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276 lines
12 KiB
C++
276 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) 2016, Los Alamos National Security, LLC
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// All rights reserved.
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//
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// Copyright 2016. Los Alamos National Security, LLC.
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// This software was produced under U.S. Government contract DE-AC52-06NA25396
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// for Los Alamos National Laboratory (LANL), which is operated by
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// Los Alamos National Security, LLC for the U.S. Department of Energy.
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// The U.S. Government has rights to use, reproduce, and distribute this
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// software. NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC
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// MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE
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// USE OF THIS SOFTWARE. If software is modified to produce derivative works,
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// such modified software should be clearly marked, so as not to confuse it
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// with the version available from LANL.
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//
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// Additionally, redistribution and use in source and binary forms, with or
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// without modification, are permitted provided that the following conditions
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// are met:
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//
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// 1. Redistributions of source code must retain the above copyright notice,
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// this list of conditions and the following disclaimer.
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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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// 3. Neither the name of Los Alamos National Security, LLC, Los Alamos
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// National Laboratory, LANL, the U.S. Government, nor the names of its
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// contributors may be used to endorse or promote products derived from
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// this software without specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND
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// CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
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// BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
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// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS
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// NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
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// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//============================================================================
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// This code is based on 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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//
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// COMMENTS:
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//
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// Essentially, a vector of data values. BUT we will want them sorted to simplify
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// processing - i.e. it's the robust way of handling simulation of simplicity
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//
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// On the other hand, once we have them sorted, we can discard the original data since
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// only the sort order matters
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//
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// Since we've been running into memory issues, we'll start being more careful.
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// Clearly, we can eliminate the values if we sort, but in this iteration we are
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// deferring doing a full sort, so we need to keep the values.
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//
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//=======================================================================================
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#ifndef vtkm_worklet_contourtree_mesh3d_dem_triangulation_h
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#define vtkm_worklet_contourtree_mesh3d_dem_triangulation_h
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#include <vtkm/cont/ArrayGetValues.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/ArrayHandleIndex.h>
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#include <vtkm/cont/ArrayHandleZip.h>
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#include <vtkm/worklet/DispatcherMapField.h>
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#include <vtkm/worklet/contourtree/ChainGraph.h>
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#include <vtkm/worklet/contourtree/LinkComponentCaseTable3D.h>
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#include <vtkm/worklet/contourtree/Mesh3D_DEM_SaddleStarter.h>
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#include <vtkm/worklet/contourtree/Mesh3D_DEM_VertexOutdegreeStarter.h>
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#include <vtkm/worklet/contourtree/Mesh3D_DEM_VertexStarter.h>
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#include <vtkm/worklet/contourtree/PrintVectors.h>
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#include <vtkm/worklet/contourtree/Types.h>
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//#define DEBUG_PRINT 1
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//#define DEBUG_TIMING 1
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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
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{
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template <typename T, typename StorageType>
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class Mesh3D_DEM_Triangulation
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{
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public:
