patterson

XRR Patterson function (Fourier transform) analysis toolkit.

Computes the Patterson function — the power spectrum of the normalized X-ray reflectivity — to extract real-space layer distances from XRR data.

Installation

pip install git+https://github.com/hgstei/patterson_xrr.git

Or clone and install locally:

git clone https://github.com/hgstei/patterson_xrr.git
cd patterson_xrr
pip install -e .

Quick start

from patterson import patterson, get_all_ft, plotXrr, plot_all

# Single file — FFT method
distance, patt = patterson(
    "sample.xrr",
    qMin=0.03, qMax=0.2,
    method=0,
    outputFile="sample",
)

# Batch process all *.xrr files in the current directory
get_all_ft(qMin=0.15, qMax=0.6, maxZ=500)

# Side-by-side XRR + Patterson plot of all files
fig, axes = plot_all(outputFile="overview", outputDir="figures")

API

patterson(dataFile, ...)

Parameter	Default	Description
dataFile	—	Path to two-column (q, I) text file
method	0	0 = FFT (fast), 1 = manual DFT
qMin/qMax	0.03/0.2	q-range (Å⁻¹) for the transform
maxZ	2000	Maximum real-space range (Å)
rrfNorm	True	Normalize by Fresnel reflectivity
zCutOff	70	Mask distances below this value (Å)
rho_sub	0.71	Substrate electron density
rho_pre	0.0	Pre-layer electron density
norm	True	Normalize output to maximum
save	True	Write result to disk
outputFile	"foo"	Base name for output file
plot	False	Linear plot
logPlot	True	Log-scale plot
ax	None	Target matplotlib axes

Returns (distance, patterson_values) as NumPy arrays.

get_all_ft(qMax, qMin, maxZ, pattern)

Batch-processes all files matching pattern (default *.xrr) in the current directory using the manual DFT method.

plotXrr(dataFile, ...)

Plot raw or Fresnel-normalized XRR data.

plot_all(...)

Side-by-side XRR + Patterson panel for all *.xrr / *.ftMan files in the current directory. Returns (fig, (ax1, ax2)).

Output files

Extension	Method	Contents
.fft	0	distance patterson
.ftMan	1	distance patterson