From 7555ca4a592ff221f68cccd1ed0d4b1bcd9dd7df Mon Sep 17 00:00:00 2001 From: marques <20172333133@m.scnu.edu.cn> Date: Sat, 11 Jan 2025 17:05:17 +0800 Subject: [PATCH] =?UTF-8?q?Main=5FQuality=5FRelabel=5FGUI.py=20=E4=BF=AE?= =?UTF-8?q?=E6=94=B9=E4=B8=80=E4=BA=9Bpathlib=E5=92=8Cos.path=E5=A4=8D?= =?UTF-8?q?=E7=94=A8=E7=9A=84=E4=BB=A3=E7=A0=81=20=E5=8C=85=E7=9A=84?= =?UTF-8?q?=E5=BC=95=E7=94=A8=E6=94=B9=E6=88=90from=E5=AF=BC=E5=85=A5=20?= =?UTF-8?q?=E5=87=8F=E5=B0=91=E6=89=93=E5=8C=85=E5=90=8E=E7=9A=84=E7=A8=8B?= =?UTF-8?q?=E5=BA=8F=E4=BD=93=E7=A7=AF=20Preprocessing.py=20=E8=BE=83?= =?UTF-8?q?=E5=B0=91=E4=B8=8D=E5=BF=85=E8=A6=81=E5=8C=85=E7=9A=84=E5=BC=95?= =?UTF-8?q?=E5=85=A5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .gitignore | 1 + MainWindow.py | 1 + Main_Quality_Relabel_GUI.py | 566 ++++++++++++++++++++---------------- PSG_label_2_BCG_label.py | 2 +- utils/Preprocessing.py | 191 ++---------- 5 files changed, 344 insertions(+), 417 deletions(-) diff --git a/.gitignore b/.gitignore index 3eba565..8695265 100644 --- a/.gitignore +++ b/.gitignore @@ -252,6 +252,7 @@ ipython_config.py # Remove previous ipynb_checkpoints # git rm -r .ipynb_checkpoints/ +SaLabel/ data/* logs/* .idea/* diff --git a/MainWindow.py b/MainWindow.py index bf7fc03..000ef47 100644 --- a/MainWindow.py +++ b/MainWindow.py @@ -11,6 +11,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_MainWindow(object): def setupUi(self, MainWindow): MainWindow.setObjectName("MainWindow") diff --git a/Main_Quality_Relabel_GUI.py b/Main_Quality_Relabel_GUI.py index 0f8760b..7076c90 100644 --- a/Main_Quality_Relabel_GUI.py +++ b/Main_Quality_Relabel_GUI.py @@ -5,26 +5,26 @@ @time:2025/1/4 """ -import os import sys -import logging -import time -import numpy as np -import pandas as pd -import matplotlib -import pyedflib -import traceback +from logging import NOTSET, getLogger, FileHandler, Formatter, StreamHandler, info, error, debug +from time import time, strftime, localtime +from numpy import load, nan, zeros, append, linspace, place +from pandas import DataFrame, read_csv, read_excel, Series, concat +from matplotlib import use +from matplotlib import pyplot as plt, gridspec +from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT +from pyedflib import EdfReader from datetime import datetime from tqdm import tqdm from pathlib import Path -from PyQt5 import QtCore, QtWidgets -from PyQt5.QtWidgets import QFileDialog, QMainWindow, QMessageBox, QButtonGroup -from matplotlib import pyplot as plt, gridspec -from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT -from MainWindow import Ui_MainWindow -from utils.Preprocessing import BCG_Operation +from PyQt5.QtCore import QCoreApplication, QThread, pyqtSignal +from PyQt5.QtWidgets import QFileDialog, QMainWindow, QMessageBox, QButtonGroup, QApplication -matplotlib.use("Qt5Agg") # 声明使用QT5 +from MainWindow import Ui_MainWindow +from utils.Preprocessing import Butterworth + + +use("Qt5Agg") # 声明使用QT5 plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签 plt.rcParams['axes.unicode_minus'] = False # 用来正常显示负号 @@ -36,25 +36,25 @@ plt.rcParams['axes.unicode_minus'] = False # 用来正常显示负号 # 'EEG A1-A2', 'Imp'] # 设置日志 -logger = logging.getLogger() -logger.setLevel(logging.NOTSET) -realtime = time.strftime('%Y%m%d', time.localtime(time.time())) -if not os.path.exists(Path("logs")): - os.makedirs(Path("logs")) -fh = logging.FileHandler(Path("logs") / (realtime + ".log"), mode='a') -fh.setLevel(logging.NOTSET) -fh.setFormatter(logging.Formatter("%(asctime)s: %(message)s")) +logger = getLogger() +logger.setLevel(NOTSET) +realtime = strftime('%Y%m%d', localtime(time())) +if not Path("logs").exists(): + Path("logs").mkdir(exist_ok=True) +fh = FileHandler(Path("logs") / (realtime + ".log"), mode='a') +fh.setLevel(NOTSET) +fh.setFormatter(Formatter("%(asctime)s: %(message)s")) logger.addHandler(fh) -ch = logging.StreamHandler() -ch.setLevel(logging.NOTSET) -ch.setFormatter(logging.Formatter("%(asctime)s: %(message)s")) +ch = StreamHandler() +ch.setLevel(NOTSET) +ch.setFormatter(Formatter("%(asctime)s: %(message)s")) logger.addHandler(ch) -logging.getLogger('matplotlib.font_manager').disabled = True -logging.info("------------------------------------") +getLogger('matplotlib.font_manager').disabled = True +info("------------------------------------") + class MainWindow(QMainWindow, Ui_MainWindow): - # 可选择的通道 base_channel = ['EEG F3-A2', 'EEG F4-A1', 'EEG C3-A2', 'EEG C4-A1', 'EEG O1-A2', 'EEG O2-A1', 'EOG Right', 'EOG Left', 'EMG Chin', 'ECG I', 'RR', 'ECG II', 'Effort Tho', 'Flow Patient', 'Flow Patient', 'HR', @@ -178,72 +178,76 @@ class MainWindow(QMainWindow, Ui_MainWindow): fileDialog.setOption(QFileDialog.ShowDirsOnly, True) if fileDialog.exec_() == QFileDialog.Accepted: self.dir_path = fileDialog.selectedFiles()[0] - if self.dir_path: - logging.info("Loading Data Path...") - self.PSG_Data_Path = Path(os.path.join(self.dir_path, "PSG")) - self.BCG_Data_Path = Path(os.path.join(self.dir_path, "BCG")) - self.BCG_Label_Path = Path(os.path.join(self.dir_path, "BCG_label")) - self.Artifact_Label_Path = Path(os.path.join(self.dir_path, "Artifact_label")) - self.Artifact_Offset_Path = Path(os.path.join(self.dir_path, "Artifact_label", "20220421Artifact_offset_value.xlsx")) - if self.PSG_Data_Path.exists() and self.BCG_Data_Path.exists() and self.BCG_Label_Path.exists() and self.Artifact_Label_Path.exists() and self.Artifact_Label_Path.exists(): - sampIDs = os.listdir(self.BCG_Data_Path) - sampID_for_comboBox = [] - for sampID in sampIDs: - sampID = sampID.replace("samp.npy", "") - sampID_for_comboBox.append(sampID) - bcg_path = self.BCG_Data_Path / f"{sampID}samp.npy" - ecg_path = self.PSG_Data_Path / f"A{str(sampID).rjust(7, '0')}.edf" - bcg_label_path = self.BCG_Label_Path / f"export{sampID}_all.csv" - if not bcg_path.exists(): - logging.error(f"Can't find {bcg_path}!") - self.msgBox.setText(f"找不到数据{bcg_path}") - self.msgBox.setIcon(QMessageBox.Critical) - self.msgBox.exec() - return - if not ecg_path.exists(): - logging.error(f"Can't find {ecg_path}!") - self.msgBox.setText(f"找不到数据{ecg_path}") - self.msgBox.setIcon(QMessageBox.Critical) - self.msgBox.exec() - return - if not bcg_label_path.exists(): - logging.error(f"Can't find {bcg_label_path}!") - self.msgBox.setText(f"找不到数据{bcg_label_path}") - self.msgBox.setIcon(QMessageBox.Critical) - self.msgBox.exec() - return - self.comboBox_sampID.setEnabled(True) - self.lineEdit_start_bcg_index.setEnabled(True) - self.comboBox_sampID.addItems(sampID_for_comboBox) - self.lineEdit_start_bcg_index.setEnabled(True) - self.lineEdit_frequency.setEnabled(True) - self.lineEdit_bcg_frequency.setEnabled(True) - self.lineEdit_front_add_second.setEnabled(True) - self.lineEdit_back_add_second.setEnabled(True) - self.checkBox_OSA.setEnabled(True) - self.checkBox_CSA.setEnabled(True) - self.checkBox_MSA.setEnabled(True) - self.checkBox_HPY.setEnabled(True) - self.action_selectPath.setEnabled(False) - self.pushButton_confirmLabel.setEnabled(True) - self.pushButton_confirmLabel.setText("开始打标") - MainWindow.setWindowTitle(self, QtCore.QCoreApplication.translate("MainWindow", "Main_Quality_Relabel_GUI - Data Path: " + self.dir_path)) - logging.info("Successfully Loaded Data Path.") - self.textBrowser_update("操作：数据路径选择成功") - else: - logging.info("Failed to Load Data Path.") - self.textBrowser_update("操作：数据路径选择错误，缺乏必要数据文件夹") - self.msgBox.setText("数据路径选择错误，缺乏必要数据文件夹") - self.msgBox.setIcon(QMessageBox.Critical) - self.msgBox.exec() - else: - logging.info("Data Path not Exist...") + if not self.dir_path: + info("Data Path not Exist...") self.textBrowser_update("操作：载入存档错误，存档不存在") self.msgBox.setText("载入存档错误，存档不存在") self.msgBox.setIcon(QMessageBox.Critical) self.msgBox.exec() + return + + self.dir_path = Path(self.dir_path) + info("Loading Data Path...") + self.PSG_Data_Path = self.dir_path / "PSG" + self.BCG_Data_Path = self.dir_path / "BCG" + self.BCG_Label_Path = self.dir_path / "BCG_label" + self.Artifact_Label_Path = self.dir_path / "Artifact_label" + self.Artifact_Offset_Path = self.dir_path / "Artifact_label" / "20220421Artifact_offset_value.xlsx" + if self.PSG_Data_Path.exists() and self.BCG_Data_Path.exists() and self.BCG_Label_Path.exists() and self.Artifact_Label_Path.exists() and self.Artifact_Label_Path.exists(): + sampIDs = self.BCG_Data_Path.glob() + sampID_for_comboBox = [] + for sampID in sampIDs: + sampID = sampID.replace("samp.npy", "") + sampID_for_comboBox.append(sampID) + bcg_path = self.BCG_Data_Path / f"{sampID}samp.npy" + ecg_path = self.PSG_Data_Path / f"A{str(sampID).rjust(7, '0')}.edf" + bcg_label_path = self.BCG_Label_Path / f"export{sampID}_all.csv" + if not bcg_path.exists(): + error(f"Can't find {bcg_path}!") + self.msgBox.setText(f"找不到数据{bcg_path}") + self.msgBox.setIcon(QMessageBox.Critical) + self.msgBox.exec() + return + if not ecg_path.exists(): + error(f"Can't find {ecg_path}!") + self.msgBox.setText(f"找不到数据{ecg_path}") + self.msgBox.setIcon(QMessageBox.Critical) + self.msgBox.exec() + return + if not bcg_label_path.exists(): + error(f"Can't find {bcg_label_path}!") + self.msgBox.setText(f"找不到数据{bcg_label_path}") + self.msgBox.setIcon(QMessageBox.Critical) + self.msgBox.exec() + return + self.comboBox_sampID.setEnabled(True) + self.lineEdit_start_bcg_index.setEnabled(True) + self.comboBox_sampID.addItems(sampID_for_comboBox) + self.lineEdit_start_bcg_index.setEnabled(True) + self.lineEdit_frequency.setEnabled(True) + self.lineEdit_bcg_frequency.setEnabled(True) + self.lineEdit_front_add_second.setEnabled(True) + self.lineEdit_back_add_second.setEnabled(True) + self.checkBox_OSA.setEnabled(True) + self.checkBox_CSA.setEnabled(True) + self.checkBox_MSA.setEnabled(True) + self.checkBox_HPY.setEnabled(True) + self.action_selectPath.setEnabled(False) + self.pushButton_confirmLabel.setEnabled(True) + self.pushButton_confirmLabel.setText("开始打标") + MainWindow.setWindowTitle(self, QCoreApplication.translate("MainWindow", + "Main_Quality_Relabel_GUI - Data Path: " + self.dir_path)) + info("Successfully Loaded Data Path.") + self.textBrowser_update("操作：数据路径选择成功") + else: + info("Failed to Load Data Path.") + self.textBrowser_update("操作：数据路径选择错误，缺乏必要数据文件夹") + self.msgBox.setText("数据路径选择错误，缺乏必要数据文件夹") + self.msgBox.setIcon(QMessageBox.Critical) + self.msgBox.exec() + else: - logging.info("Canceled Loading Data Path.") + info("Canceled Loading Data Path.") self.textBrowser_update("提示：数据路径选择取消") self.msgBox.setText("数据路径选择取消") self.msgBox.setIcon(QMessageBox.Warning) @@ -264,7 +268,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.pushButton_left.setEnabled(False) self.pushButton_right.setEnabled(True) self.pushButton_confirmLabel.setText("确定打标参数(S)") - self.pushButton_confirmLabel.setShortcut(QtCore.QCoreApplication.translate("MainWindow", "S")) + self.pushButton_confirmLabel.setShortcut(QCoreApplication.translate("MainWindow", "S")) self.pushButton_confirmLabel.clicked.disconnect(self.slot_btn_run) self.pushButton_confirmLabel.clicked.connect(self.slot_btn_confirmLabel) self.pushButton_quick_remark_input_waitingForTalk.setEnabled(True) @@ -297,49 +301,61 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.lineEdit_remark.setEnabled(True) self.lineEdit_correctStart.setEnabled(True) self.lineEdit_correctEnd.setEnabled(True) - self.pd = pd.read_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_all.csv")), encoding="gbk") - csv_headers = self.pd.columns.tolist() - if not (("score" in csv_headers) and ("remark" in csv_headers) and ("correct_Start" in csv_headers) and ("correct_End") in csv_headers and ("isLabeled" in csv_headers)): - self.pd["score"] = "-1" - self.pd["remark"] = "" - self.pd["correct_Start"] = "-1" - self.pd["correct_End"] = "-1" - self.pd["correct_EventsType"] = "" - self.pd["isLabeled"] = "-1" - self.pd["score"] = self.pd["score"].astype(int) - self.pd["remark"] = self.pd["remark"].astype(str) - self.pd["correct_Start"] = self.pd["correct_Start"].astype(int) - self.pd["correct_End"] = self.pd["correct_End"].astype(int) - self.pd["correct_EventsType"] = self.pd["correct_EventsType"].astype(str) - self.pd["isLabeled"] = self.pd["isLabeled"].astype(int) + self.df_saLabel = read_csv( + self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_all.csv", + encoding="gbk") + csv_headers = self.df_saLabel.columns.tolist() + if not (("score" in csv_headers) and ("remark" in csv_headers) and ("correct_Start" in csv_headers) and ( + "correct_End") in csv_headers and ("isLabeled" in