mirror of https://github.com/CGAL/cgal
ImageIO no longer depends on VTK
* The non-documented WITH_VTK is no longer supported. * The function CGAL::Image_3::read_vtk_image_data has been replaced by a global function. * Added Mesh_3/examples/Mesh_3/mesh_3D_gray_vtk_image.cpp
This commit is contained in:
Andreas Fabri
parent
4afa8a7813
commit
57ad151cd4
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@ -64,6 +64,7 @@ public:
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class CGAL_IMAGEIO_EXPORT Image_3
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{
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struct Image_deleter {
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void operator()(_image* image)
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{
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@ -164,7 +165,7 @@ public:
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vx,vy,vz,offset));
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}
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#ifdef CGAL_USE_VTK
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#if 0
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bool read_vtk_image_data(vtkImageData*);
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#endif // CGAL_USE_VTK
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@ -157,7 +157,7 @@ void Image_3::gl_draw_bbox(const float line_width,
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} // end namespace CGAL
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#ifdef CGAL_USE_VTK
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#if 0
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#include <vtkImageData.h>
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#include <CGAL/Image_3_vtk_interface.h>
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@ -23,7 +23,6 @@
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#include <CGAL/config.h>
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#ifdef CGAL_USE_VTK
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#include <CGAL/Image_3.h>
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#include <vtkImageData.h>
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#include <vtkPointData.h>
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@ -126,7 +125,5 @@ struct VTK_type_generator<boost::uint32_t> {
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} //end namespace CGAL
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#endif // CGAL_USE_VTK
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#endif // CGAL_IMAGE_3_VTK_INTERFACE_H
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@ -0,0 +1,95 @@
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// Copyright (c) 2005-2008 INRIA Sophia-Antipolis (France).
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// 2008 GeometryFactory
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// All rights reserved.
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//
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// This file is part of CGAL (www.cgal.org); you can redistribute it and/or
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// modify it under the terms of the GNU Lesser General Public License as
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// published by the Free Software Foundation; either version 3 of the License,
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// or (at your option) any later version.
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//
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// Licensees holding a valid commercial license may use this file in
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// accordance with the commercial license agreement provided with the software.
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//
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// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
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// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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//
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// $URL$
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// $Id$
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//
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//
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// Author(s) : Laurent Rineau, Pierre Alliez
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#ifndef CGAL_READ_VTK_IMAGE_DATA_H
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#define CGAL_READ_VTK_IMAGE_DATA_H
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#include <CGAL/Image_3.h>
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#include <CGAL/Image_3_vtk_interface.h>
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namespace CGAL {
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namespace {
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struct VTK_to_ImageIO_type_mapper {
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WORD_KIND wordKind;
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SIGN sign;
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unsigned int wdim;
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};
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static const VTK_to_ImageIO_type_mapper VTK_to_ImageIO_type[VTK_ID_TYPE] =
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{ { WK_UNKNOWN, SGN_UNKNOWN, 0}, // 0=VTK_VOID
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{ WK_UNKNOWN, SGN_UNKNOWN, 0}, // 1=VTK_BIT
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{ WK_FIXED, SGN_SIGNED, 1}, // 2=VTK_CHAR
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{ WK_FIXED, SGN_UNSIGNED, 1}, // 3=VTK_UNSIGNED_CHAR
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{ WK_FIXED, SGN_SIGNED, 2}, // 4=VTK_SHORT
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{ WK_FIXED, SGN_UNSIGNED, 2}, // 5=VTK_UNSIGNED_SHORT
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{ WK_FIXED, SGN_SIGNED, 4}, // 6=VTK_INT
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{ WK_FIXED, SGN_UNSIGNED, 4}, // 7=VTK_UNSIGNED_INT
