misleep 0.2.8__tar.gz → 0.2.9__tar.gz

{misleep-0.2.8 → misleep-0.2.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.8
+Version: 0.2.9
 Summary: MiSleep: Mice Sleep EEG/EMG visualization, scoring and analysis.
 Home-page: https://github.com/BryanWang0702/MiSleep/
 Download-URL: https://github.com/BryanWang0702/MiSleep/

{misleep-0.2.8 → misleep-0.2.9}/misleep/__init__.py

@@ -5,6 +5,7 @@ from .preprocessing import *
 from .utils import *
 from .viz import *
 from .gui import *
+from .analysis import *
 
 __author__ = "Xueqiang Wang <swang9194@gmail.com>"
 __version__ = "0.0.1"

{misleep-0.2.8 → misleep-0.2.9}/misleep/config.ini

@@ -1,7 +1,7 @@
 [gui]
-version = v0.2.8
-updatetime = 2025/4/1
-marker = ['good', 'first REM', 'WindEEG', 'W-R ', 'maker']
+version = v0.2.9
+updatetime = 2025/4/23
+marker = ['half_signal', 'first REM', 'WindEEG', 'W-R ', 'maker']
 startend = ['burst-supression', 'REM', 'Wake', 'Spindle', 'SWA', 'start end label', 'start end label']
 statemap = {"1": "NREM", "2": "REM", "3": "Wake", "4": "INIT", "5": "IS", "6": "MicroArousal"}
 statecolor = {"1": "orange", "2": "skyblue", "3": "red", "4": "white", "5": "green", "6": "pink"}

{misleep-0.2.8 → misleep-0.2.9}/misleep/gui/dialog.py

@@ -20,6 +20,7 @@ from misleep.gui.uis.horizontal_line_dialog_ui import Ui_horizontal_line_dialog
 from misleep.gui.uis.SWA_detect_dialog_ui import Ui_SWADetectDialog
 from misleep.gui.uis.spindle_detect_dialog_ui import Ui_SpindleDetectDialog
 from misleep.gui.uis.auto_stage_dialog_ui import Ui_AutoStageDialog
+from misleep.gui.uis.save_data_dialog_ui import Ui_SaveDataDialog
 from misleep.gui.thread import SaveThread
 from misleep.io.annotation_io import transfer_result
 from misleep.utils.signals import signal_filter
@@ -981,6 +982,68 @@ class AutoStageDialog(QDialog, Ui_AutoStageDialog):
         event.ignore()
         self.closed = True
         self.hide()
+
+
+class SaveData_dialog(QDialog, Ui_SaveDataDialog):
+    def __init__(self, parent=None):
+        """
+        Initialize the save data dialog of MiSleep
+        """
+        super().__init__(parent)
+
+        self.setupUi(self)
+
+        self.CropStartTimeEditor.setDisabled(True)
+        self.CropEndTimeEditor.setDisabled(True)
+
+        self.CropStartTimeEditor.setDisabled(True)
+        self.CropEndTimeEditor.setDisabled(True)
+        self.CropDataStartCheckBox.clicked.connect(self.crop_start_time_editor_changed)
+        self.CropDataEndCheckBox.clicked.connect(self.crop_end_time_editor_changed)
+        
+        self.channel_slm = QStringListModel()
+        
+        self.OKBtn.clicked.connect(self.okEvent)
+        self.CancelBtn.clicked.connect(self.cancelEvent)
+        self.closed = True
+
+    def crop_start_time_editor_changed(self):
+        if self.CropDataStartCheckBox.isChecked():
+            self.CropStartTimeEditor.setEnabled(True)
+        if not self.CropDataStartCheckBox.isChecked():
+            self.CropStartTimeEditor.setDisabled(True)
+
+    def crop_end_time_editor_changed(self):
+        if self.CropDataEndCheckBox.isChecked():
+            self.CropEndTimeEditor.setEnabled(True)
+        if not self.CropDataEndCheckBox.isChecked():
+            self.CropEndTimeEditor.setDisabled(True)
+
+    def fill_midata_params(self, midata):
+        """
+        Fill the midata params to the dialog, including time, channels, sf, etc.
+        """
+        self.channel_slm.setStringList(midata.channels)
+        self.ChannelListView.setModel(self.channel_slm)
+
+        self.CropStartTimeEditor.setDateTime(datetime.datetime.strptime(midata.time, "%Y%m%d-%H:%M:%S"))
+        # End time should add the midata.duration to format the time
+        end_time = datetime.datetime.strptime(midata.time, "%Y%m%d-%H:%M:%S") + datetime.timedelta(seconds=midata.duration)
+        self.CropEndTimeEditor.setDateTime(end_time)
+
+    def okEvent(self):
+        self.closed = False
+        self.hide()
+
+    def cancelEvent(self):
+        """Triggered by the `cancel` button"""
+        self.closed = True
+        self.hide()
+    
+    def closeEvent(self, event):
+        event.ignore()
+        self.closed = True
+        self.hide()
         
