diff --git a/CTAI_flask/core/get_feature.py b/CTAI_flask/core/get_feature.py new file mode 100644 index 0000000..c08f4f1 --- /dev/null +++ b/CTAI_flask/core/get_feature.py @@ -0,0 +1,200 @@ +import inspect + +import SimpleITK as sitk +import cv2 +import numpy as np +import pandas as pd +from numba import jit + +np.set_printoptions(suppress=True) # 输出时禁止科学表示法,直接输出小数值 + +column_all_c = ['面积', '周长', '重心x', '重心y', '似圆度', '灰度均值', '灰度方差', '灰度偏度', + '灰度峰态', '小梯度优势', '大梯度优势', '灰度分布不均匀性', '梯度分布不均匀性', '能量', '灰度平均', '梯度平均', + '灰度均方差', '梯度均方差', '相关', '灰度熵', '梯度熵', '混合熵', '惯性', '逆差矩'] + +features_list = ['area', 'perimeter', 'focus_x', 'focus_y', 'ellipse', 'mean', 'std', 'piandu', 'fengdu', + 'small_grads_dominance', + 'big_grads_dominance', 'gray_asymmetry', 'grads_asymmetry', 'energy', 'gray_mean', 'grads_mean', + 'gray_variance', 'grads_variance', 'corelation', 'gray_entropy', 'grads_entropy', 'entropy', 'inertia', + 'differ_moment'] + + +# 最后俩偏度 峰度 + + +# 获取变量的名 +def get_variable_name(variable): + callers_local_vars = inspect.currentframe().f_back.f_locals.items() + return [var_name for var_name, var_val in callers_local_vars if var_val is variable] + + +def glcm(img_gray, ngrad=16, ngray=16): + '''Gray Level-Gradient Co-occurrence Matrix,取归一化后的灰度值、梯度值分别为16、16''' + # 利用sobel算子分别计算x-y方向上的梯度值 + gsx = cv2.Sobel(img_gray, cv2.CV_64F, 1, 0, ksize=3) + gsy = cv2.Sobel(img_gray, cv2.CV_64F, 0, 1, ksize=3) + height, width = img_gray.shape + grad = (gsx ** 2 + gsy ** 2) ** 0.5 # 计算梯度值 + grad = np.asarray(1.0 * grad * (ngrad - 1) / grad.max(), dtype=np.int16) + gray = np.asarray(1.0 * img_gray * (ngray - 1) / img_gray.max(), dtype=np.int16) # 0-255变换为0-15 + gray_grad = np.zeros([ngray, ngrad]) # 灰度梯度共生矩阵 + for i in range(height): + for j in range(width): + gray_value = gray[i][j] + grad_value = grad[i][j] + gray_grad[gray_value][grad_value] += 1 + gray_grad = 1.0 * gray_grad / (height * width) # 归一化灰度梯度矩阵,减少计算量 + get_glcm_features(gray_grad) + + +@jit +def get_gray_feature(): + # 灰度特征提取算法 + hist = cv2.calcHist([image_ROI_uint8[index]], [0], None, [256], [0, 256]) + # 假的 还没用灰度直方图 + + c_features['mean'].append(np.mean(image_ROI[index])) + c_features['std'].append(np.std(image_ROI[index])) + + s = pd.Series(image_ROI[index]) + c_features['piandu'].append(s.skew()) + c_features['fengdu'].append(s.kurt()) + + +def get_glcm_features(mat): + '''根据灰度梯度共生矩阵计算纹理特征量,包括小梯度优势,大梯度优势,灰度分布不均匀性,梯度分布不均匀性,能量,灰度平均,梯度平均, + 灰度方差,梯度方差,相关,灰度熵,梯度熵,混合熵,惯性,逆差矩''' + sum_mat = mat.sum() + small_grads_dominance = big_grads_dominance = gray_asymmetry = grads_asymmetry = energy = gray_mean = grads_mean = 0 + gray_variance = grads_variance = corelation = gray_entropy = grads_entropy = entropy = inertia = differ_moment = 0 + for i in range(mat.shape[0]): + gray_variance_temp = 0 + for j in range(mat.shape[1]): + small_grads_dominance += mat[i][j] / ((j + 1) ** 2) + big_grads_dominance += mat[i][j] * j ** 2 + energy += mat[i][j] ** 2 + if mat[i].sum() != 0: + gray_entropy -= mat[i][j] * np.log(mat[i].sum()) + if mat[:, j].sum() != 0: + grads_entropy -= mat[i][j] * np.log(mat[:, j].sum()) + if mat[i][j] != 0: + entropy -= mat[i][j] * np.log(mat[i][j]) + inertia += (i - j) ** 2 * np.log(mat[i][j]) + differ_moment += mat[i][j] / (1 + (i - j) ** 2) + gray_variance_temp += mat[i][j] ** 0.5 + + gray_asymmetry += mat[i].sum() ** 2 + gray_mean += i * mat[i].sum() ** 2 + gray_variance += (i - gray_mean) ** 2 * gray_variance_temp + for j in