def test_psf1d_kernel_model(caplog):
"""Access the kernel data: subkernel=True"""
k = Box1D()
k.xlow = 1
k.xhi = 3
m = PSFModel(kernel=k)
dfold = Data1D('fold', np.arange(10), np.zeros(10))
with caplog.at_level(logging.INFO, logger='sherpa'):
ans = m.get_kernel(dfold)
assert len(caplog.records) == 1
r = caplog.record_tuples[0]
assert r[0] == 'sherpa.instrument'
assert r[1] == logging.INFO
assert r[2] == "PSF frac: 1.0"
assert isinstance(ans, Data1D)
assert ans.name == 'kernel'
# integers, so treat as exact
assert (ans.x == np.arange(10)).all()
# box1D between 1 and 3 inclusive
y = np.asarray([0, 1, 1, 1, 0, 0, 0, 0, 0, 0])
assert ans.y == pytest.approx(y / y.sum())
assert ans.staterror is None
assert ans.syserror is None
def test_psf1d_combined_v2():
"""See test_psf1d_step_v2"""
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
gsmooth = Gauss1D()
psf = PSFModel('psf', gsmooth)
x = np.arange(0, 200, 0.5)
d = Data1D('fake', x, x * 0)
psf.fold(d)
smoothed = psf(imdl)
y = smoothed(x)
# So the output is not easy to describe analytically, hence
# we just check parts of it.
#
assert y[(x >= 19.5) & (x <= 100)] == pytest.approx([-490] * 162, abs=1e-4)
assert y[x >= 119] == pytest.approx([-500] * 162, abs=1e-4)
# check that the x <= 19 values are in ascending order
y1 = y[x <= 19]
assert (y1[1:] > y1[:-1]).all()
def test_psf1d_model_given_2d_dataset():
"""Do we error out or not?
This is a regression test.
"""
psf = PSFModel('psf', make_1d_model())
d = make_2d_data()
# Does this error out?
psf.fold(d)
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
# Or maybe this errors out?
smoothed = psf(imdl)
with pytest.raises(TypeError) as err:
smoothed(np.arange(1, 7))
# It is not at all obvious why we have 36 for the source dim.
#
assert str(
err.value
) == "input array sizes do not match dimensions, source size: 6 vs source dim: 36"
def test_psf1d_kernel_data(caplog):
"""Access the kernel data: subkernel=True"""
k = np.asarray([2, 5, 3])
x = 5 + np.arange(k.size)
d = Data1D('my-kernel', x, k)
m = PSFModel(kernel=d)
dfold = Data1D('fold', np.arange(10), np.zeros(10))
with caplog.at_level(logging.INFO, logger='sherpa'):
ans = m.get_kernel(dfold)
assert len(caplog.records) == 1
r = caplog.record_tuples[0]
assert r[0] == 'sherpa.instrument'
assert r[1] == logging.INFO
assert r[2] == "PSF frac: 1.0"
assert isinstance(ans, Data1D)
assert ans.name == 'kernel'
# integers, so treat as exact
assert (ans.x == np.arange(5, 8)).all()
assert ans.y == pytest.approx(k / k.sum())
assert ans.staterror is None
assert ans.syserror is None
def test_psf2d_data_given_1d_dataset():
"""Do we error out or not?
This is a regression test.
"""
psf = PSFModel('psf', make_2d_data())
d = make_1d_data()
# Does this error out?
psf.fold(d)
smdl = Gauss2D()
smdl.ampl = 1000
cmdl = Const2D()
cmdl.c0 = -500
imdl = smdl + cmdl
# Or maybe this errors out?
smoothed = psf(imdl)
with pytest.raises(TypeError) as err:
smoothed(np.arange(1, 7))
assert str(
err.value) == "function missing required argument 'x1lo' (pos 3)"
def test_psf1d_data_given_2d_dataset():
"""Do we error out or not?
This is a regression test.
