/* Begin Funtion Definitions */
int main (int argc, const char * argv[]) {
cl_int error;
GPUInit(&context, &queue, &is_nvidia, &program, "remap_kern.cl");
cHash_kernel = clCreateKernel(program, "cellHash_kern", &error);
remap1_kernel = clCreateKernel(program, "remap1_kern", &error);
printf(" REMAP\n\n");
if (is_nvidia)
printf("size, Brute Force, CPU kD Tree, CPU Hash1, CPU Hash2, NVIDIA Hash1\n");
else
printf("size, Brute Force, CPU kD Tree, CPU Hash1, CPU Hash2, ATI Hash1\n");
for( int levmx = 1; levmx < 10; levmx++) {
printf("\nlevmx is %d\n\n",levmx);
for( int i = 1024; i < 50000000; i *= 2) {
printf("%d, ", i);
remaps(i, i, 1.0, (double)levmx, 0.0);
printf("\n");
}
}
}
inline void merge_segments_with_function( const volume_ptr<ID>& seg_ptr,
const region_graph_ptr<ID,F> rg_ptr,
std::vector<std::size_t>& counts,
const FN& func,
const M& lowt )
{
zi::disjoint_sets<ID> sets(counts.size());
region_graph<ID,F>& rg = *rg_ptr;
for ( auto& it: rg )
{
std::size_t size = func(std::get<0>(it));
if ( size == 0 )
{
break;
}
ID s1 = sets.find_set(std::get<1>(it));
ID s2 = sets.find_set(std::get<2>(it));
if ( s1 != s2 && s1 && s2 )
{
if ( (counts[s1] < size) || (counts[s2] < size) )
{
counts[s1] += counts[s2];
counts[s2] = 0;
ID s = sets.join(s1,s2);
std::swap(counts[s], counts[s1]);
}
}
}
std::cout << "Done with merging" << std::endl;
std::vector<ID> remaps(counts.size());
ID next_id = 1;
std::size_t low = static_cast<std::size_t>(lowt);
for ( ID id = 0; id < counts.size(); ++id )
{
ID s = sets.find_set(id);
if ( s && (remaps[s] == 0) && (counts[s] >= low) )
{
remaps[s] = next_id;
counts[next_id] = counts[s];
++next_id;
}
}
counts.resize(next_id);
std::ptrdiff_t xdim = seg_ptr->shape()[0];
std::ptrdiff_t ydim = seg_ptr->shape()[1];
std::ptrdiff_t zdim = seg_ptr->shape()[2];
std::ptrdiff_t total = xdim * ydim * zdim;
ID* seg_raw = seg_ptr->data();
for ( std::ptrdiff_t idx = 0; idx < total; ++idx )
{
seg_raw[idx] = remaps[sets.find_set(seg_raw[idx])];
}
std::cout << "Done with remapping, total: " << (next_id-1) << std::endl;
region_graph<ID,F> new_rg;
for ( auto& it: rg )
{
ID s1 = remaps[sets.find_set(std::get<1>(it))];
ID s2 = remaps[sets.find_set(std::get<2>(it))];
if ( s1 != s2 && s1 && s2 )
{
auto mm = std::minmax(s1,s2);
new_rg.emplace_back(std::get<0>(it), mm.first, mm.second);
}
}
rg.swap(new_rg);
std::cout << "Done with updating the region graph, size: "
<< rg.size() << std::endl;
}
inline cube_p<int>
get_segmentation( std::vector<cube_p<real>> affs,
real threshold = 0.5 )
{
// only takes 3D affinity graph
ZI_ASSERT(affs.size==3);
vec3i s = size(*affs[0]);
size_t n = s[0]*s[1]*s[2];
cube<real> const & xaff = *affs[0];
cube<real> const & yaff = *affs[1];
cube<real> const & zaff = *affs[2];
zi::disjoint_sets<uint32_t> sets(n+1);
