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various updates from review
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@jemorrison
jemorrison committed Sep 18, 2024
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41 changes: 0 additions & 41 deletions docs/jwst/cube_build/arguments.rst
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Expand Up @@ -167,44 +167,3 @@ An example of making an offset file for an association containing three files is
Below is an example of making an offset file for `num` files.
The user has set up three lists `file`, `ra_offset` and `dec_offset`. The `file` list
contains the filenames and the `ra_offset` and `dec_offset` contain the Ra and Dec offsets respectively.
In this example, all the list have five values. The units of the of Ra and Dec offsets are given in
the `units` value and this value must be arc seconds.

.. code-block:: python
import asdf
import astropy.units as u
def create_offset_asdf(files, ra_offset, dec_offset):
filename = []
raoffset = []
decoffset = []
num = len(files)
for i in range(num):
filename.append(files[i])
raoffset.append(ra_offset[i])
decoffset.append(dec_offset[i])
tree = {
"units": str(u.arcsec),
"filename": filename,
"raoffset": raoffset,
"decoffset": decoffset
}
af = asdf.AsdfFile(tree)
af.write_to( 'offsets.asdf')
Set up the lists and call the above function:

.. code-block:: python
files = ['test1.fits', 'test2.fits', 'test3.fits', 'test4,fits', 'test5.fits']
ra_offset = [0.1, 0.12, 0.13, 0.11, 0.12]
dec_offset = [0.14, 0.15, 0.16, 0.01, 0.1]
create_offset_asdf(files, ra_offset, dec_offset)
34 changes: 12 additions & 22 deletions jwst/cube_build/cube_build_step.py
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Expand Up @@ -11,7 +11,7 @@
from ..assign_wcs.util import update_s_region_keyword
from ..stpipe import Step, record_step_status
from pathlib import Path

from astropy import units
__all__ = ["CubeBuildStep"]


Expand Down Expand Up @@ -564,51 +564,41 @@ def check_offset_file(self):
try:
af = asdf.open(self.offset_file, custom_schema=DATA_PATH/'ifuoffset.schema.yaml')
except:
self.log.error('Validation Error for offset file')
self.log.error('Turning off adjusting by offsets')
return None
schema_message = ('Validation Error for offset file. Fix the offset file. \n' + \
'The offset file needs to have the same number of elements the filename, raoffset and decoffset lists.\n' +\
'The units need to provided and only arcsec is allowed.')

raise Exception(schema_message)

offset_filename = af['filename']
offset_ra = af['raoffset']
offset_dec = af['decoffset']
offset_unit = af['units']

if offset_unit != 'arcsec':
self.log.error('Provide the offset units in units of arcsec ')
self.log.error('Turning off adjusting by offsets ')
af.close()
return None

# check that all the file names in input_model are in the offset filename
for model in self.input_models:
file_check = model.meta.filename
if file_check in offset_filename:
continue
else:
self.log.error('File in assocation is not found in offset list list %s', file_check)
self.log.error('Turning off adjusting by offsets')
af.close()
return None
raise Exception('Error in offset file. A file in assocation is not found in offset list list %s', file_check)

# check that all the lists have the same length
len_file = len(offset_filename)
len_ra = len(offset_ra)
len_dec = len(offset_dec)
if (len_file != len_ra or len_ra != len_dec or len_file != len_dec):
self.log.error('The offset file does not have the same number of values for filename, offset_ra, offset_dec')
self.log.error('Turning off adjusting by offsets')
af.close()
return None
raise Exception('Offset file error. The offset file does not have the same number of values for filename, offset_ra, offset_dec')

offset_ra = offset_ra* units.arcsec
offset_dec = offset_dec* units.arcsec

# The offset file has passed tests so set the offset dictionary
offsets = {}
offsets['filename'] = offset_filename
offsets['raoffset'] = offset_ra
offsets['decoffset'] = offset_dec
n = len(offsets['raoffset'])
# convert to degrees
for i in range(n):
offsets['raoffset'][i] = offsets['raoffset'][i]/3600.0
offsets['decoffset'][i] = offsets['decoffset'][i]/3600.0

