1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
|
# This file is used to configure the behavior of pytest when using the Astropy
# test infrastructure. It needs to live inside the package in order for it to
# get picked up when running the tests inside an interpreter using
# packagename.test
from copy import copy
import numpy as np
import pytest
from astropy import units as u
from astropy.modeling import models
from specutils.spectra import Spectrum1D
try:
from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
ASTROPY_HEADER = True
except ImportError:
ASTROPY_HEADER = False
def pytest_configure(config):
if ASTROPY_HEADER:
config.option.astropy_header = True
# Customize the following lines to add/remove entries from the list of
# packages for which version numbers are displayed when running the tests.
PYTEST_HEADER_MODULES.pop('Pandas', None)
PYTEST_HEADER_MODULES.pop('h5py', None)
PYTEST_HEADER_MODULES['astropy'] = 'astropy'
PYTEST_HEADER_MODULES['gwcs'] = 'gwcs'
PYTEST_HEADER_MODULES['asdf'] = 'asdf'
PYTEST_HEADER_MODULES['asdf-astropy'] = 'asdf_astropy'
PYTEST_HEADER_MODULES['stdatamodels'] = 'stdatamodels'
PYTEST_HEADER_MODULES['ndcube'] = 'ndcube'
PYTEST_HEADER_MODULES['spectral-cube'] = 'spectral_cube'
from specutils import __version__
TESTED_VERSIONS['specutils'] = __version__
class SpectraExamples:
"""
The ``SpectralExamples`` class is a *container class* that has
several examples of simple spectra that are to be used in the tests
(e.g., arithmetic tests, smoothing tests etc).
The purpose of this being a test class instead of using a `Spectrum1D`
directly is that it contains both the `Spectrum1D` object and the flux
that was used to *create* the Spectrum. That's for tests that ensure
the simpler operations just on the flux arrays are carried through to
the `Spectrum1D` operations.
Each of the spectra are created from a base noise-less spectrum
constructed from 4 Gaussians and a ramp. Then three example spectra
are created, and then gaussian random noise is added.
1. s1_um_mJy_e1 - 4 Gaussians + ramp with one instantion of noise
dispersion: um, flux: mJy
2. s1_um_mJy_e2 - same as 1, but with a different instance of noise
dispersion: um, flux: mJy
3. s1_AA_mJy_e3 - same as 1, but with a third instance of noise
dispersion: Angstroms, flux: mJy
4. s1_AA_nJy_e3 - same as 1, but with a fourth instance of noise
dispersion: Angstroms, flux: nJy
5. s1_um_mJy_e1_masked - same as 1, but with a random set of pixels
masked.
6. s1_um_mJy_e1_desc - same as 1, but with the spectral axis in
descending rather than ascending order.
"""
def __init__(self):
#
# Create the base wavelengths and flux
#
self.wavelengths_um = np.linspace(0.4, 1.05, 100)
g1 = models.Gaussian1D(amplitude=2000, mean=0.56, stddev=0.01)
g2 = models.Gaussian1D(amplitude=500, mean=0.62, stddev=0.02)
g3 = models.Gaussian1D(amplitude=-400, mean=0.80, stddev=0.02)
g4 = models.Gaussian1D(amplitude=-350, mean=0.52, stddev=0.01)
ramp = models.Linear1D(slope=300, intercept=0.0)
self.base_flux = (g1(self.wavelengths_um) + g2(self.wavelengths_um) +
g3(self.wavelengths_um) + g4(self.wavelengths_um) +
ramp(self.wavelengths_um) + 1000)
#
# Initialize the seed so the random numbers are not quite as random
#
np.random.seed(42)
#
# Create two spectra with the only difference in the instance of noise
#
self._flux_e1 = self.base_flux + 400 * np.random.random(self.base_flux.shape)
self._s1_um_mJy_e1 = Spectrum1D(spectral_axis=self.wavelengths_um * u.um,
flux=self._flux_e1 * u.mJy)
self._flux_e2 = self.base_flux + 400 * np.random.random(self.base_flux.shape)
self._s1_um_mJy_e2 = Spectrum1D(spectral_axis=self.wavelengths_um * u.um,
flux=self._flux_e2 * u.mJy)
#
# Create one spectrum with the same flux but in angstrom units
#
self.wavelengths_AA = self.wavelengths_um * 10000
self._s1_AA_mJy_e3 = Spectrum1D(spectral_axis=self.wavelengths_AA * u.AA,
flux=self._flux_e1 * u.mJy)
#
# Create one spectrum with the same flux but in angstrom units and nJy
#
self._flux_e4 = (self.base_flux + 400 * np.random.random(self.base_flux.shape)) * 1000000
self._s1_AA_nJy_e4 = Spectrum1D(spectral_axis=self.wavelengths_AA * u.AA,
flux=self._flux_e4 * u.nJy)
#
# Create one spectrum like 1 but with a mask
#
self._s1_um_mJy_e1_masked = copy(self._s1_um_mJy_e1) # SHALLOW copy - the data are shared with the above non-masked case # noqa
self._s1_um_mJy_e1_masked.mask = (np.random.randn(*self.base_flux.shape) + 1) > 0
# Create a spectrum like 1, but with descending spectral axis
self._s1_um_mJy_e1_desc = Spectrum1D(spectral_axis=self.wavelengths_um[::-1] * u.um,
flux=self._flux_e1[::-1] * u.mJy)
@property
def s1_um_mJy_e1(self):
return self._s1_um_mJy_e1
@property
def s1_um_mJy_e1_flux(self):
return self._flux_e1
@property
def s1_um_mJy_e2(self):
return self._s1_um_mJy_e2
@property
def s1_um_mJy_e2_flux(self):
return self._flux_e2
@property
def s1_AA_mJy_e3(self):
return self._s1_AA_mJy_e3
@property
def s1_AA_mJy_e3_flux(self):
return self._flux_e1
@property
def s1_AA_nJy_e4(self):
return self._s1_AA_nJy_e4
@property
def s1_AA_nJy_e4_flux(self):
return self._flux_e4
@property
def s1_um_mJy_e1_masked(self):
return self._s1_um_mJy_e1_masked
@property
def s1_um_mJy_e1_desc(self):
return self._s1_um_mJy_e1_desc
@pytest.fixture
def simulated_spectra():
"""
The method will be called as a fixture to tests.
Parameters
----------
N/A
Return
------
``SpectralExamples``
An instance of the SpectraExamples class.
Examples
--------
This fixture can be used in a test as:
```
from .spectral_examples import spectral_examples
def test_add_spectra(spectral_examples):
# Get the numpy array of data
flux1 = define_spectra.s1_um_mJy_e1_flux
flux2 = define_spectra.s1_um_mJy_e2_flux
flux3 = flux1 + flux2
# Calculate using the spectrum1d/nddata code
spec3 = define_spectra.s1_um_mJy_e1 + define_spectra.s1_um_mJy_e2
assert np.allclose(spec3.flux.value, flux3)
```
"""
return SpectraExamples()
|