APAV: Python for atom probe tomography
APAV (Atom Probe Analysis and Visualization) is a Python package for analysis and visualization of atom probe tomography datasets, some features:
File read support for traditional (*.pos, *.epos, *.ato, *.rng, *.rrng) or new (*.apt) formats
File write support for *.pos and *.epos
Mass spectrum quantification with configurable background correction
Calculation and configuration of correlation histograms
Roi primitive shapes for localized analysis
Most analyses can be parameterized by multiple-detection events
Fast generation of the compositional grid using conventional 1st/2nd pass delocalization
Calculation of arbitrary molecular isotopic distributions
Source code repository: https://gitlab.com/jesseds/apav
Basic usage
Essential APT analysis typically involves loading some data and doing some calculation(s). Import the core functions and classes:
>>> import apav as ap
Load an apt file from AP Suite or some other source, along with a suitable range file (or build one programtically):
>>> roi = ap.load_apt("data/NiTiHf.apt")
>>> rng = ap.load_rrng("data/NiTiHf_FWHM.rrng")
Now import the analysis components and compute the total (uncorrected) decomposed composition:
>>> import apav.analysis as anl
>>> mass = anl.RangedMassSpectrum(roi, rng, decompose=True)
>>> mass.print()
Ion Composition Counts
----- ------------- --------
Ti 0.307084 2381757
Ni 0.595634 4619772
Hf 0.0907196 703626
O 0.00656261 50900
Estimate the (uncorrected) composition of a grain in the upper part of the ROI using a sphere:
>>> precip_roi = ap.RoiSphere(roi, center=(-8.5, 2.1, -20), radius=20)
>>> precip_mass = anl.RangedMassSpectrum(precip_roi, rng, decompose=True)
>>> precip_mass.print()
Ion Composition Counts
----- ------------- --------
Ti 0.397016 261053
Ni 0.532445 350102
Hf 0.0665544 43762
O 0.00398457 2620
Check the documentation for more analyses and background corrections.
How to cite
If you use APAV in your work, please cite:
Smith et al., (2023). APAV: An Open-Source Python Package for Mass Spectrum Analysis
in Atom Probe Tomography. Journal of Open Source Software, 8(83), 4862,
https://doi.org/10.21105/joss.04862