def test_trim(capsys):
# eureka.lib.util.trim test
#Let's trim by giving metadata some xwindow and ywindow information which is normally given by the user in the S3_ecf
trim_x0 = 10
trim_x1 = 90
trim_y0 = 2
trim_y1 = 14
meta = MetaClass()
data = DataClass()
n = 7
ny = 20
nx = 100
#Let's assume we have a dataset with 7 integrations and every spectrum has the dimensions of 100x20
data.data = np.ones((n, ny, nx))
data.err = np.ones((n, ny, nx))
data.dq = np.ones((n, ny, nx))
data.wave = np.ones((n, ny, nx))
data.v0 = np.ones((n, ny, nx))
meta.ywindow = [trim_y0, trim_y1]
meta.xwindow = [trim_x0, trim_x1]
res_dat, res_md = util.trim(data, meta)
#Let's check if the dimensions agree
assert res_dat.subdata.shape == (n, (trim_y1 - trim_y0),
(trim_x1 - trim_x0))
def test_eclipsemodel(self):
"""Tests for the BatmanEclipseModel class"""
# Set the intial parameters
params = Parameters()
params.rp = 0.22, 'fixed' # rprs
params.fp = 0.08, 'free', 0.0, 0.1, 'U' # fprs
params.per = 10.721490, 'fixed'
params.t0 = 0.48, 'free', 0, 1, 'U'
params.inc = 89.7, 'free', 80., 90., 'U'
params.a = 18.2, 'free', 15., 20., 'U' # aprs
params.ecc = 0., 'fixed'
params.w = 90., 'fixed' # omega
params.Rs = 1., 'independent'
# Make the eclipse model
meta = MetaClass()
meta.sharedp = False
longparamlist, paramtitles = s5_fit.make_longparamlist(meta, params, 1)
log = logedit.Logedit('./data/test.log')
self.e_model = models.BatmanEclipseModel(parameters=params,
name='transit',
fmt='r--',
log=log,
longparamlist=longparamlist,
nchan=1,
paramtitles=paramtitles)
# Remove the temporary log file
os.system("rm ./data/test.log")
# Evaluate and test output
self.e_model.time = self.time
vals = self.e_model.eval()
self.assertEqual(vals.size, self.time.size)
def test_transitmodel(self):
"""Tests for the BatmanTransitModel class"""
# Set the intial parameters
params = Parameters()
params.rp = 0.22, 'free', 0.0, 0.4, 'U' # rprs
params.per = 10.721490, 'fixed'
params.t0 = 0.48, 'free', 0, 1, 'U'
params.inc = 89.7, 'free', 80., 90., 'U'
params.a = 18.2, 'free', 15., 20., 'U' # aprs
params.ecc = 0., 'fixed'
params.w = 90., 'fixed' # omega
params.limb_dark = '4-parameter', 'independent'
params.u1 = 0.1, 'free', 0., 1., 'U'
params.u2 = 0.1, 'free', 0., 1., 'U'
params.u3 = 0.1, 'free', 0., 1., 'U'
params.u4 = 0.1, 'free', 0., 1., 'U'
# Make the transit model
meta = MetaClass()
meta.sharedp = False
longparamlist, paramtitles = s5_fit.make_longparamlist(meta, params, 1)
self.t_model = models.BatmanTransitModel(parameters=params,
name='transit',
fmt='r--',
longparamlist=longparamlist,
nchan=1,
paramtitles=paramtitles)
# Evaluate and test output
self.t_model.time = self.time
vals = self.t_model.eval()
self.assertEqual(vals.size, self.time.size)
def test_WFC3(capsys):
with capsys.disabled():
# is able to display any message without failing a test
# useful to leave messages for future users who run the tests
print(
"\n\nIMPORTANT: Make sure that any changes to the ecf files are " +
"included in demo ecf files and documentation (docs/source/ecf.rst)"
)
print("\nWFC3 S3 test: ", end='', flush=True)
# explicitly define meta variables to be able to run pathdirectory fn locally
meta = MetaClass()
meta.eventlabel = 'WFC3'
meta.topdir = '../tests'
ecf_path = './WFC3_ecfs/'
reload(s3)
s3_meta = s3.reduceJWST(meta.eventlabel, ecf_path=ecf_path)
# run assertions for S3
meta.outputdir_raw = 'data/WFC3/Stage3/'
name = pathdirectory(meta, 'S3', 1, ap=8, bg=40)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# remove temporary files
