def create_kb_for_testing():
experiment = model.Experiment()
so1 = model.Subject('Robert')
experiment.put_subject(so1)
setup = model.Setup(experiment)
modality1 = model.Modality(setup, 15, identifier='emg')
model.Sample(modality1, 'm1')
model.Sample(modality1, 'm2')
model.Sample(modality1, 'm3')
model.Sample(modality1, 'm4')
modality2 = model.Modality(setup, 5, identifier='pos')
model.Sample(modality2, 'length')
model.Sample(modality2, 'width')
session = model.Session(experiment, setup, so1)
emg_data = np.column_stack(
(np.arange(0, 150, dtype='float'), np.arange(200, 350, dtype='float'),
np.arange(400, 550, dtype='float'), np.arange(600, 750,
dtype='float')))
recording = model.Recording(session=session,
data=emg_data,
identifier='emg_recording',
modality=modality1.Identifier)
model.Trial(recording, 1, 2, 'trial1', label='cool')
model.Trial(recording, 4, 1, 'trial2', label='cool')
model.Trial(recording, 6, 3, 'trial3', label='hot')
pos_data = np.column_stack(
(np.arange(800, 850, dtype='float'), np.arange(900, 950,
dtype='float')))
recording = model.Recording(session=session,
data=pos_data,
identifier='pos_recording',
modality=modality2.Identifier)
model.Trial(recording, 1, 2, 'trial1', label='hot')
model.Trial(recording, 4, 1, 'trial2', label='hot')
model.Trial(recording, 6, 3, 'trial3', label='cool')
return experiment
def small_sport_kb():
experiment = model.Experiment()
# Subjects
# -----------------------------------------------------------------------------------
so3 = model.Subject('subject3')
experiment.put_subject(so3)
# Setups
# ===================================================================================
setup = model.Setup(experiment)
modality = model.Modality(setup=setup, frequency=4000, identifier='arm')
model.Sample(modality, 'bizeps')
model.Sample(modality, 'triceps')
model.Sample(modality, 'extensor_digitorum')
model.Sample(modality, 'flexor_digitorum')
# Sessions
# ===================================================================================
# Session 3
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_01.pkl',
modality=modality.Identifier)
t = model.Trial(rec, 0, 4, 'calm')
t.add_marker((4, 'start_trials'))
t.add_marker((4.1, 'another'))
model.Trial(rec, 4, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 8, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 12, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 16, 4, 'hantel1', label='hantel')
model.Trial(rec, 20, 4, 'hantel2', label='hantel')
model.Trial(rec, 24, 4, 'hantel3', label='hantel')
model.Trial(rec, 28, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 32, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 36, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 44, 4, 'max_triceps').add_marker((0, 'start_max_tests'))
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_bizeps')
model.Trial(rec, 60, 4, 'max_extensor')
return experiment
def create_kb(data=None):
if data is None:
print 'Create new dataset...'
rec1 = np.arange(100)
rec1 = np.column_stack((rec1, rec1, rec1))
rec2 = np.arange(100, 200)
rec2 = np.column_stack((rec2, rec2, rec2))
rec3 = np.arange(200, 300)
rec3 = np.column_stack((rec3, rec3, rec3))
data = np.row_stack((rec1, rec2, rec3))
df = pd.DataFrame(data, dtype='float')
experiment = model.Experiment()
# Subjects
#==========
so1 = model.Subject('Robert')
so2 = model.Subject('Therese')
so3 = model.Subject('Michael')
experiment.put_subject(so1)
experiment.put_subject(so2)
experiment.put_subject(so3)
# Setups
# =======
setup = model.Setup(experiment)
modality = model.Modality(setup, 1, 'arm')
model.Sample(modality, 'bizeps')
model.Sample(modality, 'trizeps')
modality = model.Modality(setup, 'leg')
model.Sample(modality, 'gluteus maximus')
# Sessions
# =========
# Session1
#---------
session = model.Session(experiment, setup, so1)
recording = model.Recording(session=session, data=df)
model.Trial(recording, 10, 10, 'curl_simple')
model.Trial(recording, 30, 11, 'squat')
model.Trial(recording, 50, 12, 'curl_difficult')
model.Trial(recording, 70, 20, 'leg_lever')
# Session 2
# ----------
df = pd.DataFrame(np.copy(data), dtype='float')
session = model.Session(experiment, setup, so2)
recording = model.Recording(session=session, data=df)
model.Trial(recording, 10, 10, 'curl_simple')
model.Trial(recording, 30, 11, 'squat')
model.Trial(recording, 50, 12, 'curl_difficult')
model.Trial(recording, 70, 20, 'leg_lever')
df = pd.DataFrame(np.copy(data), dtype='float')
recording = model.Recording(session=session, data=df)
model.Trial(recording, 10, 10, 'curl_simple2')
