# TODO:
#
import glob
from os import makedirs, mkdir
from os.path import join, exists
import pandas as pd
import numpy as np
import json
import ipdb
import re
import pickle
import sys
import time
from zipfile import ZipFile
from joblib import dump, load
import argparse
from datetime import datetime, timedelta, timezone, timedelta
import pytz
import matplotlib.pyplot as plt
from functools import partial
from collections import Counter
from itertools import repeat, chain, combinations
from multiprocessing import Pool, cpu_count
import tensorflow as tf
from sklearn.decomposition import PCA
from sklearn.preprocessing import StandardScaler, MinMaxScaler, OneHotEncoder
from sklearn.preprocessing import PolynomialFeatures, LabelEncoder
from sklearn.model_selection import KFold, train_test_split
from sklearn.metrics import accuracy_score
from tsfresh.feature_extraction import extract_features
from tsfresh.feature_extraction import settings as tsfresh_settings
from tsfresh.utilities.string_manipulation import get_config_from_string
from modules.datapipeline import get_file_list, load_and_snip, load_data, \
load_split_data, load_harness_data
from modules.digitalsignalprocessing import vectorized_slide_win as vsw
from modules.digitalsignalprocessing import imu_signal_processing
from modules.digitalsignalprocessing import bvp_signal_processing
from modules.digitalsignalprocessing import hernandez_sp, reject_artefact
from modules.digitalsignalprocessing import do_pad_fft,\
pressure_signal_processing, infer_frequency, movingaverage
from modules.utils import *
from modules.evaluations import Evaluation
from modules.datapipeline import get_windowed_data, DataSynchronizer,\
parallelize_dataframe
from modules.datapipeline import ProjectFileHandler
from models.ardregression import ARDRegressionClass
from models.knn import KNNClass
from models.svm import SVMClass
from models.lda import LDAClass
from models.svr import SVRClass
from models.logisticregression import LogisticRegressionClass
from models.linearregression import LinearRegressionClass
from models.neuralnet import FNN_HyperModel, LSTM_HyperModel, TunerClass,\
CNN1D_HyperModel
from models.ridgeclass import RidgeClass
from models.resnet import Regressor_RESNET, Classifier_RESNET
from models.xgboostclass import XGBoostClass
from pprint import PrettyPrinter
from sktime.transformations.panel.rocket import (
MiniRocket,
MiniRocketMultivariate,
MiniRocketMultivariateVariable,
)
from config import WINDOW_SIZE, WINDOW_SHIFT, IMU_FS, DATA_DIR, BR_FS\
, FS_RESAMPLE, PPG_FS
from regress_rr import *
N_SUBJECT_MAX = 6
IMU_COLS = ['acc_x', 'acc_y', 'acc_z', 'gyro_x', 'gyro_y', 'gyro_z']
def load_and_sync_xsens(subject, sens_list:list=['imu', 'bvp']):
"""
Loads requested sensors from the subject folder and synchronises each to
the beginning and end timestamps. Linearly interpolates the data and
timestamps to match the higher frequency data.
