misleep 0.2.2__tar.gz → 0.2.3__tar.gz

{misleep-0.2.2 → misleep-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.2
+Version: 0.2.3
 Summary: MiSleep: Mice Sleep EEG/EMG visualization, scoring and analysis.
 Home-page: https://github.com/BryanWang0702/MiSleep/
 Download-URL: https://github.com/BryanWang0702/MiSleep/
@@ -82,7 +82,7 @@ There is a config.ini in the root directory of MiSleep source package, multiple
 
 4. Auto stage
 
-Finally, now we have the auto stage function! Check it in the tool.
+Finally, now we have the auto stage function! Check it in the tool. The overall test accuracy of NREM and Wake is higher than 90%, and for REM, the accuracy is higher than 80%. Currently the model's result is rather fragmented in the state transition segments, we will add some constraints to fix this.
 
 **Future**: Open for suggestions :).
 

{misleep-0.2.2 → misleep-0.2.3}/README.md

@@ -48,7 +48,7 @@ There is a config.ini in the root directory of MiSleep source package, multiple
 
 4. Auto stage
 
-Finally, now we have the auto stage function! Check it in the tool.
+Finally, now we have the auto stage function! Check it in the tool. The overall test accuracy of NREM and Wake is higher than 90%, and for REM, the accuracy is higher than 80%. Currently the model's result is rather fragmented in the state transition segments, we will add some constraints to fix this.
 
 **Future**: Open for suggestions :).
 

{misleep-0.2.2 → misleep-0.2.3}/misleep/analysis/auto_stage.py

@@ -5,6 +5,7 @@ import pandas as pd
 from scipy import stats
 import antropy
 import joblib
+import copy
 
 
 def filter_power_line_noise(data, sf, noise_band='50-100-150'):
@@ -36,8 +37,10 @@ def split_window_data(data, sf, state, window_length=20, stride_length=5):
         return []
     
     window_data = []
-    for i in range(0, len(data) - int(window_length*sf) + 1, int(stride_length*sf)):
-        window = data[i:i + int(window_length*sf)]
+    # Make sure we have enough data point of the final segment
+    data_sec_length = floor(data.shape[0] / sf)
+    for i in range(0, data_sec_length-stride_length, stride_length):
+        window = data[int(i*sf):int((i+window_length)*sf)]
         window_data.append([window, state])
 
     return window_data
@@ -99,6 +102,24 @@ def get_data_features(data, sf, data_format='EEG'):
 
     return window_feature_df
 
+def result_constraints(pred_label):
+    """
+    Once finished the prediction, add some constraints to make the result more smooth
+    1. No REM after Wake, set to NREM
+    2. All one epoch between two same state will be set to the around state
+    """
+
+    pred_label = copy.deepcopy(pred_label)
+    for idx in range(1, len(pred_label)-1):
+        label_ = pred_label[idx]
+        if label_ == 3 and pred_label[idx+1] == 2:  # REM after Wake
+            pred_label[idx+1] = 1
+        if pred_label[idx-1] ==pred_label[idx+1]:  # Same state previous and after
+            pred_label[idx] = pred_label[idx-1]
+    
+    return pred_label
+
+
 def auto_stage_gbm(EEG, EMG, sf, EEG_channel='F'):
     """
     Auto stage with lightgbm method
@@ -132,5 +153,6 @@ def auto_stage_gbm(EEG, EMG, sf, EEG_channel='F'):
         gbm_model = joblib.load(r'./misleep/analysis/auto_stage_model/EEG_P_lightgbm_20241221.pkl')
 
     pred_label = gbm_model.predict(window_feature_df, num_iteration=gbm_model.best_iteration_)
+    pred_label = result_constraints(pred_label)
     pred_label = [item for each in pred_label for item in [each]*5]
     return pred_label

{misleep-0.2.2 → misleep-0.2.3}/misleep/config.ini

@@ -1,5 +1,5 @@
 [gui]
-version = v0.2.2
+version = v0.2.3
 updatetime = 2024/12/23
 marker = ['long REM', 'first REM', 'WindEEG', 'W-R ', 'maker']
 startend = ['burst-supression', 'REM', 'Wake', 'Spindle', 'SWA', 'start end label', 'start end label']

{misleep-0.2.2 → misleep-0.2.3}/misleep/gui/dialog.py

@@ -916,6 +916,7 @@ class AutoStageDialog(QDialog, Ui_AutoStageDialog):
 
         return pred_label
 
+
     def okEvent(self):
         self.closed = False
         self.hide()

{misleep-0.2.2 → misleep-0.2.3}/misleep/gui/main_window.py

@@ -1626,8 +1626,8 @@ class main_window(QMainWindow, Ui_MiSleep):
                 return
             auto_stage_lst = self.auto_stage_dialog.auto_stage(self.midata)
             
-            # start_end = self.mianno.start_end + 
-            self.mianno._sleep_state[:len(auto_stage_lst)] = auto_stage_lst
+            # Not sure which one is shorter, so get the minimum one
+            self.mianno._sleep_state[:min(len(self.mianno._sleep_state),len(auto_stage_lst))] = auto_stage_lst[:min(len(self.mianno._sleep_state),len(auto_stage_lst))] 
 
             self.is_saved = False
             self.AnnotationPathLabel.setText('*Annotation path:')

{misleep-0.2.2 → misleep-0.2.3}/misleep.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: misleep
-Version: 0.2.2
+Version: 0.2.3
 Summary: MiSleep: Mice Sleep EEG/EMG visualization, scoring and analysis.
 Home-page: https://github.com/BryanWang0702/MiSleep/
 Download-URL: https://github.com/BryanWang0702/MiSleep/
@@ -82,7 +82,7 @@ There is a config.ini in the root directory of MiSleep source package, multiple
 
 4. Auto stage
 
-Finally, now we have the auto stage function! Check it in the tool.
+Finally, now we have the auto stage function! Check it in the tool. The overall test accuracy of NREM and Wake is higher than 90%, and for REM, the accuracy is higher than 80%. Currently the model's result is rather fragmented in the state transition segments, we will add some constraints to fix this.
 
 **Future**: Open for suggestions :).
 

{misleep-0.2.2 → misleep-0.2.3}/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 = "0.2.2"
+VERSION = "0.2.3"
 
 INSTALL_REQUIRES = [
     "numpy>=1.18.1",