class SmokeTest(unittest.TestCase):
"""
Smoke test test case.
Historically, CIAO software has been accompanied by "smoke tests", tests that are shipped with the
main code distribution and that can be run to assess whether the software was properly installed.
The Smoke Test is not a full tests suite, but simply tries to detect obvious failures that signal an
improper setup.
This class implements the Smoke Test as a standalone unittest test case. This means that there are no
external dependencies required for the Smoke Test to run, and the only data files it may use are shipped
with the main distribution as well.
It is also run as part fo the full Sherpa tests suite.
Some methods require external dependencies. If such dependencies are not found the tests are skipped.
There is more logic (see the run method in this module) that checks the requirements are actually installed
and fails the Smoke Test if they are not.
"""
def setUp(self):
self._old_level = logger.getEffectiveLevel()
logger.setLevel(logging.ERROR)
from sherpa.astro import datastack
folder = os.path.dirname(datastack.__file__)
self.fits = os.path.join(folder, "tests", "data",
"acisf07867_000N001_r0002_pha3.fits")
self.x = [1, 2, 3]
self.y = [1, 2, 3]
def tearDown(self):
if hasattr(self, "old_level"):
logger.setLevel(self._old_level)
def test_fit(self):
"""
Perform a very simple fit with built-in models, and check that the results make sense.
"""
ui.load_arrays(1, self.x, self.y)
ui.set_source("polynom1d.p")
ui.thaw("p.c1")
ui.set_method("levmar")
ui.fit()
model = ui.get_model_component("p")
expected = [0, 1]
observed = [model.c0.val, model.c1.val]
assert_almost_equal(observed, expected)
# Using skipIf directly as we need these tests to run when there is no pytest installed, so we can't use
# the decorators in sherpa.utils.testing
@unittest.skipIf(not has_package_from_list('astropy.io.fits', 'pycrates'),
reason="Requires fits backend")
def test_fits_io(self):
"""
Test that basic FITS I/O functions work.
This test ensures that the FITS backend can be used to perform basic
I/O functions.
"""
ui.load_pha(self.fits)
with NamedTemporaryFile() as f:
ui.save_pha(f.name, ascii=False, clobber=True)
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
reason="Requires xspec")
def test_xspec(self):
"""
Perform a very simple fit with an xspec model.
Also check that the results make sense.
This test proves that the xspec extension properly works, and that there are no obvious building, linking, or
environment issues that would prevent the xspec model from running.
"""
ui.load_arrays(1, self.x, self.y)
ui.set_source("xspowerlaw.p")
ui.set_method("moncar")
ui.set_stat("chi2xspecvar")
ui.fit()
model = ui.get_model_component("p")
expected = [-1.3686404, 0.5687635]
observed = [model.PhoIndex.val, model.norm.val]
assert_almost_equal(observed, expected)
def test_failure(self):
"""
This is a debug test that always fails.
It may be used to check that error conditions upstream are correctly
handled by scripts calling the Smoke Test. Whether or not this test is run depends on the option passed to the
run function in this module.