Arguments
---------
subject : str
subject to extract data from (i.e. 'Pilot02', 'S02')
sens_list : list
a list that contains either or both 'imu' and 'bvp'
Returns
-------
pd.DataFrame
"""
assert 'imu' in sens_list or 'bvp' in sens_list, \
f"{sens_list} is not supported, must contain"\
"'imu', 'bvp' or 'imu, bvp'"
pss_df, br_df, imu_df, bvp_df = None, None, None, None
acc_data, gyr_data, bvp_data = None, None, None
# load imu
if 'imu' in sens_list:
imu_list = get_file_list('imudata.gz', sbj=subject)
imu_df_all, imu_hdr_df_all = load_imu_files(imu_list)
# load bioharness
pss_list = get_file_list('*Breathing.csv', sbj=subject)
if len(pss_list) == 0:
pss_list = get_file_list('BR*.csv', sbj=subject)
br_list = get_file_list('*Summary*.csv', sbj=subject)
# load e4 wristband
if 'bvp' in sens_list:
e4_list = get_file_list('*.zip', sbj=subject)
bvp_df_all, bvp_hdr = load_e4_files(e4_list)
bvp_fs = bvp_hdr[0]['fs']
xsens_list = []
# skip the first and last x minute(s)
minutes_to_skip = .5
br_skiprows = br_skipfooter = int(minutes_to_skip*60)
pss_skiprows = pss_skipfooter = int(minutes_to_skip*60*BR_FS)
# load each bioharness file and sync the imu to it
for pss_file, br_file in zip(pss_list, br_list):
xsens_data = {}
pss_df = load_bioharness_file(pss_file, skiprows=pss_skiprows,
skipfooter=pss_skipfooter,
engine='python')
pss_time = pss_df['Time'].map(bioharness_datetime_to_seconds).values\
.reshape(-1, 1)
pss_df['sec'] = pss_time
br_df = load_bioharness_file(br_file, skiprows=br_skiprows,
skipfooter=br_skipfooter,
engine='python')
br_time = br_df['Time'].map(bioharness_datetime_to_seconds).values\
.reshape(-1, 1)
br_df['sec'] = br_time
# sync
if 'imu' in sens_list and 'bvp' in sens_list:
br_df, imu_df = sync_to_ref(br_df, imu_df_all.copy())
pss_df, _ = sync_to_ref(pss_df, imu_df_all.copy())
bvp_df, _ = sync_to_ref(bvp_df_all.copy(), pss_df.copy())
elif 'imu' in sens_list and not 'bvp' in sens_list:
br_df, imu_df = sync_to_ref(br_df, imu_df_all.copy())
pss_df, _ = sync_to_ref(pss_df, imu_df_all.copy())
elif not 'imu' in sens_list and 'bvp' in sens_list:
br_df, bvp_df = sync_to_ref(br_df, bvp_df_all.copy())
pss_df, _ = sync_to_ref(pss_df, bvp_df_all.copy())
# extract relevant data
if 'imu' in sens_list:
axes = ['x', 'y', 'z']
acc_data = np.stack(imu_df['accelerometer'].values)
gyr_data = np.stack(imu_df['gyroscope'].values)
x_time = imu_df['sec'].values.reshape(-1, 1)
if 'bvp' in sens_list and 'imu' in sens_list:
bvp_data = bvp_df['bvp'].values
bvp_data = np.interp(x_time, bvp_df['sec'].values, bvp_data)\
.reshape(-1, 1)
elif 'bvp' in sens_list and not 'imu' in sens_list:
bvp_data = bvp_df['bvp'].values
x_time = bvp_df['sec'].values
xsens_data['sec'] = x_time.flatten()
br_col = [col for col in pss_df.columns.values if\
'breathing' in col.lower()][0]
pss_data = pss_df[br_col].values
pss_data = np.interp(x_time, pss_df['sec'].values, pss_data)\
.reshape(-1, 1)
xsens_data['PSS'] = pss_data.flatten()
br_lbl = [col for col in br_df.columns.values if\
'br' in col.lower()][0]
br_data = br_df['BR'].values
br_data = np.interp(x_time, br_df['sec'].values, br_data)\
.reshape(-1, 1)
xsens_data['BR'] = br_data.flatten()
if 'imu' in sens_list:
for i, axis in enumerate(axes):
xsens_data['acc_'+axis] = acc_data.T[i].flatten()
xsens_data['gyro_'+axis] = gyr_data.T[i].flatten()
if 'bvp' in sens_list:
xsens_data['bvp'] = bvp_data.flatten()
xsens_df_tmp = pd.DataFrame(xsens_data)
xsens_list.append(xsens_df_tmp)
if len(xsens_list) > 1:
