def Fig2(): ##### View,filter, and average spectra of PbS dots with Methoxythiophenol in the 2300-3400 cm-1 range
subplot(121)
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/7_.txt")
takeout(a)
a.plot()
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/7_.txt")
b = RamanTools.FourierFilter(b, width=380)
takeout(b, centers=(456, 483), demo=True)
b.plot()
c = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/8_.txt")
takeout(c)
c.plot()
m = RamanTools.add_RamanSpectra(a, b)
n = RamanTools.add_RamanSpectra(m, c)
legend(["1", "2", "3"])
subplot(122)
MTP = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141014/4_methoxythiophenol_1.csv")
MTP -= min(MTP[0:1000])
MTP /= max(MTP[0:1000])
MTP *= 1000
MTP.plot(color="b", linewidth=3)
n.autobaseline((2300, 3400))
n /= 10
n.plot()
xlim(2300, 3400)
ylim(-500, 1500)
return 0
def Fig1(): ##### View,filter, and average spectra of PbS dots with Methoxythiophenol in the 800-1600 cm-1 range
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/5_.txt")
# takeout(a)
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/6_.txt")
takeout(b)
c = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/8_.txt")
takeout(c)
d = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/6_.txt")
takeout(d)
e = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/3_.txt")
for l in [a, b, c, d, e]:
noise = l.calc_noise((1100, 1200))
signal = l.values[argmin(abs(array(l.index) - 1596))] - l.values[argmin(abs(array(l.index) - 1650))]
print "S/N:", signal / noise
l = RamanTools.add_RamanSpectra(a, b)
m = RamanTools.add_RamanSpectra(l, c)
o = RamanTools.add_RamanSpectra(m, d)
# o = RamanTools.add_RamanSpectra(o,e)
noise = l.calc_noise((1100, 1200))
signal = l.iloc[argmin(abs(array(l.index) - 1596))] - l.iloc[argmin(abs(array(l.index) - 1650))]
print "S/N:", signal / noise
noise = m.calc_noise((1100, 1200))
signal = m.iloc[argmin(abs(array(m.index) - 1596))] - m.iloc[argmin(abs(array(m.index) - 1650))]
print "S/N:", signal / noise
noise = o.calc_noise((1100, 1200))
signal = o.iloc[argmin(abs(array(m.index) - 1596))] - o.iloc[argmin(abs(array(o.index) - 1650))]
print "S/N:", signal / noise
figure()
subplot(311)
a.plot(color="r")
b.plot(color="k")
c.plot(color="b")
d.plot(color="g")
legend(["a", "b", "c", "d"])
# n = FourierFilter(n, width = 400)
subplot(312)
o.plot()
subplot(313)
n = RamanTools.FourierFilter(o, width=170)
n.autobaseline((700, 1700))
n.plot(color="k")
#### Reference Spectrum of MTP on Cd
MTP = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141014/4_methoxythiophenol_1.csv")
MTP -= min(MTP[0:1000])
MTP /= max(MTP[0:1000])
MTP *= 1000
MTP.plot(color="b", linewidth=3)
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/10_control pbs.txt")
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/11_control.txt")
c = RamanTools.add_RamanSpectra(a, b)
control = RamanTools.FourierFilter(c, width=170)
control.autobaseline((700, 1700))
control.plot(color="r")
xlim(700, 1700)
ylim(-500, 1500)
return 0
def Fig3(): ### Combine final spectra from fig1 and fig2. Display side by side. Showing no SH stretch but some modes for phenyl ring in MTP.
subplot(121)
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/5_.txt")
takeout(a)
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/6_.txt")
takeout(b)
c = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/8_.txt")
takeout(c)
d = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/6_.txt")
takeout(d)
e = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/3_.txt")
##### total of 4500 s measurement for a-e, for a-d total is 2500 s
l = RamanTools.add_RamanSpectra(a, b)
m = RamanTools.add_RamanSpectra(l, c)
o = RamanTools.add_RamanSpectra(m, d)
n = RamanTools.FourierFilter(o, width=170)
n.autobaseline((700, 1700))
n /= 2500
MTP = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141014/4_methoxythiophenol_1.csv")
MTP -= min(MTP[0:1000])
MTP /= max(MTP[0:1000])
MTP += 1
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/10_control pbs.txt")
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/11_control.txt")
c = RamanTools.add_RamanSpectra(a, b)
####total colection time for a and b is 1700
control = RamanTools.FourierFilter(c, width=170)
control.autobaseline((700, 1700))
control[:] /= 1700
control += 0.5
MTP.plot(color="b", linewidth=3, label="MTP reference")
control.plot(color="r", label="PbS-oleate only")
n.plot(color="k", label="PbS-oleate + MTP")
annotate(
"C-S-H bend",
(910, 1.25),
xytext=(910, 2.0),
arrowprops={"width": 1, "headwidth": 3, "frac": 0.05, "color": "k"},
fontsize=14,
)
annotate(
"Ring expansion",
(804, 2.1),
xytext=(804, 2.6),
arrowprops={"width": 1, "headwidth": 3, "frac": 0.05, "color": "k"},
fontsize=14,
)
annotate(
"Ring expansion",
(1095, 1.85),
xytext=(1140, 1.9),
arrowprops={"width": 1, "headwidth": 3, "frac": 0.05, "color": "k"},
fontsize=14,
)
annotate(
"Ring asymmetric rocking",
(1600, 1.7),
xytext=(1300, 1.8),
arrowprops={"width": 1, "headwidth": 3, "frac": 0.05, "color": "k"},
fontsize=14,
)
legend()
xlim(700, 1700)
ylim(-0.5, 3)
ylabel("Intensity (a.u.)")
xlabel("Raman Shift (cm$^{-1}$)")
subplot(122)
a = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141125/7_.txt")
takeout(a)
b = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/7_.txt")
b = RamanTools.FourierFilter(b, width=380)
takeout(b, centers=(456, 483))
c = RamanTools.RamanSpectrum("/home/chris/Documents/DataWeiss/141126/8_.txt")
takeout(c)
#### Total collection time is 2500 s
m = RamanTools.add_RamanSpectra(a, b)
g = RamanTools.add_RamanSpectra(m, c)
g.autobaseline((2300, 3400))
g[:] /= 2500
MTP.plot(color="b", label="MTP reference", linewidth=3)
g.plot(color="k", label="PbS-oleate + MTP")
annotate(
"S-H stretch",
(2556, 1.4),
xytext=(2556, 1.6),
fontsize=14,
arrowprops={"width": 1, "headwidth": 3, "frac": 0.05, "color": "k"},
)
legend()
xlim(2300, 3400)
ylim(-0.5, 3.0)
xlabel("Raman Shift (cm$^{-1}$)")
return 0
