AnniesLasso.tests.TestBaseCannonModel.get_model() - Code Metrics - Inspection of "Merge pull request #1 from andycasey/code" - andycasey/AnniesLasso - Measure and Improve Code Quality continuously with Scrutinizer

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by Andy

created 2015-11-21 10:08 UTC

AnniesLasso.tests.TestBaseCannonModel.get_model() A

↳ Parent: AnniesLasso.tests.TestBaseCannonModel

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Metric	Value
dl	0
loc	4
rs	10
cc	1

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
Unit tests for the base model class and associated functions.
"""

import numpy as np
import unittest
from AnniesLasso import model, utils


class NullObject(object):
    pass


class TestRequiresTrainingWheels(unittest.TestCase):
    def test_not_trained(self):
        o = NullObject()
        o.is_trained = False
        with self.assertRaises(TypeError):
            model.requires_training_wheels(lambda x: None)(o)

    def test_is_trained(self):
        o = NullObject()
        o.is_trained = True
        self.assertIsNone(model.requires_training_wheels(lambda x: None)(o))


class TestRequiresLabelVector(unittest.TestCase):
    def test_with_label_vector(self):
        o = NullObject()
        o.label_vector = ""
        self.assertIsNone(model.requires_label_vector(lambda x: None)(o))

    def test_without_label_vector(self):
        o = NullObject()
        o.label_vector = None
        with self.assertRaises(TypeError):
            model.requires_label_vector(lambda x: None)(o)


class TestBaseCannonModel(unittest.TestCase):

    def setUp(self):
        # Initialise some faux data and labels.
        labels = "ABCDE"
        N_labels = len(labels)
        N_stars = np.random.randint(10, 500)
        N_pixels = np.random.randint(1, 10000)
        shape = (N_stars, N_pixels)

        self.valid_training_labels = np.rec.array(
            np.random.uniform(low=0.5, high=1.5, size=(N_stars, N_labels)),
            dtype=[(label, '<f8') for label in labels])

        self.valid_fluxes = np.random.uniform(low=0.5, high=1.5, size=shape)
        self.valid_flux_uncertainties = np.random.uniform(low=0.5, high=1.5,
            size=shape)

    def runTest(self):
        None
    
    def get_model(self, **kwargs):
        return model.BaseCannonModel(
            self.valid_training_labels, self.valid_fluxes,
            self.valid_flux_uncertainties, **kwargs)

    def test_repr(self):
        self.runTest() # Just for that 100%, baby.
        m = self.get_model()
        print("{0} {1}".format(m.__str__(), m.__repr__()))

    def test_get_dispersion(self):
        m = self.get_model()
        self.assertSequenceEqual(
            tuple(m.dispersion), 
            tuple(np.arange(self.valid_fluxes.shape[1])))

    def test_set_dispersion(self):
        m = self.get_model()
        for item in (None, False, True):
            # Incorrect data type (not an iterable)
            with self.assertRaises(TypeError):
                m.dispersion = item

        for item in ("", {}, [], (), set()):
            # These are iterable but have the wrong lengths.
            with self.assertRaises(ValueError):
                m.dispersion = item

        with self.assertRaises(ValueError):
            m.dispersion = [3,4,2,1]

        # These should work.
        m.dispersion = 10 + np.arange(self.valid_fluxes.shape[1])
        m.dispersion = -100 + np.arange(self.valid_fluxes.shape[1])
        m.dispersion = 520938.4 + np.arange(self.valid_fluxes.shape[1])

        # Disallow non-finite numbers.
        with self.assertRaises(ValueError):
            d = np.arange(self.valid_fluxes.shape[1], dtype=float)
            d[0] = np.nan
            m.dispersion = d

        with self.assertRaises(ValueError):
            d = np.arange(self.valid_fluxes.shape[1], dtype=float)
            d[0] = np.inf
            m.dispersion = d

        with self.assertRaises(ValueError):
            d = np.arange(self.valid_fluxes.shape[1], dtype=float)
            d[0] = -np.inf
            m.dispersion = d

