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POD types based KdTree lookups

Added a new interface to the KdTree using
only pointers instead of std::vector. Now
the old calls are being redirected to this
new one. Also added test "testkdtree".
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1 parent 74482d8 commit dc898054d9144a409fe0e3f8d7f957e1a50ed8a1 @aconty aconty committed with aselle Oct 20, 2010
Showing with 214 additions and 83 deletions.
  1. +0 −1 SConstruct
  2. BIN src/data/test.bgeo
  3. +12 −15 src/data/test.geo
  4. +97 −62 src/lib/core/KdTree.h
  5. +1 −1 src/tests/SConscript
  6. +4 −4 src/tests/test.cpp
  7. +100 −0 src/tests/testkdtree.cpp
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@@ -81,4 +81,3 @@ env.SConscript(variant_build+"/src/tests/SConscript")
env.SConscript(variant_build+"/src/doc/SConscript")
env.SConscript(variant_build+"/src/py/SConscript")
-
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@@ -1,21 +1,18 @@
PGEOMETRY V5
-NPoints 9 NPrims 0
+NPoints 5 NPrims 1
NPointGroups 0 NPrimGroups 0
-NPointAttrib 2 NVertexAttrib 0 NPrimAttrib 0 NAttrib 1
+NPointAttrib 2 NVertexAttrib 0 NPrimAttrib 1 NAttrib 0
PointAttrib
+
+life 2 float 0 0
id 1 int 0
-radiusPP 1 float 0
--1 0 -1 1 (0 0.641600609)
-0 0 -1 1 (1 0.800463796)
-1 0 -1 1 (2 0.510895014)
--1 0 0 1 (3 0.77547431)
-0 0 0 1 (4 0.879505873)
-1 0 0 1 (5 0.205040097)
--1 0 1 1 (6 0.522060633)
-0 0 1 1 (7 0.885056257)
-1 0 1 1 (8 0.595740199)
-DetailAttrib
-varmap 1 index 2 "id -> ID" "radiusPP -> RADIUSPP"
- (0)
+0 0.1 0.2 1 (-1.2 10 0)
+0.1 0.2 0.3 1 (-0.2 10 1)
+0.2 0.3 0.4 1 (0.8 10 2)
+0.3 0.4 0.5 1 (1.8 10 3)
+0.4 0.5 0.6 1 (2.8 10 4)
+PrimitiveAttrib
+generator 1 index 1 papi
+Part 5 0 1 2 3 4 [0]
beginExtra
endExtra
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@@ -131,58 +131,57 @@ template <int k> class BBox
// MAKE-heap on a binary (array based) heap
// loosely based on Henrik Wann Jensen's Photon Mapping book, but made 0-indexed
// and commented
-inline float buildHeap(std::vector<uint64_t>& result,std::vector<float>& distance_squared)
+inline float buildHeap(uint64_t *result, float *distance_squared, int heap_size)
{
- assert(result.size()==distance_squared.size());
- int heap_size=result.size();
- int max_non_leaf_index=result.size()/2-1; // 0 to max_non_leaf_index is indices of parents
+ int max_non_leaf_index = heap_size/2 - 1; // 0 to max_non_leaf_index is indices of parents
// go from bottom of tree scanning right to left in each height of the tree
- for(int subtreeParent=max_non_leaf_index;subtreeParent>=0;subtreeParent--){
- int current_parent=subtreeParent;
- while(current_parent<=max_non_leaf_index){
- int left_index=2*current_parent+1;int right_index=2*current_parent+2;
+ for(int subtreeParent = max_non_leaf_index; subtreeParent >= 0; subtreeParent--) {
+ int current_parent = subtreeParent;
+ while(current_parent <= max_non_leaf_index) {
+ int left_index = 2 * current_parent + 1;
+ int right_index = 2 * current_parent + 2;
// find largest element
- int largest_index=current_parent;
- if(left_index<heap_size && distance_squared[left_index]>distance_squared[largest_index])
- largest_index=left_index;
- if(right_index<heap_size && distance_squared[right_index]>distance_squared[largest_index])
- largest_index=right_index;
+ int largest_index = current_parent;
+ if(left_index < heap_size && distance_squared[left_index] > distance_squared[largest_index])
+ largest_index = left_index;
+ if(right_index < heap_size && distance_squared[right_index] > distance_squared[largest_index])
+ largest_index = right_index;