csv_headers)): + self.df_saLabel["score"] = "-1" + self.df_saLabel["remark"] = "" + self.df_saLabel["correct_Start"] = "-1" + self.df_saLabel["correct_End"] = "-1" + self.df_saLabel["correct_EventsType"] = "" + self.df_saLabel["isLabeled"] = "-1" + self.df_saLabel["score"] = self.df_saLabel["score"].astype(int) + self.df_saLabel["remark"] = self.df_saLabel["remark"].astype(str) + self.df_saLabel["correct_Start"] = self.df_saLabel["correct_Start"].astype(int) + self.df_saLabel["correct_End"] = self.df_saLabel["correct_End"].astype(int) + self.df_saLabel["correct_EventsType"] = self.df_saLabel["correct_EventsType"].astype(str) + self.df_saLabel["isLabeled"] = self.df_saLabel["isLabeled"].astype(int) self.change_radioButton_events(self.bcg_event_label_index_list[self.plotEventIndex]) - if not Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_addNew.csv")).exists(): - self.pd_examineBySecond = pd.DataFrame(columns=self.pd.columns) + if not Path(self.BCG_Label_Path / + f"export{self.comboBox_sampID.currentText()}_addNew.csv").exists(): + self.pd_examineBySecond = DataFrame(columns=self.df_saLabel.columns) self.pd_examineBySecond["score"] = self.pd_examineBySecond["score"].astype(int) self.pd_examineBySecond["remark"] = self.pd_examineBySecond["remark"].astype(str) self.pd_examineBySecond["correct_Start"] = self.pd_examineBySecond["correct_Start"].astype(int) self.pd_examineBySecond["correct_End"] = self.pd_examineBySecond["correct_End"].astype(int) - self.pd_examineBySecond["correct_EventsType"] = self.pd_examineBySecond["correct_EventsType"].astype(str) + self.pd_examineBySecond["correct_EventsType"] = self.pd_examineBySecond["correct_EventsType"].astype( + str) self.pd_examineBySecond["isLabeled"] = self.pd_examineBySecond["isLabeled"].astype(int) - self.pd_examineBySecond.to_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_addNew.csv")), index=False, encoding="gbk") + self.pd_examineBySecond.to_csv( + self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_addNew.csv", + index=False, encoding="gbk") else: - self.pd_examineBySecond = pd.read_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_addNew.csv")), encoding="gbk") - if (self.pd["isLabeled"] == 1).all(): + self.pd_examineBySecond = read_csv( + self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_addNew.csv", + encoding="gbk") + if (self.df_saLabel["isLabeled"] == 1).all(): self.checkBox_examineLabeled.setChecked(False) self.msgBox.setText("该份数据打标已全部完成") self.msgBox.setIcon(QMessageBox.Information) self.msgBox.exec() - self.pd.to_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_all.csv")), mode='w', index=None, encoding="gbk") - self.show_one_event(self.plotEventIndex, front_add_second=self.front_add_second, back_add_second=self.back_add_second) - if not str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": - self.lineEdit_remark.setText(str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) + self.df_saLabel.to_csv(self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_all.csv", + mode='w', index=None, encoding="gbk") + self.show_one_event(self.plotEventIndex, front_add_second=self.front_add_second, + back_add_second=self.back_add_second) + if not str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": + self.lineEdit_remark.setText( + str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) else: self.lineEdit_remark.setText("") - if str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": + if str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": self.radioButton_1_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": self.radioButton_2_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": self.radioButton_3_class.setChecked(True) else: self.radioButton_2_class.setChecked(True) @@ -350,20 +366,22 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.figure.clear() self.plotEventIndex = self.plotEventIndex - 1 if self.checkBox_examineLabeled.isChecked() == True: - while self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == 1 and self.plotEventIndex > self.start_bcg_index: + while self.df_saLabel.at[self.bcg_event_label_index_list[ + self.plotEventIndex], "isLabeled"] == 1 and self.plotEventIndex > self.start_bcg_index: self.plotEventIndex = self.plotEventIndex - 1 self.show_one_event(self.plotEventIndex, front_add_second=self.front_add_second, back_add_second=self.back_add_second) - if not str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": - self.lineEdit_remark.setText(str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) + if not str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": + self.lineEdit_remark.setText( + str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) else: self.lineEdit_remark.setText("") self.change_radioButton_events(self.bcg_event_label_index_list[self.plotEventIndex]) - if str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": + if str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": self.radioButton_1_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": self.radioButton_2_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": self.radioButton_3_class.setChecked(True) else: self.radioButton_2_class.setChecked(True) @@ -383,20 +401,23 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.figure.clear() self.plotEventIndex = self.plotEventIndex + 1 if self.checkBox_examineLabeled.isChecked() == True: - while self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == 1 and self.plotEventIndex < len(self.bcg_event_label_filtered_df) - 1: + while self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == 1 and self.plotEventIndex < len( + self.bcg_event_label_filtered_df) - 1: self.plotEventIndex = self.plotEventIndex + 1 self.show_one_event(self.plotEventIndex, front_add_second=self.front_add_second, back_add_second=self.back_add_second) - if not str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": - self.lineEdit_remark.setText(str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) + if not str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"]) == "nan": + self.lineEdit_remark.setText( + str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"])) else: self.lineEdit_remark.setText("") self.change_radioButton_events(self.bcg_event_label_index_list[self.plotEventIndex]) - if str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": + if