2018-08-08 18:38:06 +00:00
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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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2019-04-15 23:24:21 +00:00
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//
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2018-08-08 18:38:06 +00:00
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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 (c) 2018, The Regents of the University of California, through
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// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
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// from the U.S. Dept. of Energy). All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without modification,
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// are permitted provided that the following conditions are met:
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//
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// (1) Redistributions of source code must retain the above copyright notice, this
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// list of conditions and the following disclaimer.
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//
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// (2) Redistributions in binary form must reproduce the above copyright notice,
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// this list of conditions and the following disclaimer in the documentation
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// and/or other materials provided with the distribution.
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//
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// (3) Neither the name of the University of California, Lawrence Berkeley National
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// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
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// used to endorse or promote products derived from this software without
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// specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
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// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
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// OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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//=============================================================================
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//
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// This code is an extension of the algorithm presented in the paper:
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// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
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// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
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// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
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// (LDAV), October 2016, Baltimore, Maryland.
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//
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// The PPP2 algorithm and software were jointly developed by
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// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
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// Oliver Ruebel (LBNL)
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//==============================================================================
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2018-09-26 17:48:37 +00:00
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#ifndef vtk_m_worklet_ContourTreeUniformAugmented_h
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#define vtk_m_worklet_ContourTreeUniformAugmented_h
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2018-08-08 18:38:06 +00:00
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2018-09-11 19:31:01 +00:00
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2020-01-22 09:11:45 +00:00
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#include <sstream>
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2018-08-08 18:38:06 +00:00
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#include <utility>
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// VTKM includes
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#include <vtkm/Math.h>
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#include <vtkm/Types.h>
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#include <vtkm/cont/ArrayHandle.h>
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#include <vtkm/cont/ArrayHandleCounting.h>
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#include <vtkm/cont/Field.h>
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#include <vtkm/cont/Timer.h>
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#include <vtkm/worklet/DispatcherMapField.h>
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#include <vtkm/worklet/WorkletMapField.h>
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// Contour tree worklet includes
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2018-09-26 17:48:37 +00:00
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#include <vtkm/worklet/contourtree_augmented/ActiveGraph.h>
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#include <vtkm/worklet/contourtree_augmented/ContourTree.h>
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#include <vtkm/worklet/contourtree_augmented/ContourTreeMaker.h>
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#include <vtkm/worklet/contourtree_augmented/MergeTree.h>
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#include <vtkm/worklet/contourtree_augmented/MeshExtrema.h>
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#include <vtkm/worklet/contourtree_augmented/Mesh_DEM_Triangulation.h>
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#include <vtkm/worklet/contourtree_augmented/Types.h>
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2019-08-28 18:34:42 +00:00
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#include <vtkm/worklet/contourtree_augmented/mesh_dem_meshtypes/ContourTreeMesh.h>
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2019-09-07 00:48:45 +00:00
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#include <vtkm/worklet/contourtree_augmented/mesh_dem_meshtypes/MeshBoundary.h>
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2018-08-08 18:38:06 +00:00
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namespace vtkm
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{
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namespace worklet
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{
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2020-01-22 09:40:49 +00:00
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class ContourTreeAugmented
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2018-08-08 18:38:06 +00:00
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{
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public:
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2019-08-28 18:34:42 +00:00
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/*!
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* Run the contour tree to merge an existing set of contour trees
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2019-09-07 00:48:45 +00:00
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*
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* meshBoundary : Is computed by calling mesh.GetMeshBoundaryExecutionObject.
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* It is technically only needed if computeRegularStructure==2.
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary
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2019-08-28 18:34:42 +00:00
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*/
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template <typename FieldType, typename StorageType>
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void Run(const vtkm::cont::ArrayHandle<FieldType, StorageType>
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fieldArray, // TODO: We really should not need this
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contourtree_augmented::ContourTreeMesh<FieldType>& mesh,
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType sortOrder,
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vtkm::Id& nIterations,
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2019-09-07 00:48:45 +00:00
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unsigned int computeRegularStructure,
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const contourtree_augmented::MeshBoundaryContourTreeMeshExec& meshBoundary)
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{
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RunContourTree(
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fieldArray, // Just a place-holder to fill the required field. Used when calling SortData on the contour tree which is a no-op
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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2019-09-07 00:48:45 +00:00
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computeRegularStructure,
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meshBoundary);
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2019-08-28 18:34:42 +00:00
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return;
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}
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2018-08-08 18:38:06 +00:00
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/*!
