t_jit_err o_jit_pcl_supervoxel_matrix_calc(t_o_jit_pcl_supervoxel *x, t_symbol *s, long argc, t_atom *argv)
{
void *matrix = NULL;
t_jit_err err = JIT_ERR_NONE;
long in_savelock;
t_jit_matrix_info in_minfo;
char *in_bp;
long i, j;
long dimcount;
long planecount;
long dim[JIT_MATRIX_MAX_DIMCOUNT];
char *fip;
if( argc && argv )
{
matrix = jit_object_findregistered(jit_atom_getsym(argv));
}
else
return JIT_ERR_INVALID_INPUT;
if( matrix == NULL || !jit_object_method(matrix, _jit_sym_class_jit_matrix))
return JIT_ERR_INVALID_PTR;
in_savelock = (long)jit_object_method(matrix, _jit_sym_lock, 1);
jit_object_method(matrix, _jit_sym_getinfo, &in_minfo);
jit_object_method(matrix, _jit_sym_getdata, &in_bp);
if (!in_bp)
return JIT_ERR_INVALID_INPUT;
//get dimensions/planecount
dimcount = in_minfo.dimcount;
planecount = in_minfo.planecount;
if( planecount < 6 )
{
object_error((t_object *)x, "requires a 6 plane matrix (xyzrgb)");
err = JIT_ERR_INVALID_INPUT;
goto out;
}
if( in_minfo.type != _jit_sym_float32)
{
object_error((t_object *)x, "received: %s jit.pcl uses only float32 matrixes", in_minfo.type->s_name );
err = JIT_ERR_INVALID_INPUT;
goto out;
}
//if dimsize is 1, treat as infinite domain across that dimension.
//otherwise truncate if less than the output dimsize
for (i=0; i<dimcount; i++) {
dim[i] = in_minfo.dim[i];
if ( in_minfo.dim[i]<dim[i] && in_minfo.dim[i]>1) {
dim[i] = in_minfo.dim[i];
}
}
{
//convert to point cloud
pcl::PointCloud<pcl::PointXYZRGBA>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZRGBA>);
cloud->width = (uint32_t)dim[0];
cloud->height = (uint32_t)dim[1];
cloud->points.resize (cloud->width * cloud->height);
size_t count = 0;
float _x, _y, _z;
uint8_t _r, _g, _b;
const float bad_point = std::numeric_limits<float>::quiet_NaN();
for (j = 0; j < dim[0]; ++j)
{
fip = in_bp + j * in_minfo.dimstride[0];
for( i = 0; i < dim[1]; ++i)
{
if(count < cloud->points.size())
{
_x = ((float *)fip)[0];
_y = ((float *)fip)[1];
_z = ((float *)fip)[2];
_r = (uint8_t)(((float *)fip)[3] * 255.0);
_g = (uint8_t)(((float *)fip)[4] * 255.0);
_b = (uint8_t)(((float *)fip)[5] * 255.0);
if( !_x && !_y && !_z && !_r && !_g && !_b )
{
cloud->points[count].x = bad_point;
cloud->points[count].y = bad_point;
cloud->points[count].z = bad_point;
cloud->points[count].r = bad_point;
cloud->points[count].g = bad_point;
cloud->points[count].b = bad_point;
cloud->points[count].a = bad_point;
}
else
{
cloud->points[count].x = _x;
cloud->points[count].y = _y;
cloud->points[count].z = _z;
cloud->points[count].r = _r;
cloud->points[count].g = _g;
cloud->points[count].b = _b;
cloud->points[count].a = 255;
}
}
count++;
fip += in_minfo.dimstride[1];
}
}
{
typedef pcl::PointXYZRGBA PointT;
pcl::SupervoxelClustering<PointT> super (x->voxel_resolution, x->seed_resolution);
float concavity_tolerance_threshold = 10;
float smoothness_threshold = 0.1;
uint32_t min_segment_size = 0;
bool use_extended_convexity = false;
bool use_sanity_criterion = false;
if (x->disable_transform)
super.setUseSingleCameraTransform (false);
super.setInputCloud ( cloud );
super.setColorImportance (x->color_importance);
