Create preprocessing_physio.py

analysis/preprocessing_physio.py

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+import os
+
+import matplotlib.pyplot as plt
+import neurokit2 as nk
+import numpy as np
+import pandas as pd
+
+# Variables =======================================================
+# Change the path to your local data folder.
+# The data can be downloaded from OpenNeuro (TODO).
+path = "C:/Users/domma/Box/Data/PrimalsInteroception/pilots/physio/"
+
+
+# Convenience functions ============================================
+def load_data(path, task="HBC"):
+    files = os.listdir(path)
+    df, info = nk.read_xdf(filename=path + [file for file in files if task in file][0])
+
+    # # Test
+    # df1 = df.iloc[0:3000]
+    # df2 = info["data"][0].iloc[0:300]
+    # plt.plot(df1.index, df1["TP9"])
+    # plt.plot(df2.index, df2["TP9"])
+
+    # df3 = info["data"][4].iloc[0:1000]
+    # plt.plot(df1.index, df1["ECG"])
+    # plt.plot(df3.index, df3["ECGBIT1"])
+
+    df = df.reset_index()
+
+    df = df.drop(
+        columns=[
+            "Right AUX",
+            "X",
+            "Y",
+            "Z",
+            "RED",
+            "GYRO_X",
+            "GYRO_Y",
+            "GYRO_Z",
+            "nSeq",
+            "index",
+        ]
+    )
+
+    df = df.rename(
+        columns={
+            "PPG": "PPG_Muse",
+            "RESPBIT0": "RSP",
+            "ECGBIT1": "ECG",
+            "PULSEOXI2": "PPG",
+            "LUX3": "PHOTO",
+        }
+    )
+
+    return df, info
+
+
+# Load Data =======================================================
+participants = os.listdir(path)
+
+for participant in participants:
+    # participant = "sub-pilot2"
+    path_sub = path + participant + "/ses-S001/beh/"
+
+    df, info = load_data(path=path_sub, task="HBC")
+
+    nk.signal_plot(df, subplots=True)