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vtk-m/vtkm/worklet/contourtree_augmented/ContourTree.h

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//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
// Copyright (c) 2018, The Regents of the University of California, through
// Lawrence Berkeley National Laboratory (subject to receipt of any required approvals
// from the U.S. Dept. of Energy). All rights reserved.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// (1) Redistributions of source code must retain the above copyright notice, this
// list of conditions and the following disclaimer.
//
// (2) Redistributions in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// (3) Neither the name of the University of California, Lawrence Berkeley National
// Laboratory, U.S. Dept. of Energy nor the names of its contributors may be
// used to endorse or promote products derived from this software without
// specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
// INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
// OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
// OF THE POSSIBILITY OF SUCH DAMAGE.
//
//=============================================================================
//
// This code is an extension of the algorithm presented in the paper:
// Parallel Peak Pruning for Scalable SMP Contour Tree Computation.
// Hamish Carr, Gunther Weber, Christopher Sewell, and James Ahrens.
// Proceedings of the IEEE Symposium on Large Data Analysis and Visualization
// (LDAV), October 2016, Baltimore, Maryland.
//
// The PPP2 algorithm and software were jointly developed by
// Hamish Carr (University of Leeds), Gunther H. Weber (LBNL), and
// Oliver Ruebel (LBNL)
//==============================================================================
#ifndef vtk_m_worklet_contourtree_augmented_contourtree_h
#define vtk_m_worklet_contourtree_augmented_contourtree_h
// global includes
#include <algorithm>
#include <iomanip>
#include <iostream>
#include <sstream>
#include <string>
// local includes
#include <vtkm/worklet/contourtree_augmented/PrintVectors.h>
#include <vtkm/worklet/contourtree_augmented/Types.h>
//VTKM includes
#include <vtkm/Pair.h>
#include <vtkm/Types.h>
#include <vtkm/cont/Algorithm.h>
#include <vtkm/cont/ArrayHandleConstant.h>
namespace vtkm
{
namespace worklet
{
namespace contourtree_augmented
{
constexpr int N_NODE_COLORS = 12;
constexpr const char* NODE_COLORS[N_NODE_COLORS] = { // nodeColors
"red", "red4", "green", "green4", "royalblue", "royalblue4",
"cyan", "cyan4", "magenta", "magenta4", "yellow", "yellow4"
}; // nodeColors
struct SaddlePeakSort
{
VTKM_EXEC_CONT
inline bool operator()(const vtkm::Pair<vtkm::Id, vtkm::Id>& a,
const vtkm::Pair<vtkm::Id, vtkm::Id>& b) const
{
if (a.first < b.first)
return true;
if (a.first > b.first)
return false;
if (a.second < b.second)
return true;
if (a.second > b.second)
return false;
return false;
}
};
class ContourTree
{ // class ContourTree
public:
// VECTORS INDEXED ON N = SIZE OF DATA
// the list of nodes is implicit - but for some purposes, it's useful to have them pre-sorted by superarc
IdArrayType Nodes;
// vector of (regular) arcs in the merge tree
IdArrayType Arcs;
// vector storing which superarc owns each node
IdArrayType Superparents;
// VECTORS INDEXED ON T = SIZE OF TREE
// vector storing the list of supernodes by ID
// WARNING: THESE ARE NOT SORTED BY INDEX
// Instead, they are sorted by hyperarc, secondarily on index
IdArrayType Supernodes;
// vector of superarcs in the merge tree
// stored as supernode indices
IdArrayType Superarcs;
// for boundary augmented contour tree (note: these use the same convention as supernodes/superarcs)
IdArrayType Augmentnodes;
IdArrayType Augmentarcs;
// vector of Hyperarcs to which each supernode/arc belongs
