def test_c3d_analysis_data():
"""Test analysis var reads from c3d"""
c3dfile = _c3d_path('double_contact.c3d')
an_ = read_data.get_analysis(c3dfile, 'c3dtest')
assert 'c3dtest' in an_
an = an_['c3dtest']
an_vars = [
'Stride Time',
'Opposite Foot Off',
'Double Support',
'Step Time',
'Single Support',
'Step Length',
'Foot Off',
'Walking Speed',
'Stride Length',
'Opposite Foot Contact',
'Cadence',
]
assert all([var in an for var in an_vars])
assert all(['Left' in an[var] for var in an_vars])
assert all(['Right' in an[var] for var in an_vars])
an_file = _file_path('analysis_testdata.p')
an_g = pickle.load(open(an_file, 'rb'))
for var in an_vars:
for context in ['Left', 'Right']:
assert_allclose(an_g['unknown'][var][context], an[var][context])
def test_c3d_marker_data():
"""Test marker data reads from c3d"""
# lowerbody PiG marker set
c3dfile = _c3d_path('double_contact.c3d')
mkrset = list(utils._pig_markerset().keys())
mkrdata = read_data.get_marker_data(c3dfile, mkrset)
assert utils.is_plugingait_set(mkrdata)
assert len(mkrdata) == 5 * len(mkrset) # vars = P*2, V, A & gaps
# check array dimensions for all markers (gap data has different dims)
for mkr in mkrdata:
if '_gaps' not in mkr:
assert mkrdata[mkr].shape == (442, 3)
# LHEE gaps from 360 to 388
assert_equal(mkrdata['LHEE_gaps'], np.arange(360, 389))
lhee_file = _file_path('lhee_data.npy')
lhee_data = np.load(lhee_file)
# allow some deviation from saved reference data (was read using btk)
assert_allclose(mkrdata['LHEE'], lhee_data, rtol=1e-4)
import pytest
import numpy as np
import logging
import tempfile
import os
import os.path as op
from gaitutils.report import pdf, web
from utils import _file_path, cfg
logger = logging.getLogger(__name__)
# test session
sessiondir_ = 'test_subjects/D0063_RR/2018_12_17_preOp_RR'
sessiondir_abs = _file_path(sessiondir_)
sessiondir2_ = 'test_subjects/D0063_RR/2018_12_17_preOp_tuet_RR'
sessiondir2_abs = _file_path(sessiondir2_)
sessiondir__ = op.split(sessiondir_)[-1]
tmpdir = tempfile.gettempdir()
def test_pdf_report():
"""Test creation of pdf report + time-distance text report"""
pdfname = sessiondir__ + '.pdf'
pdfpath = op.join(tmpdir, pdfname)
timedist_name = sessiondir__ + '_time_distance.txt'
timedist_path = op.join(tmpdir, timedist_name)
if op.isfile(pdfpath):
os.remove(pdfpath)
if op.isfile(timedist_path):
import logging
import pytest
from numpy.testing import assert_allclose
from gaitutils.utils import (
is_plugingait_set,
_point_in_poly,
_pig_markerset,
_check_markers_flipped,
marker_gaps,
)
from utils import _file_path
logger = logging.getLogger(__name__)
trial_enf = _file_path('anon.Trial.enf')
trial_enf_write = _file_path('writetest.enf')
def test_marker_gaps():
"""Test marker_gaps"""
mdata = np.random.randn(1000, 3)
assert not marker_gaps(mdata)
mdata[100:200, :] = 0
gaps = marker_gaps(mdata)
assert_allclose(gaps, np.arange(100, 200))
mdata[0, :] = 0
gaps = marker_gaps(mdata)
assert 0 not in gaps
gaps = marker_gaps(mdata, ignore_edge_gaps=False)
assert 0 in gaps
""" Normaldata unit tests @author: jussi ([email protected]) """ from numpy.testing import assert_allclose import logging from gaitutils import normaldata, models from utils import _file_path logger = logging.getLogger(__name__) fn_xlsx = _file_path('normaldata.xlsx') def test_read_xlsx_normaldata(): """Test read of default xlsx normaldata""" ndata = normaldata._read_xlsx(fn_xlsx) normaldata._check_normaldata(ndata) ndata_vars = ndata.keys() pigvars = models.pig_lowerbody.varlabels_nocontext.keys() # no normaldata for following vars not_in_normal = { 'AnkleAnglesY', 'ForeFootAnglesX', 'ForeFootAnglesY', 'ForeFootAnglesZ', }
@author: Jussi ([email protected]) """ import logging import tempfile from gaitutils import videos, sessionutils import time from utils import _file_path, cfg logger = logging.getLogger(__name__) # test session sessiondir_ = 'test_subjects/D0063_RR/2018_12_17_preOp_RR' # rel path sessiondir_abs = _file_path(sessiondir_) # absolute path tmpdir = tempfile.gettempdir() def test_convert_videos(): c3d_file = sessionutils.get_c3ds( sessiondir_abs, tags=None, trial_type='dynamic', check_if_exists=False )[0] original_vids = videos.get_trial_videos(c3d_file, vid_ext='.avi', overlay=False) assert len(original_vids) == 3 target_vids = videos.get_trial_videos(c3d_file, vid_ext='.ogv', overlay=False) # remove target videos if they exist for vidfile in target_vids: vidfile.unlink() # check should not find target videos any more assert not videos.convert_videos(original_vids, check_only=True)