def wcs_from_spec_footprints(wcslist, refwcs=None, transform=None, domain=None):
"""
Create a WCS from a list of spatial/spectral WCS.
Build-7 workaround.
"""
if not isiterable(wcslist):
raise ValueError("Expected 'wcslist' to be an iterable of gwcs.WCS")
if not all([isinstance(w, WCS) for w in wcslist]):
raise TypeError("All items in 'wcslist' must have instance of gwcs.WCS")
if refwcs is None:
refwcs = wcslist[0]
else:
if not isinstance(refwcs, WCS):
raise TypeError("Expected refwcs to be an instance of gwcs.WCS.")
# TODO: generalize an approach to do this for more than one wcs. For
# now, we just do it for one, using the api for a list of wcs.
# Compute a fiducial point for the output frame at center of input data
fiducial = compute_spec_fiducial(wcslist, domain=domain)
# Create transform for output frame
transform = compute_spec_transform(fiducial, refwcs)
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the domain in the output frame wcs object by running the input wcs
# footprints through the backward transform of the output wcs
sky = [spec_footprint(w) for w in wcslist]
domain_grid = [wnew.backward_transform(*f) for f in sky]
sky0 = sky[0]
det = domain_grid[0]
offsets = []
input_frame = refwcs.input_frame
for axis in input_frame.axes_order:
axis_min = np.nanmin(det[axis])
offsets.append(axis_min)
transform = Shift(offsets[0]) & Shift(offsets[1]) | transform
wnew = WCS(output_frame=output_frame, input_frame=input_frame,
forward_transform=transform)
domain = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(domain_grid[0][axis])
axis_max = np.nanmax(domain_grid[0][axis]) + 1
domain.append({'lower': axis_min, 'upper': axis_max,
'includes_lower': True, 'includes_upper': False})
wnew.domain = domain
return wnew
def compute_scale(wcs: WCS, fiducial: Union[tuple, np.ndarray]) -> float:
"""Compute scaling transform.
Parameters
----------
wcs : `~gwcs.wcs.WCS`
Reference WCS object from which to compute a scaling factor.
fiducial : tuple
Input fiducial of (RA, DEC) used in calculating reference points.
Returns
-------
scale : float
Scaling factor for x and y.
"""
if len(fiducial) != 2:
raise ValueError(f'Input fiducial must contain only (RA, DEC); Instead recieved: {fiducial}')
crpix = np.array(wcs.invert(*fiducial))
crpix_with_offsets = np.vstack((crpix, crpix + (1, 0), crpix + (0, 1))).T
crval_with_offsets = wcs(*crpix_with_offsets)
coords = SkyCoord(ra=crval_with_offsets[0], dec=crval_with_offsets[1], unit="deg")
xscale = np.abs(coords[0].separation(coords[1]).value)
yscale = np.abs(coords[0].separation(coords[2]).value)
return np.sqrt(xscale * yscale)
def compute_scale(wcs: WCS,
fiducial: Union[tuple, np.ndarray],
disp_axis: int = None,
pscale_ratio: float = None) -> float:
"""Compute scaling transform.
Parameters
----------
wcs : `~gwcs.wcs.WCS`
Reference WCS object from which to compute a scaling factor.
fiducial : tuple
Input fiducial of (RA, DEC) or (RA, DEC, Wavelength) used in calculating reference points.
disp_axis : int
Dispersion axis integer. Assumes the same convention as `wcsinfo.dispersion_direction`
pscale_ratio : int
Ratio of input to output pixel scale
Returns
-------
scale : float
Scaling factor for x and y or cross-dispersion direction.
"""
spectral = 'SPECTRAL' in wcs.output_frame.axes_type
if spectral and disp_axis is None:
raise ValueError('If input WCS is spectral, a disp_axis must be given')
crpix = np.array(wcs.invert(*fiducial))
delta = np.zeros_like(crpix)
spatial_idx = np.where(
np.array(wcs.output_frame.axes_type) == 'SPATIAL')[0]
delta[spatial_idx[0]] = 1
crpix_with_offsets = np.vstack(
(crpix, crpix + delta, crpix + np.roll(delta, 1))).T
crval_with_offsets = wcs(*crpix_with_offsets)
coords = SkyCoord(ra=crval_with_offsets[spatial_idx[0]],
dec=crval_with_offsets[spatial_idx[1]],
unit="deg")
xscale = np.abs(coords[0].separation(coords[1]).value)
yscale = np.abs(coords[0].separation(coords[2]).value)
if pscale_ratio is not None:
xscale = xscale * pscale_ratio
yscale = yscale * pscale_ratio
if spectral:
# Assuming scale doesn't change with wavelength
# Assuming disp_axis is consistent with DataModel.meta.wcsinfo.dispersion.direction
return yscale if disp_axis == 1 else xscale
return np.sqrt(xscale * yscale)
def gwcs_1d():
detector_frame = cf.CoordinateFrame(
name="detector",
naxes=1,
axes_order=(0, ),
axes_type=("pixel"),
axes_names=("x"),
unit=(u.pix))
spec_frame = cf.SpectralFrame(name="spectral", axes_order=(2, ), unit=u.nm)
return WCS(forward_transform=Identity(1), input_frame=detector_frame, output_frame=spec_frame)
def assign_moving_target_wcs(input_model):
if not isinstance(input_model, datamodels.ModelContainer):
raise ValueError("Expected a ModelContainer object")
# Get the MT RA/Dec values from all the input exposures
mt_ra = np.array(
[model.meta.wcsinfo.mt_ra for model in input_model._models])
mt_dec = np.array(
[model.meta.wcsinfo.mt_dec for model in input_model._models])
# Compute the mean MT RA/Dec over all exposures
if (None in mt_ra) or (None in mt_dec):
log.warning("One or more MT RA/Dec values missing in input images")
log.warning("Step will be skipped, resulting in target misalignment")
for model in input_model:
model.meta.cal_step.assign_mtwcs = 'SKIPPED'
return input_model
else:
mt_avra = mt_ra.mean()
mt_avdec = mt_dec.mean()
for model in input_model:
pipeline = model.meta.wcs._pipeline[:-1]
mt = deepcopy(model.meta.wcs.output_frame)
mt.name = 'moving_target'
mt_ra = model.meta.wcsinfo.mt_ra
mt_dec = model.meta.wcsinfo.mt_dec
model.meta.wcsinfo.mt_avra = mt_avra
model.meta.wcsinfo.mt_avdec = mt_avdec
rdel = mt_avra - mt_ra
ddel = mt_avdec - mt_dec
if isinstance(mt, cf.CelestialFrame):
transform_to_mt = Shift(rdel) & Shift(ddel)
elif isinstance(mt, cf.CompositeFrame):
transform_to_mt = Shift(rdel) & Shift(ddel) & Identity(1)
else:
raise ValueError("Unrecognized coordinate frame.")
pipeline.append((model.meta.wcs.output_frame, transform_to_mt))
pipeline.append((mt, None))
new_wcs = WCS(pipeline)
del model.meta.wcs
model.meta.wcs = new_wcs
model.meta.cal_step.assign_mtwcs = 'COMPLETE'
return input_model
def wcs_from_spec_footprints(wcslist,
refwcs=None,
transform=None,
domain=None):
"""
Create a WCS from a list of spatial/spectral WCS.
Build-7 workaround.
"""
if not isiterable(wcslist):
raise ValueError("Expected 'wcslist' to be an iterable of gwcs.WCS")
if not all([isinstance(w, WCS) for w in wcslist]):
raise TypeError(
"All items in 'wcslist' must have instance of gwcs.WCS")
if refwcs is None:
refwcs = wcslist[0]
else:
if not isinstance(refwcs, WCS):
raise TypeError("Expected refwcs to be an instance of gwcs.WCS.")
# TODO: generalize an approach to do this for more than one wcs. For
# now, we just do it for one, using the api for a list of wcs.
# Compute a fiducial point for the output frame at center of input data
fiducial = compute_spec_fiducial(wcslist, domain=domain)
# Create transform for output frame
transform = compute_spec_transform(fiducial, refwcs)
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the domain in the output frame wcs object by running the input wcs
# footprints through the backward transform of the output wcs
sky = [spec_footprint(w) for w in wcslist]
domain_grid = [wnew.backward_transform(*f) for f in sky]
sky0 = sky[0]
det = domain_grid[0]
offsets = []
input_frame = refwcs.input_frame
for axis in input_frame.axes_order:
axis_min = np.nanmin(det[axis])
offsets.append(axis_min)
transform = Shift(offsets[0]) & Shift(offsets[1]) | transform
wnew = WCS(output_frame=output_frame,
input_frame=input_frame,
forward_transform=transform)
domain = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(domain_grid[0][axis])
axis_max = np.nanmax(domain_grid[0][axis]) + 1
domain.append({
'lower': axis_min,
'upper': axis_max,
'includes_lower': True,
'includes_upper': False
})
wnew.domain = domain
return wnew
def gwcs_3d():
detector_frame = cf.CoordinateFrame(
name="detector",
naxes=3,
axes_order=(0, 1, 2),
axes_type=("pixel", "pixel", "pixel"),
axes_names=("x", "y", "z"),
unit=(u.pix, u.pix, u.pix))
sky_frame = cf.CelestialFrame(reference_frame=Helioprojective(), name='hpc')
spec_frame = cf.SpectralFrame(name="spectral", axes_order=(2, ), unit=u.nm)
out_frame = cf.CompositeFrame(frames=(sky_frame, spec_frame))
return WCS(forward_transform=spatial_like_model(),
input_frame=detector_frame, output_frame=out_frame)
def add_mt_frame(wcs, ra_average, dec_average, mt_ra, mt_dec):
""" Add a "moving_target" frame to the WCS pipeline.