 
 

{misleep-0.2.8 → misleep-0.2.9}/misleep/gui/main_window.py

@@ -28,7 +28,7 @@ from misleep.gui.utils import create_new_mianno, identify_startend_color
 from misleep.utils.annotation import lst2group
 from misleep.gui.about import about_dialog
 from misleep.gui.dialog import label_dialog, transferResult_dialog, stateSpectral_dialog, \
-horizontalLine_dialog, SWADetectionDialog, SpindleDetectionDialog, AutoStageDialog
+horizontalLine_dialog, SWADetectionDialog, SpindleDetectionDialog, AutoStageDialog, SaveData_dialog
 from misleep.gui.spec_window import SpecWindow
 from misleep.gui.uis.main_window_ui import Ui_MiSleep
 from misleep.preprocessing.spectral import spectrogram, spectrum, band_power
@@ -129,6 +129,9 @@ class main_window(QMainWindow, Ui_MiSleep):
         # Initial state spectral dialog
         self.state_spectral_dialog = stateSpectral_dialog()
 
+        # Initial data saving dialog
+        self.save_data_dialog = SaveData_dialog()
+
         # Initial horizontal line dialog
         self.horizontal_line_dialog = horizontalLine_dialog()
         # The horizontal_line dict contains the line value, line color, line comment
@@ -166,6 +169,7 @@ class main_window(QMainWindow, Ui_MiSleep):
         self.actionSWA_detection.triggered.connect(self.swa_detection)
         self.actionSpindle_Detection.triggered.connect(self.spindle_detection)
         self.actionAuto_Stage.triggered.connect(self.auto_stage)
+        self.actionSaveData.triggered.connect(self.save_data)
 
         # Spectrogram percentile change
         self.PercentileSpin.setValue(self.spectrogram_percentile)
@@ -384,12 +388,17 @@ class main_window(QMainWindow, Ui_MiSleep):
 
     def load_anno(self):
         """Triggered by actionLoad_Annotation"""
-        anno_path, _ = QFileDialog.getOpenFileName(
+        anno_path, _ = QFileDialog.getSaveFileName(
             self, "Select annotation file", 
             f"{self.config['gui']['openpath']}", 
             "txt Files (*.txt *.TXT)"
         )
 
+        if not os.path.exists(anno_path):
+            # Create the file if it doesn't exist
+            with open(anno_path, 'w') as file:
+                file.write("")
+
         if anno_path == "":
             return
         self.anno_path = anno_path
@@ -1009,10 +1018,11 @@ class main_window(QMainWindow, Ui_MiSleep):
                 # Clear start end label
                 self.start_end = []
                 self.start_end.append(sec)
+            elif sec < self.start_end[0]:
+                # Clear start end label and add the second as start
+                self.start_end = []
+                self.start_end.append(sec)
             else:
-                if sec < self.start_end[0]:
-                    QMessageBox.about(self, "Error", "End should be larger than Start!")
-                    return
                 self.start_end.append(sec + 1)
 
             self.plot_start_end_line()
@@ -1365,28 +1375,36 @@ class main_window(QMainWindow, Ui_MiSleep):
             int(end_*self.midata.sf[channel])
         ]
         
-        freq, psd = spectrum(signal=signal_data,
-                             sf=self.midata.sf[channel],
-                             relative=True)
-        
-        f, t, Sxx = spectrogram(signal=signal_data,
+        try:
+            freq, psd = spectrum(signal=signal_data,
                                 sf=self.midata.sf[channel],
-                                step=1, window=5, norm=True)
+                                relative=True)
+            
+            f, t, Sxx = spectrogram(signal=signal_data,
+                                    sf=self.midata.sf[channel],
+                                    step=1, window=5, norm=True)
 
