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adding more nodes

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matei jordache
2026-04-03 23:11:52 -07:00
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GWYDDION_FEATURE_GAP.md
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# Gwyddion Features Not Yet in tono
# Gwyddion Feature Gap — tono
Reference for future implementation. Grouped by value to typical SPM workflows.
Comprehensive comparison against Gwyddion r29630. Excludes force curves, force volumes, and spectroscopic measurements. Grouped by priority for typical SPM workflows.
---
## High Value
## Completed
| # | Feature | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| ~~1~~ | ~~Line Correction~~ | ~~linecorrect.c, linematch.c~~ | ~~Row-by-row median/polynomial alignment. Essential for raw SPM data with scan-line artifacts.~~ **DONE** |
| ~~2~~ | ~~Scar Removal~~ | ~~scars.c~~ | ~~Detect and interpolate scan-line defects (horizontal streaks).~~ **DONE** |
| ~~3~~ | ~~Facet Leveling~~ | ~~facet-level.c~~ | ~~Orient the dominant surface facet to horizontal. Better than plane level for terraced/stepped surfaces.~~ **DONE** |
| ~~4~~ | ~~Morphological Mask Ops~~ | ~~mask_morph.c~~ | ~~Erode, dilate, open, close on grain masks. Needed to clean up thresholded masks.~~ **DONE** |
| ~~5~~ | ~~1D FFT Filter~~ | ~~fft_filter_1d.c~~ | ~~Bandpass/lowpass/highpass filtering of LINE profiles.~~ **DONE** |
| ~~6~~ | ~~2D FFT Filter~~ | ~~fft_filter_2d.c~~ | ~~Frequency-domain filtering of DATA_FIELDs (remove periodic noise, etc.).~~ **DONE** |
| ~~7~~ | ~~Autocorrelation (ACF)~~ | ~~acf2d.c~~ | ~~2D autocorrelation function. Reveals periodic structures and correlation lengths.~~ **DONE** |
| ~~8~~ | ~~PSDF~~ | ~~psdf2d.c~~ | ~~Radial/2D power spectral density function. Complementary to ACF for roughness characterization.~~ **DONE** |
| ~~9~~ | ~~Fractal Dimension~~ | ~~fractal.c~~ | ~~Multiple methods: partitioning, cube counting, triangulation, PSDF, HHCF. Quantifies surface complexity.~~ **DONE** |
| ~~10~~ | ~~Curvature~~ | ~~curvature.c~~ | ~~Quadratic-surface curvature fit with principal radii/directions. Useful for apex and dome characterization.~~ **DONE** |
| ~~11~~ | ~~Grain Distance Transform~~ | ~~mask_edt.c~~ | ~~Euclidean distance from grain boundaries. Useful for spatial distribution analysis.~~ **DONE** |
| ~~12~~ | ~~Watershed Segmentation~~ | ~~grain_wshed.c~~ | ~~Automatic grain detection without manual threshold. More robust than simple thresholding.~~ **DONE** |
| ~~13~~ | ~~Rotate / Flip~~ | ~~rotate.c, basicops.c~~ | ~~Basic geometric transforms (90°, arbitrary angle, mirror).~~ **DONE** |
| ~~14~~ | ~~Crop~~ | ~~crop.c~~ | ~~Extract sub-region of a field.~~ **DONE** |
All features from the original gap analysis are implemented:
## Medium Value
| # | Feature | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| ~~15~~ | ~~Correlation / Pattern Matching~~ | ~~crosscor.c, maskcor.c~~ | ~~Find repeated features or align images via cross-correlation.~~ **DONE** |
| ~~16~~ | ~~Slope Distribution~~ | ~~slope_dist.c~~ | ~~Angular histogram of surface slopes. Characterizes surface texture directionality.~~ **DONE** |
| ~~17~~ | ~~Grain Filtering~~ | ~~grain_filter.c~~ | ~~Remove grains by size, height, or border contact. Refine grain masks post-detection.~~ **DONE** |
| ~~18~~ | ~~Field Arithmetic~~ | ~~arithmetic.c~~ | ~~Add/subtract/multiply/divide two DATA_FIELDs. Useful for difference maps, normalization.~~ **DONE** |
| ~~19~~ | ~~Spot Removal~~ | ~~spotremove.c~~ | ~~Interpolate over selected point defects (dust, spikes).~~ **DONE** |
| ~~20~~ | ~~Tip Modeling / Deconvolution~~ | ~~tip_blind.c, tip_model.c~~ | ~~Estimate tip shape from image, deconvolve to recover true surface.~~ **DONE** |
| ~~21~~ | ~~Radial Profile~~ | ~~rprofile tool~~ | ~~Azimuthally averaged profile from a center point. Good for circular features.~~ **DONE** |
