Created
August 14, 2021 02:49
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A simple script to plot some STXM spectra for comparison.
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import numpy as np | |
import matplotlib.pyplot as plt | |
from scipy.signal import medfilt, convolve | |
from scipy.signal.windows import gaussian | |
import os, sys | |
STXMPath = os.path.join("..", "210628", "NS_210628066 Fe-L", "Spectra") | |
PtychoPath = os.path.join("..", "210629", "NS_210629000 - Fe-L ptycho", "Spectra Abs") | |
SpectraFiles = {"3+ inclusion (ptycho)": os.path.join(PtychoPath, "3+ inclusion.txt"), | |
"Kosmo1 CPX (STXM)": os.path.join(STXMPath, "Top CPX.txt"), | |
"Kosmo2 CPX (ptycho)": os.path.join(PtychoPath, "Bottom KosmoCPX.txt"), | |
"OPX1 (STXM)": os.path.join(STXMPath, "OPX.txt"), | |
"OPX1 rim (ptycho)": os.path.join(PtychoPath, "OPX rim.txt"), | |
"Fe-rich CPX (STXM)": os.path.join(STXMPath, "Fe-rich.txt"), | |
"K-rich (STXM)": os.path.join(STXMPath, "K-rich.txt"), | |
"Sulfide (STXM)": os.path.join(STXMPath, "Sulfide.txt")} | |
SpectraColors = {"3+ inclusion (ptycho)": "black", | |
"Kosmo1 CPX (STXM)": "darkturquoise", | |
"Kosmo2 CPX (ptycho)": "teal", | |
"OPX1 (STXM)": "limegreen", | |
"OPX1 rim (ptycho)": "forestgreen", | |
"Fe-rich CPX (STXM)": "firebrick", | |
"K-rich (STXM)": "royalblue", | |
"Sulfide (STXM)": "gold"} | |
Spectra = dict() | |
for Name, FileName in SpectraFiles.items(): | |
Spectra[Name] = np.genfromtxt(FileName) | |
def NormMe(I): | |
I -= np.min(I) | |
I /= np.max(I) | |
return I | |
def SubtractPreEdge(S): | |
MaxInd = np.argmin(np.abs(S[:,0]-703.0)) | |
Pline = np.polyfit(S[:MaxInd,0], S[:MaxInd,1], 1) | |
Bkg = Pline[0]*S[:,0] + Pline[1] | |
S[:,1] -= Bkg | |
return S | |
def Preprocess(S): | |
S[:,1] = NormMe(S[:,1]) | |
S = SubtractPreEdge(S) | |
# k = gaussian(9, 2) | |
# print(k) | |
# S[:,1] = convolve(S[:,1], k, mode='same') | |
# S[:,1] = medfilt(S[:,1], [0.25, 0.5, 0.25]) | |
return S | |
plt.figure() | |
Offset = 0 | |
for Name, S in Spectra.items(): | |
Sprime = Preprocess(S) | |
plt.plot(S[:,0], Sprime[:,1]+Offset, label=Name, color=SpectraColors[Name]) | |
Offset -= 0.5 | |
plt.xlabel("eV") | |
plt.ylabel("OD (arb)") | |
plt.xlim(695,730) | |
plt.legend(bbox_to_anchor=(1,0.5)) | |
plt.tight_layout() | |
plt.show() |
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