-        bandPower = band_power(psd=psd, freq=freq, 
-                               bands=[[0.5, 4, 'delta'], [4, 9, 'theta']])
-        
-        ratio = bandPower['delta'] / bandPower['theta']
-        
-        self.spec_window.show_(spectrum=[psd, freq], 
-                               spectrogram=[f, t, Sxx],
-                               percentile_=self.spectrogram_percentile,
-                               ratio=ratio, start_end=[start_, end_])
-        
-        self.spec_window.activateWindow()
-        self.spec_window.setWindowState(
-                self.spec_window.windowState() & ~Qt.WindowMinimized | Qt.WindowActive)
-        self.spec_window.showNormal()
+            bandPower = band_power(psd=psd, freq=freq, 
+                                bands=[[0.5, 4, 'delta'], [4, 9, 'theta']])
+            
+            ratio = bandPower['delta'] / bandPower['theta']
+            
+            self.spec_window.show_(spectrum=[psd, freq], 
+                                spectrogram=[f, t, Sxx],
+                                percentile_=self.spectrogram_percentile,
+                                ratio=ratio, start_end=[start_, end_])
+            
+            self.spec_window.activateWindow()
+            self.spec_window.setWindowState(
+                    self.spec_window.windowState() & ~Qt.WindowMinimized | Qt.WindowActive)
+            self.spec_window.showNormal()
+        except Exception as e:
+            QMessageBox.about(
+                self,
+                "Error",
+                "Filter error.",
+            )
+            return
 
     def set_show_duration(self, type_="Combo"):
         """Set show_duration with ShowRangeCombo or SecondNumSpin"""
@@ -1646,12 +1664,17 @@ class main_window(QMainWindow, Ui_MiSleep):
             For when I only want to save a file but not cover the current labels
         """
         if self.anno_path == "":
-            anno_path, _ = QFileDialog.getOpenFileName(
+            anno_path, _ = QFileDialog.getSaveFileName(
             self, "Select annotation file", 
             f"{self.config['gui']['openpath']}", 
             "txt Files (*.txt *.TXT)"
             )
 
+            if not os.path.exists(anno_path):
+                # Create the file if it doesn't exist
+                with open(anno_path, 'w') as file:
+                    file.write("")
+
             if anno_path == "":
                 return
             if not just_save:
@@ -1667,7 +1690,59 @@ class main_window(QMainWindow, Ui_MiSleep):
         save_thread.quit()
 
     def save_data(self):
-        """Save data into file"""        
+        """Save data into file"""
+        
+        # Pop up dialog to get save data options
+        self.save_data_dialog.fill_midata_params(midata=self.midata)
+        self.save_data_dialog.exec()
+        if self.save_data_dialog.closed:
+            return
+        
+        # Get the selected channels to save data
+        selected_channels = [each.row() for each in self.save_data_dialog.ChannelListView.selectedIndexes()]
+        # If did not select any channel, save all channels
+        if selected_channels == []:
+            selected_channels = list(range(self.midata.n_channels))
+        midata_to_save = self.midata.pick_chs([self.midata.channels[each] for each in selected_channels])
+
+        # Crop data with the checkbox and time editor
+        start_sec = 0
+        end_sec = self.midata.duration
+        
+        if self.save_data_dialog.CropDataStartCheckBox.isChecked():
+            start_time = self.save_data_dialog.CropStartTimeEditor.dateTime().toPyDateTime()
+            midata_to_save._time = start_time.strftime("%Y%m%d-%H:%M:%S")
+            start_sec = int(datetime.timedelta.total_seconds(start_time - self.ac_time))
+            if start_sec < 0:
+                start_sec = 0
+        
+        if self.save_data_dialog.CropDataEndCheckBox.isChecked():
+            end_time = self.save_data_dialog.CropEndTimeEditor.dateTime().toPyDateTime()
+            end_sec = int(datetime.timedelta.total_seconds(end_time - self.ac_time))
+            if end_sec > self.midata.duration:
+                end_sec = self.midata.duration
+
+        if end_sec <= start_sec:
+            start_sec = 0
+            end_sec = self.midata.duration
+            
+        midata_to_save = midata_to_save.crop([start_sec, end_sec])
+
+        data_path, _ = QFileDialog.getSaveFileName(
+            self, "Select a file to save data", 
+            f"{self.config['gui']['openpath']}_misleep_saved", 
+            "*mat Files (*.mat *.MAT);;*edf Files (*.edf *.EDF);"
+        )
+        if data_path == "":
+                return
+
+        save_thread = SaveThread(file=midata_to_save, file_path=data_path)
+        saved = save_thread.save_data()
+        if saved:
+            QMessageBox.about(self, "Info", f"Data Saved to {data_path}")
+        else:
+            QMessageBox.about(self, "Error", "Data save ERROR")
+        save_thread.quit()        
     
     def auto_save(self):
         """Auto save every 5 mins"""

