michaelplews/materials-research

This repository holds Python scripts used for day-to-day data analysis required by my graduate degree.

Contents

1. Installation Requirements
2. X-Ray Absorption Spectroscopy (XAS.py)
3. Thermogravimetric Analysis (TGA.py)
4. X-Ray Diffraction (XRD.py)
5. Electrochemistry (EChem.py)
6. Transmission Electron Microscopy (TEM.py)

Installation Requirements

Requirements can be installed with:

conda create -n cabanalab python=3.6
source activate cabanalab
git clone git@github.com:michaelplews/materials-research.git
pip3 install -r materials-research/requirements.txt
pip3 install ipykernel
ipython kernel install --user --name=cabanalab

Jupyter Commands

Requirements to be used in Jupyter Lab/Notebook - use cabanalab kernel

import sys

# Showing which directory you installed this to
sys.path.append('/path/to/materials-research/')

# Example importing of XAS module
from cabanapy import XAS as xas

X-Ray Absorption Spectroscopy (XAS.py)

Use

• The IDC4 object exports data collected at beamline 4-ID-C at the Advanced Photon Source at Argonne National Laboratory.
• Syntax for use is as follows:

from cabanapy import XAS as xas

dire = "./data/4-ID-C/my_data/" #The directory that contains your data
base = "MyData" 				#The base name for all your files (e.g. MyData.0001)

my_sample = xas.IDC4(dire, base, start="1", end="2", shortname = "My Sample")

This will load filed 'MyData.0001' and 'MyData.0002' to the IDC4 object and process the data into my_sample.processed_dataframe. 'shortname' defines the legend label for this sample.

To plot data:

fig = plt.figure(1, figsize=(16, 4))

my_sample.plot('STD', color='black')
plt.xlabel(r'Energy / eV', fontsize=15)

This plots the 'STD' or Standard data. Other options include 'TEY' (Electron Yield), 'TFY' (Fluorescence Yield), and 'sTFY' (Smoothed Fluorescence Yield).

Example

Loading each sample edge into a IDC4 object

dire = "./data/4-ID-C/my_data/"
base = "MyData" 
sample_a = xas.IDC4(dire, base, start="248", end="250", shortname ='Sample A') 
sample_b = xas.IDC4(dire, base, start="244", end="246", shortname = 'Sample B')

Plotting STD data

fig = plt.figure(1, figsize=(16, 4))

sample_a.plot('STD', color='black')
sample_b.plot('STD', color='red')
plt.xlabel(r'Energy / eV', fontsize=15)

show()

Aligning STD data to account for beamdrift

#Find the peak max value between 705 eV and 710 eV and set the x value to 'x_target'
x_target, y = sample_a.max_in_range('STD', low=705, high=710, plot=False, do_return=True)

#Assign the sample_b peak max value to x1 within the same range
x1, y1 = sample_b.max_in_range('STD', low=705, high=710, plot=False, do_return=True)

#Align the sample_b object to sample_a
sample_b.align(x1, x_target)

#Replot STD data
fig = plt.figure(1, figsize=(16, 4))

sample_a.plot('STD', color='black')
sample_b.plot('STD', color='red')
plt.xlabel(r'Energy / eV', fontsize=15)

show()

Supported Importers

Object	Beamline	Facility
IDC4	4-ID-C	APS, Argonne National Laboratory
ALS6312	6.3.1	ALS, Lawrence Berkeley National Laboratory
ALS801	8.0.1	ALS, Lawrence Berkeley National Laboratory

Thermogravimetric Analysis (TGA.py)

Use

• The TGAFile object loads data to an object from a .txt file created in Universal Analysis 2000 by TA Instruments.

Example

from cabanapy import TGA as tga

my_sample = tga.TGAFile("../path/to/file.txt", shortname=r'My Sample')

fig = plt.figure(1, figsize=(6, 4))

#plots weight percent on the y axis
my_sample.plot_percent()

#plots a point and hline for a given x value 
my_sample.plot_step(550)
my_sample.plot_step(700)
adjust_axes(50, 800, 70, 110) # a custom function not included in this repo

show()

X-Ray Diffraction (XRD.py)

Use

• The BrukerBrmlFile object imports v4 .brml files taken on a Bruker D8 Advance diffractometer (credit to m3wolf/scimap project).
• The XYFile object imports .xy (ASCII) files taken on the above diffractometer (if .brml file is unavailable)
• ICDDXmlFile object imports .xml files exported from 'PDF-2 2013' software to add line patterns for reference materials.
• MaterProjJSON object imports the .json files downloaded from The Materials Project to add line patterns for reference materials.

Example

from cabanapy import XRD as xrd

my_sample = xrd.BrukerBrmlFile("./path/to/file.brml", shortname=r'LiF as purchased')
ref_LiF = xrd.ICDDXmlFile("./path/to/file.xml") #defaults to the file name for the legend

fig = plt.figure(1, figsize=(16, 5))

plt.subplot(211)
my_sample.plot(color='black')
hide_x_axis() # a custom function not included in this repo

plt.subplot(212)
ref_LiF.plot('red')

adjust_axes(10,80,0,110)	# a custom function not included in this repo
plt.xlabel(r'2$\theta$ / $^\circ$', fontsize=20)
show()

Electrochemistry (EChem.py)

Use

• The MPTFile and processedMPTFile objects exports data collected on Bio-Logic machines.
• Tested on VMP3, BCS, and SP-50 models.

Example

from cabanapy import EChem as echem

my_battery = echem.MPTFile("./path/to/mptfile", shortname = "My Battery")
my_battery.show_columns #Shows all columns with index numbers in the file

Output:

00 | mode
01 | ox/red
02 | error
03 | control changes
04 | Ns changes
05 | counter inc.
06 | Ns
07 | time/s
08 | control/V/mA
09 | Ewe/V
10 | dq/mA.h
11 | <I>/mA
12 | P/W
13 | (Q-Qo)/mA.h
14 | x
15 | Capacity/mA.h

Plotting the data:

fig = plt.figure(1, figsize=(6, 4))

#Plotting Ewe vs x
my_battery.plot(x=14, y=9, color='black')
plt.xlabel('x', fontsize=12)
plt.ylabel('Ewe / V', fontsize=12)

show()

Transmission Electron Microscopy (TEM.py)

Requirements

This script is a wrapper for _dm3_lib.py which should be placed in the same folder as this script. See documentation for _dm3_lib.py for use. This is included in the requirements.txt file.

Other functions

from cabanapy import TEM as tem

myDM3image = tem.DM3File("./path/to/dm3file", shortname = "My Image")
myDM3image.plot()

show()

This .plot() function plots a TEM image with axes showing the scale in nanometers. Scale bars are also supported with the scale_bar keyword argument.

Known Issues

Error: fromstring has been removed, use frombytes() instead.

This can happen if you have installed an old instance of _dm3_lib.py. It is, however, easily fixable. Go to your installation of '_dm3_lib.py', mine was at:

/usr/local/lib/python3.5/dist-packages/dm3_lib/_dm3_lib.py

Edit the file and change all instances of fromstring (mine had 2) to frombytes. Restart your python kernel and the issue should be fixed.