def test_tabular1d_inverse():
"""Test that the Tabular1D inverse is defined"""
points = np.arange(5)
values = np.array([1.5, 3.4, 6.7, 7, 32])
t = models.Tabular1D(points, values)
result = t.inverse((3.4, 6.7))
assert_allclose(result, np.array((1., 2.)))
# Check that it works for descending values in lookup_table
t2 = models.Tabular1D(points, values[::-1])
assert_allclose(t2.inverse.points[0], t2.lookup_table[::-1])
result2 = t2.inverse((7, 6.7))
assert_allclose(result2, np.array((1., 2.)))
# Check that it errors on double-valued lookup_table
points = np.arange(5)
values = np.array([1.5, 3.4, 3.4, 32, 25])
t = models.Tabular1D(points, values)
with pytest.raises(NotImplementedError):
t.inverse((3.4, 7.))
# Check that Tabular2D.inverse raises an error
table = np.arange(5*5).reshape(5, 5)
points = np.arange(0, 5)
points = (points, points)
t3 = models.Tabular2D(points=points, lookup_table=table)
with pytest.raises(NotImplementedError):
t3.inverse((3, 3))
def test_tabular_str():
points = np.arange(5)
lt = np.arange(5)
t = models.Tabular1D(points, lt)
assert str(t) == ("Model: Tabular1D\n"
"N_inputs: 1\n"
"N_outputs: 1\n"
"Parameters: \n"
" points: (array([0, 1, 2, 3, 4]),)\n"
" lookup_table: [0 1 2 3 4]\n"
" method: linear\n"
" fill_value: nan\n"
" bounds_error: True")
table = np.arange(5 * 5).reshape(5, 5)
points = np.arange(0, 5)
points = (points, points)
t = models.Tabular2D(points=points, lookup_table=table)
assert str(t) == (
"Model: Tabular2D\n"
"N_inputs: 2\n"
"N_outputs: 1\n"
"Parameters: \n"
" points: (array([0, 1, 2, 3, 4]), array([0, 1, 2, 3, 4]))\n"
" lookup_table: [[ 0 1 2 3 4]\n"
" [ 5 6 7 8 9]\n"
" [10 11 12 13 14]\n"
" [15 16 17 18 19]\n"
" [20 21 22 23 24]]\n"
" method: linear\n"
" fill_value: nan\n"
" bounds_error: True")
def fitswcs_transform_from_model(wcsinfo, wavetable=None):
"""
Create a WCS object using from datamodel.meta.wcsinfo.
Transforms assume 0-based coordinates.
Parameters
----------
wcsinfo : dict-like
``~jwst.meta.wcsinfo`` structure.
Return
------
transform : `~astropy.modeling.core.Model`
WCS forward transform - from pixel to world coordinates.
"""
spatial_axes, spectral_axes, unknown = gwutils.get_axes(wcsinfo)
transform = gwutils.make_fitswcs_transform(wcsinfo)
if spectral_axes:
sp_axis = spectral_axes[0]
if wavetable is None:
# Subtract one from CRPIX which is 1-based.
spectral_transform = astmodels.Shift(-(wcsinfo['CRPIX'][sp_axis] - 1)) | \
astmodels.Scale(wcsinfo['CDELT'][sp_axis]) | \
astmodels.Shift(wcsinfo['CRVAL'][sp_axis])
else:
# Wave dimension is an array that needs to be converted to a table
waves = wavetable['wavelength'].flatten()
spectral_transform = astmodels.Tabular1D(lookup_table=waves)
transform = transform & spectral_transform
return transform
def test_tabular_with_bounding_box():
points = np.arange(5)
values = np.array([1.5, 3.4, 6.7, 7, 32])
t = models.Tabular1D(points, values)
result = t(1, with_bounding_box=True)
assert result == 3.4
assert t.inverse(result, with_bounding_box=True) == 1.
