misleep 0.2.7__tar.gz → 0.2.8__tar.gz

{misleep-0.2.7 → misleep-0.2.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.7
+Version: 0.2.8
 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-0.2.7 → misleep-0.2.8}/misleep/config.ini

@@ -1,6 +1,6 @@
 [gui]
-version = v0.2.7
-updatetime = 2025/3/25
+version = v0.2.8
+updatetime = 2025/4/1
 marker = ['good', '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"}
@@ -9,5 +9,5 @@ startendcolor = {"NREM": "orange", "REM": "skyblue", "Wake": "red"}
 statecolorbgalpha = 0.1
 markerlinecolor = "red"
 startendlinecolor = "blue"
-openpath = //172.16.41.188/wangtianyi/Sleep architecture/Female/Sham/P30/DOB250214_250318_28/annotation.txt
+openpath = D:
 

{misleep-0.2.7 → misleep-0.2.8}/misleep/gui/dialog.py

@@ -403,7 +403,7 @@ class stateSpectral_dialog(QDialog, Ui_StateSpectralDialog):
         Wake_hour_spec = []
         if self.HourSegmentCheckBox.isChecked():
             for sec in range(0, end_sec-start_sec, 3600):
-                sleep_state = mianno.sleep_state[sec:sec+3600]
+                sleep_state = mianno.sleep_state[start_sec+sec: start_sec+sec+3600]
                 sleep_state = lst2group([[idx+sec, each] for idx, each in enumerate(sleep_state)])
 
                 # Merge 4 states' data
@@ -466,7 +466,6 @@ class stateSpectral_dialog(QDialog, Ui_StateSpectralDialog):
             Init_figure.savefig(fd + '/Init_spectrum.pdf')
 
         writer.close()
-
         QMessageBox.about(self, "Info", "Spectral analysis finished")
 
     def okEvent(self):

{misleep-0.2.7 → misleep-0.2.8}/misleep/io/annotation_io.py

@@ -6,7 +6,6 @@
 @Date: 2024/3/6
 @Description:  Annotation io, default is for MiSleep annotation, `NAME.txt`
 """
-from misleep.io.base import MiAnnotation
 from misleep.utils.annotation import marker2mianno, start_end2mianno, lst2group, sleep_state2mianno, transfer_time
 import pandas as pd
 
@@ -43,6 +42,8 @@ def load_misleep_anno(file_path, state_map=None):
 
     sleep_state = annotation[sleep_state_idx + 1:]
     sleep_state = sleep_state2mianno(sleep_state)
+    
+    from misleep.io.base import MiAnnotation
 
     return MiAnnotation(sleep_state=sleep_state, start_end=start_end, marker=marker, state_map=state_map)
 
@@ -62,6 +63,8 @@ def load_bio_anno(file_path):
     }
 
     state_list = [state_map[each] for each in state_list]
+    
+    from misleep.io.base import MiAnnotation
     return MiAnnotation(sleep_state=state_list, marker=[], start_end=[])
 
 

{misleep-0.2.7 → misleep-0.2.8}/misleep/io/base.py

@@ -9,7 +9,7 @@
 import math
 
 import numpy as np
-from misleep.utils.signals import signal_filter
+
 
 
 class MiData:
@@ -143,6 +143,7 @@ class MiData:
         low : float
         high : float
         """
+        from misleep.utils.signals import signal_filter
         if chans is None or not isinstance(chans, list):
             raise TypeError(f"'chans' should be a list of channel names, got {type(chans)}")
 

{misleep-0.2.7 → misleep-0.2.8}/misleep/io/signal_io.py

@@ -13,7 +13,6 @@
 from hdf5storage import savemat
 import pyedflib
 import datetime
-from misleep.io.base import MiData
 from misleep.utils.logger_handler import logger
 
