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Update jwst_utils.py
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@gbrammer
gbrammer authored Oct 8, 2024
1 parent 13497af commit 865f27d
Showing 1 changed file with 40 additions and 89 deletions.
129 changes: 40 additions & 89 deletions grizli/jwst_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -489,7 +489,10 @@ def img_with_flat(
use_skyflats : bool
Apply sky flat corrections if True.
Note: Some of this documentation is AI-generated and will be reviewed.
Returns
-------
output : `jwst.datamodels.ImageModel`
Updated data model
"""
import gc

Expand Down Expand Up @@ -663,7 +666,6 @@ def img_with_wcs(
with_wcs : `jwst.datamodels.ImageModel`
Image model with full `~gwcs` in `with_wcs.meta.wcs`.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from jwst.datamodels import util
from jwst.assign_wcs import AssignWcsStep
Expand Down Expand Up @@ -783,8 +785,6 @@ def img_with_wcs(


def match_gwcs_to_sip(input, step=64, transform=None, verbose=True, overwrite=True):
# TODO: (docs review) `img` was not a param so docs removed for it.
# It seems to be set in the method directly. (K.V.)
"""
Calculate transformation of gwcs to match SIP header, which may have been
realigned (shift, rotation, scale)
Expand Down Expand Up @@ -1063,7 +1063,6 @@ def copy_jwst_keywords(header, orig_keys=ORIG_KEYS, verbose=True):
verbose : bool
Print status messages.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
for k in orig_keys:
newk = "O" + k[:7]
Expand Down Expand Up @@ -1334,7 +1333,7 @@ def initialize_jwst_image(
Make copies of some header keywords to make the headers look like
and HST instrument
1) Apply gain correction [x remove]
1) Apply gain correction [*NOT PERFORMED*]
2) Clip DQ bits
3) Copy header keywords
4) Apply exposure-level 1/f correction
Expand Down Expand Up @@ -1372,7 +1371,6 @@ def initialize_jwst_image(
status : bool
True if finished successfully
Note: Some of this documentation is AI-generated and will be reviewed.
"""
frame = inspect.currentframe()
utils.log_function_arguments(
Expand Down Expand Up @@ -1623,15 +1621,6 @@ def initialize_jwst_image(
msg = f"exposure_oneoverf_correction: NIRCam grism sky {filename}"
utils.log_comment(utils.LOGFILE, msg)

# # Subtract simple median
# exposure_oneoverf_correction(filename,
# in_place=True,
# erode_mask=False,
# thresholds=[4,3],
# axis=_disp_axis,
# dilate_iterations=5,
# deg_pix=0)

# Subtract average along dispersion axis
exposure_oneoverf_correction(
filename,
Expand All @@ -1647,7 +1636,7 @@ def initialize_jwst_image(

get_phot_keywords(filename)

# Add TIME
# Add TIME extension
if "TIME" not in img:
img = pyfits.open(filename)

Expand Down Expand Up @@ -1715,7 +1704,6 @@ def set_jwst_to_hst_keywords(
img : `~astropy.io.fits.HDUList`
Modified FITS HDUList object.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
frame = inspect.currentframe()
utils.log_function_arguments(
Expand Down Expand Up @@ -1764,19 +1752,6 @@ def set_jwst_to_hst_keywords(
# img[0].header[f'ATODGN{x}'] = gain
# img[0].header[f'READNSE{x}'] = 12.9

##### This now done in get_phot_keywords
# if img[0].header['OINSTRUM'] == 'NIRISS':
# _filter = img[0].header['OPUPIL']
# if _filter in NIS_PHOT_KEYS:
# img[0].header['PHOTFLAM'] = NIS_PHOT_KEYS[_filter][0]
# img[0].header['PHOTFNU'] = NIS_PHOT_KEYS[_filter][1]
# img[0].header['PHOTPLAM'] = NIS_PHOT_KEYS[_filter][2] * 1.e4
#
# elif 'PHOTFNU' not in img[0].header:
# img[0].header['PHOTFLAM'] = 1.e-21
# img[0].header['PHOTFNU'] = 1.e-31
# img[0].header['PHOTPLAM'] = 1.5e4

# TIME keyword seems to get corrupted?
if "TIME" in img:
img["TIME"].header["PIXVALUE"] = img[0].header["EXPTIME"]
Expand Down Expand Up @@ -1804,7 +1779,6 @@ def strip_telescope_header(header, simplify_wcs=True):
new_header : `~astropy.io.fits.Header`
Modified FITS header.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
new_header = header.copy()

