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Commit 51f73704 authored by Gunther Weber's avatar Gunther Weber
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Clean-up. Move functor class outside template.

parent 74923266
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2 merge requests!2615Draft: DONTMERGE ME: TEST FOR 1.7.0-rc1 is our 9th official release of VTK-m.,!2443Contour tree performance improvements (ContourTreeMesh)
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vtkm/worklet/contourtree_augmented/ArrayTransforms.h
+ 0
− 10
View file @ 51f73704
......@@ -110,16 +110,6 @@ inline void PermuteArray(const ArrayType& input, IdArrayType& permute, ArrayType
} // permuteValues()
// transform functor needed for ScanExclusive calculation. Return 0 if noSuchElement else 1
struct OneIfArcValid
{
VTKM_EXEC_CONT
OneIfArcValid() {}
VTKM_EXEC_CONT
vtkm::Id operator()(vtkm::Id a) const { return NoSuchElement(a) ? 0 : 1; }
};
// transform functor used in ContourTreeMesh to flag indicies as other when using the CombinedVectorClass
struct MarkOther
{
......
vtkm/worklet/contourtree_augmented/meshtypes/ContourTreeMesh.h
+ 63
− 33
View file @ 51f73704
......@@ -85,9 +85,9 @@
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/AddToArrayElementsWorklet.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/ApplyLookupTableDecorator.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/ArcComparator.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/ArcValidDecorator.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CombinedSimulatedSimplicityIndexComparator.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CombinedVectorDifferentFromNext.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CompressNeighborsWorklet.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CopyIntoCombinedArrayWorklet.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CopyIntoCombinedNeighborsWorklet.h>
#include <vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CopyNeighborsToPackedArray.h>
......@@ -446,7 +446,7 @@ inline void CopyVecArrayByIndices(const PT1& srcArray,
// Initalize the contour tree from the arcs array and sort order
// Initalize the contour tree from the arcs array
template <typename FieldType>
inline void ContourTreeMesh<FieldType>::InitializeNeighborConnectivityFromArcs(
const IdArrayType& arcs)
......@@ -456,51 +456,81 @@ inline void ContourTreeMesh<FieldType>::InitializeNeighborConnectivityFromArcs(
// i and arc[i]. For the neighbor connectiviy in the contour tree mesh, we first convert these
// into two directed arcs that are then used to compute a list of neighbors in the mesh for
// each node.
// Step 1: Identify valid arcs (i.e., those that are not marked by the NO_SUCH_ELEMENT as having
// no target) as well as find target indices for valid arcs in neighbors array ...
IdArrayType arcTargetIndex;
arcTargetIndex.Allocate(arcs.GetNumberOfValues());
OneIfArcValid oneIfArcValidFunctor;
auto oneIfArcValidArrayHandle =
vtkm::cont::ArrayHandleTransform<IdArrayType, OneIfArcValid>(arcs, oneIfArcValidFunctor);
vtkm::cont::Algorithm::ScanExclusive(oneIfArcValidArrayHandle, arcTargetIndex);
vtkm::Id nValidArcs = ArrayGetValue(arcTargetIndex.GetNumberOfValues() - 1, arcTargetIndex) +
oneIfArcValidFunctor(ArrayGetValue(arcs.GetNumberOfValues() - 1, arcs));
// ... and compress array
this->NeighborConnectivity.ReleaseResources();
this->NeighborConnectivity.Allocate(
2 * nValidArcs); // Number of directed arcs = 2 * number of undirected arcs
this->Invoke(contourtree_mesh_inc_ns::CompressNeighborsWorklet{},
arcs,
arcTargetIndex,
this->NeighborConnectivity);
// Sort arcs so that all arcs originating at the same vertex are adjacent. All arcs are in neighbors array based on
// sort index of their 'from' vertex (and then within a run sorted by sort index of their 'to' vertex).
