Merge branch 'master' into dq-bits-fix

grizli/aws/field_tiles.py

@@ -57,6 +57,10 @@ def make_all_fields():
     sextansa 152.7749473 -4.7061916 46 46
     rxcj0600 90.04 -20.145 46 46
     ulasj1342 205.555 9.462 46 46
+    izw18 143.5087276 55.2404070 46 46
+    q2343p12 356.60847 12.80712 46 46
+    abell1703 198.76667958333334 51.821752 46 46
+    sunburst 237.5295615 -78.1917929 46 46
     """
 
     # 46 46 for tile ref 9 9

grizli/aws/recalibrate.py

@@ -228,11 +228,12 @@ def do_recalibrate(rate_file='jw06541001001_03101_00001_nrs1_rate.fits', cores='
     output_path, base_file = os.path.split(rate_file)
     mastquery.utils.download_from_mast([base_file.replace('_rate.fits','_uncal.fits')])
 
-    try:
-        ncores = int(cores)
-    except ValueError:
-        ncores = cores
-
+    # try:
+    #     ncores = int(cores)
+    # except ValueError:
+    #     ncores = cores
+    ncores = cores
+
     steps = {
         "jump": {
             "save_results": True,

grizli/data/cwi_badpix.py

@@ -0,0 +1,35 @@
+"""
+update LW badpix table from C. Willott
+
+https://github.com/gbrammer/grizli/issues/200
+
+"""
+
+import os
+import astropy.io.fits as pyfits
+import numpy as np
+from grizli import utils
+
+new_list = ['https://github.com/gbrammer/grizli/files/13878784/badpixlist_along_20240108.txt', 
+ 'https://github.com/gbrammer/grizli/files/13878785/badpixlist_blong_20240108.txt']
+
+old_list = ['nrc_badpix_231206_NRCALONG.fits.gz', 'nrc_badpix_231206_NRCBLONG.fits.gz']
+
+for new_file, old_file in zip(new_list, old_list):
+    det = os.path.basename(new_file).split('_')[1]
+
+    new_data = utils.read_catalog(new_file, format='ascii')
+
+    with pyfits.open(old_file) as im:
+        orig_bad = im[0].data.sum()
+
+        for x, y in zip(new_data['col1'], new_data['col2']):
+            im[0].data[y,x] |= 1
+
+        new_bad = im[0].data.sum()
+
+        msg = f'{det} prev = {orig_bad.sum()}  new = {new_bad.sum()}'
+        print(msg)
+
+    out_file = f'nrc_badpix_240112_NRC{det.upper()}.fits.gz'
+    im.writeto(out_file, overwrite=True)

grizli/data/photom_correction.yml

@@ -184,3 +184,42 @@ NRCALONG-F410M-CLEAR: 0.9788
 # From j1235 COM-1063 commissioning field
 NRCBLONG-F300M-CLEAR: 1.0000
 NRCALONG-F300M-CLEAR: 0.9681
+
+## From PRIMER UDS split by detector
+## jwst_0989.pmap
+
+# NRCA1-F090W-CLEAR: 0.9761
+# NRCA2-F090W-CLEAR: 1.0069
+# NRCA3-F090W-CLEAR: 0.9625
+# NRCA4-F090W-CLEAR: 0.9987
+# NRCB1-F090W-CLEAR: 1.0233
+# NRCB2-F090W-CLEAR: 1.0143
+# NRCB3-F090W-CLEAR: 1.0121
+# NRCB4-F090W-CLEAR: 1.0000
+
+# NRCA1-F115W-CLEAR: 0.9828
+# NRCA2-F115W-CLEAR: 1.0133
+# NRCA3-F115W-CLEAR: 0.9726
+# NRCA4-F115W-CLEAR: 1.0189
+# NRCB1-F115W-CLEAR: 1.0283
+# NRCB2-F115W-CLEAR: 1.0005
+# NRCB3-F115W-CLEAR: 1.0120
+# NRCB4-F115W-CLEAR: 1.0000
+
+# NRCA1-F150W-CLEAR: 1.0045
+# NRCA2-F150W-CLEAR: 1.0373
+# NRCA3-F150W-CLEAR: 0.9785
+# NRCA4-F150W-CLEAR: 1.0192
+# NRCB1-F150W-CLEAR: 1.0375
+# NRCB2-F150W-CLEAR: 1.0055
+# NRCB3-F150W-CLEAR: 1.0240
+# NRCB4-F150W-CLEAR: 1.0000
+
+# NRCA1-F200W-CLEAR: 0.9953
+# NRCA2-F200W-CLEAR: 1.0397
+# NRCA3-F200W-CLEAR: 0.9788
+# NRCA4-F200W-CLEAR: 1.0196
+# NRCB1-F200W-CLEAR: 1.0293
+# NRCB2-F200W-CLEAR: 1.0053
+# NRCB3-F200W-CLEAR: 1.0175
+# NRCB4-F200W-CLEAR: 1.0000

grizli/galfit/psf.py

@@ -367,7 +367,10 @@ def objfun(params, self, ra, dec, wcs_slice, filter, drz_cutout):
         print(params, chi2)
         return chi2
 
-    def get_psf(self, ra=53.06967306, dec=-27.72333015, filter='F140W', pixfrac=0.1, kernel='point', verbose=True, wcs_slice=None, get_extended=True, get_weight=False, ds9=None, npix=13, renormalize=True):
+    def get_psf(self, ra=53.06967306, dec=-27.72333015, filter='F140W', pixfrac=0.1, kernel='point', verbose=True, wcs_slice=None, get_extended=True, get_weight=False, ds9=None, npix=13, renormalize=True, xphase=0, yphase=0):
+        """
+        """
+
         from drizzlepac import adrizzle
         from shapely.geometry import Polygon, Point
 