xsens_df = pd.concat(xsens_list, axis=0, ignore_index=True)
xsens_df.reset_index(drop=True, inplace=True)
else:
xsens_df = xsens_list[0]
return xsens_df
def get_test_data(cal_df, activity_df, xsens_df, test_standing):
"""
Loads and retrieves the activity timestamps from sitting and standing
events
Arguments
---------
cal_df : pandas.DataFrame
synchronised and frequency matched respiration calibration data
activity_df : pandas.DataFrame
timestamps of activity events
xsens_df : pandas.DataFrame
synchronised and frequency matched DataFrame with all data and labels
test_standing : bool
list of column str
Returns
-------
pd.DataFrame
"""
fmt = "%d/%m/%Y %H:%M:%S"
start_time = cal_df.iloc[0]['data'].sec.values[0]
data_df = xsens_df[xsens_df.sec < start_time]
activity_start = 0
activity_end = 0
activity_list = []
for index, row in activity_df.iterrows():
sec = datetime.strptime(row['Timestamps'], fmt).timestamp()
if not test_standing and row['Activity'] == 'standing':
continue
if row['Event'] == 'start':
activity_start = sec
elif row['Event'] == 'end':
activity_stop = sec
dsync = DataSynchronizer()
dsync.set_bounds(data_df['sec'].values, activity_start,
activity_stop)
sync_df = dsync.sync_df(data_df.copy())
activity_data = {'activity': row['Activity'], 'data': sync_df}
activity_list.append(activity_data)
return pd.DataFrame(activity_list)
def sens_rr_model(subject='S02-repeat',
window_size=12,
window_shift=0.2,
lbl_str='pss',
mdl_str='linreg',
overwrite=False,
feature_method='minirocket',
train_len:int=5,
test_standing=True,
data_input:str='imu',
):
"""Loads, preprocesses, and trains a select model using the configured
settings.
Attributes
----------
subject: str
specify the subject code (i.e. 'Pilot02', 'S02')
window_size : float
a numpy array of the respiration rate ground truth values from the
bioharness
window_shift : float
a portion of the window size between 0 and 1
mdl_str : str
a string to infoa portion of the window size between 0 and 1rm what model was used
overwrite : bool
overwrites the evaluations, models, and graphs (default False)
feature_method : str
choose between 'minirocket', 'tsfresh', or 'None'
train_len : int
number of minutes to sample from, choose between 1 to 7
test_standing : bool
boolean to use standing data
data_input : str
sensors to use, choose from 'imu', 'bvp', 'imu+bvp'
Returns
------
None
"""
cal_str = 'cpm'
tmp = []
imu_cols = IMU_COLS
bvp_cols = ['bvp']
if 'imu' in data_input and 'bvp' in data_input:
data_cols = ['acc_x', 'acc_y', 'acc_z',
'gyro_x', 'gyro_y', 'gyro_z',
'bvp']
parent_directory_string = "imu-bvp_rr"
data_input = 'imu+bvp'
sens_list = ['imu', 'bvp']
fs = IMU_FS
elif 'imu' in data_input and not 'bvp' in data_input:
data_cols = ['acc_x', 'acc_y', 'acc_z',
'gyro_x', 'gyro_y', 'gyro_z',]
parent_directory_string = "imu_rr"
sens_list = ['imu']
fs = IMU_FS
elif not 'imu' in data_input and 'bvp' in data_input:
data_cols = ['bvp']
parent_directory_string = "bvp_rr"
sens_list = ['bvp']
fs = PPG_FS
do_minirocket = False
use_tsfresh = False
overwrite_tsfresh = overwrite
train_size = int(train_len)
minirocket = None
if feature_method == 'tsfresh':
use_tsfresh = True
elif feature_method == 'minirocket':
do_minirocket = True
config = {'window_size' : window_size,
'window_shift' : window_shift,
'lbl_str' : lbl_str,
'do_minirocket' : do_minirocket,
'use_tsfresh' : use_tsfresh,
'train_len' : train_len,
'test_standing' : test_standing,
'sens_list' : data_input
}
pfh = ProjectFileHandler(config)