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* Run the contour tree analysis. This helper function is used to
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* allow one to run the contour tree in a consistent fashion independent
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* of whether the data is 2D, 3D, or 3D_MC. This function just calls
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* Run2D, Run3D, or Run3D_MC depending on the type
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2019-09-07 00:48:45 +00:00
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*
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary
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2018-08-08 18:38:06 +00:00
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*/
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2018-08-30 15:53:18 +00:00
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template <typename FieldType, typename StorageType>
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2018-08-08 18:38:06 +00:00
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void Run(const vtkm::cont::ArrayHandle<FieldType, StorageType> fieldArray,
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2018-09-26 17:48:37 +00:00
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType& sortOrder,
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2018-08-08 18:38:06 +00:00
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vtkm::Id& nIterations,
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const vtkm::Id nRows,
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const vtkm::Id nCols,
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const vtkm::Id nSlices = 1,
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bool useMarchingCubes = false,
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unsigned int computeRegularStructure = 1)
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2018-08-08 18:38:06 +00:00
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{
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2018-09-26 17:48:37 +00:00
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using namespace vtkm::worklet::contourtree_augmented;
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2018-08-08 18:38:06 +00:00
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// 2D Contour Tree
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if (nSlices == 1)
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{
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// Build the mesh and fill in the values
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2018-09-11 19:31:01 +00:00
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Mesh_DEM_Triangulation_2D_Freudenthal<FieldType, StorageType> mesh(nRows, nCols);
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2018-08-08 18:38:06 +00:00
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// Run the contour tree on the mesh
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2019-09-07 00:48:45 +00:00
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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2019-08-28 18:34:42 +00:00
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return;
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2018-08-08 18:38:06 +00:00
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}
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// 3D Contour Tree using marching cubes
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else if (useMarchingCubes)
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{
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// Build the mesh and fill in the values
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2018-09-11 19:31:01 +00:00
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Mesh_DEM_Triangulation_3D_MarchingCubes<FieldType, StorageType> mesh(nRows, nCols, nSlices);
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2018-08-08 18:38:06 +00:00
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// Run the contour tree on the mesh
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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2019-08-28 18:34:42 +00:00
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return;
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2018-08-08 18:38:06 +00:00
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}
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// 3D Contour Tree with Freudenthal
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else
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{
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// Build the mesh and fill in the values
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2018-09-11 19:31:01 +00:00
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Mesh_DEM_Triangulation_3D_Freudenthal<FieldType, StorageType> mesh(nRows, nCols, nSlices);
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2018-08-08 18:38:06 +00:00
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// Run the contour tree on the mesh
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2019-09-07 00:48:45 +00:00
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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2019-08-28 18:34:42 +00:00
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return;
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2018-08-08 18:38:06 +00:00
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}
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}
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private:
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/*!
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* Run the contour tree for the given mesh. This function implements the main steps for
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* computing the contour tree after the mesh has been constructed using the approbrite
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2019-09-07 00:48:45 +00:00
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* contour tree mesh class.
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*
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* meshBoundary : This parameter is generated by calling mesh.GetMeshBoundaryExecutionObject
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* For regular 2D/3D meshes this required no extra parameters, however, for a
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* ContourTreeMesh additional information about the block must be given. Rather
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* than generating the MeshBoundary descriptor here, we therefore, require it
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* as an input. The MeshBoundary is used to augment the contour tree with the
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* mesh boundary vertices. It is needed only if we want to augement by the
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* mesh boundary and computeRegularStructure is False (i.e., if we compute
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* the full regular strucuture this is not needed because all vertices
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* (including the boundary) will be addded to the tree anyways.