{misleep-0.2.8 → misleep-0.2.9}/misleep/gui/thread.py

@@ -1,7 +1,7 @@
 from PyQt5.QtCore import QObject, QThread
 from misleep.gui.utils import second2time
 from misleep.utils.annotation import lst2group
-from misleep.io.signal_io import load_mat
+from misleep.io.signal_io import load_mat, write_edf, write_mat
 import datetime
 
 class SaveThread(QThread):
@@ -69,6 +69,20 @@ class SaveThread(QThread):
         with open(self.file_path, 'w') as f:
             f.write('\n'.join(annos))
         return True
+    
+    def save_data(self):
+        """Data save function"""
+        midata= self.file
+        if midata is None:
+            return False
+
+        if self.file_path.endswith('.mat'):
+            write_mat(midata.signals, midata.channels, midata.sf, midata.time, self.file_path)
+        elif self.file_path.endswith('.edf'):
+            write_edf(midata.signals, midata.channels, midata.sf, midata.time, self.file_path)
+        else:
+            raise ValueError("File type not supported!")
+        return True
 
 class LoadThread(QThread):
 

{misleep-0.2.8 → misleep-0.2.9}/misleep/gui/uis/main_window_ui.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file '.\main_window.ui'
+# Form implementation generated from reading ui file 'misleep/gui/uis/main_window.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -14,7 +14,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
 class Ui_MiSleep(object):
     def setupUi(self, MiSleep):
         MiSleep.setObjectName("MiSleep")
-        MiSleep.resize(1445, 971)
+        MiSleep.resize(1451, 967)
         MiSleep.setFocusPolicy(QtCore.Qt.WheelFocus)
         icon = QtGui.QIcon()
         icon.addPixmap(QtGui.QPixmap(":/logo/logo.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
@@ -35,7 +35,7 @@ class Ui_MiSleep(object):
         self.HypnoArea.setWidgetResizable(True)
         self.HypnoArea.setObjectName("HypnoArea")
         self.scrollAreaWidgetContents_2 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_2.setGeometry(QtCore.QRect(0, 0, 1063, 128))
+        self.scrollAreaWidgetContents_2.setGeometry(QtCore.QRect(0, 0, 1069, 128))
         self.scrollAreaWidgetContents_2.setObjectName("scrollAreaWidgetContents_2")
         self.HypnoArea.setWidget(self.scrollAreaWidgetContents_2)
         self.gridLayout_3.addWidget(self.HypnoArea, 2, 0, 1, 1)
@@ -44,7 +44,7 @@ class Ui_MiSleep(object):
         self.SignalArea.setWidgetResizable(True)
         self.SignalArea.setObjectName("SignalArea")
         self.scrollAreaWidgetContents = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents.setGeometry(QtCore.QRect(0, 0, 1063, 756))
+        self.scrollAreaWidgetContents.setGeometry(QtCore.QRect(0, 0, 1069, 764))
         self.scrollAreaWidgetContents.setObjectName("scrollAreaWidgetContents")
         self.SignalArea.setWidget(self.scrollAreaWidgetContents)
         self.gridLayout_3.addWidget(self.SignalArea, 0, 0, 1, 1)
@@ -291,7 +291,7 @@ class Ui_MiSleep(object):
         self.TimeDock.setWidget(self.dockWidgetContents_7)
         MiSleep.addDockWidget(QtCore.Qt.DockWidgetArea(2), self.TimeDock)
         self.menuBar = QtWidgets.QMenuBar(MiSleep)
-        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1445, 26))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1451, 22))
         self.menuBar.setObjectName("menuBar")
         self.menuFile = QtWidgets.QMenu(self.menuBar)
         self.menuFile.setObjectName("menuFile")
@@ -322,8 +322,14 @@ class Ui_MiSleep(object):
         self.actionSpindle_Detection.setObjectName("actionSpindle_Detection")
         self.actionAuto_Stage = QtWidgets.QAction(MiSleep)
         self.actionAuto_Stage.setObjectName("actionAuto_Stage")
+        self.actionLoad_AccuSleep_Data = QtWidgets.QAction(MiSleep)
+        self.actionLoad_AccuSleep_Data.setObjectName("actionLoad_AccuSleep_Data")
+        self.actionSaveData = QtWidgets.QAction(MiSleep)
+        self.actionSaveData.setObjectName("actionSaveData")
         self.menuFile.addAction(self.actionLoadData)
         self.menuFile.addAction(self.actionLoadAnnotation)
+        self.menuFile.addSeparator()
+        self.menuFile.addAction(self.actionSaveData)
         self.menuEvent_Detection.addAction(self.actionSWA_detection)
         self.menuEvent_Detection.addAction(self.actionSpindle_Detection)
         self.menuTools.addAction(self.actionAddLine)
@@ -399,4 +405,6 @@ class Ui_MiSleep(object):
         self.actionSWA_detection.setText(_translate("MiSleep", "SWA Detection"))
         self.actionSpindle_Detection.setText(_translate("MiSleep", "Spindle Detection"))
         self.actionAuto_Stage.setText(_translate("MiSleep", "Auto Stage"))
+        self.actionLoad_AccuSleep_Data.setText(_translate("MiSleep", "Load AccuSleep Data"))
+        self.actionSaveData.setText(_translate("MiSleep", "Save Data"))
 from misleep.gui.resources import misleep

