mpba / pyphysio Goto Github PK

from __future__ import division
import numpy as np
import pandas as pd
import pyphysio as ph

FILE = '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/sample_data/medical.txt'
FSAMP = 2048
TSTART = 0

data = np.loadtxt(FILE, delimiter='\t')
ecg = ph.EvenlySignal(data[:, 0], sampling_freq = FSAMP, signal_nature = 'ECG', start_time = TSTART)

ecg_bp = ph.IIRFilter(fp=[10, 50], fs=[0.01, 70])(ecg) # <== 

Traceback (most recent call last):

  File "<ipython-input-43-61d61d81a620>", line 1, in <module>
    ecg_bp = ph.IIRFilter(fp=[10, 50], fs=[0.01, 70])(ecg)  # OK

  File "pyphysio/BaseAlgorithm.py", line 50, in __call__
    return self.get(data, self._params)

  File "pyphysio/BaseAlgorithm.py", line 79, in get
    return cls.algorithm(data, kwargs)

  File "pyphysio/filters/Filters.py", line 175, in algorithm
    cls.warn(cls.__name__ + ': Filter parameters allow no solution. Returning original signal.')

  File "pyphysio/BaseAlgorithm.py", line 144, in warn
    cls.emulate_log([l])

  File "pyphysio/BaseAlgorithm.py", line 168, in emulate_log
    map(lambda f, m: f(m), log)

TypeError: <lambda>() takes exactly 2 arguments (1 given)

# import libraries
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt

# for windowed plots
get_ipython().magic(u'matplotlib qt')

# import all pyphysio classes and methods
import pyphysio as ph 


# In[2]:

# import data and creating a signal

ecg_data = ph.TestData.ecg()

fsamp = 2048
ecg = ph.EvenlySignal(values = ecg_data, sampling_freq = fsamp, signal_nature = 'ecg')


# In[3]:

ecg.plot()


# ** Step 1: Filtering and preprocessing **

# In[4]:

# (optional) IIR filtering : remove high frequency noise
ecg = ph.IIRFilter(fp=45, fs = 50, ftype='ellip')(ecg)


# In[5]:

# normalization : normalize data
ecg = ph.Normalize(norm_method='standard')(ecg)


# In[6]:

# resampling : increase the sampling frequency by cubic interpolation
ecg = ecg.resample(fout=4096, kind='cubic')
fsamp = 4096


# In[7]:

ecg.plot()


# ** Step 2: Information Extraction **
# 
# The information we want to extract from the ECG signal is the position of the heartbeats and the Inter Beat Interval signal.

# In[8]:

ibi = ph.BeatFromECG()(ecg)


# In[9]:

# check results so far
ax1 = plt.subplot(211)
ecg.plot()
plt.vlines(ibi.get_times(), np.min(ecg), np.max(ecg))

plt.subplot(212, sharex = ax1)
ibi.plot('o-')
plt.vlines(ibi.get_times(), np.min(ibi), np.max(ibi))
plt.show()


# ** Step 3: Physiological Indicators **

# In[10]:

# define a list of indicators we want to compute
hrv_indicators = [ph.Mean(name='RRmean'), ph.StDev(name='RRstd'), ph.RMSSD(name='rmsSD'), 
              ph.PowerInBand(name = 'HF', interp_freq=4, freq_max=0.4, freq_min=0.15, method = 'ar'),
              ph.PowerInBand(name = 'LF', interp_freq=4, freq_max=0.15, freq_min=0.04, method = 'ar')
             ]


# In[11]:

# create fake label
label = np.zeros(1200)

label[300:600] = 1

label[900:1200] = 2

label = ph.EvenlySignal(label, sampling_freq = 10, signal_nature = 'label')


# In[25]:

# check label
ax1 = plt.subplot(211)
ibi.plot('.-')

plt.subplot(212, sharex = ax1)
label.plot('.-')
plt.show()


# In[16]:

#fixed length windowing
fixed_length = ph.FixedSegments(step = 5, width = 20, labels = label)

indicators, col_names = ph.fmap(fixed_length(ibi), hrv_indicators)