Parameters
----------
wcs : `~gwcs.WCS`
WCS object for the observation or slit.
ra_average : float
The average RA of all observations.
dec_average : float
The average DEC of all observations.
mt_ra, mt_dec : float
The RA, DEC of the moving target in the observation.
Returns
-------
new_wcs : `~gwcs.WCS`
The WCS for the moving target observation.
"""
pipeline = wcs._pipeline[:-1]
mt = deepcopy(wcs.output_frame)
mt.name = 'moving_target'
rdel = ra_average - mt_ra
ddel = dec_average - mt_dec
if isinstance(mt, cf.CelestialFrame):
transform_to_mt = Shift(rdel) & Shift(ddel)
elif isinstance(mt, cf.CompositeFrame):
transform_to_mt = Shift(rdel) & Shift(ddel) & Identity(1)
else:
raise ValueError("Unrecognized coordinate frame.")
pipeline.append((
wcs.output_frame, transform_to_mt))
pipeline.append((mt, None))
new_wcs = WCS(pipeline)
return new_wcs
def assign_moving_target_wcs(input_model):
if not isinstance(input_model, datamodels.ModelContainer):
raise ValueError("Expected a ModelContainer object")
mt_ra = np.array(
[model.meta.wcsinfo.mt_ra for model in input_model._models])
mt_dec = np.array(
[model.meta.wcsinfo.mt_dec for model in input_model._models])
mt_avra = mt_ra.mean()
mt_avdec = mt_dec.mean()
for model in input_model:
pipeline = model.meta.wcs._pipeline[:-1]
mt = deepcopy(model.meta.wcs.output_frame)
mt.name = 'moving_target'
mt_ra = model.meta.wcsinfo.mt_ra
mt_dec = model.meta.wcsinfo.mt_dec
model.meta.wcsinfo.mt_avra = mt_avra
model.meta.wcsinfo.mt_avdec = mt_avdec
rdel = mt_avra - mt_ra
ddel = mt_avdec - mt_dec
if isinstance(mt, cf.CelestialFrame):
transform_to_mt = Shift(rdel) & Shift(ddel)
elif isinstance(mt, cf.CompositeFrame):
transform_to_mt = Shift(rdel) & Shift(ddel) & Identity(1)
else:
raise ValueError("Unrecognized coordinate frame.")
pipeline.append((model.meta.wcs.output_frame, transform_to_mt))
pipeline.append((mt, None))
new_wcs = WCS(pipeline)
del model.meta.wcs
model.meta.wcs = new_wcs
model.meta.cal_step.assign_mtwcs = 'COMPLETE'
return input_model
def build_nirspec_output_wcs(self, refmodel=None):
"""
Create a spatial/spectral WCS covering footprint of the input
"""
all_wcs = [m.meta.wcs for m in self.input_models if m is not refmodel]
if refmodel:
all_wcs.insert(0, refmodel.meta.wcs)
else:
refmodel = self.input_models[0]
refwcs = refmodel.meta.wcs
s2d = refwcs.get_transform('slit_frame', 'detector')
d2s = refwcs.get_transform('detector', 'slit_frame')
s2w = refwcs.get_transform('slit_frame', 'world')
# estimate position of the target without relying in the meta.target:
bbox = refwcs.bounding_box
grid = wcstools.grid_from_bounding_box(bbox)
_, s, lam = np.array(d2s(*grid))
sd = s * refmodel.data
ld = lam * refmodel.data
good_s = np.isfinite(sd)
if np.any(good_s):
total = np.sum(refmodel.data[good_s])
wmean_s = np.sum(sd[good_s]) / total
wmean_l = np.sum(ld[good_s]) / total
else:
wmean_s = 0.5 * (refmodel.slit_ymax - refmodel.slit_ymin)
wmean_l = d2s(*np.mean(bbox, axis=1))[2]
targ_ra, targ_dec, _ = s2w(0, wmean_s, wmean_l)
ref_lam = _find_nirspec_output_sampling_wavelengths(
all_wcs,
targ_ra, targ_dec
)
ref_lam = np.array(ref_lam)
n_lam = ref_lam.size
if not n_lam:
raise ValueError("Not enough data to construct output WCS.")
x_slit = np.zeros(n_lam)
lam = 1e-6 * ref_lam
# Find the spatial pixel scale:
y_slit_min, y_slit_max = self._max_virtual_slit_extent(all_wcs, targ_ra, targ_dec)
nsampl = 50
xy_min = s2d(
nsampl * [0],
nsampl * [y_slit_min],
lam[(tuple((i * n_lam) // nsampl for i in range(nsampl)), )]
)
xy_max = s2d(
nsampl * [0],
nsampl * [y_slit_max],
lam[(tuple((i * n_lam) // nsampl for i in range(nsampl)), )]
)
good = np.logical_and(np.isfinite(xy_min), np.isfinite(xy_max))
if not np.any(good):
raise ValueError("Error estimating output WCS pixel scale.")
xy1 = s2d(x_slit, np.full(n_lam, refmodel.slit_ymin), lam)
xy2 = s2d(x_slit, np.full(n_lam, refmodel.slit_ymax), lam)
xylen = np.nanmax(np.linalg.norm(np.array(xy1) - np.array(xy2), axis=0)) + 1
pscale = (refmodel.slit_ymax - refmodel.slit_ymin) / xylen
# compute image span along Y-axis (length of the slit in the detector plane)
# det_slit_span = np.linalg.norm(np.subtract(xy_max, xy_min))
det_slit_span = np.nanmax(np.linalg.norm(np.subtract(xy_max, xy_min), axis=0))
ny = int(np.ceil(det_slit_span * self.pscale_ratio + 0.5)) + 1
border = 0.5 * (ny - det_slit_span * self.pscale_ratio) - 0.5
if xy_min[1][1] < xy_max[1][1]:
y_slit_model = Linear1D(
slope=pscale / self.pscale_ratio,
intercept=y_slit_min - border * pscale * self.pscale_ratio
)
else:
y_slit_model = Linear1D(
slope=-pscale / self.pscale_ratio,
intercept=y_slit_max + border * pscale * self.pscale_ratio
)
# extrapolate 1/2 pixel at the edges and make tabular model w/inverse:
lam = lam.tolist()
pixel_coord = list(range(n_lam))
if len(pixel_coord) > 1:
# left:
slope = (lam[1] - lam[0]) / pixel_coord[1]
lam.insert(0, -0.5 * slope + lam[0])
pixel_coord.insert(0, -0.5)
# right:
slope = (lam[-1] - lam[-2]) / (pixel_coord[-1] - pixel_coord[-2])
lam.append(slope * (pixel_coord[-1] + 0.5) + lam[-2])
pixel_coord.append(pixel_coord[-1] + 0.5)
else:
lam = 3 * lam
pixel_coord = [-0.5, 0, 0.5]
wavelength_transform = Tabular1D(points=pixel_coord,
lookup_table=lam,
bounds_error=False, fill_value=np.nan)
wavelength_transform.inverse = Tabular1D(points=lam,
lookup_table=pixel_coord,
bounds_error=False,
fill_value=np.nan)
self.data_size = (ny, len(ref_lam))
# Construct the final transform
mapping = Mapping((0, 1, 0))
mapping.inverse = Mapping((2, 1))
out_det2slit = mapping | Identity(1) & y_slit_model & wavelength_transform
# Create coordinate frames
det = cf.Frame2D(name='detector', axes_order=(0, 1))
slit_spatial = cf.Frame2D(name='slit_spatial', axes_order=(0, 1),
unit=("", ""), axes_names=('x_slit', 'y_slit'))
spec = cf.SpectralFrame(name='spectral', axes_order=(2,),
unit=(u.micron,), axes_names=('wavelength',))
slit_frame = cf.CompositeFrame([slit_spatial, spec], name='slit_frame')
sky = cf.CelestialFrame(name='sky', axes_order=(0, 1),
reference_frame=coord.ICRS())
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, out_det2slit), (slit_frame, s2w), (world, None)]
output_wcs = WCS(pipeline)
# Compute bounding box and output array shape. Add one to the y (slit)
# height to account for the half pixel at top and bottom due to pixel
# coordinates being centers of pixels
bounding_box = resample_utils.wcs_bbox_from_shape(self.data_size)
output_wcs.bounding_box = bounding_box
output_wcs.array_shape = self.data_size
return output_wcs
def build_nirspec_lamp_output_wcs(self):
"""
Create a spatial/spectral WCS output frame for NIRSpec lamp mode
Creates output frame by linearly fitting x_msa, y_msa along the slit and
producing a lookup table to interpolate wavelengths in the dispersion
direction.
