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filter_emg.py
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filter_emg.py
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#!/usr/bin/env python3
import os
import sys
import glob
import pandas as pd
from putemg_features import biolab_utilities
def usage():
print()
print("Applies denoising filter")
print()
print("Usage: {:s} <input_hdf5_folder> <output_hdf5_folder>".format(os.path.basename(__file__)))
print(" <input_hdf5_folder>: putEMG HDF5 file folder containing raw experiment data")
print(" <output_hdf5_folder>: output HDF5 file folder for filtered data")
print()
print("Example:")
print("{:s} ../putEMG/Data-HDF5 ../putEMG/Data-HDF5-filtered".
format(os.path.basename(__file__)))
exit(1)
if __name__ == '__main__':
if '-h' in sys.argv or '--help' in sys.argv:
usage()
if len(sys.argv) != 3:
print("Invalid parameter count")
usage()
putemg_folder = sys.argv[1]
output_folder = sys.argv[2]
all_files = [f for f in sorted(glob.glob(os.path.join(putemg_folder, "*.hdf5")))]
if not os.path.exists(output_folder):
os.makedirs(output_folder)
for file in all_files:
basename = os.path.basename(file)
filename = os.path.splitext(basename)[0]
print('Denoising file: {:s}'.format(basename))
# read raw putEMG data file and run filter
df: pd.DataFrame = pd.read_hdf(file)
biolab_utilities.apply_filter(df)
output_file = filename + '_filtered.hdf5'
print('Saving to file: {:s}'.format(output_file))
df.to_hdf(os.path.join(output_folder, output_file), 'data', format='table', mode='w', complevel=5)