misleep-0.2.9/misleep/gui/uis/save_data_dialog_ui.py

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'misleep/gui/uis/save_data_dialog.ui'
+#
+# Created by: PyQt5 UI code generator 5.15.9
+#
+# WARNING: Any manual changes made to this file will be lost when pyuic5 is
+# run again.  Do not edit this file unless you know what you are doing.
+
+
+from PyQt5 import QtCore, QtGui, QtWidgets
+
+
+class Ui_SaveDataDialog(object):
+    def setupUi(self, SaveDataDialog):
+        SaveDataDialog.setObjectName("SaveDataDialog")
+        SaveDataDialog.resize(409, 516)
+        self.gridLayout_2 = QtWidgets.QGridLayout(SaveDataDialog)
+        self.gridLayout_2.setObjectName("gridLayout_2")
+        self.OKBtn = QtWidgets.QPushButton(SaveDataDialog)
+        self.OKBtn.setObjectName("OKBtn")
+        self.gridLayout_2.addWidget(self.OKBtn, 1, 0, 1, 1)
+        self.CancelBtn = QtWidgets.QPushButton(SaveDataDialog)
+        self.CancelBtn.setObjectName("CancelBtn")
+        self.gridLayout_2.addWidget(self.CancelBtn, 1, 1, 1, 1)
+        self.ACTimeEdit = QtWidgets.QGroupBox(SaveDataDialog)
+        self.ACTimeEdit.setObjectName("ACTimeEdit")
+        self.gridLayout = QtWidgets.QGridLayout(self.ACTimeEdit)
+        self.gridLayout.setObjectName("gridLayout")
+        self.CropDataStartCheckBox = QtWidgets.QCheckBox(self.ACTimeEdit)
+        self.CropDataStartCheckBox.setObjectName("CropDataStartCheckBox")
+        self.gridLayout.addWidget(self.CropDataStartCheckBox, 2, 0, 1, 1)
+        self.CropStartTimeEditor = QtWidgets.QDateTimeEdit(self.ACTimeEdit)
+        self.CropStartTimeEditor.setObjectName("CropStartTimeEditor")
+        self.gridLayout.addWidget(self.CropStartTimeEditor, 3, 0, 1, 1)
+        self.ChannelListView = QtWidgets.QListView(self.ACTimeEdit)
+        self.ChannelListView.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustIgnored)
+        self.ChannelListView.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
+        self.ChannelListView.setTabKeyNavigation(True)
+        self.ChannelListView.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
+        self.ChannelListView.setObjectName("ChannelListView")
+        self.gridLayout.addWidget(self.ChannelListView, 1, 0, 1, 2)
+        self.label_3 = QtWidgets.QLabel(self.ACTimeEdit)
+        self.label_3.setObjectName("label_3")
+        self.gridLayout.addWidget(self.label_3, 0, 0, 1, 1)
+        self.CropDataEndCheckBox = QtWidgets.QCheckBox(self.ACTimeEdit)
+        self.CropDataEndCheckBox.setObjectName("CropDataEndCheckBox")
+        self.gridLayout.addWidget(self.CropDataEndCheckBox, 4, 0, 1, 1)
+        self.CropEndTimeEditor = QtWidgets.QDateTimeEdit(self.ACTimeEdit)
+        self.CropEndTimeEditor.setObjectName("CropEndTimeEditor")
+        self.gridLayout.addWidget(self.CropEndTimeEditor, 5, 0, 1, 1)
+        self.gridLayout_2.addWidget(self.ACTimeEdit, 0, 0, 1, 2)
+
+        self.retranslateUi(SaveDataDialog)
+        QtCore.QMetaObject.connectSlotsByName(SaveDataDialog)
+
+    def retranslateUi(self, SaveDataDialog):
+        _translate = QtCore.QCoreApplication.translate
+        SaveDataDialog.setWindowTitle(_translate("SaveDataDialog", "Dialog"))
+        self.OKBtn.setText(_translate("SaveDataDialog", "OK"))
+        self.CancelBtn.setText(_translate("SaveDataDialog", "Cancel"))
+        self.ACTimeEdit.setTitle(_translate("SaveDataDialog", "Save data options"))
+        self.CropDataStartCheckBox.setText(_translate("SaveDataDialog", "Crop data - Set Start Time"))
+        self.CropStartTimeEditor.setDisplayFormat(_translate("SaveDataDialog", "yyyy/MM/dd HH:mm:ss"))
+        self.label_3.setText(_translate("SaveDataDialog", "Select Channels to Save"))
+        self.CropDataEndCheckBox.setText(_translate("SaveDataDialog", "Crop data - Set End Time"))
+        self.CropEndTimeEditor.setDisplayFormat(_translate("SaveDataDialog", "yyyy/MM/dd HH:mm:ss"))

