Release 1.5.2

nodtem66 · Aug 8, 2021 · 91e6f66 · 91e6f66
1 parent 678630d
commit 91e6f66
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Showing 29 changed files with 1,343 additions and 999 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -117,23 +117,17 @@ endif()
 if(BUILD_SCAFFOLDER)
 	# Add your project files
 	file(GLOB MAIN_SOURCES
-		"${PROJECT_SOURCE_DIR}/include/*.c"
-		"${PROJECT_SOURCE_DIR}/include/*.cpp"
-		"${PROJECT_SOURCE_DIR}/include/*.tpp"
-		"${PROJECT_SOURCE_DIR}/include/*.h"
-		"${PROJECT_SOURCE_DIR}/include/*.hpp"
 		"${PROJECT_SOURCE_DIR}/include/*/*.c"
 		"${PROJECT_SOURCE_DIR}/include/*/*.cpp"
-		"${PROJECT_SOURCE_DIR}/include/*/*.tpp"
-		"${PROJECT_SOURCE_DIR}/include/*/*.h"
-		"${PROJECT_SOURCE_DIR}/include/*/*.hpp"
 		"${PROJECT_SOURCE_DIR}/src/utils.cpp"
+		"${PROJECT_SOURCE_DIR}/src/Scaffolder.cpp"
 		"${VCG_INCLUDE_DIR}/wrap/ply/plylib.cpp"
 		"${OpenCTM_INCLUDE_DIR}/*.c"
 		"${OpenCTM_INCLUDE_DIR}/liblzma/*.c"
 	)
 	include(update_deps_file)
 	update_deps_file("main_sources" "${MAIN_SOURCES}")
+
 
 	# Build binary
 	add_executable(${PROJECT_NAME} ${MAIN_SOURCES} ${PROJECT_SOURCE_DIR}/src/Main.cpp)
@@ -145,6 +139,7 @@ if(BUILD_SCAFFOLDER)
 		${SOL2_INCLUDE_DIR}
 		${LUA_INCLUDE_DIR}
 		${OpenCTM_INCLUDE_DIR}
+		${LIBIGL_INCLUDE_DIR}
 		"${OpenCTM_INCLUDE_DIR}/liblzma/"
 	)
 	target_link_libraries(${PROJECT_NAME} PRIVATE
@@ -155,10 +150,15 @@ if(BUILD_SCAFFOLDER)
 		${LUA_LIBRARIES}
 	)
 
-	add_executable("${PROJECT_NAME}.SliceTest" ${MAIN_SOURCES} ${PROJECT_SOURCE_DIR}/src/SliceTest.cpp)
+	add_executable("${PROJECT_NAME}.SliceTest" 
+		${PROJECT_SOURCE_DIR}/src/SliceTest.cpp
+		${PROJECT_SOURCE_DIR}/src/utils.cpp
+		${VCG_INCLUDE_DIR}/wrap/ply/plylib.cpp
+	)
 	target_include_directories("${PROJECT_NAME}.SliceTest" PRIVATE
 		"${PROJECT_SOURCE_DIR}/include"
 		${VCG_INCLUDE_DIR}
+		${LIBIGL_INCLUDE_DIR}
 		${EIGEN3_INCLUDE_DIR}
 		${OpenCTM_INCLUDE_DIR}
 		"${OpenCTM_INCLUDE_DIR}/liblzma/"
@@ -177,19 +177,21 @@ if(BUILD_PYSCAFFOLDER)
 
 	file(GLOB PYTHON_SOURCES
 		"${PROJECT_SOURCE_DIR}/src/python/*.cpp"
-		"${PROJECT_SOURCE_DIR}/src/python/*.hpp"
-		"${PROJECT_SOURCE_DIR}/src/utils.cpp"
+		${PROJECT_SOURCE_DIR}/src/Scaffolder.cpp
+		${PROJECT_SOURCE_DIR}/src/utils.cpp
 	)
 	include(update_deps_file)
 	update_deps_file("python_sources" "${PYTHON_SOURCES}")
 
