EMG_Biometrics_2021/Handle_emg_data.py

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2021-07-07 07:46:18 +00:00
from typing import List
from numpy.core.arrayprint import IntegerFormat
from numpy.lib import math
import pandas as pd
from pathlib import Path
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import numpy as np
from pandas.core.frame import DataFrame
import sys
sys.path.insert(0, '/Users/Markus/Prosjekter git/Slovakia 2021/psf_lib/python_speech_features/python_speech_features')
from psf_lib.python_speech_features.python_speech_features import mfcc
import json
import os
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# Global variables for MFCC
MFCC_STEPSIZE = 0.5 # Seconds
MFCC_WINDOWSIZE = 2 # Seconds
NR_COEFFICIENTS = 13 # Number of coefficients
NR_MEL_BINS = 40 # Number of mel-filter-bins
class Data_container:
# Initiates personal data container for each subject. Dict for each session with keys 'left' and 'right',
# and values equal to lists of EMG data indexed 0-7
def __init__(self, subject_nr:int, subject_name:str, nr_sessions:int):
self.subject_nr = subject_nr
self.subject_name = subject_name
self.dict_list = [{'left': [None]*8, 'right': [None]*8} for i in range(nr_sessions)]
def __str__(self) -> str:
return 'Name: {}, \tID: {}'.format(self.subject_name, self.subject_nr)
class CSV_handler:
# Initiates object to store all datapoints in the experiment
def __init__(self, nr_subjects:int, nr_sessions:int):
self.working_dir = str(Path.cwd())
self.nr_subjects = nr_subjects
self.nr_sessions = nr_sessions
# Dict with keys equal subject numbers and values equal to its respective datacontainer
self.data_container_dict = {i+1: None for i in range(nr_subjects)}
# String describing which type of data is stored in the object
self.data_type = None
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# Makes dataframe from the csv files in the working directory
# Input: filename of a csv-file
# Output: DataFrame
def make_df(self, filename):
#filepath = self.working_dir + str(filename)
filepath = str(filename)
df = pd.read_csv(filepath)
return df
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# Extracts out the timestamp and the selected emg signal into a new dataframe
# Input: filename of a csv-file, EMG nr
# Output: DataFrame(timestamp/EMG)
def get_emg_table_from_file(self, filename:str, emg_nr:int):
tot_data_frame = self.make_df(filename)
emg_str = 'emg' + str(emg_nr)
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filtered_df = tot_data_frame[["timestamp", emg_str]]
return filtered_df
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# Takes in a df and stores the information in a Data_container object
# Input: filename of a csv-file, EMG nr, left/right arm, subject's data_container, session nr
# Output: None -> stores EMG data in data container
def store_df_in_container(self, filename:str, emg_nr:int, which_arm:str, data_container:Data_container, session:int):
df = self.get_emg_table_from_file(filename, emg_nr+1)
if df.isnull().values.any():
print('NaN in: subject', data_container.subject_nr, 'arm:', which_arm, 'session:', session, 'emg nr:', emg_nr)
# Places the data correctly:
data_container.dict_list[session-1][which_arm][emg_nr] = df
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# Links the data container for a subject to the csv_handler object
# Input: the subject's data_container
# Output: None -> places the data container correctly in the CSV_handler data_container_dict
def link_container_to_handler(self, data_container:Data_container):
# Links the retrieved data with the subjects data_container
subject_nr = data_container.subject_nr
self.data_container_dict[subject_nr] = data_container
# Retrieves df via the data_dict in the CSV_handler object
# Input: Experiment detailes
# Output: DataFrame
def get_df_from_data_dict(self, subject_nr, which_arm, session, emg_nr):
container:Data_container = self.data_container_dict.get(subject_nr)
df = container.dict_list[session - 1].get(which_arm)[emg_nr - 1]
return df
# Loads data the to the CSV_handler(general load func). Choose data_type: hard, hardPP, soft og softPP as str.
# Input: String(datatype you want), direction name of that type
# Output: None -> load and stores data
def load_data(self, type:str, type_dir_name:str):
data_path = self.working_dir + '/data/' + type_dir_name
subject_id = 100
subject_name = 'bruh'
nr_sessions = 101
container = None
session_count = 0
for i, (path, subject_dir, session_dir) in enumerate(os.walk(data_path)):
if path is not data_path:
if subject_dir:
session_count = 0
subject_id = int(path[-1])
subject_name = subject_dir[0].split('_')[0]
nr_sessions = len(subject_dir)
container = Data_container(subject_id, subject_name, nr_sessions)
continue
else:
session_count += 1
for f in session_dir:
spes_path = os.path.join(path, f)
if f == 'myoLeftEmg.csv':
for emg_nr in range(8):
self.store_df_in_container(spes_path, emg_nr, 'left', container, session_count)
elif f == 'myoRightEmg.csv':
for emg_nr in range(8):
self.store_df_in_container(spes_path, emg_nr, 'right', container, session_count)
self.link_container_to_handler(container)
