import numpy as np import open3d as o3d from sklearn.cluster import DBSCAN def mini_color_table(index, norm=True): colors = [ [0.5000, 0.5400, 0.5300], [0.8900, 0.1500, 0.2100], [0.6400, 0.5800, 0.5000], [1.0000, 0.3800, 0.0100], [1.0000, 0.6600, 0.1400], [0.4980, 1.0000, 0.0000], [0.4980, 1.0000, 0.8314], [0.9412, 0.9725, 1.0000], [0.5412, 0.1686, 0.8863], [0.5765, 0.4392, 0.8588], [0.3600, 0.1400, 0.4300], [0.5600, 0.3700, 0.6000], ] color = colors[index % len(colors)] if not norm: color[0] *= 255 color[1] *= 255 color[2] *= 255 return color def clusterToColor(cluster, cluster_idx): colors = np.zeros(shape=(len(cluster), 3)) point_idx = 0 for point in cluster: colors[point_idx, :] = mini_color_table(cluster_idx) point_idx += 1 return colors def read_pointcloud(path, delimiter=' ', hasHeader=True): with open(path, 'r') as f: if hasHeader: # Get rid of the Header _ = f.readline() # This itrates over all lines, splits them anc converts values to floats. Will fail on wrong values. pc = [[float(x) for x in line.rstrip().split(delimiter)] for line in f if line != ''] return np.asarray(pc) def write_pointcloud(file, pc, numCols=6): np.savetxt(file, pc[:,:numCols], header=str(len(pc)) + ' ' + str(numCols), comments='') def farthest_point_sampling(pts, K): if pts.shape[0] < K: return pts def calc_distances(p0, points): return ((p0[:3] - points[:, :3]) ** 2).sum(axis=1) farthest_pts = np.zeros((K, pts.shape[1])) farthest_pts[0] = pts[np.random.randint(len(pts))] distances = calc_distances(farthest_pts[0], pts) for i in range(1, K): farthest_pts[i] = pts[np.argmax(distances)] distances = np.minimum(distances, calc_distances(farthest_pts[i], pts)) return farthest_pts def cluster_per_column(pc, column): clusters = [] for i in range(0, int(np.max(pc[:, column]))): cluster_pc = pc[pc[:, column] == i, :] clusters.append(cluster_pc) return clusters def cluster_cubes(data, cluster_dims): max = data[:,:3].max(axis=0) max += max * 0.01 min = data[:,:3].min(axis=0) min -= min * 0.01 size = (max - min) clusters = {} cluster_size = size / np.array(cluster_dims, dtype=np.float32) print('Min: ' + str(min) + ' Max: ' + str(max)) print('Cluster Size: ' + str(cluster_size)) for row in data: # print('Row: ' + str(row)) cluster_pos = ((row[:3] - min) / cluster_size).astype(int) cluster_idx = cluster_dims[0] * cluster_dims[2] * cluster_pos[1] + cluster_dims[0] * cluster_pos[2] + cluster_pos[0] clusters.setdefault(cluster_idx, []).append(row) # Apply farthest point sampling to each cluster for key, cluster in clusters.items(): c = np.vstack(cluster) clusters[key] = c # farthest_point_sampling(c, max_points_per_cluster) return clusters.values() def cluster_dbscan(data, selected_indices, eps, min_samples, metric='euclidean', algo='auto'): min_samples = min_samples * len(data) print('Clustering. Min Samples: ' + str(min_samples) + ' EPS: ' + str(eps) + "Selected Indices: " + str(selected_indices)) # 0,1,2 : pos # 3,4,5 : normal # 6: type index # 7,8,9,10: type index one hot encoded # 11,12: normal as angles db_res = DBSCAN(eps=eps, metric=metric, n_jobs=-1, algorithm=algo, min_samples=min_samples).fit(data[:, selected_indices]) labels = db_res.labels_ n_clusters = len(set(labels)) - (1 if -1 in labels else 0) n_noise = list(labels).count(-1) print("Noise: " + str(n_noise) + " Clusters: " + str(n_clusters)) clusters = {} for idx, l in enumerate(labels): if l is -1: continue clusters.setdefault(str(l), []).append(data[idx, :]) npClusters = [] for cluster in clusters.values(): npClusters.append(np.array(cluster)) return npClusters def draw_clusters(clusters): clouds = [] for cluster_idx, cluster in enumerate(clusters): cloud = o3d.PointCloud() cloud.points = o3d.Vector3dVector(cluster[:,:3]) cloud.colors = o3d.Vector3dVector(clusterToColor(cluster, cluster_idx)) clouds.append(cloud) o3d.draw_geometries(clouds) def write_clusters(path, clusters, type_column=6): file = open(path, "w") file.write(str(len(clusters)) + "\n") for cluster in clusters: print("Types: ", cluster[:, type_column]) types = np.unique(cluster[:, type_column], axis=0) np.savetxt(file, types, header='', comments='') np.savetxt(file, cluster[:, :6], header=str(len(cluster)) + ' ' + str(6), comments='')