def test_tabular_bounding_box_with_units():
points = np.arange(5) * u.pix
lt = np.arange(5) * u.AA
t = models.Tabular1D(points, lt)
result = t(1 * u.pix, with_bounding_box=True)
assert result == 1. * u.AA
assert t.inverse(result, with_bounding_box=True) == 1 * u.pix
def test_format_output():
points = np.arange(5)
values = np.array([1.5, 3.4, 6.7, 7, 32])
t = models.Tabular1D(points, values)
pipe = [('detector', t), ('world', None)]
w = wcs.WCS(pipe)
assert_allclose(w(1), 3.4)
assert_allclose(w([1, 2]), [3.4, 6.7])
assert np.isscalar(w(1))
def test_units_with_bounding_box():
points = np.arange(10, 20)
table = np.arange(10) * u.Angstrom
t = models.Tabular1D(points, lookup_table=table)
assert isinstance(t(10), u.Quantity)
assert isinstance(t(10, with_bounding_box=True), u.Quantity)
assert_quantity_allclose(t(10), t(10, with_bounding_box=True))
def test_bare_baseframe():
# This is a regression test for the following call:
frame = cf.CoordinateFrame(1, "SPATIAL", (0,), unit=(u.km,))
assert u.allclose(frame.coordinate_to_quantity((1*u.m,)), 1*u.m)
# Now also setup the same situation through the whole call stack to be safe.
w = WCS(forward_transform=m.Tabular1D(points=np.arange(10)*u.pix,
lookup_table=np.arange(10)*u.km),
output_frame=frame,
input_frame=cf.CoordinateFrame(1, "PIXEL", (0,), unit=(u.pix,), name="detector_frame")
)
assert u.allclose(w.world_to_pixel(0*u.km), 0)
def test_tabular_evaluate():
points = np.arange(5)
lt = np.arange(5)[::-1]
t = models.Tabular1D(points, lt)
assert (t.evaluate([1, 2, 3]) == [3, 2, 1]).all()
assert (t.evaluate(np.array([1, 2, 3]) * u.m) == [3, 2, 1]).all()
t.n_outputs = 2
value = [np.array([3, 2, 1]), np.array([1, 2, 3])]
with mk.patch.object(tabular_models, 'interpn', autospec=True, return_value=value) as mkInterpn:
outputs = t.evaluate([1, 2, 3])
for index, output in enumerate(outputs):
assert np.all(value[index] == output)
assert mkInterpn.call_count == 1
def test_tabular_model(tmpdir):
points = np.arange(0, 5)
values = [1., 10, 2, 45, -3]
model = astmodels.Tabular1D(points=points, lookup_table=values)
tree = {'model': model}
helpers.assert_roundtrip_tree(tree, tmpdir)
table = np.array([[ 3., 0., 0.],
[ 0., 2., 0.],
[ 0., 0., 0.]])
points = ([1, 2, 3], [1, 2, 3])
model2 = astmodels.Tabular2D(points, lookup_table=table, bounds_error=False,
fill_value=None, method='nearest')
tree = {'model': model2}
helpers.assert_roundtrip_tree(tree, tmpdir)
def gwcs_stokes_lookup():
transform = models.Tabular1D([0, 1, 2, 3] * u.pix, [0, 1, 2, 3] * u.one,
method="nearest",
fill_value=np.nan,
bounds_error=False)
frame = cf.StokesFrame()
detector_frame = cf.CoordinateFrame(name="detector",
naxes=1,
axes_order=(0, ),
axes_type=("pixel", ),
axes_names=("x", ),
unit=(u.pix, ))
return wcs.WCS(forward_transform=transform,
output_frame=frame,
input_frame=detector_frame)
def generate_lookup_table(lookup_table,
interpolation='linear',
points_unit=u.pix,
**kwargs):
if not isinstance(lookup_table, u.Quantity):
raise TypeError("lookup_table must be a Quantity.")
