def cluster_procedure(self):
cl_array = []
try:
for i,scan in enumerate(self.points):
if len(scan) < self.num_c:
continue
Eps, cluster_labels= mt.dbscan(scan, self.num_c, eps=self.eps)
max_label=int(np.amax(cluster_labels)) #(-1 is for outliers)
#for every cluster/label (-> denotes a new cluster)
for k in range(1,max_label+1) :
filter = np.where(cluster_labels==k)
if len(filter) == 0:
continue
#get the x,y points of the specific cluster and create a <ScanCluster> instance
if (len(filter[0]) >= self.num_c):
x_ = zip(*scan)[0]
xCl = np.array(x_)[filter]
y_ = zip(*scan)[1]
yCl = np.array(y_)[filter]
cluster_ = ScanCluster(xCl, yCl, i)
cl_array.append(cluster_)
if not (len(cl_array) == 0):
self.combine_clusters(cl_array)
cl_array = []
print 'total number of clusters = ',len(self.clusters.boxes)
return self.clusters
except Exception as ex:
print 'Exception in cluster procedure ',ex
raise ex
def clustering_procedure(buffer):
global num_c, clusters_publisher, frame_id, publish_cluster_labels, cluster_labels_publisher
if len(buffer.x) == 0: #the area is empty!
clustersmsg = ClustersMsg()
clustersmsg.header.stamp = rospy.Time.now()
clustersmsg.header.frame_id = frame_id
clustersmsg.x = []
clustersmsg.y = []
clustersmsg.z = []
#empty array_sizes means that anyone listening to this message won't loop through the data
clustersmsg.array_sizes = []
clustersmsg.num_clusters = []
clusters_publisher.publish(clustersmsg)
else:
scan_time = buffer.scan_time
clear_data = np.zeros((len(buffer.x), 3))
for i in range(0, len(buffer.x)):
clear_data[i] = ([buffer.x[i], buffer.y[i], buffer.z[i]])
arr_sz = []
x_ = []
y_ = []
z_ = []
num_clusters = []
if use_overlap:
Eps, cluster_labels = mt.dbscan(clear_data, num_c)
max_label = int(np.amax(cluster_labels))
for k in range(1, max_label + 1):
filter = np.where(cluster_labels == k)
if len(filter[0]) > 40:
xk = np.array(buffer.x)[filter]
yk = np.array(buffer.y)[filter]
zk = np.array(buffer.z)[filter]
for i in range(0, len(xk)):
x_.append(xk[i])
y_.append(yk[i])
z_.append(zk[i])
arr_sz.append(len(xk))
else:
prev_clusters, cluster_label = oncl.onlineDBscan(clear_data, num_c)
for cl in prev_clusters:
if len(x_) == 0:
x_.append(cl.getPoints()[:, 0])
y_.append(cl.getPoints()[:, 1])
z_.append(cl.getPoints()[:, 2])
else:
x_[0] = np.append(x_[0], cl.getPoints()[:, 0], axis=0)
y_[0] = np.append(y_[0], cl.getPoints()[:, 1], axis=0)
z_[0] = np.append(z_[0], cl.getPoints()[:, 2], axis=0)
if len(num_clusters) == 0:
num_clusters = np.array(cl.getSizes())
arr_sz = [cl.getNumPts()]
else:
num_clusters = np.append(num_clusters,
cl.getSizes(),
axis=0)
arr_sz.append(cl.getNumPts())
if 0 in arr_sz:
arr_sz = [i for i in arr_sz if i != 0]
x_ = x_[0]
y_ = y_[0]
z_ = z_[0]
clustersmsg = ClustersMsg()
clustersmsg.header.stamp = rospy.Time.now()
clustersmsg.header.frame_id = frame_id
#clustersmsg.clusters = cluster_labels
clustersmsg.x = x_
clustersmsg.y = y_
clustersmsg.z = z_
clustersmsg.array_sizes = arr_sz
clustersmsg.num_clusters = num_clusters
clustersmsg.scan_time = scan_time
clusters_publisher.publish(clustersmsg)
if publish_cluster_labels:
clusterlabelsmsg = ClusterLabelsMsg()
clusterlabelsmsg.header = clustersmsg.header
clusterlabelsmsg.cluster_labels = cluster_labels
cluster_labels_publisher.publish(clusterlabelsmsg)
def clustering_procedure(buffer):
global num_c, clusters_publisher, frame_id, publish_cluster_labels, cluster_labels_publisher
if len(buffer.x) == 0: #the area is empty!
