16367188041

Committed 18 Jul 2025 09:29AM UTC coverage: 83.006% (+8.7%) from 74.269%

Build # 16367188041

Build Type

Pull #167

github

Committed by

web-flow

Commit Message

Merge ad4c2a75f into 9db9e1feb

Pull Request Pull Request #167: Debug

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54.55

/tests/test_extractor.py

import matplotlib as mpl
mpl.use('Agg')  # must be run first! But therefore requires noqa E402 on all other imports

from spectractor import parameters  # noqa: E402
from spectractor.extractor.extractor import Spectractor  # noqa: E402
from spectractor.logbook import LogBook  # noqa: E402
from spectractor.config import load_config, apply_rebinning_to_parameters  # noqa: E402
import os  # noqa: E402
import sys  # noqa: E402
import numpy as np  # noqa: E402
import unittest  # noqa: E402
import astropy.config  # noqa: E402


def test_logbook():
    logbook = LogBook('./tests/data/ctiofulllogbook_jun2017_v5.csv')
    # target, xpos, ypos = logbook.search_for_image('reduc_20170529_085.fits')
    # assert xpos is None
    disperser_label, target, xpos, ypos = logbook.search_for_image('reduc_20170603_020.fits')
    assert target == "PKS1510-089"
    assert xpos == 830
    assert ypos == 590
    # logbook = LogBook('./ctiofulllogbook_jun2017_v5.csv')
    # logbook.plot_columns_vs_date(['T', 'seeing', 'W'])


@astropy.config.set_temp_cache(os.path.join(os.path.abspath(os.path.dirname(__file__)), "data", "cache"))
def test_extractor_ctio():
    file_names = ['tests/data/reduc_20170530_134.fits']
    output_directory = "./outputs"

    logbook = LogBook(logbook='./tests/data/ctiofulllogbook_jun2017_v5.csv')
    parameters.VERBOSE = True
    load_config("ctio.ini")
    parameters.VERBOSE = True
    parameters.DEBUG = False
    parameters.CCD_REBIN = 1  # rebin=1 to build tests/data spectrum
    apply_rebinning_to_parameters()

    for file_name in file_names:
        tag = file_name.split('/')[-1].replace("sim", "reduc")
        disperser_label, target_label, xpos, ypos = logbook.search_for_image(tag)
        if target_label is None or xpos is None or ypos is None:
            continue
        spectrum = Spectractor(file_name, output_directory, target_label, [xpos, ypos], disperser_label, config="")
        assert spectrum.data is not None
        spectrum.my_logger.warning(f"\n\tQuantities to test:"
                                   f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
                                   f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
                                   f"\n\t\tspectrum.x0={spectrum.x0}"
                                   f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
                                   f"\n\t\tspectrum total flux={np.sum(spectrum.data) * parameters.CCD_REBIN ** 2}"
                                   f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
                                   f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
        assert np.sum(spectrum.data) * parameters.CCD_REBIN**2 > 2e-11 / parameters.CCD_REBIN
        if parameters.CCD_REBIN == 1:
            if parameters.SPECTRACTOR_DECONVOLUTION_PSF2D or parameters.SPECTRACTOR_DECONVOLUTION_FFM:
                assert np.isclose(spectrum.lambdas[0], 345, atol=1)
                assert np.isclose(spectrum.lambdas[-1], 1083.0, atol=1)
            else:
                assert np.isclose(spectrum.lambdas[0], 347, atol=1)
                assert np.isclose(spectrum.lambdas[-1], 1085.0, atol=1)
            assert np.isclose(spectrum.spectrogram_x0, -280, atol=1)
        assert np.isclose(spectrum.x0[0] * parameters.CCD_REBIN, 743.6651370068676, atol=0.5 * parameters.CCD_REBIN)
        assert np.isclose(spectrum.x0[1] * parameters.CCD_REBIN, 683.0577836601408, atol=1 * parameters.CCD_REBIN)
        assert 2 < np.mean(spectrum.chromatic_psf.table['gamma']) * parameters.CCD_REBIN < 3.5
        assert os.path.isfile(os.path.join(output_directory, tag.replace('.fits', '_spectrum.fits'))) is True


