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.
289 lines
12 KiB
C++
289 lines
12 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_distributed_boundary_restricted_augmented_contour_tree_h
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#define vtk_m_worklet_contourtree_distributed_boundary_restricted_augmented_contour_tree_h
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#include <vtkm/Types.h>
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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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#include <vtkm/worklet/contourtree_augmented/mesh_dem/IdRelabeler.h>
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#include <vtkm/worklet/contourtree_augmented/mesh_dem_meshtypes/ContourTreeMesh.h>
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#include <sstream>
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#include <string>
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#include <utility>
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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_distributed
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{
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/// \brief Boundary Restricted Augmented Contour Tree (BRACT)
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///
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/// A contour tree for boundary vertices with the interior abstracted.
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/// This is primarily a data storage class. The actual constuction of
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/// the BRACT is performed by the BoundaryRestrictedAugmentedContourTreeMaker
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/// (BRACTMaker). As a data store, this class primarily stores a set of
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/// arrays and provides convenience functions for interacting with the
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/// the data, e.g., to export the data to dot.
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class BoundaryRestrictedAugmentedContourTree
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{ // class BRACT
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public:
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// for each vertex, we store the index
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vtkm::worklet::contourtree_augmented::IdArrayType VertexIndex;
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// and the ID of the vertex it connects to (or NO_SUCH_ELEMENT)
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vtkm::worklet::contourtree_augmented::IdArrayType Superarcs;
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// prints the contents of the BRACT for comparison with sweep and merge
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std::string Print();
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// secondary version which takes the mesh as a parameter
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template <typename Mesh, typename FieldArrayType>
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std::string PrintGlobalDot(const char* label,
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const Mesh& mesh,
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const FieldArrayType& fieldArray,
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const vtkm::Id3 blockOrigin,
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const vtkm::Id3 globalSize) const;
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// prints the contents of the BRACT as a dot file using global IDs (version for CT mesh)
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template <typename FieldType>
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std::string PrintGlobalDot(
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const char* label,
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vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType>& mesh);
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// prints the contents of the BRACT in debug format
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std::string DebugPrint(const char* message, const char* fileName, long lineNum);
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};
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// prints the contents of the BRACT for comparison with sweep and merge
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std::string BoundaryRestrictedAugmentedContourTree::Print()
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{ // Print
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// Use string steam to record text so the user can print it however they like
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std::stringstream resultStream;
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resultStream << "Boundary-Restricted Augmented Contour Tree" << std::endl;
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resultStream << "==========================================" << std::endl;
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// fill it up
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auto superarcsPortal = this->Superarcs.ReadPortal();
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auto vertexIndexPortal = this->VertexIndex.ReadPortal();
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for (vtkm::Id node = 0; node < superarcsPortal.GetNumberOfValues(); node++)
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{
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// retrieve ID of target supernode
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vtkm::Id from = vertexIndexPortal.Get(node);
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vtkm::Id to = superarcsPortal.Get(node);
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// if this is true, it is the last pruned vertex & is omitted
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if (vtkm::worklet::contourtree_augmented::NoSuchElement(to))
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{
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continue;
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}
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// print out the from & to
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resultStream << std::setw(vtkm::worklet::contourtree_augmented::PRINT_WIDTH) << from << " ";
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resultStream << std::setw(vtkm::worklet::contourtree_augmented::PRINT_WIDTH) << to << std::endl;
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}
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return resultStream.str();
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} // Print
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// secondary version which takes the mesh as a parameter
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template <typename Mesh, typename FieldArrayType>
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std::string BoundaryRestrictedAugmentedContourTree::PrintGlobalDot(const char* label,
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const Mesh& mesh,
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const FieldArrayType& fieldArray,
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const vtkm::Id3 blockOrigin,
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const vtkm::Id3 globalSize) const
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{ // PrintGlobalDot
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std::stringstream resultStream;
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// print the header information
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resultStream << "digraph BRACT" << std::endl;
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resultStream << "\t{" << std::endl;
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resultStream << "\tlabel=\"" << label << "\"\n\tlabelloc=t\n\tfontsize=30" << std::endl;
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// create a relabeler
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vtkm::worklet::contourtree_augmented::mesh_dem::IdRelabeler relabeler(blockOrigin[0],
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blockOrigin[1],
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blockOrigin[2],
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mesh.NumRows,
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mesh.NumCols,
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globalSize[0],
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globalSize[1]);
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// loop through all nodes
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auto vertexIndexPortal = this->VertexIndex.ReadPortal();
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auto superarcsPortal = this->Superarcs.ReadPortal();
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auto sortOrderPortal = mesh.SortOrder.ReadPortal();
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auto fieldArrayPortal = fieldArray.ReadPortal();
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for (vtkm::Id node = 0; node < this->Superarcs.GetNumberOfValues(); node++)
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{
