cleanup docs

docs/src/api.md

@@ -4,7 +4,7 @@
 
 Given 3D levelset data such as a CT scan, we can do:
 
-```
+```julia
 using Meshing
 
 A = rand(50,50,50) # 3D Matrix
@@ -14,43 +14,17 @@ points,faces = isosurface(A)
 
 An iso-level is specified within the algorithm specification as follows:
 
-```
+```julia
 using Meshing
 
 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:
 
-## Quick Start - GeometryBasics
-
-Meshing is well-integrated with [GeometryBasics.jl](https://github.com/JuliaGeometry/GeometryBasics.jl)  by extending the [mesh constructors](http://juliageometry.github.io/GeometryBasics.jl/latest/types.html#Meshes-1) for convience.
-
-The algorithms operate on a `Function`, `AbstractArray`, or `SignedDistanceField` and output a concrete `AbstractMesh`.
-For example, we can use the GeometryBasics API as follows, using `Rect` to specify the bounds:
-
-```
-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
@@ -66,60 +40,19 @@ points, faces = isosurface(MarchingTetrahedra(), origin=SVector(-1,-1,-1.), widt
 end
 ```
 
-## Quick Start - GeometryTypes
-
-
-!!! warning
-
-    GeometryTypes is in the process of being deprecated across the Julia ecosystem.
-    GeometryBasics is the recommended replacement.
-
-
-Meshing is well-integrated with [GeometryTypes.jl](https://github.com/JuliaGeometry/GeometryTypes.jl)  by extending the [mesh constructors](http://juliageometry.github.io/GeometryTypes.jl/latest/types.html#Meshes-1) for convience.
-
-The algorithms operate on a `Function`, `AbstractArray`, or `SignedDistanceField` and output a concrete `AbstractMesh`.
-For example, we can use the GeometryTypes API as follows, using `HyperRectangle` to specify the bounds:
-
-```
-using Meshing
-using GeometryTypes
-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(HyperRectangle(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 [GeometryTypes.jl mesh documentation](http://juliageometry.github.io/GeometryTypes.jl/latest/types.html#Meshes-1).
-
-Alternatively, we can use the `isosurface` API to sample a function:
-
-```
-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
+## Isosurface
 
-# by default MarchingCubes() is used, but we may specify a different algorithm as follows
+`isosurface` is the common and generic API for isosurface extraction with any type of abstract vector/vertex/face type.
 
-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
+```@docs
+isosurface
 ```
 