super.setSpatialImportance (x->spatial_importance);
super.setNormalImportance (x->normal_importance);
if( cloud->height > 1)
{
super.setUseSingleCameraTransform (false);
}
std::map <uint32_t, pcl::Supervoxel<PointT>::Ptr > supervoxel_clusters;
super.extract (supervoxel_clusters);
pcl::PointCloud<PointT>::Ptr voxel_centroid_cloud = super.getVoxelCentroidCloud ();
pcl::PointCloud<pcl::PointXYZL>::Ptr labeled_voxel_cloud = super.getLabeledVoxelCloud ();
pcl::PointCloud<pcl::PointNormal>::Ptr sv_normal_cloud = super.makeSupervoxelNormalCloud (supervoxel_clusters);
std::multimap<uint32_t, uint32_t> supervoxel_adjacency;
super.getSupervoxelAdjacency (supervoxel_adjacency);
// LCCP
pcl::LCCPSegmentation<PointT> lccp;
lccp.setConcavityToleranceThreshold (concavity_tolerance_threshold);
lccp.setSanityCheck (use_sanity_criterion);
lccp.setSmoothnessCheck (true, x->voxel_resolution, x->seed_resolution, smoothness_threshold);
uint k_factor = 0;
if (use_extended_convexity)
k_factor = 1;
lccp.setKFactor (k_factor);
lccp.segment (supervoxel_clusters, supervoxel_adjacency);
if (min_segment_size > 0)
{
post ("Merging small segments\n");
lccp.mergeSmallSegments (min_segment_size);
}
pcl::PointCloud<pcl::PointXYZL>::Ptr sv_labeled_cloud = super.getLabeledCloud ();
pcl::PointCloud<pcl::PointXYZL>::Ptr lccp_labeled_cloud = sv_labeled_cloud->makeShared ();
lccp.relabelCloud (*lccp_labeled_cloud);
/*
typedef pcl::LCCPSegmentation<PointT>::SupervoxelAdjacencyList SuperVoxelAdjacencyList;
typedef pcl::LCCPSegmentation<PointT>::VertexIterator VertexIterator;
typedef pcl::LCCPSegmentation<PointT>::AdjacencyIterator AdjacencyIterator;
typedef pcl::LCCPSegmentation<PointT>::EdgeID EdgeID;
SuperVoxelAdjacencyList sv_adjacency_list;
lccp.getSVAdjacencyList (sv_adjacency_list);
*/
std::map<uint32_t, std::set<uint32_t> > segment_supervoxel_map;
lccp.getSegmentSupervoxelMap( segment_supervoxel_map );
std::map<uint32_t, std::set<uint32_t> >::iterator map_iter;
t_osc_bndl_u *bndl = osc_bundle_u_alloc();
char buf[2048];
ssize_t count = 0;
for( map_iter = segment_supervoxel_map.begin(); map_iter != segment_supervoxel_map.end(); ++map_iter)
{
uint32_t group_label = map_iter->first;
// ssize_t ngroup_voxel_pts = map_iter->second.size();
std::set<uint32_t>::iterator pt_id_iter;
for( pt_id_iter = map_iter->second.begin(); pt_id_iter != map_iter->second.end(); ++pt_id_iter)
{
sprintf(buf, "/supervoxel/pt/%ld", ++count);
t_osc_msg_u *supervoxel_group = osc_message_u_allocWithAddress(buf);
t_osc_bndl_u *subbndl = osc_bundle_u_alloc();
t_osc_msg_u *pt_num = osc_message_u_allocWithAddress((char *)"/pt_id");
osc_message_u_appendInt64(pt_num, count);
osc_bundle_u_addMsg(subbndl, pt_num);
t_osc_msg_u *segment_num = osc_message_u_allocWithAddress((char *)"/group_id");
osc_message_u_appendInt32(segment_num, group_label);
osc_bundle_u_addMsg(subbndl, segment_num);
pcl::Supervoxel<pcl::PointXYZRGBA>::Ptr supervoxel = supervoxel_clusters.at( *pt_id_iter );
t_osc_msg_u *centroid = osc_message_u_allocWithAddress((char *)"/centroid/xyz");
osc_message_u_appendFloat(centroid, supervoxel->centroid_.x);
