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apps/demo/Mesh_Segementation_MeshSegNet_17_classes_60samples_best.tar

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apps/demo/ZOUIF2W4_upper.obj

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apps/demo/file.obj

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-size 18769177

apps/demo/pages/01_🦷 Segment.py

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-from streamlit import session_state as session
-import shutil
-
-import os
-import numpy as np
-from sklearn import neighbors
-from scipy.spatial import distance_matrix
-from pygco import cut_from_graph
-import open3d as o3d
-import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
-import json
-from stpyvista import stpyvista
-import torch
-import torch.nn as nn
-from torch.autograd import Variable
-import torch.nn.functional as F
-import streamlit as st
-import pyvista as pv
-
-from PIL import Image
-
-class TeethApp:
-    def __init__(self):
-        # Font
-        with open("utils/style.css") as css:
-            st.markdown(f"<style>{css.read()}</style>", unsafe_allow_html=True)
-
-        # Logo
-        self.image_path = "utils/teeth-295404_1280.png"
-        self.image = Image.open(self.image_path)
-        width, height = self.image.size
-        scale = 12
-        new_width, new_height = width / scale, height / scale
-        self.image = self.image.resize((int(new_width), int(new_height)))
-
-        # Streamlit side navigation bar
-        st.sidebar.markdown("# AI ToothSeg")
-        st.sidebar.markdown("Automatic teeth segmentation with Deep Learning")
-        st.sidebar.markdown(" ")
-        st.sidebar.image(self.image, use_column_width=False)
-        st.markdown(
-            """
-                <style>
-                .css-1bxukto {
-                background-color: rgb(255, 255, 255) ;""",
-            unsafe_allow_html=True,
-        )
-
-
-class STN3d(nn.Module):
-    def __init__(self, channel):
-        super(STN3d, self).__init__()
-        self.conv1 = torch.nn.Conv1d(channel, 64, 1)
-        self.conv2 = torch.nn.Conv1d(64, 128, 1)
-        self.conv3 = torch.nn.Conv1d(128, 1024, 1)
-        self.fc1 = nn.Linear(1024, 512)
-        self.fc2 = nn.Linear(512, 256)
-        self.fc3 = nn.Linear(256, 9)
-        self.relu = nn.ReLU()
-
-        self.bn1 = nn.BatchNorm1d(64)
-        self.bn2 = nn.BatchNorm1d(128)
-        self.bn3 = nn.BatchNorm1d(1024)
-        self.bn4 = nn.BatchNorm1d(512)
-        self.bn5 = nn.BatchNorm1d(256)
-
-    def forward(self, x):
-        batchsize = x.size()[0]
-        x = F.relu(self.bn1(self.conv1(x)))
-        x = F.relu(self.bn2(self.conv2(x)))
-        x = F.relu(self.bn3(self.conv3(x)))
-        x = torch.max(x, 2, keepdim=True)[0]
-        x = x.view(-1, 1024)
-
-        x = F.relu(self.bn4(self.fc1(x)))
-        x = F.relu(self.bn5(self.fc2(x)))
-        x = self.fc3(x)
-
-        iden = Variable(torch.from_numpy(np.array([1, 0, 0, 0, 1, 0, 0, 0, 1]).astype(np.float32))).view(1, 9).repeat(
-            batchsize, 1)
-        if x.is_cuda:
-            iden = iden.to(x.get_device())
-        x = x + iden
-        x = x.view(-1, 3, 3)
-        return x
-
-class STNkd(nn.Module):
-    def __init__(self, k=64):
-        super(STNkd, self).__init__()
-        self.conv1 = torch.nn.Conv1d(k, 64, 1)
-        self.conv2 = torch.nn.Conv1d(64, 128, 1)
-        self.conv3 = torch.nn.Conv1d(128, 512, 1)
-        self.fc1 = nn.Linear(512, 256)
-        self.fc2 = nn.Linear(256, 128)
-        self.fc3 = nn.Linear(128, k * k)
-        self.relu = nn.ReLU()
-
-        self.bn1 = nn.BatchNorm1d(64)
-        self.bn2 = nn.BatchNorm1d(128)
-        self.bn3 = nn.BatchNorm1d(512)
-        self.bn4 = nn.BatchNorm1d(256)
-        self.bn5 = nn.BatchNorm1d(128)
-
-        self.k = k
-
-    def forward(self, x):
-        batchsize = x.size()[0]
-        x = F.relu(self.bn1(self.conv1(x)))
-        x = F.relu(self.bn2(self.conv2(x)))
-        x = F.relu(self.bn3(self.conv3(x)))
-        x = torch.max(x, 2, keepdim=True)[0]
-        x = x.view(-1, 512)
-
-        x = F.relu(self.bn4(self.fc1(x)))
-        x = F.relu(self.bn5(self.fc2(x)))
-        x = self.fc3(x)
-
-        iden = Variable(torch.from_numpy(np.eye(self.k).flatten().astype(np.float32))).view(1, self.k * self.k).repeat(
-            batchsize, 1)
-        if x.is_cuda:
-            iden = iden.to(x.get_device())
-        x = x + iden
-        x = x.view(-1, self.k, self.k)
-        return x
-
-class MeshSegNet(nn.Module):
-    def __init__(self, num_classes=17, num_channels=15, with_dropout=True, dropout_p=0.5):
-        super(MeshSegNet, self).__init__()
-        self.num_classes = num_classes
-        self.num_channels = num_channels
-        self.with_dropout = with_dropout
-        self.dropout_p = dropout_p
-
-        # MLP-1 [64, 64]
-        self.mlp1_conv1 = torch.nn.Conv1d(self.num_channels, 64, 1)
-        self.mlp1_conv2 = torch.nn.Conv1d(64, 64, 1)
-        self.mlp1_bn1 = nn.BatchNorm1d(64)
-        self.mlp1_bn2 = nn.BatchNorm1d(64)