af.close()
return offsets
138 changes: 45 additions & 93 deletions jwst/cube_build/ifu_cube.py
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Expand Up @@ -8,14 +8,13 @@
import math

from astropy.stats import circmean
from astropy import units as u
from gwcs import wcstools

from stdatamodels.jwst import datamodels
from stdatamodels.jwst.datamodels import dqflags
from stdatamodels.jwst.transforms.models import _toindex
from astropy import units
from astropy.coordinates import SkyCoord
from astropy import units as u

from ..model_blender import blendmeta
from ..assign_wcs import pointing
Expand Down Expand Up @@ -116,7 +115,6 @@ def __init__(self,
self.naxis3 = None
self.cdelt3_normal = None
self.rot_angle = None # rotation angle between Ra-Dec and IFU local instrument plane
self.median_dec = None

self.a_min = 0
self.a_max = 0
Expand Down Expand Up @@ -1319,10 +1317,7 @@ def setup_ifucube_wcs(self):
decoffset = 0.0
# pull out ra dec offset if it exists
if self.offsets is not None:
filename = input_model.meta.filename
index = self.offsets['filename'].index(filename)
raoffset = self.offsets['raoffset'][index]
decoffset = self.offsets['decoffset'][index]
raoffset, decoffset = self.find_ra_dec_offset(input_model.meta.filename)
# ________________________________________________________________________________
# Find the footprint of the image
spectral_found = hasattr(input_model.meta.wcsinfo, 'spectral_region')
Expand Down Expand Up @@ -1380,28 +1375,11 @@ def setup_ifucube_wcs(self):

# now append this model spatial and spectral corner
if self.offsets is not None:
c1 = SkyCoord(ca1, cb1, unit='deg')
c2 = SkyCoord(ca2, cb2, unit='deg')
c3 = SkyCoord(ca3, cb3, unit='deg')
c4 = SkyCoord(ca4, cb4, unit='deg')
raoffset = raoffset* units.deg
decoffset = decoffset* units.deg

c1_new = c1.spherical_offsets_by(raoffset, decoffset)
c2_new = c2.spherical_offsets_by(raoffset, decoffset)
c3_new = c3.spherical_offsets_by(raoffset, decoffset)
c4_new = c4.spherical_offsets_by(raoffset, decoffset)
ca1 = c1_new.ra.value
cb1 = c1_new.dec.value

ca2 = c2_new.ra.value
cb2 = c2_new.dec.value

ca3 = c3_new.ra.value
cb3 = c3_new.dec.value

ca4 = c4_new.ra.value
cb4 = c4_new.dec.value
ca1, cb1 = self.offset_coord(ca1, cb1, raoffset, decoffset)
ca2, cb2 = self.offset_coord(ca2, cb2, raoffset, decoffset)
ca3, cb3 = self.offset_coord(ca3, cb3, raoffset, decoffset)
ca4, cb4 = self.offset_coord(ca4, cb4, raoffset, decoffset)

corner_a.append(ca1)
corner_a.append(ca2)
corner_a.append(ca3)
Expand Down Expand Up @@ -1758,15 +1736,11 @@ def map_miri_pixel_to_sky(self, input_model, this_par1, subtract_background,
decoffset = 0.0
# pull out ra dec offset if it exists
if offsets is not None:
filename = input_model.meta.filename
index = offsets['filename'].index(filename)
raoffset = offsets['raoffset'][index]
decoffset = offsets['decoffset'][index]
raoffset, decoffset = self.find_ra_dec_offset(input_model.meta.filename)
log.info("Ra and Dec offset (arc seconds) applied to file :%8.6f, %8.6f, %s",
raoffset*3600.0,
decoffset*3600.0, filename)
raoffset = raoffset* units.deg
decoffset = decoffset* units.deg
raoffset.value,
decoffset.value, input_model.meta.filename)

# check if background sky matching as been done in mrs_imatch step
# If it has not been subtracted and the background has not been
# subtracted - subtract it.
Expand Down Expand Up @@ -1805,10 +1779,7 @@ def map_miri_pixel_to_sky(self, input_model, this_par1, subtract_background,