"""
psf = PSFModel('psf', make_1d_data())
d = make_2d_data()
# Does this error out?
psf.fold(d)
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
# Or maybe this errors out?
smoothed = psf(imdl)
with pytest.raises(TypeError) as err:
smoothed(np.arange(1, 7))
assert str(
err.value
) == "input array sizes do not match, dims_src: 2 vs dims_kern: 1"
def fold(self, data):
_PSFModel.fold(self, data)
# Set WCS coordinates of kernel data set to match source data set.
if (isinstance(data, DataIMG) and
isinstance(self.kernel, DataIMG)):
self.kernel.set_coord(data.coord)
def test_psf2d_model_show():
"""What happens when the kernel is a model?"""
m = PSFModel("pmodel2", make_2d_model())
yy, xx = np.mgrid[1:10, 1:9]
xx = xx.flatten()
yy = yy.flatten()
zz = np.arange(xx.size)
dfold = Data2D('fold', xx, yy, zz)
m.fold(dfold)
print(m)
out = str(m).split("\n")
assert len(out) == 8
assert out[0] == "pmodel2"
assert out[
1] == " Param Type Value Min Max Units"
assert out[
2] == " ----- ---- ----- --- --- -----"
assert out[3] == " pmodel2.kernel frozen box2"
assert out[
4] == " pmodel2.size frozen (72, 72) (72, 72) (72, 72)"
assert out[
5] == " pmodel2.center frozen (36, 36) (36, 36) (36, 36)"
assert out[
6] == " pmodel2.radial frozen 0 0 1 "
assert out[
7] == " pmodel2.norm frozen 1 0 1 "
def test_psf2d_data_show():
"""What happens when the kernel is a Data2D instance?"""
y, x = np.mgrid[1:4, 1:3]
x = x.flatten()
y = y.flatten()
z = np.ones(x.size)
data2 = Data2D('data2', x, y, z)
m = PSFModel("pdata2", data2)
yy, xx = np.mgrid[1:10, 1:9]
xx = xx.flatten()
yy = yy.flatten()
zz = np.arange(xx.size)
dfold = Data2D('fold', xx, yy, zz)
m.fold(dfold)
out = str(m).split("\n")
assert len(out) == 8
assert out[0] == "pdata2"
assert out[
1] == " Param Type Value Min Max Units"
assert out[
2] == " ----- ---- ----- --- --- -----"
assert out[3] == " pdata2.kernel frozen data2"
assert out[
4] == " pdata2.size frozen (6, 6) (6, 6) (6, 6)"
assert out[
5] == " pdata2.center frozen (3, 3) (3, 3) (3, 3)"
assert out[
6] == " pdata2.radial frozen 0 0 1 "
assert out[
7] == " pdata2.norm frozen 1 0 1 "
def test_psf1d_model_show():
"""What happens when the kernel is a model?"""
box1 = make_1d_model()
m = PSFModel("pmodel1", box1)
dfold = Data1D('fold', np.arange(10), np.zeros(10))
m.fold(dfold)
out = str(m).split("\n")
assert len(out) == 8
assert out[0] == "pmodel1"
assert out[
1] == " Param Type Value Min Max Units"
assert out[
2] == " ----- ---- ----- --- --- -----"
assert out[3] == " pmodel1.kernel frozen box1"
assert out[
4] == " pmodel1.size frozen 10 10 10"
assert out[
5] == " pmodel1.center frozen 5 5 5"
assert out[
6] == " pmodel1.radial frozen 0 0 1 "
assert out[
7] == " pmodel1.norm frozen 1 0 1 "
def test_psf1d_combined():
"""This is based on
sherpa.models.tests.test_regrid_unit.test_regrid1_works_with_convolution_style
but I wanted to make sure we have an explicit check of the underlying
code.
"""
smdl = StepLo1D()
smdl.xcut = 12.5
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
gsmooth = Gauss1D()
gsmooth.fwhm = 3
psf = PSFModel('psf', gsmooth)
x = np.arange(5, 23, 3)
d = Data1D('fake', x, x * 0)
psf.fold(d)
smoothed = psf(imdl)
y = smoothed(x)
assert y == pytest.approx([-490, -490, -490, -500, -500, -500], rel=7e-3)
def test_psf1d_step_v2():
"""Trying to track down why we have seen different behavior in
test_regrid_unit.py.