"""
self.fail("Requested to fail")
def mycal_staterror(data):
return numpy.ones_like(data)
@staticmethod
def chi_nobkg(data, model, staterror=None, syserror=None, weight=None):
fvec = ((data - model) / staterror)**2
stat = fvec.sum()
return (stat, fvec)
calc_stat = chi_nobkg
calc_staterror = mycal_staterror
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
class test_stats(SherpaTestCase):
_fit_mycash_results_bench = {
'succeeded': 1,
'numpoints': 446,
'dof': 443,
'istatval': 796.401435754,
'statval': -14889.3202844,
'parnames': ('abs1.nH', 'abs1.gamma', 'abs1.ampl'),
'parvals': numpy.array(
[5886.0660236942495, 1.6556198746259132, 30098.968589487202])
}
class test_image(SherpaTestCase):
if (os.environ.has_key("DISPLAY") == True):
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_ds9(self):
im = sherpa.image.ds9_backend.DS9.DS9Win(
sherpa.image.ds9_backend.DS9._DefTemplate, False)
im.doOpen()
im.showArray(data.y)
data_out = get_arr_from_imager(im)
im.xpaset("quit")
self.assertEqualWithinTol((data.y - data_out).sum(), 0.0, 1e-4)
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_image(self):
im = Image()
im.image(data.y)
data_out = get_arr_from_imager(im)
im.xpaset("quit")
self.assertEqualWithinTol((data.y - data_out).sum(), 0.0, 1e-4)
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_data_image(self):
im = DataImage()
im.prepare_image(data)
im.image()
data_out = get_arr_from_imager(im)
im.xpaset("quit")
self.assertEqualWithinTol((data.y - data_out).sum(), 0.0, 1e-4)
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_model_image(self):
im = ModelImage()
im.prepare_image(data, 1)
im.image()
data_out = get_arr_from_imager(im)
im.xpaset("quit")
self.assertEqualWithinTol((data.y - data_out).sum(), 0.0, 1e-4)
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_ratio_image(self):
im = RatioImage()
im.prepare_image(data, 1)
im.image()
data_out = get_arr_from_imager(im)
im.xpaset("quit")
# The sum is 99, because the first model pixel
# will be zero, and therefore the ratio function
# reassigns the ratio there to be one.
self.assertEqualWithinTol(data_out.sum(), 99.0, 1e-4)
@unittest.skipIf(
not has_package_from_list('sherpa.image.ds9_backend'),
"required package sherpa.image.ds9_backend not available")
def test_resid_image(self):
im = ResidImage()
im.prepare_image(data, 1)
im.image()
data_out = get_arr_from_imager(im)
im.xpaset("quit")
self.assertEqualWithinTol(data_out.sum(), 0.0, 1e-4)
else:
pass
from sherpa.utils import has_package_from_list, has_fits_support
import logging
error = logging.getLogger(__name__).error
def is_proper_subclass(obj, cls):
if type(cls) is not tuple:
cls = (cls, )
if obj in cls:
return False
return issubclass(obj, cls)
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
class test_xspec(SherpaTestCase):
def test_create_model_instances(self):
import sherpa.astro.xspec as xs
count = 0
for cls in dir(xs):
if not cls.startswith('XS'):
continue
cls = getattr(xs, cls)
if is_proper_subclass(
cls, (xs.XSAdditiveModel, xs.XSMultiplicativeModel)):
m = cls()
class test_threads(SherpaTestCase):
def setUp(self):
self.is_crates_io = False
try:
import sherpa.astro.io
if ("sherpa.astro.io.crates_backend" ==
sherpa.astro.io.backend.__name__):
self.is_crates_io = True
except:
self.is_crates_io = False
self.startdir = os.getcwd()
self.old_state = ui._session.__dict__.copy()
self.old_level = logger.getEffectiveLevel()
logger.setLevel(logging.CRITICAL)
def tearDown(self):
os.chdir(self.startdir)
ui._session.__dict__.update(self.old_state)
logger.setLevel(self.old_level)
def assign_model(self, name, obj):
self.locals[name] = obj
def run_thread(self, name, scriptname='fit.py'):
ui.clean()
ui.set_model_autoassign_func(self.assign_model)
self.locals = {}
os.chdir(os.path.join(self.datadir, 'ciao4.3', name))
execfile(scriptname, {}, self.locals)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_pha_intro(self):
self.run_thread('pha_intro')
# astro.ui imported as ui, instead of
# being in global namespace
self.assertEqualWithinTol(ui.get_fit_results().statval, 37.9079, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 0.902569, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 0.651155, 1e-4)
self.assertEqualWithinTol(self.locals['p1'].gamma.val, 2.15852, 1e-4)
self.assertEqualWithinTol(self.locals['p1'].ampl.val, 0.00022484, 1e-4)
self.assertEqualWithinTol(ui.calc_photon_flux(), 0.000469964, 1e-4)
self.assertEqualWithinTol(ui.calc_energy_flux(), 9.614847e-13, 1e-4)
self.assertEqualWithinTol(ui.calc_data_sum(), 706.85714092, 1e-4)
self.assertEqualWithinTol(ui.calc_model_sum(), 638.45693377, 1e-4)
self.assertEqualWithinTol(ui.calc_source_sum(), 0.046996409, 1e-4)
self.assertEqualWithinTol(
ui.eqwidth(self.locals['p1'], ui.get_source()), -0.57731725, 1e-4)
self.assertEqualWithinTol(
ui.calc_kcorr([1, 1.2, 1.4, 1.6, 1.8, 2], 0.5, 2), [
0.93341286, 0.93752836, 0.94325233, 0.94990140, 0.95678054,
0.96393515
], 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 22)
self.assertEqual(ui.get_fit_results().numpoints, 44)
self.assertEqual(ui.get_fit_results().dof, 42)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_pha_read(self):
self.run_thread('pha_read')
self.assertEqual(type(ui.get_data()), DataPHA)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_basic(self):