IdArrayType Hyperparents;
// vector tracking which superarc was transferred on which iteration
IdArrayType WhenTransferred;
// VECTORS INDEXED ON H = SIZE OF HYPERTREE
// vector of sort indices for the hypernodes
IdArrayType Hypernodes;
// vector of Hyperarcs in the merge tree
// NOTE: These are supernode IDs, not hypernode IDs
// because not all Hyperarcs lead to hypernodes
IdArrayType Hyperarcs;
// counter for the number of iterations it took to construct the tree
// this is also used for hypersweep computations
vtkm::Id NumIterations;
// vectors tracking the segments used in each iteration of the hypersweep
IdArrayType FirstSupernodePerIteration;
IdArrayType FirstHypernodePerIteration;
// ROUTINES
// initialises contour tree arrays - rest is done by another class
inline ContourTree();
// initialises contour tree arrays - rest is done by another class
inline void Init(vtkm::Id dataSize);
// debug routine
inline std::string DebugPrint(const char* message, const char* fileName, long lineNum) const;
// print contents
inline void PrintContent(std::ostream& outStream = std::cout) const;
// print routines
inline void PrintDotSuperStructure() const;
inline std::string PrintHyperStructureStatistics(bool print = true) const;
inline std::string PrintArraySizes() const;
}; // class ContourTree
inline ContourTree::ContourTree()
: Arcs()
, Superparents()
, Supernodes()
, Superarcs()
, Hyperparents()
, Hypernodes()
, Hyperarcs()
{ // ContourTree()
} // ContourTree()
// initialises contour tree arrays - rest is done by another class
inline void ContourTree::Init(vtkm::Id dataSize)
{ // Init()
vtkm::cont::ArrayHandleConstant<vtkm::Id> noSuchElementArray(
static_cast<vtkm::Id>(NO_SUCH_ELEMENT), dataSize);
vtkm::cont::Algorithm::Copy(noSuchElementArray, this->Arcs);
vtkm::cont::Algorithm::Copy(noSuchElementArray, this->Superparents);
} // Init()
inline void ContourTree::PrintContent(std::ostream& outStream /*= std::cout*/) const
{
PrintHeader(this->Arcs.GetNumberOfValues(), outStream);
PrintIndices("Arcs", this->Arcs, -1, outStream); // -1 -> thisArcs.size()
PrintIndices("Superparents", this->Superparents, -1, outStream);
outStream << std::endl;
PrintHeader(this->Supernodes.GetNumberOfValues(), outStream);
PrintIndices("Supernodes", this->Supernodes, -1, outStream);
PrintIndices("Superarcs", this->Superarcs, -1, outStream);
PrintIndices("Hyperparents", this->Hyperparents, -1, outStream);
PrintIndices("When Xferred", this->WhenTransferred, -1, outStream);
outStream << std::endl;
PrintHeader(this->Hypernodes.GetNumberOfValues(), outStream);
PrintIndices("Hypernodes", this->Hypernodes, -1, outStream);
PrintIndices("Hyperarcs", this->Hyperarcs, -1, outStream);
PrintHeader(Augmentnodes.GetNumberOfValues(), outStream);
PrintIndices("Augmentnodes", Augmentnodes, -1, outStream);
PrintIndices("Augmentarcs", this->Augmentarcs, -1, outStream);
outStream << std::endl;
outStream << "NumIterations: " << this->NumIterations << std::endl;
PrintHeader(this->FirstSupernodePerIteration.GetNumberOfValues(), outStream);
PrintIndices("First SN Per Iter", this->FirstSupernodePerIteration, -1, outStream);
PrintIndices("First HN Per Iter", this->FirstHypernodePerIteration, -1, outStream);
}
inline std::string ContourTree::DebugPrint(const char* message,
const char* fileName,
long lineNum) const
{ // DebugPrint()
std::stringstream resultStream;
resultStream << std::endl;
resultStream << "---------------------------" << std::endl;
resultStream << std::setw(30) << std::left << fileName << ":" << std::right << std::setw(4)
<< lineNum << std::endl;
resultStream << std::left << std::string(message) << std::endl;
resultStream << "Contour Tree Contains: " << std::endl;
resultStream << "---------------------------" << std::endl;
resultStream << std::endl;