Returns
-------
output_wcs : `~gwcs.WCS` object
A gwcs WCS object defining the output frame WCS
"""
model = self.input_models[0]
wcs = model.meta.wcs
bbox = wcs.bounding_box
grid = wcstools.grid_from_bounding_box(bbox)
x_msa, y_msa, lam = np.array(wcs(*grid))
# Handle vertical (MIRI) or horizontal (NIRSpec) dispersion. The
# following 2 variables are 0 or 1, i.e. zero-indexed in x,y WCS order
spectral_axis = find_dispersion_axis(model)
spatial_axis = spectral_axis ^ 1
# Compute the wavelength array, trimming NaNs from the ends
# In many cases, a whole slice is NaNs, so ignore those warnings
warnings.simplefilter("ignore")
wavelength_array = np.nanmedian(lam, axis=spectral_axis)
warnings.resetwarnings()
wavelength_array = wavelength_array[~np.isnan(wavelength_array)]
# Find the center ra and dec for this slit at central wavelength
lam_center_index = int((bbox[spectral_axis][1] -
bbox[spectral_axis][0]) / 2)
x_msa_array = x_msa.T[lam_center_index]
y_msa_array = y_msa.T[lam_center_index]
x_msa_array = x_msa_array[~np.isnan(x_msa_array)]
y_msa_array = y_msa_array[~np.isnan(y_msa_array)]
# Estimate and fit the spatial sampling
fitter = LinearLSQFitter()
fit_model = Linear1D()
xstop = x_msa_array.shape[0] / self.pscale_ratio
xstep = 1 / self.pscale_ratio
ystop = y_msa_array.shape[0] / self.pscale_ratio
ystep = 1 / self.pscale_ratio
pix_to_x_msa = fitter(fit_model, np.arange(0, xstop, xstep), x_msa_array)
pix_to_y_msa = fitter(fit_model, np.arange(0, ystop, ystep), y_msa_array)
step = 1 / self.pscale_ratio
stop = wavelength_array.shape[0] / self.pscale_ratio
points = np.arange(0, stop, step)
pix_to_wavelength = Tabular1D(points=points,
lookup_table=wavelength_array,
bounds_error=False, fill_value=None,
name='pix2wavelength')
# Tabular models need an inverse explicitly defined.
# If the wavelength array is descending instead of ascending, both
# points and lookup_table need to be reversed in the inverse transform
# for scipy.interpolate to work properly
points = wavelength_array
lookup_table = np.arange(0, stop, step)
if not np.all(np.diff(wavelength_array) > 0):
points = points[::-1]
lookup_table = lookup_table[::-1]
pix_to_wavelength.inverse = Tabular1D(points=points,
lookup_table=lookup_table,
bounds_error=False, fill_value=None,
name='wavelength2pix')
# For the input mapping, duplicate the spatial coordinate
mapping = Mapping((spatial_axis, spatial_axis, spectral_axis))
mapping.inverse = Mapping((2, 1))
# The final transform
# define the output wcs
transform = mapping | pix_to_x_msa & pix_to_y_msa & pix_to_wavelength
det = cf.Frame2D(name='detector', axes_order=(0, 1))
sky = cf.Frame2D(name=f'resampled_{model.meta.wcs.output_frame.name}', axes_order=(0, 1))
spec = cf.SpectralFrame(name='spectral', axes_order=(2,),
unit=(u.micron,), axes_names=('wavelength',))
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, transform),
(world, None)]
output_wcs = WCS(pipeline)
# Compute the output array size and bounding box
output_array_size = [0, 0]
output_array_size[spectral_axis] = int(np.ceil(len(wavelength_array) / self.pscale_ratio))
x_size = len(x_msa_array)
output_array_size[spatial_axis] = int(np.ceil(x_size / self.pscale_ratio))
# turn the size into a numpy shape in (y, x) order
output_wcs.array_shape = output_array_size[::-1]
output_wcs.pixel_shape = output_array_size
bounding_box = resample_utils.wcs_bbox_from_shape(output_array_size[::-1])
output_wcs.bounding_box = bounding_box
return output_wcs
def build_interpolated_output_wcs(self, refmodel=None):
"""
Create a spatial/spectral WCS output frame
Creates output frame by linearly fitting RA, Dec along the slit and
producing a lookup table to interpolate wavelengths in the dispersion
direction.
Parameters
----------
refmodel : `~jwst.datamodels.DataModel`
The reference input image from which the fiducial WCS is created.
If not specified, the first image in self.input_models is used.
Returns
-------
output_wcs : `~gwcs.WCS` object
A gwcs WCS object defining the output frame WCS
"""
if refmodel is None:
refmodel = self.input_models[0]
refwcs = refmodel.meta.wcs
bb = refwcs.bounding_box
grid = wcstools.grid_from_bounding_box(bb)
ra, dec, lam = np.array(refwcs(*grid))
spectral_axis = find_dispersion_axis(lam)
spatial_axis = spectral_axis ^ 1
# Compute the wavelength array, trimming NaNs from the ends
wavelength_array = np.nanmedian(lam, axis=spectral_axis)
wavelength_array = wavelength_array[~np.isnan(wavelength_array)]
# Compute RA and Dec up the slit (spatial direction) at the center
# of the dispersion. Use spectral_axis to determine slicing dimension
lam_center_index = int((bb[spectral_axis][1] - bb[spectral_axis][0]) / 2)
if not spectral_axis:
ra_array = ra.T[lam_center_index]
dec_array = dec.T[lam_center_index]
else:
ra_array = ra[lam_center_index]
dec_array = dec[lam_center_index]
ra_array = ra_array[~np.isnan(ra_array)]
dec_array = dec_array[~np.isnan(dec_array)]
fitter = LinearLSQFitter()
fit_model = Linear1D()
pix_to_ra = fitter(fit_model, np.arange(ra_array.shape[0]), ra_array)
pix_to_dec = fitter(fit_model, np.arange(dec_array.shape[0]), dec_array)
# Tabular interpolation model, pixels -> lambda
pix_to_wavelength = Tabular1D(lookup_table=wavelength_array,
bounds_error=False, fill_value=None, name='pix2wavelength')
# Tabular models need an inverse explicitly defined.
# If the wavelength array is decending instead of ascending, both
# points and lookup_table need to be reversed in the inverse transform
# for scipy.interpolate to work properly
points = wavelength_array
lookup_table = np.arange(wavelength_array.shape[0])
if not np.all(np.diff(wavelength_array) > 0):
points = points[::-1]
lookup_table = lookup_table[::-1]
pix_to_wavelength.inverse = Tabular1D(points=points,
lookup_table=lookup_table,
bounds_error=False, fill_value=None, name='wavelength2pix')
# For the input mapping, duplicate the spatial coordinate
mapping = Mapping((spatial_axis, spatial_axis, spectral_axis))
# Sometimes the slit is perpendicular to the RA or Dec axis.
# For example, if the slit is perpendicular to RA, that means
# the slope of pix_to_ra will be nearly zero, so make sure
# mapping.inverse uses pix_to_dec.inverse. The auto definition
# of mapping.inverse is to use the 2nd spatial coordinate, i.e. Dec.
if np.isclose(pix_to_dec.slope, 0, atol=1e-8):
mapping_tuple = (0, 1)
# Account for vertical or horizontal dispersion on detector
if spatial_axis:
mapping.inverse = Mapping(mapping_tuple[::-1])
else:
mapping.inverse = Mapping(mapping_tuple)
# The final transform
transform = mapping | pix_to_ra & pix_to_dec & pix_to_wavelength
det = cf.Frame2D(name='detector', axes_order=(0, 1))
sky = cf.CelestialFrame(name='sky', axes_order=(0, 1),
reference_frame=coord.ICRS())
spec = cf.SpectralFrame(name='spectral', axes_order=(2,),
unit=(u.micron,), axes_names=('wavelength',))
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, transform),
(world, None)]
output_wcs = WCS(pipeline)
# compute the output array size in WCS axes order, i.e. (x, y)
output_array_size = [0, 0]
output_array_size[spectral_axis] = len(wavelength_array)
output_array_size[spatial_axis] = len(ra_array)
# turn the size into a numpy shape in (y, x) order
self.data_size = tuple(output_array_size[::-1])
bounding_box = resample_utils.wcs_bbox_from_shape(self.data_size)
output_wcs.bounding_box = bounding_box
return output_wcs
def build_interpolated_output_wcs(self, refmodel=None):
"""
Create a spatial/spectral WCS output frame
Creates output frame by linearly fitting RA, Dec along the slit and
producing a lookup table to interpolate wavelengths in the dispersion
direction.
Parameters
----------
refmodel : `~jwst.datamodels.DataModel`
The reference input image from which the fiducial WCS is created.
If not specified, the first image in self.input_models is used.
