From 1b5a2fc24786720b21f9604df2c4de178bdaa4a1 Mon Sep 17 00:00:00 2001
From: Raymond Chia <rqchia@janus0.ihpc.uts.edu.au>
Date: Sun, 26 Nov 2023 01:24:41 +1100
Subject: [PATCH] tsfresh tested
---
create_features.py | 14 +-
logs/singularity_2776358.out | 18 ++
logs/singularity_2776834.out | 42 +++
logs/singularity_2810990.out | 7 +
.../__pycache__/datapipeline.cpython-38.pyc | Bin 25878 -> 16921 bytes
modules/datapipeline.py | 273 ------------------
regress_rr.py | 101 ++++---
7 files changed, 135 insertions(+), 320 deletions(-)
create mode 100644 logs/singularity_2776358.out
create mode 100644 logs/singularity_2776834.out
create mode 100644 logs/singularity_2810990.out
diff --git a/create_features.py b/create_features.py
index b180232..bcf8f46 100644
--- a/create_features.py
+++ b/create_features.py
@@ -32,7 +32,7 @@ from modules.animationplotter import AnimationPlotter, AnimationPlotter2D
from modules.digitalsignalprocessing import imu_signal_processing
from modules.digitalsignalprocessing import vectorized_slide_win
from modules.digitalsignalprocessing import get_video_features
-from modules.datapipeline import SubjectData, datetime_to_sec\
+from modules.datapipeline import datetime_to_sec\
,sec_to_datetime, DataSynchronizer
from modules.datapipeline import get_file_list, load_files_conditions
from modules.evaluations import Evaluation
@@ -183,16 +183,14 @@ def plot_video_features(video_fname, nframes=1000):
ipdb.set_trace()
def map_imu_tsfresh_subject(subject,
- tlx_df=None,
- conditions=['R', 'L0', 'L1', 'L2', 'L3'],
window_size=5, window_shift=0.2):
- sbj_data = SubjectData(subject=subject)
- sbj_data.set_imu_fname()
- sbj_dir = sbj_data.subject_dir
+ pfh = ProjectFileHandler({})
+ pfh.set_home_directory(join(DATA_DIR, 'subject_specific', subject))
for condition in conditions:
tsfresh_pkl = path_join(
- sbj_dir, "{0}__winsize_{1}__winshift_{2}_imu_tsfresh_df.pkl"\
- .format(condition, window_size, window_shift))
+ pfh.home_directory,
+ "{0}__winsize_{1}__winshift_{2}_tsfresh_df.pkl"\
+ .format(window_size, window_shift))
if path_exists(tsfresh_pkl): continue
print(f"trying {subject} for {condition}")
data_df = load_df(subject, condition)
diff --git a/logs/singularity_2776358.out b/logs/singularity_2776358.out
new file mode 100644
index 0000000..23dd6d6
--- /dev/null
+++ b/logs/singularity_2776358.out
@@ -0,0 +1,18 @@
+2023-11-26 00:44:07.923231: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
+To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
+Traceback (most recent call last):
+ File "regress_rr.py", line 23, in <module>
+ import tensorflow as tf
+ File "/home/rqchia/.local/lib/python3.8/site-packages/tensorflow/__init__.py", line 54, in <module>
+ from ._api.v2 import data
+ File "/home/rqchia/.local/lib/python3.8/site-packages/tensorflow/_api/v2/data/__init__.py", line 11, in <module>
+ from . import experimental
+ File "/home/rqchia/.local/lib/python3.8/site-packages/tensorflow/_api/v2/data/experimental/__init__.py", line 87, in <module>
+ from . import service
+ File "<frozen importlib._bootstrap>", line 991, in _find_and_load
+ File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
+ File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
+ File "<frozen importlib._bootstrap_external>", line 844, in exec_module
+ File "<frozen importlib._bootstrap_external>", line 939, in get_code
+ File "<frozen importlib._bootstrap_external>", line 1037, in get_data
+KeyboardInterrupt
diff --git a/logs/singularity_2776834.out b/logs/singularity_2776834.out
new file mode 100644
index 0000000..4b9cae6
--- /dev/null
+++ b/logs/singularity_2776834.out
@@ -0,0 +1,42 @@
