def plot_Qpeaks(self):
proj3d.persp_transformation = self.orthogonal_proj
try:
# Find size of screen
import curses
stdscr = curses.initscr()
self.screen_x, self.screen_y = stdscr.getmaxyx()
self.screen_x = min(self.screen_x, self.screen_y)
self.screen_y = self.screen_x
except:
self.screen_x = 40
self.screen_y = 40
plt.rcParams.update({'font.size': 10})
if len(self.mod) == 0:
IndexPeaks(PeaksWorkspace=self.peaks_ws,
Tolerance=self.tolerance,
RoundHKLs=False,
CommonUBForAll=True)
elif len(self.mod) > 0:
IndexPeaksWithSatellites(PeaksWorkspace=self.peaks_ws,
RoundHKLs=False,
ModVector1=self.mod,
MaxOrder=1)
npeaksTotal = self.peaks_ws.getNumberPeaks()
self.c = []
self.x = []
self.y = []
self.z = []
self.s = []
for i in range(npeaksTotal):
peak = self.peaks_ws.getPeak(i)
hklp = V3D(peak.getH() - math.floor(peak.getH()),
peak.getK() - math.floor(peak.getK()),
peak.getL() - math.floor(peak.getL()))
if peak.getSigmaIntensity() != 0.0:
IsigI = peak.getIntensity() / peak.getSigmaIntensity()
else:
IsigI = 0.0
#if IsigI < 50:
#continue
intensity = max(self.minIntensity, peak.getIntensity())
for i in range(-1, 1):
for j in range(-1, 1):
for k in range(-1, 1):
if (abs(hklp[0] + i) < 1.0 and abs(hklp[1] + j) < 1.0
and abs(hklp[2] + k) < 1.0):
self.x.append(hklp[0] + i)
self.y.append(hklp[1] + j)
self.z.append(hklp[2] + k)
self.c.append(intensity)
self.s.append(5)
nPts = 100
x_grid = np.linspace(-1, 1, nPts + 1)
x_half = np.zeros(nPts)
for j in range(nPts):
x_half[j] = 0.5 * (x_grid[j] + x_grid[j + 1])
sumIntensityX = np.zeros(nPts)
for i in range(len(self.x)):
for j in range(nPts):
if self.x[i] > x_grid[j] and self.x[i] < x_grid[j + 1]:
sumIntensityX[j] = sumIntensityX[j] + self.c[i]
sumIntensityY = np.zeros(nPts)
for i in range(len(self.y)):
for j in range(nPts):
if self.y[i] > x_grid[j] and self.y[i] < x_grid[j + 1]:
sumIntensityY[j] = sumIntensityY[j] + self.c[i]
sumIntensityZ = np.zeros(nPts)
for i in range(len(self.z)):
for j in range(nPts):
if self.z[i] > x_grid[j] and self.z[i] < x_grid[j + 1]:
sumIntensityZ[j] = sumIntensityZ[j] + self.c[i]
# Plot figure with subplots of different sizes
fig = plt.figure("Modulated Structures",
figsize=(self.screen_x, self.screen_y))
# set up subplot grid
gridspec.GridSpec(3, 3)
ax = plt.subplot2grid((3, 3), (0, 2))
plt.plot(x_half, sumIntensityX)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.55 or abs(x_half[i]) < 0.05:
continue
if sumIntensityX[i] > sumIntensityX[
i - 1] and sumIntensityX[i] > sumIntensityX[
i + 1] and sumIntensityX[i - 1] > sumIntensityX[
i - 2] and sumIntensityX[i + 1] > sumIntensityX[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('H')
ax.set_ylabel(r'$\Sigma$I')
ax = plt.subplot2grid((3, 3), (1, 2))
plt.plot(x_half, sumIntensityY)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.5 or abs(x_half[i]) < 0.05:
continue
if sumIntensityY[i] > sumIntensityY[
i - 1] and sumIntensityY[i] > sumIntensityY[
i + 1] and sumIntensityY[i - 1] > sumIntensityY[
i - 2] and sumIntensityY[i + 1] > sumIntensityY[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('K')
ax.set_ylabel(r'$\Sigma$I')
ax = plt.subplot2grid((3, 3), (2, 2))
plt.plot(x_half, sumIntensityZ)
maxGrid = "max\n"
for i in range(2, nPts - 2):
if abs(x_half[i]) > 0.5 or abs(x_half[i]) < 0.05:
continue
if sumIntensityZ[i] > sumIntensityZ[
i - 1] and sumIntensityZ[i] > sumIntensityZ[
i + 1] and sumIntensityZ[i - 1] > sumIntensityZ[
i - 2] and sumIntensityZ[i + 1] > sumIntensityZ[i +
2]:
maxGrid += "{:f}\n".format(x_half[i])
ax.text(0.05, 0.60, maxGrid, fontsize=10, transform=ax.transAxes)
ax.set_yscale('log')