Returns
-------
output_wcs : `~gwcs.WCS` object
A gwcs WCS object defining the output frame WCS
"""
if refmodel is None:
refmodel = self.input_models[0]
refwcs = refmodel.meta.wcs
bb = refwcs.bounding_box
grid = wcstools.grid_from_bounding_box(bb)
ra, dec, lam = np.array(refwcs(*grid))
spectral_axis = find_dispersion_axis(lam)
spatial_axis = spectral_axis ^ 1
# Compute the wavelength array, trimming NaNs from the ends
wavelength_array = np.nanmedian(lam, axis=spectral_axis)
wavelength_array = wavelength_array[~np.isnan(wavelength_array)]
# Compute RA and Dec up the slit (spatial direction) at the center
# of the dispersion. Use spectral_axis to determine slicing dimension
lam_center_index = int(
(bb[spectral_axis][1] - bb[spectral_axis][0]) / 2)
if not spectral_axis:
ra_array = ra.T[lam_center_index]
dec_array = dec.T[lam_center_index]
else:
ra_array = ra[lam_center_index]
dec_array = dec[lam_center_index]
ra_array = ra_array[~np.isnan(ra_array)]
dec_array = dec_array[~np.isnan(dec_array)]
fitter = LinearLSQFitter()
fit_model = Linear1D()
pix_to_ra = fitter(fit_model, np.arange(ra_array.shape[0]), ra_array)
pix_to_dec = fitter(fit_model, np.arange(dec_array.shape[0]),
dec_array)
# Tabular interpolation model, pixels -> lambda
pix_to_wavelength = Tabular1D(lookup_table=wavelength_array,
bounds_error=False,
fill_value=None,
name='pix2wavelength')
# Tabular models need an inverse explicitly defined.
# If the wavelength array is decending instead of ascending, both
# points and lookup_table need to be reversed in the inverse transform
# for scipy.interpolate to work properly
points = wavelength_array
lookup_table = np.arange(wavelength_array.shape[0])
if not np.all(np.diff(wavelength_array) > 0):
points = points[::-1]
lookup_table = lookup_table[::-1]
pix_to_wavelength.inverse = Tabular1D(points=points,
lookup_table=lookup_table,
bounds_error=False,
fill_value=None,
name='wavelength2pix')
# For the input mapping, duplicate the spatial coordinate
mapping = Mapping((spatial_axis, spatial_axis, spectral_axis))
# Sometimes the slit is perpendicular to the RA or Dec axis.
# For example, if the slit is perpendicular to RA, that means
# the slope of pix_to_ra will be nearly zero, so make sure
# mapping.inverse uses pix_to_dec.inverse. The auto definition
# of mapping.inverse is to use the 2nd spatial coordinate, i.e. Dec.
if np.isclose(pix_to_dec.slope, 0, atol=1e-8):
mapping_tuple = (0, 1)
# Account for vertical or horizontal dispersion on detector
if spatial_axis:
mapping.inverse = Mapping(mapping_tuple[::-1])
else:
mapping.inverse = Mapping(mapping_tuple)
# The final transform
transform = mapping | pix_to_ra & pix_to_dec & pix_to_wavelength
det = cf.Frame2D(name='detector', axes_order=(0, 1))
sky = cf.CelestialFrame(name='sky',
axes_order=(0, 1),
reference_frame=coord.ICRS())
spec = cf.SpectralFrame(name='spectral',
axes_order=(2, ),
unit=(u.micron, ),
axes_names=('wavelength', ))
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, transform), (world, None)]
output_wcs = WCS(pipeline)
# compute the output array size in WCS axes order, i.e. (x, y)
output_array_size = [0, 0]
output_array_size[spectral_axis] = len(wavelength_array)
output_array_size[spatial_axis] = len(ra_array)
# turn the size into a numpy shape in (y, x) order
self.data_size = tuple(output_array_size[::-1])
bounding_box = resample_utils.wcs_bbox_from_shape(self.data_size)
output_wcs.bounding_box = bounding_box
return output_wcs
def build_nirspec_output_wcs(self, refmodel=None):
"""
Create a spatial/spectral WCS covering footprint of the input
"""
if not refmodel:
refmodel = self.input_models[0]
refwcs = refmodel.meta.wcs
bb = refwcs.bounding_box
ref_det2slit = refwcs.get_transform('detector', 'slit_frame')
ref_slit2world = refwcs.get_transform('slit_frame', 'world')
grid = x, y = wcstools.grid_from_bounding_box(bb, step=(1, 1))
Grid = namedtuple('Grid', refwcs.slit_frame.axes_names)
grid_slit = Grid(*ref_det2slit(*grid))
# Compute spatial transform from detector to slit
ref_wavelength = np.nanmean(grid_slit.wavelength)
# find the number of pixels sampled by a single shutter
fid = np.array([[0., 0.], [-.5, .5], np.repeat(ref_wavelength, 2)])
slit_extents = np.array(ref_det2slit.inverse(*fid)).T
pix_per_shutter = np.linalg.norm(slit_extents[0] - slit_extents[1])
# Get min and max of slit in pixel units
ymin = np.nanmin(grid_slit.y_slit) * pix_per_shutter
ymax = np.nanmax(grid_slit.y_slit) * pix_per_shutter
slit_height_pix = int(abs(ymax - ymin + 0.5))
# Compute grid of wavelengths and make tabular model w/inverse
lookup_table = np.nanmean(grid_slit.wavelength, axis=0)
wavelength_transform = Tabular1D(lookup_table=lookup_table,
bounds_error=False,
fill_value=np.nan)
wavelength_transform.inverse = Tabular1D(
points=lookup_table,
lookup_table=np.arange(grid_slit.wavelength.shape[1]),
bounds_error=False,
fill_value=np.nan)
# Define detector to slit transforms
yslit_transform = Scale(-1 / pix_per_shutter) | Shift(
ymax / pix_per_shutter)
xslit_transform = Const1D(-0.)
xslit_transform.inverse = Const1D(0.)
# Construct the final transform
coord_mapping = Mapping((0, 1, 0))
coord_mapping.inverse = Mapping((2, 1))
the_transform = xslit_transform & yslit_transform & wavelength_transform
out_det2slit = coord_mapping | the_transform
# Create coordinate frames
det = cf.Frame2D(name='detector', axes_order=(0, 1))
slit_spatial = cf.Frame2D(name='slit_spatial',
axes_order=(0, 1),
unit=("", ""),
axes_names=('x_slit', 'y_slit'))
spec = cf.SpectralFrame(name='spectral',
axes_order=(2, ),
unit=(u.micron, ),
axes_names=('wavelength', ))
slit_frame = cf.CompositeFrame([slit_spatial, spec], name='slit_frame')
sky = cf.CelestialFrame(name='sky',
axes_order=(0, 1),
reference_frame=coord.ICRS())
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, out_det2slit), (slit_frame, ref_slit2world),
(world, None)]
output_wcs = WCS(pipeline)
self.data_size = (slit_height_pix, len(lookup_table))
bounding_box = resample_utils.bounding_box_from_shape(self.data_size)
output_wcs.bounding_box = bounding_box
return output_wcs
def wcs_from_footprints(dmodels, refmodel=None, transform=None, bounding_box=None):
"""
Create a WCS from a list of input data models.
A fiducial point in the output coordinate frame is created from the
footprints of all WCS objects. For a spatial frame this is the center
of the union of the footprints. For a spectral frame the fiducial is in
the beginning of the footprint range.
If ``refmodel`` is None, the first WCS object in the list is considered
a reference. The output coordinate frame and projection (for celestial frames)
is taken from ``refmodel``.
If ``transform`` is not suplied, a compound transform is created using
CDELTs and PC.
If ``bounding_box`` is not supplied, the bounding_box of the new WCS is computed
from bounding_box of all input WCSs.
Parameters
----------
dmodels : list of `~jwst.datamodels.DataModel`
A list of data models.
refmodel : `~jwst.datamodels.DataModel`, optional
This model's WCS is used as a reference.
WCS. The output coordinate frame, the projection and a
scaling and rotation transform is created from it. If not supplied
the first model in the list is used as ``refmodel``.
transform : `~astropy.modeling.core.Model`, optional
A transform, passed to :meth:`~gwcs.wcstools.wcs_from_fiducial`
If not supplied Scaling | Rotation is computed from ``refmodel``.
bounding_box : tuple, optional
Bounding_box of the new WCS.
If not supplied it is computed from the bounding_box of all inputs.
