mfhars
mfhars
/ Quant Bruker spx.ipynb
Created
March 13, 2024 09:24
— forked from ZGainsforth/Quant Bruker spx.ipynb
Read in a Bruker spx spectrum and do basic TEM quantification to get area under the peaks.
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mfhars
/ ExtractSpectrumFromBruker.py
Created
March 13, 2024 09:24
— forked from ZGainsforth/ExtractSpectrumFromBruker.py
Script to manually extract spectra out of a bruker bcf file by using a mask image. Written by Michael and Roger.
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| #1/5/2022 Michael Ofengenden & Roger Yu & A LOT A LOT of help from Zack Gainsforth | |
| import sys, os | |
| import hyperspy.api as hs | |
| import numpy as np | |
| import warnings | |
| with warnings.catch_warnings(): | |
| warnings.simplefilter("ignore") | |
| import tifffile as tif | |
| import skimage | |
| from skimage.transform import resize |
mfhars
/ DrawSpec.py
Created
March 13, 2024 09:24
— forked from ZGainsforth/DrawSpec.py
Draw a spectrum and compare it against another. Using streamlit enable rescaling, shifting and gaussian convolution of spectra.
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| import streamlit as st | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| import os, sys | |
| from scipy.ndimage.filters import gaussian_filter1d | |
| from scipy.interpolate import interp1d | |
| def ConvolveGaussian(Eraw, Iraw, Sigma): | |
| E = np.linspace(Eraw[0], Eraw[-1], 10000) | |
| dE = E[1] - E[0] |
mfhars
/ PlotIR.py
Created
March 13, 2024 09:23
— forked from ZGainsforth/PlotIR.py
A quick way to plot some IR spectra extracted from a NanoIR stack.
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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 | |
| SpectraPath = os.path.join(".") | |
| SpectraFiles = { | |
| "Top Crystal" : os.path.join(SpectraPath, "Top Crystal.txt"), |
mfhars
/ BackgroundSubtractBrukerSpectra.ipynb
Created
March 13, 2024 09:23
— forked from ZGainsforth/BackgroundSubtractBrukerSpectra.ipynb
Subtract the elements from one Bruker quant from another after normalizing one element. Useful for getting the composition of an inclusion or one phase out of a mixed phase where the other phase is known.
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mfhars
/ ReadSPA.py
Created
March 13, 2024 09:23
— forked from ZGainsforth/ReadSPA.py
Read an SPA file from Omnic
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| # Created 2015, Zack Gainsforth | |
| import matplotlib | |
| import matplotlib.pyplot as plt | |
| import numpy as np | |
| import struct | |
| from numpy.fft import fft, fftfreq | |
| def LoadSPAInterferogram(FileName): | |
| # Open the SPA file. |
mfhars
/ Decomposition on FTIR map.ipynb
Created
March 13, 2024 09:23
— forked from ZGainsforth/Decomposition on FTIR map.ipynb
PCA, ICA, NMF on an FTIR map
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mfhars
/ PlotSPA.ipynb
Created
March 13, 2024 09:22
— forked from ZGainsforth/PlotSPA.ipynb
Read Omnic spa files and plot them.
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