"""
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
gsmooth = Gauss1D()
psf = PSFModel('psf', gsmooth)
x = np.arange(0, 200, 0.5)
d = Data1D('fake', x, x * 0)
psf.fold(d)
smoothed = psf(smdl)
y = smoothed(x)
# So the output is not easy to describe analytically, hence
# we just check parts of it.
#
assert y[(x >= 19.5) & (x <= 100)] == pytest.approx([10] * 162, abs=1e-4)
assert y[x >= 119] == pytest.approx([0] * 162, abs=1e-4)
# check that the x <= 19 values are in ascending order
y1 = y[x <= 19]
assert (y1[1:] > y1[:-1]).all()
def test_psf1d_show():
"""Test the __str__ method
Loop through basic data and then add in the options
(but not all possible combinations).
"""
def check(x, n, ans):
toks = x[n].split()
assert toks == ans
NAME = ['psfmodel']
PARAMS = ['Param', 'Type', 'Value', 'Min', 'Max', 'Units']
LINES = ['-----', '----', '-----', '---', '---', '-----']
KERNEL = ['psfmodel.kernel', 'frozen', 'oned']
SIZE = ['psfmodel.size', 'frozen', '7', '7', '7']
CENTER = ['psfmodel.center', 'frozen', '3', '3', '3']
RADIAL = ['psfmodel.radial', 'frozen', '0', '0', '1']
NORM = ['psfmodel.norm', 'frozen', '1', '0', '1']
m = PSFModel()
# basic settings
out = str(m).split('\n')
assert len(out) == 5
check(out, 0, NAME)
check(out, 1, PARAMS)
check(out, 2, LINES)
check(out, 3, RADIAL)
check(out, 4, NORM)
m.kernel = make_1d_data()
# before a fold you don't get the size and center parameters
out = str(m).split('\n')
assert len(out) == 6
check(out, 0, NAME)
check(out, 1, PARAMS)
check(out, 2, LINES)
check(out, 3, KERNEL)
check(out, 4, RADIAL)
check(out, 5, NORM)
dfold = Data1D('fold', np.arange(10), np.zeros(10))
m.fold(dfold)
out = str(m).split('\n')
assert len(out) == 8
check(out, 0, NAME)
check(out, 1, PARAMS)
check(out, 2, LINES)
check(out, 3, KERNEL)
check(out, 4, SIZE)
check(out, 5, CENTER)
check(out, 6, RADIAL)
check(out, 7, NORM)
def test_psf1d_fold_no_kernel():
"""Error out if there's no kernel"""
m = PSFModel('bob')
dfold = Data1D('fold', np.arange(10), np.zeros(10))
with pytest.raises(PSFErr) as exc:
m.fold(dfold)
assert "model 'bob' does not have an associated PSF function" == str(exc.value)
def test_psf_set_model_to_bool(kernel_func):
"""Can we change the model field? boolean
This is a regression test.
"""
m = PSFModel(kernel=kernel_func())
# This does not error out
m.model = False
def test_psf_set_model_to_model(kernel_func):
"""Can we change the model field? model
This is a regression test.