# In[19]:

# extract column with the labels for each window
label_w = indicators[:, np.where(col_names == 'label')[0]]

# extract column with the RRmean values computed from each window
rrmean_w = indicators[:, np.where(col_names == 'RRmean')[0]]

# create a box and whisker plot
plt.boxplot([rrmean_w[label_w==1], rrmean_w[label_w==2]],  
            labels=['image1', 'image2'])
plt.show()


# In[21]:

#label based windowing
label_based = ph.LabelSegments(labels = label)

indicators, col_names = ph.fmap(label_based(ibi), hrv_indicators)


# In[23]:

indicators[:,0:2]


# In[32]:

custom_based = ph.CustomSegments(begins = [0, 30, 60, 90], ends = [30, 60, 90, label.get_duration()], labels=label, drop_shorter=False, drop_mixed=False)

indicators, col_names = ph.fmap(custom_based, hrv_indicators, ibi)

indicators[:,0:2]


# In[29]:

len(label)


# In[ ]:




# ### 2.2 EDA processing pipeline

# ** Step 0: Import data **

# In[ ]:

# import data and creating a signal

eda_data = ph.TestData.eda()

fsamp = 2048
eda = ph.EvenlySignal(values = eda_data, sampling_freq = fsamp, signal_nature = 'eda')

eda.plot()


# ** Step 1: Filtering and preprocessing **

# In[ ]:

# resampling : decrease the sampling frequency by cubic interpolation
eda = eda.resample(fout=8, kind='cubic')


# In[ ]:

# IIR filtering : remove high frequency noise
eda = ph.IIRFilter(fp=0.8, fs = 1.1, ftype='ellip')(eda)


# In[ ]:

eda.plot()


# ** Step 2: Information Extraction **
# 
# The information we want to extract from the EDA signal is the phasic component associated to the sympathetic activity.

# In[ ]:

# estimate the driver function
driver = ph.DriverEstim(delta=0.02)(eda)


# In[ ]:

# compute the phasic component
phasic, tonic, _ = ph.PhasicEstim(delta=0.02)(driver)
phasic.plot()


# In[ ]:

# check results so far
ax1 = plt.subplot(211)
eda.plot()

plt.subplot(212, sharex = ax1)
driver.plot()
phasic.plot()
plt.grid()
plt.show()


# ** Step 3: Physiological Indicators **

# In[ ]:

# define a list of indicators we want to compute
indicators = [ph.Mean(), ph.StDev(), ph.AUC(), 
              ph.PeaksMean(delta=0.02),
              ph.DurationMean(delta=0.02)
             ]


# In[ ]:

# define the windowing method

In : type(ibi_curr_th)
Out : pyphysio.Signal.UnevenlySignal
In : ph.Mean()(ibi_curr_th)
Warning: The data must be a Signal (see class EvenlySignal and UnevenlySignal).
Out : 0.57361778846153844
In : isinstance(ibi_curr_th, Signal)
Out : True

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-31-f8c2fba97632> in <module>()
      1 # compute indicators over the segments
----> 2 result = ph.fmap(fixed_length, indicators, ibi)

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/__init__.pyc in fmap(segments, algorithms, alt_signal)
    136     from numpy import asarray as _asarray
    137     values = _asarray([[seg.get_begin_time(), seg.get_end_time()] + [alg(seg(alt_signal)) for alg in algorithms]
--> 138                        for seg in segments])
    139     labels = _asarray([seg.get_label() for seg in segments])
    140     col_names = ["begin", "end"] + map(lambda x: x.__repr__(), algorithms)

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/BaseSegmentation.pyc in __call__(self, data)
     48         if data is None:
     49             data = self._signal
---> 50         return data.segment_time(self.get_begin_time(), self.get_end_time())
     51 
     52     def __repr__(self):

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/Signal.pyc in segment_time(self, t_start, t_stop)
    425 
    426         return self.segment_idx(self.get_idx(t_start) if t_start is not None else None,
--> 427                                 self.get_idx(t_stop) if t_stop is not None else None)
    428 
    429     def segment_idx(self, idx_start, idx_stop=None):

