StlSaver

class io.savers.StlSaver

Bases: io.savers.BaseSaver

STLSAVER - Saver for binary STL (Stereolithography) isosurface mesh output.

Handles one format: ‘STL isosurface as binary (*.stl)’ - one binary STL file per material, e.g. ‘Labels_stack_Nucleus.stl’, ‘Labels_stack_ER.stl’

This saver is labels-only. It extracts a triangular isosurface mesh for each segmentation material using mibRenderModel(), optionally reducing (isosurface decimation) and smoothing the mesh, then writes each surface to a separate binary STL file using stlwrite().

The result is a set of STL files suitable for visualisation in Blender, Paraview, or 3-D printing pipelines.

The saver delegates mesh generation to utils.isosurfaceMibRendering(), which is ported and refactored from MIB2’s mibRenderModel.

DATA DIMENSIONS Input data : [H, W, D, C, T] (MIB3 native order) mibRenderModel() expects [H, W, D] - squeezed from data(:,:,:,1,1).

OUTPUT FILENAMES Each material is written to: <fnBase>_<materialName>.stl where fnBase is the output path without extension, e.g.: /output/Labels_myStack_Nucleus.stl /output/Labels_myStack_ER.stl

MESH GENERATION OPTIONS (passed inside savingOptions to mibRenderModel) savingOptions.reduce - face-count reduction target (0 = no reduction; default 500 if image width > 500, else 0) savingOptions.smooth - number of Laplacian smoothing iterations (default 5) savingOptions.maxFaces - maximum face count per surface (default 300000) savingOptions.slice - (logical) 0 = full 3-D surface (default)

MATERIAL SELECTION options.MaterialIndex - [] = all materials (default) scalar = index of a single material to export

USAGE EXAMPLES

%% 1. Export all materials as STL for Blender / 3-D printing
saver = io.SaverFactory.create('STL isosurface as binary (``*.stl``)');

opts.Format         = 'STL isosurface as binary (``*.stl``)';
opts.showWaitbar    = false;
opts.silent         = true;
opts.overwrite      = true;
opts.layerType      = 'labels';
opts.MaterialIndex  = [];     % [] = export all materials
opts.reduce         = 500;    % decimate to 500 faces
opts.smooth         = 5;      % 5 smoothing iterations
opts.maxFaces       = 300000;
opts.slice          = 0;

meta.filename       = 'source_stack.tif';
meta.pixSize        = struct('x',0.065,'y',0.065,'z',0.2, ...
                             'units','um','t',1,'tunits','s');
meta.boundingBox    = [0 33.3 0 33.3 0 10];
meta.materialNames  = {'Nucleus'; 'ER'; 'Mitochondria'};
meta.materialColors = [0 0 1; 0 1 0; 1 0 0];

labels = uint8(rand(512,512,50,1,1)*3);  % [H W D C T]
fnOut = saver.save(labels, meta, '/output/Labels_myStack.stl', opts);
% Creates: /output/Labels_myStack_Nucleus.stl
%          /output/Labels_myStack_ER.stl
%          /output/Labels_myStack_Mitochondria.stl

%% 2. Export only the second material (index 2)
opts.MaterialIndex = 2;
fnOut = saver.save(labels, meta, '/output/Labels_myStack.stl', opts);
% Creates: /output/Labels_myStack_ER.stl

%% 3. Via MibModel batch
BatchOpt.LayerType       = {'labels'};
BatchOpt.Format          = {'STL isosurface as binary (``*.stl``)'};
BatchOpt.OutputDirectoryPolicy = {'Full path'};
BatchOpt.DestinationDirectory  = '/output/stl';
BatchOpt.FilenamePolicy  = {'Use existing name'};
BatchOpt.showWaitbar     = false;
BatchOpt.mibBatchTooltip.LayerType = '';
model.save('labels', [], BatchOpt);

SEE ALSO io.SaverFactory, io.savers.BaseSaver, io.savers.MrcSaver, core.MibDataset.save, models.MibModel.save

Constructor Summary
StlSaver(options)

STLSAVER - Constructor for StlSaver class.

Syntax:
saver = io.savers.StlSaver(options)
Input Arguments:

  • options - (optional) struct, saver-level options (usually empty; per-save options are passed to save() instead)

Output Arguments:

  • obj - instance of the StlSaver class

Method Summary
getSupportedFormats(~)

GETSUPPORTEDFORMATS - Return format strings handled by StlSaver.

Syntax:
formats = obj.getSupportedFormats()
Input Arguments:

(none)

Output Arguments:

  • formats - cell array of format strings for STL output

save(data, metadata, filename, options)

SAVE - Write labels data as binary STL isosurface mesh files.

Syntax:
fnOut = obj.save(data, metadata, filename, options)

One STL file is produced per material (or one file if options.MaterialIndex is a scalar). File names follow the pattern: <fnBase>_<materialName>.stl

Input Arguments:

  • data - [H, W, D, C, T] numeric label array; only the first channel (C=1) and first time point (T=1) are processed

  • metadata - struct with fields:

    • pixSize - struct {.x, .y, .z, .units, .t, .tunits}

    • boundingBox - [xmin xmax ymin ymax zmin zmax]

    • materialNames - cell array of material name strings

    • materialColors - [M × 3] material RGB colours (0-1 range)

  • filename - [char] full output path template, e.g. '/out/Labels_myStack.stl'

  • options - struct with fields:

    • Format - format string

    • layerType - expected 'labels' or 'mask'; warning if not

    • MaterialIndex - (optional) [numeric] material index or array; default: [] (all materials)

    • reduce - (optional) [double] face reduction target; default: 500 if width > 500, else 0

    • smooth - (optional) [integer] smoothing iterations; default: 5

    • maxFaces - (optional) [integer] max faces per mesh; default: 300000

    • slice - (optional) [logical] full 3-D mesh (0) or 2-D slices (1); default: 0

    • showWaitbar - logical; default: true

    • silent - logical, suppress dialogs; default: false

    • overwrite - logical; default: true

Output Arguments:

  • fnOut - cell of char with paths of all saved .stl files, or single char when only one material is exported; [] on failure

Example - see class-level documentation above.