self.data_type = type
return self.data_container_dict
# Retrieved data. Send in loaded csv_handler and data detailes you want.
# Input: Experiment detailes
# Output: DataFrame, samplerate:int
def get_data(self, subject_nr, which_arm, session, emg_nr):
data_frame = self.get_df_from_data_dict(subject_nr, which_arm, session, emg_nr)
samplerate = get_samplerate(data_frame)
return data_frame, samplerate
# OBSOLETE
def load_hard_PP_emg_data(self):
# CSV data from subject 1
file1_subject1_left = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1810/myoLeftEmg.csv"
file2_subject1_left = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1830/myoLeftEmg.csv"
file3_subject1_left = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1845/myoLeftEmg.csv"
file4_subject1_left = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1855/myoLeftEmg.csv"
subject1_left_files = [file1_subject1_left, file2_subject1_left, file3_subject1_left, file4_subject1_left]
file1_subject1_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1810/myoRightEmg.csv"
file2_subject1_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1830/myoRightEmg.csv"
file3_subject1_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1845/myoRightEmg.csv"
file4_subject1_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMarek_20201207_1855/myoRightEmg.csv"
subject1_right_files = [file1_subject1_rigth, file2_subject1_rigth, file3_subject1_rigth, file4_subject1_rigth]
# CSV data from subject 2
file1_subject2_left = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2010/myoLeftEmg.csv"
file2_subject2_left = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2025/myoLeftEmg.csv"
file3_subject2_left = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2035/myoLeftEmg.csv"
file4_subject2_left = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2045/myoLeftEmg.csv"
subject2_left_files = [file1_subject2_left, file2_subject2_left, file3_subject2_left, file4_subject2_left]
file1_subject2_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2010/myoRightEmg.csv"
file2_subject2_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2025/myoRightEmg.csv"
file3_subject2_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2035/myoRightEmg.csv"
file4_subject2_rigth = "/Exp20201205_2myo_hardTypePP/HaluskaMaros_20201205_2045/myoRightEmg.csv"
subject2_right_files = [file1_subject2_rigth, file2_subject2_rigth, file3_subject2_rigth, file4_subject2_rigth]
# CSV data from subject 3
file1_subject3_left = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1700/myoLeftEmg.csv"
file2_subject3_left = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1715/myoLeftEmg.csv"
file3_subject3_left = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1725/myoLeftEmg.csv"
file4_subject3_left = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1735/myoLeftEmg.csv"
subject3_left_files = [file1_subject3_left, file2_subject3_left, file3_subject3_left, file4_subject3_left]
file1_subject3_rigth = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1700/myoRightEmg.csv"
file2_subject3_rigth = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1715/myoRightEmg.csv"
file3_subject3_rigth = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1725/myoRightEmg.csv"
file4_subject3_rigth = "/Exp20201205_2myo_hardTypePP/HaluskovaBeata_20201205_1735/myoRightEmg.csv"
subject3_right_files = [file1_subject3_rigth, file2_subject3_rigth, file3_subject3_rigth, file4_subject3_rigth]
# CSV data from subject 4
file1_subject4_left = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1900/myoLeftEmg.csv"
file2_subject4_left = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1915/myoLeftEmg.csv"
file3_subject4_left = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1925/myoLeftEmg.csv"
file4_subject4_left = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1935/myoLeftEmg.csv"
subject4_left_files = [file1_subject4_left, file2_subject4_left, file3_subject4_left, file4_subject4_left]
file1_subject4_rigth = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1900/myoRightEmg.csv"
file2_subject4_rigth = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1915/myoRightEmg.csv"
file3_subject4_rigth = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1925/myoRightEmg.csv"
file4_subject4_rigth = "/Exp20201205_2myo_hardTypePP/KelisekDavid_20201209_1935/myoRightEmg.csv"
subject4_right_files = [file1_subject4_rigth, file2_subject4_rigth, file3_subject4_rigth, file4_subject4_rigth]
# CSV data from subject 5
file1_subject5_left = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2030/myoLeftEmg.csv"
file2_subject5_left = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2040/myoLeftEmg.csv"
file3_subject5_left = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2050/myoLeftEmg.csv"
file4_subject5_left = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2100/myoLeftEmg.csv"
subject5_left_files = [file1_subject5_left, file2_subject5_left, file3_subject5_left, file4_subject5_left]
file1_subject5_rigth = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2030/myoRightEmg.csv"
file2_subject5_rigth = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2040/myoRightEmg.csv"
file3_subject5_rigth = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2050/myoRightEmg.csv"