 
@@ -40,6 +39,8 @@ def load_mat(data_path):
 
     from scipy.io import loadmat as scipy_loadmat
     from mat73 import loadmat as mat73_loadmat
+    
+    from misleep.io.base import MiData
 
     try:
         # Use scipy to load
@@ -183,6 +184,8 @@ def load_edf(data_path):
     """
 
     signals, signal_headers, meta = pyedflib.highlevel.read_edf(edf_file=data_path)
+    
+    from misleep.io.base import MiData
 
     return MiData(signals=signals,
                   channels=[each['label'] for each in signal_headers],

misleep-0.2.8/misleep/utils/signals.py

@@ -0,0 +1,120 @@
+# -*- coding: UTF-8 -*-
+"""
+@Project: misleep
+@File: signals.py
+@Author: Xueqiang Wang
+@Date: 2024/2/29
+@Description:  
+"""
+import numpy as np
+from scipy import signal
+from copy import deepcopy
+from misleep.io.base import MiData
+from misleep.utils.annotation import lst2group
+
+
+def signal_filter(data, sf=256., btype='lowpass', low=0.5, high=30.):
+    """
+    Filter the signal data, use butter filter in scipy
+
+    Parameters
+    ----------
+    data : ndarray
+        1D array. Signal data need to be filtered.
+    sf : float
+        Sampling frequency of signal data. Default is 305.
+    btype : {'lowpass', 'highpass', 'bandpass'}, optional
+        The type of filter. Default is 'lowpass'.
+    low : float
+        Higher than this frequency can pass, used in 'highpass' and 'bandpass'
+        filter. Default is 0.5.
+    high : float
+        Lower than this frequency can pass, used in 'lowpass' and 'bandpass'
+        filter. Default is 30.
+
+    Returns
+    ----------
+    filtered_data : 1D-array
+        Filtered data of signal data using butter filter
+    fname : str
+
+    """
+    if not isinstance(sf, (int, float)):
+        raise TypeError(f"Sample frequency should be a float, got {type(sf)}")
+
+    if not isinstance(low, (int, float)):
+        raise TypeError(f"Low threshold should be a float, got {type(sf)}")
+
+    if not isinstance(high, (int, float)):
+        raise TypeError(f"high threshold should be a float, got {type(sf)}")
+
+    if btype == 'lowpass':
+        fnorm = high / (.5 * sf)
+        fname = f"{btype}_{high}"
+    elif btype == 'highpass':
+        fnorm = low / (.5 * sf)
+        fname = f"{btype}_{low}"
+    elif btype == 'bandpass':
+        fnorm = np.divide([low, high], .5 * sf)
+        fname = f"{btype}_{low}_{high}"
+    elif btype == 'bandstop':
+        fnorm = np.divide([low, high], .5 * sf)
+        fname = f"{btype}_{low}_{high}"
+    else:
+        raise ValueError("'%s' is an invalid type for filter, "
+                         "you can only choose 'lowpass', 'highpass', 'bandpass' or 'bandstop'"
+                         % 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)
+
+    filtered_data = signal.filtfilt(b=b, a=a, x=data)
+
+    return filtered_data, fname
+
+
+def crop_state_data(midata, mianno):
+    """Crop the data with annotation into different state data, typically seperate the data into NREM data, REM data, Wake and Init data
+    Apply this to every channels
+    """
+    # Get the sleep state data
+    sleep_state = deepcopy(mianno.sleep_state)
+    sleep_state = lst2group([[idx, each] for idx, each in enumerate(sleep_state)])
+    signals = deepcopy(midata.signals)
+    NREM_signals = []
+    REM_signals = []
+    Wake_signals = []
+    Init_signals = []
+
+    for idx, signal in enumerate(signals):
+        sf = midata.sf[idx]
+
+        NREM_data = [signal[int(each[0]*sf): int(each[1]*sf)] 
+                        for each in sleep_state if each[2] == 1]
+        NREM_data = np.array([element for sublist in NREM_data for element in sublist])
+        NREM_signals.append(NREM_data)
+
+        REM_data = [signal[int(each[0]*sf): int(each[1]*sf)] 
+                        for each in sleep_state if each[2] == 2]
+        REM_data = np.array([element for sublist in REM_data for element in sublist])
+        REM_signals.append(REM_data)
+
+        Wake_data = [signal[int(each[0]*sf): int(each[1]*sf)] 
+                        for each in sleep_state if each[2] == 3]
+        Wake_data = np.array([element for sublist in Wake_data for element in sublist])
+        Wake_signals.append(Wake_data)
+        
+        Init_data = [signal[int(each[0]*sf): int(each[1]*sf)] 
+                        for each in sleep_state if each[2] == 4]
+        Init_data = np.array([element for sublist in Init_data for element in sublist])
+        Init_signals.append(Init_data)
+
+    NREM_data = MiData(signals=NREM_signals, channels=midata.channels, sf=midata.sf, time=midata.time, describe='NREM cropped data')
+    REM_data = MiData(signals=REM_signals, channels=midata.channels, sf=midata.sf, time=midata.time, describe='REM cropped data')
+    Wake_data = MiData(signals=Wake_signals, channels=midata.channels, sf=midata.sf, time=midata.time, describe='Wake cropped data')
+    Init_data = MiData(signals=Init_signals, channels=midata.channels, sf=midata.sf, time=midata.time, describe='Init cropped data')
+
+    return NREM_data, REM_data, Wake_data, Init_data
+
+