Expand Down Expand Up @@ -1900,7 +1874,7 @@ def model_wcs_header(
**kwargs,
):
"""
Make a header with approximate WCS for use in DS9.
Make a header with a better SIP WCS derived from the JWST `gwcs` object
Parameters
----------
Expand Down Expand Up @@ -1950,7 +1924,6 @@ def model_wcs_header(
header : '~astropy.io.fits.Header`
Header with simple WCS definition: CD rotation but no distortion.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from astropy.io.fits import Header
from scipy.optimize import least_squares
Expand All @@ -1967,22 +1940,6 @@ def model_wcs_header(
degree = kwargs["order"]

if crpix is None:
# try:
# pipe = datamodel.meta.wcs.pipeline[0][1]
# if 'offset_2' in pipe.param_names:
# # NIRISS WCS
# c_x = pipe.offset_2.value + pipe.offset_0.value
# c_y = pipe.offset_3.value + pipe.offset_1.value
#
# else:
# # Simple WCS
# c_x = pipe.offset_0.value
# c_y = pipe.offset_1.value
#
# crpix = np.array([-c_x+1, -c_y+1])
# #print('xxx ', crpix)
#
# except:
crpix = np.array(sh)[::-1] / 2.0 + 0.5
else:
crpix = np.array(crpix)
Expand Down Expand Up @@ -2302,7 +2259,6 @@ def pipeline_model_wcs_header(
fast_coeffs=True,
uvxy=None,
):
# TODO (docs review) fast_coeffs passed to model_wcs_header as it was not used.
"""
Iterative pipeline to refine the SIP headers
Expand Down Expand Up @@ -2349,9 +2305,8 @@ def pipeline_model_wcs_header(
Returns
-------
header : '~astropy.io.fits.Header`
Header with simple WCS definition: CD rotation but no distortion.
Header with SIP WCS
Note: Some of this documentation is AI-generated and will be reviewed.
"""

frame = inspect.currentframe()
Expand Down Expand Up @@ -2438,10 +2393,10 @@ def _objective_sip(
List of SIP coefficients.
u, v, ra, dec : array
Detector and sky coordinates.
Grid of detector and sky coordinates.
crval, crpix : array
Reference pixel and sky coordinates.
Reference pixel
a_names, b_names : list
List of SIP coefficient names.
Expand All @@ -2453,16 +2408,16 @@ def _objective_sip(
Bitmask for fitting rotation, scale, and CRVAL offsets.
ret : int
Return status.
Return behavior
Returns
-------
if ret == 1:
pp, cd_i, crval_i, a_coeff, b_coeff, ra_nmad, dec_nmad
pp, cd_i, crval_i, a_coeff, b_coeff, ra_nmad, dec_nmad : values derived from the input ``params``
else:
dr
dr : array-like
Residuals for fit optimization
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from astropy.modeling import models, fitting

Expand Down Expand Up @@ -2557,8 +2512,7 @@ def _objective_lstsq_sip(
params, u, v, ra, dec, crval, crpix, a_names, b_names, cd, fit_type, ret
):
"""
Objective function for fitting SIP header with coefficients determined
with lst squares
Objective function for fitting SIP header
Parameters
----------
Expand Down Expand Up @@ -2586,11 +2540,11 @@ def _objective_lstsq_sip(
Returns
-------
if ret == 1:
pp, cd_i, crval_i, a_coeff, b_coeff, ra_nmad, dec_nmad
pp, cd_i, crval_i, a_coeff, b_coeff, ra_nmad, dec_nmad : values derived from input ``params``
else:
dr
dr : array-like
Residuals for fit optimization
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from astropy.modeling.fitting import LinearLSQFitter
from astropy.modeling.polynomial import Polynomial2D
Expand Down Expand Up @@ -2712,7 +2666,6 @@ def _objective_lstsq_sip(