file4_subject5_rigth = "/Exp20201205_2myo_hardTypePP/KelisekRichard_20201209_2100/myoRightEmg.csv"
subject5_right_files = [file1_subject5_rigth, file2_subject5_rigth, file3_subject5_rigth, file4_subject5_rigth]
left_list = [subject1_left_files, subject2_left_files, subject3_left_files, subject4_left_files, subject5_left_files]
right_list = [subject1_right_files, subject2_right_files, subject3_right_files, subject4_right_files, subject5_right_files]
subject1_data_container = Data_container(1, 'HaluskaMarek')
subject2_data_container = Data_container(2, 'HaluskaMaros')
subject3_data_container = Data_container(3, 'HaluskovaBeata')
subject4_data_container = Data_container(4, 'KelisekDavid')
subject5_data_container = Data_container(5, 'KelisekRichard')
subject_data_container_list = [subject1_data_container, subject2_data_container, subject3_data_container,
subject4_data_container, subject5_data_container]
for subject_nr in range(5):
data_container = subject_data_container_list[subject_nr]
# left variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = left_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'left', data_container, round+1)
# right variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = right_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'right', data_container, round+1)
# Links the stored data in the data_container to the Handler
self.link_container_to_handler(data_container)
self.data_type = 'hardPP'
return self.data_container_dict
def load_soft_PP_emg_data(self):
# CSV data from subject 1
file1_subject1_left = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1910/myoLeftEmg.csv"
file2_subject1_left = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1920/myoLeftEmg.csv"
file3_subject1_left = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1935/myoLeftEmg.csv"
file4_subject1_left = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1945/myoLeftEmg.csv"
subject1_left_files = [file1_subject1_left, file2_subject1_left, file3_subject1_left, file4_subject1_left]
file1_subject1_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1910/myoRightEmg.csv"
file2_subject1_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1920/myoRightEmg.csv"
file3_subject1_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1935/myoRightEmg.csv"
file4_subject1_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMarek_20201207_1945/myoRightEmg.csv"
subject1_right_files = [file1_subject1_rigth, file2_subject1_rigth, file3_subject1_rigth, file4_subject1_rigth]
# CSV data from subject 2
file1_subject2_left = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2055/myoLeftEmg.csv"
file2_subject2_left = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2110/myoLeftEmg.csv"
file3_subject2_left = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2125/myoLeftEmg.csv"
file4_subject2_left = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2145/myoLeftEmg.csv"
subject2_left_files = [file1_subject2_left, file2_subject2_left, file3_subject2_left, file4_subject2_left]
file1_subject2_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2055/myoRightEmg.csv"
file2_subject2_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2110/myoRightEmg.csv"
file3_subject2_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2125/myoRightEmg.csv"
file4_subject2_rigth = "/Exp20201205_2myo_softTypePP/HaluskaMaros_20201205_2145/myoRightEmg.csv"
subject2_right_files = [file1_subject2_rigth, file2_subject2_rigth, file3_subject2_rigth, file4_subject2_rigth]
# CSV data from subject 3
file1_subject3_left = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1745/myoLeftEmg.csv"
file2_subject3_left = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1755/myoLeftEmg.csv"
file3_subject3_left = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1810/myoLeftEmg.csv"
file4_subject3_left = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1825/myoLeftEmg.csv"
subject3_left_files = [file1_subject3_left, file2_subject3_left, file3_subject3_left, file4_subject3_left]
file1_subject3_rigth = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1745/myoRightEmg.csv"
file2_subject3_rigth = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1755/myoRightEmg.csv"
file3_subject3_rigth = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1810/myoRightEmg.csv"
file4_subject3_rigth = "/Exp20201205_2myo_softTypePP/HaluskovaBeata_20201205_1825/myoRightEmg.csv"
subject3_right_files = [file1_subject3_rigth, file2_subject3_rigth, file3_subject3_rigth, file4_subject3_rigth]
# CSV data from subject 4
file1_subject4_left = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_1945/myoLeftEmg.csv"
file2_subject4_left = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_1955/myoLeftEmg.csv"
file3_subject4_left = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_2010/myoLeftEmg.csv"
file4_subject4_left = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_2025/myoLeftEmg.csv"
subject4_left_files = [file1_subject4_left, file2_subject4_left, file3_subject4_left, file4_subject4_left]
file1_subject4_rigth = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_1945/myoRightEmg.csv"
file2_subject4_rigth = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_1955/myoRightEmg.csv"
file3_subject4_rigth = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_2010/myoRightEmg.csv"
