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Voxelise atom probe data, compute a concentration field, and render a 3D isosurface at a chosen at.% threshold (e.g. for interfaces, precipitates, or grain boundaries). Use when the user wants an isoconcentration surface or isosurface from their APT data.
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
SOC 직업 분류 기준
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-isosurface |
| description | Voxelise atom probe data, compute a concentration field, and render a 3D isosurface at a chosen at.% threshold (e.g. for interfaces, precipitates, or grain boundaries). Use when the user wants an isoconcentration surface or isosurface from their APT data. |
| argument-hint | [isovalue] |
Voxelise the reconstruction, compute the concentration of one or more species per voxel, and draw an isosurface at a chosen at.% level. Use the MATLAB MCP server.
The MATLAB workspace must contain:
pos — loaded atom probe data with ions allocated (has ion column, from /apt-composition)colorScheme — color scheme (from /apt-setup)If ions have not been allocated yet, tell the user to run /apt-composition first.
Build a 3D binning grid from the atom coordinates. bin is the voxel size in nm and may be isotropic [2 2 2] or anisotropic [1 2 2]. Mode is always 'distance' for 3D voxelisation:
dist = [pos.x pos.y pos.z];
bin = [2 2 2]; % voxel size in nm (1 = fine detail, 2 = general, 3 = fast overview)
mode = 'distance';
[binCenters, binEdges] = binVectorsFromDistance(dist, bin, mode);
Voxelise all atoms, then voxelise only the species of interest, and take the ratio to get the per-voxel concentration:
gridVec = binCenters;
vox = posToVoxel(pos, gridVec); % counts of all species per voxel
species = {'Al', 'Ti'}; % species defining the isosurface; ask the user
voxIon = posToVoxel(pos, gridVec, species); % counts of selected species per voxel
conc = voxIon ./ vox; % concentration field (fraction, 0..1)
Ask the user which species the isosurface should be built on. conc is a fraction; an isovalue of 8 below means 8 at.%.
isovalue = 8; % at.% threshold (typical 1-40 depending on the system)
fv = isosurface(gridVec{2}, gridVec{1}, gridVec{3}, conc, isovalue);
RGB = [1 1 0]; % face color
p = patch(fv, 'FaceColor', RGB); axis equal; rotate3d on;
axisSpatialAptify; % switch to the standard APT viewing orientation
Use $ARGUMENTS for the isovalue if the user gave one; otherwise start at 8 and suggest trying several values to best capture the feature.
Critical axis-ordering note: MATLAB's isosurface treats the first array dimension as Y and the second as X, so the grid vectors are passed as gridVec{2}, gridVec{1}, gridVec{3} (X and Y swapped). Do not "fix" this to {1},{2},{3} — if the surface looks mirrored or rotated, this swap is what keeps it aligned with the data.
If conc is single precision and isosurface complains, cast to double: conc = double(conc);.
Live scripts cannot drive the app, so tell the user to paste this into the MATLAB command window themselves (manual GUI step — do not automate). It opens a slider to sweep the isovalue live, recolor patches, and split/export patches to the workspace:
species = {'Cr'}; % numerator species
speciesAll = {'Al','Ni','Co','Cr'}; % denominator species (must include numerator); {} = use raw counts
bin = 2; % voxel size in nm
isosurfaceWidget(pos, species, speciesAll, bin, colorScheme, ax);
Plot ions first, then add the isosurface patch into the same axes:
species = {'C'};
sample = 1; % fraction (<1) or absolute number (>1) of atoms to plot
size = 1; % marker size
pPlot = scatterPlotPosData(pos, species, sample, colorScheme, size, axes(figure()));
ax = pPlot.Parent;
patch(ax, fv, 'DisplayName', 'Isosurface');
Or add ions into an existing isosurface plot: ax = gca; scatterPlotPosData(pos, {'Mo','B'}, sample, colorScheme, size, ax);
Export to OBJ (e.g. for Blender):
patchToObj(fv, 'grain boundary', 'fileName.obj');
Re-import an edited OBJ (call with no argument to pick a file via dialog):
[obj, gr] = objToPatch('isosurface.obj');
Tell the user:
fv (faces/vertices) and conc (concentration field) are in the workspace.isosurfaceWidget for interactive tuning.Suggested follow-ups: /apt-proxigram (proxigram across this isosurface) or exporting via patchToObj for external rendering.