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https://gitlab.kitware.com/vtk/vtk-m
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66c96a983f
This merge request is Phase 1 of several to implement the distributed parallel contour tree in VTKm. This merge requests adds the base outline for the algorithm. The implementation of the details of the algorithm in the BoundaryRestrictedAugmentedContourTree.h is currently still missing. However, these will require a substantial (~3000) lines of additional code. The goal is to stage the integration process across merge requests to make the review process simpler.
416 lines
15 KiB
C++
416 lines
15 KiB
C++
//============================================================================
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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 (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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#ifndef vtk_m_worklet_contourtree_augmented_contourtree_h
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#define vtk_m_worklet_contourtree_augmented_contourtree_h
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// global includes
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#include <algorithm>
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#include <iomanip>
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#include <iostream>
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#include <sstream>
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#include <string>
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// local includes
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#include <vtkm/worklet/contourtree_augmented/PrintVectors.h>
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#include <vtkm/worklet/contourtree_augmented/Types.h>
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//VTKM includes
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#include <vtkm/Pair.h>
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#include <vtkm/Types.h>
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#include <vtkm/cont/Algorithm.h>
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#include <vtkm/cont/ArrayHandleConstant.h>
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namespace vtkm
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{
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namespace worklet
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{
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namespace contourtree_augmented
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{
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constexpr int N_NODE_COLORS = 12;
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constexpr const char* NODE_COLORS[N_NODE_COLORS] = { // nodeColors
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"red", "red4", "green", "green4", "royalblue", "royalblue4",
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"cyan", "cyan4", "magenta", "magenta4", "yellow", "yellow4"
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}; // nodeColors
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struct SaddlePeakSort
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{
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VTKM_EXEC_CONT
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inline bool operator()(const vtkm::Pair<vtkm::Id, vtkm::Id>& a,
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const vtkm::Pair<vtkm::Id, vtkm::Id>& b) const
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{
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if (a.first < b.first)
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return true;
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if (a.first > b.first)
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return false;
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if (a.second < b.second)
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return true;
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if (a.second > b.second)
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return false;
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return false;
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}
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};
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class ContourTree
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{ // class ContourTree
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public:
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// VECTORS INDEXED ON N = SIZE OF DATA
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// the list of nodes is implicit - but for some purposes, it's useful to have them pre-sorted by superarc
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IdArrayType Nodes;
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// vector of (regular) arcs in the merge tree
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IdArrayType Arcs;
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// vector storing which superarc owns each node
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IdArrayType Superparents;
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// VECTORS INDEXED ON T = SIZE OF TREE
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// vector storing the list of supernodes by ID
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// WARNING: THESE ARE NOT SORTED BY INDEX
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// Instead, they are sorted by hyperarc, secondarily on index
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IdArrayType Supernodes;
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// vector of superarcs in the merge tree
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// stored as supernode indices
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IdArrayType Superarcs;
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// for boundary augmented contour tree (note: these use the same convention as supernodes/superarcs)
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IdArrayType Augmentnodes;
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IdArrayType Augmentarcs;
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// vector of Hyperarcs to which each supernode/arc belongs
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IdArrayType Hyperparents;
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// vector tracking which superarc was transferred on which iteration
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IdArrayType WhenTransferred;
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// VECTORS INDEXED ON H = SIZE OF HYPERTREE
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// vector of sort indices for the hypernodes
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IdArrayType Hypernodes;
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// vector of Hyperarcs in the merge tree
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// NOTE: These are supernode IDs, not hypernode IDs
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// because not all Hyperarcs lead to hypernodes
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IdArrayType Hyperarcs;
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// counter for the number of iterations it took to construct the tree
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// this is also used for hypersweep computations
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vtkm::Id NumIterations;
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// vectors tracking the segments used in each iteration of the hypersweep
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IdArrayType FirstSupernodePerIteration;
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IdArrayType FirstHypernodePerIteration;
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// ROUTINES
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// initialises contour tree arrays - rest is done by another class
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inline ContourTree();
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// initialises contour tree arrays - rest is done by another class
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inline void Init(vtkm::Id dataSize);
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// debug routine
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inline void DebugPrint(const char* message, const char* fileName, long lineNum) const;
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// print contents
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inline void PrintContent() const;
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// print routines
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inline void PrintDotSuperStructure() const;
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inline std::string PrintHyperStructureStatistics(bool print = true) const;
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}; // class ContourTree
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ContourTree::ContourTree()
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: Arcs()
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, Superparents()
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, Supernodes()
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, Superarcs()
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, Hyperparents()