file4_subject4_rigth = "/Exp20201205_2myo_softTypePP/KelisekDavid_20201209_2025/myoRightEmg.csv"
subject4_right_files = [file1_subject4_rigth, file2_subject4_rigth, file3_subject4_rigth, file4_subject4_rigth]
# CSV data from subject 5
file1_subject5_left = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2110/myoLeftEmg.csv"
file2_subject5_left = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2120/myoLeftEmg.csv"
file3_subject5_left = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2130/myoLeftEmg.csv"
file4_subject5_left = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2140/myoLeftEmg.csv"
subject5_left_files = [file1_subject5_left, file2_subject5_left, file3_subject5_left, file4_subject5_left]
file1_subject5_rigth = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2110/myoRightEmg.csv"
file2_subject5_rigth = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2120/myoRightEmg.csv"
file3_subject5_rigth = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2130/myoRightEmg.csv"
file4_subject5_rigth = "/Exp20201205_2myo_softTypePP/KelisekRichard_20201209_2140/myoRightEmg.csv"
subject5_right_files = [file1_subject5_rigth, file2_subject5_rigth, file3_subject5_rigth, file4_subject5_rigth]
left_list = [subject1_left_files, subject2_left_files, subject3_left_files, subject4_left_files, subject5_left_files]
right_list = [subject1_right_files, subject2_right_files, subject3_right_files, subject4_right_files, subject5_right_files]
subject1_data_container = Data_container(1, 'HaluskaMarek')
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subject2_data_container = Data_container(2, 'HaluskaMaros')
subject3_data_container = Data_container(3, 'HaluskovaBeata')
subject4_data_container = Data_container(4, 'KelisekDavid')
subject5_data_container = Data_container(5, 'KelisekRichard')
subject_data_container_list = [subject1_data_container, subject2_data_container, subject3_data_container,
subject4_data_container, subject5_data_container]
for subject_nr in range(5):
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data_container = subject_data_container_list[subject_nr]
# left variant proccessed here
for round in range(4):
for emg_nr in range(8):
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filename = left_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'left', data_container, round+1)
# right variant proccessed here
for round in range(4):
for emg_nr in range(8):
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filename = right_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'right', data_container, round+1)
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# Links the stored data in the data_container to the Handler
self.link_container_to_handler(data_container)
self.data_type = 'softPP'
return self.data_container_dict
def load_hard_original_emg_data(self):
# CSV data from subject 1
file1_subject1_left = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1810/myoLeftEmg.csv"
file2_subject1_left = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1830/myoLeftEmg.csv"
file3_subject1_left = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1845/myoLeftEmg.csv"
file4_subject1_left = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1855/myoLeftEmg.csv"
subject1_left_files = [file1_subject1_left, file2_subject1_left, file3_subject1_left, file4_subject1_left]
file1_subject1_rigth = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1810/myoRightEmg.csv"
file2_subject1_rigth = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1830/myoRightEmg.csv"
file3_subject1_rigth = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1845/myoRightEmg.csv"
file4_subject1_rigth = "/Exp20201205_2myo_hardType/HaluskaMarek_20201207_1855/myoRightEmg.csv"
subject1_right_files = [file1_subject1_rigth, file2_subject1_rigth, file3_subject1_rigth, file4_subject1_rigth]
# CSV data from subject 2
file1_subject2_left = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2010/myoLeftEmg.csv"
file2_subject2_left = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2025/myoLeftEmg.csv"
file3_subject2_left = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2035/myoLeftEmg.csv"
file4_subject2_left = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2045/myoLeftEmg.csv"
subject2_left_files = [file1_subject2_left, file2_subject2_left, file3_subject2_left, file4_subject2_left]
file1_subject2_rigth = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2010/myoRightEmg.csv"
file2_subject2_rigth = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2025/myoRightEmg.csv"
file3_subject2_rigth = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2035/myoRightEmg.csv"
file4_subject2_rigth = "/Exp20201205_2myo_hardType/HaluskaMaros_20201205_2045/myoRightEmg.csv"
subject2_right_files = [file1_subject2_rigth, file2_subject2_rigth, file3_subject2_rigth, file4_subject2_rigth]
# CSV data from subject 3
file1_subject3_left = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1700/myoLeftEmg.csv"
file2_subject3_left = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1715/myoLeftEmg.csv"
file3_subject3_left = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1725/myoLeftEmg.csv"
file4_subject3_left = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1735/myoLeftEmg.csv"
