ENH: Improve reconstruction order of vertices to change normals orientation

Common.cmake

@@ -18,9 +18,9 @@ if(NOT COMMAND SETIFEMPTY)
 endif()
 
 #-----------------------------------------------------------------------------
-SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}-build/lib)
-SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}-build/lib)
-SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}-build/bin)
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}build/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}build/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${PRIMARY_PROJECT_NAME}build/bin)
 
 #-----------------------------------------------------------------------------
 SETIFEMPTY(CMAKE_INSTALL_LIBRARY_DESTINATION lib)

README.md

@@ -0,0 +1,60 @@
+## Surface Remesh
+
+## Description
+
+Surface reconstruction from rotated spheres (after RigidAlignment) or from coefficients (after GROUPS).
+
+
+## Build
+
+#### Requirements 
+
+Building SurfRemesh requires to have built previously:
+
+* MeshLib (https://github.com/pdedumast/MeshLib)
+* SlicerExecutionModel
+
+SurfRemesh can either be built from GROUPS SuperBuild.
+
+
+###### Linux or MacOSX 
+
+Consider this tree of repertories:
+```
+~/Project/SurfRemesh
+         /SurfRemesh-build
+```
+
+Start a terminal.
+First change your current working directory to the build directory ```SurfRemesh-build```
+```
+cd ~/Project/SurfRemesh-build
+```
+
+Generate the project using ```cmake```
+```
+cmake -DMeshLib_DIR:PATH=path/to/MeshLib -DSlicerExecutionModel:PATH=path/to/SlicerExecutionModel ../SurfRemesh
+make
+```
+
+
+## Usage
+
+Reconstruction from new rotated sphere, after RigidAlignment:
+Output surface will have the same parametrization with one specified by the reference sphere.
+```
+./SurfRemesh --input [<std::string> input surface model] --tempModel [<std::string> rotate sphere] 
+--ref [<std::string> common sphere model (same as refSphere in RigidAlignment)] 
+--output [<std::string> reconstructed surface]
+```
+
+Reconstruction from coefficients, after GROUPS:
+```
+./SurfRemesh --input [<std::string> input surface model] --tempModel [<std::string> sphere model used in GROUPS] 
+--ref [<std::string> common sphere model] --coeff [<std::string> Coefficients file from GROUPS]
+--output [<std::string> reconstructed surface]
+```
+
+## Licence
+
+See LICENSE.txt for information on using and contributing.

src/CMakeLists.txt

@@ -1,3 +1,4 @@
 add_library(SurfRemesh 
     STATIC
-    SurfaceRemeshing.cpp)
+    SurfaceRemeshing.cpp)
+

src/SurfaceRemeshing.cpp

@@ -102,6 +102,7 @@ SurfaceRemeshing::SurfaceRemeshing(const char *subject, const char *sphere, cons
 		m_coeff[0] = 0;
 		m_coeff[1] = 0;
 	}
+
 	float phi, theta;
 	Coordinate::cart2sph(m_pole, &phi, &theta);
 
@@ -137,7 +138,7 @@ SurfaceRemeshing::SurfaceRemeshing(const char *subject, const char *sphere, cons
 			if (fabs(phi - phi_) < eps && fabs(theta - theta_) < eps) continue;
 			SphericalHarmonics::basis(m_degree, (float *)v->fv(), Y);
 			reconsCoord(v->fv(), v1, Y, m_coeff, m_degree, m_pole);
-			MathVector V(v1); V.unit();
+			MathVector V(v1); V.unit(); 
 			v->setVertex(V.fv());
 		}
 	}
@@ -194,6 +195,7 @@ SurfaceRemeshing::SurfaceRemeshing(const char *subject, const char *sphere, cons
 	}
 }
 
+
 void SurfaceRemeshing::reconsCoord(const float *v0, float *v1, float *Y, float *coeff, int degree, float *pole)
 {
 	// spharm basis
@@ -244,8 +246,8 @@ void SurfaceRemeshing::reconsCoord(const float *v0, float *v1, float *Y, float *
 	// inverse rotation
 	Coordinate::rotPoint(rv, rot, v1);
 }
-
-/*void SurfaceRemeshing::reconsCoord(const float *v0, float *v1, float *Y, float *coeff, float degree, float *pole)
+/*
+void SurfaceRemeshing::reconsCoord(const float *v0, float *v1, float *Y, float *coeff, float degree, float *pole)
 {
 	// spharm basis
 	int n = (degree + 1) * (degree + 1);
@@ -354,7 +356,7 @@ void SurfaceRemeshing::deformSurface()
 			d_v[0] = dataInterpolation(m_x, id, coeff, m_sphere_subj);
 			d_v[1] = dataInterpolation(m_y, id, coeff, m_sphere_subj);
 			d_v[2] = dataInterpolation(m_z, id, coeff, m_sphere_subj);
-			
+
 			if (m_keepColor)
 			{
 				int *d_c = new int[3];
@@ -372,6 +374,7 @@ void SurfaceRemeshing::deformSurface()
 			d_v[2] = dataMedian(m_z, id, m_sphere_subj);
 		}
 		Vertex *new_v = (Vertex *)m_remesh->vertex(i);
+
 		new_v->setVertex(d_v);
 	}
 }

wrapper/CMakeLists.txt

@@ -1,5 +1,4 @@
 
-
 if(UNIX)
     set( INSTALL_RUNTIME_DESTINATION bin)
     set( INSTALL_LIBRARY_DESTINATION lib)
@@ -20,4 +19,5 @@ SEMMacroBuildCLI(
     	INSTALL_ARCHIVE_DESTINATION ${INSTALL_ARCHIVE_DESTINATION}
 )
 
-install(TARGETS SRemesh RUNTIME DESTINATION ${INSTALL_RUNTIME_DESTINATION})
+install(TARGETS SRemesh RUNTIME DESTINATION ${INSTALL_RUNTIME_DESTINATION})
+

wrapper/SRemesh.cxx

@@ -7,6 +7,8 @@ int main(int argc, char* argv[])
 {
 	PARSE_ARGS;
 
+	std::cout<<std::endl<<std::endl;
+
 	if (argc < 2)
 	{
 		std::cout << "Usage: " << argv[0] << " --help" << std::endl;