# In data1.dat for this test, there is a comment with one
# word at the beginning -- deliberately would break when reading
# with DM ASCII kernel, but passes because we have Sherpa code
# to bypass that.
self.run_thread('basic')
self.assertEqualWithinTol(ui.get_fit_results().statval, 151.827, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 16.8697, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 3.68798e-28, 1e-4)
self.assertEqualWithinTol(self.locals['m1'].c0.val, 1.49843, 1e-4)
self.assertEqualWithinTol(self.locals['m1'].c1.val, 0.1447, 1e-4)
self.assertEqualWithinTol(self.locals['m1'].c2.val, 0.0322936, 1e-4)
self.assertEqualWithinTol(self.locals['m1'].c3.val, -0.00277729, 1e-4)
self.assertEqualWithinTol(self.locals['m2'].c0.val, 1.75548, 1e-4)
self.assertEqualWithinTol(self.locals['m2'].c1.val, 0.198455, 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 9)
self.assertEqual(ui.get_fit_results().numpoints, 11)
self.assertEqual(ui.get_fit_results().dof, 9)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_simultaneous(self):
self.run_thread('simultaneous')
self.assertEqualWithinTol(ui.get_fit_results().statval, 7.4429, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 0.531636, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 0.916288, 1e-4)
self.assertEqualWithinTol(self.locals['abs1'].nh.val, 0.898162, 1e-2)
self.assertEqualWithinTol(self.locals['pl1'].gamma.val, 1.645, 1e-4)
self.assertEqualWithinTol(self.locals['pl1'].ampl.val, 2.28323e-05,
1e-3)
self.assertEqualWithinTol(self.locals['pl2'].ampl.val, 2.44585e-05,
1e-3)
self.assertEqual(ui.get_fit_results().numpoints, 18)
self.assertEqual(ui.get_fit_results().dof, 14)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_sourceandbg(self):
self.run_thread('sourceandbg')
self.assertEqualWithinTol(ui.get_fit_results().statval, 947.5, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 0.715094, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 1, 1e-4)
self.assertEqualWithinTol(self.locals['a1'].nh.val, 0.0342266, 1e-2)
self.assertEqualWithinTol(self.locals['b1'].kt.val, 20, 1e-2)
self.assertEqualWithinTol(self.locals['b1'].norm.val, 0.00953809, 1e-2)
self.assertEqualWithinTol(self.locals['b2'].kt.val, 0.563109, 1e-2)
self.assertEqualWithinTol(self.locals['b2'].norm.val, 1.16118e-05,
1e-2)
self.assertEqual(ui.get_fit_results().numpoints, 1330)
self.assertEqual(ui.get_fit_results().dof, 1325)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_spatial(self):
self.run_thread('spatial')
self.assertEqualWithinTol(ui.get_fit_results().statval, -59229.749441,
1e-4)
self.assertEqualWithinTol(self.locals['g1'].fwhm.val, 61.5615, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].xpos.val, 4070.45, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].ypos.val, 4251.35, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].ampl.val, 22.1269, 1e-4)
self.assertEqualWithinTol(self.locals['g2'].fwhm.val, 6.20409, 1e-4)
self.assertEqualWithinTol(self.locals['g2'].xpos.val, 4070.78, 1e-4)
self.assertEqualWithinTol(self.locals['g2'].ypos.val, 4249.33, 1e-4)
self.assertEqualWithinTol(self.locals['g2'].ampl.val, 226.563, 1e-4)
#self.assertEqual(ui.get_fit_results().nfev,371)
self.assertEqual(ui.get_fit_results().numpoints, 4881)
self.assertEqual(ui.get_fit_results().dof, 4877)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_pileup(self):
