def test_new_physio_like():
fname = testutils.get_test_data_path('ECG.csv')
data = physio.Physio(np.loadtxt(fname), fs=1000.)
data._history = [('does history', 'copy?')]
data._metadata['peaks'] = np.array([1, 2, 3])
# assert all copies happen by default
new_data = utils.new_physio_like(data, data[:])
assert np.allclose(data, utils.new_physio_like(data, data[:]))
assert new_data.fs == data.fs
assert new_data.data.dtype == data.data.dtype
assert new_data.history == data.history
assert new_data._metadata == data._metadata
# check if changes apply
new_data = utils.new_physio_like(data,
data[:],
fs=50,
dtype=int,
copy_history=False,
copy_metadata=False)
assert np.allclose(data, utils.new_physio_like(data, data[:]))
assert new_data.fs == 50
assert new_data.data.dtype == int
assert new_data.history == []
for k, v in new_data._metadata.items():
assert v.size == 0
def test_save_history(tmpdir):
# get paths of data, original history, new history
fname = get_test_data_path('ECG.csv')
orig_history = get_test_data_path('history.json')
temp_history = tmpdir.join('tmp').purebasename
# make physio object and perform some operations
phys = physio.Physio(np.loadtxt(fname), fs=1000.)
with pytest.warns(UserWarning): # no history = warning
io.save_history(temp_history, phys)
filt = operations.filter_physio(phys, [5., 15.], 'bandpass')
path = io.save_history(temp_history, filt) # dump history=
# load both original and new json and ensure equality
with open(path, 'r') as src:
hist = json.load(src)
with open(orig_history, 'r') as src:
orig = json.load(src)
assert hist == orig
def test_load_rtpeaks():
for channel in [1, 2, 9]:
with pytest.warns(UserWarning):
hist = dict(fname=DATA, channel=channel, fs=1000.)
phys = external.load_rtpeaks(DATA, channel=channel, fs=1000.)
assert phys.history == [('load_rtpeaks', hist)]
assert phys.fs == 1000.
with pytest.raises(ValueError):
external.load_rtpeaks(testutils.get_test_data_path('ECG.csv'),
channel=channel, fs=1000.)
def test_check_physio():
fname = testutils.get_test_data_path('ECG.csv')
data = physio.Physio(np.loadtxt(fname), fs=1000.)
# check that `ensure_fs` is functional
with pytest.raises(ValueError):
utils.check_physio(fname)
assert isinstance(utils.check_physio(fname, False), physio.Physio)
# "normal" instance should just pass
assert isinstance(utils.check_physio(data), physio.Physio)
# check that copy works
assert utils.check_physio(data) == data
assert utils.check_physio(data, copy=True) != data
def test_load_physio():
# try loading pickle file (from io.save_physio)
pckl = io.load_physio(get_test_data_path('ECG.phys'), allow_pickle=True)
assert isinstance(pckl, physio.Physio)
assert pckl.data.size == 44611
assert pckl.fs == 1000.
with pytest.warns(UserWarning):
pckl = io.load_physio(get_test_data_path('ECG.phys'),
fs=500.,
allow_pickle=True)
assert pckl.fs == 500.
# try loading CSV file
csv = io.load_physio(get_test_data_path('ECG.csv'))
assert isinstance(csv, physio.Physio)
assert np.allclose(csv, pckl)
assert np.isnan(csv.fs)
assert csv.history[0][0] == 'load_physio'
# try loading array
with pytest.warns(UserWarning):
arr = io.load_physio(np.loadtxt(get_test_data_path('ECG.csv')))
assert isinstance(arr, physio.Physio)
arr = io.load_physio(np.loadtxt(get_test_data_path('ECG.csv')),
history=[('np.loadtxt', {
'fname': 'ECG.csv'
})])
assert isinstance(arr, physio.Physio)
# try loading physio object (and resetting dtype)
out = io.load_physio(arr, dtype='float32')
assert out.data.dtype == np.dtype('float32')
assert out.history[0][0] == 'np.loadtxt'
assert out.history[-1][0] == 'load_physio'
with pytest.raises(TypeError):
io.load_physio([1, 2, 3])
def test_load_history(tmpdir):
# get paths of data, new history
fname = get_test_data_path('ECG.csv')
temp_history = tmpdir.join('tmp').purebasename
# make physio object and perform some operations
phys = io.load_physio(fname, fs=1000.)
filt = operations.filter_physio(phys, [5., 15.], 'bandpass')
# save history to file and recreate new object from history
path = io.save_history(temp_history, filt)
replayed = io.load_history(path, verbose=True)
# ensure objects are the same
assert np.allclose(filt, replayed)
assert filt.history == replayed.history
assert filt.fs == replayed.fs
def test_save_physio(tmpdir):
pckl = io.load_physio(get_test_data_path('ECG.phys'), allow_pickle=True)
out = io.save_physio(tmpdir.join('tmp').purebasename, pckl)
assert os.path.exists(out)
assert isinstance(io.load_physio(out, allow_pickle=True), physio.Physio)
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'peakdetdoc'
# -- Extension configuration -------------------------------------------------
intersphinx_mapping = {
'matplotlib': ('https://matplotlib.org', None),
'numpy': ('https://docs.scipy.org/doc/numpy', None),
'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
}
doctest_global_setup = """
import os
from peakdet.tests.utils import get_test_data_path
os.chdir(get_test_data_path())
"""
from peakdet.tests.utils import get_test_data_path # noqa
plot_working_directory = get_test_data_path()
plot_include_source = True
plot_formats = [("png", 90)]
plot_html_show_formats = False
plot_html_show_source_link = False
# -*- coding: utf-8 -*-
import pytest
from peakdet import external
from peakdet.tests import utils as testutils
DATA = testutils.get_test_data_path('rtpeaks.csv')
def test_load_rtpeaks():
for channel in [1, 2, 9]:
with pytest.warns(UserWarning):
hist = dict(fname=DATA, channel=channel, fs=1000.)
phys = external.load_rtpeaks(DATA, channel=channel, fs=1000.)
assert phys.history == [('load_rtpeaks', hist)]
assert phys.fs == 1000.
with pytest.raises(ValueError):
external.load_rtpeaks(testutils.get_test_data_path('ECG.csv'),
channel=channel, fs=1000.)
# -*- coding: utf-8 -*-
import numpy as np
import pytest
from peakdet.physio import Physio
from peakdet.tests import utils as testutils
DATA = np.loadtxt(testutils.get_test_data_path('ECG.csv'))
PROPERTIES = ['data', 'fs', 'history', 'peaks', 'troughs', '_masked']
PHYSIO_TESTS = [
# accepts "correct" inputs for history
dict(kwargs=dict(data=DATA, history=[('good', 'history')])),
# fails on bad inputs for history
dict(kwargs=dict(data=DATA, history=['malformed', 'history']),
raises=TypeError),
dict(kwargs=dict(data=DATA, history='not real history'), raises=TypeError),
# accepts "correct" for metadata
dict(kwargs=dict(data=DATA, metadata=dict())),
dict(kwargs=dict(data=DATA, metadata=dict(peaks=[], reject=[],
troughs=[]))),
# fails on bad inputs for metadata
dict(kwargs=dict(data=DATA, metadata=[]), raises=TypeError),
dict(kwargs=dict(data=DATA, metadata=dict(peaks={})), raises=TypeError),
# fails on bad inputs for data
dict(kwargs=dict(data=np.column_stack([DATA, DATA])), raises=ValueError),
dict(kwargs=dict(data='hello'), raises=ValueError)
]
def test_physio():
phys = Physio(DATA, fs=1000)