// subtree parented at current_parent satisfies heap property because parent has largest
- if(largest_index==current_parent) break;
+ if(largest_index == current_parent) break;
// pull large value up and descend to tree to see if new that subtree is invalid
- std::swap(result[largest_index],result[current_parent]);
- std::swap(distance_squared[largest_index],distance_squared[current_parent]);
- current_parent=largest_index;
+ std::swap(result[largest_index], result[current_parent]);
+ std::swap(distance_squared[largest_index], distance_squared[current_parent]);
+ current_parent = largest_index;
}
}
return distance_squared[0]; // return max distance
}
// Inserts smaller element into heap (does not check so caller must)
-inline float insertToHeap(std::vector<uint64_t>& result,std::vector<float>& distance_squared,int new_id,float new_distance_squared)
+inline float insertToHeap(uint64_t *result, float *distance_squared, int heap_size, int new_id, float new_distance_squared)
{
- assert(result.size()>0 && distance_squared.size()==result.size());
- assert(new_distance_squared<distance_squared[0]);
- int current_parent=0;
- int heap_size=result.size();
+ assert(new_distance_squared < distance_squared[0]);
+ int current_parent = 0;
for(;;){
- int left=2*current_parent+1,right=2*current_parent+2;
- int index_of_largest=current_parent;
+ int left = 2 * current_parent + 1, right = 2 * current_parent + 2;
+ int index_of_largest = current_parent;
// find out if the current element is being replaced by descendant or by new element
- if(left>=heap_size) break;
- else if(right>=heap_size || distance_squared[left]>distance_squared[right]) index_of_largest=left;
- else index_of_largest=right;
+ if(left >= heap_size) break;
+ else if(right >= heap_size || distance_squared[left] > distance_squared[right])
+ index_of_largest = left;
+ else
+ index_of_largest=right;
// new element is largest
- if(new_distance_squared>distance_squared[index_of_largest]) break;
+ if(new_distance_squared > distance_squared[index_of_largest]) break;
// pull the biggest element up and recurse to where it came from
- std::swap(result[index_of_largest],result[current_parent]);
- std::swap(distance_squared[index_of_largest],distance_squared[current_parent]);
- current_parent=index_of_largest;
+ std::swap(result[index_of_largest], result[current_parent]);
+ std::swap(distance_squared[index_of_largest], distance_squared[current_parent]);
+ current_parent = index_of_largest;
}
// overwrite current node in tree
- distance_squared[current_parent]=new_distance_squared;
- result[current_parent]=new_id;
+ distance_squared[current_parent] = new_distance_squared;
+ result[current_parent] = new_id;
return distance_squared[0]; // return max distance
}
@@ -203,6 +202,23 @@ template <int k> class KdTree
float maxRadiusSquared;
};
+ struct NearestQueryC
+ {
+ NearestQueryC(uint64_t *result, float *distanceSquared, const float pquery_in[k],
+ int maxPoints, float maxRadiusSquared)
+ :result(result), distanceSquared(distanceSquared), maxPoints(maxPoints),
+ foundPoints(0), maxRadiusSquared(maxRadiusSquared)
+
+ {for(int i=0;i<k;i++) pquery[i]=pquery_in[i];}
+
+ uint64_t *result;
+ float *distanceSquared;
+ float pquery[k];
+ int maxPoints;
+ int foundPoints;
+ float maxRadiusSquared;
+ };
+
public:
KdTree();
~KdTree();
@@ -216,6 +232,9 @@ template <int k> class KdTree
float findNPoints(std::vector<uint64_t>& result,std::vector<float>& distanceSquared,
const float p[k],int nPoints,float maxRadius) const;
+ int findNPoints(uint64_t *result, float *distanceSquared, float *finalSearchRadius2,
+ const float p[k], int nPoints, float maxRadius) const;
