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 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 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
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
# 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
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