-        # FTM (feature-transformer module)
-        self.fstn = STNkd(k=64)
-        # GLM-1 (graph-contrained learning modulus)
-        self.glm1_conv1_1 = torch.nn.Conv1d(64, 32, 1)
-        self.glm1_conv1_2 = torch.nn.Conv1d(64, 32, 1)
-        self.glm1_bn1_1 = nn.BatchNorm1d(32)
-        self.glm1_bn1_2 = nn.BatchNorm1d(32)
-        self.glm1_conv2 = torch.nn.Conv1d(32+32, 64, 1)
-        self.glm1_bn2 = nn.BatchNorm1d(64)
-        # MLP-2
-        self.mlp2_conv1 = torch.nn.Conv1d(64, 64, 1)
-        self.mlp2_bn1 = nn.BatchNorm1d(64)
-        self.mlp2_conv2 = torch.nn.Conv1d(64, 128, 1)
-        self.mlp2_bn2 = nn.BatchNorm1d(128)
-        self.mlp2_conv3 = torch.nn.Conv1d(128, 512, 1)
-        self.mlp2_bn3 = nn.BatchNorm1d(512)
-        # GLM-2 (graph-contrained learning modulus)
-        self.glm2_conv1_1 = torch.nn.Conv1d(512, 128, 1)
-        self.glm2_conv1_2 = torch.nn.Conv1d(512, 128, 1)
-        self.glm2_conv1_3 = torch.nn.Conv1d(512, 128, 1)
-        self.glm2_bn1_1 = nn.BatchNorm1d(128)
-        self.glm2_bn1_2 = nn.BatchNorm1d(128)
-        self.glm2_bn1_3 = nn.BatchNorm1d(128)
-        self.glm2_conv2 = torch.nn.Conv1d(128*3, 512, 1)
-        self.glm2_bn2 = nn.BatchNorm1d(512)
-        # MLP-3
-        self.mlp3_conv1 = torch.nn.Conv1d(64+512+512+512, 256, 1)
-        self.mlp3_conv2 = torch.nn.Conv1d(256, 256, 1)
-        self.mlp3_bn1_1 = nn.BatchNorm1d(256)
-        self.mlp3_bn1_2 = nn.BatchNorm1d(256)
-        self.mlp3_conv3 = torch.nn.Conv1d(256, 128, 1)
-        self.mlp3_conv4 = torch.nn.Conv1d(128, 128, 1)
-        self.mlp3_bn2_1 = nn.BatchNorm1d(128)
-        self.mlp3_bn2_2 = nn.BatchNorm1d(128)
-        # output
-        self.output_conv = torch.nn.Conv1d(128, self.num_classes, 1)
-        if self.with_dropout:
-            self.dropout = nn.Dropout(p=self.dropout_p)
-
-    def forward(self, x, a_s, a_l):
-        batchsize = x.size()[0]
-        n_pts = x.size()[2]
-        # MLP-1
-        x = F.relu(self.mlp1_bn1(self.mlp1_conv1(x)))
-        x = F.relu(self.mlp1_bn2(self.mlp1_conv2(x)))
-        # FTM
-        trans_feat = self.fstn(x)
-        x = x.transpose(2, 1)
-        x_ftm = torch.bmm(x, trans_feat)
-        # GLM-1
-        sap = torch.bmm(a_s, x_ftm)
-        sap = sap.transpose(2, 1)
-        x_ftm = x_ftm.transpose(2, 1)
-        x = F.relu(self.glm1_bn1_1(self.glm1_conv1_1(x_ftm)))
-        glm_1_sap = F.relu(self.glm1_bn1_2(self.glm1_conv1_2(sap)))
-        x = torch.cat([x, glm_1_sap], dim=1)
-        x = F.relu(self.glm1_bn2(self.glm1_conv2(x)))
-        # MLP-2
-        x = F.relu(self.mlp2_bn1(self.mlp2_conv1(x)))
-        x = F.relu(self.mlp2_bn2(self.mlp2_conv2(x)))
-        x_mlp2 = F.relu(self.mlp2_bn3(self.mlp2_conv3(x)))
-        if self.with_dropout:
-            x_mlp2 = self.dropout(x_mlp2)
-        # GLM-2
-        x_mlp2 = x_mlp2.transpose(2, 1)
-        sap_1 = torch.bmm(a_s, x_mlp2)
-        sap_2 = torch.bmm(a_l, x_mlp2)
-        x_mlp2 = x_mlp2.transpose(2, 1)
-        sap_1 = sap_1.transpose(2, 1)
-        sap_2 = sap_2.transpose(2, 1)
-        x = F.relu(self.glm2_bn1_1(self.glm2_conv1_1(x_mlp2)))
-        glm_2_sap_1 = F.relu(self.glm2_bn1_2(self.glm2_conv1_2(sap_1)))
-        glm_2_sap_2 = F.relu(self.glm2_bn1_3(self.glm2_conv1_3(sap_2)))
-        x = torch.cat([x, glm_2_sap_1, glm_2_sap_2], dim=1)
-        x_glm2 = F.relu(self.glm2_bn2(self.glm2_conv2(x)))
-        # GMP
-        x = torch.max(x_glm2, 2, keepdim=True)[0]
-        # Upsample
-        x = torch.nn.Upsample(n_pts)(x)
-        # Dense fusion
-        x = torch.cat([x, x_ftm, x_mlp2, x_glm2], dim=1)
-        # MLP-3
-        x = F.relu(self.mlp3_bn1_1(self.mlp3_conv1(x)))
-        x = F.relu(self.mlp3_bn1_2(self.mlp3_conv2(x)))
-        x = F.relu(self.mlp3_bn2_1(self.mlp3_conv3(x)))
-        if self.with_dropout:
-            x = self.dropout(x)
-        x = F.relu(self.mlp3_bn2_2(self.mlp3_conv4(x)))
-        # output
-        x = self.output_conv(x)
-        x = x.transpose(2,1).contiguous()
-        x = torch.nn.Softmax(dim=-1)(x.view(-1, self.num_classes))
-        x = x.view(batchsize, n_pts, self.num_classes)
-
-        return x
-
-def clone_runoob(li1):
-    li_copy = li1[:]
-    return li_copy
-
-# 对离群点重新进行分类
-def class_inlier_outlier(label_list, mean_points,cloud, ind, label_index, points, labels):
-    label_change = clone_runoob(labels)
-    outlier_index = clone_runoob(label_index)
-    ind_reverse = clone_runoob(ind)
-    # 得到离群点的label下标
-    ind_reverse.reverse()
-    for i in ind_reverse:
-        outlier_index.pop(i)
-
-    # 获取离群点
-    inlier_cloud = cloud.select_by_index(ind)
-    outlier_cloud = cloud.select_by_index(ind, invert=True)
-    outlier_points = np.array(outlier_cloud.points)
-
-    for i in range(len(outlier_points)):
-        distance = []
-        for j in range(len(mean_points)):
-            dis = np.linalg.norm(outlier_points[i] - mean_points[j], ord=2)  # 计算tooth和GT质心之间的距离
-            distance.append(dis)
-        min_index = distance.index(min(distance))  # 获取和离群点质心最近label的index
-        outlier_label = label_list[min_index]  # 获取离群点应该的label