# The integer location is at the centre of the pixel.
points = (np.arange(lookup_table.size) - 0) * points_unit
kwargs = {
'bounds_error': False,
'fill_value': np.nan,
'method': interpolation,
**kwargs
}
return m.Tabular1D(points, lookup_table, **kwargs)
def test_tabular_repr():
points = np.arange(5)
lt = np.arange(5)
t = models.Tabular1D(points, lt)
assert repr(t) ==\
"<Tabular1D(points=(array([0, 1, 2, 3, 4]),), lookup_table=[0 1 2 3 4])>"
table = np.arange(5 * 5).reshape(5, 5)
points = np.arange(0, 5)
points = (points, points)
t = models.Tabular2D(points=points, lookup_table=table)
assert repr(t) ==\
"<Tabular2D(points=(array([0, 1, 2, 3, 4]), array([0, 1, 2, 3, 4])), " +\
"lookup_table=[[ 0 1 2 3 4]\n" +\
" [ 5 6 7 8 9]\n" +\
" [10 11 12 13 14]\n" +\
" [15 16 17 18 19]\n" +\
" [20 21 22 23 24]])>"
assert_allclose(positional, model(1, 2))
with pytest.raises(ValueError):
model(1, 2, 3)
with pytest.raises(ValueError):
model(1)
with pytest.raises(ValueError):
model(1, 2, t=12, r=3)
@pytest.mark.parametrize('model', [
models.Gaussian1D(),
models.Polynomial1D(1, ),
models.Tabular1D(lookup_table=np.ones((5, ))),
models.Rotation2D(),
models.Pix2Sky_TAN()
])
@pytest.mark.skipif('not HAS_SCIPY')
def test_call_keyword_args_1(model):
"""
Test calling a model with positional, keywrd and a mixture of both arguments.
"""
positional = model(1)
assert_allclose(positional, model(x=1))
model.inputs = ('r', )
assert_allclose(positional, model(r=1))
with pytest.raises(ValueError):
def test_tabular_with_bounding_box():
points = np.arange(5)
values = np.array([1.5, 3.4, 6.7, 7, 32])
t = models.Tabular1D(points, values)
result = t(1, with_bounding_box=True)
def test_bounding_box_with_units():
points = np.arange(5)*u.pix
lt = np.arange(5)*u.AA
t = models.Tabular1D(points, lt)
assert(t(1*u.pix, with_bounding_box=True) == 1.*u.AA)
def v2v3lamtoxy(v2in, v3in, lamin, stype):
# Open relevant distortion file
specfile = fits.open(get_fitsreffile())
# Convert input vectors to numpy arrays
v2 = np.array(v2in)
v3 = np.array(v3in)
lam = np.array(lamin)
# Global header
hdr = specfile[0].header
# File data
lrsdata = np.array([l for l in specfile[1].data])
# Define zero points (in subarray frame), subarray location, subarray size
if (stype.lower() == 'slit'):
xsub0, ysub0 = 0, 0
xsub1, ysub1 = 1031, 1023
zero_point = hdr['imx'] - 1, hdr['imy'] - 1
elif (stype.lower() == 'slitless'):
xsub0, ysub0 = 0, 528
xsub1, ysub1 = 71, 415
zero_point = hdr['imxsltl'] - 1 - xsub0, hdr['imysltl'] - 1 - ysub0
else:
print('Invalid operation type: specify either slit or slitless')
# In the lrsdata reference table, X_center,y_center,wavelength describe the location of the
# centroid trace along the detector in pixels relative to nominal location.
# The box corners for this wavelength are x0,y0(ul) x1,y1 (ur) x2,y2(lr) x3,y3(ll)
# Use these to create the bounding box for all valid detector locations in units of subarray pixels
xcen = lrsdata[:, 0]
ycen = lrsdata[:, 1]
wavetab = lrsdata[:, 2]
x0 = lrsdata[:, 3]
y0 = lrsdata[:, 4]
x1 = lrsdata[:, 5]
y2 = lrsdata[:, 8]
bb = ((x0.min() - 0.5 + zero_point[0], x1.max() + 0.5 + zero_point[0]),
(y2.min() - 0.5 + zero_point[1], y0.max() + 0.5 + zero_point[1]))