osc_message_u_appendFloat(centroid, supervoxel->centroid_.y);
osc_message_u_appendFloat(centroid, supervoxel->centroid_.z);
osc_bundle_u_addMsg(subbndl, centroid);
t_osc_msg_u *centroid_color = osc_message_u_allocWithAddress((char *)"/centroid/rgb");
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.r);
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.g);
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.b);
osc_bundle_u_addMsg(subbndl, centroid_color);
pcl::PointCloud<pcl::PointXYZRGBA> adjacent_supervoxel_centers;
t_osc_msg_u *adjx = osc_message_u_allocWithAddress((char *)"/adjacent/x");
t_osc_msg_u *adjy = osc_message_u_allocWithAddress((char *)"/adjacent/y");
t_osc_msg_u *adjz = osc_message_u_allocWithAddress((char *)"/adjacent/z");
std::multimap<uint32_t,uint32_t>::iterator adjacent_itr = supervoxel_adjacency.equal_range(*pt_id_iter).first;
for ( ; adjacent_itr!=supervoxel_adjacency.equal_range(*pt_id_iter).second; ++adjacent_itr)
{
pcl::Supervoxel<pcl::PointXYZRGBA>::Ptr neighbor_supervoxel = supervoxel_clusters.at(adjacent_itr->second);
osc_message_u_appendFloat(adjx, neighbor_supervoxel->centroid_.x);
osc_message_u_appendFloat(adjy, neighbor_supervoxel->centroid_.y);
osc_message_u_appendFloat(adjz, neighbor_supervoxel->centroid_.z);
// line from supervoxel->centroid_ to each adjacent_supervoxel_centers
}
osc_bundle_u_addMsg(subbndl, adjx);
osc_bundle_u_addMsg(subbndl, adjy);
osc_bundle_u_addMsg(subbndl, adjz);
osc_message_u_appendBndl_u(supervoxel_group, subbndl);
osc_bundle_u_addMsg(bndl, supervoxel_group);
}
// post("%d %d", group_label, ngroup_voxel_pts);
}
// for( int i = 0; i < lccp_labeled_cloud->points.size(); i++ )
// post("%d %d", lccp_labeled_cloud->points.size(), lccp_labeled_cloud->points[i].label);
/*
std::set<EdgeID> edge_drawn;
//The vertices in the supervoxel adjacency list are the supervoxel centroids
//This iterates through them, finding the edges
std::pair<VertexIterator, VertexIterator> vertex_iterator_range;
vertex_iterator_range = boost::vertices (sv_adjacency_list);
t_osc_bndl_u *bndl = osc_bundle_u_alloc();
char buf[2048];
for (VertexIterator itr = vertex_iterator_range.first; itr != vertex_iterator_range.second; ++itr)
{
const uint32_t sv_label = sv_adjacency_list[*itr];
pcl::Supervoxel<PointT>::Ptr supervoxel = supervoxel_clusters.at (sv_label);
pcl::PointXYZRGBA vert_curr = supervoxel->centroid_;
// pcl::PointXYZL lccp_pt = lccp_labeled_cloud->at ( sv_label );
const uint32_t group_label = lccp_labeled_cloud->at ( sv_label ).label;
// const uint32_t group_label = lccp_labeled_cloud->points[ sv_label ].label;
sprintf(buf, "/supervoxel/%d/%d", group_label, sv_label);
post("%s", buf);
t_osc_msg_u *supervoxel_group = osc_message_u_allocWithAddress(buf);
t_osc_bndl_u *subbndl = osc_bundle_u_alloc();
t_osc_msg_u *centroid = osc_message_u_allocWithAddress((char *)"/centroid/xyz");
osc_message_u_appendFloat(centroid, vert_curr.x);
osc_message_u_appendFloat(centroid, vert_curr.y);
osc_message_u_appendFloat(centroid, vert_curr.z);
osc_bundle_u_addMsg(subbndl, centroid);
t_osc_msg_u *centroid_color = osc_message_u_allocWithAddress((char *)"/centroid/rgb");