model.Trial(recording, 30, 11, 'squat2')
model.Trial(recording, 50, 12, 'curl_difficult2')
model.Trial(recording, 70, 20, 'leg_lever2')
# Session 3
# ----------
df = pd.DataFrame(np.copy(data), dtype='float')
session = model.Session(experiment, setup, so3)
recording = model.Recording(session=session, data=df)
model.Trial(recording, 10, 10, 'curl_simple')
model.Trial(recording, 30, 11, 'squat')
model.Trial(recording, 50, 12, 'curl_difficult')
model.Trial(recording, 70, 20, 'leg_lever')
return experiment
def create_emg_eeg_kb(meta, sessions, markers=None):
""" Builds an `emgframework.model.model.Experiment` using information extracted from
`P#_AllLifts.mat` and data extracted from `HS_P#_S#.mat`.
Builds the model with EMG and EEG data only (Kinematic, Environmental and
Miscellaneous data not included)
Args:
meta (pandas.core.DataFrame): Meta information to sessions
session (Dictionary): Data of one session
Returns:
emgframework.model.model.Experiment
"""
cols = [
col for col in meta.columns
if col.startswith('t') or col.startswith('Dur_')
]
meta.loc[:, cols] = meta.loc[:, cols] - 2.002
# Define mapping for weights and surface
weights = {}
weights[1] = '165g'
weights[2] = '330g'
weights[4] = '660g'
surface = {}
surface[1] = 'sandpaper'
surface[2] = 'suede'
surface[3] = 'silk'
# Create Experiment
# ==================================================================================
exp = model.Experiment()
subj = model.Subject(sessions[0]['initials'])
# Creating Setup and Modalities
# ==================================================================================
setup = model.Setup(exp)
kin_cols = [
'Px1 - position x sensor 1', 'Px2 - position x sensor 2',
'Px3 - position x sensor 3', 'Px4 - position x sensor 4',
'Py1 - position y sensor 1', 'Py2 - position y sensor 2',
'Py3 - position y sensor 3', 'Py4 - position y sensor 4',
'Pz1 - position z sensor 1', 'Pz2 - position z sensor 2',
'Pz3 - position z sensor 3', 'Pz4 - position z sensor 4'
]
mod_emg = model.Modality(setup, sessions[0]['emg_sr'], 'emg')
for s in sessions[0]['emg_data'].columns:
model.Sample(mod_emg, s)
mod_eeg = model.Modality(setup, sessions[0]['eeg_sr'], 'eeg')
for s in sessions[0]['eeg_data'].columns:
model.Sample(mod_eeg, s)
mod_kin = model.Modality(setup, sessions[0]['kin_sr'], 'kin')
for s in sessions[0]['kin_data'].columns:
if s in kin_cols:
model.Sample(mod_kin, s)
# Creating Session, Recordings and Trials
# ==================================================================================
for session in sessions:
# Select data of from metadata belonging to in `session` specified session
meta_session = meta.loc[meta.loc[:, 'Run'] == session['session'], :]
meta_session.reset_index(inplace=True)
sess = model.Session(exp, setup, subj,
'session_' + str(session['session']))
# Creating Recordings
# ----------------------------------------------------------------------------------
rec_emg = model.Recording(sess,
data=session['emg_data'],
identifier='emg_data',
modality=mod_emg.Identifier)
rec_eeg = model.Recording(sess,
data=session['eeg_data'],
identifier='eeg_data',
modality=mod_eeg.Identifier)
rec_kin = model.Recording(sess,
data=session['kin_data'].loc[:, kin_cols],
identifier='kin_data',
modality=mod_kin.Identifier)
# Creating Trials
# ----------------------------------------------------------------------------------
for i in range(meta_session.shape[0]):
start = meta_session.loc[i, 'StartTime']
if i == meta_session.shape[0] - 1:
duration = float(session['emg_data'].shape[0]
) / 4000. - meta_session.loc[i, 'StartTime']
else:
duration = meta_session.loc[
i + 1, 'StartTime'] - meta_session.loc[i, 'StartTime']
if (start + duration
) * session['emg_sr'] > session['emg_data'].shape[0]:
warning = (
'WARNING - EMG data does not contain enough data points. Has '
+
'{samples:d} data points but {needed:d} are required. Skipped '
+ 'Lift {lift:d}').format(
samples=session['emg_data'].shape[0],
needed=int((start + duration) * session['emg_sr']),
lift=i)
warnings.warn(warning)
continue
if (start + duration
) * session['eeg_sr'] > session['eeg_data'].shape[0]:
warning = (
'WARNING - EEG data does not contain enough data points. Has '
+
'{samples:d} data points but {needed:d} are required. Skipped '
+ 'Lift {lift:d}').format(
samples=session['eeg_data'].shape[0],
needed=int((start + duration) * session['eeg_sr']),
lift=i)
warnings.warn(warning)
continue
t_emg = model.Trial(
recording=rec_emg,
start=start,
duration=duration,
identifier='emg_lift' + str(i),
label=weights[meta_session.loc[
i, 'CurW']] # + '_' + surface[meta_session.loc[i, 'CurS']]