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, Hypernodes()
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, Hyperarcs()
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{ // ContourTree()
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} // ContourTree()
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// initialises contour tree arrays - rest is done by another class
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void ContourTree::Init(vtkm::Id dataSize)
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{ // Init()
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vtkm::cont::ArrayHandleConstant<vtkm::Id> noSuchElementArray(
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static_cast<vtkm::Id>(NO_SUCH_ELEMENT), dataSize);
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vtkm::cont::Algorithm::Copy(noSuchElementArray, this->Arcs);
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vtkm::cont::Algorithm::Copy(noSuchElementArray, this->Superparents);
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} // Init()
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inline void ContourTree::PrintContent() const
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{
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PrintHeader(this->Arcs.GetNumberOfValues());
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PrintIndices("Arcs", this->Arcs);
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PrintIndices("Superparents", this->Superparents);
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std::cout << std::endl;
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PrintHeader(this->Supernodes.GetNumberOfValues());
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PrintIndices("Supernodes", this->Supernodes);
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PrintIndices("Superarcs", this->Superarcs);
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PrintIndices("Hyperparents", this->Hyperparents);
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PrintIndices("When Xferred", this->WhenTransferred);
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std::cout << std::endl;
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PrintHeader(this->Hypernodes.GetNumberOfValues());
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PrintIndices("Hypernodes", this->Hypernodes);
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PrintIndices("Hyperarcs", this->Hyperarcs);
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PrintHeader(Augmentnodes.GetNumberOfValues());
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PrintIndices("Augmentnodes", Augmentnodes);
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PrintIndices("Augmentarcs", this->Augmentarcs);
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std::cout << std::endl;
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std::cout << "NumIterations: " << this->NumIterations << std::endl;
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PrintHeader(this->FirstSupernodePerIteration.GetNumberOfValues());
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PrintIndices("First SN Per Iter", this->FirstSupernodePerIteration);
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PrintIndices("First HN Per Iter", this->FirstHypernodePerIteration);
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}
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void ContourTree::DebugPrint(const char* message, const char* fileName, long lineNum) const
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{ // DebugPrint()
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#ifdef DEBUG_PRINT
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std::cout << "---------------------------" << std::endl;
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std::cout << std::setw(30) << std::left << fileName << ":" << std::right << std::setw(4)
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<< lineNum << std::endl;
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std::cout << std::left << std::string(message) << std::endl;
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std::cout << "Contour Tree Contains: " << std::endl;
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std::cout << "---------------------------" << std::endl;
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std::cout << std::endl;
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this->PrintContent();
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#else
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// Avoid unused parameter warnings
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(void)message;
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(void)fileName;
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(void)lineNum;
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#endif
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} // DebugPrint()
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void ContourTree::PrintDotSuperStructure() const
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{ // PrintDotSuperStructure()
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// print the header information
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printf("digraph G\n\t{\n");
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printf("\tsize=\"6.5, 9\"\n\tratio=\"fill\"\n");
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auto whenTransferredPortal = this->WhenTransferred.ReadPortal();
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auto supernodesPortal = this->Supernodes.ReadPortal();
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auto superarcsPortal = this->Superarcs.ReadPortal();
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auto hypernodesPortal = this->Hypernodes.ReadPortal();
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auto hyperparentsPortal = this->Hyperparents.ReadPortal();
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auto hyperarcsPortal = this->Hyperarcs.ReadPortal();
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// colour the nodes by the iteration they transfer (mod # of colors) - paired iterations have similar colors RGBCMY
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for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
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{ // per supernode
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vtkm::Id iteration = MaskedIndex(whenTransferredPortal.Get(supernode));
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printf("\tnode s%lli [style=filled,fillcolor=%s]\n",
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static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
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NODE_COLORS[iteration % N_NODE_COLORS]);
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} // per supernode
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// loop through supernodes
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for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
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{ // per supernode
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// skip the global root
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if (NoSuchElement(superarcsPortal.Get(supernode)))
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continue;
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if (IsAscending(superarcsPortal.Get(supernode)))
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printf(
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"\tedge s%lli -> s%lli[label=S%lli,dir=back]\n",
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static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(superarcsPortal.Get(supernode)))),
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static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
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static_cast<vtkm::Int64>(supernode));
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else
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printf(
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"\tedge s%lli -> s%lli[label=S%lli]\n",
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static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
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static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(superarcsPortal.Get(supernode)))),
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static_cast<vtkm::Int64>(supernode));
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} // per supernode
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// now loop through hypernodes to show hyperarcs
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for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
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{ // per hypernode
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// skip the global root
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if (NoSuchElement(hyperarcsPortal.Get(hypernode)))
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continue;
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printf(
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"\ts%lli -> s%lli [constraint=false][width=5.0][label=\"H%lli\\nW%lli\"]\n",
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static_cast<vtkm::Int64>(supernodesPortal.Get(hypernodesPortal.Get(hypernode))),