self.run_thread('pileup')
self.assertEqualWithinTol(ui.get_fit_results().statval, 53.6112, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 1.44895, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 0.0379417, 1e-4)
self.assertEqualWithinTol(self.locals['jdp'].alpha.val, 0.522593, 1e-1)
self.assertEqualWithinTol(self.locals['jdp'].f.val, 0.913458, 1e-2)
self.assertEqualWithinTol(self.locals['abs1'].nh.val, 6.12101, 1e-2)
self.assertEqualWithinTol(self.locals['power'].gamma.val, 1.41887,
1e-2)
self.assertEqualWithinTol(self.locals['power'].ampl.val, 0.00199457,
1e-2)
self.assertEqual(ui.get_fit_results().numpoints, 42)
self.assertEqual(ui.get_fit_results().dof, 37)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_radpro(self):
self.run_thread('radpro')
self.assertEqualWithinTol(ui.get_fit_results().statval, 217.450, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 6.21287, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 0.0, 1e-4)
self.assertEqualWithinTol(self.locals['src'].r0.val, 125.829, 1e-4)
self.assertEqualWithinTol(self.locals['src'].beta.val, 4.1633, 1e-4)
self.assertEqualWithinTol(self.locals['src'].xpos.val, 0.0, 1e-4)
self.assertEqualWithinTol(self.locals['src'].ampl.val, 4.42821, 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 92)
self.assertEqual(ui.get_fit_results().numpoints, 38)
self.assertEqual(ui.get_fit_results().dof, 35)
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_radpro_dm(self):
# This test is completely redundant to test_radpro above.
# The only difference is that here I test if using DM syntax
# in the file name returns the correct arrays from CRATES.
# Since any other I/O backend would not understand DM syntax,
# I make this test a no-op unless CRATES is used as the I/O
# backend. SMD 05/23/13
if (True == self.is_crates_io):
self.run_thread('radpro_dm')
self.assertEqualWithinTol(ui.get_fit_results().statval, 217.450,
1e-4)
self.assertEqualWithinTol(ui.get_fit_results().rstat, 6.21287,
1e-4)
self.assertEqualWithinTol(ui.get_fit_results().qval, 0.0, 1e-4)
self.assertEqualWithinTol(self.locals['src'].r0.val, 125.829, 1e-4)
self.assertEqualWithinTol(self.locals['src'].beta.val, 4.1633,
1e-4)
self.assertEqualWithinTol(self.locals['src'].xpos.val, 0.0, 1e-4)
self.assertEqualWithinTol(self.locals['src'].ampl.val, 4.42821,
1e-4)
self.assertEqual(ui.get_fit_results().nfev, 92)
self.assertEqual(ui.get_fit_results().numpoints, 38)
self.assertEqual(ui.get_fit_results().dof, 35)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_psf2d(self):
self.run_thread('psf')
self.assertEqualWithinTol(ui.get_fit_results().statval, 4066.78, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].fwhm.val, 2.80117, 1e-2)
self.assertEqualWithinTol(self.locals['g1'].ypos.val, 77.2271, 1e-2)
self.assertEqualWithinTol(self.locals['g1'].xpos.val, 88.661, 1e-2)
self.assertEqualWithinTol(self.locals['g1'].ampl.val, 166.649, 1e-2)
#self.assertEqual(ui.get_fit_results().nfev,342)
self.assertEqual(ui.get_fit_results().numpoints, 4899)
self.assertEqual(ui.get_fit_results().dof, 4895)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_fpsf2d(self):
self.run_thread('fpsf')
self.assertEqualWithinTol(ui.get_fit_results().statval, -4053.6635,
1e-4)