clustersmsg = ClustersMsg()
clustersmsg.header.stamp = rospy.Time.now()
clustersmsg.header.frame_id = frame_id
clustersmsg.x = []
clustersmsg.y = []
clustersmsg.z = []
#empty array_sizes means that anyone listening to this message won't loop through the data
clustersmsg.array_sizes = []
clustersmsg.num_clusters = []
clusters_publisher.publish(clustersmsg)
else:
scan_time = buffer.scan_time
clear_data = np.zeros((len(buffer.x), 3))
for i in range(0,len(buffer.x)):
clear_data[i] = ([buffer.x[i], buffer.y[i], buffer.z[i]])
Eps, cluster_labels= mt.dbscan(clear_data, num_c)
max_label=int(np.amax(cluster_labels))
arr_sz = []
x_ = []
y_ = []
z_ = []
for k in range(1,max_label+1) :
filter = np.where(cluster_labels==k)
if len(filter[0])>40 :
xk = np.array(buffer.x)[filter]
yk = np.array(buffer.y)[filter]
zk = np.array(buffer.z)[filter]
for i in range(0, len(xk)):
x_.append(xk[i])
y_.append(yk[i])
z_.append(zk[i])
arr_sz.append(len(xk))
clustersmsg = ClustersMsg()
clustersmsg.header.stamp = rospy.Time.now()
clustersmsg.header.frame_id = frame_id
#clustersmsg.clusters = cluster_labels
clustersmsg.x = x_
clustersmsg.y = y_
clustersmsg.z = z_
clustersmsg.array_sizes = arr_sz
clustersmsg.num_clusters = []
clustersmsg.scan_time = scan_time
clusters_publisher.publish(clustersmsg)
if publish_cluster_labels:
clusterlabelsmsg = ClusterLabelsMsg()
clusterlabelsmsg.header = clustersmsg.header
clusterlabelsmsg.cluster_labels = cluster_labels
cluster_labels_publisher.publish(clusterlabelsmsg)
def cluster_train(clear_data):
global cc, ccnames, kat, ax, fig1, wall_cart, fig3, hogs_temp
global annotated_humans, annotated_obstacles, cc, point_clouds
hogs=[]
surfaces=[]
ann=[]
cluster_points=[]
Eps, cluster_labels= dbscan(clear_data,3) # DB SCAN
print 'eps = ',Eps,' , ',len(clear_data),' points in ', np.amax(cluster_labels),'clusters'
#print 'Eps = ', Eps, ', outliers=' ,len(np.where(cluster_labels==-1))
max_label=int(np.amax(cluster_labels))
human=np.zeros(len(clear_data))
[xi,yi,zi] = [clear_data[:,0] , clear_data[:,1] , clear_data[:,2]]
fig1.clear()
kat.clear()
kat.plot(wall_cart[:,0],wall_cart[:,1])
for k in range(1,max_label+1) :
filter=np.where(cluster_labels==k)
if len(filter[0])>timewindow :
ax.scatter(xi[filter],yi[filter], zi[filter], 'z', 30,c=cc[k%12])
fig1.add_axes(ax)
#kat.scatter(xi[filter],yi[filter],s=20, c=cc[k-1])
kat.scatter(xi[filter],yi[filter],s=20, c=cc[k%12])
[xk,yk,zk] = [xi[filter],yi[filter], zi[filter]]
point_clouds.append([xk,yk,zk])
grid=gridfit(yi[filter], zi[filter], xi[filter], 16, 16) #extract surface
grid=grid-np.amin(grid) #build surface grid
fig3.clear()
ax3 = fig3.add_subplot(1,1,1, projection='3d')
X, Y = np.mgrid[:16, :16]
surf = ax3.plot_surface(X, Y, grid, rstride=1, cstride=1, cmap=cm.gray,
linewidth=0, antialiased=False)
surfaces.append(grid)
hogs.append(hog(grid)) #extract features
#list_dist=euclidean_distance(hogs_temp, hog(grid))
plt.pause(0.0001)
#print ccnames[k-1],' cluster size :',len(filter[0]), 'Is',ccnames[k-1],'human? '
print ccnames[k%12],' cluster size :',len(filter[0]), 'Is',ccnames[k%12],'human? '
while True:
ha = raw_input()
if RepresentsInt(timewindow) and (int(ha)==1 or int(ha)==0):
#print timewindow
ha = int(ha)
if ha == 1:
annotated_humans = annotated_humans + 1
else :
annotated_obstacles = annotated_obstacles + 1
break
else:
print 'Try again, 1 for human or 0 for obstacle'
#grid=gridfit(yi[filter], zi[filter], xi[filter], 16, 16) #extract surface
#grid=grid-np.amin(grid) #build surface grid
#surfaces.append(grid)
#hogs.append(hog(grid)) #extract features