//
// Take this simple graph for example:
//
// 4
// \
// \> 3 -> 1 <- 0
// /
// /
// 2
//
// (This is a graph with nodes 0 through 4 and edges 0 -> 1, 2 -> 3, 3 -> 1, 4 -> 3).
// The way the graph is structured, each nodes has at most one outgoing edge.
// The contour tree algorithm stores this in an arcs array:
//
// idx: 0 1 2 3 4
// arcs: 1 - 3 1 3 (- = NO_SUCH_ELEMENT, meaning no arc originating from this node)
//
// This function translates this into the internal contour tree mesh represnetation,
// which is "regular" vtk-m connectivity format, i.e., the connectity array is a
// flat list of neighbor vertices and offsets give the start index of the
// neighbor list for each vertex:
//
// connectivity: 1 0 3 3 1 2 4 3
// counts: 1 2 1 3 1
// offset: 0 1 3 4 7 8
// Step 1: Implictely view arc array as directed arcs and add arcs in the opposite
// direction. In the resulting arc list, arc 2*idx is the arc idx->arcs[idx] and arc
// 2*idx+1 is the arc arcs[idx]->idx, i.e., in our example,
// idx: 0 1 2 3 4 5 6 7 8 9
// from: 0 1 1 - 2 3 3 1 4 3
// to: 1 0 - 1 3 2 1 3 3 4
vtkm::Id nArcsTotal = 2 * arcs.GetNumberOfValues();
vtkm::cont::ArrayHandleIndex indexArray(nArcsTotal);
auto arcIsValidArray = make_ArrayHandleDecorator(
nArcsTotal, mesh_dem_contourtree_mesh_inc::ArcValidDecoratorImpl{}, arcs);
// We first generate a list of "valid" arcs in this->NeighborConnectivity, in our
// example:
// connectivity: 0 1 4 5 6 7 8 9
vtkm::cont::Algorithm::CopyIf(indexArray, arcIsValidArray, this->NeighborConnectivity);
vtkm::Id nValidArcs = this->NeighborConnectivity.GetNumberOfValues();
// Step 2: Sort arcs---by permuting their indices in the connectiviy array---so
// that all arcs originating at the same vertex (same `from`) are adjacent.
// All arcs are in neighbors array based on sort index of their 'from' vertex
// (and then within a run sorted by sort index of their 'to' vertex).
// In our example this results in:
// connectivity: 0 1 7 4 6 5 9 8
// corresponding to an arc order of
// from: 0 1 1 2 3 3 3 4
// to: 1 0 3 3 1 2 4 3
vtkm::cont::Algorithm::Sort(this->NeighborConnectivity,
contourtree_mesh_inc_ns::ArcComparator(arcs));
// Find start index for each vertex into neighbors array (per vtk-m convention, connectivy array has
// one extra element not corresponding to a vertex to avoid special case)
auto arcFrom = make_ArrayHandleDecorator(this->NeighborConnectivity.GetNumberOfValues(),
// We can now obtain counts of the connectivity array by counting the number
// of consecutive `from` entries with the same value. In our example:
// counts: 1 2 1 3 1
auto arcFrom = make_ArrayHandleDecorator(nValidArcs,
mesh_dem_contourtree_mesh_inc::GetArcFromDecoratorImpl{},
this->NeighborConnectivity,
arcs);
auto constOne = vtkm::cont::make_ArrayHandleConstant(
vtkm::Id{ 1 }, this->NeighborConnectivity.GetNumberOfValues());
auto constOne = vtkm::cont::make_ArrayHandleConstant(vtkm::Id{ 1 }, nValidArcs);
vtkm::cont::ArrayHandle<vtkm::Id> uniqueKeys;
vtkm::cont::ArrayHandle<vtkm::Id> counts;
vtkm::cont::Algorithm::ReduceByKey(arcFrom, constOne, uniqueKeys, counts, vtkm::Add());
VTKM_ASSERT(uniqueKeys.GetNumberOfValues() == this->NumVertices);
// Convert counts into offsts for the connectivity array
vtkm::Id neighborOffsetsSize;
//this->NeighborOffsets.Allocate(this->NumVertices + 1);
vtkm::cont::ConvertNumComponentsToOffsets(counts, this->NeighborOffsets, neighborOffsetsSize);
// Replace arc number with 'to' vertex in neighbors array
// Finally, the correct connectivity array correspons to the `to` array,
// so replace arc indices with its `to`vertex. In our example, this results in:
// connectivity: 1 0 3 3 1 2 4 3
// which is exactly the array we needed to compute
contourtree_mesh_inc_ns::ReplaceArcNumWithToVertexWorklet replaceArcNumWithToVertexWorklet;
this->Invoke(replaceArcNumWithToVertexWorklet,
this->NeighborConnectivity, // input/output
......
vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/CompressNeighborsWorklet.h → vtkm/worklet/contourtree_augmented/meshtypes/contourtreemesh/ArcValidDecorator.h
+ 16
− 37
View file @ 51f73704
......@@ -60,11 +60,8 @@
// Oliver Ruebel (LBNL)
//==============================================================================
#ifndef vtk_m_worklet_contourtree_augmented_contourtree_mesh_inc_compress_neighbors_worklet_h
#define vtk_m_worklet_contourtree_augmented_contourtree_mesh_inc_compress_neighbors_worklet_h
#include <vtkm/worklet/WorkletMapField.h>
#include <vtkm/worklet/contourtree_augmented/Types.h>
#ifndef vtk_m_worklet_contourtree_augmented_contourtree_mesh_inc_arc_valid_decorator_h
#define vtk_m_worklet_contourtree_augmented_contourtree_mesh_inc_arc_valid_decorator_h
namespace vtkm
{
......@@ -74,45 +71,27 @@ namespace contourtree_augmented
{
namespace mesh_dem_contourtree_mesh_inc
{
class CompressNeighborsWorklet : public vtkm::worklet::WorkletMapField
class ArcValidDecoratorImpl
{
public:
typedef void ControlSignature(
FieldIn arcs, // (input) arcs
FieldIn arcTargetIndex, // (input) arcTargetIndex
WholeArrayOut neighborConnectivity); // (output) neighborConnectivity
typedef void ExecutionSignature(_1, InputIndex, _2, _3);
typedef _1 InputDomain;
template <typename OutFieldPortalType>
VTKM_EXEC void operator()(vtkm::Id& to,
vtkm::Id from,
vtkm::Id& arcTargetIndexFrom,
const OutFieldPortalType& neighborConnectivityPortal) const
template <typename PortalType>
struct Functor
{
if (!NoSuchElement(to))
PortalType ArcsPortal;
VTKM_EXEC_CONT
vtkm::Id operator()(vtkm::Id arcNo) const
{
neighborConnectivityPortal.Set(2 * arcTargetIndexFrom + 0, 2 * from + 0);
neighborConnectivityPortal.Set(2 * arcTargetIndexFrom + 1, 2 * from + 1);
return NoSuchElement(ArcsPortal.Get(arcNo / 2)) ? 0 : 1;
}
};
// In serial this worklet implements the following operation
// for (indexVector::size_type from = 0; from < arcs.size(); ++from)
// {
// indexType to = arcs[from];
// if (!NoSuchElement(to))
// {
// assert(MaskedIndex(to) != from);
// neighbors[2*arcTargetIndex[from]+0] = 2*from+0;
// neighbors[2*arcTargetIndex[from]+1] = 2*from+1;
// }
template <typename PT>
Functor<PT> CreateFunctor(PT arcsPortal) const
{
return { arcsPortal };
}
}; // CompressNeighborsWorklet
}; // ArcValidDecoratorImpl
} // namespace mesh_dem_contourtree_mesh_inc
} // namespace contourtree_augmented
......
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