# self.assertEqualWithinTol(self.locals['b1'].xlow.val, -4.70832, 1e-4)
# self.assertEqualWithinTol(self.locals['b1'].xhi.val, 164.687, 1e-4)
# self.assertEqualWithinTol(self.locals['b1'].ylow.val, 0.83626, 1e-4)
# self.assertEqualWithinTol(self.locals['b1'].yhi.val, 142.603, 1e-4)
# self.assertEqualWithinTol(self.locals['b1'].ampl.val, 0.956766, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].fwhm.val, 6.420237, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].xpos.val, 88.940712, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].ypos.val, 76.577265, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].ampl.val, 36344.48324,
1e-4)
#self.assertEqual(ui.get_fit_results().nfev,978)
self.assertEqual(ui.get_fit_results().numpoints, 4899)
self.assertEqual(ui.get_fit_results().dof, 4895)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_radpro_psf(self):
self.run_thread('radpro_psf')
self.assertEqualWithinTol(ui.get_fit_results().statval, 200.949, 1e-4)
self.assertEqualWithinTol(self.locals['src'].r0.val, 83.0997, 1e-4)
self.assertEqualWithinTol(self.locals['src'].beta.val, 2.97737, 1e-4)
self.assertEqualWithinTol(self.locals['src'].ampl.val, 5.27604, 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 48)
self.assertEqual(ui.get_fit_results().numpoints, 38)
self.assertEqual(ui.get_fit_results().dof, 35)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_linepro(self):
self.run_thread('linepro')
self.assertEqualWithinTol(ui.get_fit_results().statval, 203.34, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].r0.val, 4.25557, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].beta.val, 0.492232, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].ampl.val, 11.8129, 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 17)
self.assertEqual(ui.get_fit_results().numpoints, 75)
self.assertEqual(ui.get_fit_results().dof, 72)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_kernel(self):
self.run_thread('kernel')
self.assertEqualWithinTol(ui.get_fit_results().statval, 98.5793, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].r0.val, 19.2278, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].beta.val, 0.555464, 1e-4)
self.assertEqualWithinTol(self.locals['b1'].ampl.val, 1.93706, 1e-4)
self.assertEqual(ui.get_fit_results().nfev, 21)
self.assertEqual(ui.get_fit_results().numpoints, 75)
self.assertEqual(ui.get_fit_results().dof, 72)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_spectrum(self):
self.run_thread('spectrum')
self.assertEqualWithinTol(ui.get_fit_results().statval, 0.0496819,
1e-4)
self.assertEqualWithinTol(self.locals['abs2'].nh.val, 1.1015, 1e-4)
self.assertEqualWithinTol(self.locals['mek1'].kt.val, 0.841025, 1e-4)
self.assertEqualWithinTol(self.locals['mek1'].norm.val, 0.699761, 1e-4)
self.assertEqualWithinTol(self.locals['mek2'].kt.val, 2.35845, 1e-4)
self.assertEqualWithinTol(self.locals['mek2'].norm.val, 1.03724, 1e-4)
self.assertEqual(ui.get_fit_results().numpoints, 446)
self.assertEqual(ui.get_fit_results().dof, 441)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_histo(self):
self.run_thread('histo')
self.assertEqualWithinTol(ui.get_fit_results().statval, 14.7264, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].fwhm.val, 0.0232473, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].pos.val, 1.26713, 1e-4)
self.assertEqualWithinTol(self.locals['g1'].ampl.val, 40.4503, 1e-4)
#self.assertEqual(ui.get_fit_results().nfev,19)
self.assertEqual(ui.get_fit_results().numpoints, 50)
