ZGainsforth

ZGainsforth

ZGainsforth

#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

ZGainsforth

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]

ZGainsforth

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"),

ZGainsforth

import numpy as np
import matplotlib.pyplot as plt
from skimage.io import imread, imsave
from icecream import ic
# from QuickPlot import PrettyPlot

E = np.genfromtxt('532_210619074_energies.txt')
x = imread('532_210619074_CPX_Linescan.tif')

# The pixels are 100 nm in length, and the image was rotated 65 degrees.  Therefore, the length of a pixel in this raster is (about 110 nm):

ZGainsforth

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"),

ZGainsforth

ZGainsforth

from astropy.constants import c, h, e
from astropy.io import fits
import numpy as np
from sys import argv

def LoadSpectrum(SpectrumName='0090340201.fluxed'):
    spectrumfits = fits.open(SpectrumName)

    spec = spectrumfits[1]
    angstrom = np.nan_to_num(spec.data.field('CHANNEL').copy())

ZGainsforth

# Filenames are: RxxxxxxxxxxRyS00zAAAAAA1001.FTZ
# xxxxxxxxxx is the observation ID.
# Ry = R1 or R2 depending on whether it is RGS instrument 1 or 2.
# S00z can be s004 or 5 depending on which RGS.
# AAAAAA is SRSPEC for the spectrum, RSPMAT for the response matrix, BGSPEC for the background spectrum.

# Also need fluxedto2col.py to do the conversion of the fluxed file into a two column output.

# For each ObsID, combine the RGS 1 and RGS 2 first order spectrum, produce a fluxed output, and convert that into a 2 column file.
for OBSID in 0693490201 0090340201