str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "1": self.radioButton_1_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "2": self.radioButton_2_class.setChecked(True) - elif str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": + elif str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) == "3": self.radioButton_3_class.setChecked(True) else: self.radioButton_2_class.setChecked(True) @@ -437,36 +458,59 @@ class MainWindow(QMainWindow, Ui_MainWindow): elif self.radioButton_HPY.isChecked() == True: correct_EventsType = "Hypopnea" isLabeled = int(1) - self.pd_examineBySecond = self.pd_add_new_row(self.pd_examineBySecond, score, remark, correct_Start, correct_End, correct_EventsType, isLabeled) - self.pd_examineBySecond.to_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_addNew.csv")), mode='w', index=None, encoding="gbk") - self.textBrowser_update("操作：保存新事件打标结果到csv。" + "score:" + str(score) + "，correct_Start:" + str(correct_Start) + "，correct_End:" + str(correct_End) + "，correct_EventsType:" + str(correct_EventsType)) + self.pd_examineBySecond = self.pd_add_new_row(self.pd_examineBySecond, score, remark, correct_Start, + correct_End, correct_EventsType, isLabeled) + self.pd_examineBySecond.to_csv( + self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_addNew.csv", + mode='w', index=None, encoding="gbk") + self.textBrowser_update( + "操作：保存新事件打标结果到csv。" + "score:" + str(score) + "，correct_Start:" + str( + correct_Start) + "，correct_End:" + str(correct_End) + "，correct_EventsType:" + str( + correct_EventsType)) else: self.msgBox.setText("起始时间和终止时间输入错误") self.msgBox.setIcon(QMessageBox.Critical) self.msgBox.exec() - elif self.checkBox_examineBySecond.isChecked() == False: + elif not self.checkBox_examineBySecond.isChecked(): if int(self.lineEdit_correctStart.text()) < int(self.lineEdit_correctEnd.text()): - if self.radioButton_1_class.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(1) - elif self.radioButton_2_class.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(2) - elif self.radioButton_3_class.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(3) - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "remark"] = self.lineEdit_remark.text() - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"] = int(self.lineEdit_correctStart.text()) - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"] = int(self.lineEdit_correctEnd.text()) - if self.radioButton_OSA.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Obstructive apnea" - elif self.radioButton_CSA.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Central apnea" - elif self.radioButton_MSA.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Mixed apnea" - elif self.radioButton_HPY.isChecked() == True: - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Hypopnea" - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] = int(1) - self.pd.to_csv(Path(os.path.join(self.BCG_Label_Path, f"export{self.comboBox_sampID.currentText()}_all.csv")), mode='w', index=None, encoding="gbk") - self.textBrowser_update("操作：保存index" + str(self.plotEventIndex + 1) + "打标结果到csv。" + "score:" + str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"]) + "，correct_Start:" + str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"]) + "，correct_End:" + str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"]) + "，correct_EventsType:" + str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"])) - if (self.pd.loc[self.bcg_event_label_index_list]["isLabeled"] == 1).all(): + if self.radioButton_1_class.isChecked(): + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(1) + elif self.radioButton_2_class.isChecked(): + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(2) + elif self.radioButton_3_class.isChecked(): + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "score"] = int(3) + self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "remark"] = self.lineEdit_remark.text() + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"] = int( + self.lineEdit_correctStart.text()) + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"] = int( + self.lineEdit_correctEnd.text()) + if self.radioButton_OSA.isChecked(): + self.df_saLabel.at[self.bcg_event_label_index_list[ + self.plotEventIndex], "correct_EventsType"] = "Obstructive apnea" + elif self.radioButton_CSA.isChecked(): + self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Central apnea" + elif self.radioButton_MSA.isChecked(): + self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Mixed apnea" + elif self.radioButton_HPY.isChecked(): + self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] = "Hypopnea" + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] = int(1) + self.df_saLabel.to_csv(self.BCG_Label_Path / f"export{self.comboBox_sampID.currentText()}_all.csv", + mode='w', index=None, encoding="gbk") + self.textBrowser_update( + "操作：保存index" + str(self.plotEventIndex + 1) + "打标结果到csv。" + "score:" + str( + self.df_saLabel.at[ + self.bcg_event_label_index_list[ + self.plotEventIndex], "score"]) + "，correct_Start:" + str( + self.df_saLabel.at[self.bcg_event_label_index_list[ + self.plotEventIndex], "correct_Start"]) + "，correct_End:" + str(self.df_saLabel.at[ + self.bcg_event_label_index_list[ + self.plotEventIndex], "correct_End"]) + "，correct_EventsType:" + str( + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"])) + if (self.df_saLabel.loc[self.bcg_event_label_index_list]["isLabeled"] == 1).all(): self.msgBox.setText("该份数据打标已全部完成") self.msgBox.setIcon(QMessageBox.Information) self.msgBox.exec() @@ -570,7 +614,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): # +60s的槽函数 def enable_checkBox_examineLabeled(self): if self.checkBox_examineLabeled.isChecked(): - if (self.pd.loc[self.bcg_event_label_index_list]["isLabeled"] == 1).all(): + if (self.df_saLabel.loc[self.bcg_event_label_index_list]["isLabeled"] == 1).all(): self.checkBox_examineLabeled.setChecked(False) self.msgBox.setText("该份数据打标已全部完成") self.msgBox.setIcon(QMessageBox.Information) @@ -636,23 +680,23 @@ class MainWindow(QMainWindow, Ui_MainWindow): # 修改了事件类型单选框后执行的函数 def change_radioButton_events(self, index): - if not (self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == -1): - if self.pd.at[index, "correct_EventsType"] == "Obstructive apnea": + if not (self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == -1): + if