-        index = outlier_index[i]
-        label_change[index] = outlier_label
-
-    return label_change
-
-# 利用knn算法消除离群点
-def remove_outlier(points, labels):
-    # points = np.array(point_cloud_o3d_orign.points)
-    # global label_list
-    same_label_points = {}
-
-    same_label_index = {}
-
-    mean_points = []  # 所有label种类对应点云的质心坐标
-
-    label_list = []
-    for i in range(len(labels)):
-        label_list.append(labels[i])
-    label_list = list(set(label_list))  # 去重获从小到大排序取GT_label=[0, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]
-    label_list.sort()
-    label_list = label_list[1:]
-
-    for i in label_list:
-        key = i
-        points_list = []
-        all_label_index = []
-        for j in range(len(labels)):
-            if labels[j] == i:
-                points_list.append(points[j].tolist())
-                all_label_index.append(j)  # 得到label为 i 的点对应的label的下标
-        same_label_points[key] = points_list
-        same_label_index[key] = all_label_index
-
-        tooth_mean = np.mean(points_list, axis=0)
-        mean_points.append(tooth_mean)
-        # print(mean_points)
-
-    for i in label_list:
-        points_array = same_label_points[i]
-        # 建立一个o3d的点云对象
-        pcd = o3d.geometry.PointCloud()
-        # 使用Vector3dVector方法转换
-        pcd.points = o3d.utility.Vector3dVector(points_array)
-
-        # 对label i 对应的点云进行统计离群值去除，找出离群点并显示
-        # 统计式离群点移除
-        cl, ind = pcd.remove_statistical_outlier(nb_neighbors=200, std_ratio=2.0)  # cl是选中的点，ind是选中点index
-        # 可视化
-        # display_inlier_outlier(pcd, ind)
-
-        # 对分出来的离群点重新分类
-        label_index = same_label_index[i]
-        labels = class_inlier_outlier(label_list, mean_points, pcd, ind, label_index, points, labels)
-        # print(f"label_change{labels[4400]}")
-
-    return labels
-
-
-# 消除离群点，保存最后的输出
-def remove_outlier_main(jaw, pcd_points, labels, instances_labels):
-    # point_cloud_o3d_orign = o3d.io.read_point_cloud('E:/tooth/data/MeshSegNet-master/test_upsample_15/upsample_01K17AN8_upper_refined.pcd')
-    # 原始点
-    points = pcd_points.copy()
-    label = remove_outlier(points, labels)
-
-    # 保存json文件
-    label_dict = {}
-    label_dict["id_patient"] = ""
-    label_dict["jaw"] = jaw
-    label_dict["labels"] = label.tolist()
-    label_dict["instances"] = instances_labels.tolist()
-    b = json.dumps(label_dict)
-    with open('dental-labels4' + '.json', 'w') as f_obj:
-        f_obj.write(b)
-    f_obj.close()
-
-
-same_points_list = {}
-
-
-# 体素下采样
-def voxel_filter(point_cloud, leaf_size):
-    same_points_list = {}
-    filtered_points = []
-    # step1 计算边界点
-    x_max, y_max, z_max = np.amax(point_cloud, axis=0)  # 计算 x,y,z三个维度的最值
-    x_min, y_min, z_min = np.amin(point_cloud, axis=0)
-
-    # step2 确定体素的尺寸
-    size_r = leaf_size
-
-    # step3 计算每个 volex的维度 voxel grid
-    Dx = (x_max - x_min) // size_r + 1
-    Dy = (y_max - y_min) // size_r + 1
-    Dz = (z_max - z_min) // size_r + 1
-
-    # print("Dx x Dy x Dz is {} x {} x {}".format(Dx, Dy, Dz))
-
-    # step4 计算每个点在volex grid内每一个维度的值
-    h = list()  # h 为保存索引的列表
-    for i in range(len(point_cloud)):
-        hx = np.floor((point_cloud[i][0] - x_min) // size_r)
-        hy = np.floor((point_cloud[i][1] - y_min) // size_r)
-        hz = np.floor((point_cloud[i][2] - z_min) // size_r)
-        h.append(hx + hy * Dx + hz * Dx * Dy)
-    # print(h[60581])
-
-    # step5 对h值进行排序
-    h = np.array(h)
-    h_indice = np.argsort(h)  # 提取索引,返回h里面的元素按从小到大排序的  索引
-    h_sorted = h[h_indice]  # 升序
-    count = 0  # 用于维度的累计
-    step = 20
-    # 将h值相同的点放入到同一个grid中，并进行筛选
-    for i in range(1, len(h_sorted)):  # 0-19999个数据点
-        # if i == len(h_sorted)-1:
-        #     print("aaa")
-        if h_sorted[i] == h_sorted[i - 1] and (i != len(h_sorted) - 1):
-            continue
-        elif h_sorted[i] == h_sorted[i - 1] and (i == len(h_sorted) - 1):
-            point_idx = h_indice[count:]
-            key = h_sorted[i - 1]
-            same_points_list[key] = point_idx
-            _G = np.mean(point_cloud[point_idx], axis=0)  # 所有点的重心
-            _d = np.linalg.norm(point_cloud[point_idx] - _G, axis=1, ord=2)  # 计算到重心的距离
-            _d.sort()
-            inx = [j for j in range(0, len(_d), step)]  # 获取指定间隔元素下标
-            for j in inx:
-                index = point_idx[j]
-                filtered_points.append(point_cloud[index])
-            count = i
-        elif h_sorted[i] != h_sorted[i - 1] and (i == len(h_sorted) - 1):
-            point_idx1 = h_indice[count:i]
-            key1 = h_sorted[i - 1]
-            same_points_list[key1] = point_idx1
-            _G = np.mean(point_cloud[point_idx1], axis=0)  # 所有点的重心
-            _d = np.linalg.norm(point_cloud[point_idx1] - _G, axis=1, ord=2)  # 计算到重心的距离
-            _d.sort()
-            inx = [j for j in range(0, len(_d), step)]  # 获取��定间隔元素下标
-            for j in inx:
-                index = point_idx1[j]
-                filtered_points.append(point_cloud[index])
-
-            point_idx2 = h_indice[i:]
-            key2 = h_sorted[i]