"""
bb = bounding_box
wcslist = [im.meta.wcs for im in dmodels]
if not isiterable(wcslist):
raise ValueError("Expected 'wcslist' to be an iterable of WCS objects.")
if not all([isinstance(w, WCS) for w in wcslist]):
raise TypeError("All items in wcslist are to be instances of gwcs.WCS.")
if refmodel is None:
refmodel = dmodels[0]
else:
if not isinstance(refmodel, DataModel):
raise TypeError("Expected refmodel to be an instance of DataModel.")
fiducial = compute_fiducial(wcslist, bb)
ref_fiducial = compute_fiducial([refmodel.meta.wcs])
prj = astmodels.Pix2Sky_TAN()
if transform is None:
transform = []
wcsinfo = pointing.wcsinfo_from_model(refmodel)
sky_axes, spec, other = gwutils.get_axes(wcsinfo)
# Need to put the rotation matrix (List[float, float, float, float]) returned from calc_rotation_matrix into the
# correct shape for constructing the transformation
pc = np.reshape(
calc_rotation_matrix(
np.deg2rad(refmodel.meta.wcsinfo.roll_ref),
np.deg2rad(refmodel.meta.wcsinfo.v3yangle),
vparity=refmodel.meta.wcsinfo.vparity),
(2, 2)
)
rotation = astmodels.AffineTransformation2D(pc)
transform.append(rotation)
if sky_axes:
scale = compute_scale(refmodel.meta.wcs, ref_fiducial)
transform.append(astmodels.Scale(scale) & astmodels.Scale(scale))
if transform:
transform = functools.reduce(lambda x, y: x | y, transform)
out_frame = refmodel.meta.wcs.output_frame
input_frame = dmodels[0].meta.wcs.input_frame
wnew = wcs_from_fiducial(fiducial, coordinate_frame=out_frame, projection=prj, transform=transform)
# temporary fix before gwcs 0.14 is released
# wnew = wcs_from_fiducial(fiducial, coordinate_frame=out_frame, projection=prj,
# transform=transform, input_frame=input_frame)
pipe = wnew.pipeline[:]
pipe[0] = (input_frame, pipe[0][1])
wnew = WCS(pipe)
footprints = [w.footprint().T for w in wcslist]
domain_bounds = np.hstack([wnew.backward_transform(*f) for f in footprints])
for axs in domain_bounds:
axs -= (axs.min() + .5)
bounding_box = []
for axis in out_frame.axes_order:
axis_min, axis_max = domain_bounds[axis].min(), domain_bounds[axis].max()
bounding_box.append((axis_min, axis_max))
bounding_box = tuple(bounding_box)
ax1, ax2 = np.array(bounding_box)[sky_axes]
offset1 = (ax1[1] - ax1[0]) / 2
offset2 = (ax2[1] - ax2[0]) / 2
offsets = astmodels.Shift(-offset1) & astmodels.Shift(-offset2)
wnew.insert_transform('detector', offsets, after=True)
wnew.bounding_box = bounding_box
return wnew
def build_nirspec_output_wcs(self, refwcs=None):
"""
Create a simple output wcs covering footprint of the input datamodels
"""
# TODO: generalize this for more than one input datamodel
# TODO: generalize this for imaging modes with distorted wcs
input_model = self.input_models[0]
if refwcs == None:
refwcs = input_model.meta.wcs
# Generate grid of sky coordinates for area within bounding box
bb = refwcs.bounding_box
det = x, y = wcstools.grid_from_bounding_box(bb,
step=(1, 1),
center=True)
sky = ra, dec, lam = refwcs(*det)
x_center = int((bb[0][1] - bb[0][0]) / 2)
y_center = int((bb[1][1] - bb[1][0]) / 2)
log.debug("Center of bounding box: {} {}".format(x_center, y_center))
# Compute slit angular size, slit center sky coords
xpos = []
sz = 3
for row in lam:
if np.isnan(row[x_center]):
xpos.append(np.nan)
else:
f = interpolate.interp1d(row[x_center - sz + 1:x_center + sz],
x[y_center,
x_center - sz + 1:x_center + sz],
bounds_error=False,
fill_value='extrapolate')
xpos.append(f(lam[y_center, x_center]))
x_arg = np.array(xpos)[~np.isnan(lam[:, x_center])]
y_arg = y[~np.isnan(lam[:, x_center]), x_center]
# slit_coords, spect0 = refwcs(x_arg, y_arg, output='numericals_plus')
slit_ra, slit_dec, slit_spec_ref = refwcs(x_arg, y_arg)
slit_coords = SkyCoord(ra=slit_ra, dec=slit_dec, unit=u.deg)
pix_num = np.flipud(np.arange(len(slit_ra)))
# pix_num = np.arange(len(slit_ra))
interpol_ra = interpolate.interp1d(pix_num, slit_ra)
interpol_dec = interpolate.interp1d(pix_num, slit_dec)
slit_center_pix = len(slit_spec_ref) / 2. - 1
log.debug('Slit center pix: {0}'.format(slit_center_pix))
slit_center_sky = SkyCoord(ra=interpol_ra(slit_center_pix),
dec=interpol_dec(slit_center_pix),
unit=u.deg)
log.debug('Slit center: {0}'.format(slit_center_sky))
log.debug('Fiducial: {0}'.format(
resample_utils.compute_spec_fiducial([refwcs])))
angular_slit_size = np.abs(slit_coords[0].separation(slit_coords[-1]))
log.debug('Slit angular size: {0}'.format(angular_slit_size.arcsec))
dra, ddec = slit_coords[0].spherical_offsets_to(slit_coords[-1])
offset_up_slit = (dra.to(u.arcsec), ddec.to(u.arcsec))
log.debug('Offset up the slit: {0}'.format(offset_up_slit))
# Compute spatial and spectral scales
xposn = np.array(xpos)[~np.isnan(xpos)]
dx = xposn[-1] - xposn[0]
slit_npix = np.sqrt(dx**2 + np.array(len(xposn) - 1)**2)
spatial_scale = angular_slit_size / slit_npix
log.debug('Spatial scale: {0}'.format(spatial_scale.arcsec))
spectral_scale = lam[y_center, x_center] - lam[y_center, x_center - 1]
# Compute slit angle relative (clockwise) to y axis
slit_rot_angle = (np.arcsin(dx / slit_npix) * u.radian).to(u.degree)
slit_rot_angle = slit_rot_angle.value
log.debug('Slit rotation angle: {0}'.format(slit_rot_angle))
# Compute transform for output frame
roll_ref = input_model.meta.wcsinfo.roll_ref
min_lam = np.nanmin(lam)
offset = Shift(-slit_center_pix) & Shift(-slit_center_pix)
# TODO: double-check the signs on the following rotation angles
rot = Rotation2D(roll_ref + slit_rot_angle)
scale = Scale(spatial_scale.value) & Scale(spatial_scale.value)
tan = Pix2Sky_TAN()
lon_pole = _compute_lon_pole(slit_center_sky, tan)
skyrot = RotateNative2Celestial(slit_center_sky.ra.value,
slit_center_sky.dec.value,
lon_pole.value)
spatial_trans = offset | rot | scale | tan | skyrot
spectral_trans = Scale(spectral_scale) | Shift(min_lam)
mapping = Mapping((1, 1, 0))
mapping.inverse = Mapping((2, 1))
transform = mapping | spatial_trans & spectral_trans
transform.outputs = ('ra', 'dec', 'lamda')
# Build the output wcs
input_frame = refwcs.input_frame
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the bounding_box in the output frame wcs object
bounding_box_grid = wnew.backward_transform(ra, dec, lam)
bounding_box = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(bounding_box_grid[axis])
axis_max = np.nanmax(bounding_box_grid[axis])
bounding_box.append((axis_min, axis_max))
wnew.bounding_box = tuple(bounding_box)
# Update class properties
self.output_spatial_scale = spatial_scale
self.output_spectral_scale = spectral_scale
self.output_wcs = wnew
def test_round_trip_gwcs(tmpdir):
"""
Add a 2-step gWCS instance to NDAstroData, save to disk, reload & compare.
"""
from gwcs import coordinate_frames as cf
from gwcs import WCS
arr = np.zeros((10, 10), dtype=np.float32)
ad1 = astrodata.create(fits.PrimaryHDU(), [fits.ImageHDU(arr, name='SCI')])
# Transformation from detector pixels to pixels in some reference row,
# removing relative distortions in wavelength:
det_frame = cf.Frame2D(name='det_mosaic',
axes_names=('x', 'y'),
unit=(u.pix, u.pix))
dref_frame = cf.Frame2D(name='dist_ref_row',
axes_names=('xref', 'y'),
unit=(u.pix, u.pix))
# A made-up example model that looks vaguely like some real distortions:
fdist = models.Chebyshev2D(2,
2,
c0_0=4.81125,
c1_0=5.43375,
c0_1=-0.135,
c1_1=-0.405,
c0_2=0.30375,
c1_2=0.91125,
x_domain=[0., 9.],
y_domain=[0., 9.])
# This is not an accurate inverse, but will do for this test:
idist = models.Chebyshev2D(2,
2,
c0_0=4.89062675,
c1_0=5.68581232,
c2_0=-0.00590263,
c0_1=0.11755526,
c1_1=0.35652358,
c2_1=-0.01193828,
c0_2=-0.29996306,
c1_2=-0.91823397,
c2_2=0.02390594,
x_domain=[-1.5, 12.],
y_domain=[0., 9.])
