inaxes == ax0: # hor=X, ver=Y
endpoint[2], endpoint[1] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax1: # hor=X, ver=rocking curve
endpoint[2], endpoint[0] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax2: # hor=Y, ver=rocking curve
endpoint[1], endpoint[0] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax3: # print the resolution at the mouse position
res_text.remove()
res_text = fig_prtf.text(
0.55,
0.25,
f"Resolution={2*np.pi/(10*event.xdata):.1f} nm",
size=10)
plt.draw()
update_cut = False
else:
update_cut = False
if update_cut:
res_text.remove()
res_text = fig_prtf.text(0.55, 0.25, "", size=10)
print(f"endpoint = {endpoint}")
cut = gu.linecut(
linecut_prtf,
indices=list(zip(starting_point, endpoint)),
interp_order=1,
)
plt0.remove()
plt1.remove()
plt2.remove()
(plt0, ) = ax0.plot([x0, endpoint[2]], [y0, endpoint[1]],
"ro-") # sum axis 0
(plt1, ) = ax1.plot([x0, endpoint[2]], [z0, endpoint[0]],
"ro-") # sum axis 1
(plt2, ) = ax2.plot([y0, endpoint[1]], [z0, endpoint[0]],
"ro-") # sum axis 2
ax3.cla()
ax3.plot(
np.linspace(
distances_q[z0, y0, x0],
distances_q[endpoint[0], endpoint[1], endpoint[2]],
num=len(cut),
),
cut,
"-or",
markersize=3,
)
ax3.axhline(y=1 / np.e, linestyle="dashed", color="k", linewidth=1)
ax3.set_xlabel("q (1/A)")
ax3.set_ylabel("PRTF")
ax3.axis("auto")
plt.tight_layout()
plt.draw()
scale="linear",
vmin=0,
reciprocal_space=True,
)
np.savez_compressed(setup.detector.savedir + "linecut_prtf.npz",
data=linecut_prtf)
else:
linecut_prtf = prtf_matrix
plt.ioff()
max_colorbar = 5
starting_point = [z0, y0, x0]
endpoint = [0, 0, 0]
cut = gu.linecut(
prtf_matrix,
indices=list(zip(starting_point, endpoint)),
interp_order=1,
)
diff_pattern[np.isnan(diff_pattern)] = 0 # discard nans
fig_prtf, ((ax0, ax1), (ax2, ax3)) = plt.subplots(nrows=2,
ncols=2,
figsize=(12, 6))
fig_prtf.canvas.mpl_disconnect(
fig_prtf.canvas.manager.key_press_handler_id)
ax0.imshow(np.log10(diff_pattern.sum(axis=0)),
vmin=0,
vmax=max_colorbar,
cmap=my_cmap)
ax1.imshow(np.log10(diff_pattern.sum(axis=1)),
vmin=0,
vmax=max_colorbar,
if load_qvalues:
print(
f'COM[qx, qz, qy] = {qxCOM:.3f} 1/A, {qzCOM:.3f} 1/A, {qyCOM:.3f} 1/A')
else:
print(f'COM[qx, qz, qy] = {qxCOM:.3f}, {qzCOM:.3f}, {qyCOM:.3f}')
####################
# interactive plot #
####################
plt.ioff()
starting_point = starting_point or [nz // 2, 0, nx // 2]
endpoint = endpoint or [nz // 2, ny - 1, nx // 2]
cut = gu.linecut(diff_pattern,
start_indices=starting_point,
stop_indices=endpoint,
interp_order=1,
debugging=False)
if qx.ndim == 1:
dq = np.sqrt((qx[endpoint[0]] - qx[starting_point[0]])**2 +
(qz[endpoint[1]] - qz[starting_point[1]])**2 +
(qy[endpoint[2]] - qy[starting_point[2]])**2)
else:
dq = np.sqrt(
(qx[endpoint[0], endpoint[1], endpoint[2]] -
qx[starting_point[0], starting_point[1], starting_point[2]])**2 +
(qz[endpoint[0], endpoint[1], endpoint[2]] -
qz[starting_point[0], starting_point[1], starting_point[2]])**2 +
(qy[endpoint[0], endpoint[1], endpoint[2]] -
qy[starting_point[0], starting_point[1], starting_point[2]])**2)
distance = np.linspace(0, dq, num=len(cut))
def on_click(event):
"""
Function to interact with a plot, return the position of clicked pixel. If flag_pause==1 or
if the mouse is out of plot axes, it will not register the click
