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.


Indices and tables