 	pybind11_add_module("Py${PROJECT_NAME}" ${PYTHON_SOURCES})
 	target_include_directories("Py${PROJECT_NAME}" PRIVATE
 		"${PROJECT_SOURCE_DIR}/include"
+		"${PROJECT_SOURCE_DIR}/src/python/"
 		${TBB_INCLUDE_DIR}
 		${VCG_INCLUDE_DIR}
 		${EIGEN3_INCLUDE_DIR}
 		${SOL2_INCLUDE_DIR}
+		${LIBIGL_INCLUDE_DIR}
 		${LUA_INCLUDE_DIR}
 		${PyBind11_INCLUDE_DIR}
 		${OpenCTM_INCLUDE_DIR}

diff --git a/blender/SCAFFOLDER_OP_generate_mesh.py b/blender/SCAFFOLDER_OP_generate_mesh.py
@@ -79,7 +79,10 @@ def callback(v):
                 f = read_faces(mesh)
 
                 def gen(self):
-                    mesh = PyScaffolder.generate_mesh(v, f, params, callback)
+                    if ('__version__' in PyScaffolder.__dict__):
+                        mesh = PyScaffolder.generate_scaffold(v, f, params, callback)
+                    else:
+                        mesh = PyScaffolder.generate_mesh(v, f, params, callback)
                     template_str = "Porosity: %.3f\nSurface Area: %.3f\nSurface Area Ratio: %.3f"
                     props.result1 = template_str % (mesh.porosity, mesh.surface_area, mesh.surface_area_ratio)
 

diff --git a/blender/SCAFFOLDER_settings.py b/blender/SCAFFOLDER_settings.py
@@ -38,8 +38,8 @@ def set_coff(self, context):
     is_build_inverse: BoolProperty(name="Build inverse", default=False)
 
     grid_size: IntProperty(name="Grid size", default=100, min=10)
-    grid_offset: IntProperty(name="Grid offset", default=5, min=0)
-    smooth_step: IntProperty(name="smooth step", default=5, min=0)
+    grid_offset: IntProperty(name="Grid offset", default=3, min=0)
+    smooth_step: IntProperty(name="smooth step", default=0, min=0)
     k_slice: IntProperty(name="k slice", default=100, min=1)
     k_polygon: IntProperty(name="k polygon", default=4, min=1)
 

diff --git a/cmake/FindLIBIGL.cmake b/cmake/FindLIBIGL.cmake
@@ -30,7 +30,7 @@ set(LIBIGL_USE_STATIC_LIBRARY OFF CACHE INTERNAL "prefer STATIC build")
 set(LIBIGL_SKIP_DOWNLOAD ON CACHE INTERNAL "Skip download libigl")
 # set(HUNTER_ENABLED ON CACHE INTERNAL "Enable Hunter package manager support")
 
-message(STATUS "USE DIR: ${LIBIGL_INCLUDE_DIR}")
+message(STATUS "USE IGL DIR: ${LIBIGL_INCLUDE_DIR}")
 list(APPEND CMAKE_MODULE_PATH "${LIBIGL_INCLUDE_DIR}/../cmake")
 if (NOT EIGEN3_INCLUDE_DIR)
   set(EIGEN3_INCLUDE_DIR "${LIBIGL_INCLUDE_DIR}/../external/eigen")

diff --git a/cmake/FindSol2.cmake b/cmake/FindSol2.cmake
@@ -56,7 +56,7 @@ file(GLOB SOL2_HEADER_SOURCES ${SOL2_INCLUDE_DIR}/sol*.hpp)
 source_group(sol2 FILES ${SOL2_HEADER_SOURCES})
 
 list(APPEND CMAKE_MODULE_PATH "${SOL2_INCLUDE_DIR}/../cmake/Modules")
-message(STATUS "USE DIR: ${SOL2_INCLUDE_DIR}")
+message(STATUS "USE SOL2 DIR: ${SOL2_INCLUDE_DIR}")
 
 # # # Libraries
 # Here, we pull in all the necessary libraries for building examples and tests
@@ -143,4 +143,4 @@ endif()
 if (NOT LUA_FOUND AND NOT LUABUILD_FOUND)
 	message(FATAL_ERROR "sol2 Lua \"${SOL2_LUA_VERSION}\" not found and could not be targeted for building")
 endif()
-message(STATUS "USE DIR: ${LUA_LIBRARIES} ${LUA_INCLUDE_DIR}")
+message(STATUS "USE LUA DIR: ${LUA_LIBRARIES} ${LUA_INCLUDE_DIR}")
diff --git a/docs/cmd.md b/docs/cmd.md
@@ -5,9 +5,9 @@ Usage:
   Scaffolder [OPTION...] INPUT OUTPUT PARAMETERS
 