"""
m = PSFModel(kernel=kernel_func())
with pytest.raises(AttributeError) as err:
m.model = Box1D()
assert str(
err.value
) == "'PSFModel' object attribute 'model' cannot be replaced with a callable attribute"
def test_psf2d_kernel_model(caplog):
"""Access the kernel data: no subkernel"""
k = Box2D()
k.xlow = -1
k.xhi = 1
k.ylow = 10
k.yhi = 12
m = PSFModel('x', kernel=k)
d1, d0 = np.mgrid[5:15, -5:4]
ds = d0.shape
d0 = d0.flatten()
d1 = d1.flatten()
z = np.zeros(ds).flatten()
dfold = Data2D('fold', d0, d1, z, shape=ds)
with caplog.at_level(logging.INFO, logger='sherpa'):
ans = m.get_kernel(dfold)
assert len(caplog.records) == 1
r = caplog.record_tuples[0]
assert r[0] == 'sherpa.instrument'
assert r[1] == logging.INFO
assert r[2] == "PSF frac: 1.0"
assert isinstance(ans, Data2D)
assert ans.name == 'kernel'
assert (ans.shape == [10, 9]).all()
# integers, so treat as exact
assert (ans.x0 == d0).all()
assert (ans.x1 == d1).all()
# This is the old check, converted to what I assume is meant to be
# the correct form - see #1428 - but ans.y is all zeros except for
# a single 1 whilst k is not (it has 9 True values and the rest
# False). I do not have time to identify the truth here.
#
k = (ans.x0 >= -1) & (ans.x0 <= 1) & (ans.x1 >= 10) & (ans.x1 <= 12)
assert ans.y == pytest.approx(k / k.sum())
assert ans.staterror is None
assert ans.syserror is None
def test_psf1d_no_kernel():
"""Error out if there's no kernel"""
m = PSFModel('bob')
b = Box1D()
with pytest.raises(PSFErr) as exc:
m(b)
assert "PSF kernel has not been set" == str(exc.value)
def test_psf2d_kernel_data(caplog):
"""Access the kernel data: no subkernel"""
x1, x0 = np.mgrid[-5:-3, 10:13]
s = x0.shape
k = np.ones(s)
k[1, 1] = 2
x0 = x1.flatten()
x1 = x1.flatten()
k = k.flatten()
d = Data2D('my-kernel', x0, x1, k, shape=s)
m = PSFModel('x', kernel=d)
d1, d0 = np.mgrid[5:15, -5:5]
ds = d0.shape
z = np.zeros(ds)
dfold = Data2D('fold', d0.flatten(), d1.flatten(), z.flatten(), shape=ds)
with caplog.at_level(logging.INFO, logger='sherpa'):
ans = m.get_kernel(dfold)
assert len(caplog.records) == 1
r = caplog.record_tuples[0]
assert r[0] == 'sherpa.instrument'
assert r[1] == logging.INFO
assert r[2] == "PSF frac: 1.0"
assert isinstance(ans, Data2D)
assert ans.name == 'kernel'
assert (ans.shape == [2, 3]).all()
# integers, so treat as exact
assert (ans.x0 == x0).all()
assert (ans.x1 == x1).all()
assert ans.y == pytest.approx(k / k.sum())
assert ans.staterror is None
assert ans.syserror is None
def test_psf2d_set_invalid_field(kernel_func, field, vals):
"""What happens if we send in a 2D array?
This is a regression test (since it currently does not error out).
"""
kernel = kernel_func()
m = PSFModel("p2", kernel)
setattr(m, field, vals)
assert getattr(m, field) == pytest.approx(vals)
def test_psf2d_kernel_model(caplog):
"""Access the kernel data: no subkernel"""
k = Box2D()
k.xlow = -1
k.xhi = 1
k.ylow = 10
k.yhi = 12
m = PSFModel('x', kernel=k)
d1, d0 = np.mgrid[5:15, -5:4]
ds = d0.shape
d0 = d0.flatten()
d1 = d1.flatten()
z = np.zeros(ds).flatten()
dfold = Data2D('fold', d0, d1, z, shape=ds)
with caplog.at_level(logging.INFO, logger='sherpa'):
ans = m.get_kernel(dfold)
assert len(caplog.records) == 1
r = caplog.record_tuples[0]
assert r[0] == 'sherpa.instrument'
assert r[1] == logging.INFO
assert r[2] == "PSF frac: 1.0"
assert isinstance(ans, Data2D)
assert ans.name == 'kernel'
assert (ans.shape == [10, 9]).all()
# integers, so treat as exact
assert (ans.x0 == d0).all()
assert (ans.x1 == d1).all()
k = (ans.x0 >= -1) & (ans.x0 <= 1) & (ans.x1 >= 10) & (ans.x1 <= 12)
assert pytest.approx(k / k.sum(), ans.y)
assert ans.staterror is None
assert ans.syserror is None
def test_psf1d_no_fold():
"""Error out if there's no kernel"""
box = Box1D()
psf = PSFModel('bob', box)
cpt = Gauss1D()
sm = psf(cpt)
with pytest.raises(PSFErr) as exc:
sm([1, 2, 3, 4, 5])
assert "PSF model has not been folded" == str(exc.value)
def test_psf1d_flat():
"""This is based on
sherpa.models.tests.test_regrid_unit.test_regrid1_works_with_convolution_style
but I wanted to make sure we have an explicit check of the underlying
code.