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// now convert to mesh IDs from node IDs
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vtkm::Id from = vertexIndexPortal.Get(node);
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// find the local & global IDs & data value
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vtkm::Id fromLocal = sortOrderPortal.Get(from);
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vtkm::Id fromGlobal = relabeler(fromLocal);
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auto fromValue = fieldArrayPortal.Get(fromLocal);
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// print the vertex
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resultStream << node << " [style=filled,fillcolor="
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<< "grey"
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<< ",label=\"" << fromGlobal << "\\nv" << fromValue << "\"];" << std::endl;
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}
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for (vtkm::Id node = 0; node < this->Superarcs.GetNumberOfValues(); node++)
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{
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// retrieve ID of target supernode
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vtkm::Id to = superarcsPortal.Get(node);
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// if this is true, it is the last pruned vertex & is omitted
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if (vtkm::worklet::contourtree_augmented::NoSuchElement(to))
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{
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continue;
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}
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if (node < to)
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{
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resultStream << to << " -> " << node << std::endl;
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}
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else
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{
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resultStream << node << " -> " << to << std::endl;
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}
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}
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resultStream << "\t}" << std::endl;
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// return the result
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return resultStream.str();
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} // PrintGlobalDot
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// prints the contents of the BRACT as a dot file using global IDs (version for CT mesh)
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template <typename FieldType>
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std::string BoundaryRestrictedAugmentedContourTree::PrintGlobalDot(
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const char* label,
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vtkm::worklet::contourtree_augmented::ContourTreeMesh<FieldType>& mesh)
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{ //PrintGlobalDot
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std::stringstream resultStream;
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// print the header information
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resultStream << "digraph BRACT\n\t{\n";
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resultStream << "\tsize=\"6.5, 9\"\n\tratio=\"fill\"\n";
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resultStream << "\tlabel=\"" << label << "\"\n\tlabelloc=t\n\tfontsize=30\n" << std::endl;
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// loop through all nodes
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auto vertexIndexPortal = this->VertexIndex.ReadPortal();
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auto globalMeshIndexPortal = mesh.GlobalMeshIndex.ReadPortal();
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auto sortedValuesPortal = mesh.SortedValued.ReadPortal();
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auto superarcsPortal = this->Superarcs.ReadPortal();
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for (vtkm::Id node = 0; node < this->VertexIndex.GetNumberOfValues(); node++)
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{ // per node
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// work out the node and it's value
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vtkm::Id meshIndex = vertexIndexPortal.Get(node);
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vtkm::Id from = globalMeshIndexPortal.Get(meshIndex);
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auto fromValue = sortedValuesPortal.Get(meshIndex);
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// print the vertex
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resultStream << node << " [style=filled,fillcolor="
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<< "grey"
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<< ",label=\"" << from << "\\nv" << fromValue << "\"];" << std::endl;
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} // per node
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for (vtkm::Id node = 0; node < this->Superarcs.GetNumberOfValues(); node++)
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{ // per node
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// retrieve ID of target supernode
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vtkm::Id to = superarcsPortal.Get(node);
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// if this is true, it is the last pruned vertex & is omitted
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if (vtkm::worklet::contourtree_augmented::NoSuchElement(to))
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{
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continue;
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}
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if (node < to)
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{
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resultStream << to << " -> " << node << std::endl;
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}
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else
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{
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resultStream << node << " -> " << to << std::endl;
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}
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} // per node
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resultStream << "\t}" << std::endl;
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// Return the resulting strin
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return resultStream.str();
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} //PrintGlobalDot
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// debug routine
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inline std::string BoundaryRestrictedAugmentedContourTree::DebugPrint(const char* message,
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const char* fileName,
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long lineNum)
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{ // DebugPrint
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std::stringstream resultStream;
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resultStream << "[CUTHERE]-------------------------------------------------------" << 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 << "Boundary Restricted Augmented Contour Tree Contains: " << std::endl;
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resultStream << "----------------------------------------------------------------" << std::endl;
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vtkm::worklet::contourtree_augmented::PrintHeader(this->VertexIndex.GetNumberOfValues(),
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resultStream);
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vtkm::worklet::contourtree_augmented::PrintIndices(
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"Vertex Index", this->VertexIndex, -1, resultStream);
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vtkm::worklet::contourtree_augmented::PrintIndices(
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"Superarcs", this->Superarcs, -1, resultStream);
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resultStream << "---------------------------" << std::endl;
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resultStream << std::endl;
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resultStream << std::flush;
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return resultStream.str();
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} // DebugPrint
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} // namespace contourtree_distributed
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} // namespace worklet
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} // namespace vtkm
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#endif
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