def test_arf_get_x_unit(): session = Session() arf_x_lo, arf_x_hi = np.array([12.0, 12.1, 12.2]), np.array([12.1, 12.2, 12.3]) arf = session.create_arf(arf_x_lo, arf_x_hi) expected_arf_x = (arf_x_hi + arf_x_lo)/2 actual_arf_x = arf.get_x() np.testing.assert_array_almost_equal(expected_arf_x, actual_arf_x)
def test_source_component_arbitrary_grid_int(): from sherpa.astro.ui.utils import Session from sherpa.models import Const1D from sherpa.data import Data1DInt ui = Session() x = numpy.array([1, 2, 3]), numpy.array([2, 3, 4]) y = [1.5, 2.5, 3.5] re_x = numpy.array([10, 20, 30]), numpy.array([20, 30, 40]) ui.load_arrays(1, x[0], x[1], y, Data1DInt) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(*re_x) with pytest.warns(UserWarning): ui.plot_source_component(regrid_model) x_points = (x[0] + x[1])/2 re_x_points = (re_x[0] + re_x[1])/2 points = numpy.concatenate((x_points, re_x_points)) numpy.testing.assert_array_equal(ui._compsrcplot.x, points) numpy.testing.assert_array_equal(ui._compsrcplot.y, [10, 10, 10, 100, 100, 100])
def test_rmf_get_x_unit(): session = Session() rmf_x_lo, rmf_x_hi = np.array([21.0, 21.1, 21.2]), np.array([21.1, 21.2, 21.3]) rmf = session.create_rmf(rmf_x_lo, rmf_x_hi) expected_rmf_x = (rmf_x_hi + rmf_x_lo)/2 actual_rmf_x = rmf.get_x() np.testing.assert_array_almost_equal(expected_rmf_x, actual_rmf_x)
def test_rmf_get_x_unit(): session = Session() rmf_x_lo, rmf_x_hi = np.array([21.0, 21.1, 21.2]), np.array([21.1, 21.2, 21.3]) rmf = session.create_rmf(rmf_x_lo, rmf_x_hi) expected_rmf_x = (rmf_x_hi + rmf_x_lo) / 2 actual_rmf_x = rmf.get_x() np.testing.assert_array_almost_equal(expected_rmf_x, actual_rmf_x)
def test_arf_get_x_unit(): session = Session() arf_x_lo, arf_x_hi = np.array([12.0, 12.1, 12.2]), np.array([12.1, 12.2, 12.3]) arf = session.create_arf(arf_x_lo, arf_x_hi) expected_arf_x = (arf_x_hi + arf_x_lo) / 2 actual_arf_x = arf.get_x() np.testing.assert_array_almost_equal(expected_arf_x, actual_arf_x)
def test_bug_275(make_data_path): session = Session() session.load_data(make_data_path('3c273.pi')) str(session.get_data()) str(session.get_rmf()) str(session.get_arf()) session.load_data(make_data_path('img.fits')) str(session.get_data())
def test_load_table_model(make_data_path): """What does load_table_model do? Even though this is not a FITS file, the code appears to need the I/O module to work. """ s = Session() s.load_table_model('tbl', make_data_path('double.dat')) tbl = s.get_model_component('tbl') assert tbl.ndim is None
def test_create_rmf(make_data_path): from sherpa.astro.ui.utils import Session ui = Session() energ = np.arange(0.05, 1.1, 0.05) rmflo = energ[:-1] rmfhi = energ[1:] fname= make_data_path('test_rmfimg.fits') datarmf = ui.create_rmf(rmflo, rmfhi, fname=fname) assert len(datarmf._fch) == 1039 assert len(datarmf._nch) == 1039 assert len(datarmf.n_grp) == 900 assert datarmf._rsp.shape[0] == 380384
def test_create_rmf(make_data_path): from sherpa.astro.ui.utils import Session ui = Session() energ = np.arange(0.05, 1.1, 0.05) rmflo = energ[:-1] rmfhi = energ[1:] fname = make_data_path('test_rmfimg.fits') datarmf = ui.create_rmf(rmflo, rmfhi, fname=fname) assert len(datarmf._fch) == 1039 assert len(datarmf._nch) == 1039 assert len(datarmf.n_grp) == 900 assert datarmf._rsp.shape[0] == 380384
def test_list_ids(): session = Session() session.load_arrays(1, TEST, TEST) session.load_arrays("1", TEST, TEST2) # order of 1 and "1" is not determined assert {1, "1"} == set(session.list_data_ids()) assert_array_equal(TEST2, session.get_data('1').get_dep()) assert_array_equal(TEST, session.get_data(1).get_dep())