-            same_points_list[key2] = point_idx2
-            _G = np.mean(point_cloud[point_idx2], axis=0)  # 所有点的重心
-            _d = np.linalg.norm(point_cloud[point_idx2] - _G, axis=1, ord=2)  # 计算到重心的距离
-            _d.sort()
-            inx = [j for j in range(0, len(_d), step)]  # 获取指定间隔元素下标
-            for j in inx:
-                index = point_idx2[j]
-                filtered_points.append(point_cloud[index])
-            count = i
-
-        else:
-            point_idx = h_indice[count: i]
-            key = h_sorted[i - 1]
-            same_points_list[key] = point_idx
-            _G = np.mean(point_cloud[point_idx], axis=0)  # 所有点的重心
-            _d = np.linalg.norm(point_cloud[point_idx] - _G, axis=1, ord=2)  # 计算到重心的距离
-            _d.sort()
-            inx = [j for j in range(0, len(_d), step)]  # 获取指定间隔元素下标
-            for j in inx:
-                index = point_idx[j]
-                filtered_points.append(point_cloud[index])
-            count = i
-
-    # 把点云格式改成array，并对外返回
-    # print(f'filtered_points[0]为{filtered_points[0]}')
-    filtered_points = np.array(filtered_points, dtype=np.float64)
-    return filtered_points,same_points_list
-
-
-# 体素上采样
-def voxel_upsample(same_points_list, point_cloud, filtered_points, filter_labels, leaf_size):
-    upsample_label = []
-    upsample_point = []
-    upsample_index = []
-    # step1 计算边界点
-    x_max, y_max, z_max = np.amax(point_cloud, axis=0)  # 计算 x,y,z三个维度的最值
-    x_min, y_min, z_min = np.amin(point_cloud, axis=0)
-    # step2 确定体素的尺寸
-    size_r = leaf_size
-    # step3 计算每个 volex的维度 voxel grid
-    Dx = (x_max - x_min) // size_r + 1
-    Dy = (y_max - y_min) // size_r + 1
-    Dz = (z_max - z_min) // size_r + 1
-    print("Dx x Dy x Dz is {} x {} x {}".format(Dx, Dy, Dz))
-
-    # step4 计算每个点（采样后的点）在volex grid内每一个维度的值
-    h = list()
-    for i in range(len(filtered_points)):
-        hx = np.floor((filtered_points[i][0] - x_min) // size_r)
-        hy = np.floor((filtered_points[i][1] - y_min) // size_r)
-        hz = np.floor((filtered_points[i][2] - z_min) // size_r)
-        h.append(hx + hy * Dx + hz * Dx * Dy)
-
-    # step5 根据h值查询字典same_points_list
-    h = np.array(h)
-    count = 0
-    for i in range(1, len(h)):
-        if h[i] == h[i - 1] and i != (len(h) - 1):
-            continue
-        elif h[i] == h[i - 1] and i == (len(h) - 1):
-            label = filter_labels[count:]
-            key = h[i - 1]
-            count = i
-            # 累计label次数，classcount：{‘A’:2,'B':1}
-            classcount = {}
-            for i in range(len(label)):
-                vote = label[i]
-                classcount[vote] = classcount.get(vote, 0) + 1
-            # 对map的value排序
-            sortedclass = sorted(classcount.items(), key=lambda x: (x[1]), reverse=True)
-            # key = h[i-1]
-            point_index = same_points_list[key]  # h对应的point index列表
-            for j in range(len(point_index)):
-                upsample_label.append(sortedclass[0][0])
-                index = point_index[j]
-                upsample_point.append(point_cloud[index])
-                upsample_index.append(index)
-        elif h[i] != h[i - 1] and (i == len(h) - 1):
-            label1 = filter_labels[count:i]
-            key1 = h[i - 1]
-            label2 = filter_labels[i:]
-            key2 = h[i]
-            count = i
-
-            classcount = {}
-            for i in range(len(label1)):
-                vote = label1[i]
-                classcount[vote] = classcount.get(vote, 0) + 1
-            sortedclass = sorted(classcount.items(), key=lambda x: (x[1]), reverse=True)
-            # key1 = h[i-1]
-            point_index = same_points_list[key1]
-            for j in range(len(point_index)):
-                upsample_label.append(sortedclass[0][0])
-                index = point_index[j]
-                upsample_point.append(point_cloud[index])
-                upsample_index.append(index)
-
-            # label2 = filter_labels[i:]
-            classcount = {}
-            for i in range(len(label2)):
-                vote = label2[i]
-                classcount[vote] = classcount.get(vote, 0) + 1
-            sortedclass = sorted(classcount.items(), key=lambda x: (x[1]), reverse=True)
-            # key2 = h[i]
-            point_index = same_points_list[key2]
-            for j in range(len(point_index)):
-                upsample_label.append(sortedclass[0][0])
-                index = point_index[j]
-                upsample_point.append(point_cloud[index])
-                upsample_index.append(index)
-        else:
-            label = filter_labels[count:i]
-            key = h[i - 1]
-            count = i
-            classcount = {}
-            for i in range(len(label)):
-                vote = label[i]
-                classcount[vote] = classcount.get(vote, 0) + 1
-            sortedclass = sorted(classcount.items(), key=lambda x: (x[1]), reverse=True)
-            # key = h[i-1]
-            point_index = same_points_list[key]  # h对应的point index列表
-            for j in range(len(point_index)):