# TODO: DM-33441 Fix broken spectractor tests
@unittest.skip('Skipping due broken test (TypeError: argument of type bool is not iterable)')
def test_extractor_ctio_planetary_nebula():
    file_names = ['tests/data/reduc_20170605_028.fits']
    output_directory = "./outputs"

    logbook = LogBook(logbook='./tests/data/ctiofulllogbook_jun2017_v5.csv')
    load_config("ctio.ini")
    parameters.VERBOSE = True
    parameters.DEBUG = False
    parameters.CCD_REBIN = 1  # do not work with other values
    parameters.LAMBDA_MIN = 450
    parameters.LAMBDA_MAX = 1000

    for file_name in file_names:
        tag = file_name.split('/')[-1]
        disperser_label, target_label, xpos, ypos = logbook.search_for_image(tag)
        if target_label is None or xpos is None or ypos is None:
            continue
        spectrum = Spectractor(file_name, output_directory, target_label, [xpos, ypos], disperser_label)
        assert spectrum.data is not None
        spectrum.my_logger.warning(f"\n\tQuantities to test:"
                                   f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
                                   f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
                                   f"\n\t\tspectrum.x0={spectrum.x0}"
                                   f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
                                   f"\n\t\tspectrum total flux={np.sum(spectrum.data) * parameters.CCD_REBIN ** 2}"
                                   f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
                                   f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
        if parameters.SPECTRACTOR_DECONVOLUTION_PSF2D or parameters.SPECTRACTOR_DECONVOLUTION_FFM:
            assert np.isclose(spectrum.lambdas[0], 449, atol=1)
            assert np.isclose(spectrum.lambdas[-1], 996.5, atol=1)
        else:
            assert np.isclose(spectrum.lambdas[0], 443, atol=1)
            assert np.isclose(spectrum.lambdas[-1], 981, atol=1)
        assert np.isclose(spectrum.spectrogram_x0, -368, atol=1)
        assert np.sum(spectrum.data) * parameters.CCD_REBIN ** 2 > 1e-11 / parameters.CCD_REBIN
        assert np.isclose(spectrum.x0[0] * parameters.CCD_REBIN, 816.75, atol=0.5 * parameters.CCD_REBIN)
        assert np.isclose(spectrum.x0[1] * parameters.CCD_REBIN, 587.67, atol=1 * parameters.CCD_REBIN)
        assert 1 < np.mean(spectrum.chromatic_psf.table['gamma']) * parameters.CCD_REBIN < 2.5
        assert os.path.isfile(os.path.join(output_directory, tag.replace('.fits', '_spectrum.fits'))) is True


def extractor_auxtel():
    file_names = ['tests/data/calexp_2020031500162-EMPTY_ronchi90lpmm-det000.fits']  # image 1
    # file_names = ['tests/data/calexp_2020031200313-EMPTY_ronchi90lpmm-det000.fits']  # image 2
    # file_names = ['tests/data/calexp_2020022100767-EMPTY_ronchi90lpmm-det000.fits']  # image 3
    # file_names = ['tests/data//calexp_2020021800154-EMPTY_ronchi90lpmm-det000.fits']  # image 4
    file_names = ['tests/data/Cor_holo4_003_empty_HD60753_2021-02-18_585.fits']  # ronchi170lpmm
    # tests/data/auxtel_first_light-1.fits']