std::vector<uint32_t> sizes(n+1);
cube_p<int> ids_ptr = get_cube<int>(s);
cube<int> & ids = *ids_ptr;
for ( size_t i = 0; i < n; ++i )
{
ids.data()[i] = i+1;
sizes[i+1] = 1;
}
typedef std::pair<uint32_t,uint32_t> edge_type;
std::vector<edge_type> edges;
// thresholded affinity graph
for ( size_t z = 0; z < s[0]; ++z )
{
for ( size_t y = 0; y < s[1]; ++y )
{
for ( size_t x = 0; x < s[2]; ++x )
{
long id1 = ids[z][y][x];
if ( x > 0 )
{
// skip disconnected (black) edges
// only count connected (white) edges
if ( xaff[z][y][x] > threshold )
{
long id2 = ids[z][y][x-1];
edges.push_back(edge_type(id1, id2));
}
}
if ( y > 0 )
{
// skip disconnected (black) edges
// only count connected (white) edges
if ( yaff[z][y][x] > threshold )
{
long id2 = ids[z][y-1][x];
edges.push_back(edge_type(id1, id2));
}
}
if ( z > 0 )
{
// skip disconnected (black) edges
// only count connected (white) edges
if ( zaff[z][y][x] > threshold )
{
long id2 = ids[z-1][y][x];
edges.push_back(edge_type(id1, id2));
}
}
}
}
}
// connected components of the thresholded affinity graph
// computed the size of each connected component
for ( auto& e: edges )
{
uint32_t set1 = sets.find_set(e.first);
uint32_t set2 = sets.find_set(e.second);
if ( set1 != set2 )
{
uint32_t new_set = sets.join(set1, set2);
sizes[set1] += sizes[set2];
sizes[set2] = 0;
std::swap(sizes[new_set], sizes[set1]);
}
}
std::vector<uint32_t> remaps(n+1);
uint32_t next_id = 1;
// assign a unique segment ID to each of
// the pixel in a connected component
for ( size_t i = 0; i < n; ++i )
{
uint32_t id = sets.find_set(ids.data()[i]);
if ( sizes[id] > 1 )
{
if ( remaps[id] == 0 )
{
remaps[id] = next_id;
ids.data()[i] = next_id;
++next_id;
}
else
{
ids.data()[i] = remaps[id];
}
}
else
{
remaps[id] = 0;
ids.data()[i] = 0;
}
}
return ids_ptr;
}
inline std::vector<double>
merge_segments_with_function_err( const volume_ptr<ID>& seg_ptr,
const volume_ptr<ID>& gt_ptr,
const region_graph_ptr<ID,F> rg_ptr,
std::vector<std::size_t>& counts,
const FN& func,
const M& lowt )
{
std::vector<double> ret;
std::ptrdiff_t xdim = seg_ptr->shape()[0];
std::ptrdiff_t ydim = seg_ptr->shape()[1];
std::ptrdiff_t zdim = seg_ptr->shape()[2];
volume<ID>& seg = *seg_ptr;
volume<ID>& gt = *gt_ptr;
zi::disjoint_sets<ID> sets(counts.size());
std::size_t tot = 0;
std::vector<std::size_t> s_i(counts.size());
std::map<ID,std::size_t> t_j;
std::vector<std::map<ID,std::size_t>> p_ij(counts.size());
for ( std::ptrdiff_t z = 0; z < zdim; ++z )
for ( std::ptrdiff_t y = 0; y < ydim; ++y )
for ( std::ptrdiff_t x = 0; x < xdim; ++x )
{
uint32_t sgv = seg[x][y][z];
uint32_t gtv = gt[x][y][z];
if ( gtv )
{
tot += 1;
++p_ij[sgv][gtv];
++s_i[sgv];
++t_j[gtv];
}
}
double sum_p_ij = 0;
for ( auto& a: p_ij )
{
for ( auto& b: a )
{
sum_p_ij += (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