        # Disallow non-float like things.
        with self.assertRaises(ValueError):
            d = np.array([""] * self.valid_fluxes.shape[1])
            m.dispersion = d

        with self.assertRaises(ValueError):
            d = np.array([None] * self.valid_fluxes.shape[1])
            m.dispersion = d
        
    def test_get_training_data(self):
        m = self.get_model()
        self.assertIsNotNone(m.training_labels)
        self.assertIsNotNone(m.training_fluxes)
        self.assertIsNotNone(m.training_flux_uncertainties)

    def test_invalid_label_names(self):
        m = self.get_model()
        for character in m._forbidden_label_characters:

            invalid_labels = [] + list(m.labels_available)
            invalid_labels[0] = "HELLO_{}".format(character)

            N_stars = len(self.valid_training_labels)
            N_labels = len(invalid_labels)
            invalid_training_labels = np.rec.array(
                np.random.uniform(size=(N_stars, N_labels)),
                dtype=[(l, '<f8') for l in invalid_labels])

            m = model.BaseCannonModel(invalid_training_labels,
                self.valid_fluxes, self.valid_flux_uncertainties,
                live_dangerously=True)

            m._forbidden_label_characters = None
            self.assertTrue(m._verify_labels_available())

            with self.assertRaises(ValueError):
                m = model.BaseCannonModel(invalid_training_labels,
                    self.valid_fluxes, self.valid_flux_uncertainties)

    def test_get_label_vector(self):
        m = self.get_model()
        m.label_vector = "A + B + C"
        self.assertEqual(m.pixel_label_vector(1), [
            [("A", 1)],
            [("B", 1)],
            [("C", 1)]
        ])

    def test_set_label_vector(self):
        m = self.get_model()
        label_vector = "A + B + C + D + E"

        m.label_vector = label_vector
        self.assertEqual(m.label_vector, utils.parse_label_vector(label_vector))
        self.assertEqual("1 + A + B + C + D + E", m.human_readable_label_vector)

        with self.assertRaises(ValueError):
            m.label_vector = "A + G"

        m.label_vector = None
        self.assertIsNone(m.label_vector)

        for item in (True, False, 0, 1.0):
            with self.assertRaises(TypeError):
                m.label_vector = item

    def test_label_getsetters(self):

        m = self.get_model()
        self.assertEqual((), m.labels)

        m.label_vector = "A + B + C"
        self.assertSequenceEqual(("A", "B", "C"), tuple(m.labels))

        with self.assertRaises(AttributeError):
            m.labels = None

    def test_inheritence(self):
        m = self.get_model()
        m.label_vector = "A + B + C"
        with self.assertRaises(NotImplementedError):
            m.train()
        m._trained = True
        with self.assertRaises(NotImplementedError):
            m.predict()
        with self.assertRaises(NotImplementedError):
            m.fit()
        
    def test_get_label_indices(self):
        m = self.get_model()
        m.label_vector = "A^5 + A^2 + B^3 + C + C*D + D^6"
        self.assertEqual([1, 2, 3, 5], m._get_lowest_order_label_indices())

    def test_data_verification(self):
        m = self.get_model()
        m._training_fluxes = m._training_fluxes.reshape(1, -1)
        with self.assertRaises(ValueError):
            m._verify_training_data()

        m._training_flux_uncertainties = \
            m._training_flux_uncertainties.reshape(m._training_fluxes.shape)
        with self.assertRaises(ValueError):
            m._verify_training_data()

        with self.assertRaises(ValueError):
            m = self.get_model(dispersion=[1,2,3])

        N_labels = 2
        N_stars, N_pixels = self.valid_fluxes.shape
        invalid_training_labels = np.random.uniform(
            low=0.5, high=1.5, size=(N_stars, N_labels))
        with self.assertRaises(ValueError):
            m = model.BaseCannonModel(invalid_training_labels,
                self.valid_fluxes, self.valid_flux_uncertainties)

    def test_labels_array(self):
        m = self.get_model()
        m.label_vector = "A^2 + B^3 + C^5"

        for i, label in enumerate("ABC"):
            foo = m.labels_array[:, i]
            bar = np.array(m.training_labels[label]).flatten()
            self.assertTrue(np.allclose(foo, bar))

        with self.assertRaises(AttributeError):
            m.labels_array = None

    def test_label_vector_array(self):
        m = self.get_model()
        m.label_vector = "A^2.0 + B^3.4 + C^5"

        self.assertTrue(np.allclose(
            np.array(m.training_labels["A"]**2).flatten(),
            m.label_vector_array[1],
        ))
        self.assertTrue(np.allclose(
            np.array(m.training_labels["B"]**3.4).flatten(),
            m.label_vector_array[2]
        ))
        self.assertTrue(np.allclose(
            np.array(m.training_labels["C"]**5).flatten(),
            m.label_vector_array[3]
        ))

        m.training_labels["A"][0] = np.nan
        m.label_vector_array # For Coveralls.