-                upsample_label.append(sortedclass[0][0])
-                index = point_index[j]
-                upsample_point.append(point_cloud[index])
-                upsample_index.append(index)
-            # count = i
-
-    # 恢复原始顺序
-    # print(f'upsample_index[0]的值为{upsample_index[0]}')
-    # print(f'upsample_index的总长度为{len(upsample_index)}')
-
-    # 恢复index原始顺序
-    upsample_index = np.array(upsample_index)
-    upsample_index_indice = np.argsort(upsample_index)  # 提取索引,返回h里面的元素按从小到大排序的  索引
-    upsample_index_sorted = upsample_index[upsample_index_indice]
-
-    upsample_point = np.array(upsample_point)
-    upsample_label = np.array(upsample_label)
-    # 恢复point和label的原始顺序
-    upsample_point_sorted = upsample_point[upsample_index_indice]
-    upsample_label_sorted = upsample_label[upsample_index_indice]
-
-    return upsample_point_sorted, upsample_label_sorted
-
-
-# 利用knn算法上采样
-def KNN_sklearn_Load_data(voxel_points, center_points, labels):
-    # 载入数据
-    # x_train, x_test, y_train, y_test = train_test_split(center_points, labels, test_size=0.1)
-    # 构建模型
-    model = neighbors.KNeighborsClassifier(n_neighbors=3)
-    model.fit(center_points, labels)
-    prediction = model.predict(voxel_points.reshape(1, -1))
-    # meshtopoints_labels = classification_report(voxel_points, prediction)
-    return prediction[0]
-
-
-# 加载点进行knn上采样
-def Load_data(voxel_points, center_points, labels):
-    meshtopoints_labels = []
-    # meshtopoints_labels.append(SVC_sklearn_Load_data(voxel_points[i], center_points, labels))
-    for i in range(0, voxel_points.shape[0]):
-        meshtopoints_labels.append(KNN_sklearn_Load_data(voxel_points[i], center_points, labels))
-    return np.array(meshtopoints_labels)
-
-# 将三角网格数据上采样回原始点云数据
-def mesh_to_points_main(jaw, pcd_points, center_points, labels):
-    points = pcd_points.copy()
-    # 下采样
-    voxel_points, same_points_list = voxel_filter(points, 0.6)
-
-    after_labels = Load_data(voxel_points, center_points, labels)
-
-    upsample_point, upsample_label = voxel_upsample(same_points_list, points, voxel_points, after_labels, 0.6)
-
-    new_pcd = o3d.geometry.PointCloud()
-    new_pcd.points = o3d.utility.Vector3dVector(upsample_point)
-    instances_labels = upsample_label.copy()
-    # '''
-    # o3d.io.write_point_cloud(os.path.join(save_path, 'upsample_' + name + '.pcd'), new_pcd, write_ascii=True)
-    for i in range(0, upsample_label.shape[0]):
-        if jaw == 'upper':
-            if (upsample_label[i] >= 1) and (upsample_label[i] <= 8):
-                upsample_label[i] = upsample_label[i] + 10
-            elif (upsample_label[i] >= 9) and (upsample_label[i] <= 16):
-                upsample_label[i] = upsample_label[i] + 12
-        else:
-            if (upsample_label[i] >= 1) and (upsample_label[i] <= 8):
-                upsample_label[i] = upsample_label[i] + 30
-            elif (upsample_label[i] >= 9) and (upsample_label[i] <= 16):
-                upsample_label[i] = upsample_label[i] + 32
-    remove_outlier_main(jaw, pcd_points, upsample_label, instances_labels)
-
-
-# 将原始点云数据转换为三角网格
-def mesh_grid(pcd_points):
-    new_pcd,_ = voxel_filter(pcd_points, 0.6)
-    # pcd需要有法向量
-
-    # estimate radius for rolling ball
-    pcd_new = o3d.geometry.PointCloud()
-    pcd_new.points = o3d.utility.Vector3dVector(new_pcd)
-    pcd_new.estimate_normals()
-    distances = pcd_new.compute_nearest_neighbor_distance()
-    avg_dist = np.mean(distances)
-    radius = 6 * avg_dist
-    mesh = o3d.geometry.TriangleMesh.create_from_point_cloud_ball_pivoting(
-        pcd_new,
-        o3d.utility.DoubleVector([radius, radius * 2]))
-    # o3d.io.write_triangle_mesh("./tooth date/test.ply", mesh)
-
-    return mesh
-
-
-# 读取obj文件内容
-def read_obj(obj_path):
-    jaw = None
-    with open(obj_path) as file:
-        points = []
-        faces = []
-        while 1:
-            line = file.readline()
-            if not line:
-                break
-            strs = line.split(" ")
-            if strs[0] == "v":
-                points.append((float(strs[1]), float(strs[2]), float(strs[3])))
-            elif strs[0] == "f":
-                faces.append((int(strs[1]), int(strs[2]), int(strs[3])))
-            elif strs[1][0:5] == 'lower':
-                jaw = 'lower'
-            elif strs[1][0:5] == 'upper':
-                jaw = 'upper'
-
-    points = np.array(points)
-    faces = np.array(faces)
-
-    if jaw is None:
-        raise ValueError("Jaw type not found in OBJ file")
-
-    return points, faces, jaw
-
-
-# obj文件转为pcd文件
-def obj2pcd(obj_path):
-    if os.path.exists(obj_path):
-        print('yes')
-    points, _, jaw = read_obj(obj_path)
-    pcd_list = []
-    num_points = np.shape(points)[0]
-    for i in range(num_points):
-        new_line = str(points[i, 0]) + ' ' + str(points[i, 1]) + ' ' + str(points[i, 2])
-        pcd_list.append(new_line.split())
-
-    pcd_points = np.array(pcd_list).astype(np.float64)
-    return pcd_points, jaw
-
-# Configure Streamlit page
-st.set_page_config(page_title="Teeth Segmentation", page_icon="🦷")