self.df_saLabel.at[index, "correct_EventsType"] == "Obstructive apnea": self.radioButton_OSA.setChecked(True) - elif self.pd.at[index, "correct_EventsType"] == "Central apnea": + elif self.df_saLabel.at[index, "correct_EventsType"] == "Central apnea": self.radioButton_CSA.setChecked(True) - elif self.pd.at[index, "correct_EventsType"] == "Mixed apnea": + elif self.df_saLabel.at[index, "correct_EventsType"] == "Mixed apnea": self.radioButton_MSA.setChecked(True) - elif self.pd.at[index, "correct_EventsType"] == "Hypopnea": + elif self.df_saLabel.at[index, "correct_EventsType"] == "Hypopnea": self.radioButton_HPY.setChecked(True) else: - if self.pd.at[index, "Event type"] == "Obstructive apnea": + if self.df_saLabel.at[index, "Event type"] == "Obstructive apnea": self.radioButton_OSA.setChecked(True) - elif self.pd.at[index, "Event type"] == "Central apnea": + elif self.df_saLabel.at[index, "Event type"] == "Central apnea": self.radioButton_CSA.setChecked(True) - elif self.pd.at[index, "Event type"] == "Mixed apnea": + elif self.df_saLabel.at[index, "Event type"] == "Mixed apnea": self.radioButton_MSA.setChecked(True) - elif self.pd.at[index, "Event type"] == "Hypopnea": + elif self.df_saLabel.at[index, "Event type"] == "Hypopnea": self.radioButton_HPY.setChecked(True) # 点击开始打标按钮后的初始化变量函数 @@ -684,7 +728,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): def check_channel(self): for i in self.channel_list: if i not in self.base_channel: - logging.debug(f"{i} 不存在于常见通道名中") + debug(f"{i} 不存在于常见通道名中") print(f"常见通道名：{self.channel_list}") def set_focus_event_list(self): @@ -704,19 +748,19 @@ class MainWindow(QMainWindow, Ui_MainWindow): ecg_path = self.PSG_Data_Path / f"A{str(self.sampNo).rjust(7, '0')}.edf" if not bcg_path.exists(): - logging.error(f"Can't find {bcg_path} !") + error(f"Can't find {bcg_path} !") raise FileNotFoundError(f"Can't find {bcg_path} !") if not ecg_path.exists(): - logging.error(f"Can't find {ecg_path} !") + error(f"Can't find {ecg_path} !") raise FileNotFoundError(f"Can't find {ecg_path} !") - with pyedflib.EdfReader(str(ecg_path.resolve())) as file: + with EdfReader(str(ecg_path.resolve())) as file: signal_num = file.signals_in_file - logging.debug(f"{self.sampNo} EDF file signal number is {signal_num}") + debug(f"{self.sampNo} EDF file signal number is {signal_num}") signal_label = file.getSignalLabels() - logging.debug(f"{self.sampNo} EDF file signal label : {signal_label}") + debug(f"{self.sampNo} EDF file signal label : {signal_label}") # 打印PSG信息 file.file_info_long() @@ -724,7 +768,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): # sub_index 用于区分两个flow patient sub_index = 1 - logging.info("Loading PSG signal...") + info("Loading PSG signal...") self.textBrowser_update("提示：正在加载PSG信号") for i, index in enumerate(signal_label): # 仅加载选中的通道 @@ -744,44 +788,43 @@ class MainWindow(QMainWindow, Ui_MainWindow): elif sample_frequency > self.frequency: signal = signal[::int(sample_frequency / self.frequency)] self.signal_select[index] = signal - logging.info(f"Finished load PSG: {index}") + info(f"Finished load PSG: {index}") self.textBrowser_update("提示：完成加载PSG信号") # 加载心晓信号 - logging.info("Loading XinXiao signal...") + info("Loading XinXiao signal...") self.textBrowser_update("提示：正在加载心晓信号") - signal = np.load(bcg_path) - preprocessing = BCG_Operation(sample_rate=self.bcg_frequency) + signal = load(bcg_path) # 20Hz低通去噪 - signal1 = preprocessing.Butterworth(signal, 'lowpass', low_cut=20, order=3) + signal1 = Butterworth(signal, self.bcg_frequency, 'lowpass', low_cut=20, order=3) # 0.7Hz 低通提取呼吸 - signal2 = preprocessing.Butterworth(signal, 'lowpass', low_cut=0.7, order=3) + signal2 = Butterworth(signal, self.bcg_frequency, 'lowpass', low_cut=0.7, order=3) # 进行降采样 signal1 = signal1[::int(self.bcg_frequency / self.frequency)] signal2 = signal2[::int(self.bcg_frequency / self.frequency)] # 根据心晓事件长度生成事件记录 - self.bcg_event_label = np.zeros(len(signal) + self.extend_second * self.frequency) + self.bcg_event_label = zeros(len(signal) + self.extend_second * self.frequency) self.signal_select['orgdata'] = signal1 self.signal_select['0.7lowpass_resp'] = signal2 for signal_key in self.signal_select.keys(): - self.signal_select[signal_key] = np.append(self.signal_select[signal_key], + self.signal_select[signal_key] = append(self.signal_select[signal_key], self.signal_select[signal_key].mean().astype(int).repeat( self.extend_second * self.frequency)) - logging.info("Finished load XinXiao signal") + info("Finished load XinXiao signal") self.textBrowser_update("提示：完成加载心晓信号") def read_event(self): bcg_label_path = self.BCG_Label_Path / f"export{self.sampNo}_all.csv" if not bcg_label_path.exists(): - logging.error(f"Can't find {bcg_label_path} !") + error(f"Can't find {bcg_label_path} !") raise FileNotFoundError(f"Can't find {bcg_label_path} !") # 读取心晓事件 - df = pd.read_csv(bcg_label_path, encoding="gbk") + df = read_csv(bcg_label_path, encoding="gbk") df["Start"] = df["Start"].astype("int") df["End"] = df["End"].astype("int") self.bcg_event_label_df = df @@ -791,7 +834,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): df2 = df2.sort_values(by='Epoch') self.bcg_event_label_filtered_df = df2 self.bcg_event_label_index_list = df2.index.tolist() - logging.info("Traversaling XinXiao events...") + info("Traversaling XinXiao events...") self.textBrowser_update("提示：正在遍历心晓事件") for one_data in tqdm(df.index): one_data = df.loc[one_data] @@ -806,16 +849,16 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.bcg_event_label[SP:EP] = 3 elif one_data["Event type"] == "Mixed apnea": self.bcg_event_label[SP:EP] = 4 - logging.info("Finished Traversal XinXiao events") + info("Finished Traversal XinXiao events") self.textBrowser_update("提示：完成遍历心晓事件") def read_artifact_label(self): - all_offset_length = pd.read_excel(self.Artifact_Offset_Path) + all_offset_length = read_excel(self.Artifact_Offset_Path) offset_length = all_offset_length[all_offset_length['数据编号'] == self.sampNo]['from_code'].values[0] artifact_label_path = self.Artifact_Label_Path / f"Artifact_{self.sampNo}.txt" - artifact_label = pd.read_csv(artifact_label_path, header=None).to_numpy().reshape(-1, 4) + artifact_label = read_csv(artifact_label_path, header=None).to_numpy().reshape(-1, 4) - self.artifact_event_label = np.zeros(len(self.bcg_event_label) + self.extend_second * self.frequency) + self.artifact_event_label = zeros(len(self.bcg_event_label) + self.extend_second * self.frequency) for i, artifact_type, SP, EP in artifact_label: SP = (int(SP) + offset_length) // (1000 // self.frequency) @@ -849,12 +892,10 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.bcg_EP = bcg_EP bcg_duration = bcg_EP - bcg_SP - logging.info(f"sampNo:{self.sampNo} " + info(f"sampNo:{self.sampNo} " f"bcg[index:{bcg_index} epoch:{one_bcg_data['Epoch']} event:{one_bcg_data['Event type']}] " f"ecg:[index:{bcg_index} epoch:{one_bcg_data['Epoch']} event:{one_bcg_data['Event type']}]") - - # 进行向两边延展 bcg_SP = bcg_SP - front_add_second bcg_EP = bcg_EP + back_add_second @@ -867,12 +908,16 @@ class MainWindow(QMainWindow, Ui_MainWindow): plt.xticks([]) plt.yticks([]) - if not (self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == -1): - bcg_duration_new = self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"] - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"] - self.lineEdit_correctStart.setText(str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"])) - self.lineEdit_correctEnd.setText(str(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"])) - self.label_BCG_event.setText(f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)} " - f"Epoch:{one_bcg_data['Epoch']} Duration:{bcg_duration}s New Duration:{bcg_duration_new}s") + if not (self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "isLabeled"] == -1): + bcg_duration_new = self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"] - \ + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"] + self.lineEdit_correctStart.setText( + str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"])) + self.lineEdit_correctEnd.setText( + str(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"])) + self.label_BCG_event.setText( + f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)} " + f"Epoch:{one_bcg_data['Epoch']} Duration:{bcg_duration}s New Duration:{bcg_duration_new}s") else: bcg_duration_new = -1 self.lineEdit_correctStart.setText(str(self.bcg_SP)) @@ -883,20 +928,25 @@ class MainWindow(QMainWindow, Ui_MainWindow): # 绘制 Flow1 self.ax0 = self.figure.add_subplot(gs[0]) - self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Flow T", bcg_duration_new=bcg_duration_new, show_mode="one") + self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Flow T", bcg_duration_new=bcg_duration_new, + show_mode="one") # 绘制 Flow2 self.ax1 = self.figure.add_subplot(gs[1], sharex=self.ax0) - self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Flow P", bcg_duration_new=bcg_duration_new, show_mode="one") + self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Flow P", bcg_duration_new=bcg_duration_new, + show_mode="one") self.ax2 = self.figure.add_subplot(gs[2], sharex=self.ax0) - self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Effort Tho", bcg_duration_new=bcg_duration_new, show_mode="one") + self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Effort Tho", bcg_duration_new=bcg_duration_new, + show_mode="one") self.ax3 = self.figure.add_subplot(gs[3], sharex=self.ax0) - self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Effort Abd", bcg_duration_new=bcg_duration_new, show_mode="one") + self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="Effort Abd", bcg_duration_new=bcg_duration_new, + show_mode="one") self.ax4 = self.figure.add_subplot(gs[4], sharex=self.ax0) - self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="SpO2", event_code=[5], bcg_duration_new=bcg_duration_new, show_mode="one") + self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="SpO2", event_code=[5], + bcg_duration_new=bcg_duration_new, show_mode="one") self.ax5 = self.figure.add_subplot(gs[5], sharex=self.ax0) self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="orgdata", @@ -907,7 +957,8 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="0.7lowpass_resp", event_code=[6, 7, 8, 9, 10, 1, 2, 3, 4], event_show_under=False, - title=f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)}", bcg_duration_new=bcg_duration_new, show_mode="one") + title=f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)}", + bcg_duration_new=bcg_duration_new, show_mode="one") # figManager = plt.get_current_fig_manager() # figManager.window.showMaximized() @@ -915,7 +966,8 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.ax0.callbacks.connect('xlim_changed', lambda ax: self.on_xlim_change(ax)) def plt_channel(self, plt_, SP, EP, channel, event_code=[1, 2, 3, 4], event_show_under=False, - ax_top=True, ax_bottom=True, ax_left=True, ax_right=True, title=None, bcg_duration_new=-1, show_mode=None): + ax_top=True, ax_bottom=True, ax_left=True, ax_right=True, title=None, bcg_duration_new=-1, + show_mode=None): """ :param plt_: :param SP: 显示开始秒数 @@ -931,7 +983,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): """ linestyle = "-" SP = 0 if SP < 0 else SP - plt_.plot(np.linspace(SP, EP, (EP - SP) * self.frequency), + plt_.plot(linspace(SP, EP, (EP - SP) * self.frequency), self.signal_select[channel][SP * self.frequency:EP * self.frequency], label=channel, color=self.color_cycle[0]) @@ -951,12 +1003,12 @@ class MainWindow(QMainWindow, Ui_MainWindow): min_point = self.signal_select[channel][SP * self.frequency:EP * self.frequency].min() len_segment = EP * self.frequency - SP * self.frequency y = (min_point.repeat(len_segment) * mask).astype('float') - np.place(y, y == 0, np.nan) + place(y, y == 0, nan) else: y = (self.signal_select[channel][SP * self.frequency:EP * self.frequency] * mask).astype('float') - np.place(y, y == 0, np.nan) - plt_.plot(np.linspace(SP, EP, (EP - SP) * self.frequency), y, color=self.color_cycle[j], + place(y, y == 0, nan) + plt_.plot(linspace(SP, EP, (EP - SP) * self.frequency), y, color=self.color_cycle[j], linestyle=linestyle) plt_.legend(fontsize=8, loc=1) if title is not None: @@ -971,42 +1023,58 @@ class MainWindow(QMainWindow, Ui_MainWindow): # 绘制半透明矩形框 if show_mode == "one": - if not(bcg_duration_new == -1): - if self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Obstructive apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], color='red', - alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Central apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], color='blue', - alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Mixed apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], color='gray', - alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Hypopnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], color='pink', - alpha=0.3) + if not (bcg_duration_new == -1): + if self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Obstructive apnea": + ax.axvspan( + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], + color='red', + alpha=0.3) + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Central apnea": + ax.axvspan( + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], + color='blue', + alpha=0.3) + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Mixed apnea": + ax.axvspan( + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], + color='gray', + alpha=0.3) + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "correct_EventsType"] == "Hypopnea": + ax.axvspan( + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "correct_End"], + color='pink', + alpha=0.3) else: - if self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Obstructive apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], + if self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Obstructive apnea": + ax.axvspan(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], color='red', alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Central apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Central apnea": + ax.axvspan(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], color='blue', alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Mixed apnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Mixed apnea": + ax.axvspan(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], color='gray', alpha=0.3) - elif self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Hypopnea": - ax.axvspan(self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], - self.pd.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], + elif self.df_saLabel.at[ + self.bcg_event_label_index_list[self.plotEventIndex], "Event type"] == "Hypopnea": + ax.axvspan(self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "Start"], + self.df_saLabel.at[self.bcg_event_label_index_list[self.plotEventIndex], "End"], color='pink', alpha=0.3) # xticks = [[]] if xticks else [range(SP, EP, 5), [str(i) for i in range(0, (EP - SP), 5)]] @@ -1030,7 +1098,7 @@ class MainWindow(QMainWindow, Ui_MainWindow): bcg_EP = one_bcg_data["End"] bcg_duration = bcg_EP - bcg_SP - logging.info(f"sampNo:{self.sampNo} " + info(f"sampNo:{self.sampNo} " f"bcg[index:{bcg_index} epoch:{one_bcg_data['Epoch']} event:{one_bcg_data['Event type']}] " f"ecg:[index:{bcg_index} epoch:{one_bcg_data['Epoch']} event:{one_bcg_data['Event type']}]") @@ -1077,7 +1145,8 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.plt_channel(plt_=plt, SP=bcg_SP, EP=bcg_EP, channel="0.7lowpass_resp", event_code=[6, 7, 8, 9, 10, 1, 2, 3, 4], event_show_under=False, - title=f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)}", show_mode="new") + title=f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)}", + show_mode="new") self.label_BCG_event.setText( f"sampNo:{self.sampNo} Index:{bcg_index + 1}/{len(self.bcg_event_label_filtered_df)} " @@ -1088,20 +1157,21 @@ class MainWindow(QMainWindow, Ui_MainWindow): self.canvas.draw() self.ax0.callbacks.connect('xlim_changed', lambda ax: self.on_xlim_change(ax)) - - def pd_add_new_row(self, df, score: int, remark: str, correct_Start: int, correct_End: int, correct_EventsType: str, isLabeled: int): - new_row = pd.Series(index=df.columns, data=np.nan) + def pd_add_new_row(self, df, score: int, remark: str, correct_Start: int, correct_End: int, correct_EventsType: str, + isLabeled: int): + new_row = Series(index=df.columns, data=nan) new_row["score"] = score new_row["remark"] = remark new_row["correct_Start"] = correct_Start new_row["correct_End"] = correct_End new_row["correct_EventsType"] = correct_EventsType new_row["isLabeled"] = isLabeled - return pd.concat([df, pd.DataFrame([new_row])], ignore_index=True) + return concat([df, DataFrame([new_row])], ignore_index=True) + # 此线程类用于更新textBrowser的内容 -class Thread_textbrowserUpdate(QtCore.QThread): - trigger = QtCore.pyqtSignal(str) +class Thread_textbrowserUpdate(QThread): + trigger = pyqtSignal(str) def __init__(self): super(Thread_textbrowserUpdate, self).__init__() @@ -1109,6 +1179,7 @@ class Thread_textbrowserUpdate(QtCore.QThread): def run_(self, message): self.trigger.emit(message) + # 此类用于继承matplot的NavigationToolbar类，然后写回调函数 class CustomNavigationToolbar(NavigationToolbar2QT): def __init__(self, canvas, parent, callback): @@ -1120,9 +1191,10 @@ class CustomNavigationToolbar(NavigationToolbar2QT): if self.callback: self.callback() # 执行自定义回调 + # 主函数 if __name__ == '__main__': - app = QtWidgets.QApplication(sys.argv) + app = QApplication(sys.argv) mainWindow = MainWindow() mainWindow.show() sys.exit(app.exec_()) diff --git a/PSG_label_2_BCG_label.py b/PSG_label_2_BCG_label.py index bd6aa92..3fdb4e4 100644 --- a/PSG_label_2_BCG_label.py +++ b/PSG_label_2_BCG_label.py @@ -40,7 +40,7 @@ df_PSG_label['End'] = df_PSG_label['Start'] + df_PSG_label['Duration'].astype(fl print(df_PSG_label) # 写入csv文件 -df_PSG_label.to_csv(r"E:\data_annotation\6SleepApnea_annotation_GUI_demo\data\BCG_label\export" + str(sampID) + "_all.csv", index=False, encoding="gbk") +df_PSG_label.to_csv(dir_path + r"\BCG_label\export" + str(sampID) + "_all.csv", index=False, encoding="gbk") # 打印结果 print("sampID_" + str(sampID) + "写入csv成功") \ No newline at end of file diff --git a/utils/Preprocessing.py b/utils/Preprocessing.py index 2085357..ea47142 100644 --- a/utils/Preprocessing.py +++ b/utils/Preprocessing.py @@ -6,174 +6,27 @@ @ illustration: Pre-processing """ -import sys -import numpy as np -import pandas as pd -import matplotlib.pyplot as plt +from scipy.signal import butter, lfilter, filtfilt -import pywt -from scipy import signal -from scipy import fftpack +def Butterworth(data, sample_rate, type, low_cut=0.0, high_cut=0.0, order=10): + """ + :param type: Type of Butter. filter, lowpass, bandpass, ... + :param lowcut: Low cutoff frequency + :param highcut: High cutoff frequency + :param order: Order