        kwd1 = {
            "A": float(m.training_labels["A"][1]),
            "B": float(m.training_labels["B"][1]),
            "C": float(m.training_labels["C"][1])
        }
        kwd2 = {
            "A": [m.training_labels["A"][1][0]],
            "B": [m.training_labels["B"][1][0]],
            "C": [m.training_labels["C"][1][0]]
        }
        self.assertTrue(np.allclose(
            model._build_label_vector_rows(m.label_vector, kwd1),
            model._build_label_vector_rows(m.label_vector, kwd2)
        ))

    def test_format_input_labels(self):
        m = self.get_model()
        m.label_vector = "A^2.0 + B^3.4 + C^5"

        kwds = {"A": [5], "B": [3], "C": [0.43]}
        for k, v in m._format_input_labels(None, **kwds).items():
            self.assertEqual(kwds[k], v)
        for k, v in m._format_input_labels([5, 3, 0.43]).items():
            self.assertEqual(kwds[k], v)

        kwds_input = {k: v[0] for k, v in kwds.items() }
        for k, v in m._format_input_labels(None, **kwds_input).items():
            self.assertEqual(kwds[k], v)




    # The trained attributes and I/O functions will be tested in the sub-classes


1			#!/usr/bin/env python
2			# -- coding: utf-8 --
3
4			"""
5			Unit tests for the base model class and associated functions.
6			"""
7
8			import numpy as np
9			import unittest
10			from AnniesLasso import model, utils
11
12
13			class NullObject(object):
14			pass
15
16
17			class TestRequiresTrainingWheels(unittest.TestCase):
18			def test_not_trained(self):
19			o = NullObject()
20			o.is_trained = False
21			with self.assertRaises(TypeError):
22			model.requires_training_wheels(lambda x: None)(o)
23
24			def test_is_trained(self):
25			o = NullObject()
26			o.is_trained = True
27			self.assertIsNone(model.requires_training_wheels(lambda x: None)(o))
28
29
30			class TestRequiresLabelVector(unittest.TestCase):
31			def test_with_label_vector(self):
32			o = NullObject()
33			o.label_vector = ""
34			self.assertIsNone(model.requires_label_vector(lambda x: None)(o))
35
36			def test_without_label_vector(self):
37			o = NullObject()
38			o.label_vector = None
39			with self.assertRaises(TypeError):
40			model.requires_label_vector(lambda x: None)(o)
41
42
43			class TestBaseCannonModel(unittest.TestCase):
44
45			def setUp(self):
46			# Initialise some faux data and labels.
47			labels = "ABCDE"
48			N_labels = len(labels)
49			N_stars = np.random.randint(10, 500)
50			N_pixels = np.random.randint(1, 10000)
51			shape = (N_stars, N_pixels)
52
53			self.valid_training_labels = np.rec.array(
54			np.random.uniform(low=0.5, high=1.5, size=(N_stars, N_labels)),
55			dtype=[(label, '<f8') for label in labels])
56
57			self.valid_fluxes = np.random.uniform(low=0.5, high=1.5, size=shape)
58			self.valid_flux_uncertainties = np.random.uniform(low=0.5, high=1.5,
59			size=shape)
60
61			def runTest(self):
62			None
63
64			def get_model(self, **kwargs):
65			return model.BaseCannonModel(
66			self.valid_training_labels, self.valid_fluxes,
67			self.valid_flux_uncertainties, **kwargs)
68
69			def test_repr(self):
70			self.runTest() # Just for that 100%, baby.
71			m = self.get_model()
72			print("{0} {1}".format(m.__str__(), m.__repr__()))
73
74			def test_get_dispersion(self):
75			m = self.get_model()
76			self.assertSequenceEqual(
77			tuple(m.dispersion),
78			tuple(np.arange(self.valid_fluxes.shape[1])))
79
80			def test_set_dispersion(self):
81			m = self.get_model()
82			for item in (None, False, True):
83			# Incorrect data type (not an iterable)