+2023-11-26 00:44:26.282311: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
+To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
+Using TensorFlow backend
+Namespace(data_input='imu-bvp', feature_method='tsfresh', lbl_str='pss', model='linreg', overwrite=0, subject=3, test_standing=1, train_len=5, win_shift=0.2, win_size=12)
+unable to find matching config id
+Data id not set, auto assigned to: 2
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/65 [00:00<?, ?it/s]
Feature Extraction: 2%|â– | 1/65 [00:00<00:08, 7.47it/s]
Feature Extraction: 12%|█■| 8/65 [00:00<00:01, 38.61it/s]
Feature Extraction: 25%|██■| 16/65 [00:00<00:00, 53.36it/s]
Feature Extraction: 37%|███▋ | 24/65 [00:00<00:00, 58.89it/s]
Feature Extraction: 49%|████▉ | 32/65 [00:00<00:00, 63.82it/s]
Feature Extraction: 62%|██████■| 40/65 [00:00<00:00, 65.14it/s]
Feature Extraction: 74%|███████■| 48/65 [00:00<00:00, 67.87it/s]
Feature Extraction: 86%|████████▌ | 56/65 [00:00<00:00, 69.75it/s]
Feature Extraction: 98%|█████████▊| 64/65 [00:01<00:00, 72.31it/s]
Feature Extraction: 100%|██████████| 65/65 [00:01<00:00, 63.53it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/47 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 47/47 [00:00<00:00, 997.74it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/47 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 47/47 [00:00<00:00, 975.44it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/47 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 47/47 [00:00<00:00, 1034.00it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/47 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 47/47 [00:00<00:00, 1018.94it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/49 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 49/49 [00:00<00:00, 1008.80it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/47 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 47/47 [00:00<00:00, 950.21it/s]
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/49 [00:00<?, ?it/s]
Feature Extraction: 100%|██████████| 49/49 [00:00<00:00, 1035.00it/s]
+imu-bvp_rr_Pilot03_id2_combi5.0-7.0-10.0-12.0-15.0
+train
+(101, 74)
+test
+(978, 73)
+---LinearRegression---
+Traceback (most recent call last):
+ File "regress_rr.py", line 1374, in <module>
+ sens_rr_model(subject,
+ File "regress_rr.py", line 1268, in sens_rr_model
+ x_test = transforms.transform(x_test)
+ File "/usr/local/lib/python3.8/dist-packages/sklearn/utils/_set_output.py", line 140, in wrapped
+ data_to_wrap = f(self, X, *args, **kwargs)
+ File "/usr/local/lib/python3.8/dist-packages/sklearn/preprocessing/_polynomial.py", line 432, in transform
+ X = self._validate_data(
+ File "/usr/local/lib/python3.8/dist-packages/sklearn/base.py", line 625, in _validate_data
+ self._check_n_features(X, reset=reset)
+ File "/usr/local/lib/python3.8/dist-packages/sklearn/base.py", line 414, in _check_n_features
+ raise ValueError(
+ValueError: X has 70 features, but PolynomialFeatures is expecting 71 features as input.
diff --git a/logs/singularity_2810990.out b/logs/singularity_2810990.out
new file mode 100644
index 0000000..179501a
--- /dev/null
+++ b/logs/singularity_2810990.out
@@ -0,0 +1,7 @@
+2023-11-26 01:21:46.434356: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
+To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
+Using TensorFlow backend
+Namespace(data_input='imu-bvp', feature_method='tsfresh', lbl_str='pss', model='linreg', overwrite=1, subject=3, test_standing=1, train_len=5, win_shift=0.2, win_size=12)
+Using pre-set data id: 2
+Dependency not available for matrix_profile, this feature will be disabled!