# Now deal with the fact that the spectral trace isn't perfectly up and down along detector.
# This information is contained in the xcenter/ycenter values in the CDP table, but we'll handle it
# as a simple rotation using a linear fit to this relation provided by the CDP.
z = np.polyfit(xcen, ycen, 1)
slope = 1. / z[0]
traceangle = np.arctan(slope) * 180. / np.pi # trace angle in degrees
rot = models.Rotation2D(traceangle) # Rotation model
# Now include this rotation in our overall transform
# First shift to a frame relative to the trace zeropoint, then apply the rotation
# to correct for the curved trace. End in a rotated frame relative to zero at the reference point
# and where yrot is aligned with the spectral trace)
xysubtoxyrot = models.Shift(-zero_point[0]) & models.Shift(
-zero_point[1]) | rot
# Work out the spectral component of the transform
# First compute the reference trace in the rotated-Y frame
xcenrot, ycenrot = rot(xcen, ycen)
# The input table of wavelengths isn't perfect, and the delta-wavelength steps show some unphysical behaviour
# Therefore fit with a spline for the ycenrot->wavelength transform
# Reverse vectors so that yinv is increasing (needed for spline fitting function)
wavetab = lrsdata[:, 2]
yrev = ycenrot[::-1]
wrev = wavetab[::-1]
# Spline fit with enforced smoothness
spl = UnivariateSpline(yrev, wrev, s=0.002)
# Evaluate the fit at the rotated-y reference points
wavereference = spl(yrev)
# wavereference now contains the wavelengths corresponding to regularly-sampled ycenrot, create the model
wavemodel = models.Tabular1D(lookup_table=wavereference,
points=yrev,
name='waveref',
bounds_error=False,
fill_value=np.nan)
# Now construct the inverse spectral transform.
# First we need to create a spline going from wavereference -> ycenrot
spl2 = UnivariateSpline(wavereference[::-1], ycenrot, s=0.002)
# Compute the nominal x,y pixels in subarray frame for this v2,v3
xnom, ynom = mt.v2v3toxy(v2, v3, 'F770W')
xnom = xnom - xsub0
ynom = ynom - ysub0
# Compute this in the rotated frame
xrot, _ = xysubtoxyrot(xnom, ynom)
# Get the real yrot from the wavelength
yrot = spl2(lam)
# Convert rotated x,y to subarray x,y
xsub, ysub = xysubtoxyrot.inverse(xrot, yrot)
return xsub, ysub
def lrs_distortion(input_model, reference_files):
"""
The LRS-FIXEDSLIT and LRS-SLITLESS WCS pipeline.
Transform from subarray (x, y) to (v2, v3, lambda) using
the "specwcs" and "distortion" reference files.
"""
# subarray to full array transform
subarray2full = subarray_transform(input_model)
# full array to v2v3 transform for the ordinary imager
with DistortionModel(reference_files['distortion']) as dist:
distortion = dist.model
# Combine models to create subarray to v2v3 distortion
if subarray2full is not None:
subarray_dist = subarray2full | distortion
else:
subarray_dist = distortion
# Read in the reference table data and get the zero point (SIAF reference point)
# of the LRS in the subarray ref frame
with fits.open(reference_files['specwcs']) as ref:
lrsdata = np.array([l for l in ref[1].data])
# Get the zero point from the reference data.
# The zero_point is X, Y (which should be COLUMN, ROW)
# These are 1-indexed in CDP-7 (i.e., SIAF convention) so must be converted to 0-indexed
if input_model.meta.exposure.type.lower() == 'mir_lrs-fixedslit':
zero_point = ref[0].header['imx'] - 1, ref[0].header['imy'] - 1
elif input_model.meta.exposure.type.lower() == 'mir_lrs-slitless':
zero_point = ref[0].header['imxsltl'] - 1, ref[0].header[
'imysltl'] - 1
# Transform to slitless subarray from full array
zero_point = subarray2full.inverse(zero_point[0], zero_point[1])
