[FIXED] Append multiple biopac files into one dataframe with python?

Issue

I am trying to put many AcqKnowledge data files from a folder into different data frames based on the channel data so that I may do additional operations etc with them. When I try to use the following syntax, I cannot get the data files to join with one another. Any suggestions would be appreciated!

I am able to read one file at a time with a similar approach.

this is a resource on bioread: https://github.com/uwmadison-chm/bioread

import pandas as pd
from bioread import read_file

# Specify the folder containing your Acq files
folder_path = r"C:\path\to\your\acq_files"

# Initialize empty lists for EDA and ECG data
eda_data = []
ecg_data = []

# Iterate through Acq files in the folder
for file_name in os.listdir(folder_path):
    if file_name.endswith(".acq"):
        file_path = os.path.join(folder_path, file_name)

        # Read the Acq file
        acq_data = read_file(file_path)

        # Extract data for EDA channel
        eda_channel_name = 'GSR - EDA100C'
        if eda_channel_name in acq_data.channels:
            eda_data.extend(acq_data[eda_channel_name].data.tolist())

        # Extract data for ECG channel
        ecg_channel_name = 'ECG - ECG100C'
        if ecg_channel_name in acq_data.channels:
            ecg_data.extend(acq_data[ecg_channel_name].data.tolist())

# Create DataFrames for EDA and ECG
df_eda = pd.DataFrame({"GSR - EDA100C": eda_data})
df_ecg = pd.DataFrame({"ECG - ECG100C": ecg_data})

# Print the first 10 rows of the EDA DataFrame
print("First 10 rows of the EDA DataFrame:")
print(df_eda.head(10))

# Print the first 10 rows of the ECG DataFrame
print("\nFirst 10 rows of the ECG DataFrame:")
print(df_ecg.head(10))

First 10 rows of the combined DataFrame: Empty DataFrame Columns: [] Index: []

Could you help me resolve this?

Solution

I think the main problem here is that you're doing membership test operations using an str against a list of Channel objects. This is why the checks, you do, never evalute to True, the lists remain empty and hence the DataFrames too. So, here is a proposition to fix your code :

Move lines 20 and 25 outside the loop (put them before) and update the inner if blocks to this :

        channels = acq_data.channels

        for idx, ch in enumerate(map(str, channels)):
            if eda_channel_name in ch:
                eda_data.extend(channels[idx].data)

            elif ecg_channel_name in ch:
                ecg_data.extend(channels[idx].data)

Answered By - Timeless