more parameters

main.py

@@ -63,6 +63,25 @@ SECTIONS = [
             {"name": "DOWNSAMPLE_FREQUENCY", "default": 25, "type": int, "help": "Frequency (Hz) to downsample to. If this is set higher than the input data, new data will be interpolated. Only used if DOWNSAMPLE is set to True"},
         ]
     },
+    {
+        "title": "Trimming",
+        "params": [
+            {"name": "TRIM", "default": True, "type": bool, "help": "Trim the file start."},
+            {"name": "SECONDS_TO_KEEP", "default": 5, "type": float, "help": "Seconds to keep at the beginning of all loaded snirf files before the first annotation/event occurs. Calculation is done seperatly on all loaded snirf files. Setting this to 0 will have the first annotation/event be at time point 0."},
+        ]
+    },
+    {
+        "title": "Verify Optode Placement",
+        "params": [
+            {"name": "OPTODE_PLACEMENT", "default": True, "type": bool, "help": "Generate an image for each participant outlining their optode placement."},
+        ]
+    },
+    {
+        "title": "Heart Rate",
+        "params": [
+            {"name": "HEART_RATE", "default": True, "type": bool, "help": "Attempt to calculate the participants heart rate."},
+        ]
+    },
     {
         "title": "Scalp Coupling Index",
         "params": [
@@ -108,6 +127,15 @@ SECTIONS = [
             {"name": "TDDR", "default": True, "type": bool, "help": "Apply Temporal Derivitave Distribution Repair filtering - a method that removes baseline shift and spike artifacts from the data."},
         ]
     },
+    {
+        "title": "Wavelet filtering",
+        "params": [
+            {"name": "WAVELET", "default": True, "type": bool, "help": "Apply Wavelet filtering."},
+            {"name": "IQR", "default": 1.5, "type": float, "help": "Inter-Quartile Range."},
+            {"name": "WAVELET_TYPE", "default": "db4", "type": str, "help": "Wavelet type."},
+            {"name": "WAVELET_LEVEL", "default": 3, "type": int, "help": "Wavelet level."},
+        ]
+    },
     {
         "title": "Haemoglobin Concentration",
         "params": [
@@ -117,22 +145,23 @@ SECTIONS = [
     {
         "title": "Enhance Negative Correlation",
         "params": [
-            #{"name": "ENHANCE_NEGATIVE_CORRELATION", "default": False, "type": bool, "help": "Calculate Peak Spectral Power."},
+            {"name": "ENHANCE_NEGATIVE_CORRELATION", "default": False, "type": bool, "help": "Apply Enhance Negative Correlation."},
         ]
     },
     {
         "title": "Filtering",
         "params": [
+            {"name": "FILTER", "default": True, "type": bool, "help": "Filter the data."},
             {"name": "L_FREQ", "default": 0.005, "type": float, "help": "Any frequencies lower than this value will be removed."},
             {"name": "H_FREQ", "default": 0.3, "type": float, "help": "Any frequencies higher than this value will be removed."},
-            #{"name": "FILTER", "default": True, "type": bool, "help": "Calculate Peak Spectral Power."},
-
         ]
     },
     {
-        "title": "Short Channels",
+        "title": "Short/Long Channels",
         "params": [
             {"name": "SHORT_CHANNEL", "default": True, "type": bool, "help": "This should be set to True if the data has a short channel present in the data."},
+            {"name": "SHORT_CHANNEL_THRESH", "default": 0.015, "type": float, "help": "The maximum distance the short channel can be in metres."},
+            {"name": "LONG_CHANNEL_THRESH", "default": 0.045, "type": float, "help": "The maximum distance the long channel can be in metres."},
         ]
     },
     {
@@ -151,7 +180,7 @@ SECTIONS = [
         "title": "Design Matrix",
         "params": [
             {"name": "REMOVE_EVENTS", "default": "None", "type": list, "help": "Remove events matching the names provided before generating the Design Matrix"},
-            # {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Drift model for GLM."},
+            {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Drift model for GLM."},
             # {"name": "DURATION_BETWEEN_ACTIVITIES", "default": 35, "type": int, "help": "Time between activities (s)."},
             # {"name": "SHORT_CHANNEL_REGRESSION", "default": True, "type": bool, "help": "Use short channel regression."},
         ]
@@ -1200,7 +1229,7 @@ class ProgressBubble(QWidget):
         self.progress_layout = QHBoxLayout()
 
         self.rects = []
-        for _ in range(20):
+        for _ in range(25):
             rect = QFrame()
             rect.setFixedSize(10, 18)
             rect.setStyleSheet("background-color: white; border: 1px solid gray;")