+
Feature Extraction: 0%| | 0/65 [00:00<?, ?it/s]
\ No newline at end of file
diff --git a/modules/__pycache__/datapipeline.cpython-38.pyc b/modules/__pycache__/datapipeline.cpython-38.pyc
index 450a764cdbfb582417b9f1631e429109e238e31f..112731661244257e314c326704b0de1742c5608c 100644
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diff --git a/modules/datapipeline.py b/modules/datapipeline.py
index 7c17bc4..a05ec34 100644
--- a/modules/datapipeline.py
+++ b/modules/datapipeline.py
@@ -455,279 +455,6 @@ class DataSynchronizer():
self.start_ind = start_ind
self.end_ind = end_ind
-class SubjectData(DataImporter):
- ''' Loads in data for the rigid body, breathing rate, summary files
- and syncs them accordingly '''
- def __init__(self, condition='M', subject='S01'):
- super().__init__()
- self.condition = condition
- self.subject = subject
- if subject[0] != 'S':
- self.subject_id = subject
- else:
- self.subject_id = int(re.search(r'\d+', subject).group())
- self.study_start = 0
- self.study_end = 0
-
- self.subject_dir = path_join(self.parent_dir, self.subject)
-
- self.pressure_df = pd.DataFrame()
- self.summary_df = pd.DataFrame()
- self.accel_df = pd.DataFrame()
- self.imu_df = pd.DataFrame()
-
- def get_cond_file(self, files):
- for f in files:
- if self.condition in f.split(sep)[-1] and \
- self.subject in f.split(sep)[-1]:
- return f
- return ''
-
- def list_sub_dirs(self, parent_dir, endswith=None):
- reg_str = r'[0-9]+$'
- if endswith is not None:
- reg_str = r'[0-9]+{0}$'.format(endswith)
- regex = re.compile(reg_str)
- sub_dirs = [
- path_join(parent_dir, d) for d in listdir(parent_dir) if \
- (
- isdir(path_join(parent_dir,d)) and bool(regex.search(d))
- )
- ]
- return sorted(sub_dirs)
-
- def check_times(self, sub_dirs, is_utc=False):
- ''' Parses sub directory names to datetime and checks against mat_start
- and end '''
- sep = self.sep
-
- if is_utc:
- imu_hdr_files = [path_join(sub_dir, 'recording.g3')\
- for sub_dir in sub_dirs]
- hdrs = [pd.read_json(imu_hdr_file, orient='index')\
- for imu_hdr_file in imu_hdr_files]
- times = [hdr.to_dict().pop(0)['created'] \
- for hdr in hdrs]
- times = [datetime.fromisoformat(time[:-1]) for time in times]
- times = [(time.timestamp()+ timedelta(hours=11).seconds) for time in times]
- else:
- times = [datetime_to_sec(sub_dir.split(sep)[-1])\
- for sub_dir in sub_dirs]
-
- sel_dir = sub_dirs[-1]
- for i, time in enumerate(times[:-1]):
- if self.study_start > time and self.study_start < times[i+1]:
- sel_dir = sub_dirs[i]
- return sel_dir
-
- def set_pressure_fname(self):
- subject_dir = self.subject_dir
- sub_dirs = self.list_sub_dirs(subject_dir)
- sub_dir = sub_dirs[0]
- if len(sub_dirs)> 1:
- # Check directory times with timeline
- sub_dir = self.check_times(sub_dirs)
-
- pressure_glob = path_join(sub_dir, 'BR*.csv')
- pressure_files = sorted(glob.glob(pressure_glob))
- if not pressure_files:
- dt_info = sub_dir.split(sep)[-1]
- pressure_glob = path_join(sub_dir, '*_Breathing.csv')
- pressure_files = sorted(glob.glob(pressure_glob))
- self.pressure_fname = pressure_files[-1]
-
- def set_summary_fname(self):
- subject_dir = self.subject_dir
- sub_dirs = self.list_sub_dirs(subject_dir)