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary
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2018-08-08 18:38:06 +00:00
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*/
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2019-09-07 00:48:45 +00:00
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template <typename FieldType,
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typename StorageType,
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typename MeshClass,
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typename MeshBoundaryClass>
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2018-08-08 18:38:06 +00:00
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void RunContourTree(const vtkm::cont::ArrayHandle<FieldType, StorageType> fieldArray,
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2018-09-26 17:48:37 +00:00
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType& sortOrder,
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2018-08-08 18:38:06 +00:00
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vtkm::Id& nIterations,
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MeshClass& mesh,
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2019-09-07 00:48:45 +00:00
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unsigned int computeRegularStructure,
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const MeshBoundaryClass& meshBoundary)
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2018-08-08 18:38:06 +00:00
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{
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2018-09-26 17:48:37 +00:00
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using namespace vtkm::worklet::contourtree_augmented;
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2018-10-03 18:51:13 +00:00
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// Stage 1: Load the data into the mesh. This is done in the Run() method above and accessible
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// here via the mesh parameter. The actual data load is performed outside of the
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2018-08-08 18:38:06 +00:00
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// worklet in the example contour tree app (or whoever uses the worklet)
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// Stage 2 : Sort the data on the mesh to initialize sortIndex & indexReverse on the mesh
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// Start the timer for the mesh sort
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2019-01-09 16:11:49 +00:00
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vtkm::cont::Timer timer;
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timer.Start();
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2020-01-22 09:11:45 +00:00
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std::stringstream timingsStream; // Use a string stream to log in one message
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timingsStream << std::endl;
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timingsStream << " ------------------- Contour Tree Worklet Timings ----------------------"
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<< std::endl;
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// Sort the mesh data
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2018-08-30 15:53:18 +00:00
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mesh.SortData(fieldArray);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Sort Data"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 3: Assign every mesh vertex to a peak
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2020-01-23 08:03:36 +00:00
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MeshExtrema extrema(mesh.NumVertices);
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2018-08-08 18:38:06 +00:00
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extrema.SetStarts(mesh, true);
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extrema.BuildRegularChains(true);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Regular Chains"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 4: Identify join saddles & construct Active Join Graph
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2020-01-23 08:03:36 +00:00
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MergeTree joinTree(mesh.NumVertices, true);
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2018-08-30 15:53:18 +00:00
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ActiveGraph joinGraph(true);
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2018-08-08 18:38:06 +00:00
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joinGraph.Initialise(mesh, extrema);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Initialize Active Graph"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2018-09-11 19:31:01 +00:00
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2018-08-08 18:38:06 +00:00
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#ifdef DEBUG_PRINT
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joinGraph.DebugPrint("Active Graph Instantiated", __FILE__, __LINE__);
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#endif
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 5: Compute Join Tree Hyperarcs from Active Join Graph
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joinGraph.MakeMergeTree(joinTree, extrema);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Compute"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2018-08-08 18:38:06 +00:00
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#ifdef DEBUG_PRINT
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joinTree.DebugPrint("Join tree Computed", __FILE__, __LINE__);
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joinTree.DebugPrintTree("Join tree", __FILE__, __LINE__, mesh);