# In the lrsdata reference table, X_center,y_center,wavelength describe the location of the
# centroid trace along the detector in pixels relative to nominal location.
# x0,y0(ul) x1,y1 (ur) x2,y2(lr) x3,y3(ll) define corners of the box within which the distortion
# and wavelength calibration was derived
xcen = lrsdata[:, 0]
ycen = lrsdata[:, 1]
wavetab = lrsdata[:, 2]
x0 = lrsdata[:, 3]
y0 = lrsdata[:, 4]
x1 = lrsdata[:, 5]
y2 = lrsdata[:, 8]
# If in fixed slit mode, define the bounding box using the corner locations provided in
# the CDP reference file.
if input_model.meta.exposure.type.lower() == 'mir_lrs-fixedslit':
bb_sub = ((np.floor(x0.min() + zero_point[0]) - 0.5,
np.ceil(x1.max() + zero_point[0]) + 0.5),
(np.floor(y2.min() + zero_point[1]) - 0.5,
np.ceil(y0.max() + zero_point[1]) + 0.5))
# If in slitless mode, define the bounding box X locations using the subarray x boundaries
# and the y locations using the corner locations in the CDP reference file. Make sure to
# omit the 4 reference pixels on the left edge of slitless subarray.
if input_model.meta.exposure.type.lower() == 'mir_lrs-slitless':
bb_sub = ((input_model.meta.subarray.xstart - 1 + 4 - 0.5,
input_model.meta.subarray.xsize - 1 + 0.5),
(np.floor(y2.min() + zero_point[1]) - 0.5,
np.ceil(y0.max() + zero_point[1]) + 0.5))
# Find the ROW of the zero point
row_zero_point = zero_point[1]
# The inputs to the "detector_to_v2v3" transform are
# - the indices in x spanning the entire image row
# - y is the y-value of the zero point
# This is equivalent of making a vector of x, y locations for
# every pixel in the reference row
const1d = models.Const1D(row_zero_point)
const1d.inverse = models.Const1D(row_zero_point)
det_to_v2v3 = models.Identity(1) & const1d | subarray_dist
# Now deal with the fact that the spectral trace isn't perfectly up and down along detector.
# This information is contained in the xcenter/ycenter values in the CDP table, but we'll handle it
# as a simple rotation using a linear fit to this relation provided by the CDP.
z = np.polyfit(xcen, ycen, 1)
slope = 1. / z[0]
traceangle = np.arctan(slope) * 180. / np.pi # trace angle in degrees
rot = models.Rotation2D(traceangle) # Rotation model
# Now include this rotation in our overall transform
# First shift to a frame relative to the trace zeropoint, then apply the rotation
# to correct for the curved trace. End in a rotated frame relative to zero at the reference point
# and where yrot is aligned with the spectral trace)
xysubtoxyrot = models.Shift(-zero_point[0]) & models.Shift(
-zero_point[1]) | rot
# Next shift back to the subarray frame, and then map to v2v3
xyrottov2v3 = models.Shift(zero_point[0]) & models.Shift(
zero_point[1]) | det_to_v2v3
# The two models together
xysubtov2v3 = xysubtoxyrot | xyrottov2v3
# Work out the spectral component of the transform
# First compute the reference trace in the rotated-Y frame
xcenrot, ycenrot = rot(xcen, ycen)
# The input table of wavelengths isn't perfect, and the delta-wavelength
# steps show some unphysical behaviour
# Therefore fit with a spline for the ycenrot->wavelength transform
# Reverse vectors so that yinv is increasing (needed for spline fitting function)
yrev = ycenrot[::-1]
wrev = wavetab[::-1]
# Spline fit with enforced smoothness
spl = UnivariateSpline(yrev, wrev, s=0.002)
# Evaluate the fit at the rotated-y reference points
wavereference = spl(yrev)
# wavereference now contains the wavelengths corresponding to regularly-sampled ycenrot, create the model
wavemodel = models.Tabular1D(lookup_table=wavereference,
points=yrev,
name='waveref',
bounds_error=False,
fill_value=np.nan)