def test_load_arrays_no_errors(data_no_errors): from sherpa.astro.ui.utils import Session session = Session() data = data_no_errors data_class = data.__class__ data_args = DATA_NO_ERRORS_ARGS args = data_args + (data_class, ) session.load_arrays(*args) new_data = session.get_data(data.name) assert new_data is not data # DATA-NOTE: Do we need an equality operator for data classes? These tests are very partial # Note that when they are created with load_arrays they seem to lose the name, which becomes the ID numpy.testing.assert_array_equal(new_data.get_indep(), data.get_indep()) numpy.testing.assert_array_equal(new_data.get_dep(), data.get_dep())
def test_arf_rmf_get_x(make_data_path): arf_name = make_data_path('3c120_heg_-1.arf') rmf_name = make_data_path('3c120_heg_-1.rmf') session = Session() arf = session.unpack_arf(arf_name) rmf = session.unpack_rmf(rmf_name) expected_array_10 = [0.57724115, 0.57730836, 0.57737556, 0.5774428, 0.57751006, 0.57757729, 0.57764456, 0.57771185, 0.57777914, 0.57784647] actual_arf_10 = arf.get_x()[0:10] actual_rmf_10 = rmf.get_x()[0:10] np.testing.assert_array_almost_equal(expected_array_10, actual_arf_10) np.testing.assert_array_almost_equal(expected_array_10, actual_rmf_10)
def test_zero_division_calc_stat(): ui = AstroSession() x = numpy.arange(100) y = numpy.zeros(100) ui.load_arrays(1, x, y, DataPHA) ui.group_counts(1, 100) ui.set_full_model(1, Const1D("const")) # in principle I wouldn't need to call calc_stat_info(), I could just # use _get_stat_info to reproduce the issue, However, _get_stat_info is not a public # method, so I want to double check that calc_stat_info does not throw an exception. # So, first we try to run calc_stat_info and make sure there are no exceptions. # Then, since calc_stat_info only logs something and doesn't return anything, we use # a white box approach to get the result from _get_stat_info. ui.calc_stat_info() assert ui._get_stat_info()[0].rstat is numpy.nan
def test_source_component_arbitrary_grid(): ui = Session() model = Const1D('c') model.c0 = 10 def tst(x, y, re_x, yy): ui.load_arrays(1, x, y) regrid_model = model.regrid(re_x) ui.plot_source_component(regrid_model) numpy.testing.assert_array_equal(ui._compsrcplot.x, x) numpy.testing.assert_array_almost_equal(ui._compsrcplot.y, yy) x = [1, 2, 3] y = [1, 2, 3] re_x = [10, 20, 30] tst(x, y, re_x, [0, 0, 0]) x = numpy.linspace(1, 10, 10) y = x re_x = numpy.linspace(5, 15, 15) tst(x, y, re_x, [0, 0, 0, 0, 10, 10, 10, 10, 10, 10]) re_x = numpy.linspace(1, 5, 15) tst(x, y, re_x, [10, 10, 10, 10, 10, 0, 0, 0, 0, 0]) re_x = numpy.linspace(3, 5, 15) tst(x, y, re_x, [0, 0, 10, 10, 10, 0, 0, 0, 0, 0])
def test_arf_rmf_get_x(make_data_path): arf_name = make_data_path('3c120_heg_-1.arf') rmf_name = make_data_path('3c120_heg_-1.rmf') session = Session() arf = session.unpack_arf(arf_name) rmf = session.unpack_rmf(rmf_name) expected_array_10 = [ 0.57724115, 0.57730836, 0.57737556, 0.5774428, 0.57751006, 0.57757729, 0.57764456, 0.57771185, 0.57777914, 0.57784647 ] actual_arf_10 = arf.get_x()[0:10] actual_rmf_10 = rmf.get_x()[0:10] np.testing.assert_array_almost_equal(expected_array_10, actual_arf_10) np.testing.assert_array_almost_equal(expected_array_10, actual_rmf_10)
def data_for_load_arrays(request): data_class = request.param from sherpa.astro.ui.utils import Session session = Session() data_args = INSTANCE_ARGS[data_class] args = data_args + (data_class, ) data = data_class(*data_args) return session, args, data
def setup(): const = Const1D("const") const.c0 = 0 const.c0.freeze() my_model = MyModel("my_model") my_model.integrate = False return Session(), my_model, const