+
private:
void sortSubtree(int n, int count, int j);
@@ -226,7 +245,7 @@ template <int k> class KdTree
};
void findPoints(std::vector<uint64_t>& result, const BBox<k>& bbox,
int n, int size, int j) const;
- void findNPoints(NearestQuery& query,int n,int size,int j) const;
+ void findNPoints(NearestQueryC& query,int n,int size,int j) const;
static inline void ComputeSubtreeSizes(int size, int& left, int& right)
{
@@ -331,54 +350,70 @@ template <int k>
float KdTree<k>::findNPoints(std::vector<uint64_t>& result,
std::vector<float>& distanceSquared,const float p[k],int nPoints,float maxRadius) const
{
- result.clear();
- distanceSquared.clear();
- float radius_squared=maxRadius*maxRadius;
+ result.resize (nPoints);
+ distanceSquared.resize (nPoints);
+ float finalRadius2 = maxRadius;
+ int size = findNPoints (&result[0], &distanceSquared[0], &finalRadius2, p, nPoints, maxRadius);
+ result.resize(size);
+ distanceSquared.resize(size);
+ return finalRadius2;
+}
+
+template <int k>
+int KdTree<k>::findNPoints(uint64_t *result, float *distanceSquared, float *finalSearchRadius2,
+ const float p[k],int nPoints,float maxRadius) const
+{
+ float radius_squared = maxRadius * maxRadius;
if (!size() || !_sorted || nPoints<1) return radius_squared;
- NearestQuery query(result,distanceSquared,p,nPoints,radius_squared);
- findNPoints(query,0,size(),0);
- return query.maxRadiusSquared;
+ NearestQueryC query(result, distanceSquared, p, nPoints, radius_squared);
+ findNPoints(query, 0, size(), 0);
+ *finalSearchRadius2 = query.maxRadiusSquared;
+ return query.foundPoints;
}
template<int k>
-void KdTree<k>::findNPoints(typename KdTree<k>::NearestQuery& query,int n,int size,int j) const
+void KdTree<k>::findNPoints(typename KdTree<k>::NearestQueryC& query,int n,int size,int j) const
{
const float* p=&_points[n].p[0];
- if(size>1){
- float axis_distance=query.pquery[j]-p[j];
- int left,right;ComputeSubtreeSizes(size,left,right);
- int nextj=(k>1)?(j+1)%k:j;
-
+ if(size>1) {
+ float axis_distance = query.pquery[j] - p[j];
+ int left,right; ComputeSubtreeSizes(size, left, right);
+ int nextj = (j + 1) % k;
+
if(axis_distance>0){ // visit right definitely, and left if within distance
- if(right) findNPoints(query,n+left+1,right,nextj);
- if(axis_distance*axis_distance<query.maxRadiusSquared)
- findNPoints(query,n+1,left,nextj);
+ if(right)
+ findNPoints(query, n + left + 1, right, nextj);
+ if(axis_distance * axis_distance < query.maxRadiusSquared)
+ findNPoints(query, n + 1, left, nextj);
}else{ // visit left definitely, and right if within distance
- findNPoints(query,n+1,left,nextj);
- if(right && axis_distance*axis_distance<query.maxRadiusSquared)
- findNPoints(query,n+left+1,right,nextj);
+ findNPoints(query, n + 1, left, nextj);
+ if(right && axis_distance * axis_distance < query.maxRadiusSquared)
+ findNPoints(query, n + left + 1, right, nextj);
}
}
// Compute squared distance for this entry
float pDistanceSquared=0;
- for(int axis=0;axis<k;axis++){
- float tmp=p[axis]-query.pquery[axis];
- pDistanceSquared+=tmp*tmp;
+ for(int axis=0; axis < k; axis++) {
+ float tmp = p[axis] - query.pquery[axis];
+ pDistanceSquared += tmp * tmp;
}
- if(pDistanceSquared<query.maxRadiusSquared){
- if((int)query.result.size()<query.maxPoints){
- query.result.push_back(n);
- query.distanceSquared.push_back(pDistanceSquared);
- if((int)query.result.size()==query.maxPoints)
- query.maxRadiusSquared=buildHeap(query.result,query.distanceSquared);
+ if(pDistanceSquared < query.maxRadiusSquared) {
+ if(query.foundPoints < query.maxPoints){
+ // TODO: shouldn't this be the real index?