osc_message_u_appendFloat(centroid_color, vert_curr.r);
osc_message_u_appendFloat(centroid_color, vert_curr.g);
osc_message_u_appendFloat(centroid_color, vert_curr.b);
osc_bundle_u_addMsg(subbndl, centroid_color);
t_osc_msg_u *adjx = osc_message_u_allocWithAddress((char *)"/adjacent/x");
t_osc_msg_u *adjy = osc_message_u_allocWithAddress((char *)"/adjacent/y");
t_osc_msg_u *adjz = osc_message_u_allocWithAddress((char *)"/adjacent/z");
t_osc_msg_u *is_conv = osc_message_u_allocWithAddress((char *)"/vertex/convex");
std::pair<AdjacencyIterator, AdjacencyIterator> neighbors = boost::adjacent_vertices (*itr, sv_adjacency_list);
for (AdjacencyIterator itr_neighbor = neighbors.first; itr_neighbor != neighbors.second; ++itr_neighbor)
{
EdgeID connecting_edge = boost::edge (*itr, *itr_neighbor, sv_adjacency_list).first; //Get the edge
osc_message_u_appendBool(is_conv, sv_adjacency_list[connecting_edge].is_convex);
const uint32_t sv_neighbor_label = sv_adjacency_list[*itr_neighbor];
pcl::Supervoxel<PointT>::Ptr supervoxel_neigh = supervoxel_clusters.at (sv_neighbor_label);
pcl::PointXYZRGBA vert_neigh = supervoxel_neigh->centroid_;
osc_message_u_appendFloat(adjx, vert_neigh.x);
osc_message_u_appendFloat(adjy, vert_neigh.y);
osc_message_u_appendFloat(adjz, vert_neigh.z);
}
osc_bundle_u_addMsg(subbndl, adjx);
osc_bundle_u_addMsg(subbndl, adjy);
osc_bundle_u_addMsg(subbndl, adjz);
osc_bundle_u_addMsg(subbndl, is_conv);
osc_message_u_appendBndl_u(supervoxel_group, subbndl);
osc_bundle_u_addMsg(bndl, supervoxel_group);
}
post("--------------");
*/
/*
//To make a graph of the supervoxel adjacency, we need to iterate through the supervoxel adjacency multimap
std::multimap<uint32_t,uint32_t>::iterator label_itr = supervoxel_adjacency.begin ();
for ( ; label_itr != supervoxel_adjacency.end (); )
{
//First get the label
uint32_t supervoxel_label = label_itr->first;
pcl::Supervoxel<pcl::PointXYZRGBA>::Ptr supervoxel = supervoxel_clusters.at( supervoxel_label );
sprintf(buf, "/supervoxel/%d", supervoxel_label);
t_osc_msg_u *supervoxel_group = osc_message_u_allocWithAddress(buf);
t_osc_bndl_u *subbndl = osc_bundle_u_alloc();
t_osc_msg_u *centroid = osc_message_u_allocWithAddress((char *)"/centroid/xyz");
osc_message_u_appendFloat(centroid, supervoxel->centroid_.x);
osc_message_u_appendFloat(centroid, supervoxel->centroid_.y);
osc_message_u_appendFloat(centroid, supervoxel->centroid_.z);
osc_bundle_u_addMsg(subbndl, centroid);
t_osc_msg_u *centroid_color = osc_message_u_allocWithAddress((char *)"/centroid/rgb");
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.r);
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.g);
osc_message_u_appendFloat(centroid_color, supervoxel->centroid_.b);
osc_bundle_u_addMsg(subbndl, centroid_color);
pcl::PointCloud<pcl::PointXYZRGBA>::Ptr cloud_hull_ (new pcl::PointCloud<pcl::PointXYZRGBA>);
std::vector<pcl::Vertices> vertices_;
//get convex hull of supervoxel region:
pcl::ConvexHull<pcl::PointXYZRGBA> hr;
hr.setDimension(3);
hr.setInputCloud(supervoxel->voxels_);
// cloud_hull_.reset (new Cloud); << save on reallocating memory later?