}
}
double sum_t_k = 0;
for ( auto& a: t_j )
{
sum_t_k += (static_cast<double>(a.second) / tot) *
(static_cast<double>(a.second) / tot);
}
double sum_s_k = 0;
for ( auto& a: s_i )
{
sum_s_k += (static_cast<double>(a) / tot) *
(static_cast<double>(a) / tot);
}
ret.push_back(sum_p_ij/sum_t_k);
ret.push_back(sum_p_ij/sum_s_k);
region_graph<ID,F>& rg = *rg_ptr;
int mod = 0;
F minf = 0;
for ( auto& it: rg )
{
std::size_t size = func(std::get<0>(it));
if ( size == 0 )
{
minf = std::get<0>(it);
break;
}
ID s1 = sets.find_set(std::get<1>(it));
ID s2 = sets.find_set(std::get<2>(it));
if ( s1 != s2 && s1 && s2 )
{
if ( (counts[s1] < size) || (counts[s2] < size) )
{
counts[s1] += counts[s2];
counts[s2] = 0;
sum_s_k -= (static_cast<double>(s_i[s1])/tot) *
(static_cast<double>(s_i[s1])/tot);
sum_s_k -= (static_cast<double>(s_i[s2])/tot) *
(static_cast<double>(s_i[s2])/tot);
s_i[s1] += s_i[s2];
s_i[s2] = 0;
sum_s_k += (static_cast<double>(s_i[s1])/tot) *
(static_cast<double>(s_i[s1])/tot);
for ( auto& b: p_ij[s1] )
{
sum_p_ij -= (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
}
for ( auto& b: p_ij[s2] )
{
sum_p_ij -= (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
p_ij[s1][b.first] += b.second;
}
for ( auto& b: p_ij[s1] )
{
sum_p_ij += (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
}
p_ij[s2].clear();
if ( (++mod) % 100 == 0 )
{
//std::cout << "Now Error: " << (sum_p_ij/sum_t_k) << " "
// << (sum_p_ij/sum_s_k) << "\n";
ret.push_back(sum_p_ij/sum_t_k);
ret.push_back(sum_p_ij/sum_s_k);
}
ID s = sets.join(s1,s2);
std::swap(counts[s], counts[s1]);
std::swap(s_i[s], s_i[s1]);
std::swap(p_ij[s], p_ij[s1]);
}
}
}
std::cout << "Done with merging" << std::endl;
for ( auto& it: rg )
{
break;
if ( minf > std::get<0>(it) )
{
break;
}
ID s1 = sets.find_set(std::get<1>(it));
ID s2 = sets.find_set(std::get<2>(it));
if ( s1 != s2 && s1 && s2 )
{
//if ( (counts[s1] < 100) || (counts[s2] < 100) )
{
counts[s1] += counts[s2];
counts[s2] = 0;
sum_s_k -= (static_cast<double>(s_i[s1])/tot) *
(static_cast<double>(s_i[s1])/tot);
sum_s_k -= (static_cast<double>(s_i[s2])/tot) *
(static_cast<double>(s_i[s2])/tot);
s_i[s1] += s_i[s2];
s_i[s2] = 0;
sum_s_k += (static_cast<double>(s_i[s1])/tot) *
(static_cast<double>(s_i[s1])/tot);
for ( auto& b: p_ij[s1] )
{
sum_p_ij -= (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
}
for ( auto& b: p_ij[s2] )
{
sum_p_ij -= (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
p_ij[s1][b.first] += b.second;
}
for ( auto& b: p_ij[s1] )
{
sum_p_ij += (static_cast<double>(b.second) / tot) *
(static_cast<double>(b.second) / tot);
}
p_ij[s2].clear();
//if ( (++mod) % 100 == 0 )
std::cout << "Now Error: " << (sum_p_ij/sum_t_k) << " "
<< (sum_p_ij/sum_s_k) << "\n";
ret.push_back(sum_p_ij/sum_t_k);
