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First analysis

This path uses an experimental instrument file you are permitted to analyze. SPM-Kit does not bundle redistributable experimental data with the package.

1. Inspect before computing

spmkit info scan.nid

The command reports the channels, scan direction, array shape, physical unit and field of view. Copy the exact channel name; commands do not guess when the name is wrong.

2. Run the declared pipeline

spmkit analyze scan.nid --channel Z-Axis --level plane --output results/

For scan.nid, this creates:

results/
├── scan_roughness.csv
├── scan_roughness.json
├── scan_kpfm.csv       # only when the configured CPD channel exists
└── scan_kpfm.json      # only when the configured CPD channel exists

--level plane subtracts a least-squares plane before computing Sa, Sq, Sz, Ssk and Sku. Report that preprocessing choice with the result. Use --level none only when an unlevelled height field is scientifically intended.

3. Check one result interactively

spmkit gui scan.nid

Fathom inspects the file, selects the compatible route and opens the relevant perspective. In the Image perspective, verify channel, unit, field of view and leveling before exporting a figure.

4. Preserve enough context

Keep the original file outside version control when its license or consent does not permit redistribution. Preserve alongside the results:

  • the file checksum and lawful source;
  • spmkit --version and Python version;
  • command or Fathom project/recipe;
  • channel name and scan direction;
  • field of view and physical units;
  • preprocessing and model parameters;
  • result files and interpretation limits.

An exported CSV without its channel, units and preprocessing is not a reproducible analysis.

Installation · Fathom quick start