hr.reconstruct (*cloud_hull_, vertices_);
t_osc_msg_u *cvx_x = osc_message_u_allocWithAddress((char *)"/convexhull/pts/x");
t_osc_msg_u *cvx_y = osc_message_u_allocWithAddress((char *)"/convexhull/pts/y");
t_osc_msg_u *cvx_z = osc_message_u_allocWithAddress((char *)"/convexhull/pts/z");
for( long j = 0; j < cloud_hull_->points.size(); ++j)
{
osc_message_u_appendFloat(cvx_x, cloud_hull_->points[j].x);
osc_message_u_appendFloat(cvx_y, cloud_hull_->points[j].y);
osc_message_u_appendFloat(cvx_z, cloud_hull_->points[j].z);
}
osc_bundle_u_addMsg(subbndl, cvx_x);
osc_bundle_u_addMsg(subbndl, cvx_y);
osc_bundle_u_addMsg(subbndl, cvx_z);
t_osc_msg_u *vert0 = osc_message_u_allocWithAddress((char *)"/convexhull/vertex/idx/0");
t_osc_msg_u *vert1 = osc_message_u_allocWithAddress((char *)"/convexhull/vertex/idx/1");
t_osc_msg_u *vert2 = osc_message_u_allocWithAddress((char *)"/convexhull/vertex/idx/2");
std::vector<pcl::Vertices>::iterator iter_vertices;
for( iter_vertices = vertices_.begin(); iter_vertices != vertices_.end(); ++iter_vertices)
{
osc_message_u_appendInt32(vert0, (*iter_vertices).vertices[0]);
osc_message_u_appendInt32(vert1, (*iter_vertices).vertices[1]);
osc_message_u_appendInt32(vert2, (*iter_vertices).vertices[3]);
}
osc_bundle_u_addMsg(subbndl, vert0);
osc_bundle_u_addMsg(subbndl, vert1);
osc_bundle_u_addMsg(subbndl, vert2);
//Now we need to iterate through the adjacent supervoxels and make a point cloud of them
// pcl::PointCloud<pcl::PointXYZRGBA> adjacent_supervoxel_centers;
t_osc_msg_u *adjx = osc_message_u_allocWithAddress((char *)"/adjacent/x");
t_osc_msg_u *adjy = osc_message_u_allocWithAddress((char *)"/adjacent/y");
t_osc_msg_u *adjz = osc_message_u_allocWithAddress((char *)"/adjacent/z");
std::multimap<uint32_t,uint32_t>::iterator adjacent_itr = supervoxel_adjacency.equal_range(supervoxel_label).first;
for ( ; adjacent_itr!=supervoxel_adjacency.equal_range(supervoxel_label).second; ++adjacent_itr)
{
pcl::Supervoxel<pcl::PointXYZRGBA>::Ptr neighbor_supervoxel = supervoxel_clusters.at(adjacent_itr->second);
osc_message_u_appendFloat(adjx, neighbor_supervoxel->centroid_.x);
osc_message_u_appendFloat(adjy, neighbor_supervoxel->centroid_.y);
osc_message_u_appendFloat(adjz, neighbor_supervoxel->centroid_.z);
// line from supervoxel->centroid_ to each adjacent_supervoxel_centers
}
osc_bundle_u_addMsg(subbndl, adjx);
osc_bundle_u_addMsg(subbndl, adjy);
osc_bundle_u_addMsg(subbndl, adjz);