ret.push_back(sum_p_ij/sum_s_k);
ID s = sets.join(s1,s2);
std::swap(counts[s], counts[s1]);
std::swap(s_i[s], s_i[s1]);
std::swap(p_ij[s], p_ij[s1]);
}
}
}
std::cout << "Done with merging" << std::endl;
std::vector<ID> remaps(counts.size());
ID next_id = 1;
std::size_t low = static_cast<std::size_t>(lowt);
for ( ID id = 0; id < counts.size(); ++id )
{
ID s = sets.find_set(id);
if ( s && (remaps[s] == 0) && (counts[s] >= low) )
{
remaps[s] = next_id;
counts[next_id] = counts[s];
++next_id;
}
}
counts.resize(next_id);
std::ptrdiff_t total = xdim * ydim * zdim;
ID* seg_raw = seg_ptr->data();
for ( std::ptrdiff_t idx = 0; idx < total; ++idx )
{
seg_raw[idx] = remaps[sets.find_set(seg_raw[idx])];
}
std::cout << "Done with remapping, total: " << (next_id-1) << std::endl;
region_graph<ID,F> new_rg;
std::vector<std::set<ID>> in_rg;
for ( auto& it: rg )
{
ID s1 = remaps[sets.find_set(std::get<1>(it))];
ID s2 = remaps[sets.find_set(std::get<2>(it))];
if ( s1 != s2 && s1 && s2 )
{
auto mm = std::minmax(s1,s2);
if ( in_rg[mm.first].count(mm.second) == 0 )
{
new_rg.emplace_back(std::get<0>(it), mm.first, mm.second);
in_rg[mm.first].insert(mm.second);
}
}
}
rg.swap(new_rg);
std::cout << "Done with updating the region graph, size: "
<< rg.size() << std::endl;
return ret;
}
inline void merge_segments( const volume_ptr<ID>& seg_ptr,
const region_graph_ptr<ID,F> rg_ptr,
std::vector<std::size_t>& counts,
const L& tholds,
const M& lowt )
{
zi::disjoint_sets<ID> sets(counts.size());
typename region_graph<ID,F>::iterator rit = rg_ptr->begin();
region_graph<ID,F>& rg = *rg_ptr;
for ( auto& it: tholds )
{
std::size_t size = static_cast<std::size_t>(it.first);
F thld = static_cast<F>(it.second);
while ( (rit != rg.end()) && ( std::get<0>(*rit) > thld) )
{
ID s1 = sets.find_set(std::get<1>(*rit));
ID s2 = sets.find_set(std::get<2>(*rit));
if ( s1 != s2 && s1 && s2 )
{
if ( (counts[s1] < size) || (counts[s2] < size) )
{
counts[s1] += counts[s2];
counts[s2] = 0;
ID s = sets.join(s1,s2);
std::swap(counts[s], counts[s1]);
}
}
++rit;
}
}
std::cout << "Done with merging" << std::endl;
std::vector<ID> remaps(counts.size());
ID next_id = 1;
std::size_t low = static_cast<std::size_t>(lowt);
for ( ID id = 0; id < counts.size(); ++id )
{
ID s = sets.find_set(id);
if ( s && (remaps[s] == 0) && (counts[s] >= low) )
{
remaps[s] = next_id;
counts[next_id] = counts[s];
++next_id;
}
}
counts.resize(next_id);
std::ptrdiff_t xdim = seg_ptr->shape()[0];
std::ptrdiff_t ydim = seg_ptr->shape()[1];
std::ptrdiff_t zdim = seg_ptr->shape()[2];
std::ptrdiff_t total = xdim * ydim * zdim;
ID* seg_raw = seg_ptr->data();
for ( std::ptrdiff_t idx = 0; idx < total; ++idx )
{
seg_raw[idx] = remaps[sets.find_set(seg_raw[idx])];
}
std::cout << "Done with remapping, total: " << (next_id-1) << std::endl;