)
t_eeg = model.Trial(
recording=rec_eeg,
start=start,
duration=duration,
identifier='eeg_lift' + str(i),
label=weights[meta_session.loc[
i, 'CurW']] # + '_' + surface[meta_session.loc[i, 'CurS']]
)
t_kin = model.Trial(
recording=rec_kin,
start=start,
duration=duration,
identifier='kin_lift' + str(i),
label=weights[meta_session.loc[
i, 'CurW']] # + '_' + surface[meta_session.loc[i, 'CurS']]
)
if markers is not None:
for marker in markers:
t_emg.add_marker((meta_session.loc[i, marker], marker))
t_eeg.add_marker((meta_session.loc[i, marker], marker))
t_kin.add_marker((meta_session.loc[i, marker], marker))
return exp
def sport_kb():
experiment = model.Experiment()
# Subjects
# -----------------------------------------------------------------------------------
so3 = model.Subject('subject1')
experiment.put_subject(so3)
so3 = model.Subject('subject2')
experiment.put_subject(so3)
so3 = model.Subject('subject3')
experiment.put_subject(so3)
so3 = model.Subject('subject4')
experiment.put_subject(so3)
so3 = model.Subject('subject5')
experiment.put_subject(so3)
so3 = model.Subject('subject6')
experiment.put_subject(so3)
so3 = model.Subject('subject7')
experiment.put_subject(so3)
so3 = model.Subject('subject8')
experiment.put_subject(so3)
so3 = model.Subject('subject9')
experiment.put_subject(so3)
so3 = model.Subject('subject10')
experiment.put_subject(so3)
# Setups
# ===================================================================================
setup = model.Setup(experiment)
modality = model.Modality(setup=setup, frequency=4000, identifier='arm')
model.Sample(modality, 'bizeps')
model.Sample(modality, 'triceps')
model.Sample(modality, 'extensor_digitorum')
model.Sample(modality, 'flexor_digitorum')
# Sessions
# ===================================================================================
# Session 1
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_01.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'hantel1', label='hantel')
model.Trial(rec, 8, 4, 'hantel2', label='hantel')
model.Trial(rec, 12, 4, 'hantel3', label='hantel')
model.Trial(rec, 16, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 20, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 24, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 28, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 32, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 36, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 44, 4, 'max_bizeps')
model.Trial(rec, 48, 4, 'max_triceps')
model.Trial(rec, 52, 4, 'max_flexor')
model.Trial(rec, 56, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 2
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_02.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'hantel1', label='hantel')
model.Trial(rec, 8, 4, 'hantel2', label='hantel')
model.Trial(rec, 12, 4, 'hantel3', label='hantel')
model.Trial(rec, 16, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 20, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 24, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 28, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 32, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 36, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 44, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 3
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_03.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 8, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 12, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 16, 4, 'hantel1', label='hantel')
model.Trial(rec, 20, 4, 'hantel2', label='hantel')
model.Trial(rec, 24, 4, 'hantel3', label='hantel')
model.Trial(rec, 28, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 32, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 36, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 52, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 56, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 4
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_04.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 8, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 12, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 16, 4, 'hantel1', label='hantel')
model.Trial(rec, 20, 4, 'hantel2', label='hantel')
model.Trial(rec, 24, 4, 'hantel3', label='hantel')
model.Trial(rec, 28, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 32, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 36, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 44, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 5
