insert_gmsh_fascicles.m

mesh.insert_gmsh_fascicles

gmsh = mesh.insert_gmsh_fascicles inserts fascicles (from a MBF .xml file) into a GMESH .geo file during the compilation process (using make_from_template, usually), such that the fascicles align to the X-axis in GMESH (this usually comes out as the Z-axis later).

mesh.insert_gmsh_fascicles is part of package +mesh. Before generating a mesh using models.nerve_anatomy, you should always preview the fascicle pattern which will be generated from your supplied set-up using plots.preview_fascicles.

Example

@[insert_gmsh_fascicles] // Execute spline script using SETUP

Syntax

• -setup : adds persistent options. This is used to input the data used by the make_from_template. The example script had a demonstration of this usage.
• -anat [filename] : set source file.
• -anat <struct> : use a fascicle pattern generated using MATLAB.
• -conf [filename] : select configuration file (for arrangements of fascicles from source data)
• -conf <struct> : use preloaded configuration structure

The additional following sets of options are defined:

Fascicles can be re-arranged to make test patterns using the following:

• -pIndex [1..n] : select fascicle indices from source file
• -pLocation [1..n x 2] : set fascicle XY location
• -pRotate [1..n] : set rotation (in degrees) for each fascicle around fascicle centroid

The overall resulting pattern of fascicles can be moved, shifted and scaled using the following:

• -xMove [x y] or -xMove [y]
• -xScale [xy] or -xScale [x y] (non-uniform scaling)
• -xScale [2x2 matrix] (generic matrix transform
• -xRotate [deg]

These translations, scalings, and rotations are applied around the centroid of the overall fascicle pattern and are applied in the order [scale, rotate, move].

By default, the fascicles are extruded from -z to +z with z defined using -z [range]. More complex fascicle trajectories can be specified using -path [xyz], where the xyz path of the fascicle is specified in µm. (note: path currently not re-implemented for XML input data)

Input units are assumed µm and the output units are assumed mm. For input units of mm, use -units-mm. For output units of µm, use -units-um

The additional following are configurable for parsing XML files:

• -nC [n_coeff_points], -nPxy [n_outline_points], '-invert-y'

v0.5, Calvin Eiber 9 April 2021

See also

• models.nerve_anatomy