fixed bug in SBGATSphericalHarmo, SHARMLib and CMakeLists.txt

.gitignore

@@ -4,3 +4,4 @@ doxygen_script.sh
 doc/
 .add_license.sh
 .LICENSE.hpp
+./Tests/output/*

README.md

@@ -16,32 +16,16 @@ The SBGAT User's Wiki can be found [here](https://github.com/bbercovici/SBGAT/wi
 
 ### Mac users
 
-[Homebrew](https://brew.sh/) can be used to install SBGAT's components and dependencies. Homebrew install options differ whether you want to use *SbgatGui* or just the core classes of *SbgatCore*. This is justified by *SbgatCore*'s dependency on *VTK*, as *VTK* needs to know whether it must be linked against *Qt* at build time.
-
-#### With SbgatGui
+[Homebrew](https://brew.sh/) can be used to install SBGAT's components and dependencies. 
 
     brew tap bbercovici/self
     brew update
-    brew install vtk --with-qt
+    brew install vtk
     brew install sbgat-core
     brew install sbgat-gui
 
 The *SbgatGui* executable will be simlinked to `/usr/local/bin` .
 
-#### Without SbgatGui
-
-    brew tap bbercovici/self
-    brew update
-    brew install vtk
-    brew install sbgat-core
-
-If you change your mind and decide you want the *SbgatGui* component, run:
-
-    brew uninstall sbgat-core
-    brew uninstall vtk
-
-before reinstalling.
-
 ### Linux & Mac users
 
 [Refer to the detailed installation instructions](https://github.com/bbercovici/SBGAT/wiki/2:-Compiling-and-installing-SBGAT-dependencies).
@@ -74,18 +58,25 @@ to apply the update (if any).
 
 ## Changelog
 
+### [SBGAT 2.02.3](https://github.com/bbercovici/SBGAT/releases/tag/2.02.3)
+
+#### Bug fixes
+- Fixed bug in `SBGATSphericalHarmo` that could have caused the evaluation of the spherical harmonics over a non-barycented shape to be incorrect. 
+- Pushed fix to latest version of `SHARMLib` dependency to address the same issue
+- Modified `CMakeLists.txt` in Tests to fix issue caused by a conflicting header being sometimes included by one of VTK's dependencies
+
 
 ### [SBGAT 2.02.2](https://github.com/bbercovici/SBGAT/releases/tag/2.02.2)
 
-### New
-- Shape models can now be modified from within SBGATGui, by selecting a vertex and applying a Gaussian interpolation of the vertex displacement to a neighborhood of arbitrary choice. 
+#### New
+- Shape models can now be modified from within SBGATGui, by selecting a vertex and applying a Gaussian interpolation of the vertex displacement to a k-neighbor neighborhood.
 
-### Improvements
+#### Improvements
 - Camera is now positioned at the correct distance from the targeted shape body upon loading
 - Improved visual aspect of selected facet
 - Improved visual aspect of loaded shapes
 
-### Bug fixes:
+#### Bug fixes:
 - Fixed bug in SBGATGui that prevented proper alignment of the shape model with its principal axes
 
 ### [SBGAT 2.02.1](https://github.com/bbercovici/SBGAT/releases/tag/2.02.1)
@@ -124,15 +115,13 @@ to apply the update (if any).
 ### New:
 - Facets can now be individually selected in `SbgatGui` by clicking on them. If the surface PGM of the selected shape is available, the results for the selected facet will be shown in the console
 
-
 #### Improvements
 - The `Set Shape Mapper` option was renamed to `Set Results Overlay`
 - Several GUI minors bug fixes
 
 ### Bug fixes:
 - Fixed bug in `SbgatCore` that was due to an unecessary rescaling of the computed potentials and accelerations within `SbgatCore::ComputeSurfacePGM`. This bug was manifesting itself when calling `SbgatCore::ComputeSurfacePGM` with a shape model whose coordinates were expressed in kilometers. This bug was not affecting `SbgatGui` since it automatically rescales input shapes to meters upon loading.
 