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_05.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 8, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 12, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 16, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 20, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 24, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 28, 4, 'hantel1', label='hantel')
model.Trial(rec, 32, 4, 'hantel2', label='hantel')
model.Trial(rec, 36, 4, 'hantel3', label='hantel')
model.Trial(rec, 44, 4, 'max_bizeps')
model.Trial(rec, 48, 4, 'max_triceps')
model.Trial(rec, 52, 4, 'max_flexor')
model.Trial(rec, 56, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 6
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_06.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 8, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 12, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 16, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 20, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 24, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 28, 4, 'hantel1', label='hantel')
model.Trial(rec, 32, 4, 'hantel2', label='hantel')
model.Trial(rec, 36, 4, 'hantel3', label='hantel')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 44, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 7
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_07.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'hantel1', label='hantel')
model.Trial(rec, 8, 4, 'hantel2', label='hantel')
model.Trial(rec, 12, 4, 'hantel3', label='hantel')
model.Trial(rec, 16, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 20, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 24, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 28, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 32, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 36, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 44, 4, 'max_bizeps')
model.Trial(rec, 48, 4, 'max_triceps')
model.Trial(rec, 52, 4, 'max_flexor')
model.Trial(rec, 56, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 8
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_08.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 8, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 12, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 16, 4, 'hantel1', label='hantel')
model.Trial(rec, 20, 4, 'hantel2', label='hantel')
model.Trial(rec, 24, 4, 'hantel3', label='hantel')
model.Trial(rec, 28, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 32, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 36, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 44, 4, 'max_bizeps')
model.Trial(rec, 48, 4, 'max_triceps')
model.Trial(rec, 52, 4, 'max_flexor')
model.Trial(rec, 56, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 9
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_09.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 8, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 12, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 16, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 20, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 24, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 28, 4, 'hantel1', label='hantel')
model.Trial(rec, 32, 4, 'hantel2', label='hantel')
model.Trial(rec, 36, 4, 'hantel3', label='hantel')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 44, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_extensor')
# Sessions
# ===================================================================================
# Session 10
# -----------------------------------------------------------------------------------
session = model.Session(experiment, setup, so3)
rec = model.Recording(session,
location='data/Proband_10.pkl',
modality=modality.Identifier)
model.Trial(rec, 0, 4, 'calm')
model.Trial(rec, 4, 4, 'hantel1', label='hantel')
model.Trial(rec, 8, 4, 'hantel2', label='hantel')
model.Trial(rec, 12, 4, 'hantel3', label='hantel')
model.Trial(rec, 16, 4, 'reverse_kettle1', label='reverse_kettle')
model.Trial(rec, 20, 4, 'reverse_kettle2', label='reverse_kettle')
model.Trial(rec, 24, 4, 'reverse_kettle3', label='reverse_kettle')
model.Trial(rec, 28, 4, 'stomach_kettle1', label='stomach_kettle')
model.Trial(rec, 32, 4, 'stomach_kettle2', label='stomach_kettle')
model.Trial(rec, 36, 4, 'stomach_kettle3', label='stomach_kettle')
model.Trial(rec, 40, 4, 'max_bizeps')
model.Trial(rec, 44, 4, 'max_triceps')
model.Trial(rec, 48, 4, 'max_flexor')
model.Trial(rec, 52, 4, 'max_extensor')
return experiment