- sub_dir = sub_dirs[0]
- if len(sub_dirs)> 1:
- # Check directory times with timeline
- sub_dir = self.check_times(sub_dirs)
-
- summary_glob = path_join(sub_dir, 'Summary*.csv')
- summary_files = sorted(glob.glob(summary_glob))
- if not summary_files:
- dt_info = sub_dir.split(sep)[-1]
- summary_glob = path_join(sub_dir, dt_info+'_Summary*.csv')
- summary_files = sorted(glob.glob(summary_glob))
- self.summary_fname = summary_files[-1]
-
- def set_imu_fname(self):
- subject_dir = self.subject_dir
- sub_dirs = self.list_sub_dirs(subject_dir, endswith='Z')
- sub_dir = sub_dirs[0]
- if len(sub_dirs)> 1:
- sub_dir = self.check_times(sub_dirs, is_utc=True)
-
- imu_glob = path_join(sub_dir, 'imu*')
- imu_files = sorted(glob.glob(imu_glob))
- self.imu_fname = imu_files[-1]
-
- imu_hdr_glob = path_join(sub_dir, 'recording.g3')
- imu_hdr_files = sorted(glob.glob(imu_hdr_glob))
- self.imu_hdr_fname = imu_hdr_files[-1]
- video_fname = path_join(sub_dir, 'scenevideo.mp4')
- if path_exists(video_fname):
- self.video_fname = video_fname
-
- def set_accel_fname(self):
- subject_dir = self.subject_dir
- sub_dirs = self.list_sub_dirs(subject_dir)
- sub_dir = sub_dirs[0]
- if len(sub_dirs)> 1:
- # Check directory times with timeline
- sub_dir = self.check_times(sub_dirs)
-
- accel_glob = path_join(sub_dir, 'Accel*.csv')
- accel_files = sorted(glob.glob(accel_glob))
- if not accel_files:
- dt_info = sub_dir.split(sep)[-1]
- accel_glob = path_join(sub_dir, '*_Accel.csv')
- accel_files = sorted(glob.glob(accel_glob))
- accel_files = [f for f in accel_files if 'g' not in \
- f.lower().split(sep)[-1]]
- self.accel_fname = accel_files[-1]
-
- def set_timeline(self):
- times_glob = path_join(self.subject_dir,f'*.csv')
- times_files = sorted(glob.glob(times_glob))
- self.timeline_fname = self.get_cond_file(times_files)
- self.timeline_df = self.import_time_data()
-
- mat_time = self.timeline_df['Timestamps'].map(mat_to_sec)
- mat_start_ind = self.timeline_df.index[
- self.timeline_df['Event']=='Start Test'
- ].tolist()[0]
- mat_start = mat_time.values[mat_start_ind]
- mat_end = mat_time.values[-1]
-
- self.study_start = mat_start
- self.study_end = mat_end
-
- def set_fnames(self):
- self.set_pressure_fname()
- self.set_summary_fname()
- self.set_imu_fname()
- self.set_accel_fname()
-
- def load_dataframes(self):
- self.timeline_df = self.import_time_data()
- self.pressure_df = self.import_labels(self.pressure_fname)
- self.summary_df = self.import_labels(self.summary_fname)
- self.accel_df = self.import_labels(self.accel_fname)
- self.imu_df, self.imu_hdr = self.import_imu_data()
-
- def sync_pressure_df(self):
- data_sync = DataSynchronizer()
-
- cols = self.pressure_df.columns
- if 'Year' in cols:
- year = int(self.pressure_df['Year'].values[0])
- month = int(self.pressure_df['Month'].values[0])
- day = int(self.pressure_df['Day'].values[0])
- dt_fmt = "%Y/%m/%d"
- dt_str = f"{year}/{month}/{day}"
- dt_obj = datetime.strptime(dt_str, dt_fmt)
- pressure_time = self.pressure_df['ms'].interpolate().values/1000
- pressure_time = pressure_time + dt_obj.timestamp()
- else:
- pressure_time = self.pressure_df['Time'].map(datetime_to_sec).values
-
- self.pressure_df['sec'] = pressure_time