# The resulting 2D co-ordinate mapping from detector to ref row pixels:
distrans = models.Mapping((0, 1, 1)) | (fdist & models.Identity(1))
distrans.inverse = models.Mapping((0, 1, 1)) | (idist & models.Identity(1))
# Transformation from reference row pixels to linear, row-stacked spectra:
spec_frame = cf.SpectralFrame(axes_order=(0, ),
unit=u.nm,
axes_names='lambda',
name='wavelength')
row_frame = cf.CoordinateFrame(1,
'SPATIAL',
axes_order=(1, ),
unit=u.pix,
axes_names='y',
name='row')
rss_frame = cf.CompositeFrame([spec_frame, row_frame])
# Toy wavelength model & approximate inverse:
fwcal = models.Chebyshev1D(2, c0=500.075, c1=0.05, c2=0.001, domain=[0, 9])
iwcal = models.Chebyshev1D(2,
c0=4.59006292,
c1=4.49601817,
c2=-0.08989608,
domain=[500.026, 500.126])
# The resulting 2D co-ordinate mapping from ref pixels to wavelength:
wavtrans = fwcal & models.Identity(1)
wavtrans.inverse = iwcal & models.Identity(1)
# The complete WCS chain for these 2 transformation steps:
ad1[0].nddata.wcs = WCS([(det_frame, distrans), (dref_frame, wavtrans),
(rss_frame, None)])
# Save & re-load the AstroData instance with its new WCS attribute:
testfile = str(tmpdir.join('round_trip_gwcs.fits'))
ad1.write(testfile)
ad2 = astrodata.open(testfile)
wcs1 = ad1[0].nddata.wcs
wcs2 = ad2[0].nddata.wcs
# # Temporary workaround for issue #9809, to ensure the test is correct:
# wcs2.forward_transform[1].x_domain = (0, 9)
# wcs2.forward_transform[1].y_domain = (0, 9)
# wcs2.forward_transform[3].domain = (0, 9)
# wcs2.backward_transform[0].domain = (500.026, 500.126)
# wcs2.backward_transform[3].x_domain = (-1.5, 12.)
# wcs2.backward_transform[3].y_domain = (0, 9)
# Did we actually get a gWCS instance back?
assert isinstance(wcs2, WCS)
# Do the transforms have the same number of submodels, with the same types,
# degrees, domains & parameters? Here the inverse gets checked redundantly
# as both backward_transform and forward_transform.inverse, but it would be
# convoluted to ensure that both are correct otherwise (since the transforms
# get regenerated as new compound models each time they are accessed).
compare_models(wcs1.forward_transform, wcs2.forward_transform)
compare_models(wcs1.backward_transform, wcs2.backward_transform)
# Do the instances have matching co-ordinate frames?
for f in wcs1.available_frames:
assert repr(getattr(wcs1, f)) == repr(getattr(wcs2, f))
# Also compare a few transformed values, as the "proof of the pudding":
y, x = np.mgrid[0:9:2, 0:9:2]
np.testing.assert_allclose(wcs1(x, y), wcs2(x, y), rtol=1e-7, atol=0.)
y, w = np.mgrid[0:9:2, 500.025:500.12:0.0225]
np.testing.assert_allclose(wcs1.invert(w, y),
wcs2.invert(w, y),
rtol=1e-7,
atol=0.)
def build_interpolated_output_wcs(self, refmodel=None):
"""
Create a spatial/spectral WCS output frame using all the input models
Creates output frame by linearly fitting RA, Dec along the slit and
producing a lookup table to interpolate wavelengths in the dispersion
direction.
Parameters
----------
refmodel : `~jwst.datamodels.DataModel`
The reference input image from which the fiducial WCS is created.
If not specified, the first image in self.input_models is used.
Returns
-------
output_wcs : `~gwcs.WCS` object
A gwcs WCS object defining the output frame WCS
"""
# for each input model convert slit x,y to ra,dec,lam
# use first input model to set spatial scale
# use center of appended ra and dec arrays to set up
# center of final ra,dec
# append all ra,dec, wavelength array for each slit
# use first model to initialize wavelenth array
# append wavelengths that fall outside the endpoint of
# of wavelength array when looping over additional data
all_wavelength = []
all_ra_slit = []
all_dec_slit = []
for im, model in enumerate(self.input_models):
wcs = model.meta.wcs
bb = wcs.bounding_box
grid = wcstools.grid_from_bounding_box(bb)
ra, dec, lam = np.array(wcs(*grid))
spectral_axis = find_dispersion_axis(model)
spatial_axis = spectral_axis ^ 1
# Compute the wavelength array, trimming NaNs from the ends
# In many cases, a whole slice is NaNs, so ignore those warnings
warnings.simplefilter("ignore")
wavelength_array = np.nanmedian(lam, axis=spectral_axis)
warnings.resetwarnings()
wavelength_array = wavelength_array[~np.isnan(wavelength_array)]
# We need to estimate the spatial sampling to use for the output WCS.
# Tt is assumed the spatial sampling is the same for all the input
# models. So we can use the first input model to set the spatial
# sampling.
# Steps to do this for first input model:
# 1. find the middle of the spectrum in wavelength
# 2. Pull out the ra and dec at the center of the slit.
# 3. Find the mean ra,dec and the center of the slit this will
# represent the tangent point
# 4. Convert ra,dec -> tangent plane projection: x_tan,y_tan
# 5. using x_tan, y_tan perform a linear fit to find spatial sampling
# first input model sets intializes wavelength array and defines
# the spatial scale of the output wcs
if im == 0:
for iw in wavelength_array:
all_wavelength.append(iw)
lam_center_index = int(
(bb[spectral_axis][1] - bb[spectral_axis][0]) / 2)
if spatial_axis == 0:
ra_center = ra[lam_center_index, :]
dec_center = dec[lam_center_index, :]
else:
ra_center = ra[:, lam_center_index]
dec_center = dec[:, lam_center_index]
# find the ra and dec for this slit using center of slit
ra_center_pt = np.nanmean(ra_center)
dec_center_pt = np.nanmean(dec_center)
if resample_utils.is_sky_like(model.meta.wcs.output_frame):
# convert ra and dec to tangent projection
tan = Pix2Sky_TAN()
native2celestial = RotateNative2Celestial(
ra_center_pt, dec_center_pt, 180)
undist2sky1 = tan | native2celestial
# Filter out RuntimeWarnings due to computed NaNs in the WCS
warnings.simplefilter("ignore")
# at this center of slit find x,y tangent projection - x_tan, y_tan
x_tan, y_tan = undist2sky1.inverse(ra, dec)
warnings.resetwarnings()
else:
# for non sky-like output frames, no need to do tangent plane projections
# but we still use the same variables
x_tan, y_tan = ra, dec
# pull out data from center
if spectral_axis == 0:
x_tan_array = x_tan.T[lam_center_index]
y_tan_array = y_tan.T[lam_center_index]
else:
x_tan_array = x_tan[lam_center_index]
y_tan_array = y_tan[lam_center_index]
x_tan_array = x_tan_array[~np.isnan(x_tan_array)]
y_tan_array = y_tan_array[~np.isnan(y_tan_array)]
# estimate the spatial sampling
fitter = LinearLSQFitter()
fit_model = Linear1D()
xstop = x_tan_array.shape[0] / self.pscale_ratio
xstep = 1 / self.pscale_ratio
ystop = y_tan_array.shape[0] / self.pscale_ratio
ystep = 1 / self.pscale_ratio
pix_to_xtan = fitter(fit_model, np.arange(0, xstop, xstep),
x_tan_array)
pix_to_ytan = fitter(fit_model, np.arange(0, ystop, ystep),
y_tan_array)
# append all ra and dec values to use later to find min and max
# ra and dec
ra_use = ra.flatten()
ra_use = ra_use[~np.isnan(ra_use)]
dec_use = dec.flatten()
dec_use = dec_use[~np.isnan(dec_use)]
all_ra_slit.append(ra_use)
all_dec_slit.append(dec_use)
# now check wavelength array to see if we need to add to it
this_minw = np.min(wavelength_array)
this_maxw = np.max(wavelength_array)
all_minw = np.min(all_wavelength)
all_maxw = np.max(all_wavelength)
if this_minw < all_minw:
addpts = wavelength_array[wavelength_array < all_minw]
for ip in range(len(addpts)):
all_wavelength.append(addpts[ip])
if this_maxw > all_maxw:
addpts = wavelength_array[wavelength_array > all_maxw]
for ip in range(len(addpts)):
all_wavelength.append(addpts[ip])
# done looping over set of models
all_ra = np.hstack(all_ra_slit)
all_dec = np.hstack(all_dec_slit)
all_wave = np.hstack(all_wavelength)
all_wave = all_wave[~np.isnan(all_wave)]
all_wave = np.sort(all_wave, axis=None)
# Tabular interpolation model, pixels -> lambda
wavelength_array = np.unique(all_wave)
# Check if the data is MIRI LRS FIXED Slit. If it is then
# the wavelength array needs to be flipped so that the resampled
# dispersion direction matches the disperion direction on the detector.
if self.input_models[0].meta.exposure.type == 'MIR_LRS-FIXEDSLIT':
wavelength_array = np.flip(wavelength_array, axis=None)
step = 1 / self.pscale_ratio
stop = wavelength_array.shape[0] / self.pscale_ratio
points = np.arange(0, stop, step)
pix_to_wavelength = Tabular1D(points=points,
lookup_table=wavelength_array,
bounds_error=False,
fill_value=None,
name='pix2wavelength')