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{ WK_FIXED, SGN_SIGNED, 8}, // 8=VTK_LONG
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{ WK_FIXED, SGN_UNSIGNED, 8}, // 9=VTK_UNSIGNED_LONG
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{ WK_FLOAT, SGN_SIGNED, 4}, // 10=VTK_FLOAT
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{ WK_FIXED, SGN_SIGNED, 8} // 11=VTK_DOUBLE
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};
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} //end anonymous namespace
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inline
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Image_3
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read_vtk_image_data(vtkImageData* vtk_image)
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{
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if(!vtk_image)
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return Image_3();
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_image* image = ::_initImage();
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const int* dims = vtk_image->GetDimensions();
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const double* spacing = vtk_image->GetSpacing();
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image->vectMode = VM_SCALAR;
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image->xdim = dims[0];
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image->ydim = dims[1];
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image->zdim = dims[2];
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image->vdim = 1;
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image->vx = spacing[0];
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image->vy = spacing[1];
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image->vz = spacing[2];
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image->endianness = ::_getEndianness();
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int vtk_type = vtk_image->GetScalarType();
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if(vtk_type == VTK_SIGNED_CHAR) vtk_type = VTK_CHAR;
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if(vtk_type < 0 || vtk_type > VTK_DOUBLE)
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vtk_type = VTK_DOUBLE;
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const VTK_to_ImageIO_type_mapper& imageio_type =
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VTK_to_ImageIO_type[vtk_type];
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image->wdim = imageio_type.wdim;
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image->wordKind = imageio_type.wordKind;
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image->sign = imageio_type.sign;
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image->data = ::ImageIO_alloc(dims[0]*dims[1]*dims[2]*image->wdim);
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std::cerr << "GetNumberOfTuples()=" << vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples()
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<< "\nimage->size()=" << dims[0]*dims[1]*dims[2]
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<< "\nwdim=" << image->wdim << '\n';
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CGAL_assertion(vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() == dims[0]*dims[1]*dims[2]);
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vtk_image->GetPointData()->GetScalars()->ExportToVoidPointer(image->data);
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return Image_3(image);
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}
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} // namespace CGAL
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#endif // CGAL_READ_VTK_IMAGE_DATA_H
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@ -3,11 +3,6 @@ message("Configuring libCGAL_ImageIO")
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find_package( OpenGL )
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find_package( ZLIB )
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#option(WITH_VTK "Add VTK support to libCGAL_ImageIO." OFF)
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if(WITH_VTK)
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find_package(VTK COMPONENTS vtkImagingCore vtkIOImage vtkFiltersImaging NO_MODULE REQUIRED)
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endif(WITH_VTK)
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if(OPENGL_FOUND)
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message( STATUS "OpenGL include: ${OPENGL_INCLUDE_DIR}" )
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@ -26,20 +21,6 @@ if(OPENGL_FOUND)
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set( CGAL_ImageIO_BASENAME CGAL_ImageIO)
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if(WITH_VTK)
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if( VTK_FOUND )
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message(STATUS "VTK-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}.${VTK_BUILD_VERSION} found. Build VTK support in ${CGAL_ImageIO_BASENAME}.")
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include( ${VTK_USE_FILE} )
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cache_set(CGAL_ImageIO_3RD_PARTY_DEFINITIONS ${CGAL_ImageIO_3RD_PARTY_DEFINITIONS} -DCGAL_USE_VTK)
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cache_set(CGAL_ImageIO_3RD_PARTY_INCLUDE_DIRS ${CGAL_ImageIO_3RD_PARTY_INCLUDE_DIRS} ${VTK_INCLUDE_DIRS} )
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cache_set(CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS ${CGAL_ImageIO_3RD_PARTY_LIBRARIES_DIRS} ${vtkImagingCore_RUNTIME_LIBRARY_DIRS} ${vtkImagingCore_LIBRARY_DIRS} ${vtkIOImage_RUNTIME_LIBRARY_DIRS} ${vtkIOImage_LIBRARY_DIRS} ${vtkFiltersImaging_RUNTIME_LIBRARY_DIRS} ${vtkFiltersImaging_LIBRARY_DIRS})
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cache_set(CGAL_ImageIO_3RD_PARTY_LIBRARIES ${CGAL_ImageIO_3RD_PARTY_LIBRARIES} ${VTK_LIBRARIES} )
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else()
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message(STATUS "VTK not found.")