def test_source_component_arbitrary_grid(): from sherpa.astro.ui.utils import Session from sherpa.models import Const1D ui = Session() x = [1, 2, 3] y = [1, 2, 3] re_x = [10, 20, 30] ui.load_arrays(1, x, y) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(re_x) with pytest.warns(UserWarning): ui.plot_source_component(regrid_model) numpy.testing.assert_array_equal(ui._compsrcplot.x, x + re_x) numpy.testing.assert_array_equal(ui._compsrcplot.y, [10, ]*6)
def test_source_component_arbitrary_grid_int(): from sherpa.astro.ui.utils import Session from sherpa.models import Const1D from sherpa.data import Data1DInt ui = Session() x = numpy.array([1, 2, 3]), numpy.array([2, 3, 4]) y = [1.5, 2.5, 3.5] re_x = numpy.array([10, 20, 30]), numpy.array([20, 30, 40]) ui.load_arrays(1, x[0], x[1], y, Data1DInt) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(*re_x) with pytest.warns(UserWarning): ui.plot_source_component(regrid_model) x_points = (x[0] + x[1]) / 2 re_x_points = (re_x[0] + re_x[1]) / 2 points = numpy.concatenate((x_points, re_x_points)) numpy.testing.assert_array_equal(ui._compsrcplot.x, points) numpy.testing.assert_array_equal(ui._compsrcplot.y, [10, 10, 10, 100, 100, 100])
def test_instrument_model(make_data_path): """Check the full response model""" from sherpa.astro import xspec s = Session() s.load_pha(make_data_path('3c273.pi')) a1 = xspec.XSpowerlaw() m1 = xspec.XSwabs() s.set_source(m1 * a1) src = s.get_source() mdl = s.get_model() assert src.ndim == 1 assert mdl.ndim == 1
def setup2d(): const = Const2D("const") const.c0 = 0 const.c0.freeze() x = [2, 3, 2, 3] y = [2, 2, 3, 3] xhi = [2.1, 3.5, 2.1, 3.5] yhi = [2.1, 2.1, 3.5, 3.5] # This is the result when rebinning [100, ] * 4 z = [225, ] * 4 my_model = MyModel2D("my_model") return Session(), my_model, const, (x, y, xhi, yhi, z)
def test_plot_model_arbitrary_grid_integrated(): ui = Session() x = [1, 2, 3], [2, 3, 4] y = [1, 2, 3] re_x = [10, 20, 30], [20, 30, 40] ui.load_arrays(1, x[0], x[1], y, Data1DInt) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(*re_x) ui.set_model(regrid_model) with pytest.warns(UserWarning): ui.plot_model() numpy.testing.assert_array_equal(ui._modelplot.x, [1.5, 2.5, 3.5]) numpy.testing.assert_array_equal(ui._modelplot.y, [10, 10, 10])
def psf_fixture(request): configuration = request.param fixture_data = make_images(configuration) ui = Session() ui.set_data(1, fixture_data.image) exact_expected_sigma = configuration.source_sigma approx_expected_sigma = approx(exact_expected_sigma, rel=3e-2) # Set the source model as a 2D Gaussian, and set the PSF in Sherpa source_position = configuration.source_position sherpa_source = SigmaGauss2D('source') sherpa_source.ampl = configuration.source_amplitude sherpa_source.sigma_a = exact_expected_sigma sherpa_source.sigma_b = exact_expected_sigma sherpa_source.xpos = source_position sherpa_source.ypos = source_position ui.set_source(sherpa_source) ui.set_psf(fixture_data.psf_model) return ui, sherpa_source, approx_expected_sigma
def test_source_component_arbitrary_grid_int(): ui = Session() x = numpy.array([1, 2, 3]), numpy.array([2, 3, 4]) y = [1.5, 2.5, 3.5] re_x = numpy.array([10, 20, 30]), numpy.array([20, 30, 40]) ui.load_arrays(1, x[0], x[1], y, Data1DInt) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(*re_x) ui.plot_source_component(regrid_model) x_points = (x[0] + x[1]) / 2.0 numpy.testing.assert_array_equal(ui._compsrcplot.x, x_points) numpy.testing.assert_array_equal(ui._compsrcplot.y, [0., 0., 0.])
