Releases: nodtem66/Scaffolder
Releases · nodtem66/Scaffolder
v1.5.2
Changes in v1.5.2
- add a new
--no_intersectto use only the boundary box of input mesh to generate 3d mesh - DualMC now supports parallel process with TBB (OneAPI)
- add a new
marching_cubesin python API for generating a 3D mesh with an array implicit iso-value.
This function will work well as the alternative marching cubes for SDF.
For anyone interested in Constructive Solid Geometry, SDF is a pure python library same as PyScaffolder. It has a rich of 2D/3D topology, but the marching_cubes from skimage resulted in a bad 3D mesh sometimes and that why a new marching_cubes used in Scaffolder is exposed to Python API as an alternative method.
Program options
Scaffolder - generate 3D scaffold from STL file based on implicit surface
Usage:
Scaffolder [OPTION...] INPUT OUTPUT PARAMETERS
-h, --help Print help
-i, --input INPUT Input file (STL/PLY/OFF/OBJ/VMI)
-o, --output OUTPUT Output filename with extension
stl,ply,obj,off,ctm
--params PARAMETERS Combined parameters list:
surface[,coff,isolevel,grid_size,k_slice,k_polygon]
-q, --quiet Disable verbose output [default: false]
-c, --coff DOUBLE Angular frequency (pore size adjustment)
default:PI
-t, --isolevel DOUBLE isolevel (porosity adjustment) [default: 0]
-n, --surface NAME implicit surface: rectlinear, schwarzp,
schwarzd, gyroid, double-p, double-d,
double-gyroiod, lidinoid, schoen_iwp, neovius, bcc,
tubular_g_ab, tubular_g_c (default: bcc)
-g, --grid_size INT (0..60000)
Grid size [default: 100]
-s, --shell INT (0..60000) Outer thickness (layers) [default:0]
--grid_offset INT (0..60000)
[default:3]
-m, --microstructure Analysis microstructure with Slice contour
technique ( [default: false]
--export_microstructure Analysis microstructure and export the 2D
contours (for debugging) [default: false]
--export_jpeg [X|Y|Z],INT
Export 2D JPEG (Default: Z,100)
--k_slice INT (0..60000) K_slice: the number of slicing layers in each
direction (used in microstructure analysis)
(default: 100)
--k_polygon INT (>0) K_polygon: the number of closest outer
contour (used in microstructure analysis) (default:
4)
-z, --size_optimize DOUBLE (0..1)
Experimental Quadric simplification (default:
0)
--smooth_step INT (0..60000)
Smooth with laplacian (default: 0)
--dirty Disable autoclean
--minimum_diameter DOUBLE (0..1)
used for removing small orphaned (between
0-1) (default: 0.25)
--format FORMAT (default, csv)
Format of logging output (default: default)
--output_inverse additional output inverse scaffold
--fix_self_intersect INT Experimental fix self-intersect faces
(default: 0)
--mean_curvature INT Size of mean curvature histogram (default: 0)
--no_intersect Generate 3D mesh without intersect with
original mesh (false)
Example:
Scaffolder input.stl output.stl bcc,3.14159,0,100
Generated BCC scaffold with w=3.14159 (PI), t=0, and grid size=100
Scaffolder input.stl output.stl custom.lua,3.14159,0,100,100,4 -m
Generated and evaluated scaffold with custom.lua, w=3.14159 (PI), t=0,
grid size=100, k_slice=100, k_polygon=4
Scaffolder input.stl output.stl bcc,3.14159,0 -m -q --format csv
Generated and evaluated BCC scaffold (w=3.14159, t=0) and reported in CSV
Lua file:
Define the "surface" function that return the implicit function
-----------------------------------------------------------------
function surface (x, y, z)
return sin(x) * cos(y) + sin(y) * cos(z) + sin(z) * cos(x) - params.isolevel
end
-----------------------------------------------------------------
Special symbols can be used in lua file:
params = { coff, isolevel, k_splice, k_polygon }
bbox = { min, max, length, grid_density }
winding(x,y,z): function returning the winding number of position x,y,z
signed_distance(x,y,z): function returning signed distance of position x,y,z
and all functions from math moduleSee documentation
v1.5.1
Changes from v1.4
- replace
--m1and--m2with only-moption. The pore size evaluation now only uses the slicing contour technique (-m).