{misleep-0.2.7 → misleep-0.2.8}/misleep/viz/hypnogram.py

@@ -11,7 +11,7 @@ import matplotlib.pyplot as plt
 import matplotlib
 
 
-def plot_hypno(sleep_state, state_map=None):
+def plot_hypno(sleep_state, state_map=None, time_range=[0, -1]):
     """
     Draw hypnogram with sleep_state list
 
@@ -21,10 +21,21 @@ def plot_hypno(sleep_state, state_map=None):
         List of sleep state, should be integers, and use state_map map to contents
     state_map : dict
         Dict of mapping from sleep state content to it's meaning
+    time_range : list
+        Time range to plot the hypnogram
     """
 
     if not isinstance(sleep_state, list):
         raise TypeError(f"'sleep_state' should be a list, got {type(sleep_state)}")
+    
+    try:
+        if time_range != [0, -1]:
+            sleep_state_ = sleep_state[time_range[0]:time_range[1]]
+    except Exception as e:
+        print("Invalid time range, plot as default")
+        sleep_state_ = sleep_state
+
+    sleep_state = sleep_state_
 
     if state_map is None:
         state_map = {

{misleep-0.2.7 → misleep-0.2.8}/misleep.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.7
+Version: 0.2.8
 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-0.2.7 → misleep-0.2.8}/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 = "0.2.7"
+VERSION = "0.2.8"
 
 INSTALL_REQUIRES = [
     "numpy>=1.18.1",

misleep-0.2.7/misleep/utils/signals.py

@@ -1,73 +0,0 @@
-# -*- coding: UTF-8 -*-
-"""
-@Project: misleep
-@File: signals.py
-@Author: Xueqiang Wang
-@Date: 2024/2/29
-@Description:  
-"""
-import numpy as np
-from scipy import signal
-
-
-def signal_filter(data, sf=256., btype='lowpass', low=0.5, high=30.):
-    """
-    Filter the signal data, use butter filter in scipy
-
-    Parameters
-    ----------
-    data : ndarray
-        1D array. Signal data need to be filtered.
-    sf : float
-        Sampling frequency of signal data. Default is 305.
-    btype : {'lowpass', 'highpass', 'bandpass'}, optional
-        The type of filter. Default is 'lowpass'.
-    low : float
-        Higher than this frequency can pass, used in 'highpass' and 'bandpass'
-        filter. Default is 0.5.
-    high : float
-        Lower than this frequency can pass, used in 'lowpass' and 'bandpass'
-        filter. Default is 30.
-
-    Returns
-    ----------
-    filtered_data : 1D-array
-        Filtered data of signal data using butter filter
-    fname : str
-
-    """
-    if not isinstance(sf, (int, float)):
-        raise TypeError(f"Sample frequency should be a float, got {type(sf)}")
-
-    if not isinstance(low, (int, float)):
-        raise TypeError(f"Low threshold should be a float, got {type(sf)}")
-
-    if not isinstance(high, (int, float)):
-        raise TypeError(f"high threshold should be a float, got {type(sf)}")
-
-    if btype == 'lowpass':
-        fnorm = high / (.5 * sf)
-        fname = f"{btype}_{high}"
-    elif btype == 'highpass':
-        fnorm = low / (.5 * sf)
-        fname = f"{btype}_{low}"
-    elif btype == 'bandpass':
-        fnorm = np.divide([low, high], .5 * sf)
-        fname = f"{btype}_{low}_{high}"
-    elif btype == 'bandstop':
-        fnorm = np.divide([low, high], .5 * sf)
-        fname = f"{btype}_{low}_{high}"
-    else:
-        raise ValueError("'%s' is an invalid type for filter, "
-                         "you can only choose 'lowpass', 'highpass', 'bandpass' or 'bandstop'"
-                         % 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)
-
-    filtered_data = signal.filtfilt(b=b, a=a, x=data)
-
-    return filtered_data, fname
-
-