def test_plot_model_arbitrary_grid_integrated(): ui = Session() model = Const1D('c') model.c0 = 10 def tst(x, y, re_x, yy): ui.load_arrays(1, x[0], x[1], y, Data1DInt) regrid_model = model.regrid(*re_x) ui.set_model(regrid_model) ui.plot_model() avg_x = 0.5 * (x[0] + x[1]) numpy.testing.assert_array_equal(ui._modelplot.x, avg_x) numpy.testing.assert_array_almost_equal(ui._modelplot.y, yy) tmp = numpy.arange(1, 5, 1) x = tmp[:-1], tmp[1:] y = x[0] tmp = numpy.arange(10, 50, 10) re_x = tmp[:-1], tmp[1:] tst(x, y, re_x, [0, 0, 0]) tmp = numpy.arange(1, 20, 1) x = tmp[:-1], tmp[1:] y = x[0] tmp = numpy.arange(1, 20, 0.5) re_x = tmp[:-1], tmp[1:] tst(x, y, re_x, len(y) * [10]) tmp = numpy.arange(1, 20, 1) x = tmp[:-1], tmp[1:] y = x[0] tmp = numpy.arange(10, 20, 0.5) re_x = tmp[:-1], tmp[1:] n = int(len(y) / 2) yy = numpy.append(n * [0.], n * [10.]) tst(x, y, re_x, yy)
def test_plot_model_arbitrary_grid_integrated(): from sherpa.astro.ui.utils import Session from sherpa.models import Const1D from sherpa.data import Data1DInt ui = Session() x = [1, 2, 3], [2, 3, 4] y = [1, 2, 3] re_x = [10, 20, 30], [20, 30, 40] ui.load_arrays(1, x[0], x[1], y, Data1DInt) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(*re_x) ui.set_model(regrid_model) with pytest.warns(UserWarning): ui.plot_model() numpy.testing.assert_array_equal(ui._modelplot.x, [1.5, 2.5, 3.5]) numpy.testing.assert_array_equal(ui._modelplot.y, [10, 10, 10])
def test_source_component_arbitrary_grid(): ui = Session() x = [1, 2, 3] y = [1, 2, 3] re_x = [10, 20, 30] ui.load_arrays(1, x, y) model = Const1D('c') model.c0 = 10 regrid_model = model.regrid(re_x) with pytest.warns(UserWarning): ui.plot_source_component(regrid_model) numpy.testing.assert_array_equal(ui._compsrcplot.x, x + re_x) numpy.testing.assert_array_equal(ui._compsrcplot.y, [ 10, ] * 6)
def test_show_bkg_model_with_bkg(make_data_path): session = Session() session.load_data('foo', make_data_path('3c273.pi')) session.show_bkg_model() session.show_bkg_model('foo')
def test_show_bkg_model(): session = Session() session.load_arrays(1, [1, 2], [1, 2]) session.show_bkg_model() session.show_bkg_model('xx') session.show_bkg_source() session.show_bkg_source('xx')
def test_set_log(): session = Session() assert not session.get_data_plot_prefs()['xlog'] assert not session.get_data_plot_prefs()['ylog'] session.set_xlog() assert session.get_data_plot_prefs()['xlog'] session.set_ylog() assert session.get_data_plot_prefs()['ylog'] session.set_xlinear() assert not session.get_data_plot_prefs()['xlog'] session.set_ylinear() assert not session.get_data_plot_prefs()['ylog']
def test_save_restore(tmpdir): outfile = tmpdir.join("sherpa.save") session = Session() session.load_arrays(1, TEST, TEST2) session.save(str(outfile), clobber=True) session.clean() assert set() == set(session.list_data_ids()) session.restore(str(outfile)) assert { 1, } == set(session.list_data_ids()) assert_array_equal(TEST, session.get_data(1).get_indep()[0]) assert_array_equal(TEST2, session.get_data(1).get_dep())
def convert_model(expr, postfix, groups, names): """Extract the model components. Model names go from m1 to mn (when groups is empty) or m1g1 to mng1 and then m1g2 to mng<ngrops>. Parameters ---------- expr : str The XSPEC model expression. postfix : str Add to the model + number string. groups : list of int The groups to create. It must not be empty. We special case a single group, as there's no need to add an identifier. names : set of str The names we have created (will be updated). This is just for testing. Returns ------- exprs : list of lists The model expression for each group (if groups was None then for a single group). Each list contains a pair of (str, None) or ((str, str), Model), where for the Model case the two names are the model type and the instance name. Notes ----- We require the Sherpa XSPEC module here. """ # Create our own session object to make it easy to # find out XSPEC models and the correct naming scheme. # session = Session() session._add_model_types(xspec, (xspec.XSAdditiveModel, xspec.XSMultiplicativeModel, xspec.XSConvolutionKernel)) # Let's remove the spaces dbg(f"Processing model expression: {expr}") expr = expr.translate({32: None}) if len(groups) == 1: groups = [None] def mkname(ctr, grp): n = f"m{ctr}{postfix}" if