    # logbook = LogBook(logbook='./ctiofulllogbook_jun2017_v5.csv')
    parameters.VERBOSE = True
    parameters.DEBUG = True
    #xpos = 1600
    #ypos = 2293
    #target_label = "HD107696"

    for config in ['./config/auxtel.ini']:  #'./config/auxtel_quicklook.ini',
        for file_name in file_names:
            # tag = file_name.split('/')[-1]
            # disperser_label, target, xpos, ypos = logbook.search_for_image(tag)
            #spectrum = Spectractor(file_name, './outputs/', target_label=target_label, guess=[xpos, ypos],
            #                       config=config)
            spectrum = Spectractor(file_name, './outputs/', target_label="", guess=None, config=config)
            assert spectrum.data is not None
            assert np.sum(spectrum.data) > 1e-14
            # spectrum.my_logger.warning(f"\n\tQuantities to test:"
            #                            f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
            #                            f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
            #                            f"\n\t\tspectrum.x0={spectrum.x0}"
            #                            f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
            #                            f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
            #                            f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
            # assert np.isclose(spectrum.lambdas[0], 296, atol=1)
            # assert np.isclose(spectrum.lambdas[-1], 1083.5, atol=1)
            # assert np.isclose(spectrum.x0[0], 743.6651370068676, atol=0.5)
            # assert np.isclose(spectrum.x0[1], 683.0577836601408, atol=1)
            # assert np.isclose(spectrum.spectrogram_x0, -240, atol=1)
            # assert 2 < np.mean(spectrum.chromatic_psf.table['gamma']) < 3
            # assert os.path.isfile('./outputs/' + tag.replace('.fits', '_spectrum.fits')) is True
            # assert os.path.isfile('./outputs/' + tag.replace('.fits', '_spectrogram.fits')) is True


