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https://gitlab.kitware.com/vtk/vtk-m
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392 lines
18 KiB
C++
392 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_ContourTreeUniformAugmented_h
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#define vtk_m_worklet_ContourTreeUniformAugmented_h
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#include <sstream>
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#include <utility>
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// VTKM includes
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#include <vtkm/Math.h>
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#include <vtkm/Types.h>
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#include <vtkm/cont/ArrayHandle.h>
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#include <vtkm/cont/ArrayHandleCounting.h>
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#include <vtkm/cont/Field.h>
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#include <vtkm/cont/Timer.h>
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#include <vtkm/worklet/DispatcherMapField.h>
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#include <vtkm/worklet/WorkletMapField.h>
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// Contour tree worklet includes
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#include <vtkm/worklet/contourtree_augmented/ActiveGraph.h>
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#include <vtkm/worklet/contourtree_augmented/ContourTree.h>
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#include <vtkm/worklet/contourtree_augmented/ContourTreeMaker.h>
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#include <vtkm/worklet/contourtree_augmented/DataSetMesh.h>
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#include <vtkm/worklet/contourtree_augmented/MergeTree.h>
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#include <vtkm/worklet/contourtree_augmented/MeshExtrema.h>
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#include <vtkm/worklet/contourtree_augmented/Types.h>
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#include <vtkm/worklet/contourtree_augmented/meshtypes/ContourTreeMesh.h>
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#include <vtkm/worklet/contourtree_augmented/meshtypes/mesh_boundary/MeshBoundary2D.h>
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#include <vtkm/worklet/contourtree_augmented/meshtypes/mesh_boundary/MeshBoundary3D.h>
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#include <vtkm/worklet/contourtree_augmented/meshtypes/mesh_boundary/MeshBoundaryContourTreeMesh.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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/// Compute the contour tree for 2d and 3d uniform grids and arbitrary topology graphs
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class ContourTreeAugmented
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{
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public:
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/*!
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* Log level to be used for outputting timing information. Default is vtkm::cont::LogLevel::Perf
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* Use vtkm::cont::LogLevel::Off to disable outputing the results via vtkm logging here. The
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* results are saved in the TimingsLogString variable so we can use it to do our own logging
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*/
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vtkm::cont::LogLevel TimingsLogLevel = vtkm::cont::LogLevel::Perf;
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/// Remember the results from our time-keeping so we can customize our logging
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std::string TimingsLogString;
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/*!
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* Run the contour tree to merge an existing set of contour trees
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*
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* fieldArray : Needed only as a pass-through value but not used in this case
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* mesh : The ContourTreeMesh for which the contour tree should be computed
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* contourTree : The output contour tree to be computed (output)
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* sortOrder : The sort order for the mesh vertices (output)
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* nIterations : The number of iterations used to compute the contour tree (output)
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary
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* meshBoundary : This parameter is generated by calling mesh.GetMeshBoundaryExecutionObject
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* For regular 2D/3D meshes this required no extra parameters, however, for a
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* ContourTreeMesh additional information about the block must be given. Rather
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* than generating the MeshBoundary descriptor here, we therefore, require it
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* as an input. The MeshBoundary is used to augment the contour tree with the
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* mesh boundary vertices. It is needed only if we want to augement by the
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* mesh boundary and computeRegularStructure is False (i.e., if we compute
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* the full regular strucuture this is not needed because all vertices
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* (including the boundary) will be addded to the tree anyways.
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*/
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template <typename FieldType,
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typename StorageType,
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typename MeshType,
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typename MeshBoundaryMeshExecType>
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void Run(const vtkm::cont::ArrayHandle<FieldType, StorageType> fieldArray,
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MeshType& mesh,
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType& sortOrder,
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vtkm::Id& nIterations,
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unsigned int computeRegularStructure,
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const MeshBoundaryMeshExecType& meshBoundary)
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{
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RunContourTree(
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fieldArray, // Just a place-holder to fill the required field. Used when calling SortData on the contour tree which is a no-op
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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meshBoundary);
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return;
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}
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/*!
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* Run the contour tree analysis. This helper function is used to
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* allow one to run the contour tree in a consistent fashion independent
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* of whether the data is 2D, 3D, or 3D_MC. This function initalizes
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* the approbritate mesh class from the contourtree_augmented worklet
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* and constructs ths mesh boundary exectuion object to be used. It the
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* subsequently calls RunContourTree method to compute the actual contour tree.
