A Python library for Atom Probe Tomography analysis
Project description
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
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.
Documentation
Documentation is found at: https://apav.readthedocs.io/
Support
Post discussion to the GitLab issue tracker
FAQ
Why use this over IVAS/AP Suite or program X?
APAV is not intended to be an IVAS substitute or replacement. While much of the functionality may overlap, APAV fills feature gaps in IVAS/AP Suite that are lacking or otherwise non-existent. Specifically:
- Multiple-event analysis (i.e. correlation histograms, multiple event histograms, multiple event mass quantifications).
- Manual control over mass spectrum analysis (background models, fit regions, binning, etc).
- An API to easily interface into APT data for custom data analysis.
Why is there no GUI for APAV?
APAV is intended to be used as a python library. Perhaps a GUI will one day exist along side APAV (but not in replacement). For now, APAV includes some custom interactive plotting tools for certain computations.
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