| ~~22~~ | ~~Wavelet Transform~~ | ~~dwt.c, cwt.c~~ | ~~Discrete/continuous wavelet analysis. Multi-scale roughness decomposition.~~ **DONE** |
| ~~23~~ | ~~Scale / Resample~~ | ~~scale.c, resample.c~~ | ~~Resize fields with interpolation.~~ **DONE** |
| ~~24~~ | ~~Gradient~~ | ~~gradient.c~~ | ~~Compute x/y gradient magnitude maps.~~ **DONE** |
| ~~25~~ | ~~Custom Convolution~~ | ~~convolution_filter.c~~ | ~~User-defined kernel convolution.~~ **DONE** |
| ~~26~~ | ~~Local Contrast Enhancement~~ | ~~local_contrast.c~~ | ~~Enhance visibility of local features in images.~~ **DONE** |
## Lower Priority
| # | Feature | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| 27 | Drift Correction | drift.c | Compensate for thermal/piezo drift between scan lines. |
| 28 | Affine / Perspective Correction | correct_affine.c, correct_perspective.c | Fix geometric distortions from scanner nonlinearity. |
| 29 | MFM Analysis | mfm_*.c | Magnetic force microscopy: field calculation, shift finding. |
| 30 | Lattice Measurement | measure_lattice.c | Detect and measure periodic lattice structures from ACF/FFT. |
| 31 | Hough Transform | hough.c | Detect lines and circles in images. |
| 32 | Image Stitching / Merging | merge.c, stitch.c | Combine multiple overlapping scans into one image. |
| 33 | Facet Analysis | facet_analysis.c | Orientation distribution of surface facets (stereographic projection). |
| 34 | Shape Fitting | fit-shape.c | Fit geometric primitives: sphere, paraboloid, cylinder, etc. |
| 35 | Synthetic Surface Generation | *_synth.c (~20 modules) | Generate test surfaces: FBM, noise, lattice, waves, particles, fibers, etc. |
| ~~36~~ | ~~Entropy~~ | ~~entropy.c~~ | ~~Information entropy of height distribution.~~ **DONE** |
| 37 | Indentation Analysis | indent_analyze.c, hertz.c | Nanoindentation curve fitting (Hertz model). |
| 38 | Deconvolution | deconvolve.c | Blind/regularized deconvolution for image restoration. |
| 39 | Canny / Harris Detection | filters.c | Corner and edge feature detection beyond basic Sobel/Prewitt. |
| ~~40~~ | ~~Kuwahara Filter~~ | ~~filters.c~~ | ~~Edge-preserving smoothing filter.~~ **DONE** |
| # | Feature | Gwyddion Source | tono Node |
|---|---------|---------------|-----------|
| 1 | Line Correction | linecorrect.c, linematch.c | LineCorrection |
| 2 | Scar Removal | scars.c | ScarRemoval |
| 3 | Facet Leveling | facet-level.c | FacetLevelField |
| 4 | Morphological Mask Ops | mask_morph.c | MaskMorphology |
| 5 | 1D FFT Filter | fft_filter_1d.c | FFTFilter |
| 6 | 2D FFT Filter | fft_filter_2d.c | FFTFilter |
| 7 | Autocorrelation (ACF) | acf2d.c | ACF2D |
| 8 | PSDF | psdf2d.c | PSDF |
| 9 | Fractal Dimension | fractal.c | FractalDimension |
| 10 | Curvature | curvature.c | Curvature |
| 11 | Grain Distance Transform | mask_edt.c | GrainDistanceTransform |
| 12 | Watershed Segmentation | grain_wshed.c | WatershedSegmentation |
| 13 | Rotate / Flip | rotate.c, basicops.c | RotateField, FlipField |
| 14 | Crop | crop.c | CropResizeField |
| 15 | Correlation / Pattern Matching | crosscor.c, maskcor.c | CrossCorrelate, TemplateMatch |
| 16 | Slope Distribution | slope_dist.c | SlopeDistribution |
| 17 | Grain Filtering | grain_filter.c | GrainFilter |
| 18 | Field Arithmetic | arithmetic.c | FieldArithmetic |
| 19 | Spot Removal | spotremove.c | SpotRemoval |
| 20 | Tip Modeling / Deconvolution | tip_blind.c, tip_model.c | TipModel, TipDeconvolution, BlindTipEstimate |
| 21 | Radial Profile | rprofile tool | RadialProfile |
| 22 | Wavelet Transform | dwt.c, cwt.c | WaveletDenoise |
| 23 | Scale / Resample | scale.c, resample.c | Resample |
| 24 | Gradient | gradient.c | Gradient |
| 25 | Custom Convolution | convolution_filter.c | CustomConvolution |
| 26 | Local Contrast Enhancement | local_contrast.c | LocalContrast |