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*
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* fieldArray : Needed only as a pass-through value but not used in this case
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* mesh : The ContourTreeMesh for which the contour tree should be computed
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* contourTree : The output contour tree to be computed (output)
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* sortOrder : The sort order for the mesh vertices (output)
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* nIterations : The number of iterations used to compute the contour tree (output)
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* nRows : Number of rows (i.e, x values) in the input mesh
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* nCols : Number of columns (i.e, y values) in the input mesh
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* nSlices : Number of slicex (i.e, z values) in the input mesh. Default is 1
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* to avoid having to set the nSlices for 2D input meshes
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* useMarchingCubes : Boolean indicating whether marching cubes (true) or freudenthal (false)
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* connectivity should be used. Valid only for 3D input data. Default is false.
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary.
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*/
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template <typename FieldType, typename StorageType>
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void Run(const vtkm::cont::ArrayHandle<FieldType, StorageType> fieldArray,
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType& sortOrder,
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vtkm::Id& nIterations,
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const vtkm::Id3 meshSize,
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bool useMarchingCubes = false,
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unsigned int computeRegularStructure = 1)
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{
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using namespace vtkm::worklet::contourtree_augmented;
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// 2D Contour Tree
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if (meshSize[2] == 1)
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{
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// Build the mesh and fill in the values
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DataSetMeshTriangulation2DFreudenthal mesh(vtkm::Id2{ meshSize[0], meshSize[1] });
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// Run the contour tree on the mesh
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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return;
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}
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// 3D Contour Tree using marching cubes
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else if (useMarchingCubes)
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{
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// Build the mesh and fill in the values
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DataSetMeshTriangulation3DMarchingCubes mesh(meshSize);
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// Run the contour tree on the mesh
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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return;
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}
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// 3D Contour Tree with Freudenthal
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else
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{
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// Build the mesh and fill in the values
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DataSetMeshTriangulation3DFreudenthal mesh(meshSize);
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// Run the contour tree on the mesh
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RunContourTree(fieldArray,
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contourTree,
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sortOrder,
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nIterations,
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mesh,
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computeRegularStructure,
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mesh.GetMeshBoundaryExecutionObject());
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return;
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}
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}
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private:
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/*!
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* Run the contour tree for the given mesh. This function implements the main steps for
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* computing the contour tree after the mesh has been constructed using the approbrite
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* contour tree mesh class.
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*
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* fieldArray : The values of the mesh
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* contourTree : The output contour tree to be computed (output)
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* sortOrder : The sort order for the mesh vertices (output)
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* nIterations : The number of iterations used to compute the contour tree (output)
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* mesh : The specific mesh (see vtkm/worklet/contourtree_augmented/mesh_dem_meshtypes
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* computeRegularStructure : 0=Off, 1=full augmentation with all vertices
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* 2=boundary augmentation using meshBoundary
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* meshBoundary : This parameter is generated by calling mesh.GetMeshBoundaryExecutionObject
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* For regular 2D/3D meshes this required no extra parameters, however, for a
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* ContourTreeMesh additional information about the block must be given. Rather
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* than generating the MeshBoundary descriptor here, we therefore, require it
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* as an input. The MeshBoundary is used to augment the contour tree with the
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* mesh boundary vertices. It is needed only if we want to augement by the
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* mesh boundary and computeRegularStructure is False (i.e., if we compute
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* the full regular strucuture this is not needed because all vertices
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* (including the boundary) will be addded to the tree anyways.
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*/
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template <typename FieldType,
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typename StorageType,
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typename MeshClass,
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typename MeshBoundaryClass>
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void RunContourTree(const vtkm::cont::ArrayHandle<FieldType, StorageType> fieldArray,
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contourtree_augmented::ContourTree& contourTree,
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contourtree_augmented::IdArrayType& sortOrder,
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vtkm::Id& nIterations,
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MeshClass& mesh,
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unsigned int computeRegularStructure,
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const MeshBoundaryClass& meshBoundary)
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{
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using namespace vtkm::worklet::contourtree_augmented;
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// Stage 1: Load the data into the mesh. This is done in the Run() method above and accessible
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// here via the mesh parameter. The actual data load is performed outside of the
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// worklet in the example contour tree app (or whoever uses the worklet)
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// Stage 2 : Sort the data on the mesh to initialize sortIndex & indexReverse on the mesh
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// Start the timer for the mesh sort
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vtkm::cont::Timer timer;
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timer.Start();
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std::stringstream timingsStream; // Use a string stream to log in one message
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// Sort the mesh data
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mesh.SortData(fieldArray);
