def test_get_mean_colwise(self):
"""test get_mean colwise"""
data = [[0, 1, 3], [0.01, 10, 3.5], [0.02, 21, 4.0]]
p = self.SAXSProfile()
p.add_data(data)
gp = MockGP(1, 2)
m = IMP.kernel.Model()
s = IMP.isd.Scale.setup_particle(IMP.kernel.Particle(m), 3.0)
functions = {}
functions['mean'] = MockFunction()
functions['covariance'] = MockFunction()
p.set_interpolant(gp, {'sigma': s}, functions, 'test',
IMP.kernel.Model(), None)
test = p.get_mean(colwise=True)
expected_q = numpy.linspace(0, 0.02, num=200)
expected_I = numpy.array(
map(gp.get_posterior_mean, [[i] for i in expected_q]))
expected_err = numpy.array(
map(lambda a: numpy.sqrt(gp.get_posterior_covariance([a], [1.0])),
expected_q))
expected_mean = numpy.array(
map(lambda a: functions['mean'](a), expected_q))
self.assertEqual(len(test), 4)
self.assertEqual(set(['q', 'I', 'err', 'mean']), set(test.keys()))
self.assertTrue((expected_q == test['q']).all())
self.assertTrue((expected_I == test['I']).all())
self.assertTrue((expected_err == test['err']).all())
self.assertTrue((expected_mean == test['mean']).all())
def test_get_mean_colwise(self):
"""test get_mean colwise"""
data = [[0, 1, 3], [0.01, 10, 3.5], [0.02, 21, 4.0]]
p = self.SAXSProfile()
p.add_data(data)
gp = MockGP(1, 2)
m = IMP.Model()
s = IMP.isd.Scale.setup_particle(IMP.Particle(m), 3.0)
functions = {}
functions['mean'] = MockFunction()
functions['covariance'] = MockFunction()
p.set_interpolant(
gp,
{'sigma': s},
functions,
'test',
IMP.Model(),
None)
test = p.get_mean(colwise=True)
expected_q = numpy.linspace(0, 0.02, num=200)
expected_I = numpy.array(list(map(gp.get_posterior_mean,
[[i] for i in expected_q])))
expected_err = numpy.array(list(map(lambda a:
numpy.sqrt(
gp.get_posterior_covariance(
[a], [1.0])),
expected_q)))
expected_mean = numpy.array(list(map(lambda a:
functions['mean'](a), expected_q)))
self.assertEqual(len(test), 4)
self.assertEqual(set(['q', 'I', 'err', 'mean']), set(test.keys()))
self.assertTrue((expected_q == test['q']).all())
self.assertTrue((expected_I == test['I']).all())
self.assertTrue((expected_err == test['err']).all())
self.assertTrue((expected_mean == test['mean']).all())
def test_get_raw_data_colwise(self):
"""test get_raw_data colwise """
data = [[0, 0.1, 3], [0.01, 10, 3.5], [0.02, 21, 4.0]]
self.write_data(data)
p = self.SAXSProfile()
p.add_data(self.datafile)
test = p.get_raw_data(colwise=True)
self.assertEqual(len(test), 3)
self.assertEqual(set(test.keys()), set(['q', 'I', 'err']))
self.assertEqual(test['q'], [i[0] for i in data])
self.assertEqual(test['I'], [i[1] for i in data])
self.assertEqual(test['err'], [i[2] for i in data])
def test_get_raw_data_colwise(self):
"""test get_raw_data colwise """
data = [[0, 0.1, 3], [0.01, 10, 3.5], [0.02, 21, 4.0]]
self.write_data(data)
p = self.SAXSProfile()
p.add_data(self.datafile)
test = p.get_raw_data(colwise=True)
self.assertEqual(len(test), 3)
self.assertEqual(set(test.keys()), set(['q', 'I', 'err']))
self.assertEqual(test['q'], [i[0] for i in data])
self.assertEqual(test['I'], [i[1] for i in data])
self.assertEqual(test['err'], [i[2] for i in data])
def test_get_data_colwise(self):
"""test get_data colwise """
data = [[0, 0.1, 3], [0.01, 10, 3.5], [0.02, 21, 4.0]]
self.write_data(data)
p = self.SAXSProfile()
p.add_data(self.datafile)
test = p.get_data(colwise=True)
self.assertEqual(len(test), 4)
self.assertEqual(set(test.keys()), set(["id", "q", "I", "err"]))
self.assertEqual(test["id"], range(3))
self.assertEqual(test["q"], [i[0] for i in data])
self.assertEqual(test["I"], [i[1] for i in data])
self.assertEqual(test["err"], [i[2] for i in data])