surfalize

surfalize is a python package for analyzing microscope topography measurement data in terms of surface roughness and other topographic parameters. It is intended primarily for microtextured surfaces and is supposed to replace software packages such as MountainsMap, MultiFileAnalyzer and Gwyddion for the most common tasks.

Surfalize WebApp (beta)

Surfalize is now also available as an interactive webapp under surfalize.com, running entirely clientside powered by pyodide.

Disclaimer

The authors make no guarantees for the correctness of any results obtained using this package. The package is an early work in progress and may introduce changes to both implementation details and public API at any point in time. Any results should be validated against established software to verify their correctness, especially when they are intended to be used for scientific publications.

Some parts of the package are more mature and some are in early development stage.

Cite this library

If you publish data generated with this library, please consider citing this publication:

F. Schell, C. Zwahr, A. F. Lasagni. Surfalize: A Python Library for Surface Topography and Roughness Analysis Designed for Periodic Surface Structures. Nanomaterials. 2024, 13, 1076.

How to install

To install the latest release of surfalize, run the following command:

pip install surfalize

If you want to install from source, clone this git repository and run the following command in the root folder of the cloned repository.

pip install .

While earlier versions used Cython, the current version is pure Python and can be installed without a C-compiler.

Documentation

The documentation is hosted on readthedocs.

Currently supported file formats

Manufacturer	Format	Reading	Writing
Keyence	.vk4, .vk6, .vk7	Yes	No
Keyence	.cag	Only extraction	No
Leica	.plu	Yes	No
Sensofar	.plu, .plux	Yes	No
Digital Surf	.sur	Yes	Yes
KLA Zeta	.zmg	Yes	No
Wyko	.opd	Yes	No
Nanofocus	.nms	Yes	No
Alicona	.al3d	Yes	Yes
Digital Surf	.sdf	Yes	Yes
Gwyddion	.gwy	Yes	No
Digital Metrology	.os3d	Yes	No
IAU FITS Working Group	.fits	Yes	No
Zygo	.dat	Yes	No
OpenFMC	.x3p	Yes	No
TrueMap	.tmd	Yes	Yes
General	.xyz	Yes	No

Supported roughness parameters

This package aims to implement all field parameters defined in ISO 25178-2:2021. Currently, the following parameters are supported:

Category	Parameter	Full name	Validated against
Height	Sa	Arithmetic mean height	Gwyddion, MountainsMap
	Sq	Root mean square height	Gwyddion, MountainsMap
	Sp	Maximum peak height	Gwyddion, MountainsMap
	Sv	Maximum valley depth	Gwyddion, MountainsMap
	Sz	Maximum height	Gwyddion, MountainsMap
	Ssk	Skewness	Gwyddion, MountainsMap
	Sku	Kurtosis	Gwyddion, MountainsMap
Hybrid	Sdr1	Developed interfacial area ratio	Gwyddion2, MountainsMap
	Sdq	Root mean square gradient	MountainsMap
Spatial	Sal	Autocorrelation length	-
	Str	Texture aspect ratio	-
	Std	Texture direction	-
	Ssw	Dominant spatial wavelength	-
Functional	Sk	Core roughness depth	MountainsMap
	Spk	Reduced peak height	MountainsMap
	Svk	Reduced dale height	MountainsMap
	Spkx	Maximum peak height	-
	Svkx	Maximum pit depth	-
	Sak1	Area of the hills	-
	Sak2	Area of the dales	-
	Smr1 / Smrk1	Material ratio 1	MountainsMap
	Smr2 / Smrk2	Material ratio 2	MountainsMap
	Smr©	Areal material ratio	MountainsMap
	Smc(mr)	Inverse areal material ratio	MountainsMap
	Sxp	Peak extreme height	MountainsMap
	Sdc	Material ratio height difference	-
Functional (volume)	Vmp	Peak material volume	MountainsMap
	Vmc	Core material volume	MountainsMap
	Vvv	Dale void volume	MountainsMap
	Vvc	Core void volume	MountainsMap
	Vm(p)	Material volume	-
	Vv(p)	Void volume	-

¹ Per default, Sdr calculation uses the algorithm proposed by ISO 25178 and also used by MountainsMap By keyword argument, the Gwyddion algorithm can be used instead.
² Gwyddion does not support Sdr calculation directly, but calculates surface area and projected area.

Supported profile roughness parameters

The Profile class supports the calculation of profile roughness parameters. Profiles can be extracted from a Surface (e.g. via get_horizontal_profile, get_vertical_profile or get_oblique_profile) or constructed directly. The peak/valley parameters Rp, Rv and Rz are evaluated per sampling length and averaged over the evaluation length according to ISO 4287, controlled by the n_sections argument (default 5).

Category	Parameter	Full name
Height	Ra, Rq, Rp, Rv, Rz, Rt	Amplitude parameters
	Rsk, Rku	Skewness, kurtosis
Hybrid	Rdq	Root mean square slope
Functional	Rk, Rpk, Rvk	Core / reduced peak / reduced dale
	Rpkx, Rvkx	Maximum peak height / pit depth
	Rak1, Rak2	Area of the hills / dales
	Rmr1 / Rmrk1, Rmr2 / Rmrk2	Material ratios
	Rmr©, Rmc(mr)	(Inverse) material ratio
	Rxp, Rdc	Extreme height / ratio height diff
Functional (volume)	Vmp, Vmc, Vvv, Vvc, Vm(p), Vv(p)	Volume parameters

Supported parameters of 1d-periodic surfaces

Additionally, this package supports the calculation of non-standard parameters for periodic textured surfaces with one- dimensional periodic structures. The following parameters can be calculated:

Parameter	Description
Period	Dominant spatial period of the 1d-surface texture
Depth	Peak-to-valley depth of the 1d-texture profiles
Aspect ratio	Ratio of peak-to-valley depth to spatial period
Homogeneity	Homogeneity factor (0 < H < 1) calculated from Gini analysis
Orientation	Clockwise angle of the dominant texture to the vertical axis

Supported operations

Operation	Description
Leveling	Subtraction of least squares fit to a plane
Zeroing	Sets the lowest datapoint of the surface to zero
Centering	Sets the average value of the surface elevation to zero
Zooming	Magnifies the surface by a specified factor
Cropping	Crops the surface in a specified rectangle
Rotation	Rotates the surface by a specified angle in degrees
Alignment	Aligns the surface with the dominant texture direction by rotation
Outlier removal	Removes outliers outside n standard deviation from the mean
Thresholding	Thresholding based on areal material ratio
Filtering	Applies a Gaussian highpass, lowpass or bandpass filter