human[filter]=ha
ann.append(ha)
hogs_temp = np.array(np.array(hogs))
return cluster_labels,human,hogs,ann,surfaces,cluster_points
def clustering_procedure(clear_data, num_c):
global cc, ccnames, z, z_scale, _3d_figure
global all_clusters,all_hogs,all_gridfit,all_orthogonal
global tot_results, all_annotations, metrics
global pause
hogs=[]
colors=[]
align_cl=[] #contains the aligned data clouds of each cluster
vcl=[] #Valid Cluster Labels
valid_flag=0 #this flag is only set if we have at least one valid cluster
grids=[]
cls = []
Eps, cluster_labels= mt.dbscan(clear_data,3) # DB SCAN
max_label=int(np.amax(cluster_labels))
[xi,yi,zi] = [clear_data[:,0] , clear_data[:,1] , clear_data[:,2]]
#for every created cluster - its data points
for k in range(1,max_label+1) :
filter=np.where(cluster_labels==k)
if len(filter[0])>40 :
valid_flag=1
#points of every cluster at each timewindow-frame
[xk,yk,zk]=[xi[filter],yi[filter],zi[filter]]
speed(xk,yk,zk)
trans_matrix =[[xk,yk,zk]]
all_clusters.append([xk,yk,zk])
#we get U by applying svd to the covariance matrix. U represents the rotation matrix of each cluster based on the variance of each dimension.
U,s,V=np.linalg.svd(np.cov([xk,yk,zk]), full_matrices=False)
#translate each cluster to the beginning of the axis and then do the rotation
[xnew,ynew,znew]=translate_cluster(xk,yk,zk)
#(traslation matrix) x (rotation matrix) = alignemt of cluster
alignment_result=[[sum(a*b for a,b in zip(X_row,Y_col)) for X_row in zip(*[xnew,ynew,znew])] for Y_col in U]
alignment_result=multiply_array(xnew,ynew,znew, V)
#steps2(xk,yk,zk)
cls.append([xk,yk,zk])
align_cl.append(alignment_result)
all_orthogonal.append(alignment_result)
vcl.append(k)
colors.append(ccnames[k%12])
grid=gridfit(alignment_result[0], alignment_result[1], alignment_result[2], 16, 16) #extract surface - y,z,x alignment_result[1]
all_gridfit.append(grid)
grid=grid-np.amin(grid)
grids.append(grid)
features=hog(grid)
f=hog(grid, orientations=6, pixels_per_cell=(8, 8), cells_per_block=(1, 1), visualise=False)
all_hogs.append(f)
hogs.append(f) #extract hog features
if valid_flag != 0:
overlap_trace(cls)
#3d_figure.show()
if pause_function:
print '\033[93m '+ str(pause) + ' \033[0m'
if not pause:
#_3d_figure.clear()
if num_of_diagrams > 1:
ax.clear()
ax.set_title("3D view")
ax.set_xlabel('X - Distance')
ax.set_ylabel('Y - Robot')
ax.set_zlabel('Z - Time')
update_plots(valid_flag,hogs,xi,yi,zi,cluster_labels,vcl, align_cl, grids)
def clustering_procedure(clear_data, num_c):
global cc, ccnames, z, z_scale, _3d_figure
global all_clusters, all_hogs, all_gridfit, all_orthogonal
global tot_results, all_annotations, metrics
global pause
hogs = []
colors = []
align_cl = [] #contains the aligned data clouds of each cluster
vcl = [] #Valid Cluster Labels
valid_flag = 0 #this flag is only set if we have at least one valid cluster
grids = []
cls = []
Eps, cluster_labels = mt.dbscan(clear_data, 3) # DB SCAN
max_label = int(np.amax(cluster_labels))
[xi, yi, zi] = [clear_data[:, 0], clear_data[:, 1], clear_data[:, 2]]
#for every created cluster - its data points
for k in range(1, max_label + 1):
filter = np.where(cluster_labels == k)
if len(filter[0]) > 40:
valid_flag = 1
#points of every cluster at each timewindow-frame
[xk, yk, zk] = [xi[filter], yi[filter], zi[filter]]
speed(xk, yk, zk)
trans_matrix = [[xk, yk, zk]]
all_clusters.append([xk, yk, zk])
#we get U by applying svd to the covariance matrix. U represents the rotation matrix of each cluster based on the variance of each dimension.