this->PrintContent(resultStream);
return resultStream.str();
} // DebugPrint()
inline void ContourTree::PrintDotSuperStructure() const
{ // PrintDotSuperStructure()
// print the header information
printf("digraph G\n\t{\n");
printf("\tsize=\"6.5, 9\"\n\tratio=\"fill\"\n");
// We use regular ReadPortal here since we need access to most values on the host anyways
auto whenTransferredPortal = this->WhenTransferred.ReadPortal();
auto supernodesPortal = this->Supernodes.ReadPortal();
auto superarcsPortal = this->Superarcs.ReadPortal();
auto hypernodesPortal = this->Hypernodes.ReadPortal();
auto hyperparentsPortal = this->Hyperparents.ReadPortal();
auto hyperarcsPortal = this->Hyperarcs.ReadPortal();
// colour the nodes by the iteration they transfer (mod # of colors) - paired iterations have similar colors RGBCMY
for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
{ // per supernode
vtkm::Id iteration = MaskedIndex(whenTransferredPortal.Get(supernode));
printf("\tnode s%lli [style=filled,fillcolor=%s]\n",
static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
NODE_COLORS[iteration % N_NODE_COLORS]);
} // per supernode
// loop through supernodes
for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
{ // per supernode
// skip the global root
if (NoSuchElement(superarcsPortal.Get(supernode)))
continue;
if (IsAscending(superarcsPortal.Get(supernode)))
printf(
"\tedge s%lli -> s%lli[label=S%lli,dir=back]\n",
static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(superarcsPortal.Get(supernode)))),
static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
static_cast<vtkm::Int64>(supernode));
else
printf(
"\tedge s%lli -> s%lli[label=S%lli]\n",
static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(superarcsPortal.Get(supernode)))),
static_cast<vtkm::Int64>(supernode));
} // per supernode
// now loop through hypernodes to show hyperarcs
for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
{ // per hypernode
// skip the global root
if (NoSuchElement(hyperarcsPortal.Get(hypernode)))
continue;
printf(
"\ts%lli -> s%lli [constraint=false][width=5.0][label=\"H%lli\\nW%lli\"]\n",
static_cast<vtkm::Int64>(supernodesPortal.Get(hypernodesPortal.Get(hypernode))),
static_cast<vtkm::Int64>(supernodesPortal.Get(MaskedIndex(hyperarcsPortal.Get(hypernode)))),
static_cast<vtkm::Int64>(hypernode),
static_cast<vtkm::Int64>(
MaskedIndex(whenTransferredPortal.Get(hypernodesPortal.Get(hypernode)))));
} // per hypernode
// now add the hyperparents
for (vtkm::Id supernode = 0; supernode < this->Supernodes.GetNumberOfValues(); supernode++)
{ // per supernode
printf("\ts%lli -> s%lli [constraint=false][style=dotted]\n",
static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)),
static_cast<vtkm::Int64>(
supernodesPortal.Get(hypernodesPortal.Get(hyperparentsPortal.Get(supernode)))));
} // per supernode
// now use the hyperstructure to define subgraphs
for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
{ // per hypernode
vtkm::Id firstChild = hypernodesPortal.Get(hypernode);
vtkm::Id childSentinel = (hypernode == this->Hypernodes.GetNumberOfValues() - 1)
? this->Supernodes.GetNumberOfValues()
: hypernodesPortal.Get(hypernode + 1);
printf("\tsubgraph H%lli{ ", static_cast<vtkm::Int64>(hypernode));
for (vtkm::Id supernode = firstChild; supernode < childSentinel; supernode++)
{
printf("s%lli ", static_cast<vtkm::Int64>(supernodesPortal.Get(supernode)));
}
printf("}\n");
} // per hypernode
// print the footer information
printf("\t}\n");
} // PrintDotSuperStructure()
inline std::string ContourTree::PrintHyperStructureStatistics(bool print) const
{ // PrintHyperStructureStatistics()
// arrays for collecting statistics
std::vector<vtkm::Id> minPath;
std::vector<vtkm::Id> maxPath;
std::vector<vtkm::Id> supernodeCount;
std::vector<vtkm::Id> hypernodeCount;
