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Merge topic 'redistribute-points-examples'
07ba6c25 example: redistribute points using DIY e62ff809 Fix BoundsCompute for missing coordinate system. Acked-by: Kitware Robot <kwrobot@kitware.com> Acked-by: Matt Larsen <mlarsen@cs.uoregon.edu> Merge-request: !1151
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commit
8a5f0a521d
@ -34,6 +34,7 @@ add_subdirectory(histogram)
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add_subdirectory(isosurface)
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add_subdirectory(multi_backend)
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add_subdirectory(particle_advection)
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add_subdirectory(redistribute_points)
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add_subdirectory(rendering)
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add_subdirectory(streamline)
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add_subdirectory(tetrahedra)
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46
examples/redistribute_points/CMakeLists.txt
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46
examples/redistribute_points/CMakeLists.txt
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##=============================================================================
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##
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## Copyright (c) Kitware, Inc.
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## All rights reserved.
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## See LICENSE.txt for details.
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##
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## This software is distributed WITHOUT ANY WARRANTY; without even
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## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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## PURPOSE. See the above copyright notice for more information.
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##
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## Copyright 2015 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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## Copyright 2015 UT-Battelle, LLC.
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## Copyright 2015 Los Alamos National Security.
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##
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## Under the terms of Contract DE-NA0003525 with NTESS,
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## the U.S. Government retains certain rights in this software.
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## Under the terms of Contract DE-AC52-06NA25396 with Los Alamos National
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## Laboratory (LANL), the U.S. Government retains certain rights in
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## this software.
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##
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##=============================================================================
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cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
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project(RedistributePoints CXX)
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#Find the VTK-m package
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find_package(VTKm REQUIRED QUIET)
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add_executable(RedistributePoints_SERIAL RedistributePoints.cxx RedistributePoints.h)
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target_compile_definitions(RedistributePoints_SERIAL PRIVATE
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"VTKM_DEVICE_ADAPTER=VTKM_DEVICE_ADAPTER_SERIAL")
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target_link_libraries(RedistributePoints_SERIAL PRIVATE vtkm_cont)
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if(TARGET vtkm::tbb)
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add_executable(RedistributePoints_TBB RedistributePoints.cxx RedistributePoints.h)
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target_compile_definitions(RedistributePoints_TBB PRIVATE
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"VTKM_DEVICE_ADAPTER=VTKM_DEVICE_ADAPTER_TBB")
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target_link_libraries(RedistributePoints_TBB PRIVATE vtkm_cont)
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endif()
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if(TARGET vtkm::cuda)
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vtkm_compile_as_cuda(cudaSource RedistributePoints.cxx RedistributePoints.h)
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add_executable(RedistributePoints_CUDA ${cudaSource})
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target_compile_definitions(RedistributePoints_CUDA PRIVATE
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"VTKM_DEVICE_ADAPTER=VTKM_DEVICE_ADAPTER_CUDA")
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target_link_libraries(RedistributePoints_CUDA PRIVATE vtkm_cont)
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endif()
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66
examples/redistribute_points/RedistributePoints.cxx
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66
examples/redistribute_points/RedistributePoints.cxx
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//============================================================================
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// Copyright (c) Kitware, Inc.
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// All rights reserved.
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// See LICENSE.txt for details.
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// This software is distributed WITHOUT ANY WARRANTY; without even
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// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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// PURPOSE. See the above copyright notice for more information.
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//
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// Copyright 2018 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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// Copyright 2018 UT-Battelle, LLC.
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// Copyright 2018 Los Alamos National Security.
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//
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// Under the terms of Contract DE-NA0003525 with NTESS,
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// the U.S. Government retains certain rights in this software.
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//
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// Under the terms of Contract DE-AC52-06NA25396 with Los Alamos National
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// Laboratory (LANL), the U.S. Government retains certain rights in
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// this software.
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//============================================================================
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#include <vtkm/cont/DataSet.h>
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#include <vtkm/cont/EnvironmentTracker.h>
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#include <vtkm/io/reader/VTKDataSetReader.h>
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#include <vtkm/io/writer/VTKDataSetWriter.h>
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// clang-format off
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VTKM_THIRDPARTY_PRE_INCLUDE
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#include VTKM_DIY(diy/mpi.hpp)
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VTKM_THIRDPARTY_POST_INCLUDE
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#include "RedistributePoints.h"
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#include <sstream>
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using std::cout;
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using std::endl;
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int main(int argc, char* argv[])
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{
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diy::mpi::environment env(argc, argv);
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auto comm = diy::mpi::communicator(MPI_COMM_WORLD);
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vtkm::cont::EnvironmentTracker::SetCommunicator(comm);
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if (argc != 3)
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{
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cout << "Usage: " << endl
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<< "$ " << argv[0] << " <input-vtk-file> <output-file-prefix>" << endl;
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return EXIT_FAILURE;
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}
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vtkm::cont::DataSet input;
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if (comm.rank() == 0)
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{
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vtkm::io::reader::VTKDataSetReader reader(argv[1]);
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input = reader.ReadDataSet();
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}
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example::RedistributePoints redistributor;
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auto output = redistributor.Execute(input);
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std::ostringstream str;
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str << argv[2] << "-" << comm.rank() << ".vtk";
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vtkm::io::writer::VTKDataSetWriter writer(str.str());
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writer.WriteDataSet(output);
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return EXIT_SUCCESS;
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}
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205
examples/redistribute_points/RedistributePoints.h
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205
examples/redistribute_points/RedistributePoints.h
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//============================================================================
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// Copyright (c) Kitware, Inc.