| 27 | Drift Correction | drift.c | DriftCorrection |
| 28 | Affine Correction | correct_affine.c | AffineCorrection |
| 29 | MFM Analysis | mfm_*.c | MFMAnalysis |
| 30 | Lattice Measurement | measure_lattice.c | LatticeMeasurement |
| 31 | Hough Transform | hough.c | HoughTransform |
| 32 | Image Stitching | merge.c, stitch.c | ImageStitch |
| 33 | Facet Analysis | facet_analysis.c | FacetAnalysis |
| 34 | Shape Fitting | fit-shape.c | ShapeFitting |
| 35 | Synthetic Surface Generation | *_synth.c | SyntheticSurface |
| 36 | Entropy | entropy.c | Entropy |
| 38 | Deconvolution | deconvolve.c | Deconvolution |
| 39 | Canny / Harris Detection | filters.c | FeatureDetection |
| 40 | Kuwahara Filter | filters.c | KuwaharaFilter |
---
## Already Implemented in tono
## Remaining Gaps
For reference, these Gwyddion equivalents are already covered:
### High Value — Core SPM workflow features
| tono Node | Category | Gwyddion Equivalent |
|--------------|----------|-------------------|
| Load Image / Load SPM File | io | File import (gwy, sxm, ibw) |
| Save Image | io | File export |
| Coordinate | io | — |
| Rotate Field | modify | rotate.c |
| Flip Field | modify | basicops.c |
| Plane Level | level | level.c |
| Facet Level | level | facet-level.c |
| Polynomial Level | level | polylevel.c |
| Fix Zero | level | level.c (fix_zero) |
| Line Correction | level | linecorrect.c, linematch.c |
| Gaussian Filter | filters | filters.c (gaussian) |
| Median Filter | filters | filters.c (median) |
| Edge Detect | filters | edge.c (sobel, prewitt, laplacian, LoG) |
| 1D FFT Filter | filters | fft_filter_1d.c (lowpass, highpass, bandpass, notch) |
| 2D FFT Filter | filters | fft_filter_2d.c (lowpass, highpass, bandpass, notch) |
| Scar Removal | filters | scars.c |
| Statistics | analysis | stats.c |
| Curvature | analysis | curvature.c |
| Fractal Dimension | analysis | fractal.c |
| Height Histogram | analysis | linestats.c (dh) |
| 2D FFT | analysis | fft.c |
| Cross Section | analysis | profile tool |
| Profile Roughness | analysis | roughness.c (Ra, Rq, Rsk, Rku, Rp, Rv, Rt) |
| Line Math | analysis | linestats.c |
| Threshold Mask | mask | threshold.c, otsu_threshold.c |
| Mask Morphology | mask | mask_morph.c (erode, dilate, open, close) |
| Mask Invert | mask | — |
| Mask Operations | mask | — (boolean logic on two masks: AND, OR, XOR, NAND, NOR, XNOR, implication, etc.) |
| Grain Distance Transform | mask | mask_edt.c |
| Watershed Segmentation | grains | grain_wshed.c |
| Grain Analysis | grains | grain_stat.c |
| Preview / 3D View / Print Table | display | Presentation, 3D view |
| Tip Model | tip | tip_model.c, tip.c |
| Tip Deconvolution | tip | tip_blind.c, tip.c (gwy_tip_erosion) |
| Blind Tip Estimate | tip | tip_blind.c, morph_lib.c (gwy_tip_estimate_partial/full + gwy_tip_cmap) |
| # | Feature | Gwyddion Source | tono Node | Status |
|---|---------|---------------|-----------|--------|
| 41 | Terrace Fitting | terracefit.c | TerraceFit | **DONE** |
| 42 | Laplace Interpolation | laplace.c | LaplaceInterpolation | **DONE** |
| 43 | Fractal Interpolation | fraccor.c | FractalInterpolation | **DONE** |
| 44 | Median Background Subtraction | median-bg.c | MedianBackground | **DONE** |
| 45 | Flatten Base | flatten_base.c | FlattenBase | **DONE** |
| 46 | Level Individual Grains | level_grains.c | LevelGrains | **DONE** |
| 47 | Grain Marking by Criteria | grain_mark.c | GrainMark | **DONE** |
| 48 | Grain Property Distributions | grain_dist.c | GrainDistributions | **DONE** |
| 49 | Grain Summary Statistics | grain_summary.c | GrainSummary | **DONE** |
| 50 | Outlier Masking | outliers.c | OutlierMask | **DONE** |
| 51 | Scan Line Reordering | reorder.c | ScanLineReorder | **DONE** |
### Medium Value — Analysis and correction
| # | Feature | Gwyddion Source | tono Node | Status |
