Merge pull request #96 from JuliaGeometry/sjk/nodep2

sjk/nodep2

Author: sjkelly

bench/Project.toml

@@ -7,8 +7,7 @@ makedocs(
     modules = [Meshing],
     pages = ["Index" => "index.md",
              "API" => "api.md",
-             "Examples" => "examples.md",
-             "Internals" => "internals.md"]
+             "Examples" => "examples.md"]
 )
 
 deploydocs(

bench/iso_masjk.jl

@@ -22,24 +22,6 @@ A = rand(50,50,50) # 3D Matrix
 points,faces = isosurface(A, MarchingCubes(iso=1))
 ```
 
-Alternatively, we can use the `isosurface` API to sample a function, avoiding allocations:
-
-```julia
-using Meshing
-using LinearAlgebra
-using StaticArrays
-
-points, faces = isosurface(origin=SVector(-1,-1,-1.), widths = SVector(2,2,2.), samples = (40,40,40)) do v
-    sqrt(sum(dot(v,v))) - 1
-end
-
-# by default MarchingCubes() is used, but we may specify a different algorithm as follows
-
-points, faces = isosurface(MarchingTetrahedra(), origin=SVector(-1,-1,-1.), widths = SVector(2,2,2.), samples = (40,40,40)) do v
-    sqrt(sum(dot(v,v))) - 1
-end
-```
-
 ## Isosurface
 
 `isosurface` is the common and generic API for isosurface extraction with any type of abstract vector/vertex/face type.
@@ -48,30 +30,19 @@ end
 isosurface
 ```
 
-
 ## Meshing Algorithms
 
 Three meshing algorithms exist:
 
 * `MarchingCubes()`
 * `MarchingTetrahedra()`
-* `NaiveSurfaceNets()`
 
-Each takes optional `iso`, `eps`, and `insidepositive` parameters, e.g. `MarchingCubes(iso=0.0,eps=1e-6,insidepositive=false)`.
+Each takes optional `iso` and `eps` parameters, e.g. `MarchingCubes(iso=0.0,eps=1e-6)`.
 
 Here `iso` controls the offset for the boundary detection. By default this is set to 0. `eps` is the detection tolerance for a voxel edge intersection.
-`insidepositive` sets the sign convention for inside/outside the surface (default: false).
 
 Users must construct an algorithm type and use it as an argument to a GeometryTypes mesh call or `isosurface` call.
 
-Below is a comparison of the algorithms:
-
-| Algorithm Type      | Face Type | Unique Vertices | Performance | Interpolation     |
-|---------------------|-----------|-----------------|-------------|-------------------|
-| Naive Surface Nets  | Quad      | Yes             | ~1x         | Voxel Edge Weight |
-| Marching Cubes      | Triangle  | No/Partial      | 1x          | Linear on Edge    |
-| Marching Tetrahedra | Triangle  | Yes             | 3x          | Linear on Edge    |
-
 Visual Comparison:
 From left: Marching Cubes, Naive Surface Nets, Marching Tetrahedra
 
@@ -80,6 +51,5 @@ From left: Marching Cubes, Naive Surface Nets, Marching Tetrahedra
 ```@docs
 MarchingCubes
 MarchingTetrahedra
-NaiveSurfaceNets
 Meshing.AbstractMeshingAlgorithm
 ```