osc_message_u_appendBndl_u(supervoxel_group, subbndl);
osc_bundle_u_addMsg(bndl, supervoxel_group);
//Move iterator forward to next label
label_itr = supervoxel_adjacency.upper_bound (supervoxel_label);
}
*/
omax_util_outletOSC_u(x->outlet, bndl);
if(bndl)
osc_bundle_u_free(bndl);
}
}
out:
jit_object_method(matrix, _jit_sym_lock, in_savelock);
return err;
}
int main(int argc, char **argv)
{
// create a bundle and add messages to it
t_osc_bndl_u *bndl_u = osc_bundle_u_alloc();
t_osc_msg_u *m1 = osc_message_u_alloc();
osc_message_u_setAddress(m1, "/foo");
osc_message_u_appendFloat(m1, 3.14);
osc_bundle_u_addMsg(bndl_u, m1);
t_osc_msg_u *m2 = osc_message_u_allocWithString("/bar", "whatevs");
osc_bundle_u_addMsg(bndl_u, m2);
t_osc_msg_u *m3 = osc_message_u_allocWithAddress("/bloo");
t_osc_atom_u *a = osc_atom_u_allocWithInt32(12);
osc_message_u_appendAtom(m3, a);
osc_bundle_u_addMsg(bndl_u, m3);
// serialize the bundle
long len = osc_bundle_u_nserialize(NULL, 0, bndl_u);
char bndl_s[len];
osc_bundle_u_nserialize(bndl_s, len, bndl_u);
// free the original unserialized bundle
osc_bundle_u_free(bndl_u);
bndl_u = NULL;
// deserialize the serialized bundle
osc_bundle_s_deserialize(len, bndl_s, &bndl_u);
// iterate over messages in a serialized bundle
t_osc_bndl_it_s *b_it_s = osc_bndl_it_s_get(len, bndl_s);
while(osc_bndl_it_s_hasNext(b_it_s)){
t_osc_msg_s *m = osc_bndl_it_s_next(b_it_s);
printf("%s\n", osc_message_s_getAddress(m));
}
osc_bndl_it_s_destroy(b_it_s);
// turn a serialized bundle into printable text
long tlen = osc_bundle_s_nformat(NULL, 0, len, bndl_s, 0);
char text[tlen + 1];
osc_bundle_s_nformat(text, tlen, len, bndl_s, 0);
printf("\nBUNDLE:\n");
printf("%s\n", text);
printf("\n");
// turn text into an unserialized bundle
t_osc_bndl_u *bndl_u_2 = NULL;
char *text2 = "/jean : [1, 2, 3], /john : 6.66, /jeremy : \"is cool\"";
osc_parser_parseString(strlen(text2), text2, &bndl_u_2);
// iterate over messages in an unserialized bundle
t_osc_bndl_it_u *b_it_u = osc_bndl_it_u_get(bndl_u_2);
while(osc_bndl_it_u_hasNext(b_it_u)){
t_osc_msg_u *m = osc_bndl_it_u_next(b_it_u);
printf("%s has typetags ", osc_message_u_getAddress(m));
// iterate over atoms in list
t_osc_msg_it_u *m_it_u = osc_msg_it_u_get(m);
while(osc_msg_it_u_hasNext(m_it_u)){
t_osc_atom_u *a = osc_msg_it_u_next(m_it_u);
printf("%c", osc_atom_u_getTypetag(a));
}
osc_msg_it_u_destroy(m_it_u);
printf("\n");
}
osc_bndl_it_u_destroy(b_it_u);
}