subject3_left_files = [file1_subject3_left, file2_subject3_left, file3_subject3_left, file4_subject3_left]
file1_subject3_rigth = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1700/myoRightEmg.csv"
file2_subject3_rigth = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1715/myoRightEmg.csv"
file3_subject3_rigth = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1725/myoRightEmg.csv"
file4_subject3_rigth = "/Exp20201205_2myo_hardType/HaluskovaBeata_20201205_1735/myoRightEmg.csv"
subject3_right_files = [file1_subject3_rigth, file2_subject3_rigth, file3_subject3_rigth, file4_subject3_rigth]
# CSV data from subject 4
file1_subject4_left = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1900/myoLeftEmg.csv"
file2_subject4_left = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1915/myoLeftEmg.csv"
file3_subject4_left = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1925/myoLeftEmg.csv"
file4_subject4_left = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1935/myoLeftEmg.csv"
subject4_left_files = [file1_subject4_left, file2_subject4_left, file3_subject4_left, file4_subject4_left]
file1_subject4_rigth = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1900/myoRightEmg.csv"
file2_subject4_rigth = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1915/myoRightEmg.csv"
file3_subject4_rigth = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1925/myoRightEmg.csv"
file4_subject4_rigth = "/Exp20201205_2myo_hardType/KelisekDavid_20201209_1935/myoRightEmg.csv"
subject4_right_files = [file1_subject4_rigth, file2_subject4_rigth, file3_subject4_rigth, file4_subject4_rigth]
# CSV data from subject 5
file1_subject5_left = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2030/myoLeftEmg.csv"
file2_subject5_left = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2040/myoLeftEmg.csv"
file3_subject5_left = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2050/myoLeftEmg.csv"
file4_subject5_left = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2100/myoLeftEmg.csv"
subject5_left_files = [file1_subject5_left, file2_subject5_left, file3_subject5_left, file4_subject5_left]
file1_subject5_rigth = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2030/myoRightEmg.csv"
file2_subject5_rigth = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2040/myoRightEmg.csv"
file3_subject5_rigth = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2050/myoRightEmg.csv"
file4_subject5_rigth = "/Exp20201205_2myo_hardType/KelisekRichard_20201209_2100/myoRightEmg.csv"
subject5_right_files = [file1_subject5_rigth, file2_subject5_rigth, file3_subject5_rigth, file4_subject5_rigth]
left_list = [subject1_left_files, subject2_left_files, subject3_left_files, subject4_left_files, subject5_left_files]
right_list = [subject1_right_files, subject2_right_files, subject3_right_files, subject4_right_files, subject5_right_files]
subject1_data_container = Data_container(1, 'HaluskaMarek')
subject2_data_container = Data_container(2, 'HaluskaMaros')
subject3_data_container = Data_container(3, 'HaluskovaBeata')
subject4_data_container = Data_container(4, 'KelisekDavid')
subject5_data_container = Data_container(5, 'KelisekRichard')
subject_data_container_list = [subject1_data_container, subject2_data_container, subject3_data_container,
subject4_data_container, subject5_data_container]
for subject_nr in range(5):
data_container = subject_data_container_list[subject_nr]
# left variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = left_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'left', data_container, round+1)
# right variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = right_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'right', data_container, round+1)
# Links the stored data in the data_container to the Handler
self.link_container_to_handler(data_container)
self.data_type = 'hard'
return self.data_container_dict
def load_soft_original_emg_data(self):
# CSV data from subject 1
file1_subject1_left = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1910/myoLeftEmg.csv"
file2_subject1_left = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1920/myoLeftEmg.csv"
file3_subject1_left = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1935/myoLeftEmg.csv"
file4_subject1_left = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1945/myoLeftEmg.csv"
subject1_left_files = [file1_subject1_left, file2_subject1_left, file3_subject1_left, file4_subject1_left]
file1_subject1_rigth = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1910/myoRightEmg.csv"
file2_subject1_rigth = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1920/myoRightEmg.csv"
file3_subject1_rigth = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1935/myoRightEmg.csv"
file4_subject1_rigth = "/Exp20201205_2myo_softType/HaluskaMarek_20201207_1945/myoRightEmg.csv"
subject1_right_files = [file1_subject1_rigth, file2_subject1_rigth, file3_subject1_rigth, file4_subject1_rigth]
# CSV data from subject 2
file1_subject2_left = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2055/myoLeftEmg.csv"
file2_subject2_left = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2110/myoLeftEmg.csv"
file3_subject2_left = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2125/myoLeftEmg.csv"
file4_subject2_left = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2145/myoLeftEmg.csv"