docs/make.jl

@@ -5,31 +5,29 @@
 The file for this example can be found here: [http://www.slicer.org/slicerWiki/images/0/00/CTA-cardio.nrrd](http://www.slicer.org/slicerWiki/images/0/00/CTA-cardio.nrrd)
 
 ```julia
-
+using Meshing
 using FileIO
 using NRRD
-using Meshing
-using MeshIO
+using WGLMakie
+using Downloads
 using GeometryBasics
 
+nrrd = Downloads.download("http://www.slicer.org/slicerWiki/images/0/00/CTA-cardio.nrrd")
+
 # load the file as an AxisArray
-ctacardio = load("CTA-cardio.nrrd")
+ctacardio = load(nrrd)
 
 # use marching cubes with isolevel at 100
-algo = MarchingCubes(iso=100, insidepositive=true)
+#algo = MarchingCubes(iso=100)
 # use marching tetrahedra with iso at 100
-# algo = MarchingTetrahedra(iso=100, insidepositive=true)
-# use Naive Surface Nets with iso at 100
-# algo = NaiveSurfaceNets(iso=100, insidepositive=true)
+ algo = MarchingTetrahedra(iso=100)
+
 
 # generate the mesh using marching cubes
-mc = Mesh(ctacardio, algo)
+vts, fcs = isosurface(ctacardio, algo)
 
-# we can call isosurface to get a vector of points and vector of faces indexing to the points
-# vertices, faces = isosurface(ctacardio, algo, Point{3,Float32}, TriangleFace{Int})
+WGLMakie.mesh(vts, map(v -> GeometryBasics.TriangleFace(v...), fcs))
 
-# save the file as a PLY file (change extension to save as STL, OBJ, OFF)
-save("ctacardio_mc.ply", mc)
 ```
 
 ![cta cardio](./img/ctacardio.png)
@@ -60,44 +58,11 @@ Makie.mesh(gy_mesh, color=[norm(v) for v in coordinates(gy_mesh)])
 ![gyroid](./img/gyroid.png)
 
 
-```julia
-using Meshing
-using GeometryBasics
-using LinearAlgebra: dot, norm
-using FileIO
-
-# Mesh an equation of sphere in the Axis-Aligned Bounding box starting
-# at -1,-1,-1 and widths of 2,2,2 using Marching Cubes
-m = GLNormalMesh(Rect(Vec(-1,-1,-1.), Vec(2,2,2.)), MarchingCubes()) do v
-    sqrt(sum(dot(v,v))) - 1
-end
-
-# save the Sphere as a PLY file
-save("sphere.ply",m)
-```
-
-For a full listing of concrete `AbstractMesh` types see [GeometryBasics.jl mesh documentation](http://juliageometry.github.io/GeometryBasics.jl/latest/types.html#Meshes-1).
-
-Alternatively, we can use the `isosurface` API to sample a function:
-
-```julia
-using Meshing
-using LinearAlgebra
-using StaticArrays
-
-points, faces = isosurface(origin=SVector(-1,-1,-1.), widths = SVector(2,2,2.), samples = (40,40,40)) do v
-    sqrt(sum(dot(v,v))) - 1
-end
-
-# by default MarchingCubes() is used, but we may specify a different algorithm as follows
-
-points, faces = isosurface(MarchingTetrahedra(), origin=SVector(-1,-1,-1.), widths = SVector(2,2,2.), samples = (40,40,40)) do v
-    sqrt(sum(dot(v,v))) - 1
-end
-```
-
 ## Isocaps
 
+We do not provide an equivalent to `isocaps` in Matlab, though
+a similar result may be achieved by setting the boundary to a large value:
+
 ```julia
 using GeometryTypes
 
@@ -120,4 +85,4 @@ gy_mesh = GLNormalMesh(A, MarchingCubes())
 import Makie
 using LinearAlgebra
 Makie.mesh(gy_mesh, color=[norm(v) for v in gy_mesh.vertices])
-```
+```

docs/src/api.md

@@ -6,7 +6,6 @@ Algorithms included:
 
 * [Marching Tetrahedra](https://en.wikipedia.org/wiki/Marching_tetrahedra)
 * [Marching Cubes](https://en.wikipedia.org/wiki/Marching_cubes)
-* [Naive Surface Nets](https://0fps.net/2012/07/12/smooth-voxel-terrain-part-2/)
 
 ## What is isosurface extraction?
 

docs/src/examples.md

@@ -1,18 +1,10 @@
 module Meshing
 
-"""
-    _DEFAULT_SAMPLES = (24,24,24)
-
-Global default sampling count for functions.
-"""
-const _DEFAULT_SAMPLES = (24,24,24)
-
 include("algorithmtypes.jl")
 include("common.jl")
 include("marching_tetrahedra.jl")
 include("marching_cubes.jl")
-include("roots.jl")
-include("adaptive.jl")
+include("isosurface.jl")
 
 export isosurface,
        MarchingCubes,