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// original data array
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const vtkm::cont::ArrayHandle<T, StorageType>& values;
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// size of the mesh
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vtkm::Id nRows, nCols, nSlices, NumVertices, nLogSteps;
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// array with neighbourhood masks
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vtkm::cont::ArrayHandle<vtkm::Id> neighbourhoodMask;
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// case table information for finding neighbours
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vtkm::cont::ArrayHandle<vtkm::IdComponent> neighbourOffsets3D;
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vtkm::cont::ArrayHandle<vtkm::UInt16> linkComponentCaseTable3D;
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// constructor
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Mesh3D_DEM_Triangulation(const vtkm::cont::ArrayHandle<T, StorageType>& Values,
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vtkm::Id NRows,
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vtkm::Id NCols,
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vtkm::Id NSlices);
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// sets all vertices to point along an outgoing edge (except extrema)
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void SetStarts(vtkm::cont::ArrayHandle<vtkm::Id>& chains, bool descending);
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// sets outgoing paths for saddles
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void SetSaddleStarts(ChainGraph<T, StorageType>& mergeGraph, bool descending);
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};
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// creates input mesh
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template <typename T, typename StorageType>
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Mesh3D_DEM_Triangulation<T, StorageType>::Mesh3D_DEM_Triangulation(
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const vtkm::cont::ArrayHandle<T, StorageType>& Values,
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vtkm::Id NRows,
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vtkm::Id NCols,
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vtkm::Id NSlices)
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: values(Values)
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, nRows(NRows)
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, nCols(NCols)
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, nSlices(NSlices)
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, neighbourOffsets3D()
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, linkComponentCaseTable3D()
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{
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NumVertices = nRows * nCols * nSlices;
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// compute the number of log-jumping steps (i.e. lg_2 (NumVertices))
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nLogSteps = 1;
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for (vtkm::Id shifter = NumVertices; shifter > 0; shifter >>= 1)
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nLogSteps++;
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neighbourOffsets3D =
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vtkm::cont::make_ArrayHandle(vtkm::worklet::contourtree::neighbourOffsets3D, 42);
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linkComponentCaseTable3D =
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vtkm::cont::make_ArrayHandle(vtkm::worklet::contourtree::linkComponentCaseTable3D, 16384);
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}
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// sets outgoing paths for saddles
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template <typename T, typename StorageType>
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void Mesh3D_DEM_Triangulation<T, StorageType>::SetStarts(vtkm::cont::ArrayHandle<vtkm::Id>& chains,
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bool ascending)
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{
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// create the neighbourhood mask
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neighbourhoodMask.Allocate(NumVertices);
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// For each vertex set the next vertex in the chain
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vtkm::cont::ArrayHandleIndex vertexIndexArray(NumVertices);
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Mesh3D_DEM_VertexStarter<T> vertexStarter(nRows, nCols, nSlices, ascending);
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vtkm::worklet::DispatcherMapField<Mesh3D_DEM_VertexStarter<T>> vertexStarterDispatcher(
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vertexStarter);
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vertexStarterDispatcher.Invoke(vertexIndexArray, // input
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values, // input (whole array)
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chains, // output
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neighbourhoodMask); // output
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} // SetStarts()
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// sets outgoing paths for saddles
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template <typename T, typename StorageType>
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void Mesh3D_DEM_Triangulation<T, StorageType>::SetSaddleStarts(
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ChainGraph<T, StorageType>& mergeGraph,
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bool ascending)
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{
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// we need a temporary inverse index to change vertex IDs
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vtkm::cont::ArrayHandle<vtkm::Id> inverseIndex;
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vtkm::cont::ArrayHandle<vtkm::Id> isCritical;
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vtkm::cont::ArrayHandle<vtkm::Id> outdegree;
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vtkm::cont::ArrayHandleIndex vertexIndexArray(NumVertices);
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Mesh3D_DEM_VertexOutdegreeStarter vertexOutdegreeStarter(nRows, nCols, nSlices, ascending);
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vtkm::worklet::DispatcherMapField<Mesh3D_DEM_VertexOutdegreeStarter>
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vertexOutdegreeStarterDispatcher(vertexOutdegreeStarter);