# offset the central pixel
if offsets is not None:
c1 = SkyCoord(ra, dec, unit='deg')
c1_new = c1.spherical_offsets_by(raoffset, decoffset)
ra = c1_new.ra.value
dec = c1_new.dec.value
ra, dec = self.offset_coord(ra, dec, raoffset, decoffset)

valid1 = ~np.isnan(ra)
ra = ra[valid1]
Expand Down Expand Up @@ -1851,27 +1822,11 @@ def map_miri_pixel_to_sky(self, input_model, this_par1, subtract_background,

# now offset the pixel corners
if offsets is not None:
c1 = SkyCoord(ra1, dec1, unit='deg')
c2 = SkyCoord(ra2, dec2, unit='deg')
c3 = SkyCoord(ra3, dec3, unit='deg')
c4 = SkyCoord(ra4, dec4, unit='deg')

c1_new = c1.spherical_offsets_by(raoffset, decoffset)
c2_new = c2.spherical_offsets_by(raoffset, decoffset)
c3_new = c3.spherical_offsets_by(raoffset, decoffset)
c4_new = c4.spherical_offsets_by(raoffset, decoffset)
ra1 = c1_new.ra.value
dec1 = c1_new.dec.value

ra2 = c2_new.ra.value
dec2 = c2_new.dec.value

ra3 = c3_new.ra.value
dec3 = c3_new.dec.value

ra4 = c4_new.ra.value
dec4 = c4_new.dec.value

ra1, dec1 = self.offset_coord(ra1, dec1, raoffset, decoffset)
ra2, dec2 = self.offset_coord(ra2, dec2, raoffset, decoffset)
ra3, dec3 = self.offset_coord(ra3, dec3, raoffset, decoffset)
ra4, dec4 = self.offset_coord(ra4, dec4, raoffset, decoffset)

corner_coord = [ra1, dec1, ra2, dec2, ra3, dec3, ra4, dec4]

sky_result = (x, y, ra, dec, wave, slice_no, dwave, corner_coord)
Expand Down Expand Up @@ -1901,15 +1856,10 @@ def map_nirspec_pixel_to_sky(self, input_model, offsets):
decoffset = 0.0
# pull out ra dec offset if it exists
if offsets is not None:
filename = input_model.meta.filename
index = offsets['filename'].index(filename)
raoffset = offsets['raoffset'][index]
decoffset = offsets['decoffset'][index]
raoffset, decoffset = self.find_ra_dec_offset(input_model.meta.filename)
log.info("Ra and Dec offset (arc seconds) applied to file :%8.6f, %8.6f, %s",
raoffset*3600.0, decoffset*3600.0, filename)
raoffset.value, decoffset.value, input_model.meta.filename)

raoffset = raoffset* units.deg
decoffset = decoffset* units.deg
# initialize the ra,dec, and wavelength arrays
# we will loop over slice_nos and fill in values
# the flag_det will be set when a slice_no pixel is filled in
Expand Down Expand Up @@ -2071,32 +2021,14 @@ def map_nirspec_pixel_to_sky(self, input_model, offsets):

if offsets is not None:
# central pixel
c1 = SkyCoord(ra, dec, unit='deg')
c1_new = c1.spherical_offsets_by(raoffset, decoffset)
ra = c1_new.ra.value
dec = c1_new.dec.value
ra, dec = self.offset_coord(ra, dec, raoffset, decoffset)

# pixel corners
c1 = SkyCoord(ra1, dec1, unit='deg')
c2 = SkyCoord(ra2, dec2, unit='deg')
c3 = SkyCoord(ra3, dec3, unit='deg')
c4 = SkyCoord(ra4, dec4, unit='deg')
c1_new = c1.spherical_offsets_by(raoffset, decoffset)
c2_new = c2.spherical_offsets_by(raoffset, decoffset)
c3_new = c3.spherical_offsets_by(raoffset, decoffset)
c4_new = c4.spherical_offsets_by(raoffset, decoffset)
ra1 = c1_new.ra.value
dec1 = c1_new.dec.value