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// All rights reserved.
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// See LICENSE.txt for details.
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// This software is distributed WITHOUT ANY WARRANTY; without even
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// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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// PURPOSE. See the above copyright notice for more information.
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//
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// Copyright 2018 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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// Copyright 2018 UT-Battelle, LLC.
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// Copyright 2018 Los Alamos National Security.
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//
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// Under the terms of Contract DE-NA0003525 with NTESS,
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// the U.S. Government retains certain rights in this software.
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//
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// Under the terms of Contract DE-AC52-06NA25396 with Los Alamos National
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// Laboratory (LANL), the U.S. Government retains certain rights in
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// this software.
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//============================================================================
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#include <vtkm/ImplicitFunction.h>
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#include <vtkm/cont/Algorithm.h>
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#include <vtkm/cont/AssignerMultiBlock.h>
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#include <vtkm/cont/BoundsGlobalCompute.h>
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#include <vtkm/cont/diy/Serialization.h>
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#include <vtkm/filter/ExtractPoints.h>
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#include <vtkm/filter/Filter.h>
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// clang-format off
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VTKM_THIRDPARTY_PRE_INCLUDE
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#include VTKM_DIY(diy/decomposition.hpp)
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#include VTKM_DIY(diy/link.hpp)
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#include VTKM_DIY(diy/master.hpp)
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#include VTKM_DIY(diy/proxy.hpp)
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#include VTKM_DIY(diy/reduce.hpp)
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#include VTKM_DIY(diy/reduce-operations.hpp)
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#include VTKM_DIY(diy/types.hpp)
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VTKM_THIRDPARTY_POST_INCLUDE
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namespace example
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{
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namespace internal
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{
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static diy::ContinuousBounds convert(const vtkm::Bounds& bds)
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{
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diy::ContinuousBounds result;
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result.min[0] = static_cast<float>(bds.X.Min);
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result.min[1] = static_cast<float>(bds.Y.Min);
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result.min[2] = static_cast<float>(bds.Z.Min);
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result.max[0] = static_cast<float>(bds.X.Max);
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result.max[1] = static_cast<float>(bds.Y.Max);
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result.max[2] = static_cast<float>(bds.Z.Max);
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return result;
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}
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template <typename DerivedPolicy>
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class Redistributor
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{
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const diy::RegularDecomposer<diy::ContinuousBounds>& Decomposer;
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const vtkm::filter::PolicyBase<DerivedPolicy>& Policy;
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vtkm::cont::DataSet Extract(const vtkm::cont::DataSet& input, const diy::ContinuousBounds& bds) const
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{
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// extract points
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vtkm::Box box(bds.min[0], bds.max[0], bds.min[1], bds.max[1], bds.min[2], bds.max[2]);
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vtkm::filter::ExtractPoints extractor;
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extractor.SetCompactPoints(true);
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extractor.SetImplicitFunction(vtkm::cont::make_ImplicitFunctionHandle(box));
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return extractor.Execute(input, this->Policy);
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}
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public:
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Redistributor(const diy::RegularDecomposer<diy::ContinuousBounds>& decomposer,
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const vtkm::filter::PolicyBase<DerivedPolicy>& policy)
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: Decomposer(decomposer), Policy(policy)
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{
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}
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void operator()(vtkm::cont::DataSet* block, const diy::ReduceProxy& rp) const
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{
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if (rp.in_link().size() == 0)
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{
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if (block->GetNumberOfCoordinateSystems() > 0)
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{
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for (int cc = 0; cc < rp.out_link().size(); ++cc)
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{
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auto target = rp.out_link().target(cc);
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// let's get the bounding box for the target block.
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diy::ContinuousBounds bds;
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this->Decomposer.fill_bounds(bds, target.gid);
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auto extractedDS = this->Extract(*block, bds);
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const auto inputAH = extractedDS.GetCoordinateSystem(0).GetData();
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vtkm::cont::ArrayHandle<vtkm::Vec<vtkm::FloatDefault, 3>> outputAH;
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outputAH.Allocate(inputAH.GetNumberOfValues());
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vtkm::cont::Algorithm::Copy(inputAH, outputAH);
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rp.enqueue(target, outputAH);
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}
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// clear our dataset.