self.assertEqual(ui.get_fit_results().dof, 47)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_xmm(self):
self.run_thread('xmm')
self.assertEqualWithinTol(ui.get_fit_results().statval, 118.085, 1e-4)
self.assertEqualWithinTol(self.locals['intrin'].nh.val, 11.0769, 1e-2)
self.assertEqualWithinTol(self.locals['phard'].phoindex.val, 1.49055,
1e-2)
self.assertEqualWithinTol(self.locals['phard'].norm.val, 0.00140301,
1e-2)
self.assertEqual(ui.get_fit_results().nfev, 95)
self.assertEqual(ui.get_fit_results().numpoints, 162)
self.assertEqual(ui.get_fit_results().dof, 159)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
# As of CIAO 4.5, can filter on channel number, even when
# data are grouped! Test results should exactly match CIAO 4.4
# fit results in grouped/fit.py
def test_grouped_ciao4_5(self):
self.run_thread('grouped_ciao4.5')
self.assertEqualWithinTol(ui.get_fit_results().statval, 18.8316, 1e-4)
self.assertEqual(ui.get_fit_results().numpoints, 46)
self.assertEqualWithinTol(self.locals['aa'].gamma.val, 1.83906, 1e-4)
self.assertEqualWithinTol(self.locals['aa'].ampl.val, 0.000301258,
1e-4)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_proj(self):
self.run_thread('proj')
# Fit 1
self.assertEqualWithinTol(self.locals['fit_res1'].statval, 64.3803,
1e-2)
self.assertEqualWithinTol(self.locals['g'].fwhm.val, 32.3536, 1e-2)
self.assertEqualWithinTol(self.locals['g'].pos.val, 807.863, 1e-2)
self.assertEqualWithinTol(self.locals['g'].ampl.val, 117.826, 1e-2)
# Covar 1
self.assertEqualWithinTol(self.locals['covar_res1'].parmins[0],
-0.49357, 1e-2)
self.assertEqualWithinTol(self.locals['covar_res1'].parmins[1],
-0.264056, 1e-2)
self.assertEqualWithinTol(self.locals['covar_res1'].parmins[2],
-2.58857, 1e-2)
self.assertEqualWithinTol(self.locals['covar_res1'].parmaxes[0],
0.49357, 1e-2)
self.assertEqualWithinTol(self.locals['covar_res1'].parmaxes[1],
0.264056, 1e-2)
self.assertEqualWithinTol(self.locals['covar_res1'].parmaxes[2],
2.58857, 1e-2)
# Projection 1
self.assertEqualWithinTol(self.locals['proj_res1'].parmins[0],
-0.492815, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res1'].parmins[1],
-0.263945, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res1'].parmins[2],
-2.57957, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res1'].parmaxes[0],
0.49421, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res1'].parmaxes[1],
0.26389, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res1'].parmaxes[2],
2.59695, 1e-2)
# Fit 2
self.assertEqualWithinTol(self.locals['fit_res2'].statval, 108.048,
1e-2)
self.assertEqualWithinTol(self.locals['xs1'].nh.val, 0.0532586, 1e-2)
self.assertEqualWithinTol(self.locals['p'].gamma.val, 1.4816, 1e-2)
self.assertEqualWithinTol(self.locals['p'].ampl.val, 0.302343, 1e-2)
# Covar 2
self.assertEqualWithinTol(self.locals['covar_res2'].parmins[0],
-0.0379975, 5e-1)
self.assertEqualWithinTol(self.locals['covar_res2'].parmins[1],
-0.0877478, 5e-1)
self.assertEqualWithinTol(self.locals['covar_res2'].parmins[2],
-0.0831945, 5e-1)
self.assertEqualWithinTol(self.locals['covar_res2'].parmaxes[0],
0.0379975, 5e-1)
self.assertEqualWithinTol(self.locals['covar_res2'].parmaxes[1],
0.0877478, 5e-1)
self.assertEqualWithinTol(self.locals['covar_res2'].parmaxes[2],
0.0831945, 5e-1)
# Projection 2
self.assertEqualWithinTol(self.locals['proj_res2'].parmins[0],