New features in v1.5
- introduce the third argument (PARAMETERS) to shorten the common options into one.
$ Scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
// new in v1.5
$ Scaffolder cube20mm.stl out.ctm tubulat_g_ab,3.14159,0,100
// or without generating output file
$ Scaffolder cube20mm.stl --params tubulat_g_ab,3.14159,0,100- introduce
--formatto change the stdout styles (default, csv).
// change stdout format to CSV
$ Scaffolder cube20mm.stl --params bcc,3.14159,0,100 --format csv
// When use with quiet option (-q), the stdout will show only progress bar
// and log file will be created
$ Scaffolder cube20mm.stl --params bcc,3.14159,0,100 --format csv -q- introduce LUA file to custom the implicit function
-- suppose that this is the content of my.lua
function surface (x, y, z)
return x^2+y^2+z^2-1
endThen you can fill the surface option with lua script (my.lua)
$ Scaffolder input.stl output.stl ./my.lua,3.14159,0,100 --format csv -qChanges in v1.5.1
- New special symbols in lua scripts
-- suppose that this is a content of my.lua used in command line:
-- $ Scaffolder cube1mm.stl output.stl ./my.lua,3.14159,0,150
-- The meta-table called `params` contains the program parameters, in this case:
-- params = { coff = 3.14159, isolevel = 0, k_splice = 100, k_polygon = 4 }
-- bbox = { min = [0,0,0], max = [1,1,1], length = [1,1,1], grid_density = 150 }
w = params.coff
t = params.isolevel
-- This function generate a surface from two different function combined by signed distance field (SDF) of cube1mm.stl
function surface (x, y, z)
s = signed_distance(x,y,z)
v = winding(x,y,z)
a = 2*s/bbox.length[1]
f1 = ffa(w*x*2, w*y*2, w*z*2)
f2 = ffb(w*x, w*y, w*z)
return (1-a)*f1 + (a)*f2
end
function ffa (x, y, z)
return 20*(cos(x)*sin(y)+cos(y)*sin(z)+cos(z)*sin(x))-0.5*(cos(2*x)*cos(2*y)+cos(2*y)*cos(2*z)+cos(2*z)*cos(2*x))-4
end
function ffb (x, y, z)
return 10*(cos(x)*sin(y)+cos(y)*sin(z)+cos(z)*sin(x))-2*(cos(2*x)*cos(2*y)+cos(2*y)*cos(2*z)+cos(2*z)*cos(2*x))-12
end- add
--mean_curvatureand--export_jpegoptions - support OpenCTM format (.ctm) for 3D mesh exporting
Program options
Scaffolder - generate 3D scaffold from STL file based on implicit surface
Usage:
Scaffolder [OPTION...] INPUT OUTPUT PARAMETERS
-h, --help Print help
-i, --input INPUT Input file (STL/PLY/OFF/OBJ/VMI)
-o, --output OUTPUT Output filename with extension
stl,ply,obj,off
--params PARAMETERS Combined parameters list:
surface[,coff,isolevel,grid_size,k_slice,k_polygon]
-q, --quiet Disable verbose output [default: false]
-c, --coff DOUBLE Angular frequency (pore size adjustment)
default:PI
-t, --isolevel DOUBLE isolevel (porosity adjustment) [default: 0]
-n, --surface NAME implicit surface: rectlinear, schwarzp,
schwarzd, gyroid, double-p, double-d,
double-gyroiod, lidinoid, schoen_iwp, neovius, bcc,
tubular_g_ab, tubular_g_c [default: schwarzp]
-g, --grid_size INT (0..60000)
Grid size [default: 100]
-s, --shell INT (0..60000) Outer thickness (layers) [default:0]
--grid_offset INT (0..60000)
[default:3]
-m, --microstructure Analysis microstructure with Slice contour
technique ( [default: false]
--export_microstructure Analysis microstructure and export the 2D
contours (for debugging) [default: false]
--export_jpeg [X|Y|Z],INT
Export 2D JPEG [Default: Z,100]
--k_slice INT (0..60000) K_slice: the number of slicing layers in each
direction (used in microstructure analysis)
[default: 100]
--k_polygon INT (>0) K_polygon: the number of closest outer
contour (used in microstructure analysis) [default:
4]
-z, --size_optimize DOUBLE (0..1)
Experimental Quadric simplification [default:
0]
--smooth_step INT (0..60000)
Smooth with laplacian (default: 5)
--dirty Disable autoclean [default false]
--minimum_diameter DOUBLE (0..1)