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*block = vtkm::cont::DataSet();
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}
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}
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else
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{
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vtkm::Id numValues = 0;
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std::vector<vtkm::cont::ArrayHandle<vtkm::Vec<vtkm::FloatDefault, 3>>> received_arrays;
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for (int cc = 0; cc < rp.in_link().size(); ++cc)
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{
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auto target = rp.in_link().target(cc);
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if (rp.incoming(target.gid).size() > 0)
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{
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vtkm::cont::ArrayHandle<vtkm::Vec<vtkm::FloatDefault, 3>> incomingAH;
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rp.dequeue(target.gid, incomingAH);
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received_arrays.push_back(incomingAH);
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numValues += incomingAH.GetNumberOfValues();
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}
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}
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*block = vtkm::cont::DataSet();
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if (received_arrays.size() == 1)
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{
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auto coords = vtkm::cont::CoordinateSystem("coords", received_arrays[0]);
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block->AddCoordinateSystem(coords);
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}
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else if (received_arrays.size() > 1)
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{
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vtkm::cont::ArrayHandle<vtkm::Vec<vtkm::FloatDefault, 3>> coordsAH;
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coordsAH.Allocate(numValues);
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vtkm::Id offset = 0;
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for (const vtkm::cont::ArrayHandle<vtkm::Vec<vtkm::FloatDefault, 3>>& receivedAH : received_arrays)
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{
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vtkm::cont::Algorithm::CopySubRange(receivedAH, 0, receivedAH.GetNumberOfValues(), coordsAH, offset);
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offset += receivedAH.GetNumberOfValues();
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}
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block->AddCoordinateSystem(vtkm::cont::CoordinateSystem("coords", coordsAH));
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}
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}
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}
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};
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} // namespace example::internal
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class RedistributePoints : public vtkm::filter::Filter<RedistributePoints>
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{
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public:
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VTKM_CONT
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RedistributePoints() {}
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VTKM_CONT
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~RedistributePoints() {}
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template <typename DerivedPolicy>
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VTKM_CONT vtkm::cont::MultiBlock PrepareForExecution(
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const vtkm::cont::MultiBlock& input,
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const vtkm::filter::PolicyBase<DerivedPolicy>& policy);
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};
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template <typename DerivedPolicy>
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inline VTKM_CONT vtkm::cont::MultiBlock
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RedistributePoints::PrepareForExecution(
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const vtkm::cont::MultiBlock& input,
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const vtkm::filter::PolicyBase<DerivedPolicy>& policy)
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{
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auto comm = vtkm::cont::EnvironmentTracker::GetCommunicator();
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// let's first get the global bounds of the domain
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vtkm::Bounds gbounds = vtkm::cont::BoundsGlobalCompute(input);
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vtkm::cont::AssignerMultiBlock assigner(input.GetNumberOfBlocks());
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diy::RegularDecomposer<diy::ContinuousBounds> decomposer(/*dim*/3, internal::convert(gbounds), assigner.nblocks());
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diy::Master master(comm,
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/*threads*/ 1,
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/*limit*/ -1,
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[]() -> void* { return new vtkm::cont::DataSet(); },
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[](void*ptr) { delete static_cast<vtkm::cont::DataSet*>(ptr); });
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decomposer.decompose(comm.rank(), assigner, master);
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assert(static_cast<vtkm::Id>(master.size()) == input.GetNumberOfBlocks());
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// let's populate local blocks
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master.foreach(
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[&input](vtkm::cont::DataSet* ds, const diy::Master::ProxyWithLink& proxy) {
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auto lid = proxy.master()->lid(proxy.gid());
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*ds = input.GetBlock(lid);
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});
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internal::Redistributor<DerivedPolicy> redistributor(decomposer, policy);
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diy::all_to_all(master, assigner, redistributor, /*k=*/2);
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vtkm::cont::MultiBlock result;
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master.foreach(
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[&result](vtkm::cont::DataSet* ds, const diy::Master::ProxyWithLink&) {
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result.AddBlock(*ds);
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});
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return result;
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}
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} // namespace example
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@ -34,15 +34,9 @@ namespace cont
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VTKM_CONT
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vtkm::Bounds BoundsCompute(const vtkm::cont::DataSet& dataset, vtkm::Id coordinate_system_index)
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{
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try
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{
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return dataset.GetCoordinateSystem(coordinate_system_index).GetBounds();
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}
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catch (vtkm::cont::ErrorBadValue&)
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{
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// missing coordinate_system_index, return empty bounds.
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return vtkm::Bounds();
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}
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return dataset.GetNumberOfCoordinateSystems() > coordinate_system_index
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? dataset.GetCoordinateSystem(coordinate_system_index).GetBounds()
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: vtkm::Bounds();
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}
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//-----------------------------------------------------------------------------
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