diff --git a/_mian_tensorflow_twoLayerCNN.py b/Number-Of-CNN-Layers/_mian_tensorflow_twoLayerCNN.py similarity index 94% rename from _mian_tensorflow_twoLayerCNN.py rename to Number-Of-CNN-Layers/_mian_tensorflow_twoLayerCNN.py index 7daaec7..63509ac 100644 --- a/_mian_tensorflow_twoLayerCNN.py +++ b/Number-Of-CNN-Layers/_mian_tensorflow_twoLayerCNN.py @@ -6,11 +6,11 @@ import pywt import wfdb import tensorflow as tf from tensorflow import keras -from utils import loadData, plot_history_tf, plot_heat_map +from utils_twoLayerCNN import loadData, plot_history_tf, plot_heat_map #from ECG_read_weiyuqing_without_wfdb import ECGDATAPATH #PATH of this test -Project_PATH = "./Number-Of-CNN-Layers/Two/" +Project_PATH = "../Number-Of-CNN-Layers/Two/" #PICTUREPATH= Project_PATH + "picture/" log_dir = Project_PATH + "logs/" + datetime.datetime.now().strftime("%Y%m%d-%H%M%S") model_Path_one = Project_PATH + "model/ecg_model_one_layer.h5" @@ -61,10 +61,9 @@ def CNN_model_level_one(): # take four 21*1 conv excitation function used RElu tf.keras.layers.Conv1D(filters=4, kernel_size=21, strides=1, padding='same', activation='relu'), # take four 3*1 pool,take strids 2. + tf.keras.layers.MaxPool1D(pool_size=3, strides=2, padding='same'), - tf.keras.layers.Conv1D(filters=4, kernel_size=21, strides=1, padding='same', activation='relu'), - tf.keras.layers.MaxPool1D(pool_size=3, strides=2, padding='same'), # tf.keras.layers.Conv1D(filters=4, kernel_size=21, strides=1, padding='same', activation='relu'), # tf.keras.layers.MaxPool1D(pool_size=3, strides=2, padding='same'), diff --git a/Number-Of-CNN-Layers/utils_twoLayerCNN.py b/Number-Of-CNN-Layers/utils_twoLayerCNN.py new file mode 100644 index 0000000..d06c181 --- /dev/null +++ b/Number-Of-CNN-Layers/utils_twoLayerCNN.py @@ -0,0 +1,172 @@ +# this file give +import os + +import wfdb +import pywt +import seaborn +import numpy as np +import matplotlib.pyplot as plt +from sklearn.metrics import confusion_matrix +from sklearn.model_selection import train_test_split + +# from _mian_tensorflow import Project_PATH +Project_PATH = '../Number-Of-CNN-Layers/Two/' + +PICTUREPATH = Project_PATH + 'picture/' + +# from ECG_read_weiyuqing_without_wfdb import ECGDATAPATH +MITBITECGDATAPATH = '../MIT-BIT/' + + +# wavelet denoise preprocess using mallat algorithm + +def denoise(date): + # Wavelet db5 level9 + coeffs = pywt.wavedec(data=date, wavelet='db5', level=9) + cA9, cD9, cD8, cD7, cD6, cD5, cD4, cD3, cD2, cD1 = coeffs + # noice del + threshold = (np.median(np.abs(cD1)) / 0.6745) * (np.sqrt(2 * np.log(len(cD1)))) + # take cD 1,2 turn 0 to denoise + cD1.fill(0) + cD2.fill(0) + for i in range(1, len(coeffs) - 2): + coeffs[i] = pywt.threshold(coeffs[i], threshold) + # get signal that before wavelet + rdata = pywt.waverec(coeffs=coeffs, wavelet='db5') + return rdata + + +# get ECG data,date type and denoise +# this function without return +# use append take return data to pass data +def getDataSet(number, X_data, Y_data): + ecgClassSet = ['N', 'A', 'V', 'L', 'R'] + print('get' + number + ' ECG data') + record = wfdb.rdrecord(MITBITECGDATAPATH + number, channel_names=['MLII']) + data = record.p_signal.flatten() + # use def denoise + rdata = denoise(date=data) + + # get type of ECG data + annotation = wfdb.rdann(MITBITECGDATAPATH + number, 'atr') + Rlocation = annotation.sample # annotation.sample:get R + Rclass = annotation.symbol + + # delete stable date near R + start = 10 + end = 5 + i = start + j = len(annotation.symbol) - end + + # get NAVLR type data + while i < j: + try: + lable = ecgClassSet.index(Rclass[i]) + x_train = rdata[Rlocation[i] - 99:Rlocation[i] + 201] + X_data.append(x_train) + Y_data.append(lable) + i += 1 + except ValueError: + i += 1 + return + + +# RATIO=The ratio of the training set to the test set，usually is 0.3 +def loadData(ratio, random_seed): + numberSet = ['100', '101', '103', '105', '106', '107', '108', '109', '111', '112', '113', '114', '115', + '116', '117', '119', '121', '122', '123', '124', '200', '201', '202', '203', '205', '208', + '210', '212', '213', '214', '215', '217', '219', '220', '221', '222', '223', '228', '230', + '231', '232', '233', '234'] + dataSet = [] + labelSet = [] + for n in numberSet: + getDataSet(n, dataSet, labelSet) + + # dataSet = np.array(dataSet).reshape(-1, 300) + # labelSet = np.array(labelSet).reshape(-1, 1) + + # reshape the data and split the dataset + dataSet = np.array(dataSet).reshape(-1, 300) + lableSet = np.array(labelSet).reshape(-1) + X_train, X_test, y_train, y_test = train_test_split(dataSet, lableSet, test_size=ratio, random_state=random_seed) + # print(X_train, X_test, y_train, y_test) + return X_train, X_test, y_train, y_test + + # train_ds = np.hstack((dataSet, labelSet)) + # np.random.shuffle(train_ds) + # + # X = train_ds[:, :300].reshape(-1, 300, 1) + # Y = train_ds[:, 300] + # # cut test and train data from ECG data + # shuffle_index = np.random.permutation(len(X)) + # test_length = int(RATIO * len(shuffle_index)) + # test_index = shuffle_index[:test_length] + # train_index = shuffle_index[test_index:] + # X_test, Y_test = X[test_index:], Y[test_index] + # X_train, Y_train = X[train_index], Y[train_index] + # return X_train, Y_test, X_test, Y_train + + +# confusion matrix +def plot_heat_map(y_test, y_pred): + con_mat = confusion_matrix(y_test, y_pred) + # normalize + # con_mat_norm = con_mat.astype('float') / con_mat.sum(axis=1)[:, np.newaxis] + # con_mat_norm = np.around(con_mat_norm, decimals=2) + # os.remove(PICTUREPATH+'confusion_matrix.png') + # plot + plt.figure(figsize=(8, 8)) + seaborn.heatmap(con_mat, annot=True, fmt='.20g', cmap='Blues') + plt.ylim(0, 5) + plt.xlabel('Predicted labels') + plt.ylabel('True labels') + plt.title('Confusion Matrix') + plt.savefig(PICTUREPATH + 'confusion_matrix.png') + plt.show() + + +def plot_history_tf(history): + # os.remove(PICTUREPATH+'accuracy.png') + # os.remove(PICTUREPATH+'loss.png') + + plt.figure(figsize=(8, 8)) + plt.plot(history.history['accuracy']) + plt.plot(history.history['val_accuracy']) + plt.title('Model Accuracy') + plt.ylabel('Accuracy') + plt.xlabel('Epoch') + plt.legend(['Train', 'Test'], loc='upper left') + plt.savefig(PICTUREPATH + 'accuracy.png') + plt.show() + + plt.figure(figsize=(8, 8)) + plt.plot(history.history['loss']) + plt.plot(history.history['val_loss']) + plt.title('Model Loss') + plt.ylabel('Loss') + plt.xlabel('Epoch') + plt.legend(['Train', 'Test'], loc='upper left') + plt.savefig(PICTUREPATH + 'loss.png') + plt.show() + + +def plot_history_torch(history): + plt.figure(figsize=(8, 8)) + plt.plot(history['train_acc']) + plt.plot(history['test_acc']) + plt.title('Model Accuracy') + plt.ylabel('Accuracy') + plt.xlabel('Epoch') + plt.legend(['Train', 'Test'], loc='upper left') + plt.savefig(PICTUREPATH + 'accuracy.png') + plt.show() + + plt.figure(figsize=(8, 8)) + plt.plot(history['train_loss']) + plt.plot(history['test_loss']) + plt.title('Model Loss') + plt.ylabel('Loss') + plt.xlabel('Epoch') + plt.legend(['Train', 'Test'], loc='upper left') + plt.savefig(PICTUREPATH + 'loss.png') + plt.show() diff --git a/some-test/pynvml_test.py b/some-test/pynvml_test.py new file mode 100644 index 0000000..770915d --- /dev/null +++ b/some-test/pynvml_test.py @@ -0,0 +1,35 @@ +import pynvml + +pynvml.nvmlInit() +pynvml.nvmlSystemGetDriverVersion() +pynvml.nvmlDeviceGetCount() +handle = pynvml.nvmlDeviceGetHandleByIndex(0) + +name=pynvml.nvmlDeviceGetName(handle) + +print(name) +# 每MB包含的字节数 +NUM_EXPAND = 1024 * 1024 + +gpu_id=0 +handle = pynvml.nvmlDeviceGetHandleByIndex(gpu_id) +info = pynvml.nvmlDeviceGetMemoryInfo(handle) + +gpu_Total = info.total # 总显存 +gpu_Free = info.free +gpu_Used = info.used + +print(gpu_Total) # 显卡总的显存大小,6442450944Bit +print(gpu_Free) # 显存使用大小,4401950720Bit +print(gpu_Used) # 显卡剩余显存大小,2040500224Bit + +print(gpu_Total / NUM_EXPAND) +print(gpu_Free / NUM_EXPAND) +print(gpu_Used / NUM_EXPAND) + +# meminfo.used / 1024 / 1024 +# 4198 M + + +# 可以通过这个获取显存的使用情况 +pynvml.nvmlShutdown() \ No newline at end of file