// We use regular ReadPortal here since we need access to all values anyways
auto whenTransferredPortal = this->WhenTransferred.ReadPortal();
auto hypernodesPortal = this->Hypernodes.ReadPortal();
// set an initial iteration number to negative to get it started
long whichIteration = -1;
// loop through the hypernodes
for (vtkm::Id hypernode = 0; hypernode < this->Hypernodes.GetNumberOfValues(); hypernode++)
{ // per hypernode
// retrieve corresponding supernode ID
vtkm::Id supernodeID = hypernodesPortal.Get(hypernode);
// and the iteration of transfer
vtkm::Id iterationNo = MaskedIndex(whenTransferredPortal.Get(supernodeID));
// if it doesn't match, we've hit a boundary
if (whichIteration != iterationNo)
{ // new iteration
// initialise the next iteration
// this one is larger than the maximum possible to force minimum
minPath.push_back(static_cast<vtkm::Id>(this->Supernodes.GetNumberOfValues() + 1));
maxPath.push_back(0);
supernodeCount.push_back(0);
hypernodeCount.push_back(0);
// and increment the iteration ID
whichIteration++;
} // new iteration
// now compute the new path length - default to off the end
vtkm::Id pathLength = static_cast<vtkm::Id>(this->Supernodes.GetNumberOfValues() - supernodeID);
// for all except the last, take the next one
if (hypernode != this->Hypernodes.GetNumberOfValues() - 1)
{
pathLength = hypernodesPortal.Get(hypernode + 1) - supernodeID;
}
// update the statistics
if (pathLength < minPath[static_cast<std::size_t>(whichIteration)])
{
minPath[static_cast<std::size_t>(whichIteration)] = pathLength;
}
if (pathLength > maxPath[static_cast<std::size_t>(whichIteration)])
{
maxPath[static_cast<std::size_t>(whichIteration)] = pathLength;
}
supernodeCount[static_cast<std::size_t>(whichIteration)] += pathLength;
hypernodeCount[static_cast<std::size_t>(whichIteration)]++;
} // per hypernode
// now print out the statistics
std::stringstream resultString;
for (std::size_t iteration = 0; iteration < minPath.size(); iteration++)
{ // per iteration
double averagePath = static_cast<double>(supernodeCount[iteration]) /
static_cast<double>(hypernodeCount[iteration]);
resultString << "Iteration: " << iteration << " Hyper: " << hypernodeCount[iteration]
<< " Super: " << supernodeCount[iteration] << " Min: " << minPath[iteration]
<< " Avg: " << averagePath << " Max: " << maxPath[iteration] << std::endl;
} // per iteration
resultString << "Total Hypernodes: " << this->Hypernodes.GetNumberOfValues()
<< " Supernodes: " << this->Supernodes.GetNumberOfValues() << std::endl;
if (print)
{
std::cout << resultString.str() << std::endl;
}
return resultString.str();
} // PrintHyperStructureStatistics()
inline std::string ContourTree::PrintArraySizes() const
{ // PrintArraySizes
std::stringstream arraySizeLog;
arraySizeLog << std::setw(42) << std::left << " #Nodes"
<< ": " << this->Nodes.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Arcs"
<< ": " << this->Arcs.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Superparents"
<< ": " << this->Superparents.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Superarcs"
<< ": " << this->Superarcs.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Supernodes"
<< ": " << this->Supernodes.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Hyperparents"
<< ": " << this->Hyperparents.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #WhenTransferred"
<< ": " << this->WhenTransferred.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Hypernodes"
<< ": " << this->Hypernodes.GetNumberOfValues() << std::endl
<< std::setw(42) << std::left << " #Hyperarcs"
<< ": " << this->Hyperarcs.GetNumberOfValues() << std::endl;
return arraySizeLog.str();
} // PrintArraySizes
} // namespace contourtree_augmented
} // worklet
} // vtkm
#endif
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