n in names: raise RuntimeError("Unable to handle model names with this input script") names.add(n) return n else: def mkname(ctr, grp): n = f"m{ctr}{postfix}g{grp}" if n in names: raise RuntimeError("Unable to handle model names with this input script") names.add(n) return n out = [[] for _ in groups] def add_term(start, end, ctr, storage): """storage tracks the convolution state.""" # It's not ideal we need this if start == end: return ctr name = f"xs{expr[start:end]}" dbg(f"Identified model expression '{name}'") for i, grp in enumerate(groups, 1): try: mdl = session.create_model_component(name, mkname(ctr, grp)) except ArgumentErr: raise ValueError(f"Unrecognized XSPEC model '{name[2:]}' in {expr}") from None out[i - 1].append((mdl.name.split('.'), mdl)) # This only needs to be checked for the first group. # if i == 1: if isinstance(mdl, xspec.XSConvolutionKernel): if storage['convolution'] is not None: print("Convolution found within a convolution expession. This is not handled correctly.") else: storage['convolution'] = storage['depth'] storage['lastterm'] = 'convolution' out[i - 1].append(("(", None)) elif isinstance(mdl, xspec.XSMultiplicativeModel): storage['lastterm'] = 'multiplicative' elif isinstance(mdl, xspec.XSAdditiveModel): storage['lastterm'] = 'additive' else: raise RuntimeError(f"Unrecognized XSPEC model: {mdl.__class__}") return ctr + 1 def add_sep(sep): for i, grp in enumerate(groups, 1): out[i - 1].append((sep, None)) def check_end_convolution(storage): if storage['convolution'] is None: return if storage['convolution'] > storage['depth']: return if storage['convolution'] == storage['depth']: add_sep(")") elif storage['convolution'] > storage['depth']: print("WARNING: convolution model may not be handled correctly.") storage['convolution'] = None def in_convolution(storage): return storage['convolution'] is not None \ and storage['convolution'] == storage['depth'] maxchar = len(expr) - 1 start = 0 end = 0 mnum = 1 storage = {'convolution': None, 'depth': 0, 'lastterm': None} for end, char in enumerate(expr): # Not completely sure of the supported language. # if char not in "*+-/()": continue if char == "(": if end == 0: add_sep('(') else: mnum = add_term(start, end, mnum, storage) # We want to leave ( alone for convolution models. # This is a bit messy. # if expr[end - 1] in "+*-/": add_sep(" (") elif storage['lastterm'] == 'convolution': add_sep("(") else: add_sep(" * (") start = end + 1 storage['depth'] += 1 continue if char == ")": mnum = add_term(start, end, mnum, storage) # Check to see whether we can close out the convolution. # check_end_convolution(storage) if end == maxchar: add_sep(")") elif expr[end + 1] in "+*-/": add_sep(") ") else: add_sep(") * ") start = end + 1 storage['depth'] -= 1 continue mnum = add_term(start, end, mnum, storage) # conv*a1+a2 is conv(s1) + a2 if char == '+': check_end_convolution(storage) # If we had conv*mdl then we want to drop the * # but conv*m1*a1 is conv(m1*a1) # if not(char == '*' and in_convolution(storage) and out[0][-1][1] is None and out[0][-1][0] == "("): # Add space characters to separate out the expression, # even if start==end. # add_sep(f" {char} ") start = end + 1 # Last name, which is not always present. # if start < end: add_term(start, None, mnum, storage) # I'm not sure whether this should only be done if start < end. # I am concerned we may have a case where this is needed. # check_end_convolution(storage) if storage['convolution'] is not None: print("WARNING: convolution model may not be handled correctly.") if storage['depth'] != 0: print("WARNING: unexpected issues handling brackets in the model") return out
def test_save_restore(tmpdir): outfile = tmpdir.join("sherpa.save") session = Session() session.load_arrays(1, TEST, TEST2) session.save(str(outfile), clobber=True) session.clean() assert set() == set(session.list_data_ids()) session.restore(str(outfile)) assert {1, } == set(session.list_data_ids()) assert_array_equal(TEST, session.get_data(1).get_indep()[0]) assert_array_equal(TEST2, session.get_data(1).get_dep())
def setup(make_data_path): image = make_data_path('sim_0.5bin_2g+c.fits') psf_bin1 = make_data_path('psf_0.0_00_bin1.img') psf_bin05 = make_data_path('psf_0.0_00_bin0.5.img') return Session(), image, psf_bin05, psf_bin1