pfh.set_home_directory(join(DATA_DIR, 'subject_specific', '_'+subject))
pfh.set_parent_directory(parent_directory_string)
id_check = pfh.get_id_from_config()
if id_check is None:
pfh.set_project_directory()
pfh.save_metafile()
else:
pfh.set_id(int(id_check))
pfh.set_project_directory()
print('Using pre-set data id: ', pfh.fset_id)
project_dir = pfh.project_directory
xsens_df = load_and_sync_xsens(subject, sens_list=sens_list)
activity_df = get_activity_log(subject).reset_index(drop=True)
activity_df.drop([16, 17], inplace=True)
event_df = get_respiration_log(subject).iloc[-14:]
cal_df = get_cal_data(event_df, xsens_df)
day0_event_df = get_respiration_log("S02")
second_cal_df = get_cal_data(day0_event_df, xsens_df)
# include standing or not
test_df_tmp = get_test_data(cal_df, activity_df, xsens_df, test_standing)
test_df = pd.concat([df for df in test_df_tmp['data']], axis=0)
if use_tsfresh:
cal_df_list = []
test_df = load_tsfresh(test_df,
pfh.home_directory,
window_size=window_size,
window_shift=window_shift,
fs=fs,
overwrite=overwrite_tsfresh,
data_cols=data_cols,
prefix='test',
)
for index, row in cal_df.iterrows():
data = load_tsfresh(row['data'],
pfh.home_directory,
window_size=window_size,
window_shift=window_shift,
fs=fs,
overwrite=overwrite_tsfresh,
data_cols=data_cols,
prefix=f"calcpm_{row['cpm']}"
)
cal_df_list.append({'cpm': row['cpm'], 'data': data})
cal_df = pd.DataFrame(cal_df_list)
else:
x_test_df, y_test_df = get_df_windows(
test_df, df_win_task, window_size=window_size,
window_shift=window_shift, fs=fs, cols=data_cols)
my_df = []
cal_inds = {}
for i in range(len(second_cal_df)):
df = second_cal_df.iloc[i]
data_df = df['data']
data_df['cpm'] = df.cpm
my_df.append(data_df)
my_df = pd.concat(my_df)
for combi in combinations(cal_df[cal_str].values, train_len):
combi_str = "-".join([str(x) for x in combi])
pfh.config[cal_str] = combi_str
marker = f'{parent_directory_string}_{subject}_id{pfh.fset_id}'\
f'_combi{combi_str}'
print(marker)
train_df_list = []
for cpm in combi:
df = cal_df[cal_df[cal_str] == cpm]
data_df = df['data'].iloc[0]
data_df['cpm'] = cpm
train_df_list.append(data_df)
train_df = pd.concat(train_df_list)
assert np.isin(train_df.sec.values, test_df.sec.values).any()==False,\
"overlapping test and train data"
print("train")
print(train_df.shape)
print("test")
print(test_df.shape)
if do_minirocket:
x_train_df, y_train_df = get_df_windows(train_df,
df_win_task,
window_size=window_size,
window_shift=window_shift,
fs=fs,
cols=data_cols
)
x_train = make_windows_from_id(x_train_df, data_cols)
y_train = y_train_df['cpm'].values.reshape(-1, 1)
x_test = make_windows_from_id(x_test_df, data_cols)
y_test = y_test_df[lbl_str].values.reshape(-1, 1)
# x_train = y_train_df['hr_est'].values.reshape(-1, 1)
# x_test = y_test_df['hr_est'].values.reshape(-1, 1)
x_train = np.swapaxes(x_train, 1, 2)
x_test = np.swapaxes(x_test, 1, 2)
directory = join(project_dir, '_'.join([mdl_str, marker]))
minirocket_fname = join(directory, "minirocket.joblib")
if not overwrite and exists(minirocket_fname):
with open(minirocket_fname, 'rb') as mfile:
minirocket = load(mfile)
x_train = minirocket.transform(x_train)
print("loaded minirocket...")
else:
minirocket = MiniRocketMultivariate()
x_train = minirocket.fit_transform(x_train)
x_test = minirocket.transform(x_test)
if overwrite or not exists(minirocket_fname):
if not exists(directory): makedirs(directory)
with open(minirocket_fname, 'wb') as mfile:
dump(minirocket, mfile)
print("saved new minirocket...")
