Merge pull request #11 from ZenanH/main

🎉 Release new version v0.1.9

Author: ZenanH

CondaPkg.toml

@@ -1,2 +1,4 @@
+channels = ["anaconda", "conda-forge"]
+
 [deps]
-trimesh = ""
+trimesh = "==4.6.6"

Project.toml

@@ -1,7 +1,7 @@
 name = "MaterialPointVisualizer"
 uuid = "9ce2fbfb-c269-402f-8683-a675189e795c"
 authors = ["ZenanH <[email protected]>"]
-version = "0.1.8"
+version = "0.1.9"
 
 [deps]
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"

README.md

@@ -3,7 +3,7 @@
 [![CI](https://github.com/LandslideSIM/MaterialPointVisualizer.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/LandslideSIM/MaterialPointVisualizer.jl/actions/workflows/ci.yml) 
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg?logo=quicklook)](https://LandslideSIM.github.io/MaterialPointVisualizer.jl/stable)
 [![Dev](https://img.shields.io/badge/docs-dev-red.svg?logo=quicklook)](https://LandslideSIM.github.io/MaterialPointVisualizer.jl/dev)
-[![Version](https://img.shields.io/badge/version-v0.1.8-pink)]()
+[![Version](https://img.shields.io/badge/version-v0.1.9-pink)]()
 
 With this package, we can convert the MPM simulation results (HDF5 files from ***[MaterialPointSolver.jl](https://github.com/LandslideSIM/MaterialPointSolver.jl)*** ) into `.vtp` files or create ParaView-compatible animations. Additionally, it includes some post-processing functionalities.
 