{misleep-0.2.8 → misleep-0.2.9}/misleep/io/signal_io.py

@@ -61,7 +61,7 @@ def load_mat(data_path):
         raw_data = raw_data[0][0]
         # Whether saved by python
         if 'save' in names:
-            channels = list(raw_data['channels'])
+            channels = list(names[:-4])
             sf = [float(each) for each in raw_data['sf'][0]]
             signals = [raw_data[each][0] for each in channels]
             time = raw_data['time'][0]
@@ -191,3 +191,96 @@ def load_edf(data_path):
                   channels=[each['label'] for each in signal_headers],
                   sf=[each['sample_frequency'] for each in signal_headers],
                   time=meta['startdate'].strftime('%Y%m%d-%H:%M:%S'))
+
+
+def write_edf(signals, channels, sf, time, edf_file=None):
+    """
+    Write data to an EDF (European Data Format) file.
+
+    This function saves the provided signal data, channel names, sampling frequencies, 
+    and start time into an EDF file at the specified file path.
+
+    Parameters
+    ----------
+    signals : list 
+        A list containing the signal data for each channel. Each element 
+        corresponds to the signal data for one channel.
+    channels : list of str
+        A list of channel names corresponding to the signal data.
+    sf : list of float
+        A list of sampling frequencies for each channel.
+    time : str
+        The start time of the recording in the format "YYYYMMDD-HH:MM:SS".
+    edf_file : str
+        The file path where the EDF file will be saved.
+
+    Returns
+    -------
+    None
+        The function writes the data to the specified file and does not return any value.
+
+    Notes
+    -----
+    - The function assumes that the length of `signals`, `channels`, and `sf` are the same.
+    - The `pyedflib` library is used to handle the EDF file writing process.
+    - Ensure that the `edf_file` is a valid path where the file can be created.
+
+    Example
+    -------
+    >>> signals = [[0.1, 0.2, 0.3], [0.4, 0.5, 0.6]]
+    >>> channels = ["EEG1", "EEG2"]
+    >>> sf = [256.0, 256.0]
+    >>> time = "20250423-12:00:00"
+    >>> edf_file = "output.edf"
+    >>> write_edf(signals, channels, sf, time, edf_file)
+    """
+    import pyedflib
+
+    
+    if edf_file is None:
+        edf_file = f"./{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}_saved.edf"
+
+    # Create a dictionary for the EDF header
+    header = {'technician': '',
+              'recording_additional': '',
+              'patientname': 'MiSleep',
+              'patient_additional': '',
+              'patientcode': '',
+              'equipment': '',
+              'admincode': '',
+              'sex': '',
+              'startdate': datetime.datetime.strptime(time, "%Y%m%d-%H:%M:%S"),
+              'birthdate': '',
+              'gender': '',
+              'annotations': []
+            }
+    
+    signal_headers = [
+        {'label': each,
+            'dimension': 'uV',
+            'sample_rate': sf[idx],
+            'sample_frequency': sf[idx],
+            'physical_max': 10417.0,
+            'physical_min': -10417.0,
+            'digital_max': 32767,
+            'digital_min': -32768,
+            'prefilter': '',
+            'transducer': ''
+        } for idx, each in enumerate(channels)
+    ]
+
+    try:
+
+        with pyedflib.EdfWriter(edf_file, len(signals)) as edf_writer:
+            # Set the header information
+            edf_writer.setHeader(header)
+
+            # Add each signal to the EDF file
+            for i, signal in enumerate(signals):
+                edf_writer.setSignalHeader(i, signal_headers[i])
+            edf_writer.writeSamples(signals)
+    
+    except Exception as e:
+        logger.error(f"Write data ERROR: {e}")
+  
+