subject2_left_files = [file1_subject2_left, file2_subject2_left, file3_subject2_left, file4_subject2_left]
file1_subject2_rigth = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2055/myoRightEmg.csv"
file2_subject2_rigth = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2110/myoRightEmg.csv"
file3_subject2_rigth = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2125/myoRightEmg.csv"
file4_subject2_rigth = "/Exp20201205_2myo_softType/HaluskaMaros_20201205_2145/myoRightEmg.csv"
subject2_right_files = [file1_subject2_rigth, file2_subject2_rigth, file3_subject2_rigth, file4_subject2_rigth]
# CSV data from subject 3
file1_subject3_left = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1745/myoLeftEmg.csv"
file2_subject3_left = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1755/myoLeftEmg.csv"
file3_subject3_left = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1810/myoLeftEmg.csv"
file4_subject3_left = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1825/myoLeftEmg.csv"
subject3_left_files = [file1_subject3_left, file2_subject3_left, file3_subject3_left, file4_subject3_left]
file1_subject3_rigth = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1745/myoRightEmg.csv"
file2_subject3_rigth = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1755/myoRightEmg.csv"
file3_subject3_rigth = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1810/myoRightEmg.csv"
file4_subject3_rigth = "/Exp20201205_2myo_softType/HaluskovaBeata_20201205_1825/myoRightEmg.csv"
subject3_right_files = [file1_subject3_rigth, file2_subject3_rigth, file3_subject3_rigth, file4_subject3_rigth]
# CSV data from subject 4
file1_subject4_left = "/Exp20201205_2myo_softType/KelisekDavid_20201209_1945/myoLeftEmg.csv"
file2_subject4_left = "/Exp20201205_2myo_softType/KelisekDavid_20201209_1955/myoLeftEmg.csv"
file3_subject4_left = "/Exp20201205_2myo_softType/KelisekDavid_20201209_2010/myoLeftEmg.csv"
file4_subject4_left = "/Exp20201205_2myo_softType/KelisekDavid_20201209_2025/myoLeftEmg.csv"
subject4_left_files = [file1_subject4_left, file2_subject4_left, file3_subject4_left, file4_subject4_left]
file1_subject4_rigth = "/Exp20201205_2myo_softType/KelisekDavid_20201209_1945/myoRightEmg.csv"
file2_subject4_rigth = "/Exp20201205_2myo_softType/KelisekDavid_20201209_1955/myoRightEmg.csv"
file3_subject4_rigth = "/Exp20201205_2myo_softType/KelisekDavid_20201209_2010/myoRightEmg.csv"
file4_subject4_rigth = "/Exp20201205_2myo_softType/KelisekDavid_20201209_2025/myoRightEmg.csv"
subject4_right_files = [file1_subject4_rigth, file2_subject4_rigth, file3_subject4_rigth, file4_subject4_rigth]
# CSV data from subject 5
file1_subject5_left = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2110/myoLeftEmg.csv"
file2_subject5_left = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2120/myoLeftEmg.csv"
file3_subject5_left = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2130/myoLeftEmg.csv"
file4_subject5_left = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2140/myoLeftEmg.csv"
subject5_left_files = [file1_subject5_left, file2_subject5_left, file3_subject5_left, file4_subject5_left]
file1_subject5_rigth = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2110/myoRightEmg.csv"
file2_subject5_rigth = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2120/myoRightEmg.csv"
file3_subject5_rigth = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2130/myoRightEmg.csv"
file4_subject5_rigth = "/Exp20201205_2myo_softType/KelisekRichard_20201209_2140/myoRightEmg.csv"
subject5_right_files = [file1_subject5_rigth, file2_subject5_rigth, file3_subject5_rigth, file4_subject5_rigth]
left_list = [subject1_left_files, subject2_left_files, subject3_left_files, subject4_left_files, subject5_left_files]
right_list = [subject1_right_files, subject2_right_files, subject3_right_files, subject4_right_files, subject5_right_files]
subject1_data_container = Data_container(1, 'HaluskaMarek')
subject2_data_container = Data_container(2, 'HaluskaMaros')
subject3_data_container = Data_container(3, 'HaluskovaBeata')
subject4_data_container = Data_container(4, 'KelisekDavid')
subject5_data_container = Data_container(5, 'KelisekRichard')
subject_data_container_list = [subject1_data_container, subject2_data_container, subject3_data_container,
subject4_data_container, subject5_data_container]
for subject_nr in range(5):
data_container = subject_data_container_list[subject_nr]
# left variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = left_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'left', data_container, round+1)
# right variant proccessed here
for round in range(4):
for emg_nr in range(8):
filename = right_list[subject_nr][round]
self.store_df_in_container(filename, emg_nr, 'right', data_container, round+1)
# Links the stored data in the data_container to the Handler
self.link_container_to_handler(data_container)
self.data_type = 'soft'
return self.data_container_dict
def load_data_OLD(self, data_type):
if data_type == 'hard':
self.load_hard_original_emg_data()
elif data_type == 'hardPP':
self.load_hard_PP_emg_data()
elif data_type == 'soft':
self.load_soft_original_emg_data()
elif data_type == 'softPP':
self.load_soft_PP_emg_data()
else:
raise Exception('Wrong input')