|---|---------|---------------|-----------|--------|
| 52 | Perspective Correction | correct_perspective.c | PerspectiveCorrection | **DONE** |
| 53 | Polynomial Distortion | polydistort.c | PolynomialDistortion | **DONE** |
| 54 | Frequency Splitting | freq_split.c | FrequencySplit | **DONE** |
| 55 | Phase/Value Wrapping | wrapvalue.c | WrapValue | **DONE** |
| 56 | Shaded Presentation | shade.c | Shade | **DONE** |
| 57 | Pixel Binning | binning.c | PixelBinning | **DONE** |
| 58 | Extend / Pad | extend.c | ExtendPad | **DONE** |
| 59 | Tilt | tilt.c | Tilt | **DONE** |
| 60 | Trimmed Mean Filter | trimmed-mean.c | TrimmedMean | **DONE** |
| 61 | Rank Filter | rank-filter.c | RankFilter | **DONE** |
| 62 | Zero Crossing Detection | zero_crossing.c | ZeroCrossing | **DONE** |
| 63 | Log-Polar PSDF | psdf_logphi.c | LogPolarPSDF | **DONE** |
| 64 | Grain Edge Detection | grain_edge.c | GrainEdge | **DONE** |
| 65 | Grain Cross-Correlation | grain_cross.c | GrainCross | **DONE** |
| 66 | Mutual Crop | mcrop.c | MutualCrop | **DONE** |
| 67 | Immerse Detail | immerse.c | ImmerseDetail | **DONE** |
| 68 | Multiple Profiles | multiprofile.c | MultipleProfiles | **DONE** |
| 69 | Straighten Path | straighten_path.c | StraightenPath | **DONE** |
| 70 | Relate Two Fields | relate.c | RelateFields | **DONE** |
### SPM Mode-Specific
| # | Feature | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| 71 | PFM Analysis | pfm.c | Piezoresponse Force Microscopy: compute in-plane and 3D polarization vectors from VPFM/LPFM amplitude and phase at multiple rotations. |
| 72 | Lateral Force Simulation | latsim.c | Simulate topography artifacts in lateral force (friction) channels given friction coefficient, adhesion, and normal load parameters. |
| 73 | SEM Simulation | semsim.c | Simulate Scanning Electron Microscopy signal from topography data using integration or Monte Carlo methods. |
| 74 | Scanning Microwave Microscopy | smm.c, smm_apply.c | Fit complex reflection coefficients from SMM impedance measurements to extract capacitance and material properties. |
| 75 | MFM Current Simulation | mfm_current.c | Simulate current distribution from magnetization for MFM. Extends existing MFMAnalysis node. |
| 76 | MFM Domain Generation | mfm_parallel.c | Generate parallel magnetic domain patterns for MFM simulation and testing. |
### Lower Priority — Specialized or niche
| # | Feature | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| 77 | Mark Disconnected Regions | mark_disconn.c | Mask topologically isolated surface regions using threshold and radius criteria. |
| 78 | Mask Shift | mask_shift.c | Translate mask by pixel offset in any direction. |
| 79 | Mask Noisify | mask_noisify.c | Add random perturbation to mask boundaries. Useful for testing mask sensitivity. |
| 80 | DWT Anisotropy | dwtanisotropy.c | Quantify surface anisotropy using discrete wavelet transform decomposition. |
| 81 | Displacement Field | displfield.c | Distort images using displacement fields (Gaussian, tear, image-based). Simulates scanning artifacts. |
| 82 | Pixel Classification | classify.c | Classify pixels into categories using decision trees on height, slope, and curvature criteria. |
| 83 | Neural Network Classification | neural.c | Train and apply neural networks for pixel-level feature classification. |
| 84 | Logistic Classification | logistic.c | Classify features using logistic regression on Gaussian derivative features. |
| 85 | Super-Resolution | superresolution.c | Combine multiple aligned low-resolution scans to produce a higher-resolution image. |
| 86 | PSF Estimation | psf.c, psf-fit.c | Estimate and fit point spread functions from image features for deconvolution. |
| 87 | Tip Shape from Features | tipshape.c | Estimate SPM tip shape from known calibration feature convolutions. |
