SurfaceTopography

Read and analyze surface topographies with Python. This code implements basic classes for handling uniform and nonuniform surface topography data. It contains a rich set of import filters for experimental surface topography data. Surface topographies can be easily analyzed using standard (rms height, power spectrum, ...) and some special purpose (autocorrelation function, variable bandwidth analysis, ...) statistical techniques.

Quick Start

from SurfaceTopography import read_topography

# Read a topography file (format is auto-detected)
topography = read_topography('surface.opd')

# Get basic properties
print(f"Grid size: {topography.nb_grid_pts}")
print(f"Physical size: {topography.physical_sizes}")
print(f"RMS height: {topography.rms_height_from_area()}")

# Compute the power spectral density (PSD)
q, psd = topography.power_spectrum_from_profile()

# Compute the autocorrelation function (ACF)
r, acf = topography.autocorrelation_from_profile()

# Plot the topography
import matplotlib.pyplot as plt
plt.pcolormesh(*topography.positions_and_heights())
plt.colorbar(label='Height')
plt.show()

Supported File Formats

SurfaceTopography supports over 35 file formats from commercial surface profilometers:

Format	Description
al3d	Alicona AL3D files
asc	ASCII text files (generic)
bcr	BCR-STM files
datx	Zygo DATX files
di	Digital Instruments / Bruker AFM files
ezd	Nanosurf EZD files
frt	FRT profilometer files
gwy	Gwyddion GWY files
h5	HDF5 files
hgt	NASA SRTM HGT elevation files
ibw	Igor Pro binary wave files (Asylum Research)
jpk	JPK Instruments files
lext	Olympus LEXT files
mat	MATLAB .mat files
metropro	Zygo MetroPro files
mi	Park Systems / Molecular Imaging files
mitutoyo	Mitutoyo surface roughness files
mnt	Digital Surf Mountains MNT files
nc	NetCDF files
nmm	PTB NMM files
nms	Nanofocus NMS files
npy	NumPy binary files
oir	Olympus OIR files
opd	Wyko OPD files
opdx	Wyko OPDx files
os3d	Digital Metrology OmniSurf3D files
plu	Sensofar PLU files
plux	Sensofar PLUX files
poir	Olympus POIR (zip) files
ps	Keyence profilometer files
sdf	ISO 25178-71 SDF files
sur	Digital Surf SUR files
tmd	TrueMap TMD files
vk	Keyence VK files
wsxm	WSxM files
x3p	ISO 25178-72 X3P files
xyz	XYZ point cloud files
zmg	KLA Zeta ZMG files
zon	Keyence ZON files

If you use this code, please cite:

• Jacobs, Junge, Pastewka, Surf. Topogr. Metrol. Prop. 1, 013001 (2017)
• Röttger el al., Surf. Topogr. Metrol. Prop. 10, 035032 (2022)

Documentation

This README file contains a brief introduction into the code. The full documentation can be found at https://contactengineering.github.io/SurfaceTopography/.

Installation

Detailed instruction for the installation are provided in the documentation. If you want to install from source you need to run git submodule update --init after a fresh checkout.

The most basic configuration of SurfaceTopography installs all requirements autonomously python3 -m pip install SurfaceTopgography

If you need an editable install (e.g. for development purposes), make sure you disable build isolation:

python3 -m pip install --no-build-isolation -e .

You need to manually install ninja, meson-python, pytest, runtests, DiscoverVersion and numpy before:

python3 -m pip install ninja meson-python pytest runtests DiscoverVersion numpy

Funding

Development of this project is funded by the European Research Council within Starting Grant 757343 and by the Deutsche Forschungsgemeinschaft within projects PA 2023/2 and EXC 2193.