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vertexOutdegreeStarterDispatcher.Invoke(vertexIndexArray, // input
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neighbourhoodMask, // input
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mergeGraph.arcArray, // input (whole array)
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neighbourOffsets3D, // input (whole array)
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linkComponentCaseTable3D, // input (whole array)
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outdegree, // output
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isCritical); // output
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vtkm::cont::Algorithm::ScanExclusive(isCritical, inverseIndex);
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// now we can compute how many critical points we carry forward
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vtkm::Id nCriticalPoints = vtkm::cont::ArrayGetValue(NumVertices - 1, inverseIndex) +
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vtkm::cont::ArrayGetValue(NumVertices - 1, isCritical);
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// allocate space for the join graph vertex arrays
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mergeGraph.AllocateVertexArrays(nCriticalPoints);
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// compact the set of vertex indices to critical ones only
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vtkm::cont::Algorithm::CopyIf(vertexIndexArray, isCritical, mergeGraph.valueIndex);
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// we initialise the prunesTo array to "NONE"
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vtkm::cont::ArrayHandleConstant<vtkm::Id> notAssigned(NO_VERTEX_ASSIGNED, nCriticalPoints);
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vtkm::cont::Algorithm::Copy(notAssigned, mergeGraph.prunesTo);
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// copy the outdegree from our temporary array
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// : mergeGraph.outdegree[vID] <= outdegree[mergeGraph.valueIndex[vID]]
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vtkm::cont::Algorithm::CopyIf(outdegree, isCritical, mergeGraph.outdegree);
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// copy the chain maximum from arcArray
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// : mergeGraph.chainExtremum[vID] = inverseIndex[mergeGraph.arcArray[mergeGraph.valueIndex[vID]]]
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using IdArrayType = vtkm::cont::ArrayHandle<vtkm::Id>;
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using PermuteIndexType = vtkm::cont::ArrayHandlePermutation<IdArrayType, IdArrayType>;
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vtkm::cont::ArrayHandle<vtkm::Id> tArray;
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tArray.Allocate(nCriticalPoints);
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vtkm::cont::Algorithm::CopyIf(mergeGraph.arcArray, isCritical, tArray);
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vtkm::cont::Algorithm::Copy(PermuteIndexType(tArray, inverseIndex), mergeGraph.chainExtremum);
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// and set up the active vertices - initially to identity
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vtkm::cont::ArrayHandleIndex criticalVertsIndexArray(nCriticalPoints);
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vtkm::cont::Algorithm::Copy(criticalVertsIndexArray, mergeGraph.activeVertices);
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// now we need to compute the firstEdge array from the outdegrees
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vtkm::cont::Algorithm::ScanExclusive(mergeGraph.outdegree, mergeGraph.firstEdge);
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vtkm::Id nCriticalEdges = vtkm::cont::ArrayGetValue(nCriticalPoints - 1, mergeGraph.firstEdge) +
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vtkm::cont::ArrayGetValue(nCriticalPoints - 1, mergeGraph.outdegree);
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// now we allocate the edge arrays
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mergeGraph.AllocateEdgeArrays(nCriticalEdges);
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// and we have to set them, so we go back to the vertices
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Mesh3D_DEM_SaddleStarter saddleStarter(nRows, // input
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nCols, // input
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nSlices, // input
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ascending); // input
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vtkm::worklet::DispatcherMapField<Mesh3D_DEM_SaddleStarter> saddleStarterDispatcher(
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saddleStarter);
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vtkm::cont::ArrayHandleZip<vtkm::cont::ArrayHandle<vtkm::Id>, vtkm::cont::ArrayHandle<vtkm::Id>>
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outDegFirstEdge = vtkm::cont::make_ArrayHandleZip(mergeGraph.outdegree, mergeGraph.firstEdge);
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saddleStarterDispatcher.Invoke(criticalVertsIndexArray, // input
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outDegFirstEdge, // input (pair)
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mergeGraph.valueIndex, // input
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neighbourhoodMask, // input (whole array)
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mergeGraph.arcArray, // input (whole array)
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inverseIndex, // input (whole array)
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neighbourOffsets3D, // input (whole array)
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linkComponentCaseTable3D, // input (whole array)
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mergeGraph.edgeNear, // output (whole array)
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mergeGraph.edgeFar, // output (whole array)
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mergeGraph.activeEdges); // output (whole array)
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// finally, allocate and initialise the edgeSorter array
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vtkm::cont::ArrayCopy(mergeGraph.activeEdges, mergeGraph.edgeSorter);
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} // SetSaddleStarts()
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}
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}
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}
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#endif
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