-
-class Segment(TeethApp):
-    def __init__(self):
-        TeethApp.__init__(self)
-        self.build_app()
-
-    def build_app(self):
-
-        st.title("Segment Intra-oral Scans")
-        st.markdown("Select scan for segmentation")
-
-        inputs = st.radio(
-            "Select scan for segmentation:",
-            ("Upload Scan", "Example Scan"),
-        )
-        import pyvista as pv
-        if inputs == "Example Scan":
-            mesh = pv.read("ZOUIF2W4_upper.obj")
-            plotter = pv.Plotter()
-
-            # Add the mesh to the plotter
-            plotter.add_mesh(mesh, color='black', show_edges=True)
-            visualize = st.button("Segment")
-            if visualize:
-                stpyvista(plotter)
-
-        elif inputs == "Upload Scan":
-            file = st.file_uploader("Please upload an OBJ Object file", type=["OBJ"])
-
-            if file is not None:
-                # save the uploaded file to disk
-                with open("file.obj", "wb") as buffer:
-                    shutil.copyfileobj(file, buffer)
-                # 复制数据
-
-
-                obj_path = "file.obj"
-                upsampling_method = 'KNN'
-
-                model_path = 'Mesh_Segementation_MeshSegNet_17_classes_60samples_best.tar'
-                num_classes = 17
-                num_channels = 15
-
-                # set model
-                device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-                model = MeshSegNet(num_classes=num_classes, num_channels=num_channels).to(device, dtype=torch.float)
-
-                # load trained model
-                # checkpoint = torch.load(os.path.join(model_path, model_name), map_location='cpu')
-                checkpoint = torch.load(model_path, map_location='cpu')
-                model.load_state_dict(checkpoint['model_state_dict'])
-                del checkpoint
-                model = model.to(device, dtype=torch.float)
-
-                # cudnn
-                torch.backends.cudnn.benchmark = True
-                torch.backends.cudnn.enabled = True
-
-                # Predicting
-                model.eval()
-                with torch.no_grad():
-                    pcd_points, jaw = obj2pcd(obj_path)
-                    mesh = mesh_grid(pcd_points)
-
-                    # move mesh to origin
-                    with st.spinner("Patience please, AI at work. Grab a coffee while you wait☕!"):
-                        vertices_points = np.asarray(mesh.vertices)
-                        triangles_points = np.asarray(mesh.triangles)
-                        N = triangles_points.shape[0]
-                        cells = np.zeros((triangles_points.shape[0], 9))
-                        cells = vertices_points[triangles_points].reshape(triangles_points.shape[0], 9)
-
-                        mean_cell_centers = mesh.get_center()
-                        cells[:, 0:3] -= mean_cell_centers[0:3]
-                        cells[:, 3:6] -= mean_cell_centers[0:3]
-                        cells[:, 6:9] -= mean_cell_centers[0:3]
-
-                        v1 = np.zeros([triangles_points.shape[0], 3], dtype='float32')
-                        v2 = np.zeros([triangles_points.shape[0], 3], dtype='float32')
-                        v1[:, 0] = cells[:, 0] - cells[:, 3]
-                        v1[:, 1] = cells[:, 1] - cells[:, 4]
-                        v1[:, 2] = cells[:, 2] - cells[:, 5]
-                        v2[:, 0] = cells[:, 3] - cells[:, 6]
-                        v2[:, 1] = cells[:, 4] - cells[:, 7]
-                        v2[:, 2] = cells[:, 5] - cells[:, 8]
-                        mesh_normals = np.cross(v1, v2)
-                        mesh_normal_length = np.linalg.norm(mesh_normals, axis=1)
-                        mesh_normals[:, 0] /= mesh_normal_length[:]
-                        mesh_normals[:, 1] /= mesh_normal_length[:]
-                        mesh_normals[:, 2] /= mesh_normal_length[:]
-
-                        # prepare input
-                        points = vertices_points.copy()
-                        points[:, 0:3] -= mean_cell_centers[0:3]
-                        normals = np.nan_to_num(mesh_normals).copy()
-                        barycenters = np.zeros((triangles_points.shape[0], 3))
-                        s = np.sum(vertices_points[triangles_points], 1)
-                        barycenters = 1 / 3 * s
-                        center_points = barycenters.copy()
-                        barycenters -= mean_cell_centers[0:3]
-
-                        # normalized data
-                        maxs = points.max(axis=0)
-                        mins = points.min(axis=0)
-                        means = points.mean(axis=0)
-                        stds = points.std(axis=0)
-                        nmeans = normals.mean(axis=0)
-                        nstds = normals.std(axis=0)
-
-                        for i in range(3):
-                            cells[:, i] = (cells[:, i] - means[i]) / stds[i]  # point 1
-                            cells[:, i + 3] = (cells[:, i + 3] - means[i]) / stds[i]  # point 2