U, s, V = np.linalg.svd(np.cov([xk, yk, zk]), full_matrices=False)
#translate each cluster to the beginning of the axis and then do the rotation
[xnew, ynew, znew] = translate_cluster(xk, yk, zk)
#(traslation matrix) x (rotation matrix) = alignemt of cluster
alignment_result = [[
sum(a * b for a, b in zip(X_row, Y_col))
for X_row in zip(*[xnew, ynew, znew])
] for Y_col in U]
alignment_result = multiply_array(xnew, ynew, znew, V)
#steps2(xk,yk,zk)
cls.append([xk, yk, zk])
align_cl.append(alignment_result)
all_orthogonal.append(alignment_result)
vcl.append(k)
colors.append(ccnames[k % 12])
grid = gridfit(alignment_result[0], alignment_result[1],
alignment_result[2], 16,
16) #extract surface - y,z,x alignment_result[1]
all_gridfit.append(grid)
grid = grid - np.amin(grid)
grids.append(grid)
features = hog(grid)
f = hog(grid,
orientations=6,
pixels_per_cell=(8, 8),
cells_per_block=(1, 1),
visualise=False)
all_hogs.append(f)
hogs.append(f) #extract hog features
if valid_flag != 0:
overlap_trace(cls)
#3d_figure.show()
if pause_function:
print '\033[93m ' + str(pause) + ' \033[0m'
if not pause:
#_3d_figure.clear()
if num_of_diagrams > 1:
ax.clear()
ax.set_title("3D view")
ax.set_xlabel('X - Distance')
ax.set_ylabel('Y - Robot')
ax.set_zlabel('Z - Time')
update_plots(valid_flag, hogs, xi, yi, zi, cluster_labels, vcl,
align_cl, grids)
def cluster_train(clear_data):
global cc, ccnames, kat, ax, fig1, wall_cart, TP, FP, TN, FN, annotations_checked, fig3
hogs=[]
surfaces=[]
ann=[]
Eps, cluster_labels= dbscan(clear_data,3) # DB SCAN
print len(clear_data),' points in ', np.amax(cluster_labels),'clusters'
#print 'Eps = ', Eps, ', outliers=' ,len(np.where(cluster_labels==-1))
max_label=int(np.amax(cluster_labels))
human=np.zeros(len(clear_data))
[xi,yi,zi] = [clear_data[:,0] , clear_data[:,1] , clear_data[:,2]]
fig1.clear()
kat.clear()
kat.plot(wall_cart[:,0],wall_cart[:,1])
for k in range(1,max_label+1) :
filter=np.where(cluster_labels==k)
if len(filter[0])>timewindow :
ax.scatter(xi[filter],yi[filter], zi[filter], 'z', 30,c=cc[k%12])
fig1.add_axes(ax)
#kat.scatter(xi[filter],yi[filter],s=20, c=cc[k-1])
kat.scatter(xi[filter],yi[filter],s=20, c=cc[k%12])
grid=gridfit(yi[filter], zi[filter], xi[filter], 16, 16) #extract surface
grid=grid-np.amin(grid) #build surface grid
fig3.clear()
ax3 = fig3.add_subplot(1,1,1, projection='3d')
X, Y = np.mgrid[:16, :16]
surf = ax3.plot_surface(X, Y, grid, rstride=1, cstride=1, cmap=cm.gray,
linewidth=0, antialiased=False)
surfaces.append(grid)
hogs.append(hog(grid)) #extract features
plt.pause(0.0001)
#print ccnames[k-1],' cluster size :',len(filter[0]), 'Is',ccnames[k-1],'human? '
print ccnames[k%12],' cluster size :',len(filter[0]), 'Is',ccnames[k%12],'human? '
while True:
ha = raw_input()
if RepresentsInt(timewindow) and (int(ha)==1 or int(ha)==0):
#print timewindow
ha = int(ha)
break
else:
print 'Try again, 1 for human or 0 for obstacle'
if ha == classifier_annotations[0,annotations_checked]:
if ha == 1:
TP+=1
print 'TP'
print TP
else:
TN+=1
print 'TN'
print TN
else:
if classifier_annotations[0,annotations_checked] == 1:
FP+=1
print 'FP'
print FP
else:
FN+=1
print 'FN'
print FN
annotations_checked+=1
human[filter]=ha
ann.append(ha)
return cluster_labels,human,hogs,ann,surfaces