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/Signal.pyc in segment_idx(self, idx_start, idx_stop)
    448             idx_start = 0
    449 
--> 450         iidx_start = int(self.get_iidx_from_idx(idx_start))
    451         iidx_stop = int(self.get_iidx_from_idx(idx_stop))
    452 

TypeError: int() argument must be a string or a number, not 'NoneType'



---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-33-f8c2fba97632> in <module>()
      1 # compute indicators over the segments
----> 2 result = ph.fmap(fixed_length, indicators, ibi)

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/__init__.pyc in fmap(segments, algorithms, alt_signal)
    136     from numpy import asarray as _asarray
    137     values = _asarray([[seg.get_begin_time(), seg.get_end_time()] + [alg(seg(alt_signal)) for alg in algorithms]
--> 138                        for seg in segments])
    139     labels = _asarray([seg.get_label() for seg in segments])
    140     col_names = ["begin", "end"] + map(lambda x: x.__repr__(), algorithms)

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/BaseSegmentation.pyc in __iter__(self)
     87 
     88     def __iter__(self):
---> 89         return SegmentationIterator(self)
     90 
     91     @classmethod

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/BaseSegmentation.pyc in __init__(self, win)
    118         assert isinstance(win, SegmentsGenerator)
    119         self._win = _cpy(win)
--> 120         self._win.init_segmentation()
    121 
    122     def next(self):

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/segmentation/SegmentsGenerators.pyc in init_segmentation(self)
    133         self._labsig = self._params["labels"]
    134         s = self._params["start"]
--> 135         self._t = s if s is not None else self._signal.get_start_time()
    136 
    137     def next_times(self):

AttributeError: 'NoneType' object has no attribute 'get_start_time'

import numpy as np
import pyphysio as ph

FSAMP = 100
n = np.arange(1000)
t = n / FSAMP
freq = 1
#create reference signal
sinusoid = ph.EvenlySignal(np.sin(2 * np.pi * freq * t), sampling_freq = FSAMP, signal_nature = '', start_time = 0)

# remove some samples
sinusoid_unevenly = ph.UnevenlySignal(np.delete(sinusoid.get_values(), [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]),
                                      sampling_freq = FSAMP, signal_nature = '', start_time = 0,
                                      x_values = np.delete(sinusoid.get_times(), [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]),
                                      x_type='instants')

np.sum(sinusoid_unevenly.get_times() - np.delete(sinusoid.get_times(), [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24])) # NOT EQUAL TO ZERO

# create a signal

## create fake data
signal_values = np.arange(100)

## create fake indices
idx = np.arange(100)
idx[-1] = 125

## set the sampling frequency
fsamp = 10 # Hz

## set the starting time
tstart = 0 # s

## create an Unevenly signal defining the indices
x_values_idx = idx

s_fake_idx = UnevenlySignal(values = signal_values, sampling_freq = fsamp, signal_nature = 'fake', start_time = tstart,
                       x_values = x_values_idx, x_type = 'indices')

## create an Unevenly signal defining the indices
x_values_time = idx/fsamp + 1

s_fake_time = UnevenlySignal(values = signal_values, sampling_freq = fsamp, signal_nature = 'fake',# start_time = tstart,
                       x_values = x_values_time, x_type = 'instants')

# segmentation of US

s_fake_idx_segment = s_fake_idx.segment_time(4.5, 5)
s_fake_time_segment = s_fake_time.segment_time(4.5, 5)

# plot
ax1 = plt.subplot(211)
s_fake_idx.plot('.-')
s_fake_idx_segment.plot('.-r')

plt.subplot(212, sharex=ax1)
s_fake_time.plot('.-')
s_fake_time_segment.plot('.-r')

signal_unevenly = ph.UnevenlySignal(np.array([1,2,3,4,5,6,8,9,10]),
                                      sampling_freq = 100, signal_nature = '', start_time = 0,
                                      x_values = np.array([1,2,3,4,5,6,7,9,10]),
                                      x_type='instants')
signal_unevenly.get_times()[0] # = 1 <=OK

signal_evenly = signal_unevenly.to_evenly()
signal_evenly.get_times()[0] # = 0 <= KO

class Asset(object):
    asset = "sample_data/"
    data = load('medical.txt')
    def ecg():
        return(data[:,0])

    def eda():
        return (etc etc)