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static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(hyperarcsPortal.Get(hypernode)))),
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static_cast<vtkm::Int64>(hypernode),
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static_cast<vtkm::Int64>(
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MaskedIndex(whenTransferredPortal.Get(hypernodesPortal.Get(hypernode)))));
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} // per hypernode
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// now add the hyperparents
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for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
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{ // per supernode
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printf("\ts%lli -> s%lli [constraint=false][style=dotted]\n",
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static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
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static_cast<vtkm::Int64>(
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supernodesPortal.Get(hypernodesPortal.Get(hyperparentsPortal.Get(supernode)))));
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} // per supernode
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// now use the hyperstructure to define subgraphs
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for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
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{ // per hypernode
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vtkm::Id firstChild = hypernodesPortal.Get(hypernode);
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vtkm::Id childSentinel = (hypernode == this->Hypernodes.GetNumberOfValues() - 1)
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? this->Supernodes.GetNumberOfValues()
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: hypernodesPortal.Get(hypernode + 1);
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printf("\tsubgraph H%lli{ ", static_cast<vtkm::Int64>(hypernode));
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for (vtkm::Id supernode = firstChild; supernode < childSentinel; supernode++)
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{
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printf("s%lli ", static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)));
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}
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printf("}\n");
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} // per hypernode
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// print the footer information
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printf("\t}\n");
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} // PrintDotSuperStructure()
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std::string ContourTree::PrintHyperStructureStatistics(bool print) const
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{ // PrintHyperStructureStatistics()
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// arrays for collecting statistics
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std::vector<vtkm::Id> minPath;
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std::vector<vtkm::Id> maxPath;
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std::vector<vtkm::Id> supernodeCount;
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std::vector<vtkm::Id> hypernodeCount;
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auto whenTransferredPortal = this->WhenTransferred.ReadPortal();
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auto hypernodesPortal = this->Hypernodes.ReadPortal();
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// set an initial iteration number to negative to get it started
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long whichIteration = -1;
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// loop through the hypernodes
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for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
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{ // per hypernode
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// retrieve corresponding supernode ID
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vtkm::Id supernodeID = hypernodesPortal.Get(hypernode);
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// and the iteration of transfer
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vtkm::Id iterationNo = MaskedIndex(whenTransferredPortal.Get(supernodeID));
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// if it doesn't match, we've hit a boundary
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if (whichIteration != iterationNo)
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{ // new iteration
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// initialise the next iteration
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// this one is larger than the maximum possible to force minimum
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minPath.push_back(static_cast<vtkm::Id>(this->Supernodes.GetNumberOfValues() + 1));
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maxPath.push_back(0);
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supernodeCount.push_back(0);
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hypernodeCount.push_back(0);
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// and increment the iteration ID
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whichIteration++;
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} // new iteration
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// now compute the new path length - default to off the end
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vtkm::Id pathLength = static_cast<vtkm::Id>(this->Supernodes.GetNumberOfValues() - supernodeID);
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// for all except the last, take the next one
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if (hypernode != this->Hypernodes.GetNumberOfValues() - 1)
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{
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pathLength = hypernodesPortal.Get(hypernode + 1) - supernodeID;
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}
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// update the statistics
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if (pathLength < minPath[static_cast<std::size_t>(whichIteration)])
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{
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minPath[static_cast<std::size_t>(whichIteration)] = pathLength;
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}
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if (pathLength > maxPath[static_cast<std::size_t>(whichIteration)])
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{
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maxPath[static_cast<std::size_t>(whichIteration)] = pathLength;
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}
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supernodeCount[static_cast<std::size_t>(whichIteration)] += pathLength;
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hypernodeCount[static_cast<std::size_t>(whichIteration)]++;
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} // per hypernode
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// now print out the statistics
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std::stringstream resultString;
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for (std::size_t iteration = 0; iteration < minPath.size(); iteration++)
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{ // per iteration
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double averagePath = static_cast<double>(supernodeCount[iteration]) /
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static_cast<double>(hypernodeCount[iteration]);
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resultString << "Iteration: " << iteration << " Hyper: " << hypernodeCount[iteration]
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<< " Super: " << supernodeCount[iteration] << " Min: " << minPath[iteration]
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<< " Avg: " << averagePath << " Max: " << maxPath[iteration] << std::endl;
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} // per iteration
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resultString << "Total Hypernodes: " << this->Hypernodes.GetNumberOfValues()
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<< " Supernodes: " << this->Supernodes.GetNumberOfValues() << std::endl;
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if (print)
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{
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std::cout << resultString.str() << std::endl;
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}
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return resultString.str();
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} // PrintHyperStructureStatistics()
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} // namespace contourtree_augmented
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} // worklet
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} // vtkm
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#endif
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