"""
cmdl = Const1D()
cmdl.c0 = -500
gsmooth = Gauss1D()
gsmooth.fwhm = 3
psf = PSFModel('psf', gsmooth)
x = np.arange(5, 23, 3)
d = Data1D('fake', x, x * 0)
psf.fold(d)
smoothed = psf(cmdl)
y = smoothed(x)
assert y == pytest.approx([-500] * 6)
def test_psf1d_step():
"""This is based on
sherpa.models.tests.test_regrid_unit.test_regrid1_works_with_convolution_style
but I wanted to make sure we have an explicit check of the underlying
code.
"""
smdl = StepLo1D()
smdl.xcut = 12.5
smdl.ampl = 10
gsmooth = Gauss1D()
gsmooth.fwhm = 3
psf = PSFModel('psf', gsmooth)
x = np.arange(5, 23, 3)
d = Data1D('fake', x, x * 0)
psf.fold(d)
smoothed = psf(smdl)
y = smoothed(x)
assert y == pytest.approx([10.0, 10.0, 10.0, 0, 0, 0], abs=1e-4)
def test_psf1d_convolved_pars():
"""What does .pars mean for a PSFModel applied to a model?"""
b1 = Box1D('b1')
m = PSFModel(kernel=b1)
b2 = Box1D('b2')
c = m(b2)
b1.xlow = 1
b1.xhi = 10
b1.ampl = 0.2
b2.xlow = 4
b2.xhi = 8
b2.ampl = 0.4
bpars = b1.pars + b2.pars
assert len(bpars) == 6
cpars = c.pars
assert len(cpars) == 6
for bpar, cpar in zip(bpars, cpars):
assert cpar == bpar
def test_regrid1d_works_with_convolution_style():
"""This doesn't really test more than the previous
model-evaluation tests.
"""
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
# Set up the convolution kernel
#
gsmooth = Gauss1D()
psf = PSFModel('psf', gsmooth)
smoothed = psf(imdl)
# This is the model that will be evaluated
#
regrid = ModelDomainRegridder1D()
smoothed_regrid = regrid.apply_to(smoothed)
# Ignoring edge effects, the smoothed step function drops from
# x=100 down to x~120 (it is not clear why it doesn't smooth
# below x=100, but maybe I've set up the convolution wrong).
# So, if the regrid model evaluates x=0 to 200 but the requested
# grid is from x=102 ro 180, then we should see a difference
# to evaluating without regrid.
#
xfull = np.arange(0, 200, 0.5)
xout = np.arange(101, 180, 0.5)
regrid.grid = xfull
# fake up a data object for the fold method
# TODO: it is not clear to me what grid should be used here;
# xfull or xout
#
d = Data1D('fake', xfull, xfull * 0)
psf.fold(d)
y_regrid = smoothed_regrid(xout)
# calculate the expected values
y_full = smoothed(xfull)
# since the grids have the same binning, it is a simple extraction
idx0, = np.where(xfull == xout[0])
idx1, = np.where(xfull == xout[-1])
y_expected = y_full[idx0[0]:idx1[0] + 1]
assert_allclose(y_regrid, y_expected, atol=1e-10, rtol=0)