-
 ### [SBGAT 1.12.2](https://github.com/bbercovici/SBGAT/releases/tag/1.12.2)
 
 ### New:

SbgatCore/CMakeLists.txt

@@ -109,6 +109,13 @@ if(UNIX AND NOT APPLE AND ${CMAKE_MINOR_VERSION} GREATER 0 )
 	endif()
 endif()
 
+
+# Removing spurious include sometimes brought in by one of VTK's dependencies
+get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+list(REMOVE_ITEM dirs "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include")
+set_property(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES ${dirs})
+
+
 # Add source files in root directory
 add_library(${LIB_NAME} 
 	SHARED

SbgatCore/source/SBGATSphericalHarmo.cpp

@@ -45,6 +45,7 @@ SOFTWARE.
 #include <vtkMath.h>
 #include <vtkSmartPointer.h>
 #include <vtkInformation.h>
+#include <vtkCleanPolyData.h>
 #include <vtkInformationVector.h>
 #include <RigidBodyKinematics.hpp>
 vtkStandardNewMacro(SBGATSphericalHarmo);
@@ -89,9 +90,15 @@ int SBGATSphericalHarmo::RequestData(
   inputVector[0]->GetInformationObject(0);
 
   // call ExecuteData
-  vtkPolyData *input = vtkPolyData::SafeDownCast(
-    inInfo->Get(vtkDataObject::DATA_OBJECT()));
+  vtkPolyData * input_unclean = vtkPolyData::SafeDownCast(inInfo->Get(vtkDataObject::DATA_OBJECT()));
 
+  vtkSmartPointer<vtkCleanPolyData> cleaner =
+  vtkSmartPointer<vtkCleanPolyData>::New();
+  cleaner -> SetInputData (input_unclean);
+  cleaner -> SetOutputPointsPrecision ( vtkAlgorithm::DesiredOutputPrecision::DOUBLE_PRECISION );
+  cleaner -> Update();
+
+  vtkPolyData * input = cleaner -> GetOutput();
   vtkIdType cellId, numCells, numPts, numIds;
 
   numCells = input->GetNumberOfCells();
@@ -140,7 +147,6 @@ int SBGATSphericalHarmo::RequestData(
     numIds = ptIds->GetNumberOfIds();
     assert(numIds == 3);
 
-    // store current vertex (x,y,z) coordinates ...
     double r0[3];
     double r1[3];
     double r2[3];
@@ -149,15 +155,7 @@ int SBGATSphericalHarmo::RequestData(
     input->GetPoint(ptIds->GetId(1), r1);
     input->GetPoint(ptIds->GetId(2), r2);
 
-    double r1r0[3];
-    double r2r0[3];
-
-    vtkMath::Subtract(r1,r0,r1r0);
-    vtkMath::Subtract(r2,r0,r2r0);
-
-    double dv = vtkMath::Determinant3x3(r0,r1r0,r2r0) / 6;
-
-    arma::mat Cnm2f( this -> degree + 1, this -> degree + 1);
+    arma::mat Cnm2f(this -> degree + 1, this -> degree + 1);
     arma::mat Snm2f(this -> degree + 1, this -> degree + 1);
 
     // Call to SHARMLib here
@@ -172,11 +170,9 @@ int SBGATSphericalHarmo::RequestData(
       this -> normalized
       );
 
+    this -> Cnm += Cnm2f ;
+    this -> Snm += Snm2f ;
 
-
-    this -> Cnm += Cnm2f * dv ;
-    this -> Snm += Snm2f * dv ;
-
   }
 
   this -> Cnm /= mass_properties -> GetVolume();

SbgatGui/CMakeLists.txt

@@ -103,6 +103,13 @@ set(CMAKE_AUTOMOC ON)
 set(CMAKE_AUTOUIC ON)
 set(CMAKE_AUTORCC ON)
 
+
+# Removing spurious include sometimes brought in by one of VTK's dependencies
+get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+list(REMOVE_ITEM dirs "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include")
+set_property(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES ${dirs})
+
+
 # Add source files in root directory
 add_executable(${EXE_NAME}
 	source/main.cpp

Tests/CMakeLists.txt

@@ -96,6 +96,11 @@ include_directories(${SBGATCORE_INCLUDE_HEADER})
 find_package(VTK REQUIRED PATHS ${VTK_PATH})
 include(${VTK_USE_FILE})
 
+# Removing spurious include sometimes brought in by one of VTK's dependencies
+get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+list(REMOVE_ITEM dirs "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include")
+set_property(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES ${dirs})
+
 # Add source files in root directory
 add_executable(${EXE_NAME}
 	include/Tests.hpp
@@ -112,6 +117,7 @@ set(library_dependencies
 	)
 
 
+
 target_link_libraries(${EXE_NAME} ${library_dependencies})