used for removing small orphaned (between
0-1) [default: 0.25]
--format FORMAT (default, csv)
Format of logging output [default: default]
--output_inverse additional output inverse scaffold [default:
false]
--fix_self_intersect Experimental fix self-intersect faces
[default: false]
--mean_curvature Experimental calculate mean curvature
Example:
Scaffolder input.stl output.stl bcc,3.14159,0,100
Generated BCC scaffold with w=3.14159 (PI), t=0, and grid size=100
Scaffolder input.stl output.stl custom.lua,3.14159,0,100,100,4 -m
Generated and evaluated scaffold with custom.lua, w=3.14159 (PI), t=0,
grid size=100, k_slice=100, k_polygon=4
Scaffolder input.stl output.stl bcc,3.14159,0 -m -q --format csv
Generated and evaluated BCC scaffold (w=3.14159, t=0) and reported in CSV
Lua file:
Define the "surface" function that return the implicit function
-----------------------------------------------------------------
function surface (x, y, z)
return sin(x) * cos(y) + sin(y) * cos(z) + sin(z) * cos(x) - params.isolevel
end
-----------------------------------------------------------------
Special symbols can be used in lua file:
params = { coff, isolevel, k_splice, k_polygon }
bbox = { min, max, length, grid_density }
winding(x,y,z): function returning the winding number of position x,y,z
signed_distance(x,y,z): function returning signed distance of position x,y,z
and all functions from math moduleTips
Angular frequency (w)
w = 2PI * N / L
where PI = 3.14159, N = the number of unit cells, and L = the length of input 3D mesh
For example, if we want N=2 in cube20mm.stl (L=20), w will be 2PI*2/20 = PI/5
Please remind that the unit the same dimension with the input mesh
Example:
$ ./Scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
Program will generate the scaffold from cube20mm.stl (L=20) with theoretical N=10
v1.5.0-alpha
Changes from v1.4
- replace
--m1and--m2with only-moption. The pore size evaluation now only uses the slicing contour technique (-m).
New features in v1.5
- introduce the third arguments (PARAMETERS) to shorten the common options into one.
$ Scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
// new in v1.5
$ Scaffolder cube20mm.stl tubulat_g_ab,3.14159,0,100
// or without generating output file
$ Scaffolder cube20mm.stl --params tubulat_g_ab,3.14159,0,100- introduce
--formatto change the stdout styles (default, csv).
// change stdout format to CSV
$ Scaffolder cube20mm.stl --params bcc,3.14159,0,100 --format csv
// When use with quiet option (-q), the stdout will show only progress bar
// and log file will be created
$ Scaffolder cube20mm.stl --params bcc,3.14159,0,100 --format csv -q- introduce LUA file to custom the implicit function
-- suppose that this is the content of my.lua
function surface (x, y, z)
return sin(w*x) * cos(w*y) + sin(w*y) * cos(w*z) + sin(w*z) * cos(w*x) - t
endThen you can fill the surface option with lua script (my.lua)
$ Scaffolder input.stl output.stl ./my.lua,3.14159,0,100 --format csv -qProgram options
Scaffolder - generate 3D scaffold from STL file
Usage:
Scaffolder [OPTION...] INPUT OUTPUT PARAMETERS
-h, --help Print help
-i, --input INPUT Input file (STL)
-o, --output OUTPUT Output filename with extension
stl,ply,obj,off [default: out]
--params PARAMETERS Combined parameters list:
surface[,coff,isolevel,grid_size,k_slice,k_polygon]
-q, --quiet Disable verbose output [default: false]
-c, --coff DOUBLE Angular frequency (pore size adjustment)
default:PI
-t, --isolevel DOUBLE isolevel (porosity adjustment) [default: 0]
-n, --surface NAME implicit surface: rectlinear, schwarzp,
schwarzd, gyroid, double-p, double-d,
double-gyroiod, lidinoid, schoen_iwp, neovius, bcc,
tubular_g_ab, tubular_g_c [default: schwarzp]
-g, --grid_size INT (0..60000)
