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Create a mass spectrum from loaded atom probe data and optionally identify ions. Use when the user wants to see or analyze a mass spectrum.
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Based on SOC occupation classification
Voronoi-cell cluster determination (Felfer et al. 2015) — detect and extract clusters via Voronoi-cell volumes, Delaunay triangulation, and a Kolmogorov-Smirnov test against a randomised reference. Use when the user wants the Voronoi/clusterDetermination method specifically (this is NOT DBSCAN — for density-based DBSCAN use /apt-cluster instead).
Create a new ion color scheme or add ions/colors to the existing one. Produces/updates the `colorScheme` workspace variable used by ranging and 3D visualization everywhere else. Use when the user wants custom ion colors, a new color scheme, or to add a missing ion color.
Per-vertex concentration mapping onto a mesh/interface — compute atom-to-mesh distances, clip a slab around the interface, voxelise by nearest vertex, and apply a concentration kernel to colour each vertex. Use when the user wants a concentration map painted onto an isosurface or modelled grain boundary mesh.
Run quality-control checks on an atom probe dataset before analysis — basic stats, voltage curve, detector hit map (FDM), mass spectrum sanity, coordinate ranges, multi-hit fraction, and automated quality metrics. Use when the user wants to assess data quality or sanity-check a reconstruction.
Create a field desorption map (detector hit-density / concentration image) and optionally a movie of detector activity over the course of the experiment. Use when the user wants an FDM, desorption map, detector image, or to watch features evolve during the measurement.
Quantify interfacial excess (Gibbsian excess of solute, in at/nm^2) across an interface — either a single value via the Krakauer-Seidman integral method, or a 2D excess map over the surface. Use when the user wants the amount of an element segregated to an interface or grain boundary.
| name | apt-spectrum |
| description | Create a mass spectrum from loaded atom probe data and optionally identify ions. Use when the user wants to see or analyze a mass spectrum. |
| argument-hint | [element1 element2 ...] |
Create a mass spectrum from the pos variable in the MATLAB workspace. Use the MATLAB MCP server.
spec = massSpecPlot(pos, 0.01, 'normalised');
Use bin width 0.01 Da and normalised mode by default. If the user requests different settings, adjust accordingly.
If the user specified elements as $ARGUMENTS, add ion markers for each element. For each element, try common charge states (typically 1+ and 2+ for most elements, 3+ for transition metals):
ionAdd(spec, 'Fe', 2, isotopeTable, colorScheme);
ionAdd(spec, 'Fe', 1, isotopeTable, colorScheme);
If no elements are specified, just show the spectrum and ask the user which elements they expect in their sample. Suggest looking at the major peaks for identification.
Tell the user:
/apt-spectrum element1 element2, or define ranges with rangeAddAllisotopeTable and colorScheme must be in the workspace (from /apt-setup)load('isotopeTable_naturalAbundances.mat');
load('colorScheme_default.mat');