{misleep-0.2.8 → misleep-0.2.9}/misleep/utils/signals.py

@@ -66,8 +66,11 @@ def signal_filter(data, sf=256., btype='lowpass', low=0.5, high=30.):
                          % btype)
 
     # Use irrfilter of scipy.signal to construct a filter
-    b, a = signal.iirfilter(N=3, Wn=fnorm, btype=btype, analog=False,
-                            output='ba', ftype='butter', fs=None)
+    try:
+        b, a = signal.iirfilter(N=3, Wn=fnorm, btype=btype, analog=False,
+                                output='ba', ftype='butter', fs=None)
+    except ValueError as e:
+        raise ValueError(e)
 
     filtered_data = signal.filtfilt(b=b, a=a, x=data)
 

{misleep-0.2.8 → misleep-0.2.9}/misleep.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.8
+Version: 0.2.9
 Summary: MiSleep: Mice Sleep EEG/EMG visualization, scoring and analysis.
 Home-page: https://github.com/BryanWang0702/MiSleep/
 Download-URL: https://github.com/BryanWang0702/MiSleep/

{misleep-0.2.8 → misleep-0.2.9}/setup.py

@@ -11,7 +11,7 @@ MAINTAINER_EMAIL = "swang@gmail.com"
 URL = "https://github.com/BryanWang0702/MiSleep/"
 LICENSE = "BSD (3-clause)"
 DOWNLOAD_URL = "https://github.com/BryanWang0702/MiSleep/"
-VERSION = "0.2.8"
+VERSION = "0.2.9"
 
 INSTALL_REQUIRES = [
     "numpy>=1.18.1",

misleep-0.2.9/test/test_signal_io.py

@@ -0,0 +1,77 @@
+# -*- coding: UTF-8 -*-
+"""
+@Project: misleep
+@File: test_signal_io.py
+@Author: Xueqiang Wang
+@Date: 2024/2/22
+@Description:
+"""
+
+import pytest
+from misleep.io.signal_io import load_mat, load_edf, write_mat, write_edf
+from time import time
+import os
+
+
+class TestSignalIO():
+    def test_load_mat(self):
+        """Test load_mat"""
+        mat_path = r'./test/test_data/10mins_example_mat.mat'
+        s = time()
+        midata = load_mat(data_path=mat_path)
+        e = time()
+        print(f"Load data from .mat file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")
+
+    def test_load_edf(self):
+        """Test load_edf"""
+        edf_path = r'./test/test_data/10mins_example_edf.edf'
+        s = time()
+        midata = load_edf(data_path=edf_path)
+        e = time()
+        print(f"Load data from .edf file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")
+
+    def test_write_mat(self):
+        """Test write_mat"""
+        mat_path = r'./test/test_data/10mins_example_mat.mat'
+        s = time()
+        midata = load_mat(data_path=mat_path)
+        e = time()
+        print(f"Load data from .mat file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")
+
+        write_mat(midata.signals, midata.channels, midata.sf, midata.time, 
+                  r'./test/test_data/10mins_example_mat_saved_by_python.mat')
+        print('Saved to .mat successfully')
+
+    def test_write_edf(self):
+        """Test write_edf"""
+        mat_path = r'./test/test_data/10mins_example_mat.mat'
+        s = time()
+        midata = load_mat(data_path=mat_path)
+        e = time()
+        print(f"Load data from .mat file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")
+
+        write_edf(midata.signals, midata.channels, midata.sf, midata.time, 
+                  r'./test/test_data/10mins_example_mat_saved_by_python.edf')
+        print('Saved to .edf successfully')
+
+    def test_load_written_edf(self):
+        """Test load written edf"""
+        edf_path = r'./test/test_data/10mins_example_mat_saved_by_python.edf'
+        s = time()
+        midata = load_edf(data_path=edf_path)
+        e = time()
+        print(f"Load data from .mat file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")
+        
+    def test_load_written_mat(self):
+        """Test load written mat"""
+        mat_path = r'./test/test_data/10mins_example_mat_saved_by_python.mat'
+        s = time()
+        midata = load_mat(data_path=mat_path)
+        e = time()
+        print(f"Load data from .mat file, cost {e-s} seconds\n"
+              f"Signals shape {len(midata.signals)}, \nchannels: {midata.channels}, \nsampling frequency: {midata.sf}, \nacquisition time: {midata.time}")