Grid size [default: 100]
-s, --shell INT (0..60000) Outer thickness (layers) [default:0]
--grid_offset INT (0..60000)
[default:3]
-m, --microstructure Analysis microstructure with Slice contour
technique ( [default: false]
--export_microstructure Analysis microstructure and export the 2D
contours (for debugging) [default: false]
--k_slice INT (0..60000) K_slice: the number of slicing layers in each
direction (used in microstructure analysis)
[default: 100]
--k_polygon INT (>0) K_polygon: the number of closest outer
contour (used in microstructure analysis) [default: 4]
-z, --size_optimize DOUBLE (0..1)
Experimental Quadric simplification [default: 0]
--smooth_step INT (0..60000)
Smooth with laplacian (default: 5)
--dirty Disable autoclean [default false]
--minimum_diameter DOUBLE (0..1)
used for removing small orphaned (between 0-1) [default: 0.25]
--format FORMAT (default, csv)
Format of logging output [default: default]
--output_inverse additional output inverse scaffold [default: false]
--fix_self_intersect Experimental fix self-intersect faces
[default: false]
Example:
Scaffolder input.stl output.stl bcc,3.14159,0,100
Generated BCC scaffold with w=3.14159 (PI), t=0, and grid size=100
Scaffolder input.stl output.stl custom.lua,3.14159,0,100,100,4 -m
Generated and evaluated scaffold with custom.lua, w=3.14159 (PI), t=0,
grid size=100, k_slice=100, k_polygon=4
Scaffolder input.stl output.stl bcc,3.14159,0 -m -q --format csv
Generated and evaluated BCC scaffold (w=3.14159, t=0) and reported in CSV
Lua file:
Define the "surface" function that return the implicit function
-----------------------------------------------------------------
function surface (x, y, z)
return sin(x) * cos(y) + sin(y) * cos(z) + sin(z) * cos(x) - t
end
-----------------------------------------------------------------
Special symbols can be used in lua file:
w: value from -c, or --coff
t: value from -t, or --thickness
winding(x,y,z): function returning the winding number of position x,y,z
signed_distance(x,y,z): function returning signed distance of position x,y,z
and all functions from math moduleTips
Coefficient usage
coff = PI/target_pore_size
Please remind that use the same dimension with the input mesh
Example:
$ ./Scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
Program will generate the scaffold from cube20mm.stl with theoretical pore size 1mm of tubular_g_ab
v1.4 Release
Scaffolder - generate 3D scaffold from STL file
Usage:
Scaffolder [OPTION...] INPUT OUTPUT FORMAT
-h, --help Print help
-q, --quiet Disable verbose output [default: false]
-i, --input FILE Input file (STL)
-o, --output FILENAME Output filename without extension [default:
out]
-f, --format arg Output format (OFF,PLY,STL,OBJ) [default:
ply]
-c, --coff DOUBLE default:4*PI
-s, --shell INT [default:0]
-n, --surface NAME rectlinear, schwarzp, schwarzd, gyroid,
double-p, double-d, double-gyroiod, lidinoid,
schoen_iwp, neovius, bcc, tubular_g_ab, tubular_g_c
[default: schwarzp]
-t, --thickness DOUBLE Thickness [default: 0]
-g, --grid_size INT Grid size [default: 100]
--grid_offset INT [default:3]
--smooth_step INT Smooth with laplacian (default: 5)
-m, --microstructure Analysis microstructure ( [default: false]
--m1 Export and analysis microstructure 1 (Image
processing technique) [default: false]
--m2 Export and analysis microstructure 2 (Slice
coutour technique) [default: false]
--method 0,1 Method of microstructure analysis: 0 (Image
processing technique) or 1 (Slice contour
technique) [default: 1]
--slice_grid INT Slice Grid used in microstructure analysis
[default: 100]
--output_inverse additional output inverse scaffold [default:
false]
--inverse Enable build inverse 3D scaffold (for pore
connectivity analysis) [default: false]