1	import matplotlib as mpl	1✔
2	mpl.use('Agg') # must be run first! But therefore requires noqa E402 on all other imports	1✔
3
4	from spectractor import parameters # noqa: E402	1✔
5	from spectractor.extractor.extractor import Spectractor # noqa: E402	1✔
6	from spectractor.logbook import LogBook # noqa: E402	1✔
7	from spectractor.config import load_config, apply_rebinning_to_parameters # noqa: E402	1✔
8	import os # noqa: E402	1✔
9	import sys # noqa: E402	1✔
10	import numpy as np # noqa: E402	1✔
11	import unittest # noqa: E402	1✔
12	import astropy.config # noqa: E402	1✔
13
14
15	def test_logbook():	1✔
16	logbook = LogBook('./tests/data/ctiofulllogbook_jun2017_v5.csv')	1✔
17	# target, xpos, ypos = logbook.search_for_image('reduc_20170529_085.fits')
18	# assert xpos is None
19	disperser_label, target, xpos, ypos = logbook.search_for_image('reduc_20170603_020.fits')	1✔
20	assert target == "PKS1510-089"	1✔
21	assert xpos == 830	1✔
22	assert ypos == 590	1✔
23	# logbook = LogBook('./ctiofulllogbook_jun2017_v5.csv')
24	# logbook.plot_columns_vs_date(['T', 'seeing', 'W'])
25
26
27	@astropy.config.set_temp_cache(os.path.join(os.path.abspath(os.path.dirname(__file__)), "data", "cache"))	1✔
28	def test_extractor_ctio():	1✔
29	file_names = ['tests/data/reduc_20170530_134.fits']	1✔
30	output_directory = "./outputs"	1✔
31
32	logbook = LogBook(logbook='./tests/data/ctiofulllogbook_jun2017_v5.csv')	1✔
33	parameters.VERBOSE = True	1✔
34	load_config("ctio.ini")	1✔
35	parameters.VERBOSE = True	1✔
36	parameters.DEBUG = False	1✔
37	parameters.CCD_REBIN = 1 # rebin=1 to build tests/data spectrum	1✔
38	apply_rebinning_to_parameters()	1✔
39
40	for file_name in file_names:	1✔
41	tag = file_name.split('/')[-1].replace("sim", "reduc")	1✔
42	disperser_label, target_label, xpos, ypos = logbook.search_for_image(tag)	1✔
43	if target_label is None or xpos is None or ypos is None:	1✔
44	continue	×
45	spectrum = Spectractor(file_name, output_directory, target_label, [xpos, ypos], disperser_label, config="")	1✔
46	assert spectrum.data is not None	1✔
47	spectrum.my_logger.warning(f"\n\tQuantities to test:"	1✔
48	f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
49	f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
50	f"\n\t\tspectrum.x0={spectrum.x0}"
51	f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
52	f"\n\t\tspectrum total flux={np.sum(spectrum.data) * parameters.CCD_REBIN ** 2}"
53	f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
54	f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
55	assert np.sum(spectrum.data) * parameters.CCD_REBIN**2 > 2e-11 / parameters.CCD_REBIN	1✔
56	if parameters.CCD_REBIN == 1:	1✔
57	if parameters.SPECTRACTOR_DECONVOLUTION_PSF2D or parameters.SPECTRACTOR_DECONVOLUTION_FFM:	1✔
58	assert np.isclose(spectrum.lambdas[0], 345, atol=1)	1✔
59	assert np.isclose(spectrum.lambdas[-1], 1083.0, atol=1)	1✔
60	else:
61	assert np.isclose(spectrum.lambdas[0], 347, atol=1)	×
62	assert np.isclose(spectrum.lambdas[-1], 1085.0, atol=1)	×
63	assert np.isclose(spectrum.spectrogram_x0, -280, atol=1)	1✔
64	assert np.isclose(spectrum.x0[0] * parameters.CCD_REBIN, 743.6651370068676, atol=0.5 * parameters.CCD_REBIN)	1✔
65	assert np.isclose(spectrum.x0[1] * parameters.CCD_REBIN, 683.0577836601408, atol=1 * parameters.CCD_REBIN)	1✔
66	assert 2 < np.mean(spectrum.chromatic_psf.table['gamma']) * parameters.CCD_REBIN < 3.5	1✔
67	assert os.path.isfile(os.path.join(output_directory, tag.replace('.fits', '_spectrum.fits'))) is True	1✔
68
69
70	# TODO: DM-33441 Fix broken spectractor tests
71	@unittest.skip('Skipping due broken test (TypeError: argument of type bool is not iterable)')	1✔
72	def test_extractor_ctio_planetary_nebula():	1✔
73	file_names = ['tests/data/reduc_20170605_028.fits']	×
74	output_directory = "./outputs"	×
75
76	logbook = LogBook(logbook='./tests/data/ctiofulllogbook_jun2017_v5.csv')	×
NEW 77	load_config("ctio.ini")	×
78	parameters.VERBOSE = True	×
79	parameters.DEBUG = False	×
80	parameters.CCD_REBIN = 1 # do not work with other values	×
81	parameters.LAMBDA_MIN = 450	×
82	parameters.LAMBDA_MAX = 1000	×
83