| 88 | Presentation Ops | presentationops.c | Manage presentation overlays (extract, attach, remove presentation layers). |
| 89 | Calibration Coefficients | calcoefs_*.c, calibrate.c | Load, create, and apply lateral/height calibration corrections. |
| 90 | Distribution Coercion | coerce.c | Transform data distribution to match target (uniform, Gaussian, custom). |
| 91 | Grain Selection Visualization | grain_makesel.c | Visualize grains as discs, circles, or bounding boxes for selection. |
### Synthesis — Additional surface generation patterns
tono's SyntheticSurface node covers fbm, white_noise, lattice, steps, particles, and flat. Gwyddion has 24 separate synthesis modules. These could be added as patterns to the existing SyntheticSurface node:
| # | Pattern | Gwyddion Source | Description |
|---|---------|---------------|-------------|
| 92 | Columnar | col_synth.c | Columnar/stripe growth patterns. |
| 93 | Objects | obj_synth.c | Random spheres, pyramids, boxes, cylinders on flat surface. |
| 94 | Fibres | fibre_synth.c | Randomly oriented fibre/line features. |
| 95 | Waves | wave_synth.c | Directional wave/ripple patterns. |
| 96 | Dunes | dune_synth.c | Dune-like rippled surfaces. |
| 97 | Domains | domain_synth.c | Phase-separated domain/island patterns. |
| 98 | Ballistic Deposition | bdep_synth.c | Ballistic deposition growth simulation. |
| 99 | Particle Deposition | deposit_synth.c | Particle deposition simulation. |
| 100 | Rod Deposition | roddeposit_synth.c | Wire/rod deposition on surfaces. |
| 101 | Diffusion Aggregation | diff_synth.c | Diffusion-limited aggregation patterns. |
| 102 | Discs | disc_synth.c | Randomly distributed disc features. |
| 103 | Plateaus | plateau_synth.c | Flat-topped feature patterns. |
| 104 | Pileups | pileup_synth.c | Rounded rectangle pileup structures. |
| 105 | Annealing | anneal_synth.c | Simulated annealing surface relaxation. |
| 106 | Lattice (Voronoi) | lat_synth.c | Regular lattice with Voronoi-based variations. |
| 107 | Phase Separation | phase_synth.c | Spinodal decomposition domain patterns. |
| 108 | PDE Patterns | cpde_synth.c | Coupled partial differential equation patterns. |
| 109 | Spectral (FFT) | fft_synth.c | Surfaces with customizable power spectrum. |
| 110 | Residues | residue_synth.c | Irregular particle/residue deposits. |
| 111 | Noise Distributions | lno_synth.c, noise_synth.c | Gaussian, Poisson, exponential, and other noise types. |
| 112 | Periodic Patterns | pat_synth.c | Various periodic/modulated tiling patterns. |
| 113 | WFR Patterns | wfr_synth.c | Wave-front-related surface patterns. |
### File Format Support
Gwyddion supports 155+ file format modules. tono currently handles a smaller set. Major format gaps (not exhaustive):
| Format | Gwyddion Source | Vendor/Description |
|--------|---------------|-------------------|
| Bruker Nanoscope | nanoscope.c, nanoscope-ii.c | Bruker/Veeco/DI SPM files |
| Park Systems | parkafm.c | Park Systems SPM files |
| RHK | rhk-sm4.c, rhk-spm32.c | RHK Technology SPM files |
| Omicron | omicron.c, omicronflat.c | Omicron/Scienta SPM files |
| Asylum Research | asylum.c | Asylum Research (Igor Pro) |
| WITec | witec-asc.c | WITec SPM/Raman files |
| JEOL | jeol.c | JEOL SPM files |
| ISO 28600 | iso28600.c | Standard SPM exchange format |
| Zygo | zygo.c | Zygo surface profiler |
| ASCII matrix | asciiexport.c | Generic ASCII grid import/export |
---
## Summary
| Category | Count | Status |
|----------|-------|--------|
| Originally tracked (1–40) | 40 | 39 done, 1 excluded (force curves) |
| High Value (41–51) | 11 | **All 11 done** |
| Medium Value (52–70) | 19 | **All 19 done** |
| SPM Mode-Specific (71–76) | 6 | Pending |
| Lower Priority (77–91) | 15 | Pending |
| Synthesis Patterns (92–113) | 22 | Pending (extend SyntheticSurface) |
| File Formats | 10+ | Pending |
**69 of 70 tracked features implemented.** 43 remaining gaps identified.