-                            cells[:, i + 6] = (cells[:, i + 6] - means[i]) / stds[i]  # point 3
-                            barycenters[:, i] = (barycenters[:, i] - mins[i]) / (maxs[i] - mins[i])
-                            normals[:, i] = (normals[:, i] - nmeans[i]) / nstds[i]
-
-                        X = np.column_stack((cells, barycenters, normals))
-
-                        # computing A_S and A_L
-                        A_S = np.zeros([X.shape[0], X.shape[0]], dtype='float32')
-                        A_L = np.zeros([X.shape[0], X.shape[0]], dtype='float32')
-                        D = distance_matrix(X[:, 9:12], X[:, 9:12])
-                        A_S[D < 0.1] = 1.0
-                        A_S = A_S / np.dot(np.sum(A_S, axis=1, keepdims=True), np.ones((1, X.shape[0])))
-
-                        A_L[D < 0.2] = 1.0
-                        A_L = A_L / np.dot(np.sum(A_L, axis=1, keepdims=True), np.ones((1, X.shape[0])))
-
-                        # numpy -> torch.tensor
-                        X = X.transpose(1, 0)
-                        X = X.reshape([1, X.shape[0], X.shape[1]])
-                        X = torch.from_numpy(X).to(device, dtype=torch.float)
-                        A_S = A_S.reshape([1, A_S.shape[0], A_S.shape[1]])
-                        A_L = A_L.reshape([1, A_L.shape[0], A_L.shape[1]])
-                        A_S = torch.from_numpy(A_S).to(device, dtype=torch.float)
-                        A_L = torch.from_numpy(A_L).to(device, dtype=torch.float)
-
-                        tensor_prob_output = model(X, A_S, A_L).to(device, dtype=torch.float)
-                        patch_prob_output = tensor_prob_output.cpu().numpy()
-
-                    # refinement
-                    with st.spinner("Refining..."):
-                        round_factor = 100
-                        patch_prob_output[patch_prob_output < 1.0e-6] = 1.0e-6
-
-                        # unaries
-                        unaries = -round_factor * np.log10(patch_prob_output)
-                        unaries = unaries.astype(np.int32)
-                        unaries = unaries.reshape(-1, num_classes)
-
-                        # parawisex
-                        pairwise = (1 - np.eye(num_classes, dtype=np.int32))
-
-                        cells = cells.copy()
-
-                        cell_ids = np.asarray(triangles_points)
-                        lambda_c = 20
-                        edges = np.empty([1, 3], order='C')
-                        for i_node in range(cells.shape[0]):
-                            # Find neighbors
-                            nei = np.sum(np.isin(cell_ids, cell_ids[i_node, :]), axis=1)
-                            nei_id = np.where(nei == 2)
-                            for i_nei in nei_id[0][:]:
-                                if i_node < i_nei:
-                                    cos_theta = np.dot(normals[i_node, 0:3], normals[i_nei, 0:3]) / np.linalg.norm(
-                                        normals[i_node, 0:3]) / np.linalg.norm(normals[i_nei, 0:3])
-                                    if cos_theta >= 1.0:
-                                        cos_theta = 0.9999
-                                    theta = np.arccos(cos_theta)
-                                    phi = np.linalg.norm(barycenters[i_node, :] - barycenters[i_nei, :])
-                                    if theta > np.pi / 2.0:
-                                        edges = np.concatenate(
-                                            (edges, np.array([i_node, i_nei, -np.log10(theta / np.pi) * phi]).reshape(1, 3)), axis=0)
-                                    else:
-                                        beta = 1 + np.linalg.norm(np.dot(normals[i_node, 0:3], normals[i_nei, 0:3]))
-                                        edges = np.concatenate(
-                                            (edges, np.array([i_node, i_nei, -beta * np.log10(theta / np.pi) * phi]).reshape(1, 3)),
-                                            axis=0)
-                        edges = np.delete(edges, 0, 0)
-                        edges[:, 2] *= lambda_c * round_factor
-                        edges = edges.astype(np.int32)
-
-                        refine_labels = cut_from_graph(edges, unaries, pairwise)
-                        refine_labels = refine_labels.reshape([-1, 1])
-
-                        predicted_labels_3 = refine_labels.reshape(refine_labels.shape[0])
-                        mesh_to_points_main(jaw, pcd_points, center_points, predicted_labels_3)
-
-                import pyvista as pv
-
-                with st.spinner("Rendering..."):
-                    # Load the .obj file
-                    mesh = pv.read('file.obj')
-
-                    # Load the JSON file
-                    with open('dental-labels4.json', 'r') as file:
-                        labels_data = json.load(file)
-
-                    # Assuming labels_data['labels'] is a list of labels
-                    labels = labels_data['labels']
-