- data_sync.set_bounds(pressure_time, self.study_start, self.study_end)
- self.pressure_df = data_sync.sync_df(self.pressure_df)
-
- def sync_accel_df(self):
- data_sync = DataSynchronizer()
-
- cols = self.accel_df.columns
- if 'Year' in cols:
- year = int(self.accel_df['Year'].values[0])
- month = int(self.accel_df['Month'].values[0])
- day = int(self.accel_df['Day'].values[0])
- dt_fmt = "%Y/%m/%d"
- dt_str = f"{year}/{month}/{day}"
- dt_obj = datetime.strptime(dt_str, dt_fmt)
- accel_time = self.accel_df['ms'].interpolate().values/1000
- accel_time = accel_time + dt_obj.timestamp()
- else:
- accel_time = self.accel_df['Time'].map(datetime_to_sec).values
-
- self.accel_df['sec'] = accel_time
- data_sync.set_bounds(accel_time, self.study_start, self.study_end)
- self.accel_df = data_sync.sync_df(self.accel_df)
-
- def sync_summary_df(self):
- data_sync = DataSynchronizer()
-
- cols = self.summary_df.columns
- if 'Year' in cols:
- year = int(self.summary_df['Year'].values[0])
- month = int(self.summary_df['Month'].values[0])
- day = int(self.summary_df['Day'].values[0])
- dt_fmt = "%Y/%m/%d"
- dt_str = f"{year}/{month}/{day}"
- dt_obj = datetime.strptime(dt_str, dt_fmt)
- summary_times = self.summary_df['ms'].values/1000 + dt_obj.timestamp()
- else:
- summary_times = self.summary_df['Time'].map(datetime_to_sec).values
-
- self.summary_df['sec'] = summary_times
- data_sync.set_bounds(summary_times, self.study_start, self.study_end)
- self.summary_df = data_sync.sync_df(self.summary_df)
-
- def sync_imu_df(self):
- na_inds = self.imu_df\
- .loc[pd.isna(self.imu_df['accelerometer']), :].index.values
- self.imu_df.drop(index=na_inds, inplace=True)
- imu_times = self.imu_df['timestamp'].values
-
- ''' S21, S30 has strange time recordings '''
- mask = imu_times > 3*60*60
- if mask.any():
- bad_args = np.arange(0, len(mask))[mask]
- self.imu_df.drop(index=self.imu_df.iloc[bad_args].index,
- inplace=True)
- # self.imu_df['timestamp'] = self.imu_df['timestamp'].values - \
- # self.imu_df['timestamp'].values[0]
- imu_times = self.imu_df['timestamp'].values
-
- print(np.mean(1/(imu_times[1:] - imu_times[:-1])))
- self.imu_df['timestamp_interp'] = imu_times
- self.imu_df['timestamp_interp'] = self.imu_df['timestamp_interp']\
- .interpolate()
-
- data_sync = DataSynchronizer()
-
- iso_tz = self.imu_hdr['created']
- tzinfo = pytz.timezone(self.imu_hdr['timezone'])
- # adjust for UTC
- start_time = datetime.fromisoformat(iso_tz[:-1]) + timedelta(hours=11)
- imu_times = self.imu_df['timestamp_interp'].values
-
- imu_datetimes = [start_time + timedelta(seconds=val) \
- for val in imu_times]
- imu_sec = np.array([time.timestamp() for time in imu_datetimes])
- self.imu_df['sec'] = imu_sec
- data_sync.set_bounds(imu_sec, self.study_start, self.study_end)
- self.imu_df = data_sync.sync_df(self.imu_df)
-
- def sync_all_df(self):
- if self.study_start == 0 or self.study_start is None:
- self.set_timeline()
- self.sync_pressure_df()
- self.sync_summary_df()
- self.sync_accel_df()
- self.sync_imu_df()
-
- def get_accel_data(self):
- accel_cols = self.accel_df.columns
- if 'Time' in accel_cols:
- data_cols = ['Vertical', 'Lateral', 'Sagittal']
- else:
- data_cols = ['X Data', 'Y Data', 'Z Data']
