First Commit.

HYS/ReadEDF.py

@@ -0,0 +1,148 @@
+import os
+import pyedflib
+import numpy as np
+import pandas as pd
+import shutil
+from scipy.signal import resample
+
+def writefile(filename,data,style='w'):
+    """
+    函数说明：
+    在指定地点创建一个文件，写入data数据
+    :param filename:                需写入的文件地址和名称
+    :param data:                    需写入的数据
+    :return:                        无返回
+    """
+    data = data.astype('str')            #将data数组的数据转换成字符串
+    with open(filename,style) as f :
+        for str in data :
+            f.write(str+'\n')
+    return 0
+
+def event_handle(df):
+    if df.columns[0].strip() == 'Event type':
+        df['Event type'] = df['Event type'].replace('μ-arousal', 'u-arousal')
+    elif df.columns[0].strip() == '事件类型':
+        column_mapping = {
+            "事件类型\r\r": "Event type",
+            "睡眠期\r\r": "Stage",
+            "时间\r\r": "Time",
+            "屏\r": "Epoch",
+            "日期\r\r": "Date",
+            "持续时间\r\r": "Duration",
+            "体位记录.": "Body Position",
+            "判定\r\r": "Validation"
+        }  # 列名映射
+        df = df.rename(columns=column_mapping)  # 重命名列
+        target_columns = [
+            "Event type", "Stage", "Time", "Epoch", "Date", "Duration",
+            "HR bef.", "HR extr.", "HR delta", "O2 bef.", "O2 min.",
+            "O2 delta", "Body Position", "Validation", "Unnamed: 14"
+        ]  # 添加目标文件中要求的其他列，并赋值为None
+        df = df[target_columns]  # 按目标列顺序排序
+
+        df['Event type'] = df['Event type'].replace('腿动', 'Leg Movement')
+        df['Event type'] = df['Event type'].replace('低通气', 'Hypopnea')
+        df['Event type'] = df['Event type'].replace('混合性暂停', 'Mixed apnea')
+        df['Event type'] = df['Event type'].replace('中枢性暂停', 'Central apnea')
+        df['Event type'] = df['Event type'].replace('阻塞性暂停', 'Obstructive apnea')
+        df['Event type'] = df['Event type'].replace('氧减', 'Desaturation')
+        df['Event type'] = df['Event type'].replace('长RR间距', 'Long RR')
+        df['Event type'] = df['Event type'].replace('心率上升', 'Heart Rate Rise')
+        df['Event type'] = df['Event type'].replace('心率下降', 'Heart Rate Drop')
+        df['Event type'] = df['Event type'].replace('PTT下降', 'PTT drop')
+        df['Event type'] = df['Event type'].replace('鼾声', 'Snore')
+        df['Event type'] = df['Event type'].replace('微觉醒', 'u-arousal')
+    else:
+        assert (df.columns[0].strip() == '事件类型')
+
+    return df
+
+def upsample_resample(data,data_fs,target_fs):
+    up_ratio = target_fs / data_fs
+    target_num = int(len(data) * up_ratio)
+
+    # 执行重采样
+    if up_ratio > 1:
+        data_up = resample(data, target_num)
+        target_fs = int(target_fs)
+    else:
+        print("上采样倍数不大于1，不进行上采样操作")
+        data_up = data
+        target_fs = int(data_fs)
+
+    return data_up,target_fs
+
+def read_edf(edfpath,stagepath,eventpath,outpath):
+    list = np.array([f for f in os.listdir(edfpath) if f.endswith('.edf')])
+    for sample_num in list:
+        print("样本编号：", sample_num)
+
+        output_sample = outpath + sample_num.split('.')[0][-4:] + '/'
+        if not os.path.exists(output_sample):
+            os.makedirs(output_sample)
+
+        ##读取edf文件数据
+        fpath = edfpath + sample_num
+        shutil.copy(fpath, output_sample)
+        with pyedflib.EdfReader(fpath) as file:
+            ##读取导出的睡眠分期标签csv文件
+            df = pd.read_csv(stagepath + sample_num.split('.')[0] + '_Stage.csv')
+            stage_values = df.values[:,0].reshape(-1)
+
+            ##读edf文件信息
+            start_time = file.getStartdatetime()
+            sec = file.getFileDuration()
+            day_start = start_time.strftime("%Y") + "/" + str(start_time.month) + "/" + str(start_time.day)
+            sec_start = start_time.strftime("%H") + ":" + start_time.strftime("%M") + ":" + start_time.strftime("%S")
+            # sec_start = str(start_time.hour) + ":" + str(f"{start_time.minute:02d}") + ":" + str(f"{start_time.second:02d}")
+            assert (df.columns[3] == day_start)
+            assert (df.columns[4] == sec_start)
+            print("edf文件与睡眠分期标签开始时间一致！！！！！！！")
+
+            ##读取Event列表
+            df1 = pd.read_csv(eventpath + sample_num.split('.')[0] + '_Event.csv',header=0,encoding='GBK')
+            df1 = event_handle(df1)
+            df1.to_csv(output_sample + 'SA Label_Raw.csv', index=False, encoding='GBK')
+
+            signal_num = file.signals_in_file
+            signal_label = file.getSignalLabels()
+            min_length = int(np.min([sec,df.shape[0]]))
+            print("裁剪为最小长度:",min_length)
+            flag = 0
+            for i, index in enumerate(signal_label):
+                signal = file.readSignal(i)
+                sample_frequency = int(file.getSampleFrequency(i))
+                data_org = signal[0:min_length * sample_frequency]
+
+                if (index== 'Flow Patient') :
+                    if flag == 0:
+                        writefile(output_sample + 'Flow T_Raw_' + str(sample_frequency) + '.txt', data_org)
+                        flag = 1
+                    else:
+                        writefile(output_sample + 'Flow P_Raw_' + str(sample_frequency) + '.txt', data_org)
+
+                else:
+                    writefile(output_sample + index + '_Raw_' + str(sample_frequency) + '.txt', data_org)
+            with open(os.path.join(output_sample, "StartTime_Raw.txt"), "a") as text_file:
+                text_file.write(start_time.strftime("%Y-%m-%d %H:%M:%S\n"))
+                text_file.write("{:g}\n".format(int(sec)))
+
+            ##裁剪对齐睡眠分期标签
+            stage_values = stage_values.astype(int)
+            stage_values = np.where(stage_values == 11, 'W', stage_values)
+            stage_values = np.where(stage_values == '12', 'R', stage_values)
+            stage_values = np.where(stage_values == '13', 'N1', stage_values)
+            stage_values = np.where(stage_values == '14', 'N2', stage_values)
+            stage = np.where(stage_values == '15', 'N3', stage_values)
+            writefile(output_sample + '5_class_Raw_1.txt',stage[0:min_length])
+
+if __name__ == '__main__':
+    edf_dir = 'E:\DB\\testdata\HYS\PSG_Origin/Edf/'
+    stage_dir = 'E:\DB\\testdata\HYS\PSG_Origin/Stage/'
+    event_dir = 'E:\DB\\testdata\HYS\PSG_Origin/Event/'
+    output_dir = 'E:\DB\\testdata\HYS\PSG_Text/'
+
+    read_edf(edf_dir,stage_dir,event_dir,output_dir)
+
+    print("finished")