ax.set_xlabel('L')
ax.set_ylabel(r'$\Sigma$I')
vmin = min(self.c)
vmax = max(self.c)
logNorm = colors.LogNorm(vmin=vmin, vmax=vmax)
self.axP = plt.subplot2grid((3, 3), (0, 0),
colspan=2,
rowspan=3,
projection='3d')
sp = self.axP.scatter(self.x,
self.y,
self.z,
c=self.c,
vmin=vmin,
vmax=vmax,
norm=logNorm,
s=self.s,
cmap='rainbow',
picker=True,
alpha=0.2)
self.props = dict(boxstyle='round', facecolor='wheat', alpha=1.0)
#cid = fig.canvas.mpl_connect('pick_event', self.onpick3)
pid = fig.canvas.mpl_connect('key_press_event', self.onpress)
try:
lattice = self.peaks_ws.sample().getOrientedLattice()
except:
lattice = OrientedLattice(1, 1, 1)
astar = V3D(0.5, 0, 0)
bstar = V3D(0, 0.5, 0)
cstar = V3D(0, 0, 0.5)
hkls = np.array(
[np.array([x, y, z]) for x, y, z in zip(self.x, self.y, self.z)])
labels, centroids = self.dbscan(hkls, eps=.0425, min_points=6)
i = 0
modTest = str(self.peaks_ws.getPeak(0).getRunNumber())
lastRun = str(self.peaks_ws.getPeak(npeaksTotal - 1).getRunNumber())
if lastRun != modTest:
modTest = modTest + "-" + lastRun
modTest = modTest + " Type a, b, or c for axis alignment"
for x in centroids:
self.axP.plot([x[0]], [x[1]], [x[2]],
'wo',
ms=40,
markerfacecolor="None",
markeredgecolor='red',
markeredgewidth=3)
if x[0] * x[0] + x[1] * x[1] + x[2] * x[2] > 0.01 and x[
0] >= -0.5 and x[1] >= -0.5 and x[2] >= -0.5 and x[
0] <= 0.5 and x[1] <= 0.5 and x[2] <= 0.5:
modTest += "\nModulation Vector = " + "{:.3f}".format(
x[0]) + ", " + "{:.3f}".format(
x[1]) + ", " + "{:.3f}".format(x[2])
if len(self.mod) == 0:
self.mod = "{:.3f}".format(x[0]) + "," + "{:.3f}".format(
x[1]) + "," + "{:.3f}".format(x[2])
IndexPeaksWithSatellites(PeaksWorkspace=self.peaks_ws,
RoundHKLs=False,
ModVector1=self.mod,
MaxOrder=1)
self.axP.plot([0, astar[0]], [0, astar[1]], [0, astar[2]], color='r')
self.axP.text(astar[0],
astar[1],
astar[2],
'%s' % ('a*'),
size=20,
zorder=1,
color='r')
self.axP.plot([0, bstar[0]], [0, bstar[1]], [0, bstar[2]], color='b')
self.axP.text(bstar[0],
bstar[1],
bstar[2],
'%s' % ('b*'),
size=20,
zorder=1,
color='b')
self.axP.plot([0, cstar[0]], [0, cstar[1]], [0, cstar[2]], color='g')
self.axP.text(cstar[0],
cstar[1],
cstar[2],
'%s' % ('c*'),
size=20,
zorder=1,
color='g')
self.axP.text2D(0.05,
0.80,
modTest + "\nLattice = " + " " +
"{:.3f}".format(lattice.a()) + " " +
"{:.3f}".format(lattice.b()) + " " +
"{:.3f}".format(lattice.c()) + " " +
"{:.3f}".format(lattice.alpha()) + " " +
"{:.3f}".format(lattice.beta()) + " " +
"{:.3f}".format(lattice.gamma()) + "\nError = " + " " +
"{:.3E}".format(lattice.errora()) + " " +
"{:.3E}".format(lattice.errorb()) + " " +
"{:.3E}".format(lattice.errorc()) + " " +
"{:.3E}".format(lattice.erroralpha()) + " " +
"{:.3E}".format(lattice.errorbeta()) + " " +
"{:.3E}".format(lattice.errorgamma()),
fontsize=10,
transform=self.axP.transAxes)
self.axP.set_xlabel('H')
self.axP.set_ylabel('K')
self.axP.set_zlabel('L')
# Create cubic bounding box to simulate equal aspect ratio
max_range = max([
max(self.x) - min(self.x),
max(self.y) - min(self.y),
max(self.z) - min(self.z)
])
Xb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][0].flatten(
) + 0.5 * (max(self.x) + min(self.x))
Yb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][1].flatten(
) + 0.5 * (max(self.y) + min(self.y))
Zb = 0.5 * max_range * np.mgrid[-1:2:2, -1:2:2, -1:2:2][2].flatten(
) + 0.5 * (max(self.z) + min(self.z))
# Comment or uncomment following both lines to test the fake bounding box:
for xb, yb, zb in zip(Xb, Yb, Zb):
self.axP.plot([xb], [yb], [zb], 'w')
plt.show()
#fig.canvas.mpl_disconnect(cid)
fig.canvas.mpl_disconnect(pid)