- return self.accel_df[data_cols].values
-
class TFDataPipeline():
def __init__(self, window_size=60, batch_size=32):
self.window_size = window_size
diff --git a/regress_rr.py b/regress_rr.py
index 0255ce1..c420b0c 100644
--- a/regress_rr.py
+++ b/regress_rr.py
@@ -426,7 +426,10 @@ def df_win_task(w_inds, df, i, cols):
for col in cols:
data = w_df[col].values
# DSP
- sd_data = (data - np.mean(data, axis=0))/np.std(data, axis=0)
+ if sum(np.abs(data)) > 0:
+ sd_data = (data - np.mean(data, axis=0))/np.std(data, axis=0)
+ else:
+ sd_data = data.copy()
# ys = cubic_interp(sd_data, BR_FS, FS_RESAMPLE)
if col != 'bvp':
filt_out.append(imu_signal_processing(sd_data, fs))
@@ -455,7 +458,7 @@ def df_win_task(w_inds, df, i, cols):
if 'bvp' in cols:
xf, yf = do_pad_fft(bvp_filt, fs=fs)
bv_freq = int(xf[yf.argmax()]*60)
- y_out['bvp_est'] = bv_freq
+ # y_out['bvp_est'] = bv_freq
return x_out, y_out
@@ -590,9 +593,8 @@ def load_and_sync_xsens(subject, sens_list:list=['imu', 'bvp']):
return xsens_df
def load_tsfresh(xsens_df, home_dir,
- sens_list:list=['imu', 'bvp'],
window_size=12, window_shift=0.2, fs=IMU_FS,
- overwrite=False, data_cols=None):
+ overwrite=False, data_cols=None, prefix=None):
"""
Loads the tsfresh pickle file, or generates if it does not exist for the
given configuration
@@ -607,16 +609,26 @@ def load_tsfresh(xsens_df, home_dir,
pd.DataFrame
"""
- raise NotImplementedError("To be implemented")
+ assert data_cols is not None, "invalid selection for data columns"
+ assert 'acc_x' in xsens_df.columns.tolist() and \
+ 'gyro_x' in xsens_df.columns.tolist() and \
+ 'bvp' in xsens_df.columns.tolist(), \
+ "Does not include the full required dataset. Must have both IMU and BVP"
- # make home directory
+ # raise NotImplementedError("To be implemented")
- assert data_cols is not None, "invalid selection for data columns"
- pkl_file = join(project_dir, 'tsfresh.pkl')
+ if prefix is not None:
+ pkl_fname = f'{prefix}__winsize_{window_size}__winshift_{window_shift}__tsfresh.pkl'
+ else:
+ pkl_fname = f'winsize_{window_size}__winshift_{window_shift}__tsfresh.pkl'
+
+ pkl_dir = join(home_dir,
+ f'tsfresh__winsize_{window_size}__winshift_{window_shift}')
+ pkl_file = join(pkl_dir, pkl_fname)
+ if not exists(pkl_dir): mkdir(pkl_dir)
if exists(pkl_file) and not overwrite:
return pd.read_pickle(pkl_file)
- ipdb.set_trace()
x_df, y_df = get_df_windows(xsens_df,
df_win_task,
window_size=window_size,
@@ -630,6 +642,9 @@ def load_tsfresh(xsens_df, home_dir,
# default_fc_parameters=tsfresh_settings.MinimalFCParameters(),
)
x_features_df.fillna(0, inplace=True)
+ x_features_df.reset_index(drop=True, inplace=True)
+ x_features_df = x_features_df.reindex(sorted(x_features_df.columns.values),
+ axis=1)
cols = x_features_df.columns.values
@@ -964,7 +979,7 @@ def imu_rr_dsp(subject,
do_minirocket = False
use_tsfresh = False
- overwrite_tsfresh = True
+ overwrite_tsfresh = False
train_size = int(train_len)
config = {'window_size' : window_size,
@@ -1050,8 +1065,6 @@ def sens_rr_model(subject,
test_standing=False,
data_input:str='imu+bvp',
):
- # TODO:
- # implement tsfresh
"""Loads, preprocesses, and trains a select model using the configured
settings.