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# NOT IMPLEMENTED
def get_keyboard_data(self, filename:str, pres_or_release:str='pressed'):
filepath = self.working_dir + str(filename)
df = pd.read_csv(filepath)
if pres_or_release == 'pressed':
df = df[(df['event'] == 'KeyPressed') and (df['event'] == 'KeyPressed')]
else: pass
pass
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class NN_handler:
# Paths for data storage in json to later use in Neural_Network_Analysis.py
JSON_PATH_MFCC = "mfcc_data.json"
# Class to manipulate data from the CSV_handler and store it for further analysis
def __init__(self, csv_handler:CSV_handler) -> None:
self.csv_handler = csv_handler
# Should med 4 sessions * (~150, 208) of mfcc samples per person. One [DataFrame, session_length_list] per subject
self.mfcc_samples_per_subject = {k+1:[] for k in range(csv_handler.nr_subjects)}
# GET method for mfcc_samples_dict
def get_mfcc_samples_dict(self) -> dict:
return self.mfcc_samples_per_subject
# Retrieves all EMG data from one subject and one session, and makes a list of the DataFrames
# Input: Subject nr, Session nr (norm, not 0-indexed)
# Output: List(df_1, ..., df_16)
def get_emg_list(self, subject_nr, session_nr) -> list:
list_of_emgs = []
df, _ = self.csv_handler.get_data(subject_nr, 'left', session_nr, 1)
list_of_emgs.append(df)
for emg_nr in range(7):
df, _ = self.csv_handler.get_data(subject_nr, 'left', session_nr, emg_nr+2)
list_of_emgs.append(DataFrame(df[get_emg_str(emg_nr+2)]))
for emg_nr in range(8):
df, _ = self.csv_handler.get_data(subject_nr, 'right', session_nr, emg_nr+1)
list_of_emgs.append(DataFrame(df[get_emg_str(emg_nr+1)]))
return list_of_emgs # list of emg data
# Creates one Dataframe of all EMG data(one session, one subject). One column for each EMG array
# Input: List(emg1, ..., emg16)
# Output: DataFrame(shape[1]=16)
def make_subj_sample(self, list_of_emgs_):
# Test and fix if the left/right EMGs have different size
list_of_emgs = []
length_left_emgs = int(len(list_of_emgs_[0].index))
length_right_emgs = int(len(list_of_emgs_[-1].index))
if length_left_emgs < length_right_emgs:
for i in range(16):
new_emg_df = list_of_emgs_[i].head(length_left_emgs)
list_of_emgs.append(new_emg_df)
elif length_right_emgs < length_left_emgs:
for i in range(16):
new_emg_df = list_of_emgs_[i].head(length_right_emgs)
list_of_emgs.append(new_emg_df)
else:
list_of_emgs = list_of_emgs_
tot_session_df_list = []
for i in range(8):
df = list_of_emgs[i]
tot_session_df_list.append(df)
for i in range(1, 9):
emg_str_old = get_emg_str(i)
emg_str_new = get_emg_str(8+i)
df = list_of_emgs[7+i].rename(columns={emg_str_old: emg_str_new})
tot_session_df_list.append(df)
tot_session_df = pd.concat(tot_session_df_list, axis=1, ignore_index=True)
return tot_session_df
# Takes in all EMG session Dataframe and creates DataFrame of MFCC samples
# Input: DataFrame(shape[1]=16, EMG data)
# Output: DataFrame(merged MFCC data, shape: (n, 13*16)), length of session datapoints
def make_mfcc_df_from_session_df(self, session_df):
session_df.rename(columns={0:'timestamp'}, inplace=True)
samplerate = get_samplerate(session_df)
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attach_func = lambda list_1, list_2: list_1.extend(list_2)
signal = session_df[1]
mfcc_0 = mfcc_custom(signal, samplerate, MFCC_WINDOWSIZE, MFCC_STEPSIZE, NR_COEFFICIENTS, NR_MEL_BINS)
df = DataFrame(mfcc_0).dropna()
df['combined'] = df.values.tolist()
result_df = df['combined']
for i in range(2, 17):
signal_i = session_df[i]
mfcc_i = mfcc_custom(signal_i, samplerate, MFCC_WINDOWSIZE, MFCC_STEPSIZE, NR_COEFFICIENTS, NR_MEL_BINS)
mfcc_i = DataFrame(mfcc_i).dropna()
mfcc_i['combined'] = mfcc_i.values.tolist()
df = result_df.combine(mfcc_i['combined'], attach_func)
session_length = (len(result_df.index)) # Add the length of session data points
return result_df, session_length
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# Merges MFCC data from all sessions and stores the sample data in
# the NN_handler's mfcc_samples_per_subject dict
# Input: None(NN_handler)
# Output: None -> stores in NN_handler [samples, session_length_list] for each subject
def store_mfcc_samples(self) -> None:
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for subject_nr in range(5):
subj_samples = []
session_length_list = []
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for session_nr in range(4):
list_of_emg = self.get_emg_list(subject_nr+1, session_nr+1)
tot_session_df = self.make_subj_sample(list_of_emg)
# TESTING FOR NAN
if tot_session_df.isnull().values.any():
print('NaN in: subject', subject_nr+1, 'session:', session_nr+1, 'where? HERE')
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mfcc_df_i, session_length = self.make_mfcc_df_from_session_df(tot_session_df)
subj_samples.append(mfcc_df_i)
session_length_list.append(session_length)
result_df = pd.concat(subj_samples, axis=0, ignore_index=True)
self.mfcc_samples_per_subject[subject_nr+1] = [result_df, session_length_list]
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# Stores MFCC data from mfcc_samples_per_subject in a json file
# Input: Path to the json file
# Output: None -> stores in json
def save_json_mfcc(self, json_path=JSON_PATH_MFCC):
# dictionary to store mapping, labels, and MFCCs
data = {
"mapping": [],
"labels": [],
"mfcc": [],