def _xobjective_sip(params, u, v, x, y, crpix, a_names, b_names, ret):
# TODO (docs review) crval and cd not used in this method, removed (K.V.)
"""
Objective function for fitting SIP coefficients
Expand All @@ -2721,11 +2674,11 @@ def _xobjective_sip(params, u, v, x, y, crpix, a_names, b_names, ret):
params : list
List of SIP coefficients.
u, v, x, y : array
u, v, x, y : array-like
Detector and sky coordinates.
crpix : array
Reference pixel coordinates.
crpix : array-like
Reference pixel
a_names, b_names : list
List of SIP coefficient names.
Expand All @@ -2736,11 +2689,18 @@ def _xobjective_sip(params, u, v, x, y, crpix, a_names, b_names, ret):
Returns
-------
if ret == 1:
cdx, a_coeff, b_coeff
cdx : (2,2) array
CD matrix
a_coeff : array-like
SIP "A" coefficients
b_coeff : array-like
SIP "B" coefficients
else:
dr
dr : array-like
Residuals for fit optimization
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from astropy.modeling import models, fitting

Expand Down Expand Up @@ -2769,11 +2729,8 @@ def _xobjective_sip(params, u, v, x, y, crpix, a_names, b_names, ret):

fuv, guv = sip(u, v)
xo, yo = np.dot(cdx, np.array([u + fuv - crpix[0], v + guv - crpix[1]]))
# dr = np.sqrt((x-xo)**2+(y-yo)**2)*3600.
dr = np.append(x - xo, y - yo) * 3600.0 / 0.065

# print(params, np.abs(dr).max())

return dr


Expand Down Expand Up @@ -2811,7 +2768,6 @@ def compare_gwcs_sip(
fig : `matplotlib.figure.Figure`
Figure object
Note: Some of this documentation is AI-generated and will be reviewed.
"""
import matplotlib.pyplot as plt

Expand Down Expand Up @@ -2970,7 +2926,6 @@ def calc_jwst_filter_info(context="jwst_1130.pmap"):
Filter information dictionary for JWST instruments with the above
attributes for each filter in each instrument configuration.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
import yaml
import glob
Expand Down Expand Up @@ -3454,9 +3409,8 @@ def query_pure_parallel_wcs_to_database(
- 3990: Morishita+Mason
output : str
Output HTML file (default: /tmp/jwst_pure_parallels.html)
Output HTML table (default: /tmp/jwst_pure_parallels.html)
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from .aws import db

Expand Down Expand Up @@ -3735,7 +3689,6 @@ def update_pure_parallel_wcs_old(
status : None, True
Returns None if some problem is found
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from scipy.optimize import minimize
import pysiaf
Expand Down Expand Up @@ -3914,19 +3867,17 @@ def objfun_pysiaf_pointing(theta, ap, xy, pa, ret):
Position angle of the prime exposure.
ret : int
Return type: 0=resid, 1=attitude matrix
Return behavior
Returns
-------
if ret == 1:
att : array-like
Attitude matrix
Attitude matrix derived from the inputs
else:
resid : float
Sum of squared differences ``ap.corners - xy``
Sum of squared differences ``ap.corners - xy`` for optimization
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from pysiaf.utils import rotations

Expand Down Expand Up @@ -3980,7 +3931,7 @@ def compute_siaf_pa_offset(
Swap the coordinates to agree with APT.
verbose : bool
Messaging to the terminal.
Print messaging to the terminal.
Returns
-------
Expand All @@ -3990,7 +3941,6 @@ def compute_siaf_pa_offset(
dphi : float
Delta position angle.
Note: Some of this documentation is AI-generated and will be reviewed.
"""
from astropy.coordinates import SkyCoord
import astropy.units as u
Expand Down Expand Up @@ -4168,7 +4118,7 @@ def flag_nirspec_hot_pixels(
Parameters
----------
data : str, `~astropy.io.fits.HDUList`
NIRSpec image filename or open HDU with SCI, ERR, DQ extensions.
NIRSpec image filename or open HDU object with SCI, ERR, DQ extensions.
rnoise_percentile : float
Percentile of rnoise array for the absolute threshold
Expand All @@ -4189,12 +4139,13 @@ def flag_nirspec_hot_pixels(
S/N array derived from ``file``
dq : array-like, int
Flagged pixels where ``hot = HOT`` and ``plus = WARM``
Flagged pixels where
``hot = jwst.datamodels.mask.pixel["HOT"]`` and
``plus = jwst.datamodels.mask.pixel["WARM"]``
count : int
Number of flagged pixels
Note: Some of this documentation is AI-generated and will be reviewed.
"""
import scipy.ndimage as nd
from jwst.datamodels.mask import pixel as pixel_codes
Expand Down

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