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