# create a signal

## create fake data
signal_values = np.arange(100)

## create fake indices
idx = np.arange(100)
idx[-1] = 125

## set the sampling frequency
fsamp = 10 # Hz

## set the starting time
tstart = 10 # s

## create an Unevenly signal defining the indices
x_values_idx = idx

s_fake_idx = UnevenlySignal(values = signal_values, sampling_freq = fsamp, signal_nature = 'fake', start_time = tstart,
                       x_values = x_values_idx, x_type = 'indices')

s_fake_idx_segment = s_fake_idx.segment_time(4.5, 5)

TypeError                                 Traceback (most recent call last)
<ipython-input-16-04604a1c5589> in <module>()
      1 # segmentation of US
      2 
----> 3 s_fake_idx_segment = s_fake_idx.segment_time(4.5, 5)
      4 s_fake_time_segment = s_fake_time.segment_time(4.5, 5)

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/Signal.pyc in segment_time(self, t_start, t_stop)
    422 
    423         return self.segment_idx(self.get_idx(t_start) if t_start is not None else None,
--> 424                                 self.get_idx(t_stop) if t_stop is not None else None)
    425 
    426     def segment_idx(self, idx_start, idx_stop=None):

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/Signal.pyc in segment_idx(self, idx_start, idx_stop)
    445             idx_start = 0
    446 
--> 447         iidx_start = int(self.get_iidx_from_idx(idx_start))
    448         iidx_stop = int(self.get_iidx_from_idx(idx_stop))
    449 

TypeError: int() argument must be a string or a number, not 'NoneType'

from __future__ import division
import numpy as np
import pandas as pd
import os

import pyphysio as ph
import matplotlib.pyplot as plt

#%%
ecg = ph.EvenlySignal(ph.TestData.ecg(), 2048)

ibi = ph.BeatFromECG()(ecg)

labels = np.zeros(len(ecg))

labels[61440:122880] = 1
labels[184320:] = 2

labels = ph.EvenlySignal(labels, 2048)

#%%
windows = ph.LabelSegments(labels=labels)

indicators_td, col_names_td = ph.fmap(windows, ph.preset_hrv_td(prefix=''), ibi)
indicators_fd, col_names_fd = ph.fmap(windows, ph.preset_hrv_fd(prefix=''), ibi.to_evenly().resample(4))

print(indicators_td[:,2])
print(indicators_fd[:,2])

from __future__ import division
import numpy as np
import pyphysio as ph

ecg = ph.EvenlySignal(values = ph.TestData.ecg(), sampling_freq = 2048, signal_nature = 'ecg')
ibi = ph.BeatFromECG()(ecg)

# create fake label
label = np.zeros(1200)
label[300:600] = 1
label[900:1200] = 2
label = ph.EvenlySignal(label, sampling_freq = 10, signal_nature = 'label')

t_start = [0.5, 15, 88.7]
t_stop = [5, 21, 110.4]
custom_segments = ph.CustomSegments(begins = t_start, ends = t_stop)

indicators, col_names = ph.fmap(custom_segments, [[ph.Mean()], ibi)
print(indicators[:,2])

$> make test
pytest
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.6.0, pytest-3.0.5, py-1.4.32, pluggy-0.4.0
rootdir: /home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV, inifile: 
collected 0 items / 10 errors 