# Now construct the inverse spectral transform.
# First we need to create a spline going from wavereference -> ycenrot
spl2 = UnivariateSpline(wavereference[::-1], ycenrot, s=0.002)
# Make a uniform grid of wavelength points from min to max, sampled according
# to the minimum delta in the input table
dw = np.amin(np.absolute(np.diff(wavereference)))
wmin = np.amin(wavereference)
wmax = np.amax(wavereference)
wgrid = np.arange(wmin, wmax, dw)
# Evaluate the rotated y locations of the grid
ygrid = spl2(wgrid)
# ygrid now contains the rotated y pixel locations corresponding to
# regularly-sampled wavelengths, create the model
wavemodel.inverse = models.Tabular1D(lookup_table=ygrid,
points=wgrid,
name='waverefinv',
bounds_error=False,
fill_value=np.nan)
# Wavelength barycentric correction
try:
velosys = input_model.meta.wcsinfo.velosys
except AttributeError:
pass
else:
if velosys is not None:
velocity_corr = velocity_correction(
input_model.meta.wcsinfo.velosys)
wavemodel = wavemodel | velocity_corr
log.info("Applied Barycentric velocity correction : {}".format(
velocity_corr[1].amplitude.value))
# Construct the full distortion model (xsub,ysub -> v2,v3,wavelength)
lrs_wav_model = xysubtoxyrot | models.Mapping([1], n_inputs=2) | wavemodel
dettotel = models.Mapping((0, 1, 0, 1)) | xysubtov2v3 & lrs_wav_model
# Construct the inverse distortion model (v2,v3,wavelength -> xsub,ysub)
# Transform to get xrot from v2,v3
v2v3toxrot = subarray_dist.inverse | xysubtoxyrot | models.Mapping(
[0], n_inputs=2)
# wavemodel.inverse gives yrot from wavelength
# v2,v3,lambda -> xrot,yrot
xform1 = v2v3toxrot & wavemodel.inverse
dettotel.inverse = xform1 | xysubtoxyrot.inverse
# Bounding box is the subarray bounding box, because we're assuming subarray coordinates passed in
dettotel.bounding_box = bb_sub[::-1]
return dettotel
astropy_models.Sky2Pix_ZenithalPerspective(mu=1.5, gamma=15.0),
# astropy.modeling.rotations
astropy_models.EulerAngleRotation(23, 14, 2.3, axes_order="xzx"),
astropy_models.RotateCelestial2Native(5.63, -72.5, 180),
astropy_models.RotateCelestial2Native(5.63 * u.deg, -72.5 * u.deg,
180 * u.deg),
astropy_models.RotateNative2Celestial(5.63, -72.5, 180),
astropy_models.RotateNative2Celestial(5.63 * u.deg, -72.5 * u.deg,
180 * u.deg),
astropy_models.Rotation2D(angle=1.51),
astropy_models.RotationSequence3D([1.2, 2.3, 3.4, .3], "xyzx"),
astropy_models.SphericalRotationSequence([1.2, 2.3, 3.4, .3], "xyzy"),
# astropy.modeling.tabular
astropy_models.Tabular1D(points=np.arange(0, 5),
lookup_table=[1., 10, 2, 45, -3]),
astropy_models.Tabular1D(points=np.arange(0, 5) * u.pix,
lookup_table=[1., 10, 2, 45, -3] * u.nm),
astropy_models.Tabular2D(
points=([1, 2, 3], [1, 2, 3]),
lookup_table=np.arange(0, 9).reshape(3, 3),
bounds_error=False,
fill_value=None,
method="nearest",
),
astropy_models.Tabular2D(
points=([1, 2, 3], [1, 2, 3]) * u.pix,
lookup_table=np.arange(0, 9).reshape(3, 3) * u.nm,
bounds_error=False,
fill_value=None,
method="nearest",