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endif()
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endif()
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if(COMMAND add_config_flag)
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set( CGAL_HAS_IMAGEIO TRUE )
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add_config_flag( CGAL_HAS_IMAGEIO )
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@ -8,9 +8,6 @@ cmake_minimum_required(VERSION 2.8.11)
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include_directories(../../include)
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include_directories(../../../Triangulation_3/include)
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include_directories(../../../STL_Extension/include)
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include_directories(../../../AABB_tree/include)
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add_definitions(-DCGAL_MESH_3_NO_DEPRECATED_SURFACE_INDEX
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-DCGAL_MESH_3_NO_DEPRECATED_C3T3_ITERATORS)
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@ -48,6 +45,21 @@ if ( CGAL_FOUND )
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endif()
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set(VTK_LIBS "")
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find_package(VTK QUIET COMPONENTS vtkImagingGeneral vtkIOImage NO_MODULE)
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if(VTK_FOUND)
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include(${VTK_USE_FILE})
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if ("${VTK_VERSION_MAJOR}" GREATER "5")
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message(STATUS "VTK found")
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set( VTK_LIBS vtkImagingGeneral vtkIOImage )
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else()
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message(STATUS "VTK version 6.0 or greater is required")
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endif()
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else()
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message(STATUS "VTK was not found")
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endif()
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if ( Boost_FOUND AND Boost_VERSION GREATER 103400 )
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include( CGAL_CreateSingleSourceCGALProgram )
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@ -62,6 +74,11 @@ if ( CGAL_FOUND )
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create_single_source_cgal_program( "mesh_polyhedral_domain.cpp" )
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create_single_source_cgal_program( "mesh_polyhedral_domain_with_features.cpp" )
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if( WITH_CGAL_ImageIO )
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if( VTK_FOUND )
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add_executable ( mesh_3D_gray_vtk_image mesh_3D_gray_vtk_image.cpp )
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target_link_libraries( mesh_3D_gray_vtk_image ${CGAL_LIBRARIES} ${CGAL_3RD_PARTY_LIBRARIES} ${VTK_LIBS})
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endif()
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if( CGAL_ImageIO_USE_ZLIB )
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create_single_source_cgal_program( "mesh_optimization_example.cpp" )
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create_single_source_cgal_program( "mesh_optimization_lloyd_example.cpp" )
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@ -0,0 +1,79 @@
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#include <vtkImageData.h>
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#include <vtkDICOMImageReader.h>
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#include <vtkImageReader.h>
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#include <vtkImageGaussianSmooth.h>
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#include <vtkDemandDrivenPipeline.h>
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#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
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#include <CGAL/Mesh_triangulation_3.h>
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#include <CGAL/Mesh_complex_3_in_triangulation_3.h>
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#include <CGAL/Mesh_criteria_3.h>
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#include <CGAL/Gray_image_mesh_domain_3.h>
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#include <CGAL/make_mesh_3.h>
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#include <CGAL/Image_3.h>
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#include <CGAL/read_vtk_image_data.h>
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typedef short Image_word_type;
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// Domain
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typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
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typedef CGAL::Gray_image_mesh_domain_3<CGAL::Image_3,K,
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Image_word_type,
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std::binder1st< std::less<Image_word_type> > > Mesh_domain;
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// Triangulation
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typedef CGAL::Mesh_triangulation_3<Mesh_domain>::type Tr;
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typedef CGAL::Mesh_complex_3_in_triangulation_3<Tr> C3t3;
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// Criteria
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typedef CGAL::Mesh_criteria_3<Tr> Mesh_criteria;
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// To avoid verbose function and named parameters call
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using namespace CGAL::parameters;
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int main(int argc, char* argv[])
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{
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// Loads image
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vtkDICOMImageReader*dicom_reader = vtkDICOMImageReader::New();
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dicom_reader->SetDirectoryName(argv[1]);
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vtkDemandDrivenPipeline*executive =
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vtkDemandDrivenPipeline::SafeDownCast(dicom_reader->GetExecutive());
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if (executive)
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{
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executive->SetReleaseDataFlag(0, 0); // where 0 is the port index
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}
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vtkImageGaussianSmooth* smoother = vtkImageGaussianSmooth::New();
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smoother->SetStandardDeviations(1., 1., 1.);
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smoother->SetInputConnection(dicom_reader->GetOutputPort());
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smoother->Update();
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vtkImageData* vtk_image = smoother->GetOutput();
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vtk_image->Print(std::cerr);
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CGAL::Image_3 image = CGAL::read_vtk_image_data(vtk_image);
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if(image.image() == 0){
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std::cerr << "could not create a CGAL::Image_3 from the vtk image\n";
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return 0;
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}
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// Domain
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Mesh_domain domain(image, std::bind1st(std::less<Image_word_type>(), -555), -1000);
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// Mesh criteria
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Mesh_criteria criteria(facet_angle=30, facet_size=6, facet_distance=1,
