tono/docs/missing_gwyddion_features.md

Missing Gwyddion Features

Gwyddion 2D image/surface processing features not yet implemented in tono. Excludes force curves, force volume, spectroscopy, volume data, XYZ data, graph operations, and file I/O.

Leveling / Background Removal

• Arc Revolve — Subtract cylindrical arc background fitted by revolving an arc under the data
• Sphere Revolve — Subtract spherical cap background
• Unrotate — Auto-detect and correct in-plane scan rotation by finding dominant feature directions
• Level Rotate — Level by physically rotating the data plane rather than subtracting a polynomial
• Zero Mean Value — Shift all values so the mean is exactly zero (pure offset, no plane fit)
• Zero Maximum Value — Shift all values so the maximum is exactly zero

Filtering / Signal Processing

• 2D CWT — Continuous Wavelet Transform for scale-space analysis
• XY Denoise — Denoise by combining two orthogonal scans (forward/backward or horizontal/vertical)
• Rank Presentation — Rank transform image for local contrast enhancement
• Radial Smoothing — Smooth data in polar coordinates, averaging along radial or angular direction
• Convolve Two Images — Convolve two separate data channels together

Line Correction / Scan Artifacts

• Step Block Correction — Correct vertical step offsets between scan lines by block-matching
• Good Mean Profile — Compute a high-quality average scan line from repeated scans
• Align Rows (extended methods) — Modus and Gaussian-weighted row alignment beyond tono's current set

Correction / Restoration

• Fractal Correction — Fill masked/bad pixels using fractal interpolation (alternative to Laplace)
• Correlation Averaging — Average repeated similar structures using autocorrelation alignment
• Coerce — Force data to match the histogram distribution of another dataset
• Periodic Translate — Translate image data treating the field as periodic (wrap-around shift)
• Reorder — Reorder pixel rows/columns (interleaved to sequential, reverse scan, etc.)

Statistical Analysis

• Transfer Function Fit — Fit PSF from a known reference image and a measured blurred image
• Transfer Function Guess — Estimate PSF from a single image without a reference
• Angle Distribution — Distribution of surface normal angles (distinct from slope distribution)

Grain Operations

• Otsu Threshold — Automated grain/mask threshold using Otsu's method
• Remove Edge-Touching Grains — Remove all grains touching the image border from a mask
• Grain Selection Shapes — Create geometric selections (bounding boxes, inscribed discs, etc.) from grain masks

Mask Operations

• Mask Thin — Morphological thinning to single-pixel-wide skeletons
• Mask Distribute — Copy/distribute a mask to multiple channels simultaneously
• Mark With — Create or modify a mask using arithmetic conditions on other channels

Basic Operations

• Invert Value — Flip heights (z to -z)
• Log Scale Presentation — Log-scaled presentation layer without modifying source data
• Limit Range — Clamp data values to a specified min/max range
• Square Samples — Resample so pixels are physically square (equal x/y size)
• Null Offsets — Zero out the lateral (XY) origin offsets

SPM-Specific Modes

• MFM Field Simulation — Simulate magnetic stray field above perpendicular media
• MFM Parallel Media — Simulate MFM signal for in-plane magnetic media
• MFM Lift Shift — Simulate MFM signal change when lift height changes
• MFM Lift Estimate — Estimate lift height difference from data blur
• MFM Force Gradient — Convert MFM raw data to force gradient units
• SMM Apply Calibration — Apply Scanning Microwave Microscopy calibration coefficients

Synthetic Surface Generators

Tono has one generic Synthetic Surface node. Gwyddion has ~20+ specialized generators:

• Fractional Brownian Motion — fBm rough surfaces with controlled Hurst exponent
• Spectral Synthesis — PSD-specified random rough surfaces
• Lattice — Crystalline lattice surface with defects
• Objects — Randomly placed 3D objects (spheres, pyramids, etc.)
• Patterns — Geometric patterns (staircase, gratings, etc.)
• Waves — Sinusoidal/wave patterns
• Noise — Uncorrelated random noise with configurable distribution
• Line Noise — Synthetic scan-line noise/steps/scars for testing
• Fibres — Random fibre network surfaces
• Domain Walls — Phase-separated domain structures
• Columnar Growth — Columnar thin-film growth simulation
• Ball Deposition — Random ballistic deposition growth
• Particle Deposition — Dynamical particle deposition model
• Rod Deposition — Rod-like particle deposition
• Diffusion — Diffusion-limited aggregation surfaces
• Discs — Random overlapping disc surfaces
• CPDE / Turing — Reaction-diffusion / Turing pattern surfaces
• Sand Dunes — Aeolian sand transport simulation
• Annealing Lattice Gas — Annealed lattice-gas model textures
• Phase Separation — Spinodal decomposition textures
• Pileup — Piled-up ellipsoids or bars
• Plateaus — Stacked random plateau/terrace structures
• Film Residue — Residue left after simulated film removal
• Wetting Front — Propagating wetting front simulation