# Tabular models need an inverse explicitly defined.
# If the wavelength array is decending instead of ascending, both
# points and lookup_table need to be reversed in the inverse transform
# for scipy.interpolate to work properly
points = wavelength_array
lookup_table = np.arange(0, stop, step)
if not np.all(np.diff(wavelength_array) > 0):
points = points[::-1]
lookup_table = lookup_table[::-1]
pix_to_wavelength.inverse = Tabular1D(points=points,
lookup_table=lookup_table,
bounds_error=False,
fill_value=None,
name='wavelength2pix')
# For the input mapping, duplicate the spatial coordinate
mapping = Mapping((spatial_axis, spatial_axis, spectral_axis))
# Sometimes the slit is perpendicular to the RA or Dec axis.
# For example, if the slit is perpendicular to RA, that means
# the slope of pix_to_xtan will be nearly zero, so make sure
# mapping.inverse uses pix_to_ytan.inverse. The auto definition
# of mapping.inverse is to use the 2nd spatial coordinate, i.e. Dec.
if np.isclose(pix_to_ytan.slope, 0, atol=1e-8):
mapping_tuple = (0, 1)
# Account for vertical or horizontal dispersion on detector
if spatial_axis:
mapping.inverse = Mapping(mapping_tuple[::-1])
else:
mapping.inverse = Mapping(mapping_tuple)
# The final transform
# redefine the ra, dec center tangent point to include all data
# check if all_ra crosses 0 degress - this makes it hard to
# define the min and max ra correctly
all_ra = wrap_ra(all_ra)
ra_min = np.amin(all_ra)
ra_max = np.amax(all_ra)
ra_center_final = (ra_max + ra_min) / 2.0
dec_min = np.amin(all_dec)
dec_max = np.amax(all_dec)
dec_center_final = (dec_max + dec_min) / 2.0
tan = Pix2Sky_TAN()
if len(self.input_models
) == 1: # single model use ra_center_pt to be consistent
# with how resample was done before
ra_center_final = ra_center_pt
dec_center_final = dec_center_pt
if resample_utils.is_sky_like(model.meta.wcs.output_frame):
native2celestial = RotateNative2Celestial(ra_center_final,
dec_center_final, 180)
undist2sky = tan | native2celestial
# find the spatial size of the output - same in x,y
x_tan_all, _ = undist2sky.inverse(all_ra, all_dec)
else:
x_tan_all, _ = all_ra, all_dec
x_min = np.amin(x_tan_all)
x_max = np.amax(x_tan_all)
x_size = int(np.ceil((x_max - x_min) / np.absolute(pix_to_xtan.slope)))
# single model use size of x_tan_array
# to be consistent with method before
if len(self.input_models) == 1:
x_size = len(x_tan_array)
# define the output wcs
if resample_utils.is_sky_like(model.meta.wcs.output_frame):
transform = mapping | (pix_to_xtan & pix_to_ytan
| undist2sky) & pix_to_wavelength
else:
transform = mapping | (pix_to_xtan
& pix_to_ytan) & pix_to_wavelength
det = cf.Frame2D(name='detector', axes_order=(0, 1))
if resample_utils.is_sky_like(model.meta.wcs.output_frame):
sky = cf.CelestialFrame(name='sky',
axes_order=(0, 1),
reference_frame=coord.ICRS())
else:
sky = cf.Frame2D(
name=f'resampled_{model.meta.wcs.output_frame.name}',
axes_order=(0, 1))
spec = cf.SpectralFrame(name='spectral',
axes_order=(2, ),
unit=(u.micron, ),
axes_names=('wavelength', ))
world = cf.CompositeFrame([sky, spec], name='world')
pipeline = [(det, transform), (world, None)]
output_wcs = WCS(pipeline)
# import ipdb; ipdb.set_trace()
# compute the output array size in WCS axes order, i.e. (x, y)
output_array_size = [0, 0]
output_array_size[spectral_axis] = int(
np.ceil(len(wavelength_array) / self.pscale_ratio))
output_array_size[spatial_axis] = int(
np.ceil(x_size / self.pscale_ratio))
# turn the size into a numpy shape in (y, x) order
self.data_size = tuple(output_array_size[::-1])
bounding_box = resample_utils.wcs_bbox_from_shape(self.data_size)
output_wcs.bounding_box = bounding_box
return output_wcs
def build_nirspec_output_wcs(self, refwcs=None):
"""
Create a simple output wcs covering footprint of the input datamodels
"""
# TODO: generalize this for more than one input datamodel
# TODO: generalize this for imaging modes with distorted wcs
input_model = self.input_models[0]
if refwcs == None:
refwcs = input_model.meta.wcs
# Generate grid of sky coordinates for area within domain
det = x, y = wcstools.grid_from_domain(refwcs.domain)
sky = ra, dec, lam = refwcs(*det)
domain_xsize = refwcs.domain[0]['upper'] - refwcs.domain[0]['lower']
domain_ysize = refwcs.domain[1]['upper'] - refwcs.domain[1]['lower']
x_center, y_center = int(domain_xsize / 2), int(domain_ysize / 2)
# Compute slit angular size, slit center sky coords
xpos = []
sz = 3
for row in lam:
if np.isnan(row[x_center]):
xpos.append(np.nan)
else:
f = interpolate.interp1d(row[x_center - sz + 1:x_center + sz],
x[y_center, x_center - sz + 1:x_center + sz])
xpos.append(f(lam[y_center, x_center]))
x_arg = np.array(xpos)[~np.isnan(lam[:, x_center])]
y_arg = y[~np.isnan(lam[:,x_center]), x_center]
# slit_coords, spect0 = refwcs(x_arg, y_arg, output='numericals_plus')
slit_ra, slit_dec, slit_spec_ref = refwcs(x_arg, y_arg)
slit_coords = SkyCoord(ra=slit_ra, dec=slit_dec, unit=u.deg)
pix_num = np.flipud(np.arange(len(slit_ra)))
# pix_num = np.arange(len(slit_ra))
interpol_ra = interpolate.interp1d(pix_num, slit_ra)
interpol_dec = interpolate.interp1d(pix_num, slit_dec)
slit_center_pix = len(slit_spec_ref) / 2. - 1
log.debug('Slit center pix: {0}'.format(slit_center_pix))
slit_center_sky = SkyCoord(ra=interpol_ra(slit_center_pix),
dec=interpol_dec(slit_center_pix), unit=u.deg)
log.debug('Slit center: {0}'.format(slit_center_sky))
log.debug('Fiducial: {0}'.format(resample_utils.compute_spec_fiducial([refwcs])))
angular_slit_size = np.abs(slit_coords[0].separation(slit_coords[-1]))
log.debug('Slit angular size: {0}'.format(angular_slit_size.arcsec))
dra, ddec = slit_coords[0].spherical_offsets_to(slit_coords[-1])
offset_up_slit = (dra.to(u.arcsec), ddec.to(u.arcsec))
log.debug('Offset up the slit: {0}'.format(offset_up_slit))
# Compute spatial and spectral scales
xposn = np.array(xpos)[~np.isnan(xpos)]
dx = xposn[-1] - xposn[0]
slit_npix = np.sqrt(dx**2 + np.array(len(xposn) - 1)**2)
spatial_scale = angular_slit_size / slit_npix
log.debug('Spatial scale: {0}'.format(spatial_scale.arcsec))
spectral_scale = lam[y_center, x_center] - lam[y_center, x_center - 1]
# Compute slit angle relative (clockwise) to y axis
slit_rot_angle = (np.arcsin(dx / slit_npix) * u.radian).to(u.degree)
log.debug('Slit rotation angle: {0}'.format(slit_rot_angle))
# Compute transform for output frame
roll_ref = input_model.meta.wcsinfo.roll_ref * u.deg
min_lam = np.nanmin(lam)
offset = Shift(-slit_center_pix) & Shift(-slit_center_pix)
# TODO: double-check the signs on the following rotation angles
rot = Rotation2D(roll_ref + slit_rot_angle)
scale = Scale(spatial_scale) & Scale(spatial_scale)
tan = Pix2Sky_TAN()
lon_pole = _compute_lon_pole(slit_center_sky, tan)
skyrot = RotateNative2Celestial(slit_center_sky.ra, slit_center_sky.dec,
lon_pole)
spatial_trans = offset | rot | scale | tan | skyrot
spectral_trans = Scale(spectral_scale) | Shift(min_lam)
mapping = Mapping((1, 1, 0))
mapping.inverse = Mapping((2, 1))
transform = mapping | spatial_trans & spectral_trans
transform.outputs = ('ra', 'dec', 'lamda')
# Build the output wcs
input_frame = refwcs.input_frame
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the domain in the output frame wcs object
domain_grid = wnew.backward_transform(*sky)
domain = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(domain_grid[axis])
axis_max = np.nanmax(domain_grid[axis]) + 1
domain.append({'lower': axis_min, 'upper': axis_max,
'includes_lower': True, 'includes_upper': False})
log.debug('Domain: {0} {1}'.format(domain[1]['lower'], domain[1]['upper']))
wnew.domain = domain
# Update class properties
self.output_spatial_scale = spatial_scale
self.output_spectral_scale = spectral_scale