os.system("rm -r data/WFC3/Stage3")
def test_sinsoidalmodel(self):
"""Tests for the PolynomialModel class"""
# create dictionary
params = Parameters()
params.rp = 0.22, 'free', 0.0, 0.4, 'U' # rprs
params.fp = 0.08, 'free', 0.0, 0.1, 'U' # fprs
params.per = 10.721490, 'fixed'
params.t0 = 0.48, 'free', 0, 1, 'U'
params.inc = 89.7, 'free', 80., 90., 'U'
params.a = 18.2, 'free', 15., 20., 'U' # aprs
params.ecc = 0., 'fixed'
params.w = 90., 'fixed' # omega
params.limb_dark = '4-parameter', 'independent'
params.u1 = 0.1, 'free', 0., 1., 'U'
params.u2 = 0.1, 'free', 0., 1., 'U'
params.u3 = 0.1, 'free', 0., 1., 'U'
params.u4 = 0.1, 'free', 0., 1., 'U'
params.AmpSin1 = 0.1, 'free', -0.5, 0.5, 'U'
params.AmpCos1 = 0.3, 'free', 0.0, 0.5, 'U'
params.AmpSin2 = 0.01, 'free', -1, 1, 'U'
params.AmpCos2 = 0.01, 'free', -1, 1, 'U'
params.Rs = 1., 'independent'
# Create the model
meta = MetaClass()
meta.sharedp = False
longparamlist, paramtitles = s5_fit.make_longparamlist(meta, params, 1)
log = logedit.Logedit('./data/test.log')
self.t_model = models.BatmanTransitModel(parameters=params,
name='transit',
fmt='r--',
longparamlist=longparamlist,
nchan=1,
paramtitles=paramtitles)
self.e_model = models.BatmanEclipseModel(parameters=params,
name='transit',
fmt='r--',
log=log,
longparamlist=longparamlist,
nchan=1,
paramtitles=paramtitles)
self.phasecurve = models.SinusoidPhaseCurveModel(
parameters=params,
name='phasecurve',
fmt='r--',
longparamlist=longparamlist,
nchan=1,
paramtitles=paramtitles,
transit_model=self.t_model,
eclipse_model=self.e_model)
# Remove the temporary log file
os.system("rm ./data/test.log")
# Evaluate and test output
self.phasecurve.time = self.time
vals = self.phasecurve.eval()
self.assertEqual(vals.size, self.time.size)
def test_NIRCam(capsys):
with capsys.disabled():
# is able to display any message without failing a test
# useful to leave messages for future users who run the tests
print(
"\n\nIMPORTANT: Make sure that any changes to the ecf files are " +
"included in demo ecf files and documentation (docs/source/ecf.rst)"
)
print("\nNIRCam S3-6 test: ", end='', flush=True)
# explicitly define meta variables to be able to run pathdirectory fn locally
meta = MetaClass()
meta.eventlabel = 'NIRCam'
meta.topdir = '../tests'
ecf_path = './NIRCam_ecfs/'
reload(s3)
reload(s4)
reload(s5)
reload(s6)
s3_meta = s3.reduceJWST(meta.eventlabel, ecf_path=ecf_path)
s4_meta = s4.lcJWST(meta.eventlabel, ecf_path=ecf_path, s3_meta=s3_meta)
s5_meta = s5.fitJWST(meta.eventlabel, ecf_path=ecf_path, s4_meta=s4_meta)
s6_meta = s6.plot_spectra(meta.eventlabel,
ecf_path=ecf_path,
s5_meta=s5_meta)
# run assertions for S3
meta.outputdir_raw = 'data/JWST-Sim/NIRCam/Stage3/'
name = pathdirectory(meta, 'S3', 1, ap=20, bg=20)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S4
meta.outputdir_raw = 'data/JWST-Sim/NIRCam/Stage4/'
name = pathdirectory(meta, 'S4', 1, ap=20, bg=20)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S5
meta.outputdir_raw = 'data/JWST-Sim/NIRCam/Stage5/'
name = pathdirectory(meta, 'S5', 1, ap=20, bg=20)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S6
meta.outputdir_raw = 'data/JWST-Sim/NIRCam/Stage6/'
name = pathdirectory(meta, 'S6', 1, ap=20, bg=20)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# remove temporary files
os.system("rm -r data/JWST-Sim/NIRCam/Stage3")
os.system("rm -r data/JWST-Sim/NIRCam/Stage4")
os.system("rm -r data/JWST-Sim/NIRCam/Stage5")