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timingsStream << " " << std::setw(38) << std::left << "Sort Data"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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timer.Start();
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// Stage 3: Assign every mesh vertex to a peak
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MeshExtrema extrema(mesh.NumVertices);
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extrema.SetStarts(mesh, true);
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extrema.BuildRegularChains(true);
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Regular Chains"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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timer.Start();
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// Stage 4: Identify join saddles & construct Active Join Graph
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MergeTree joinTree(mesh.NumVertices, true);
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ActiveGraph joinGraph(true);
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joinGraph.Initialise(mesh, extrema);
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Initialize Active Graph"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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#ifdef DEBUG_PRINT
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joinGraph.DebugPrint("Active Graph Instantiated", __FILE__, __LINE__);
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#endif
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timer.Start();
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// Stage 5: Compute Join Tree Hyperarcs from Active Join Graph
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joinGraph.MakeMergeTree(joinTree, extrema);
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timingsStream << " " << std::setw(38) << std::left << "Join Tree Compute"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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#ifdef DEBUG_PRINT
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joinTree.DebugPrint("Join tree Computed", __FILE__, __LINE__);
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joinTree.DebugPrintTree("Join tree", __FILE__, __LINE__, mesh);
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#endif
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timer.Start();
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// Stage 6: Assign every mesh vertex to a pit
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extrema.SetStarts(mesh, false);
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extrema.BuildRegularChains(false);
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timingsStream << " " << std::setw(38) << std::left << "Split Tree Regular Chains"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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timer.Start();
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// Stage 7: Identify split saddles & construct Active Split Graph
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MergeTree splitTree(mesh.NumVertices, false);
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ActiveGraph splitGraph(false);
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splitGraph.Initialise(mesh, extrema);
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timingsStream << " " << std::setw(38) << std::left << "Split Tree Initialize Active Graph"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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#ifdef DEBUG_PRINT
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splitGraph.DebugPrint("Active Graph Instantiated", __FILE__, __LINE__);
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#endif
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timer.Start();
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// Stage 8: Compute Split Tree Hyperarcs from Active Split Graph
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splitGraph.MakeMergeTree(splitTree, extrema);
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timingsStream << " " << std::setw(38) << std::left << "Split Tree Compute"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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#ifdef DEBUG_PRINT
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splitTree.DebugPrint("Split tree Computed", __FILE__, __LINE__);
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// Debug split and join tree
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joinTree.DebugPrintTree("Join tree", __FILE__, __LINE__, mesh);
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splitTree.DebugPrintTree("Split tree", __FILE__, __LINE__, mesh);
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#endif
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timer.Start();
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// Stage 9: Join & Split Tree are Augmented, then combined to construct Contour Tree
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contourTree.Init(mesh.NumVertices);
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ContourTreeMaker treeMaker(contourTree, joinTree, splitTree);
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// 9.1 First we compute the hyper- and super- structure
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treeMaker.ComputeHyperAndSuperStructure();
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timingsStream << " " << std::setw(38) << std::left
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<< "Contour Tree Hyper and Super Structure"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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timer.Start();
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// 9.2 Then we compute the regular structure
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if (computeRegularStructure == 1) // augment with all vertices
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{
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treeMaker.ComputeRegularStructure(extrema);
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timingsStream << " " << std::setw(38) << std::left << "Contour Tree Regular Structure"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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}
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else if (computeRegularStructure == 2) // augment by the mesh boundary
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{
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treeMaker.ComputeBoundaryRegularStructure(extrema, mesh, meshBoundary);
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timingsStream << " " << std::setw(38) << std::left
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<< "Contour Tree Boundary Regular Structure"
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<< ": " << timer.GetElapsedTime() << " seconds" << std::endl;
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}
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timer.Start();
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// Collect the output data
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nIterations = treeMaker.ContourTreeResult.NumIterations;
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// Need to make a copy of sortOrder since ContourTreeMesh uses a smart array handle
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// TODO: Check if we can just make sortOrder a return array with variable type or if we can make the SortOrder return optional
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// TODO/FIXME: According to Ken Moreland the short answer is no. We may need to go back and refactor this when we
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// improve the contour tree API. https://gitlab.kitware.com/vtk/vtk-m/-/merge_requests/2263#note_831128 for more details.
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vtkm::cont::Algorithm::Copy(mesh.SortOrder, sortOrder);
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// ProcessContourTree::CollectSortedSuperarcs<DeviceAdapter>(contourTree, mesh.SortOrder, saddlePeak);
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// contourTree.SortedArcPrint(mesh.SortOrder);
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// contourTree.PrintDotSuperStructure();
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// Log the collected timing results in one coherent log entry
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this->TimingsLogString = timingsStream.str();
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if (this->TimingsLogLevel != vtkm::cont::LogLevel::Off)
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{
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VTKM_LOG_S(this->TimingsLogLevel,
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std::endl
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<< " ------------------- Contour Tree Worklet Timings ----------------------"
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<< std::endl
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<< this->TimingsLogString);
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}
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}
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};
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} // namespace vtkm
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} // namespace vtkm::worklet
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#endif // vtk_m_worklet_ContourTreeUniformAugmented_h
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