region_graph<ID,F> new_rg;
std::vector<std::set<ID>> in_rg;
for ( auto& it: rg )
{
ID s1 = remaps[sets.find_set(std::get<1>(it))];
ID s2 = remaps[sets.find_set(std::get<2>(it))];
if ( s1 != s2 && s1 && s2 )
{
auto mm = std::minmax(s1,s2);
if ( in_rg[mm.first].count(mm.second) == 0 )
{
new_rg.emplace_back(std::get<0>(it), mm.first, mm.second);
in_rg[mm.first].insert(mm.second);
}
}
}
rg.swap(new_rg);
std::cout << "Done with updating the region graph, size: "
<< rg.size() << std::endl;
}
inline void yet_another_watershed( const volume_ptr<ID>& seg_ptr,
const region_graph_ptr<ID,F> rg_ptr,
std::vector<std::size_t>& counts,
const L& lowl)
{
F low = static_cast<F>(lowl);
std::vector<std::size_t> new_counts({0});
std::vector<ID> remaps(counts.size());
zi::disjoint_sets<ID> sets(counts.size());
std::vector<F> maxs(counts.size());
region_graph<ID,F>& rg = *rg_ptr;
ID next_id = 1;
ID merged = 0;
for ( auto& it: rg )
{
if ( std::get<0>(it) <= low )
{
break;
}
ID s1 = std::get<1>(it);
ID s2 = std::get<2>(it);
F f = std::get<0>(it);
if ( s1 && s2 )
{
if ( (remaps[s1] == 0) || (remaps[s2] == 0) )
{
if ( remaps[s1] == 0 )
{
std::swap(s1,s2);
}
if ( remaps[s1] == 0 )
{
maxs[next_id] = f;
remaps[s1] = remaps[s2] = next_id;
new_counts.push_back(counts[s1]+counts[s2]);
++next_id;
}
else
{
ID actual = sets.find_set(remaps[s1]);
remaps[s2] = remaps[s1];
new_counts[actual] += counts[s2];
}
}
else
{
ID a1 = sets.find_set(remaps[s1]);
ID a2 = sets.find_set(remaps[s2]);
if ( 0 && a1 != a2 && ((maxs[a1]==f)||(maxs[a2]==f)) )
{
++merged;
new_counts[a1] += new_counts[a2];
new_counts[a2] = 0;
maxs[a1] = std::max(maxs[a1],maxs[a2]);
maxs[a2] = 0;
ID a = sets.join(a1,a2);
std::swap(new_counts[a], new_counts[a1]);
std::swap(maxs[a], maxs[a1]);
}
}
}
}
next_id -= merged;
std::vector<ID> remaps2(counts.size());
next_id = 1;
for ( ID id = 0; id < counts.size(); ++id )
{
ID s = sets.find_set(remaps[id]);
if ( s && (remaps2[s]==0) )
{
remaps2[s] = next_id;
new_counts[next_id] = new_counts[s];
++next_id;
}
}
new_counts.resize(next_id);
std::ptrdiff_t xdim = seg_ptr->shape()[0];
std::ptrdiff_t ydim = seg_ptr->shape()[1];
std::ptrdiff_t zdim = seg_ptr->shape()[2];
std::ptrdiff_t total = xdim * ydim * zdim;
ID* seg_raw = seg_ptr->data();
for ( std::ptrdiff_t idx = 0; idx < total; ++idx )
{
seg_raw[idx] = remaps2[remaps[seg_raw[idx]]];
}
region_graph<ID,F> new_rg;
for ( auto& it: rg )
{
ID s1 = remaps2[remaps[std::get<1>(it)]];
ID s2 = remaps2[remaps[std::get<2>(it)]];
if ( s1 != s2 && s1 && s2 )
{
auto mm = std::minmax(s1,s2);
new_rg.emplace_back(std::get<0>(it), mm.first, mm.second);
}
}
rg.swap(new_rg);
counts.swap(new_counts);
std::cout << "New count: " << counts.size() << std::endl;
std::cout << "Done with updating the region graph, size: "
<< rg.size() << std::endl;
}