os.system("rm -r data/JWST-Sim/NIRCam/Stage6")
def test_NIRSpec(capsys):
s2_installed = 'eureka.S2_calibrations.s2_calibrate' in sys.modules
if not s2_installed:
with capsys.disabled():
print(
"\n\nIMPORTANT: Make sure that any changes to the ecf files are "
+
"included in demo ecf files and documentation (docs/source/ecf.rst)"
)
print(
'\nSkipping NIRSpec Stage 2 tests as could not import eureka.S2_calibrations.s2_calibrate'
)
print("\nNIRSpec S3-5 test: ", end='', flush=True)
else:
with capsys.disabled():
# is able to display any message without failing a test
# useful to leave messages for future users who run the tests
print(
"\n\nIMPORTANT: Make sure that any changes to the ecf files are "
+
"included in demo ecf files and documentation (docs/source/ecf.rst)"
)
print("\nNIRSpec S2-5 test: ", end='', flush=True)
# explicitly define meta variables to be able to run pathdirectory fn locally
meta = MetaClass()
meta.eventlabel = 'NIRSpec'
meta.topdir = '../tests'
ecf_path = './NIRSpec_ecfs/'
if s2_installed:
# Only run S2 stuff if jwst package has been installed
reload(s2)
reload(s3)
reload(s4)
reload(s5)
if s2_installed:
# Only run S2 stuff if jwst package has been installed
s2_meta = s2.calibrateJWST(meta.eventlabel, ecf_path=ecf_path)
s3_meta = s3.reduceJWST(meta.eventlabel, ecf_path=ecf_path)
s4_meta = s4.lcJWST(meta.eventlabel, ecf_path=ecf_path, s3_meta=s3_meta)
s5_meta = s5.fitJWST(meta.eventlabel, ecf_path=ecf_path, s4_meta=s4_meta)
# run assertions for S2
if s2_installed:
# Only run S2 stuff if jwst package has been installed
meta.outputdir_raw = '/data/JWST-Sim/NIRSpec/Stage2/'
name = pathdirectory(meta, 'S2', 1)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S3
meta.outputdir_raw = '/data/JWST-Sim/NIRSpec/Stage3/'
name = pathdirectory(meta, 'S3', 1, ap=8, bg=10)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S4
meta.outputdir_raw = 'data/JWST-Sim/NIRSpec/Stage4/'
name = pathdirectory(meta, 'S4', 1, ap=8, bg=10)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# run assertions for S5
meta.outputdir_raw = 'data/JWST-Sim/NIRSpec/Stage5/'
name = pathdirectory(meta, 'S5', 1, ap=8, bg=10)
assert os.path.exists(name)
assert os.path.exists(name + '/figs')
# remove temp files
if s2_installed:
# Only run S2 stuff if jwst package has been installed
os.system("rm -r data/JWST-Sim/NIRSpec/Stage2/S2_*")
pass
os.system("rm -r data/JWST-Sim/NIRSpec/Stage3")
os.system("rm -r data/JWST-Sim/NIRSpec/Stage4")
os.system("rm -r data/JWST-Sim/NIRSpec/Stage5")
"""
import unittest
import numpy as np
import os
import sys
sys.path.insert(0, '../')
from eureka.S5_lightcurve_fitting import lightcurve, models, simulations
from eureka.lib.readEPF import Parameters, Parameter
from eureka.lib.readECF import MetaClass
from eureka.lib import logedit
from eureka.S5_lightcurve_fitting import s5_fit
meta = MetaClass()
meta.eventlabel = 'NIRCam'
'''
NOTE: Currently does not run. Since only a single function of Stage 5 is
being run here and not the whole process, the metadata from S5_NIRCam.ecf
and S5_fit_par.ecf is not read into the function. The metadata will have to be
parsed explicitly here for the test to run correctly. (or the test will need to
be restructured)
class TestLightcurve(unittest.TestCase):
"""Tests for the lightcurve.py module"""
def setUp(self):
"""Setup for the lightcurve"""
self.time = np.linspace(0, 1, 100)
self.unc = np.random.uniform(low=1E-4, high=0.01, size=100)
self.flux = np.random.normal(np.ones_like(self.time), scale=self.unc)