docs/src/usage/surfreconstruction.md

@@ -34,8 +34,9 @@ ply2surface(
     splash_dir,
     radius,
     num_threads;
-    cube_size        =0.6,
-    surface_threshold=0.6, 
-    smoothing_length =1.2
+    cube_size          = 0.6,
+    surface_threshold  = 0.6, 
+    smoothing_length   = 1.2,
+    splashsurf::String = "nothing"
 )
 ```

src/MaterialPointVisualizer.jl

@@ -18,7 +18,7 @@ import StatsBase: sample
 import MaterialPointSolver: DeviceArgs2D, DeviceGrid2D, DeviceParticle2D, DeviceProperty,
                             DeviceArgs3D, DeviceGrid3D, DeviceParticle3D     
 
-const trimesh = Ref{Py}()
+const trimesh = PythonCall.pynew()
 
 include(joinpath(@__DIR__, "mpm2vtp.jl"       ))
 include(joinpath(@__DIR__, "particle2vtp.jl"  ))
@@ -27,18 +27,8 @@ include(joinpath(@__DIR__, "plot/display.jl"  ))
 
 function __init__()
     @info "checking environment..."
-    try
-        run(pipeline(`splashsurf -V`, stdout=devnull, stderr=devnull))
-    catch e
-        if isa(e, Base.IOError)  # splashsurf 未安装
-            @warn """splashsurf
-            Cannot find splashsurf on this system. If you need surface reconstruction, please 
-            install it first, see: https://github.com/InteractiveComputerGraphics/splashsurf 
-            and make sure Julia can find it.
-            """
-        end
-    end
-    trimesh[] = pyimport("trimesh")
+    # import Python modules
+    PythonCall.pycopy!(trimesh, pyimport("trimesh"))
 end
 
 end

src/particle2surf.jl

@@ -31,7 +31,7 @@ function particle2ply(coords::Matrix; output_file::String="coord.ply")
         coords = hcat(coords, zeros(size(coords, 1)))
     end
     # export .ply file by using trimesh
-    mesh = trimesh[].Trimesh(vertices=coords)
+    mesh = trimesh.Trimesh(vertices=coords)
     mesh.export(output_file)
     # print info
     @info """PLY file ($(size(coords, 1)) pts) saved at:
@@ -55,7 +55,7 @@ function particle2ply(
     output_file = joinpath(args.project_path, args.project_name, filename)
     coords = hcat(mp.ξ, zeros(mp.np))
     # export .ply file by using trimesh
-    mesh = trimesh[].Trimesh(vertices=coords)
+    mesh = trimesh.Trimesh(vertices=coords)
     mesh.export(output_file)
     # print info
     @info """PLY file ($(size(coords, 1)) pts) saved at:
@@ -78,7 +78,7 @@ function particle2ply(
     filename = args.project_name * ".ply"
     output_file = joinpath(args.project_path, args.project_name, filename)
     # export .ply file by using trimesh
-    mesh = trimesh[].Trimesh(vertices=mp.ξ)
+    mesh = trimesh.Trimesh(vertices=mp.ξ)
     mesh.export(output_file)
     # print info
     @info """PLY file ($(mp.np) pts) saved at:
@@ -114,7 +114,7 @@ function particle2ply(hdf5_file::String, ply_dir::String)
         end
         output_file = joinpath(ply_dir, "iteration_$(i).ply")
         # export .ply file by using trimesh
-        mesh = trimesh[].Trimesh(vertices=obj)
+        mesh = trimesh.Trimesh(vertices=obj)
         mesh.export(output_file)
         next!(p)
     end
@@ -127,7 +127,7 @@ end
 
 """
     ply2surface(ply_dir, splash_dir, radius, num_threads; cube_size=0.6, 
-        surface_threshold=0.6, smoothing_length=1.2)
+        surface_threshold=0.6, smoothing_length=1.2, splashsurf="nothing")
 
 Description:
 ---
@@ -148,18 +148,49 @@ function ply2surface(
     splash_dir,
     radius,
     num_threads;
-    cube_size        =0.6,
-    surface_threshold=0.6, 
-    smoothing_length =1.2
+    cube_size          = 0.6,
+    surface_threshold  = 0.6, 
+    smoothing_length   = 1.2,
+    splashsurf::String = "nothing"
 )
+    if splashsurf == "nothing"
+        try
+            run(pipeline(`splashsurf -V`, stdout=devnull, stderr=devnull))
+        catch e
+            if isa(e, Base.IOError)  # splashsurf 未安装
+                @warn """splashsurf
+                Cannot find splashsurf on this system. If you need surface reconstruction, please
+                install it first, and make sure Julia can find it.
+                Or you can pass the path of splashsurf to ply2surface.
+                link: https://github.com/InteractiveComputerGraphics/splashsurf 
+                """
+            end
+        end
+        splashsurfcmd = "splashsurf"
+    else
+        try
+            run(pipeline(`$(splashsurf) -V`, stdout=devnull, stderr=devnull))
+        catch e
+            if isa(e, Base.IOError)  # splashsurf 未安装
+                @warn """invalid splashsurf path
+                Cannot find splashsurf on this system. If you need surface reconstruction, please
+                install it first, and make sure Julia can find it.
+                Or you can pass the path of splashsurf to ply2surface.
+                link: https://github.com/InteractiveComputerGraphics/splashsurf 
+                """
+            end
+        end
+        splashsurfcmd = splashsurf
+    end
+
     num_threads = 1 ≤ num_threads ≤ Sys.CPU_THREADS ? num_threads : Sys.CPU_THREADS
     splash_dir ≠ ply_dir || throw(ArgumentError(
         "The splash output directory should be different from the ply input directory"))
     isdir(splash_dir) || mkpath(splash_dir)
     if isfile(ply_dir)
         inputs = ply_dir
         outputs = joinpath(splash_dir, "surface.vtk")
-        run(`splashsurf reconstruct $(inputs) --output-file=$(outputs)
+        run(`$(splashsurfcmd) reconstruct $(inputs) --output-file=$(outputs)
             --particle-radius=$(radius*1.5)
             --cube-size=$(cube_size)
             --surface-threshold=$(surface_threshold)
@@ -174,7 +205,7 @@ function ply2surface(
     elseif isdir(ply_dir)
         inputs = joinpath(ply_dir, "iteration_{}.ply")
         outputs = joinpath(splash_dir, "iteration_{}.vtk")
-        run(`splashsurf reconstruct $(inputs) --output-file=$(outputs)
+        run(`$(splashsurfcmd) reconstruct $(inputs) --output-file=$(outputs)
             --particle-radius=$(radius*1.5)
             --cube-size=$(cube_size)
             --surface-threshold=$(surface_threshold)

test/runtests.jl

@@ -1,4 +1,5 @@
-using MaterialPointVisualizer 
+using MaterialPointVisualizer
+using PythonCall
 using Test
 
-@test !isnothing(MaterialPointVisualizer.trimesh[])
+@test !pyconvert(Bool, PythonCall.pyisnull(MaterialPointVisualizer.trimesh))