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cell_radius_edge_ratio=3, cell_size=8);
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// Meshing
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C3t3 c3t3 = CGAL::make_mesh_3<C3t3>(domain, criteria);
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// Output
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std::ofstream medit_file("out.mesh");
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c3t3.output_to_medit(medit_file);
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return 0;
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}
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@ -97,20 +97,18 @@ if ( CGAL_FOUND AND CGAL_Qt5_FOUND AND CGAL_ImageIO_FOUND)
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add_to_cached_list( CGAL_EXECUTABLE_TARGETS ${prj} )
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set(VTK_LIBS "")
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if (WITH_VTK)
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message(STATUS "VTK support ON, CGAL ImageIO must have been compiled with VTK support ON (WITH_VTK=ON at the cmake level)")
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find_package(VTK QUIET COMPONENTS vtkImagingCore)
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if(VTK_FOUND)
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include(${VTK_USE_FILE})
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if ("${VTK_VERSION_MAJOR}" GREATER "5")
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add_definitions(-DCGAL_USE_VTK)
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set(VTK_LIBS vtkImagingCore)
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else()
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message(STATUS "VTK support switched OFF, VTK version 6.0 or greater is required")
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endif()
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find_package(VTK QUIET COMPONENTS vtkImagingGeneral vtkIOImage NO_MODULE)
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if(VTK_FOUND)
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include(${VTK_USE_FILE})
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if ("${VTK_VERSION_MAJOR}" GREATER "5")
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message(STATUS "VTK found")
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add_definitions(-DCGAL_USE_VTK)
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set(VTK_LIBS vtkImagingGeneral vtkIOImage)
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else()
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message(STATUS "VTK support switched OFF, VTK was not found")
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message(STATUS "Vtk must be at least Rel 6")
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endif()
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else()
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message(STATUS "For reading Dicom files install VTK first")
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endif()
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# Link the executable to CGAL and third-party libraries
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@ -44,10 +44,17 @@ public:
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typedef FT_ FT;
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public:
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CBinary_image_3() : Image_3(), interpolate_(true)
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CBinary_image_3()
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: Image_3(), interpolate_(true)
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{
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}
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CBinary_image_3(const Image_3& bi)
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: Image_3(bi), interpolate_(true)
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{
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}
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CBinary_image_3(const CBinary_image_3& bi)
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: Image_3(bi), interpolate_(bi.interpolate_),labellized_(bi.labellized_)
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{
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@ -56,9 +63,6 @@ public:
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max_value = bi.max_value;
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}
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~CBinary_image_3()
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{
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}
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void finish_open() {
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CGAL_IMAGE_IO_CASE(image_ptr.get(),
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@ -325,6 +325,9 @@ void Volume::only_in()
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}
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#ifdef CGAL_USE_VTK
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#include <CGAL/read_vtk_image_data.h>
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#include <vtkImageData.h>
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#include <vtkDICOMImageReader.h>
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#include <vtkImageReader.h>
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@ -368,7 +371,8 @@ bool Volume::opendir(const QString& dirname)
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smoother->Update();
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vtk_image = smoother->GetOutput();
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vtk_image->Print(std::cerr);
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if(!m_image.read_vtk_image_data(vtk_image))
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m_image = CGAL::read_vtk_image_data(vtk_image);
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if(m_image.image() == 0)
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{
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QMessageBox::warning(mw, mw->windowTitle(),
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tr("Error with file <tt>%1/</tt>:\nunknown file format!").arg(dirname));
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@ -418,7 +422,8 @@ bool Volume::open_vtk(const QString& filename)
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vtk_reader->Print(std::cerr);
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vtk_image = vtk_reader->GetOutput();
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vtk_image->Print(std::cerr);
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if(!m_image.read_vtk_image_data(vtk_image))
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m_image = CGAL::read_vtk_image_data(vtk_image);
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if(m_image.image() == NULL)
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{
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QMessageBox::warning(mw, mw->windowTitle(),
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tr("Error with file <tt>%1</tt>:\nunknown file format!").arg(filename));
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@ -485,7 +490,8 @@ bool Volume::open_xt(const QString& filename)
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vtk_reader->Print(std::cerr);
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vtkImageData* vtk_image = vtk_reader->GetOutput();
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vtk_image->Print(std::cerr);
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if(!m_image.read_vtk_image_data(vtk_image))
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m_image = CGAL::read_vtk_image_data(vtk_image);
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if(m_image.image() != NULL)
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{
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QMessageBox::warning(mw, mw->windowTitle(),
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tr("Error with file <tt>%1</tt>:\nunknown file format!").arg(filename));
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