Skip to content

cli.md

Latest commit

 

History

History
136 lines (103 loc) · 3.47 KB

cli.md

File metadata and controls

136 lines (103 loc) · 3.47 KB

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
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

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.