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ProbeFlow CLI

The command-line entry point is:

probeflow

Run probeflow <command> --help for exact options.

Common Commands

Command Purpose
gui Launch the PySide6 GUI
info Print basic scan metadata
convert Convert or export based on input/output suffixes
dat2sxm Convert Createc .dat to .sxm
dat2png Render Createc .dat to PNG
dat2npy Export Createc .dat to NumPy bundles
sxm2png Render .sxm or supported scans to PNG
pipeline Apply ordered processing steps
prepare-png Write a PNG handoff with provenance sidecar
plane-bg Polynomial background subtraction
facet-level Plane-level using only flat-terrace pixels (stepped surfaces)
align-rows Per-row offset correction
remove-bad-lines Detect and interpolate bad scan lines
smooth Gaussian smoothing
tv-denoise Total-variation denoising (Huber-ROF / TV-L1)
edge Edge detection (Laplacian / LoG / DoG)
rotate, rotate-90, rotate-180, rotate-270 Rotate a scan (arbitrary angle or lossless quarter turns)
flip-h, flip-v Mirror a scan about the vertical / horizontal axis
fft Fourier-domain filtering
histogram Pixel-value histogram
fft-spectrum FFT magnitude spectrum
profile Line profile from endpoints or a named line ROI
periodicity Find dominant spatial periodicities via power spectrum
autoclip Suggest display clip percentiles
particles, count, classify Feature analysis workflows
grains Detect grains / islands by threshold and print statistics
lattice, unit-cell Lattice extraction and unit-cell averaging
diag-z Diagnose Z-scale candidates for a Createc .dat file
spec-info, spec-plot, spec-overlay, spec-positions Spectroscopy utilities

Some feature/lattice commands require optional dependencies from the features extra.

Examples

Inspect a file:

probeflow info scan.sxm
probeflow info scan.dat --json

Convert Createc .dat to Nanonis-compatible .sxm:

probeflow convert scan.dat scan.sxm

Export Createc .dat to NumPy bundles:

probeflow dat2npy -- --input-dir data/scans --output-dir out/npy

The NumPy exporter writes a bundle directory per input file, plus *.probeflow.json and *.provenance.json sidecars that record source path, basis, channel mapping, warnings, and other provenance metadata.

Render a scan to PNG:

probeflow sxm2png scan.sxm -o scan.png --colormap gray

Apply a processing pipeline:

probeflow pipeline scan.sxm \
    --steps remove-bad-lines align-rows:median plane-bg:1 smooth:1.2 \
    -o scan_processed.sxm

Export a processed PNG:

probeflow pipeline scan.dat \
    --steps align-rows:median plane-bg:1 \
    --png --colormap gray \
    -o scan_processed.png

Prepare a PNG for downstream analysis:

probeflow prepare-png scan.dat aisurf_input.png \
    --steps align-rows:median plane-bg:1 \
    --colormap gray

Use a named ROI saved by the GUI:

probeflow histogram scan.sxm --roi terrace
probeflow profile scan.sxm --roi line_1 -o profile.csv

Plot spectroscopy:

probeflow spec-info spectrum.VERT
probeflow spec-plot spectrum.VERT -o spectrum.png

Pipeline Step Syntax

Pipeline step syntax is:

name[:param1,param2,...]

Examples:

align-rows:median
plane-bg:1
smooth:1.2

For full accepted parameter forms, use:

probeflow pipeline --help

Output Safety

CLI exports refuse to overwrite existing output artifacts or provenance sidecars unless --force is provided.

Processing commands that derive an output path use command-specific suffixes. For example, smooth writes <input-stem>_smooth.sxm by default and pipeline writes <input-stem>_pipeline.sxm by default.