84	for file_name in file_names:	×
85	tag = file_name.split('/')[-1]	×
86	disperser_label, target_label, xpos, ypos = logbook.search_for_image(tag)	×
87	if target_label is None or xpos is None or ypos is None:	×
88	continue	×
89	spectrum = Spectractor(file_name, output_directory, target_label, [xpos, ypos], disperser_label)	×
90	assert spectrum.data is not None	×
91	spectrum.my_logger.warning(f"\n\tQuantities to test:"	×
92	f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
93	f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
94	f"\n\t\tspectrum.x0={spectrum.x0}"
95	f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
96	f"\n\t\tspectrum total flux={np.sum(spectrum.data) * parameters.CCD_REBIN ** 2}"
97	f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
98	f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
99	if parameters.SPECTRACTOR_DECONVOLUTION_PSF2D or parameters.SPECTRACTOR_DECONVOLUTION_FFM:	×
100	assert np.isclose(spectrum.lambdas[0], 449, atol=1)	×
101	assert np.isclose(spectrum.lambdas[-1], 996.5, atol=1)	×
102	else:
103	assert np.isclose(spectrum.lambdas[0], 443, atol=1)	×
104	assert np.isclose(spectrum.lambdas[-1], 981, atol=1)	×
105	assert np.isclose(spectrum.spectrogram_x0, -368, atol=1)	×
106	assert np.sum(spectrum.data) * parameters.CCD_REBIN ** 2 > 1e-11 / parameters.CCD_REBIN	×
107	assert np.isclose(spectrum.x0[0] * parameters.CCD_REBIN, 816.75, atol=0.5 * parameters.CCD_REBIN)	×
108	assert np.isclose(spectrum.x0[1] * parameters.CCD_REBIN, 587.67, atol=1 * parameters.CCD_REBIN)	×
109	assert 1 < np.mean(spectrum.chromatic_psf.table['gamma']) * parameters.CCD_REBIN < 2.5	×
110	assert os.path.isfile(os.path.join(output_directory, tag.replace('.fits', '_spectrum.fits'))) is True	×
111
112
113	def extractor_auxtel():	1✔
114	file_names = ['tests/data/calexp_2020031500162-EMPTY_ronchi90lpmm-det000.fits'] # image 1	×
115	# file_names = ['tests/data/calexp_2020031200313-EMPTY_ronchi90lpmm-det000.fits'] # image 2
116	# file_names = ['tests/data/calexp_2020022100767-EMPTY_ronchi90lpmm-det000.fits'] # image 3
117	# file_names = ['tests/data//calexp_2020021800154-EMPTY_ronchi90lpmm-det000.fits'] # image 4
118	file_names = ['tests/data/Cor_holo4_003_empty_HD60753_2021-02-18_585.fits'] # ronchi170lpmm	×
119	# tests/data/auxtel_first_light-1.fits']
120
121	# logbook = LogBook(logbook='./ctiofulllogbook_jun2017_v5.csv')
122	parameters.VERBOSE = True	×
123	parameters.DEBUG = True	×
124	#xpos = 1600
125	#ypos = 2293
126	#target_label = "HD107696"
127
128	for config in ['./config/auxtel.ini']: #'./config/auxtel_quicklook.ini',	×
129	for file_name in file_names:	×
130	# tag = file_name.split('/')[-1]
131	# disperser_label, target, xpos, ypos = logbook.search_for_image(tag)
132	#spectrum = Spectractor(file_name, './outputs/', target_label=target_label, guess=[xpos, ypos],
133	# config=config)
134	spectrum = Spectractor(file_name, './outputs/', target_label="", guess=None, config=config)	×
135	assert spectrum.data is not None	×
136	assert np.sum(spectrum.data) > 1e-14	×
137	# spectrum.my_logger.warning(f"\n\tQuantities to test:"
138	# f"\n\t\tspectrum.lambdas[0]={spectrum.lambdas[0]}"
139	# f"\n\t\tspectrum.lambdas[-1]={spectrum.lambdas[-1]}"
140	# f"\n\t\tspectrum.x0={spectrum.x0}"
141	# f"\n\t\tspectrum.spectrogram_x0={spectrum.spectrogram_x0}"
142	# f"\n\t\tnp.mean(spectrum.chromatic_psf.table['gamma']="
143	# f"{np.mean(spectrum.chromatic_psf.table['gamma'])}")
144	# assert np.isclose(spectrum.lambdas[0], 296, atol=1)
145	# assert np.isclose(spectrum.lambdas[-1], 1083.5, atol=1)
146	# assert np.isclose(spectrum.x0[0], 743.6651370068676, atol=0.5)
147	# assert np.isclose(spectrum.x0[1], 683.0577836601408, atol=1)
148	# assert np.isclose(spectrum.spectrogram_x0, -240, atol=1)
149	# assert 2 < np.mean(spectrum.chromatic_psf.table['gamma']) < 3
150	# assert os.path.isfile('./outputs/' + tag.replace('.fits', '_spectrum.fits')) is True
151	# assert os.path.isfile('./outputs/' + tag.replace('.fits', '_spectrogram.fits')) is True
152

LSSTDESC / Spectractor / 16367188041

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