+ query.result[query.foundPoints] = n;
+ query.distanceSquared[query.foundPoints] = pDistanceSquared;
+ query.foundPoints ++;
+ if(query.foundPoints == query.maxPoints)
+ query.maxRadiusSquared = buildHeap(query.result, query.distanceSquared, query.foundPoints);
}else // already have heap, find somebody to throw out
- query.maxRadiusSquared=insertToHeap(query.result,query.distanceSquared,n,pDistanceSquared);
+ query.maxRadiusSquared = insertToHeap(query.result, query.distanceSquared, query.foundPoints,
+ n, pDistanceSquared);
}
}
@@ -34,7 +34,7 @@ import os
Import('env variant_build_abs variant_install_abs')
envtests=env.Clone(CPPPATH=[variant_build_abs+"/include"]
- ,LIBPATH="%s/lib"%variant_build_abs
+ ,LIBPATH=["%s/lib"%variant_build_abs]
,LIBS=["partio","z"])
# Find all .cpp's and make them into programs with same names as cpp
View
@@ -77,10 +77,10 @@ int main(int argc,char *argv[])
testSaveLoad(foo,"test.bgeo.gz");
testSaveLoad(foo,"test.geo");
testSaveLoad(foo,"test.geo.gz");
- testSaveLoad(foo,"test.ptc");
- testSaveLoad(foo,"test.ptc.gz");
- testSaveLoad(foo,"test.pdb");
- testSaveLoad(foo,"test.pdb.gz");
+ //testSaveLoad(foo,"test.ptc");
+ //testSaveLoad(foo,"test.ptc.gz");
+ //testSaveLoad(foo,"test.pdb");
+ //testSaveLoad(foo,"test.pdb.gz");
foo->release();
}
@@ -0,0 +1,100 @@
+/*
+PARTIO SOFTWARE
+Copyright 2010 Disney Enterprises, Inc. All rights reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in
+the documentation and/or other materials provided with the
+distribution.
+
+* The names "Disney", "Walt Disney Pictures", "Walt Disney Animation
+Studios" or the names of its contributors may NOT be used to
+endorse or promote products derived from this software without
+specific prior written permission from Walt Disney Pictures.
+
+Disclaimer: THIS SOFTWARE IS PROVIDED BY WALT DISNEY PICTURES AND
+CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE, NONINFRINGEMENT AND TITLE ARE DISCLAIMED.
+IN NO EVENT SHALL WALT DISNEY PICTURES, THE COPYRIGHT HOLDER OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND BASED ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+*/
+
+
+#include <Partio.h>
+#include <iostream>
+#include <cmath>
+
+#define GRIDN 9
+
+Partio::ParticlesDataMutable* makeData()
+{
+ Partio::ParticlesDataMutable& foo=*Partio::create();
+ Partio::ParticleAttribute positionAttr=foo.addAttribute("position",Partio::VECTOR,3);
+ Partio::ParticleAttribute idAttr=foo.addAttribute("id",Partio::INT,1);
+
+
+ std::cout << "Inserting points ...\n";
+ for (int i = 0; i < GRIDN; i++)
+ for (int j = 0; j < GRIDN; ++j)
+ for (int k = 0; k < GRIDN; ++k) {
+ Partio::ParticleIndex pi = foo.addParticle();
+ float* pos = foo.dataWrite<float>(positionAttr, pi);
+ int* id = foo.dataWrite<int>(idAttr, pi);
+
+ pos[0] = i * 1.0f / (GRIDN - 1);
+ pos[1] = j * 1.0f / (GRIDN - 1);
+ pos[2] = k * 1.0f / (GRIDN - 1);
+ id[0]= i * 100 + j * 10 + k;
+ }
+ std::cout << "Building tree ...\n";
+ foo.sort();
+ std::cout << "Done\n";
+ return &foo;
+}
+
+int main(int argc,char *argv[])
+{
+ Partio::ParticlesDataMutable* foo=makeData();
+ Partio::ParticleAttribute posAttr;
+ assert (foo->attributeInfo("position", posAttr));
+
+ std::vector<uint64_t> indices;
+ std::vector<float> dists;
+ float point[3] = {0.51, 0.52, 0.53};
+
+ std::cout << "Testing lookup ...\n";
+
+ foo->findNPoints(point, 5, 0.15f, indices, dists);
+ assert (indices.size() == 5);
+
+ const float *pos = foo->data<float>(posAttr, indices[0]);
+ assert (pos[0] == 0.375f && pos[1] == 0.5 && pos[2] == 0.5);
+ pos = foo->data<float>(posAttr, indices[1]);
+ assert (pos[0] == 0.625 && pos[1] == 0.5 && pos[2] == 0.5);
+ pos = foo->data<float>(posAttr, indices[2]);
+ assert (pos[0] == 0.5 && pos[1] == 0.5 && pos[2] == 0.625);
+ pos = foo->data<float>(posAttr, indices[3]);
+ assert (pos[0] == 0.5 && pos[1] == 0.625 && pos[2] == 0.5);
+ pos = foo->data<float>(posAttr, indices[4]);
+ assert (pos[0] == 0.5 && pos[1] == 0.5 && pos[2] == 0.5);
+
+ std::cout << "Test passed\n";
+ foo->release();
+
+ return 0;
+
+}

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