misleep-0.2.8/misleep/gui/uis/save_data_dialog_ui.py

@@ -1,48 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Form implementation generated from reading ui file 'misleep/gui/uis/save_data_dialog.ui'
-#
-# Created by: PyQt5 UI code generator 5.15.10
-#
-# WARNING: Any manual changes made to this file will be lost when pyuic5 is
-# run again.  Do not edit this file unless you know what you are doing.
-
-
-from PyQt5 import QtCore, QtGui, QtWidgets
-
-
-class Ui_Dialog(object):
-    def setupUi(self, Dialog):
-        Dialog.setObjectName("Dialog")
-        Dialog.resize(432, 154)
-        self.verticalLayout = QtWidgets.QVBoxLayout(Dialog)
-        self.verticalLayout.setObjectName("verticalLayout")
-        self.ACTimeEdit = QtWidgets.QGroupBox(Dialog)
-        self.ACTimeEdit.setObjectName("ACTimeEdit")
-        self.gridLayout = QtWidgets.QGridLayout(self.ACTimeEdit)
-        self.gridLayout.setObjectName("gridLayout")
-        self.dateTimeEdit = QtWidgets.QDateTimeEdit(self.ACTimeEdit)
-        self.dateTimeEdit.setObjectName("dateTimeEdit")
-        self.gridLayout.addWidget(self.dateTimeEdit, 1, 0, 1, 1)
-        self.ResetACTimeEdit = QtWidgets.QCheckBox(self.ACTimeEdit)
-        self.ResetACTimeEdit.setObjectName("ResetACTimeEdit")
-        self.gridLayout.addWidget(self.ResetACTimeEdit, 0, 0, 1, 1)
-        spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        self.gridLayout.addItem(spacerItem, 1, 1, 1, 1)
-        self.verticalLayout.addWidget(self.ACTimeEdit)
-        self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
-        self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
-        self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok)
-        self.buttonBox.setObjectName("buttonBox")
-        self.verticalLayout.addWidget(self.buttonBox)
-
-        self.retranslateUi(Dialog)
-        self.buttonBox.accepted.connect(Dialog.accept) # type: ignore
-        self.buttonBox.rejected.connect(Dialog.reject) # type: ignore
-        QtCore.QMetaObject.connectSlotsByName(Dialog)
-
-    def retranslateUi(self, Dialog):
-        _translate = QtCore.QCoreApplication.translate
-        Dialog.setWindowTitle(_translate("Dialog", "Dialog"))
-        self.ACTimeEdit.setTitle(_translate("Dialog", "Save data options"))
-        self.ResetACTimeEdit.setText(_translate("Dialog", "Reset acquisition time?"))

misleep-0.2.8/test/test_signal_io.py

@@ -1,39 +0,0 @@
-# -*- coding: UTF-8 -*-
-"""
-@Project: misleep
-@File: test_signal_io.py
-@Author: Xueqiang Wang
-@Date: 2024/2/22
-@Description:
-"""
-
-import pytest
-from misleep.io.signal_io import load_mat, load_edf, write_mat
-from time import time
-
-
-class TestSignalIO():
-    def test_load_mat_write_mat(self):
-        """Test load_mat and write_mat"""
-        mat_path = r'E:\workplace\EEGProcessing\00_DATA\20231117_test+vid_6pin\data_mini_saved_python.mat'
-        s = time()
-        midata = load_mat(data_path=mat_path)
-        e = time()
-        print(f"Load data from .mat file, cost {e-s} seconds\n"
-              f"Signals shape {len(midata.signals)}, channels: {midata.channels}, sampling frequency: {midata.sf}")
-
-        write_mat(midata.signals, midata.channels, midata.sf, midata.time, 
-                  r'E:\workplace\EEGProcessing\00_DATA\20231117_test+vid_6pin\data_mini_saved_python.mat')
-        print('Saved to .mat successfully')
-
-    def test_load_edf_write_mat(self):
-        """Test load_edf and write_mat"""
-        edf_path = r'../datasets/learn-nsrr01.edf'
-        s = time()
-        signals, channels, sf = load_edf(data_path=edf_path)
-        e = time()
-        print(f"Load data from .edf file, cost {e-s} seconds\n"
-              f"Signals shape {len(signals)}, channels: {channels}, sampling frequency: {sf}")
-
-        write_mat(signals, channels, sf, r'../../../datasets/mat_from_edf.mat')
-        print('Saved to .mat successfully')