"session_lengths": []
}
raw_data_dict = self.get_mfcc_samples_dict()
# loop through all subjects to get samples
for key, value in raw_data_dict.items():
# save subject label in the mapping
subject_label = 'Subject ' + str(key)
print("\nProcessing: {}".format(subject_label))
data["mapping"].append(subject_label) # Subject label
data["session_lengths"].append(value[1]) # List[subject][session_length_list]
# process all samples per subject
for i, sample in enumerate(value[0]):
data["labels"].append(key-1) # Subject nr
data["mfcc"].append(sample) # MFCC sample on same index
print("sample:{} is done".format(i+1))
#print(np.array(mfcc_data).shape)
# save MFCCs to json file
with open(json_path, "w") as fp:
json.dump(data, fp, indent=4)
# OBSOLETE
def get_reg_samples_dict(self) -> dict:
return self.reg_samples_per_subject
def reshape_session_df_to_signal(self, df:DataFrame):
main_df = df[['timestamp', 1]].rename(columns={1: 'emg'})
for i in range(2, 17):
adding_df = df[['timestamp', i]].rename(columns={i: 'emg'})
main_df = pd.concat([main_df, adding_df], ignore_index=True)
samplerate = get_samplerate(main_df)
return main_df, samplerate
def store_samples(self, split_nr) -> None:
for subject_nr in range(5):
subj_samples = []
for session_nr in range(4):
list_of_emg = self.get_emg_list(subject_nr+1, session_nr+1)
tot_session_df = self.make_subj_sample(list_of_emg)
# TESTING FOR NAN
if tot_session_df.isnull().values.any():
print('NaN in: subject', subject_nr+1, 'session:', session_nr+1, 'where? HERE')
samples = np.array_split(tot_session_df.to_numpy(), split_nr)
for array in samples:
df = DataFrame(array).rename(columns={0:'timestamp'})
df_finished, samplerate = self.reshape_session_df_to_signal(df)
subj_samples.append([df_finished, samplerate])
self.reg_samples_per_subject[subject_nr+1] = subj_samples
def save_json_reg(self, json_path):
# Dictionary to store mapping, labels, and MFCCs
data = {
"mapping": [],
"labels": [],
"mfcc": []
}
raw_data_dict = self.get_reg_samples_dict()
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# Loop through all subjects to get samples
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mfcc_list = []
mfcc_frame_list = []
for key, value in raw_data_dict.items():
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# save subject label in the mapping
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subject_label = 'Subject ' + str(key)
data["mapping"].append(subject_label)
print("\nProcessing: {}".format(subject_label))
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# process all samples per subject
for i, (sample) in enumerate(value):
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# load signal from sample
signal, sample_rate = sample[0], sample[1]
signal = signal['emg'].to_numpy()
test_df_for_bugs(signal, key, i)
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#print(sample_rate)
# extract mfcc
mfcc = mfcc_custom(signal, sample_rate, MFCC_WINDOWSIZE, MFCC_STEPSIZE, NR_COEFFICIENTS, NR_MEL_BINS)
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mfcc_list.append(mfcc.tolist())
mfcc_frame_list.append(mfcc.shape[0])
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#data["mfcc"].append(mfcc.tolist())
data["labels"].append(key-1)
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print("sample:{} is done".format(i+1))
minimum = min(mfcc_frame_list)
for mfcc_data in mfcc_list:
data["mfcc"].append(mfcc_data[:minimum])
print(np.array(mfcc_data[:minimum]).shape)
# save MFCCs to json file
with open(json_path, "w") as fp:
json.dump(data, fp, indent=4)
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# HELP FUNCTIONS: ------------------------------------------------------------------------:
# Help: gets the str from emg nr
def get_emg_str(emg_nr):
return 'emg' + str(emg_nr)
# Help: gets the min/max of a df
def get_min_max_timestamp(df:DataFrame):
#min = int(np.floor(df['timestamp'].min()))
min = df['timestamp'].min()
max = df['timestamp'].max()
return min, max
# Help: returns df_time_emg
def make_df_from_xandy(x, y, emg_nr):
dict = {'timestamp': x, get_emg_str(emg_nr): y}
df = DataFrame(dict)
#print(df)
return df
# Help: returns the samplerate of a df
# REMOVE 60-SECOND-BUG IF FIXED
def get_samplerate(df:DataFrame):
min, max = get_min_max_timestamp(df)
if max > 60 and min < 60:
seconds = max - 60 - min
else:
seconds = max - min
samples = len(df.index)
samplerate = samples / seconds
return int(samplerate)
# Help: takes in a df and outputs np arrays for x and y values
def get_xory_from_df(x_or_y, df:DataFrame):
swither = {
'x': df.iloc[:,0].to_numpy(),
'y': df.iloc[:,1].to_numpy()
}
return swither.get(x_or_y, 0)
# Help: slightly modified mfcc with inputs like below. Returns N (x_values from original df) and mfcc_y_values
def mfcc_custom(signal, samplerate, windowsize=MFCC_WINDOWSIZE,
stepsize=MFCC_STEPSIZE,
nr_coefficients=NR_COEFFICIENTS,
nr_mel_filters=NR_MEL_BINS):
return mfcc(signal, samplerate, windowsize, stepsize, nr_coefficients, nr_mel_filters)
# Help: test for unregularities in DataFrame obj
def test_df_for_bugs(signal, key, placement_index):
df = DataFrame(signal)
if df.isnull().values.any():
print('NaN in subject', key, 'in sample', placement_index)
if df.shape[1] != (1):
print('Shape:', df.shape[1], 'at subject', key, 'in sample', placement_index)