-                    # Make sure the number of labels matches the number of vertices or faces
-                    assert len(labels) == mesh.n_points or len(labels) == mesh.n_cells
-
-                    # If labels correspond to vertices
-                    if len(labels) == mesh.n_points:
-                        mesh.point_data['Labels'] = labels
-                    # If labels correspond to faces
-                    elif len(labels) == mesh.n_cells:
-                        mesh.cell_data['Labels'] = labels
-                    
-                    # Create a pyvista plotter
-                    plotter = pv.Plotter()
-
-                    cmap = plt.cm.get_cmap('jet', 27)  # Using a colormap with sufficient distinct colors
-
-                    colors = cmap(np.linspace(0, 1, 27))  # Generate colors
-
-                    # Convert colors to a format acceptable by PyVista
-                    colormap = mcolors.ListedColormap(colors)
-
-                    # Add the mesh to the plotter with labels as a scalar field
-                    #plotter.add_mesh(mesh, scalars='Labels', show_scalar_bar=True, cmap='jet')
-                    plotter.add_mesh(mesh, scalars='Labels', show_scalar_bar=True, cmap=colormap, clim=[0, 27])
-
-                    # Show the plot
-                    #plotter.show()
-                    ## Send to streamlit
-                    stpyvista(plotter)
-
-if __name__ == "__main__":
-    app = Segment()

apps/demo/pages/02_📙How_it_Works.py

@@ -1,50 +0,0 @@
-import streamlit as st
-from streamlit import session_state as session
-
-from PIL import Image
-
-class TeethApp:
-    def __init__(self):
-        # Font
-        with open("utils/style.css") as css:
-            st.markdown(f"<style>{css.read()}</style>", unsafe_allow_html=True)
-    
-        # Logo
-        self.image_path = "utils/teeth-295404_1280.png"
-        self.image = Image.open(self.image_path)
-        width, height = self.image.size
-        scale = 12
-        new_width, new_height = width / scale, height / scale
-        self.image = self.image.resize((int(new_width), int(new_height)))
-
-        # Streamlit side navigation bar
-        st.sidebar.markdown("# AI ToothSeg")
-        st.sidebar.markdown("Automatic teeth segmentation with Deep Learning")
-        st.sidebar.markdown(" ")
-        st.sidebar.image(self.image, use_column_width=False)
-        st.markdown(
-            """
-                <style>
-                .css-1bxukto {
-                background-color: rgb(255, 255, 255) ;""",
-            unsafe_allow_html=True,
-        )
-
-# Configure Streamlit page
-st.set_page_config(page_title="Teeth Segmentation", page_icon="ⓘ")
-
-
-class Guide(TeethApp):
-    def __init__(self):
-        TeethApp.__init__(self)
-        self.build_app()
-
-    def build_app(self):
-        st.title("AI-assited Tooth Segmentation")
-        st.markdown("This app automatically segments intra-oral scans of teeth using machine learning.")
-        st.markdown("Head to the 'Segment' tab to try it out!")
-        st.markdown("**Example:**")
-        st.image("illu.png")
-
-if __name__ == "__main__":
-    app = Guide()

apps/demo/requirements.txt

@@ -1,10 +0,0 @@
-streamlit==1.28.2
-pyvista==0.36.1
-pythreejs==2.4.2
-stpyvista==0.0.5
-open3d==0.15.1
-torch==1.11.0
-scikit-learn==0.23.2
-scipy==1.5.2
-matplotlib==3.3.2
-pillow==10.1.0

apps/demo/utils/style.css

@@ -1,10 +0,0 @@
-@import url('https://fonts.googleapis.com/css2?family=Nunito:wght@400&display=swap');
-
-html,
-body,
-[class*="css"] {
-    font-family: 'Nunito';
-    /* font-size: 16px; */
-    font-weight: 400;
-    color: #091747;
-}

apps/demo/ⓘ_Introduction.py

@@ -1,40 +0,0 @@
-import streamlit as st
-from streamlit import session_state as session
-
-from PIL import Image
-
-class TeethApp:
-    def __init__(self):
-        # Font
-        with open("utils/style.css") as css:
-            st.markdown(f"<style>{css.read()}</style>", unsafe_allow_html=True)
-    
-        # Logo
-        self.image_path = "utils/teeth-295404_1280.png"
-        self.image = Image.open(self.image_path)
-        width, height = self.image.size
-        scale = 12
-        new_width, new_height = width / scale, height / scale
-        self.image = self.image.resize((int(new_width), int(new_height)))
-
-        # Streamlit side navigation bar
-        st.sidebar.markdown("# AI ToothSeg")
-        st.sidebar.markdown("Automatic teeth segmentation with Deep Learning")
-        st.sidebar.markdown(" ")
-        st.sidebar.image(self.image, use_column_width=False)
-        st.markdown(
-            """
-                <style>
-                .css-1bxukto {
-                background-color: rgb(255, 255, 255) ;""",
-            unsafe_allow_html=True,
-        )
-
-# Configure Streamlit page
-st.set_page_config(page_title="Teeth Segmentation", page_icon="ⓘ")
-
-st.title("AI-assited Tooth Segmentation")
-st.markdown("This app automatically segments intra-oral scans of teeth using machine learning.")
-st.markdown("Head to the 'Segment' tab to try it out!")
-st.markdown("**Example:**")
-st.image("illu.png")