   -h, --help                    Print help
-  -i, --input INPUT             Input file (STL)
+  -i, --input INPUT             Input file (STL/PLY/OFF/OBJ/VMI)
   -o, --output OUTPUT           Output filename with extension
-                                stl,ply,obj,off [default: out]
+                                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]
@@ -17,7 +17,7 @@ Usage:
   -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]
+                                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]
@@ -27,23 +27,31 @@ Usage:
                                 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]
+                                (default: 100)
       --k_polygon INT (>0)      K_polygon: the number of closest outer
-                                contour (used in microstructure analysis) [default: 4]
+                                contour (used in microstructure analysis) (default:
+                                4)
   -z, --size_optimize DOUBLE (0..1)
-                                Experimental Quadric simplification [default: 0]
+                                Experimental Quadric simplification (default:
+                                0)
       --smooth_step INT (0..60000)
-                                Smooth with laplacian (default: 5)
-      --dirty                   Disable autoclean [default false]
+                                Smooth with laplacian (default: 0)
+      --dirty                   Disable autoclean
       --minimum_diameter DOUBLE (0..1)
-                                used for removing small orphaned (between 0-1) [default: 0.25]
+                                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]
+                                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)
 ```
 
 ## Examples

diff --git a/docs/installation.md b/docs/installation.md
@@ -111,7 +111,7 @@ params = PyScaffolder.Parameter()
 params.coff = 1.0
 
 # Test the mesh generation from v,f
-a = PyScaffolder.[generate_mesh]()(v, f, params)
+a = PyScaffolder.generate_scaffold(v, f, params)
 print(a.porosity)
 print(a.surface_area_ratio)
 print(len(a.v), len(a.f))

diff --git a/docs/python.md b/docs/python.md
@@ -57,11 +57,11 @@ namespace PyScaffolder {
 }
 ```
 
-The main core functions are `generate_mesh` and `slice_test` which resemble the standalone program: `Scaffolder` and `Scaffolder.Slice`.
+The main core functions are `generate_scaffold` and `slice_test` which resemble the standalone program: `Scaffolder` and `Scaffolder.Slice`.
 
-## generate_mesh
+## generate_scaffold
 ```python
-def generate_mesh(vertices, faces, params=Parameter(), callback=None)
+def generate_scaffold(vertices, faces, params=Parameter(), callback=None)
 ```
 :   Generate 3D mesh from input vertices, faces, and parameters
     ### Parameters
@@ -113,7 +113,7 @@ def generate_mesh(vertices, faces, params=Parameter(), callback=None)
 
     # use callback to show % progression
     def progression(n):
-      print(x)
+      print(n)
 
     mesh_info = generate_mesh(v, f, callback=progression)
     ```
@@ -147,11 +147,45 @@ def slice_test(vertices, faces, k_slice=100, k_polygon=4, direction=0, callback=
     print(len(pore_size.minFeret), len(pore_size.maxFeret))
     ```
 
+## marching_cubes
+```python
+def marching_cubes(f, grid_size=(100,100,100), v_min=(0,0,0), delta=0.01, clean=False, callback=None)
+```
+:   Slice input mesh into pore sizes
+    ### Parameters
+    * `f`: numpy.array representing a discrete isosurface where F(x,y,z) = 0 is boundary   
+    * `grid_size`: *Optional* array, list, tuple, or int representing the number of voxels 
+    * `v_min`: *Optional* array, list, tuple the coordinate of the corner of grid
+    * `delta`: *Optional* array, list, tuple or double representing the dimension of a voxel 
+    * `clean` *Optional* boolean that enable mesh cleaning after marching cubes
+    * `callback`: *Optional* function with one `integer` parameter indicating the progression
+    ###Return
+    `#!python (v, f)` representing vertices and faces in `np.array`
+
+    ###Example
+    ```python
+    import PyScaffolder
+    Fxyz = [
+        1,1,1,1,
+        1,-1,-1,1,
+        1,-1,-1,1,
+        1,1,1,1
+    ]*4
+    (v, f) = PyScaffolder.marching_cubes(
+        Fxyz,
+        grid_size=4,
+        delta=0.25,
+        v_min=(-.5, -.5, -.5),
+        callback = lambda x: print(x)
+    )
+    ```
+
 ## Parameter
 ```python
 class Parameter:
     is_build_inverse = False
     is_intersect = True
+    verbose = False
     shell = 0
     grid_offset = 5
     smooth_step = 5
@@ -190,4 +224,4 @@ class MeshInfo:
 	surface_area = 0.0
 	surface_area_ratio = 0.0
 ```
-:   Collection of triangular mesh resulted from [generate_mesh](#generate_mesh)
+:   Collection of triangular mesh resulted from [generate_scaffold](#generate_scaffold)
diff --git a/docs/tutorial_1.md b/docs/tutorial_1.md
@@ -7,7 +7,7 @@ angular frequency ($w$), and isolevel ($t$) are required (See [Command line](cmd
 ## Angular frequency
 