84			with self.assertRaises(TypeError):
85			m.dispersion = item
86
87			for item in ("", {}, [], (), set()):
88			# These are iterable but have the wrong lengths.
89			with self.assertRaises(ValueError):
90			m.dispersion = item
91
92			with self.assertRaises(ValueError):
93			m.dispersion = [3,4,2,1]
94
95			# These should work.
96			m.dispersion = 10 + np.arange(self.valid_fluxes.shape[1])
97			m.dispersion = -100 + np.arange(self.valid_fluxes.shape[1])
98			m.dispersion = 520938.4 + np.arange(self.valid_fluxes.shape[1])
99
100			# Disallow non-finite numbers.
101			with self.assertRaises(ValueError):
102			d = np.arange(self.valid_fluxes.shape[1], dtype=float)
103			d[0] = np.nan
104			m.dispersion = d
105
106			with self.assertRaises(ValueError):
107			d = np.arange(self.valid_fluxes.shape[1], dtype=float)
108			d[0] = np.inf
109			m.dispersion = d
110
111			with self.assertRaises(ValueError):
112			d = np.arange(self.valid_fluxes.shape[1], dtype=float)
113			d[0] = -np.inf
114			m.dispersion = d
115
116			# Disallow non-float like things.
117			with self.assertRaises(ValueError):
118			d = np.array([""] * self.valid_fluxes.shape[1])
119			m.dispersion = d
120
121			with self.assertRaises(ValueError):
122			d = np.array([None] * self.valid_fluxes.shape[1])
123			m.dispersion = d
124
125			def test_get_training_data(self):
126			m = self.get_model()
127			self.assertIsNotNone(m.training_labels)
128			self.assertIsNotNone(m.training_fluxes)
129			self.assertIsNotNone(m.training_flux_uncertainties)
130
131			def test_invalid_label_names(self):
132			m = self.get_model()
133			for character in m._forbidden_label_characters:
134
135			invalid_labels = [] + list(m.labels_available)
136			invalid_labels[0] = "HELLO_{}".format(character)
137
138			N_stars = len(self.valid_training_labels)
139			N_labels = len(invalid_labels)
140			invalid_training_labels = np.rec.array(
141			np.random.uniform(size=(N_stars, N_labels)),
142			dtype=[(l, '<f8') for l in invalid_labels])
143
144			m = model.BaseCannonModel(invalid_training_labels,
145			self.valid_fluxes, self.valid_flux_uncertainties,
146			live_dangerously=True)
147
148			m._forbidden_label_characters = None
149			self.assertTrue(m._verify_labels_available())
150
151			with self.assertRaises(ValueError):
152			m = model.BaseCannonModel(invalid_training_labels,
153			self.valid_fluxes, self.valid_flux_uncertainties)
154
155			def test_get_label_vector(self):
156			m = self.get_model()
157			m.label_vector = "A + B + C"
158			self.assertEqual(m.pixel_label_vector(1), [
159			[("A", 1)],
160			[("B", 1)],
161			[("C", 1)]
162			])
163
164			def test_set_label_vector(self):
165			m = self.get_model()
166			label_vector = "A + B + C + D + E"
167
168			m.label_vector = label_vector
169			self.assertEqual(m.label_vector, utils.parse_label_vector(label_vector))
170			self.assertEqual("1 + A + B + C + D + E", m.human_readable_label_vector)
171
172			with self.assertRaises(ValueError):
173			m.label_vector = "A + G"
174
175			m.label_vector = None
176			self.assertIsNone(m.label_vector)
177
178			for item in (True, False, 0, 1.0):
179			with self.assertRaises(TypeError):
180			m.label_vector = item
181
182			def test_label_getsetters(self):
183
184			m = self.get_model()
185			self.assertEqual((), m.labels)
186
187			m.label_vector = "A + B + C"
188			self.assertSequenceEqual(("A", "B", "C"), tuple(m.labels))
189
190			with self.assertRaises(AttributeError):
191			m.labels = None
192
193			def test_inheritence(self):
