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Zack Gainsforth ZGainsforth

  • University of California at Berkeley
  • Los Angeles, CA, USA
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@ZGainsforth
ZGainsforth / RadialIntegrateAndFitHRTEMImageStack.py
Last active July 7, 2023 17:24
FFT an HRTEM image stack, Radially integrate it and then fit the integration with a background and gaussians.
import numpy as np
import hyperspy.api as hs
from scipy.ndimage import map_coordinates
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from tifffile import imwrite, TiffWriter, TiffFile
from lmfit import Model, CompositeModel, Parameters
from lmfit.models import GaussianModel, QuadraticModel, PseudoVoigtModel
from functools import reduce
import operator
@ZGainsforth
ZGainsforth / Decomposition on FTIR map.ipynb
Created May 17, 2023 16:57
PCA, ICA, NMF on an FTIR map
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ZGainsforth / AcquireStack.py
Created May 11, 2023 23:08
Using Tescan SharkSEM interface, acquire a stack of images rapidly in sequence.
import pdb
import os
import sys
sys.path.append(os.path.join('..', 'remote'))
import time
import sem
import struct
import base64
from sem_v3_lib import *
@ZGainsforth
ZGainsforth / Plot Oxford Stack.ipynb
Created May 11, 2023 19:51
Plot maps from h5ino file exported by Oxford Aztec SEM software. Make RGBs.
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ZGainsforth / PlotSPA.ipynb
Created January 27, 2023 02:45
Read Omnic spa files and plot them.
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ZGainsforth / Decomposition on NanoIR Spectrum Grid Array.ipynb
Created December 23, 2022 05:05
ICA, NMF, and PCA decomposition on a NanoIR spectrum grid array.
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ZGainsforth / QuantMap Bruker Stack.ipynb
Created October 7, 2022 07:47
Using hyperspy, quantify each pixel in a Bruker EDS map and output RGBs and quantitative images.
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ZGainsforth / Element Map Scatter Plots.ipynb
Created October 7, 2022 07:46
Make joint maps and pair plots from elemental maps using seaborn.
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ZGainsforth / Fityk fit three peaks together.fit
Created August 24, 2022 04:40
Fityk script file to fit three peaks in an EDS spectrum and output areas. Does all peak simultaneously and includes edge jumps pinned to fluoresence line intensities.
# Fityk script. Fityk version: 1.3.1. Created: Tue Aug 23 16:58:39 2022
set verbosity = -1 #the rest of the file is not shown
set autoplot = 0
reset
# ------------ settings ------------
set box_constraints = 1
set default_sigma = sqrt
set domain_percent = 30
set epsilon = 1e-012
@ZGainsforth
ZGainsforth / Fityk fit three peaks individually.fit
Last active August 24, 2022 04:38
Fityk script file to fit three peaks in an EDS spectrum and output areas. Does each peak independently. Does not include edge jumps.
# Fityk script. Fityk version: 1.3.1. Created: Fri Aug 19 12:09:17 2022
set verbosity = -1 #the rest of the file is not shown
set autoplot = 0
reset
# ------------ settings ------------
set box_constraints = 1
set default_sigma = sqrt
set domain_percent = 30
set epsilon = 1e-012