of filter + :return: Signal after filtering + """ + if type == "lowpass": # 低通滤波处理 + b, a = butter(order, low_cut / (sample_rate * 0.5), btype='lowpass', output='ba') + return filtfilt(b, a, data) + elif type == "bandpass": # 带通滤波处理 + low = low_cut / (sample_rate * 0.5) + high = high_cut / (sample_rate * 0.5) + b, a = butter(order, [low, high], btype='bandpass', output='ba') + return filtfilt(b, a, data) + elif type == "highpass": # 高通滤波处理 + b, a = butter(order, high_cut / (sample_rate * 0.5), btype='highpass', output='ba') + return filtfilt(b, a, data) + else: # 警告,滤波器类型必须有 + raise ValueError("Please choose a type of fliter") - -def Dilate(x, N, g, M): - returndata = np.array([]) - for num in range(N - M + 1): - returndata = np.append(returndata, np.min(np.array(x[num:num + M]) - np.array(g))) - return returndata - - -def Eorde(x, N, g, M): - returndata = np.array([]) - for num in range(N - M + 1): - returndata = np.append(returndata, np.max(np.array(x[num:num + M]) - np.array(g))) - return returndata - - -def fin_turn(data, peak): - if len(data) == 0 or len(peak) == 0: return peak - return_peak = [] - for p in peak: - minx, maxx = max(0, p - 100), min(len(data), p + 100) - return_peak.append(minx + np.argmax(data[minx: maxx])) - return return_peak - - -class BCG_Operation(): - def __init__(self, sample_rate=1000): - self.sample_rate = sample_rate - - def down_sample(self, data=None, down_radio=10): - if data is None: - raise ValueError("data is None, please given an real value!") - data = data[:len(data) // down_radio * down_radio].reshape(-1, down_radio)[:, 0] - self.sample_rate = self.sample_rate / down_radio - return data - - def Splitwin(self, data=None, len_win=None, coverage=1.0, calculate_to_end=False): - """ - 分窗 - :param len_win: length of window - :return: signal windows - """ - if (len_win is None) or (data is None): - raise ValueError("length of window or data is None, please given an real value!") - else: - length = len_win * self.sample_rate # number point of a window - # step of split windows - step = length * coverage - start = 0 - Splitdata = [] - while (len(data) - start >= length): - Splitdata.append(data[int(start):int(start + length)]) - start += step - if calculate_to_end and (len(data) - start > 2000): - remain = len(data) - start - start = start - step - step = int(remain / 2000) - start = start + step * 2000 - Splitdata.append(data[int(start):int(start + length)]) - return np.array(Splitdata), step - elif calculate_to_end: - return np.array(Splitdata), 0 - else: - return np.array(Splitdata) - - def Butterworth(self, data, type, low_cut=0.0, high_cut=0.0, order=10): - """ - :param type: Type of Butter. filter, lowpass, bandpass, ... - :param lowcut: Low cutoff frequency - :param highcut: High cutoff frequency - :param order: Order of filter - :return: Signal after filtering - """ - if type == "lowpass": # 低通滤波处理 - b, a = signal.butter(order, low_cut / (self.sample_rate * 0.5), btype='lowpass') - return signal.filtfilt(b, a, np.array(data)) - elif type == "bandpass": # 带通滤波处理 - low = low_cut / (self.sample_rate * 0.5) - high = high_cut / (self.sample_rate * 0.5) - b, a = signal.butter(order, [low, high], btype='bandpass') - return signal.filtfilt(b, a, np.array(data)) - elif type == "highpass": # 高通滤波处理 - b, a = signal.butter(order, high_cut / (self.sample_rate * 0.5), btype='highpass') - return signal.filtfilt(b, a, np.array(data)) - else: # 警告,滤波器类型必须有 - raise ValueError("Please choose a type of fliter") - - def MorphologicalFilter(self, data=None, M=200, get_bre=False): - """ - :param data: Input signal - :param M: Length of structural element - :return: Signal after filter - """ - if not data.any(): - raise ValueError("The input data is None, please given real value data") - g = np.ones(M) - Data_pre = np.insert(data, 0, np.zeros(M)) - Data_pre = np.insert(Data_pre, -1, np.zeros(M)) - # Opening: 腐蚀 + 膨胀 - out1 = Eorde(Data_pre, len(Data_pre), g, M) - out2 = Dilate(out1, len(out1), g, M) - out2 = np.insert(out2, 0, np.zeros(M - 2)) - # Closing: 膨胀 + 腐蚀 - out5 = Dilate(Data_pre, len(Data_pre), g, M) - out6 = Eorde(out5, len(out5), g, M) - out6 = np.insert(out6, 0, np.zeros(M - 2)) - - baseline = (out2 + out6) / 2 - # -------------------------保留剩余价值------------------------ - data_filtered = Data_pre[:len(baseline)] - baseline - data_filtered = data_filtered[M: M + len(data)] - baseline = baseline[M:] - data_filtered[-1] = data_filtered[-2] = data_filtered[-3] - baseline[-1] = baseline[-2] = baseline[-3] - if get_bre: - return data_filtered, baseline - else: - return data_filtered - - def Iirnotch(self, data=None, cut_fre=50, quality=3): - """陷波器""" - b, a = signal.iirnotch(cut_fre / (self.sample_rate * 0.5), quality) - return signal.filtfilt(b, a, np.array(data)) - - def ChebyFilter(self, data, rp=1, type=None, low_cut=0, high_cut=0, order=10): - """ - 切比雪夫滤波器 - :param data: Input signal - :param rp: The maximum ripple allowed - :param type: 'lowpass', 'bandpass, 'highpass' - :param low_cut: Low cut-off fre - :param high_cut: High cut-off fre - :param order: The order of filter - :return: Signal after filter - """ - if type == 'lowpass': - b, a = signal.cheby1(order, rp, low_cut, btype='lowpass', fs=self.sample_rate) - return signal.filtfilt(b, a, np.array(data)) - elif type == 'bandpass': - b, a = signal.cheby1(order, rp, [low_cut, high_cut], btype='bandpass', fs=self.sample_rate) - return signal.filtfilt(b, a, np.array(data)) - elif type == 'highpass': - b, a = signal.cheby1(order, rp, high_cut, btype='highpass', fs=self.sample_rate) - return signal.filtfilt(b, a, np.array(data)) - else: - raise ValueError("The type of filter is None, please given the real value!") - - def Envelope(self, data): - """取信号包络""" - if len(data) <= 1: raise ValueError("Wrong input data") - hx = fftpack.hilbert(data) - return np.sqrt(hx ** 2, data ** 2) - - def wavelet_trans(self, data, c_level=['aaa', 'aad'], wavelet='db4', mode='symmetric', maxlevel=10): - wp = pywt.WaveletPacket(data=data, wavelet=wavelet, mode=mode, maxlevel=maxlevel) - new_wp = pywt.WaveletPacket(data=None, wavelet=wavelet, mode=mode) - for c in c_level: - new_wp[c] = wp[c] - return new_wp.reconstruct() - - # def em_decomposition(self, data): - # from pyhht.emd import EMD - # return EMD(data).decompose()