194			m = self.get_model()
195			m.label_vector = "A + B + C"
196			with self.assertRaises(NotImplementedError):
197			m.train()
198			m._trained = True
199			with self.assertRaises(NotImplementedError):
200			m.predict()
201			with self.assertRaises(NotImplementedError):
202			m.fit()
203
204			def test_get_label_indices(self):
205			m = self.get_model()
206			m.label_vector = "A^5 + A^2 + B^3 + C + C*D + D^6"
207			self.assertEqual([1, 2, 3, 5], m._get_lowest_order_label_indices())
208
209			def test_data_verification(self):
210			m = self.get_model()
211			m._training_fluxes = m._training_fluxes.reshape(1, -1)
212			with self.assertRaises(ValueError):
213			m._verify_training_data()
214
215			m._training_flux_uncertainties = \
216			m._training_flux_uncertainties.reshape(m._training_fluxes.shape)
217			with self.assertRaises(ValueError):
218			m._verify_training_data()
219
220			with self.assertRaises(ValueError):
221			m = self.get_model(dispersion=[1,2,3])
222
223			N_labels = 2
224			N_stars, N_pixels = self.valid_fluxes.shape
225			invalid_training_labels = np.random.uniform(
226			low=0.5, high=1.5, size=(N_stars, N_labels))
227			with self.assertRaises(ValueError):
228			m = model.BaseCannonModel(invalid_training_labels,
229			self.valid_fluxes, self.valid_flux_uncertainties)
230
231			def test_labels_array(self):
232			m = self.get_model()
233			m.label_vector = "A^2 + B^3 + C^5"
234
235			for i, label in enumerate("ABC"):
236			foo = m.labels_array[:, i]
237			bar = np.array(m.training_labels[label]).flatten()
238			self.assertTrue(np.allclose(foo, bar))
239
240			with self.assertRaises(AttributeError):
241			m.labels_array = None
242
243			def test_label_vector_array(self):
244			m = self.get_model()
245			m.label_vector = "A^2.0 + B^3.4 + C^5"
246
247			self.assertTrue(np.allclose(
248			np.array(m.training_labels["A"]**2).flatten(),
249			m.label_vector_array[1],
250			))
251			self.assertTrue(np.allclose(
252			np.array(m.training_labels["B"]**3.4).flatten(),
253			m.label_vector_array[2]
254			))
255			self.assertTrue(np.allclose(
256			np.array(m.training_labels["C"]**5).flatten(),
257			m.label_vector_array[3]
258			))
259
260			m.training_labels["A"][0] = np.nan
261			m.label_vector_array # For Coveralls.
262
263			kwd1 = {
264			"A": float(m.training_labels["A"][1]),
265			"B": float(m.training_labels["B"][1]),
266			"C": float(m.training_labels["C"][1])
267			}
268			kwd2 = {
269			"A": [m.training_labels["A"][1][0]],
270			"B": [m.training_labels["B"][1][0]],
271			"C": [m.training_labels["C"][1][0]]
272			}
273			self.assertTrue(np.allclose(
274			model._build_label_vector_rows(m.label_vector, kwd1),
275			model._build_label_vector_rows(m.label_vector, kwd2)
276			))
277
278			def test_format_input_labels(self):
279			m = self.get_model()
280			m.label_vector = "A^2.0 + B^3.4 + C^5"
281
282			kwds = {"A": [5], "B": [3], "C": [0.43]}
283			for k, v in m._format_input_labels(None, **kwds).items():
284			self.assertEqual(kwds[k], v)
285			for k, v in m._format_input_labels([5, 3, 0.43]).items():
286			self.assertEqual(kwds[k], v)
287
288			kwds_input = {k: v[0] for k, v in kwds.items() }
289			for k, v in m._format_input_labels(None, **kwds_input).items():
290			self.assertEqual(kwds[k], v)
291
292
293
294
295			# The trained attributes and I/O functions will be tested in the sub-classes
296

andycasey / AnniesLasso

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AnniesLasso.tests.TestBaseCannonModel.get_model() A

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