--dirty Disable autoclean [default false]
--fix_self_intersect Experimental fix self-intersect faces
[default: false]
--qsim DOUBLE (0..1) Experimental Quadric simplification [default:
0]
--minimum_diameter DOUBLE
used for removing small orphaned (between
0-1) [default: 0.25]
Coefficient usage
coff = PI/target_pore_size
Please remind that use the same dimension with the input mesh
Example:
$ ./scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
Program will generate the scaffold from cube20mm.stl with theoretical pore size 1mm of tubular_g_ab
v1.3 Release
Scaffolder - generate 3D scaffold from STL file
Usage:
Scaffolder [OPTION...] INPUT OUTPUT FORMAT
-h, --help Print help
-q, --quiet Disable verbose output [default: false]
-i, --input FILE Input file (STL)
-o, --output FILENAME Output filename without extension [default:
out]
-f, --format arg Output format (OFF,PLY,STL,OBJ) [default:
ply]
-c, --coff DOUBLE default:4*PI
-s, --shell INT [default:0]
-n, --surface NAME rectlinear, schwarzp, schwarzd, gyroid,
double-p, double-d, double-gyroiod, lidinoid,
schoen_iwp, neovius, bcc, tubular_g_ab, tubular_g_c
[default: schwarzp]
-t, --thickness DOUBLE Thickness [default: 0]
-g, --grid_size INT Grid size [default: 100]
--grid_offset INT [default:3]
--smooth_step INT Smooth with laplacian (default: 5)
-m, --microstructure Analysis microstructure ( [default: false]
--m1 Export and analysis microstructure 1 (Image
processing technique) [default: false]
--m2 Export and analysis microstructure 2 (Slice
coutour technique) [default: false]
--method 0,1 Method of microstructure analysis: 0 (Image
processing technique) or 1 (Slice contour
technique) [default: 1]
--slice_grid INT Slice Grid used in microstructure analysis
[default: 100]
--output_inverse additional output inverse scaffold [default:
false]
--inverse Enable build inverse 3D scaffold (for pore
connectivity analysis) [default: false]
--dirty Disable autoclean [default false]
--fix_self_intersect Experimental fix self-intersect faces
[default: false]
--qsim DOUBLE (0..1) Experimental Quadric simplification [default:
0]
--minimum_diameter DOUBLE
used for removing small orphaned (between
0-1) [default: 0.25]
Coefficient usage
coff = PI/target_pore_size
Please remind that use the same dimension with the input mesh
Example:
$ ./scaffolder cube20mm.stl out.ply -c 3.14159 -g 100 -n tubulat_g_ab
Program will generate the scaffold from cube20mm.stl with theoretical pore size 1mm of tubular_g_ab
v1.1-alpha (x64-Windows)
Usage:
Scaffolder [OPTION...] [option args]
-h, --help Print help
-q, --quiet Disable verbose output
-f, --format arg Output format (OFF,PLY,STL,OBJ) [default:
ply]
-i, --input FILE Input file (STL)
-o, --output FILENAME Output filename without extension [default:
out]
-c, --coff DOUBLE default:4*PI
-s, --shell INT [default:0]
-n, --surface NAME schwarzp, schwarzd, gyroid, lidinoid,
schoen_iwp, neovius, pwhybrid [default: schwarzp]
-t, --thickness DOUBLE Thickness [default: 1.0]
-g, --grid_size INT Grid size [default: 100]
--grid_offset INT [default:2]
--dirty Disable autoclean
--minimum_diameter DOUBLE
used for removing small orphaned (between
0-1) [default: 0.25]
Requirement: vcruntime140
v1.0-alpha (x64-windows)
Usage: Scaffolder_2 [options]
Options:
-q, --quiet Disable verbose output
-f, --format Output format (OFF,PLY,STL,OBJ) [default: ply]
-i, --input Input file (STL) (Required)
-o, --output Output filename without extension [default: out]
-g, --grid Grid size [default: 100]
--thickness Thickness [default: 1.0]
--border_offset default:2
--coff default:4*PI
--minimum_diameter used for removing small orphaned (between 0-1) [default: 0.25]
--surface schwarzp, schwarzd, gyroid, lidinoid, scherk [default: schwarzp]
Requirement vcruntime140