# check that this is all worth it; i.e. that without regrid
# you just get the constant term. If this fails then it does not
# mean that the regrid code is broken, but it implies that
# something fundamental has changed with the basic model
# evaluation.
#
d = Data1D('fake', xout, xout * 0)
psf.fold(d)
y_check = smoothed(xout)
y_expected = np.zeros(xout.size) + cmdl.c0.val
assert_allclose(y_check, y_expected, rtol=0, atol=1e-7)
from matplotlib import pyplot as plt
import numpy as np
from sherpa.models.basic import Box2D
from sherpa.instrument import PSFModel
from sherpa.data import Data2D
k = np.asarray([[0, 1, 0], [1, 0, 1], [0, 1, 0]])
yg, xg = np.mgrid[:3, :3]
kernel = Data2D('kdata', xg.flatten(), yg.flatten(), k.flatten(),
shape=k.shape)
psf = PSFModel(kernel=kernel)
print("# print(psf)")
print(psf)
pt = Box2D('pt')
box = Box2D('box')
unconvolved_mdl = pt + box
pt.xlow = 1.5
pt.xhi = 2.5
pt.ylow = 2.5
pt.yhi = 3.5
pt.ampl = 10
box.xlow = 4
box.xhi = 10
box.ylow = 6.5
box.yhi = 7.5
box.ampl = 10
def test_psf1d_empty_pars():
"""What does .pars mean for an empty PSFModel?"""
m = PSFModel()
assert m.pars == ()
def fold(self, data):
_PSFModel.fold(self, data)
# Set WCS coordinates of kernel data set to match source data set.
if hasattr(self.kernel, "set_coord"):
self.kernel.set_coord(data.coord)
def fold(self, data):
_PSFModel.fold(self, data)
# Set WCS coordinates of kernel data set to match source data set.
if (isinstance(data, DataIMG) and isinstance(self.kernel, DataIMG)):
self.kernel.set_coord(data.coord)
def test_regrid1d_works_with_convolution_style():
"""This doesn't really test more than the previous
model-evaluation tests.
"""
smdl = StepLo1D()
smdl.xcut = 100
smdl.ampl = 10
cmdl = Const1D()
cmdl.c0 = -500
imdl = smdl + cmdl
# Set up the convolution kernel
#
gsmooth = Gauss1D()
psf = PSFModel('psf', gsmooth)
smoothed = psf(imdl)
# This is the model that will be evaluated
#
regrid = ModelDomainRegridder1D()
smoothed_regrid = regrid.apply_to(smoothed)
# Ignoring edge effects, the smoothed step function drops from
# x=100 down to x~120 (it is not clear why it doesn't smooth
# below x=100, but maybe I've set up the convolution wrong).
# So, if the regrid model evaluates x=0 to 200 but the requested
# grid is from x=102 ro 180, then we should see a difference
# to evaluating without regrid.
#
xfull = np.arange(0, 200, 0.5)
xout = np.arange(101, 180, 0.5)
regrid.grid = xfull
# fake up a data object for the fold method
# TODO: it is not clear to me what grid should be used here;
# xfull or xout
#
d = Data1D('fake', xfull, xfull * 0)
psf.fold(d)
y_regrid = smoothed_regrid(xout)
# calculate the expected values
y_full = smoothed(xfull)
# since the grids have the same binning, it is a simple extraction
idx0, = np.where(xfull == xout[0])
idx1, = np.where(xfull == xout[-1])
y_expected = y_full[idx0[0]:idx1[0] + 1]
assert_allclose(y_regrid, y_expected, atol=1e-10, rtol=0)
# check that this is all worth it; i.e. that without regrid
# you just get the constant term. If this fails then it does not
# mean that the regrid code is broken, but it implies that
# something fundamental has changed with the basic model
# evaluation.
#
d = Data1D('fake', xout, xout * 0)
psf.fold(d)
y_check = smoothed(xout)
y_expected = np.zeros(xout.size) + cmdl.c0.val
assert_allclose(y_check, y_expected, rtol=0, atol=1e-7)
def test_psf1d_pars():
"""What does .pars mean for a PSFModel?"""
b = Box1D()
m = PSFModel(kernel=b)
assert m.pars == ()