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442 lines
18 KiB
C++
442 lines
18 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 std::string DebugPrint(const char* message, const char* fileName, long lineNum) const;
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// print contents
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inline void PrintContent(std::ostream& outStream = std::cout) 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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inline std::string PrintArraySizes() const;
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}; // class ContourTree
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inline 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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inline 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(std::ostream& outStream /*= std::cout*/) const
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{
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PrintHeader(this->Arcs.GetNumberOfValues(), outStream);
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PrintIndices("Arcs", this->Arcs, -1, outStream); // -1 -> thisArcs.size()
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PrintIndices("Superparents", this->Superparents, -1, outStream);
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outStream << std::endl;
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PrintHeader(this->Supernodes.GetNumberOfValues(), outStream);
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PrintIndices("Supernodes", this->Supernodes, -1, outStream);
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PrintIndices("Superarcs", this->Superarcs, -1, outStream);
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PrintIndices("Hyperparents", this->Hyperparents, -1, outStream);
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PrintIndices("When Xferred", this->WhenTransferred, -1, outStream);
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outStream << std::endl;
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PrintHeader(this->Hypernodes.GetNumberOfValues(), outStream);
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PrintIndices("Hypernodes", this->Hypernodes, -1, outStream);
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PrintIndices("Hyperarcs", this->Hyperarcs, -1, outStream);
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PrintHeader(Augmentnodes.GetNumberOfValues(), outStream);
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PrintIndices("Augmentnodes", Augmentnodes, -1, outStream);
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PrintIndices("Augmentarcs", this->Augmentarcs, -1, outStream);
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outStream << std::endl;
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outStream << "NumIterations: " << this->NumIterations << std::endl;
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PrintHeader(this->FirstSupernodePerIteration.GetNumberOfValues(), outStream);
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PrintIndices("First SN Per Iter", this->FirstSupernodePerIteration, -1, outStream);
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PrintIndices("First HN Per Iter", this->FirstHypernodePerIteration, -1, outStream);
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}
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inline std::string ContourTree::DebugPrint(const char* message,
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const char* fileName,
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long lineNum) const
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{ // DebugPrint()
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std::stringstream resultStream;
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resultStream << std::endl;
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resultStream << "---------------------------" << std::endl;
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resultStream << std::setw(30) << std::left << fileName << ":" << std::right << std::setw(4)
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<< lineNum << std::endl;
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resultStream << std::left << std::string(message) << std::endl;
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resultStream << "Contour Tree Contains: " << std::endl;
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resultStream << "---------------------------" << std::endl;
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resultStream << std::endl;
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this->PrintContent(resultStream);
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return resultStream.str();
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} // DebugPrint()
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inline 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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// We use regular ReadPortal here since we need access to most values on the host anyways
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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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inline 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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// We use regular ReadPortal here since we need access to all values anyways
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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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inline std::string ContourTree::PrintArraySizes() const
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{ // PrintArraySizes
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std::stringstream arraySizeLog;
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arraySizeLog << std::setw(42) << std::left << " #Nodes"
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<< ": " << this->Nodes.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Arcs"
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<< ": " << this->Arcs.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Superparents"
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<< ": " << this->Superparents.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Superarcs"
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<< ": " << this->Superarcs.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Supernodes"
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<< ": " << this->Supernodes.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Hyperparents"
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<< ": " << this->Hyperparents.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #WhenTransferred"
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<< ": " << this->WhenTransferred.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Hypernodes"
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<< ": " << this->Hypernodes.GetNumberOfValues() << std::endl
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<< std::setw(42) << std::left << " #Hyperarcs"
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<< ": " << this->Hyperarcs.GetNumberOfValues() << std::endl;
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return arraySizeLog.str();
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} // PrintArraySizes
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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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