Attributes
@@ -1106,7 +1119,7 @@ def sens_rr_model(subject,
do_minirocket = False
use_tsfresh = False
- overwrite_tsfresh = True
+ overwrite_tsfresh = overwrite
train_size = int(train_len)
if feature_method == 'tsfresh':
@@ -1143,25 +1156,38 @@ def sens_rr_model(subject,
cal_df = get_cal_data(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:
- xsens_df = load_tsfresh(xsens_df,
- project_dir,
- sens_list=sens_list,
+ 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})
- # 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)
-
- 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)
-
+ 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)
for combi in combinations(cal_df[cal_str].values, train_len):
combi_str = "-".join([str(x) for x in combi])
@@ -1178,7 +1204,7 @@ def sens_rr_model(subject,
train_df_list.append(data_df)
train_df = pd.concat(train_df_list)
- assert np.isin(train_df.index.values, test_df.index.values).any()==False,\
+ assert np.isin(train_df.sec.values, test_df.sec.values).any()==False,\
"overlapping test and train data"
print("train")
@@ -1209,10 +1235,13 @@ def sens_rr_model(subject,
x_train = minirocket.fit_transform(x_train)
x_test = minirocket.transform(x_test)
elif use_tsfresh:
- x_train = train_df.iloc[:, 3:].values
+ 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.iloc[:, 3:].values
+ 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,
@@ -1303,7 +1332,7 @@ def arg_parser():
default='pss',
)
parser.add_argument('-tl', '--train_len', type=int,
- default=3,
+ default=5,
help='minutes of data to use for calibration'
)
parser.add_argument('-d', '--data_input', type=str,
@@ -1311,7 +1340,7 @@ def arg_parser():
help='imu, bvp, imu+bvp: select data cols for input'
)
parser.add_argument('-ts', '--test_standing', type=int,
- default=0,
+ default=1,
help='1 or 0 input, choose if standing data will be '\
'recorded or not'
)
@@ -1320,7 +1349,7 @@ def arg_parser():
if __name__ == '__main__':
np.random.seed(100)
- n_subject_max = 2
+ n_subject_max = 3
args = arg_parser()
# Load command line arguments
@@ -1356,7 +1385,7 @@ if __name__ == '__main__':
)
else:
subjects = [subject_pre_string+str(i).zfill(2) for i in \
- range(1, n_subject_max+1) if i not in imu_issues]
+ range(2, n_subject_max+1)]
rr_func = partial(sens_rr_model,
window_size=window_size,
@@ -1370,12 +1399,6 @@ if __name__ == '__main__':
data_input=data_input,
)
- if mdl_str in ['fnn', 'lstm', 'cnn1d', 'elastic', 'ard', 'xgboost']:
- for subject in subjects:
- rr_func(subject)
- else:
- ncpu = min(len(subjects), cpu_count())
- with Pool(ncpu) as p:
- p.map(rr_func, subjects)
-
+ for subject in subjects:
+ rr_func(subject)
print(args)
--
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