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# The model config:py setup file needs to be edited to fit your machine and
project.
# It is suggested that a model config.py file be made for each dataset run in
BioMesh3D.
# There are several variables in the model config:py that need to be set.
# 1) model_input_file, 2) model_output_path, 3) mats, 4) mat_names, 5)
mat_radii,
# 6) refinement_levels, 7) max_sizing_field, 8) SIZING_SCALE_VAR, 9)
num_particle_iters
# 10) tetgen)_joined_vol_flags, and 11) max_procs.

# The path for the mesh that will be input into the pipeline; in
# our case, the segmentation of the tooth (.../tooth.nrrd).

model_input_file="~/C:/ProgramFiles/SCIRun4.7/bin/FEMesher/Tooth/tooth-seg-unorient.nrrd"

# Original model_input_file definition from example.
#
model_input_file="~/software/trunk/SCIRunData/FEMesher/tooth/tooth-seg-unorient.nrrd"

# The path for the output files that will be generated by BioMesh3D
(.../tooth).

model_output_path="~/Tooth"



# The mask or data values of the materials in the input fields. In the case
# of our tooth segmentation, there are four materials: the three dierent
regions
# that we segmented, and the air around it. These are all assigned a value by
# Seg3D, beginning with 0. With the tooth file that we are using, we will
assign
# this variable (0,1,2,3).

mats = (0, 1, 2, 3)


# The names of the materials labeled in the segmentation. Each
# material labeled in the mats variable needs to have unique name. For
simplicity,
# we will assign the mat names variable (`air', `mat1', `mat2', `mat3').

mat_names = ('air', 'mat1', 'mat2', 'mat3')


# This variable is a parameter for the tightening that is performed in
# the second stage to make the meshes smoother. To turn on tightening, such as
# for very thin (one or two voxels thick) meshes, set this parameter to 0.
For the
# tooth file that we are using, we can leave the default value 0.8.

mat_radii = 0.8



# This will modify the generation and refinement of the medial
# axis points. A higher value will allow for more refinement, and thus medial
axis
# points will be closer together. This variable can be set higher if the
segmentation
# is very small or narrow.

refinement_levels=4



# Modifies the sizing field algorithm. A lower number generates
# more final elements on the tetrahedral mesh.

MAX_SIZING_FIELD = 5.0

# A lower number generates more final elements on the
# tetrahedral mesh.

SIZING_SCALE_VAR = 2.0


# The number of iterations used in the particle system in
# stage 6 of the pipeline. The particle system generates equally spaced
points to
# generate tetrahedra. For the tooth.nrrd le, set the variable to 500.

num_particle_iters = 500


# This variable is similar to the previous, except it applies
# to the tetrahedral models generated for all the materials combined into a
single
# file. The
ags available in this option are the same as the previous variable. It
# can be left as \zpAAqa10".
tetgen_joined_vol_flags = "zpAAqa10"


# Caps the number of processes used by the particle system (stage 6).
max_procs=2



# This variable came with the orginal model_config.py file for the tooth.
# It wasn't defined in "Meshing Pipeline User Guide"
CONSTAN_SIZING_FIELD = 5

Attachment: BioMesh3d_cmddotexe_error.PNG
Description: PNG image

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• [SCIRUN-USERS] Error with BioMesh3D, Trevor Aguirre, 12/23/2017
  • Re: [SCIRUN-USERS] Error with BioMesh3D, Jess, 01/04/2018

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