:param event: mouse click event
"""
global linecut_prtf, z0, y0, x0, endpoint, distances_q
global fig_prtf, ax0, ax1, ax2, ax3, plt0, plt1, plt2, cut, res_text
if event.inaxes == ax0: # hor=X, ver=Y
endpoint[2], endpoint[1] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax1: # hor=X, ver=rocking curve
endpoint[2], endpoint[0] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax2: # hor=Y, ver=rocking curve
endpoint[1], endpoint[0] = int(np.rint(event.xdata)), int(
np.rint(event.ydata))
update_cut = True
elif event.inaxes == ax3: # print the resolution at the mouse position
res_text.remove()
res_text = fig_prtf.text(
0.55,
0.25,
f'Resolution={2*np.pi/(10*event.xdata):.1f} nm',
size=10)
plt.draw()
update_cut = False
else:
update_cut = False
if update_cut:
res_text.remove()
res_text = fig_prtf.text(0.55, 0.25, '', size=10)
print(f'endpoint = {endpoint}')
cut = gu.linecut(linecut_prtf,
start_indices=(z0, y0, x0),
stop_indices=endpoint,
interp_order=1,
debugging=False)
plt0.remove()
plt1.remove()
plt2.remove()
plt0, = ax0.plot([x0, endpoint[2]], [y0, endpoint[1]],
'ro-') # sum axis 0
plt1, = ax1.plot([x0, endpoint[2]], [z0, endpoint[0]],
'ro-') # sum axis 1
plt2, = ax2.plot([y0, endpoint[1]], [z0, endpoint[0]],
'ro-') # sum axis 2
ax3.cla()
ax3.plot(np.linspace(distances_q[z0, y0, x0],
distances_q[endpoint[0], endpoint[1],
endpoint[2]],
num=len(cut)),
cut,
'-or',
markersize=3)
ax3.axhline(y=1 / np.e, linestyle='dashed', color='k', linewidth=1)
ax3.set_xlabel('q (1/A)')
ax3.set_ylabel('PRTF')
ax3.axis('auto')
plt.tight_layout()
plt.draw()
cmap=my_cmap,
title='prtf_matrix after interpolation',
scale='linear',
vmin=0,
reciprocal_space=True)
np.savez_compressed(detector.savedir + 'linecut_prtf.npz',
data=linecut_prtf)
else:
linecut_prtf = prtf_matrix
plt.ioff()
max_colorbar = 5
endpoint = [0, 0, 0]
cut = gu.linecut(prtf_matrix,
start_indices=(z0, y0, x0),
stop_indices=endpoint,
interp_order=1,
debugging=False)
diff_pattern[np.isnan(diff_pattern)] = 0 # discard nans
fig_prtf, ((ax0, ax1), (ax2, ax3)) = plt.subplots(nrows=2,
ncols=2,
figsize=(12, 6))
fig_prtf.canvas.mpl_disconnect(
fig_prtf.canvas.manager.key_press_handler_id)
ax0.imshow(np.log10(diff_pattern.sum(axis=0)),
vmin=0,
vmax=max_colorbar,
cmap=my_cmap)
ax1.imshow(np.log10(diff_pattern.sum(axis=1)),
vmin=0,
vmax=max_colorbar,
def test_2d_vertical(self):
array = np.asarray([np.ones(6) * idx for idx in range(5)])
expected = np.arange(1, 5)
output = gu.linecut(array, indices=[(1, 4), (2, 2)], interp_order=1)
self.assertTrue(np.allclose(output, expected))
def test_2d_horizontal(self):
array = np.asarray([np.arange(6) for _ in range(5)])
expected = np.arange(1, 5)
output = gu.linecut(array, indices=[(1, 1), (1, 4)], interp_order=1)
self.assertTrue(np.allclose(output, expected))
def test_1d(self):
array = np.arange(5)
expected = np.array([1.0, 2.0, 3.0])
output = gu.linecut(array, indices=[(1, 3)], interp_order=1)
self.assertTrue(np.allclose(output, expected))
def test_interp_order_null(self):
with self.assertRaises(ValueError):
gu.linecut(np.ones(3), indices=[(1, 2)], interp_order=0)
def test_interp_order_wrong_type(self):
with self.assertRaises(TypeError):
gu.linecut(np.ones(3), indices=[(1, 2)], interp_order=1.2)