 According to [prior study](https://github.com/nodtem66/Scaffolder/blob/master/data/data_visualization.ipynb),
-**$w$ is inversely proportational to the pore size** (see [Tips](tips.md)). That is when $w$ increases,
+**$w$ is inversely proportational to the pore size** (see [Tips](tips.md)). That is, when $w$ increases,
 the pore size will be decreased. For gyroid, $w \approx \pi/\text{pore size}$. If we want pore size of 0.25
 (unit as same as `sphere.stl`), we try to initially set $w = \pi/0.25 \approx 12$ 
 
@@ -107,7 +107,7 @@ We use binary search to adjust the new value of $t$ to find the optimal value wi
 | -- | -- | -- | -- | -- | -- | -- | -- | -- |
 | Porosity | 0.508 | 0.85 | 0.67 | 0.59 | 0.634 | 0.613 | 0.602 | 0.597
 
-We can also use the classic numerical method called [Secant method](https://en.wikipedia.org/wiki/Secant_method) to find the optimal $t$ for the target porosity.
+We can also use the classical numerical method called [Secant method](https://en.wikipedia.org/wiki/Secant_method) to find the optimal $t$ for the target porosity.
 
 $$
 F(t) = Porosity(t) - 0.6 = 0

diff --git a/include/MaxHeap.hpp b/include/MaxHeap.hpp
@@ -1,4 +1,5 @@
-#pragma once
+#ifndef MAXHEAP_HPP_INCLUDED
+#define MAXHEAP_HPP_INCLUDED
 
 #include <vector>
 #include <iostream>
@@ -42,4 +43,5 @@ class MaxHeap {
 		(*arr)[0] = d;
 		heapify(0);
 	}
-};
+};
+#endif
diff --git a/include/Mesh.h b/include/Mesh.h
@@ -1,6 +1,6 @@
-#pragma once
 #ifndef MESH_INCLUDED
 #define MESH_INCLUDED
+
 #include <openctm.h>
 #include <vcg/complex/complex.h>
 #include <vcg/complex/algorithms/update/halfedge_indexed.h>

diff --git a/include/MeshOperation.h b/include/MeshOperation.h
@@ -1,6 +1,6 @@
-#pragma once
 #ifndef MESHOPERATION_INCLUDED
 #define MESHOPERATION_INCLUDED
+
 #include "Mesh.h"
 #include "utils.h"
 

diff --git a/include/OptimalSlice.hpp b/include/OptimalSlice.hpp
@@ -2,9 +2,9 @@
  * This is the implement slice algorithm from Rodrigo, 2017 (An Optimal Algorithm for 3D Triangle Mesh Slicing)
  * which is claimed to be faster than slic3r and CGAL method.
  */
-#pragma once
 #ifndef OPTIMALSLICE_INCLUDED
 #define OPTIMALSLICE_INCLUDED
+
 #ifndef SLICE_PRECISION
 // There's a problem of double hashing with the precision less than 1e-8 (e.g. 1e-10)
 // when performed contour constructing

diff --git a/include/QuadricSimplification.h b/include/QuadricSimplification.h
@@ -19,9 +19,9 @@
  * for more details.                                                         *
  *                                                                           *
  ****************************************************************************/
-#pragma once
 #ifndef QUADSIM_INCLUDED
 #define QUADSIM_INCLUDED
+
 #include <vcg/container/simple_temporary_data.h>
 #include <vcg/complex/algorithms/local_optimization.h>
 #include <vcg/complex/algorithms/local_optimization/tri_edge_collapse_quadric.h>