-0.0385636, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res2'].parmins[1],
-0.0891261, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res2'].parmins[2],
-0.0737413, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res2'].parmaxes[0],
0.0388651, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res2'].parmaxes[1],
0.0896566, 1e-2)
self.assertEqualWithinTol(self.locals['proj_res2'].parmaxes[2],
0.0981627, 1e-2)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_proj_bubble(self):
self.run_thread('proj_bubble')
# Fit -- Results from reminimize
self.assertEqualWithinTol(self.locals['mek1'].kt.val, 17.8849, 1e-2)
self.assertEqualWithinTol(self.locals['mek1'].norm.val, 4.15418e-06,
1e-2)
# Covar
self.assertEqualWithinTol(ui.get_covar_results().parmins[0], -0.328832,
1e-2)
self.assertEqualWithinTol(ui.get_covar_results().parmins[1],
-8.847916e-07, 1e-2)
self.assertEqualWithinTol(ui.get_covar_results().parmaxes[0], 0.328832,
1e-2)
self.assertEqualWithinTol(ui.get_covar_results().parmaxes[1],
8.847916e-07, 1e-2)
# Proj -- Upper bound of kT can't be found
self.assertEqualWithinTol(ui.get_proj_results().parmins[0], -12.048069,
1e-2)
self.assertEqualWithinTol(ui.get_proj_results().parmins[1],
-9.510913e-07, 1e-2)
self.assertEqual(ui.get_proj_results().parmaxes[0], None)
self.assertEqualWithinTol(ui.get_proj_results().parmaxes[1],
2.403640e-06, 1e-2)
# New tests based on SDS threads -- we should catch these errors
# (if any occur) so SDS doesn't waste time tripping over them.
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_counts(self):
self.run_thread('counts')
self.assertEqualWithinTol(self.locals['counts_data1'], 52701.0, 1e-4)
self.assertEqualWithinTol(self.locals['counts_data2'], 25032.0, 1e-4)
self.assertEqualWithinTol(self.locals['counts_model1'], 73226263.55355,
1e-4)
self.assertEqualWithinTol(self.locals['eflux1'], 1.495482e-08, 1e-4)
self.assertEqualWithinTol(self.locals['counts_model2'], 46082543.21529,
1e-4)
self.assertEqualWithinTol(self.locals['eflux2'], 1.39662954483e-08,
1e-3)
self.assertEqualWithinTol(self.locals['pflux1'], 1.6178938637, 1e-2)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_stats_all(self):
self.run_thread('stats_all')
self.assertEqualWithinTol(self.locals['stat_lsqr'], 213746.236464,
1e-4)
self.assertEqualWithinTol(self.locals['stat_chi2m'], 1232.0330242,
1e-4)
self.assertEqualWithinTol(self.locals['stat_cash'], -1163566.90688,
1e-4)
self.assertEqualWithinTol(self.locals['stat_chi2c'], 1411.60090961,
1e-4)
self.assertEqualWithinTol(self.locals['stat_chi2g'], 972.388468358,
1e-4)
self.assertEqualWithinTol(self.locals['stat_chi2d'], 1204.69363458,
1e-4)
self.assertEqualWithinTol(self.locals['stat_chi2x'], 1204.69363458,
1e-4)
self.assertEqualWithinTol(self.locals['stat_cstat'], 1210.56896183,
1e-4)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_lev3fft(self):
self.run_thread('lev3fft', scriptname='bar.py')
self.assertEqualWithinTol(self.locals['src'].fwhm.val, 0.04418584,
1e-4)
self.assertEqualWithinTol(self.locals['src'].xpos.val, 150.016, 1e-4)
self.assertEqualWithinTol(self.locals['src'].ypos.val, 2.66493839,
1e-4)
self.assertEqualWithinTol(self.locals['src'].ampl.val, 1.56090546,
1e-4)
self.assertEqualWithinTol(self.locals['bkg'].c0.val, -1.513700715,
1e-4)
self.assertEqualWithinTol(ui.get_fit_results().istatval, 19496.3, 1e-4)