ra2= c2_new.ra.value
dec2 = c2_new.dec.value

ra3 = c3_new.ra.value
dec3 = c3_new.dec.value

ra4= c4_new.ra.value
dec4 = c4_new.dec.value

ra1, dec1 = self.offset_coord(ra1, dec1, raoffset, decoffset)
ra2, dec2 = self.offset_coord(ra2, dec2, raoffset, decoffset)
ra3, dec3 = self.offset_coord(ra3, dec3, raoffset, decoffset)
ra4, dec4 = self.offset_coord(ra4, dec4, raoffset, decoffset)

corner_coord = [ra1, dec1, ra2, dec2, ra3, dec3, ra4, dec4]
sky_result = (x, y, ra, dec, wave, slice_no, dwave, corner_coord)
return sky_result
Expand Down Expand Up @@ -2497,7 +2429,27 @@ def blend_output_metadata(self, IFUCube):
],
)

# ********************************************************************************
def find_ra_dec_offset(self, filename):
""" Match the filename in the offset list with input_model.meta.filename and return
the corresponding Ra and Dec offset
"""

index = self.offsets['filename'].index(filename)
raoffset = self.offsets['raoffset'][index]
decoffset = self.offsets['decoffset'][index]
return raoffset, decoffset

# ********************************************************************************
def offset_coord(self, ra, dec, raoffset, decoffset):
coord = SkyCoord(ra, dec, unit='deg')
coord_new = coord.spherical_offsets_by(raoffset, decoffset)

ra_new = coord_new.ra.value
dec_new = coord_new.dec.value

return ra_new, dec_new

class IncorrectInput(Exception):
""" Raises an exception if input parameter, Interpolation, is set to area
when more than one file is used to build the cube.
Expand Down
5 changes: 2 additions & 3 deletions jwst/cube_build/ifuoffset.schema.yaml
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Expand Up @@ -7,9 +7,8 @@ type: object
properties:
units:
description: Units of the ra and dec offset values.
anyOf:
- type: string
- $ref: http://stsci.edu/schemas/asdf/unit/unit-1.0.0
type: string
enum: ['arcsec']
filename:
description: list of filenames
type: array
Expand Down
20 changes: 10 additions & 10 deletions jwst/cube_build/tests/test_offset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,8 +158,9 @@ def test2_offset_file_config(tmp_cwd, miri_ifushort_short_2files, offset_file):

miri_ifushort_short_2files[0].meta.filename = 'test3.fits'
step.offset_file = offset_file
offsets = step.check_offset_file()
assert offsets is None

with pytest.raises(Exception):
offsets = step.check_offset_file()


def test_offset_file_units(tmp_cwd, miri_ifushort_short_2files, offset_file_arcmin):
Expand All @@ -170,9 +171,8 @@ def test_offset_file_units(tmp_cwd, miri_ifushort_short_2files, offset_file_arcm
step.input_models = miri_ifushort_short_2files

step.offset_file = offset_file_arcmin
offsets = step.check_offset_file()
assert offsets is None

with pytest.raises(Exception):
offsets = step.check_offset_file()

def test_read_offset_file(miri_ifushort_short_2files, offset_file):
""" Test offset file has been read in correctly"""
Expand Down Expand Up @@ -276,15 +276,15 @@ def test_read_offset_file(miri_ifushort_short_2files, offset_file):
raoffset = [0.0, 0.1]
decoffset = [0.0, 0.15]

ravalues = thiscube.offsets['raoffset']
ravalues = thiscube.offsets['raoffset']
decvalues = thiscube.offsets['decoffset']

assert thiscube.offsets['filename'] == filename

assert math.isclose(ravalues[0]*3600.0, raoffset[0], abs_tol=0.0001)
assert math.isclose(ravalues[1]*3600.0, raoffset[1], abs_tol=0.0001)
assert math.isclose(decvalues[0]*3600.0, decoffset[0], abs_tol=0.0001)
assert math.isclose(decvalues[1]*3600.0, decoffset[1], abs_tol=0.0001)
assert math.isclose(ravalues[0].value, raoffset[0], abs_tol=0.0001)
assert math.isclose(ravalues[1].value, raoffset[1], abs_tol=0.0001)
assert math.isclose(decvalues[0].value, decoffset[0], abs_tol=0.0001)
assert math.isclose(decvalues[1].value, decoffset[1], abs_tol=0.0001)



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