================================================================================== ERRORS ==================================================================================
__________________________________________________________________ ERROR collecting tests/test_filters.py __________________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_filters.py'.
Hint: make sure your test modules/packages have valid Python names.                                                                                                         
Traceback:                                                                                                                                                                  
tests/test_filters.py:5: in <module>                                                                                                                                        
    from context import ph, Assets, np                                                                                                                                      
E   ModuleNotFoundError: No module named 'context'                                                                                                                          
__________________________________________________________________ ERROR collecting tests/test_general.py __________________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_general.py'.
Hint: make sure your test modules/packages have valid Python names.                                                                                                         
Traceback:                                                                                                                                                                  
tests/test_general.py:4: in <module>                                                                                                                                        
    from context import ph, Assets                                                                                                                                          
E   ModuleNotFoundError: No module named 'context'                                                                                                                          
______________________________________________________________ ERROR collecting tests/test_ibi_extraction.py _______________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_ibi_extraction.py'.
Hint: make sure your test modules/packages have valid Python names.                                                                                                         
Traceback:                                                                                                                                                                  
tests/test_ibi_extraction.py:3: in <module>                                                                                                                                 
    from context import *                                                                                                                                                   
E   ModuleNotFoundError: No module named 'context'                                                                                                                          
______________________________________________________________ ERROR collecting tests/test_indicators_eda.py _______________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_indicators_eda.py'.
Hint: make sure your test modules/packages have valid Python names.                                                                                                         
Traceback:                                                                                                                                                                  
tests/test_indicators_eda.py:4: in <module>                                                                                                                                 
    from context import ph, Assets, np, approx                                                                                                                              
E   ModuleNotFoundError: No module named 'context'                                                                                                                          
______________________________________________________________ ERROR collecting tests/test_indicators_hrv.py _______________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_indicators_hrv.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_indicators_hrv.py:3: in <module>
    from context import ph, np, Assets, approx
E   ModuleNotFoundError: No module named 'context'
__________________________________________________________________ ERROR collecting tests/test_issues.py ___________________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_issues.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_issues.py:4: in <module>
    from context import ph
E   ModuleNotFoundError: No module named 'context'
_____________________________________________________________ ERROR collecting tests/test_phasic_estimation.py _____________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_phasic_estimation.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_phasic_estimation.py:3: in <module>
    from context import ph, np, Assets, approx
E   ModuleNotFoundError: No module named 'context'
______________________________________________________________ ERROR collecting tests/test_some_indicators.py ______________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_some_indicators.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_some_indicators.py:4: in <module>
    from context import ph
E   ModuleNotFoundError: No module named 'context'
__________________________________________________________________ ERROR collecting tests/test_syntax.py ___________________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_syntax.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_syntax.py:3: in <module>
    from context import ph
E   ModuleNotFoundError: No module named 'context'
___________________________________________________________________ ERROR collecting tests/test_tools.py ___________________________________________________________________
ImportError while importing test module '/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/tests/test_tools.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_tools.py:4: in <module>
    from context import ph, np, Assets, approx
E   ModuleNotFoundError: No module named 'context'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 10 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================= 10 error in 0.30 seconds =========================================================================
make: *** [Makefile:5: test] Error 2

from pyphysio import Assets 
ecg_data = Assets.ecg()

# create a signal

## create fake data
x = np.arange(100)
idx = np.arange(100)
idx[-1] = 125

## set the sampling frequency
fsamp = 100 # Hz

## set the starting time
tstart = 100 # s

## create the Evenly signal
s_fake = UnevenlySignal(values = x, sampling_freq = fsamp, signal_nature = 'fake', start_time = tstart, x_values = idx, x_type = 'indices')

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-42-30498dfacc96> in <module>()
     14 ## create the Evenly signal
     15 s_fake = UnevenlySignal(values = x, sampling_freq = fsamp, signal_nature = 'fake', start_time = tstart,
---> 16                        x_values = idx, x_type = 'indices')

/home/andrea/Trento/CODICE/workspaces/pyHRV/pyHRV/pyphysio/Signal.pyc in __new__(cls, values, sampling_freq, signal_nature, start_time, x_values, x_type)
    301                 start_time = 0
    302             else:
--> 303                 assert start_time < x_values[1] / sampling_freq, "More than one sample at or before start_time"
    304         else:
    305             if start_time is None:

AssertionError: More than one sample at or before start_time