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#endif
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 6: Assign every mesh vertex to a pit
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extrema.SetStarts(mesh, false);
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extrema.BuildRegularChains(false);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Split Tree Regular Chains"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 7: Identify split saddles & construct Active Split Graph
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2020-01-23 08:03:36 +00:00
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MergeTree splitTree(mesh.NumVertices, false);
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2018-08-30 15:53:18 +00:00
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ActiveGraph splitGraph(false);
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2018-08-08 18:38:06 +00:00
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splitGraph.Initialise(mesh, extrema);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Splot Tree Initialize Active Graph"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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2018-08-08 18:38:06 +00:00
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#ifdef DEBUG_PRINT
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splitGraph.DebugPrint("Active Graph Instantiated", __FILE__, __LINE__);
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#endif
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2019-01-09 16:11:49 +00:00
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timer.Start();
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2018-08-08 18:38:06 +00:00
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// Stage 8: Compute Split Tree Hyperarcs from Active Split Graph
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splitGraph.MakeMergeTree(splitTree, extrema);
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2020-01-22 09:11:45 +00:00
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timingsStream << " " << std::setw(38) << std::left << "Split Tree Compute"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
|
2018-08-08 18:38:06 +00:00
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#ifdef DEBUG_PRINT
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splitTree.DebugPrint("Split tree Computed", __FILE__, __LINE__);
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// Debug split and join tree
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joinTree.DebugPrintTree("Join tree", __FILE__, __LINE__, mesh);
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splitTree.DebugPrintTree("Split tree", __FILE__, __LINE__, mesh);
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#endif
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2019-01-09 16:11:49 +00:00
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timer.Start();
|
2018-08-08 18:38:06 +00:00
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// Stage 9: Join & Split Tree are Augmented, then combined to construct Contour Tree
|
2020-01-23 08:03:36 +00:00
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contourTree.Init(mesh.NumVertices);
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2018-08-30 15:53:18 +00:00
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ContourTreeMaker treeMaker(contourTree, joinTree, splitTree);
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2018-08-08 18:38:06 +00:00
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|
// 9.1 First we compute the hyper- and super- structure
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treeMaker.ComputeHyperAndSuperStructure();
|
2020-01-22 09:11:45 +00:00
|
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|
timingsStream << " " << std::setw(38) << std::left
|
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|
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<< "Contour Tree Hyper and Super Structure"
|
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|
|
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
|
2019-01-09 16:11:49 +00:00
|
|
|
timer.Start();
|
2018-08-08 18:38:06 +00:00
|
|
|
|
|
|
|
// 9.2 Then we compute the regular structure
|
2019-09-07 00:48:45 +00:00
|
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|
if (computeRegularStructure == 1) // augment with all vertices
|
2018-08-08 18:38:06 +00:00
|
|
|
{
|
|
|
|
treeMaker.ComputeRegularStructure(extrema);
|
2020-01-22 09:11:45 +00:00
|
|
|
timingsStream << " " << std::setw(38) << std::left << "Contour Tree Regular Structure"
|
|
|
|
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
|
2018-08-08 18:38:06 +00:00
|
|
|
}
|
2019-09-07 00:48:45 +00:00
|
|
|
else if (computeRegularStructure == 2) // augment by the mesh boundary
|
|
|
|
{
|
|
|
|
treeMaker.ComputeBoundaryRegularStructure(extrema, mesh, meshBoundary);
|
2020-01-22 09:11:45 +00:00
|
|
|
timingsStream << " " << std::setw(38) << std::left
|
|
|
|
<< "Contour Tree Boundary Regular Structure"
|
|
|
|
<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
|
2019-09-07 00:48:45 +00:00
|
|
|
}
|
2020-01-22 09:11:45 +00:00
|
|
|
timer.Start();
|
2018-08-08 18:38:06 +00:00
|
|
|
|
|
|
|
// Collect the output data
|
|
|
|
nIterations = treeMaker.nIterations;
|
|
|
|
sortOrder = mesh.sortOrder;
|
|
|
|
// ProcessContourTree::CollectSortedSuperarcs<DeviceAdapter>(contourTree, mesh.sortOrder, saddlePeak);
|
|
|
|
// contourTree.SortedArcPrint(mesh.sortOrder);
|
|
|
|
// contourTree.PrintDotSuperStructure();
|
2020-01-22 09:11:45 +00:00
|
|
|
|
|
|
|
// Log the collected timing results in one coherent log entry
|
|
|
|
VTKM_LOG_S(vtkm::cont::LogLevel::Info, timingsStream.str());
|
2018-08-08 18:38:06 +00:00
|
|
|
}
|
|
|
|
};
|
|
|
|
|
|
|
|
} // namespace vtkm
|
|
|
|
} // namespace vtkm::worklet
|
|
|
|
|
2018-09-26 17:48:37 +00:00
|
|
|
#endif // vtk_m_worklet_ContourTreeUniformAugmented_h
|