elif use_tsfresh:
y_cols = ['sec', 'br', 'pss', 'cpm']
x_cols = [col for col in train_df.columns.values if col not in y_cols]
x_train = train_df[x_cols].values
y_train = train_df['cpm'].values.reshape(-1, 1)
x_test = test_df[x_cols].values
y_test = test_df[lbl_str].values.reshape(-1, 1)
y_test_df = test_df[y_cols[:-1]]
else:
x_train_df, y_train_df = get_df_windows(train_df,
df_win_task,
window_size=window_size,
window_shift=window_shift,
fs=fs,
cols=data_cols,
)
x_train = make_windows_from_id(x_train_df, data_cols)
x_test = make_windows_from_id(x_test_df, data_cols)
y_train = y_train_df['cpm'].values.reshape(-1, 1)
y_test = y_test_df[lbl_str].values.reshape(-1, 1)
transforms, model = model_training(mdl_str, x_train, y_train,
marker, validation_data=None,
overwrite=overwrite,
is_regression=True,
project_directory=project_dir,
window_size=int(window_size*fs),
extra_train=200,
poly_deg=1
)
if transforms is not None:
x_test = transforms.transform(x_test)
preds = model.predict(x_test)
eval_handle = EvalHandler(y_test.flatten(), preds.flatten(), subject,
pfh, mdl_str, overwrite=overwrite)
eval_handle.update_eval_history()
eval_handle.save_eval_history()
pp = PrettyPrinter()
pp.pprint(eval_handle.load_eval_history())
fig, ax = plt.subplots(2, 1, figsize=(7.3, 4.5))
fig_title = '_'.join([mdl_str, data_input, subject]+[combi_str])
fig.suptitle(fig_title)
ax[0].plot(y_test)
ax[0].plot(preds)
ax[0].set_title('raw')
if lbl_str == 'pss':
br = y_test_df['br'].values
ax[1].plot(movingaverage(y_test, 12), color='tab:blue')
ax[1].plot(br, 'k')
ax[1].plot(movingaverage(preds, 12), color='tab:orange')
ax[1].legend([lbl_str, 'br', 'pred'])
else:
ax[1].plot(y_test, 'k')
ax[1].plot(movingaverage(preds, 12), color='tab:orange')
ax[1].legend([lbl_str, 'pred'])
ax[1].set_title('smoothened')
fig_dir = join(project_dir, 'figures')
if not exists(fig_dir): mkdir(fig_dir)
fig.savefig(join(fig_dir, fig_title+".png"))
# make PSS to lbls and preprocess data
if do_minirocket:
x_df, y_df = get_df_windows(my_df,
df_win_task,
window_size=window_size,
window_shift=window_shift,
fs=fs,
cols=data_cols
)
x = make_windows_from_id(x_df, data_cols)
y = y_df['pss'].values.reshape(-1, 1)
x = np.swapaxes(x, 1, 2)
# load and process
x = minirocket.transform(x)
elif use_tsfresh:
y_cols = ['sec', 'br', 'pss', 'cpm']
x_cols = [col for col in train_df.columns.values if col not in y_cols]
x = my_df[x_cols].values
y = my_df['pss'].values.reshape(-1, 1)
else:
x_df, y_df = get_df_windows(my_df,
df_win_task,
window_size=window_size,
window_shift=window_shift,
fs=fs,
cols=data_cols,
)
x = make_windows_from_id(x_df, data_cols)
y = y_df['pss'].values.reshape(-1, 1)
if transforms is not None:
x = transforms.transform(x)
preds = model.predict(x)
fig2, ax2 = plt.subplots()
ax2.plot(y)
ax2.plot(preds)
ax2.plot(y_df.cpm.values, '--')
ax2.legend(['label', 'pred', 'cpm'])
ax2.set_title("second day mapped to first day cal")
fig2.savefig(join(fig_dir, fig_title+"cal_check.png"))
plt.close('all')
sens_rr_model(subject='S02-repeat',
window_size=12,
window_shift=0.2,
lbl_str='pss',
mdl_str='cnn1d',
overwrite=False,
feature_method=None,
# feature_method='minirocket',
train_len=5,
test_standing=True,
data_input='bvp',
)