Improve extraction handling

- fix default parameters for smoothing - allow the graph to go to -0.05 on y range - fix smoothing issues - test file for 30FPS - add best default settings as comment
cvjena · Apr 10, 2024 · cb1aec8 · cb1aec8
1 parent f338dcd
commit cb1aec8
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Showing 6 changed files with 2,069 additions and 6 deletions.
diff --git a/frontend/jwidgets/graph.py b/frontend/jwidgets/graph.py
@@ -17,7 +17,7 @@ def __init__(self, background="default", x_lim_max=1000, **kargs):
 
         self.plot_item.setLimits(xMin=0, xMax=x_lim_max)
         self.plot_item.setXRange(0, x_lim_max)
-        self.plot_item.setYRange(0, 1)
+        self.plot_item.setYRange(-0.05, 1)
 
         self.axis_b: pg.AxisItem = self.plot_item.getAxis("bottom")
         self.curves: list[pg.PlotDataItem] = []

diff --git a/frontend/ui_eye_blinking_extraction.py b/frontend/ui_eye_blinking_extraction.py
@@ -10,12 +10,41 @@
 from qtpy.QtWidgets import QMessageBox
 from PyQt6.QtCore import pyqtSignal
 
-
 from jefapato import blinking
 from frontend import config, jwidgets
 
 logger = structlog.get_logger()
 
+#### Recommended Extracton Settings for Eye Blinking ####
+# @30 FPS
+# Minimum Distance: 10 Frames
+# Minimum Prominence: 0.1 EAR Score
+# Minimum Internal Width: 4 Frames
+# Maximum Internal Width: 20 Frames
+# Maximum Matching Distance: 15 Frames
+# Partial Threshold Left:  0.18 EAR Score
+# Partial Threshold Right: 0.18 EAR Score
+# 
+# Smoothing
+# - Window Size: 7
+# - Polynomial Degree: 3
+#
+# ---
+# 
+# @240 FPS
+# Minimum Distance: 50 Frames
+# Minimum Prominence: 0.1 EAR Score
+# Minimum Internal Width: 20 Frames
+# Maximum Internal Width: 100 Frames
+# Maximum Matching Distance: 30 Frames
+# Partial Threshold Left:  0.18 EAR Score
+# Partial Threshold Right: 0.18 EAR Score
+#
+# Smoothing
+# - Window Size: 7
+# - Polynomial Degree: 3
+
+
 DOWNSAMPLE_FACTOR = 8
 
 def to_float(value: str) -> float:
@@ -254,12 +283,12 @@ def __init__(self, parent):
 
         le_smooth_size = QtWidgets.QLineEdit()
         le_smooth_size.setValidator(int_validator)
-        self.add_handler("smooth_size", le_smooth_size, mapper=I2S, default=91)
+        self.add_handler("smooth_size", le_smooth_size, mapper=I2S, default=7)
         box_smooth_layout.addRow("Window Size", le_smooth_size)
 
         le_smooth_poly = QtWidgets.QLineEdit()
         le_smooth_poly.setValidator(int_validator)
-        self.add_handler("smooth_poly", le_smooth_poly, mapper=I2S, default=5)
+        self.add_handler("smooth_poly", le_smooth_poly, mapper=I2S, default=3)
         box_smooth_layout.addRow("Polynomial Degree", le_smooth_poly)
 
         self.set_algo.addRow(box_smooth)
@@ -274,7 +303,7 @@ def __init__(self, parent):
         self.cb_as_time.stateChanged.connect(self.compute_graph_axis)
 
         btn_reset_graph = QtWidgets.QPushButton(qta.icon("msc.refresh"), "Reset Graph Y Range")
-        btn_reset_graph.clicked.connect(lambda: self.graph.setYRange(0, 1))
+        btn_reset_graph.clicked.connect(lambda: self.graph.setYRange(-0.5, 1))
         self.set_visuals.addRow(btn_reset_graph)
 
         btn_reset_view  = QtWidgets.QPushButton(qta.icon("msc.refresh"), "View Full Graph")
@@ -635,6 +664,11 @@ def compute_intervals(self) -> bool:
         if self.comp_partial_threshold_l is np.nan or self.comp_partial_threshold_r is np.nan:
             QMessageBox.warning(None, "Blinking Extraction Warning", "No partial threshold could be found. Continued with default `complete` label.")
         self.progress.setValue(50)
+
+        # check if the blinking data frames are empty
+        if self.blinking_l.empty or self.blinking_r.empty:
+            QMessageBox.warning(None, "Blinking Extraction Warning", "No blinks found in the data. Please check the data and try again.")
+            return False
 
         try:
             self.blinking_matched = blinking.match(

diff --git a/src/jefapato/blinking/peaks.py b/src/jefapato/blinking/peaks.py
@@ -25,6 +25,10 @@ def otsu_thresholding(values: np.ndarray) -> float:
     for th in th_range:
         r = np.nansum([np.mean(cls) * np.var(values, where=cls) for cls in [values>=th, values<th]])
         res.append(r)
+
+    if len(res) == 0:
+        # if the result is empty, return np.nan
+        return np.nan
     return th_range[np.argmin(res)]
 
 def peaks(

diff --git a/src/jefapato/blinking/smooth.py b/src/jefapato/blinking/smooth.py
@@ -5,8 +5,12 @@
 
 
 def smooth(time_series: np.ndarray, smooth_size:int=91, smooth_poly:int=4) -> np.ndarray:
-    return signal.savgol_filter(
+    sig = signal.savgol_filter(
         time_series,
         window_length=smooth_size,
         polyorder=smooth_poly,
     )
+    # check all values to be 0 or 1
+    sig[sig < 0] = 0
+    sig[sig > 1] = 1
+    return sig
diff --git a/tests/files/blinking/blinking_30FPS.csv b/tests/files/blinking/blinking_30FPS.csv
@@ -0,0 +1,251 @@
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