self.output_wcs = wnew
def build_miri_output_wcs(self, refwcs=None):
"""
Create a simple output wcs covering footprint of the input datamodels
"""
# TODO: generalize this for more than one input datamodel
# TODO: generalize this for imaging modes with distorted wcs
input_model = self.input_models[0]
if refwcs == None:
refwcs = input_model.meta.wcs
x, y = wcstools.grid_from_bounding_box(refwcs.bounding_box,
step=(1, 1),
center=True)
ra, dec, lam = refwcs(x.flatten(), y.flatten())
# TODO: once astropy.modeling._Tabular is fixed, take out the
# flatten() and reshape() code above and below
ra = ra.reshape(x.shape)
dec = dec.reshape(x.shape)
lam = lam.reshape(x.shape)
# Find rotation of the slit from y axis from the wcs forward transform
# TODO: figure out if angle is necessary for MIRI. See for discussion
# https://github.com/STScI-JWST/jwst/pull/347
rotation = [m for m in refwcs.forward_transform if \
isinstance(m, Rotation2D)]
if rotation:
rot_slit = functools.reduce(lambda x, y: x | y, rotation)
rot_angle = rot_slit.inverse.angle.value
unrotate = rot_slit.inverse
refwcs_minus_rot = refwcs.forward_transform | \
unrotate & Identity(1)
# Correct for this rotation in the wcs
ra, dec, lam = refwcs_minus_rot(x.flatten(), y.flatten())
ra = ra.reshape(x.shape)
dec = dec.reshape(x.shape)
lam = lam.reshape(x.shape)
# Get the slit size at the center of the dispersion
sky_coords = SkyCoord(ra=ra, dec=dec, unit=u.deg)
slit_coords = sky_coords[int(sky_coords.shape[0] / 2)]
slit_angular_size = slit_coords[0].separation(slit_coords[-1])
log.debug('Slit angular size: {0}'.format(slit_angular_size.arcsec))
# Compute slit center from bounding_box
dx0 = refwcs.bounding_box[0][0]
dx1 = refwcs.bounding_box[0][1]
dy0 = refwcs.bounding_box[1][0]
dy1 = refwcs.bounding_box[1][1]
slit_center_pix = (dx1 - dx0) / 2
dispersion_center_pix = (dy1 - dy0) / 2
slit_center = refwcs_minus_rot(dx0 + slit_center_pix,
dy0 + dispersion_center_pix)
slit_center_sky = SkyCoord(ra=slit_center[0],
dec=slit_center[1],
unit=u.deg)
log.debug('slit center: {0}'.format(slit_center))
# Compute spatial and spectral scales
spatial_scale = slit_angular_size / slit_coords.shape[0]
log.debug('Spatial scale: {0}'.format(spatial_scale.arcsec))
tcenter = int((dx1 - dx0) / 2)
trace = lam[:, tcenter]
trace = trace[~np.isnan(trace)]
spectral_scale = np.abs((trace[-1] - trace[0]) / trace.shape[0])
log.debug('spectral scale: {0}'.format(spectral_scale))
# Compute transform for output frame
log.debug('Slit center %s' % slit_center_pix)
offset = Shift(-slit_center_pix) & Shift(-slit_center_pix)
# TODO: double-check the signs on the following rotation angles
roll_ref = input_model.meta.wcsinfo.roll_ref * u.deg
rot = Rotation2D(roll_ref)
tan = Pix2Sky_TAN()
lon_pole = _compute_lon_pole(slit_center_sky, tan)
skyrot = RotateNative2Celestial(slit_center_sky.ra,
slit_center_sky.dec, lon_pole)
min_lam = np.nanmin(lam)
mapping = Mapping((0, 0, 1))
transform = Shift(-slit_center_pix) & Identity(1) | \
Scale(spatial_scale) & Scale(spectral_scale) | \
Identity(1) & Shift(min_lam) | mapping | \
(rot | tan | skyrot) & Identity(1)
transform.inputs = (x, y)
transform.outputs = ('ra', 'dec', 'lamda')
# Build the output wcs
input_frame = refwcs.input_frame
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the bounding_box in the output frame wcs object
bounding_box_grid = wnew.backward_transform(ra, dec, lam)
bounding_box = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(bounding_box_grid[axis])
axis_max = np.nanmax(bounding_box_grid[axis])
bounding_box.append((axis_min, axis_max))
wnew.bounding_box = tuple(bounding_box)
# Update class properties
self.output_spatial_scale = spatial_scale
self.output_spectral_scale = spectral_scale
self.output_wcs = wnew
def build_miri_output_wcs(self, refwcs=None):
"""
Create a simple output wcs covering footprint of the input datamodels
"""
# TODO: generalize this for more than one input datamodel
# TODO: generalize this for imaging modes with distorted wcs
input_model = self.input_models[0]
if refwcs == None:
refwcs = input_model.meta.wcs
# Generate grid of sky coordinates for area within domain
x, y = wcstools.grid_from_domain(refwcs.domain)
ra, dec, lam = refwcs(x.flatten(), y.flatten())
# TODO: once astropy.modeling._Tabular is fixed, take out the
# flatten() and reshape() code above and below
ra = ra.reshape(x.shape)
dec = dec.reshape(x.shape)
lam = lam.reshape(x.shape)
# Find rotation of the slit from y axis from the wcs forward transform
# TODO: figure out if angle is necessary for MIRI. See for discussion
# https://github.com/STScI-JWST/jwst/pull/347
rotation = [m for m in refwcs.forward_transform if \
isinstance(m, Rotation2D)]
if rotation:
rot_slit = functools.reduce(lambda x, y: x | y, rotation)
rot_angle = rot_slit.inverse.angle.value
unrotate = rot_slit.inverse
refwcs_minus_rot = refwcs.forward_transform | \
unrotate & Identity(1)
# Correct for this rotation in the wcs
ra, dec, lam = refwcs_minus_rot(x.flatten(), y.flatten())
ra = ra.reshape(x.shape)
dec = dec.reshape(x.shape)
lam = lam.reshape(x.shape)
# Get the slit size at the center of the dispersion
sky_coords = SkyCoord(ra=ra, dec=dec, unit=u.deg)
slit_coords = sky_coords[int(sky_coords.shape[0] / 2)]
slit_angular_size = slit_coords[0].separation(slit_coords[-1])
log.debug('Slit angular size: {0}'.format(slit_angular_size.arcsec))
# Compute slit center from domain
dx0 = refwcs.domain[0]['lower']
dx1 = refwcs.domain[0]['upper']
dy0 = refwcs.domain[1]['lower']
dy1 = refwcs.domain[1]['upper']
slit_center_pix = (dx1 - dx0) / 2
dispersion_center_pix = (dy1 - dy0) / 2
slit_center = refwcs_minus_rot(dx0 + slit_center_pix, dy0 +
dispersion_center_pix)
slit_center_sky = SkyCoord(ra=slit_center[0], dec=slit_center[1],
unit=u.deg)
log.debug('slit center: {0}'.format(slit_center))
# Compute spatial and spectral scales
spatial_scale = slit_angular_size / slit_coords.shape[0]
log.debug('Spatial scale: {0}'.format(spatial_scale.arcsec))
tcenter = int((dx1 - dx0) / 2)
trace = lam[:, tcenter]
trace = trace[~np.isnan(trace)]
spectral_scale = np.abs((trace[-1] - trace[0]) / trace.shape[0])
log.debug('spectral scale: {0}'.format(spectral_scale))
# Compute transform for output frame
log.debug('Slit center %s' % slit_center_pix)
offset = Shift(-slit_center_pix) & Shift(-slit_center_pix)
# TODO: double-check the signs on the following rotation angles
roll_ref = input_model.meta.wcsinfo.roll_ref * u.deg
rot = Rotation2D(roll_ref)
tan = Pix2Sky_TAN()
lon_pole = _compute_lon_pole(slit_center_sky, tan)
skyrot = RotateNative2Celestial(slit_center_sky.ra, slit_center_sky.dec,
lon_pole)
min_lam = np.nanmin(lam)
mapping = Mapping((0, 0, 1))
transform = Shift(-slit_center_pix) & Identity(1) | \
Scale(spatial_scale) & Scale(spectral_scale) | \
Identity(1) & Shift(min_lam) | mapping | \
(rot | tan | skyrot) & Identity(1)
transform.inputs = (x, y)
transform.outputs = ('ra', 'dec', 'lamda')
# Build the output wcs
input_frame = refwcs.input_frame
output_frame = refwcs.output_frame
wnew = WCS(output_frame=output_frame, forward_transform=transform)
# Build the domain in the output frame wcs object
domain_grid = wnew.backward_transform(ra, dec, lam)
domain = []
for axis in input_frame.axes_order:
axis_min = np.nanmin(domain_grid[axis])
axis_max = np.nanmax(domain_grid[axis]) + 1
domain.append({'lower': axis_min, 'upper': axis_max,
'includes_lower': True, 'includes_upper': False})
log.debug('Domain: {0} {1}'.format(domain[0]['lower'], domain[0]['upper']))
log.debug('Domain: {0} {1}'.format(domain[1]['lower'], domain[1]['upper']))
wnew.domain = domain
# Update class properties
self.output_spatial_scale = spatial_scale
self.output_spectral_scale = spectral_scale
self.output_wcs = wnew