 
 ## Meshing Algorithms
 
 Three meshing algorithms exist:
+
 * `MarchingCubes()`
 * `MarchingTetrahedra()`
 * `NaiveSurfaceNets()`
@@ -150,54 +83,3 @@ MarchingTetrahedra
 NaiveSurfaceNets
 Meshing.AbstractMeshingAlgorithm
 ```
-
-## Isosurface
-
-`isosurface` is the common and generic API for isosurface extraction with any type of abstract vector/vertex/face type.
-
-```@docs
-isosurface
-```
-
-## GeometryBasics
-
-Meshing extends the mesh types in GeometryBasics for convenience and use with visualization tools such as Makie and MeshCat.
-Any instance of a `Mesh` may be created as follows:
-
-```
-    mesh(df::SignedDistanceField{3,ST,FT}, method::AbstractMeshingAlgorithm; pointtype=nothing, facetype=nothing) where {ST, FT}
-    mesh(f::Function, h::Rect, samples::NTuple{3,T}, method::AbstractMeshingAlgorithm; pointtype=nothing, facetype=nothing) where {T <: Integer}
-    mesh(f::Function, h::Rect, method::AbstractMeshingAlgorithm; pointtype=nothing, facetype=nothing, samples::NTuple{3,T}=_DEFAULT_SAMPLES) where {T <: Integer}
-    mesh(volume::AbstractArray{T, 3}, method::AbstractMeshingAlgorithm; pointtype=nothing, facetype=nothing, vargs...) where {T}
-```
-
-With the GeometryBasics API, the bounding box is specified by a `Rect`, or keyword specified `origin` and `widths`.
-
-Some notes on pointtype and facetype. They can be used to create a mesh with the desired point & face types.
-If they're left at nothing, the element type best matching the method and signed distancefield is used.
-Both the element type of the volume, element type of the `vertextype`, and type of `iso` in the `AbstractMeshingAlgorithm`
-are all promoted. This also allows the use of auto differentiation tools on the isosurface construction.
-
-## GeometryTypes
-
-Meshing extends the mesh types in GeometryTypes for convience and use with visualization tools such as Makie and MeshCat.
-Any instance of an `AbstractMesh` may be called with arguments as follows:
-
-```
-    (::Type{MT})(df::SignedDistanceField{3,ST,FT}, method::AbstractMeshingAlgorithm)::MT where {MT <: AbstractMesh, ST, FT}
-    (::Type{MT})(f::Function, h::HyperRectangle, samples::NTuple{3,T}, method::AbstractMeshingAlgorithm)::MT where {MT <: AbstractMesh, T <: Integer}
-    (::Type{MT})(f::Function, h::HyperRectangle, method::AbstractMeshingAlgorithm; samples::NTuple{3,T}=_DEFAULT_SAMPLES)::MT where {MT <: AbstractMesh, T <: Integer}
-    (::Type{MT})(volume::AbstractArray{T, 3}, method::AbstractMeshingAlgorithm; vargs...) where {MT <: AbstractMesh, T}
-```
-
-With the GeometryTypes API, the bounding box is specified by a `HyperRectangle`, or keyword specified `origin` and `widths`.
-
-Some notes on VertType and FaceType. Since it is common to simply call `HomogenousMesh` or `GLNormalMesh`, we have added promotion and default type logic
-to the GeometryTypes API to improve type stability and therefore performance.
-Both the element type of the volume, element type of the `vertextype`, and type of `iso` in the `AbstractMeshingAlgorithm`
-are all promoted. This also allows the use of auto differentiation tools on the isosurface construction.
-
-If for example a `HomogenousMesh` is requested, the default types will be `Point{3,Float64}` and `Face{3,Int}`
-Similarly, a `GLNormalMesh` specifies `Point{3, Float32}` and `Face{3, OffsetInteger{-1,UIn32}}` so these these types will be used.
-
-See: `isosurface` for the generic API.

docs/src/examples.md

@@ -1,7 +1,6 @@
 # Examples
 
-
-# NRRD Data
+## NRRD Data
 
 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)
 
@@ -35,7 +34,7 @@ save("ctacardio_mc.ply", mc)
 
 ![cta cardio](./img/ctacardio.png)
 
-# Functions
+## Functions
 
 ```julia
 using Meshing
@@ -59,3 +58,40 @@ 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
+```

docs/src/index.md

@@ -3,6 +3,7 @@
 This package provides a suite of meshing (isosurface extraction) algorithms.
 
 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/)
@@ -13,7 +14,8 @@ Isosurface extraction is a common technique to visualize and analyze scalar fiel
 It takes scalar data that is structured in grids and converts this into a series of points and faces suitable for 3D visualization, GPU computing, 3D Printing, or other analyses.
 
 There are several applications for these techniques such as:
-- Medical Imaging of CT and MRI data
-- Visualization of Functions
-- Solid Modeling
-- Terrain Generation
+
+* Medical Imaging of CT and MRI data
+* Visualization of Functions
+* Solid Modeling
+* Terrain Generation

docs/src/internals.md

@@ -3,7 +3,6 @@
 The internals of Meshing have been optimized for performance and to be generic.
 This is some brief documentation on the basic internal functions.
 
-
 ## Common
 
 ```@docs

src/Meshing.jl

@@ -2,7 +2,6 @@ module Meshing
 
 using StaticArrays
 
-
 """
     _DEFAULT_SAMPLES = (24,24,24)
 
@@ -17,7 +16,6 @@ include("marching_cubes.jl")
 include("surface_nets.jl")
 include("roots.jl")
 include("adaptive.jl")
-include("marching_tetrahedra_adaptive.jl")
 
 export isosurface,
        MarchingCubes,