range(mat.shape[1]): + grads_variance_temp = 0 + for i in range(mat.shape[0]): + grads_variance_temp += mat[i][j] ** 0.5 + grads_asymmetry += mat[:, j].sum() ** 2 + grads_mean += j * mat[:, j].sum() ** 2 + grads_variance += (j - grads_mean) ** 2 * grads_variance_temp + small_grads_dominance /= sum_mat + big_grads_dominance /= sum_mat + gray_asymmetry /= sum_mat + grads_asymmetry /= sum_mat + gray_variance = gray_variance ** 0.5 + grads_variance = grads_variance ** 0.5 + for i in range(mat.shape[0]): + for j in range(mat.shape[1]): + corelation += (i - gray_mean) * (j - grads_mean) * mat[i][j] + glgcm_features = [small_grads_dominance, big_grads_dominance, gray_asymmetry, grads_asymmetry, energy, gray_mean, + grads_mean, + gray_variance, grads_variance, corelation, gray_entropy, grads_entropy, entropy, inertia, + differ_moment] + for i in range(len(glgcm_features)): + t = get_variable_name(glgcm_features[i])[0] + c_features[t].append(np.round(glgcm_features[i], 4)) + + +def get_geometry_feature(): + # 形态特征 分割mask获得一些特征 + im2, contours, x = cv2.findContours(mask_array.copy(), cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE) + tarea = [] + tperimeter = [] + for c in contours: + # 生成矩 + try: + M = cv2.moments(c) + cx = int(M['m10'] / M['m00']) + cy = int(M['m01'] / M['m00']) + c_features['focus_x'].append(cx) + c_features['focus_y'].append(cy) + except: + print('error') + + # 椭圆拟合 + try: + (x, y), (MA, ma), angle = cv2.fitEllipse(c) + c_features['ellipse'].append((ma - MA)) + except: + continue + # 面积周长 + tarea.append(cv2.contourArea(c)) + tperimeter.append(cv2.arcLength(c, True)) + + # 将mask里的最大值追加 有黑洞 + try: + c_features['area'].append(max(tarea)) + c_features['perimeter'].append(round(max(tperimeter), 4)) + except: + print('area error') + + +# 提取肿瘤特征 +def get_feature(image, mask): + global w + global image_ROI_uint8, index, image_ROI_mini, image_ROI, mask_array + + mask_array = cv2.imread(mask, 0) + image = sitk.ReadImage(image) + image_arrary = sitk.GetArrayFromImage(image)[0, :, :] + # 映射到CT获得特征 + image_ROI = np.zeros(shape=image_arrary.shape) + index = np.nonzero(mask_array) + if not index[0].any(): + # c_features['no'] = True + return None + image_ROI[index] = image_arrary[index] + image_ROI_uint8 = np.uint8(image_ROI) + # 获得只有肿瘤的图片 + x, y, w, h = cv2.boundingRect(mask_array) + image_ROI_mini = np.uint8(image_arrary[y:y + h, x:x + w]) + w = image_ROI_mini + + # 灰度梯度共生矩阵提取纹理特征 + + get_geometry_feature() + + get_gray_feature() + + glcm(image_ROI_mini, 15, 15) + + return c_features + + +def main(pid): + global w + + person_id = pid + global c_features + c_features = {} + for i in range(len(features_list)): + c_features[features_list[i]] = [column_all_c[i]] + + get_feature(f'tmp/ct/{pid}.dcm', f'tmp/mask/{pid}_mask.png') + + for j in c_features: + if j == 'id': + continue + c_features[j][1] = np.round(np.mean(c_features[j][1]), 4) + + return c_features + + +if __name__ == '__main__': + main() diff --git a/CTAI_flask/core/main.py b/CTAI_flask/core/main.py new file mode 100644 index 0000000..5fd9240 --- /dev/null +++ b/CTAI_flask/core/main.py @@ -0,0 +1,15 @@ +from core import process, predict, get_feature + + +def c_main(path,model): + image_data = process.pre_process(path) + # print(image_data) + predict.predict(image_data,model) + process.last_process(image_data[1]) + image_info = get_feature.main(image_data[1]) + + return image_data[1] + '.png', image_info + + +if __name__ == '__main__': + pass