self.assertEqualWithinTol(ui.get_fit_results().statval, 592.32647,
1e-4)
self.assertEqual(ui.get_fit_results().numpoints, 3307)
self.assertEqual(ui.get_fit_results().dof, 3302)
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_setfullmodel(self):
self.run_thread('setfullmodel')
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_bug13537(self):
self.run_thread('bug13537')
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_xmm2(self):
self.run_thread('xmm2')
self.assertEqualWithinTol(ui.get_data().channel[0], 1.0, 1e-4)
self.assertEqual(ui.get_rmf().detchans, 800)
self.assertEqual(len(ui.get_rmf().energ_lo), 2400)
self.assertEqual(len(ui.get_rmf().energ_hi), 2400)
self.assertEqual(len(ui.get_rmf().n_grp), 2400)
self.assertEqual(len(ui.get_rmf().f_chan), 2394)
self.assertEqual(len(ui.get_rmf().n_chan), 2394)
self.assertEqual(len(ui.get_rmf().matrix), 1281216)
self.assertEqual(ui.get_rmf().offset, 0)
self.assertEqual(len(ui.get_rmf().e_min), 800)
self.assertEqual(len(ui.get_rmf().e_max), 800)
self.assertEqual(len(ui.get_arf().energ_lo), 2400)
self.assertEqual(len(ui.get_arf().energ_hi), 2400)
self.assertEqual(len(ui.get_arf().specresp), 2400)
class test_sim(SherpaTestCase):
@unittest.skipIf(not has_fits_support(),
'need pycrates, pyfits or astropy.io.fits')
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
def setUp(self):
try:
from sherpa.astro.io import read_pha
from sherpa.astro.xspec import XSwabs, XSpowerlaw
except:
return
# self.startdir = os.getcwd()
self.old_level = logger.getEffectiveLevel()
logger.setLevel(logging.CRITICAL)
pha = self.make_path("refake_0934_1_21_1e4.fak")
# rmf = self.make_path("ccdid7_default.rmf")
# arf = self.make_path("quiet_0934.arf")
self.simarf = self.make_path("aref_sample.fits")
self.pcaarf = self.make_path("aref_Cedge.fits")
data = read_pha(pha)
data.ignore(None, 0.3)
data.ignore(7.0, None)
rsp = Response1D(data)
self.abs1 = XSwabs('abs1')
self.p1 = XSpowerlaw('p1')
model = rsp(self.abs1 * self.p1)
self.fit = Fit(data, model, CStat(), NelderMead(), Covariance())
def tearDown(self):
# os.chdir(self.startdir)
if hasattr(self, 'old_level'):
logger.setLevel(self.old_level)
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_pragbayes_simarf(self):
mcmc = sim.MCMC()
self.abs1.nh = 0.092886
self.p1.phoindex = 0.994544
self.p1.norm = 9.26369
mcmc.set_sampler("PragBayes")
mcmc.set_sampler_opt("simarf", self.simarf)
mcmc.set_sampler_opt("p_M", 0.5)
mcmc.set_sampler_opt("nsubiter", 7)
covar_results = self.fit.est_errors()
cov = covar_results.extra_output
niter = 10
stats, accept, params = mcmc.get_draws(self.fit, cov, niter=niter)
# try:
# assert (covar_results.parmaxes < params.std(1)).all()
# except AssertionError:
# print 'covar: ', str(covar_results.parmaxes)
# print 'param: ', str(params.std(1))
# raise
@unittest.skipIf(not has_package_from_list('sherpa.astro.xspec'),
"required sherpa.astro.xspec module missing")
@unittest.skipIf(test_data_missing(), "required test data missing")
def test_pragbayes_pcaarf(self):
mcmc = sim.MCMC()
self.abs1.nh = 0.092886
self.p1.phoindex = 0.994544
self.p1.norm = 9.26369
mcmc.set_sampler("pragBayes")
mcmc.set_sampler_opt("simarf", self.pcaarf)
mcmc.set_sampler_opt("p_M", 0.5)
mcmc.set_sampler_opt("nsubiter", 5)
covar_results = self.fit.est_errors()
cov = covar_results.extra_output
niter = 10
stats, accept, params = mcmc.get_draws(self.fit, cov, niter=niter)