@@ -388,8 +391,10 @@ def get_psf(self, ra=53.06967306, dec=-27.72333015, filter='F140W', pixfrac=0.1,
 
                 xy = self.wcs[key].all_world2pix(np.array([[ra, dec]]), 0)[0]
                 xyp = np.cast[int](xy) #np.round(xy))  # +1
-                dx = xy[0]-int(xy[0])#-0.5
-                dy = xy[1]-int(xy[1])#-0.5
+                dx = xy[0] - int(xy[0]) + xphase
+                dy = xy[1] - int(xy[1]) + yphase
+                # dx = xy[0]-int(xy[0]) + 0.5
+                # dy = xy[1]-int(xy[1]) + 0.5
 
                 if ext == 2:
                     # UVIS

grizli/jwst_utils.py

@@ -923,7 +923,7 @@ def copy_jwst_keywords(header, orig_keys=ORIG_KEYS, verbose=True):
                 utils.log_comment(utils.LOGFILE, msg, verbose=verbose)
 
 
-def exposure_oneoverf_correction(file, axis=None, thresholds=[5,4,3], erode_mask=None, dilate_iterations=3, deg_pix=64, make_plot=True, init_model=0, in_place=False, skip_miri=True, verbose=True, **kwargs):
+def exposure_oneoverf_correction(file, axis=None, thresholds=[5,4,3], erode_mask=None, dilate_iterations=3, deg_pix=64, make_plot=True, init_model=0, in_place=False, skip_miri=True, force_oneoverf=False, verbose=True, **kwargs):
     """
     1/f correction for individual exposure
     
@@ -971,6 +971,9 @@ def exposure_oneoverf_correction(file, axis=None, thresholds=[5,4,3], erode_mask
     skip_miri : bool
         Don't run on MIRI exposures
     
+    force_oneoverf : bool
+        Force the correction even if the `ONEFEXP` keyword is already set
+    
     verbose : bool
         Print status messages
         
@@ -997,6 +1000,14 @@ def exposure_oneoverf_correction(file, axis=None, thresholds=[5,4,3], erode_mask
         utils.log_comment(utils.LOGFILE, msg, verbose=verbose)
 
         return None, 0
+
+    if ('ONEFEXP' in im[0].header) and im[0].header['ONEFEXP'] and (not force_oneoverf):
+        im.close()
+
+        msg = 'exposure_oneoverf_correction: Skip, already corrected'
+        utils.log_comment(utils.LOGFILE, msg, verbose=verbose)
+
+        return None, 0
 
     if axis is None:
         if im[0].header['INSTRUME'] in ('NIRISS', 'NIRSPEC'):
@@ -1456,7 +1467,7 @@ def initialize_jwst_image(filename, verbose=True, max_dq_bit=14, orig_keys=ORIG_
 #                  'F480M': [1.879639e-21, 1.453752e-30, 4.8152]}
 # 
 
-def set_jwst_to_hst_keywords(input, reset=False, verbose=True, orig_keys=ORIG_KEYS):
+def set_jwst_to_hst_keywords(input, reset=False, verbose=True, orig_keys=ORIG_KEYS, oneoverf_correction=True):
     """
     Make primary header look like an HST instrument
     """
@@ -1476,7 +1487,7 @@ def set_jwst_to_hst_keywords(input, reset=False, verbose=True, orig_keys=ORIG_KE
            'DETECTOR':'IR'}
 
     if 'OTELESCO' not in img[0].header:
-        _status = initialize_jwst_image(input, verbose=verbose)
+        _status = initialize_jwst_image(input, oneoverf_correction=oneoverf_correction, verbose=verbose)
 
         # Reopen
         if isinstance(input, str):

grizli/prep.py

@@ -4452,11 +4452,16 @@ def process_direct_grism_visit(direct={},
     if 'driz_cr_snr' in drizzle_params:
         driz_cr_snr = drizzle_params['driz_cr_snr']
         drizzle_params.pop('driz_cr_snr')
-
+        
     if 'bits' in drizzle_params:
         bits = drizzle_params['bits']
         drizzle_params.pop('bits')
-
+
+    if 'driz_cr_grow' in drizzle_params:
+        driz_cr_grow = drizzle_params.pop('driz_cr_grow')
+    else:
+        driz_cr_grow = 1
+
     # Relax CR rejection for first-pass ACS
     if isACS:
         driz_cr_snr_first = '15. 10.0'
@@ -4779,15 +4784,27 @@ def process_direct_grism_visit(direct={},
         utils.log_comment(utils.LOGFILE, logstr, verbose=True, show_date=True)
 
         if len(direct['files']) == 1:
-            AstroDrizzle(direct['files'], output=direct['product'],
-                         clean=True, final_pixfrac=0.8, context=False,
-                         resetbits=4096, final_bits=bits, driz_sep_bits=bits,
-                         preserve=False, driz_cr_snr=driz_cr_snr,
-                         driz_cr_scale=driz_cr_scale, driz_separate=False,
-                         driz_sep_wcs=False, median=False, blot=False,
-                         driz_cr=False, driz_cr_corr=False,
-                         build=False, final_wht_type='IVM',
-                         gain=_gain, rdnoise=_rdnoise,
+            AstroDrizzle(direct['files'],
+                         output=direct['product'],
+                         clean=True,
+                         final_pixfrac=0.8,
+                         context=False,
+                         resetbits=4096,
+                         final_bits=bits,
+                         driz_sep_bits=bits,
+                         preserve=False,
+                         driz_cr_snr=driz_cr_snr,
+                         driz_cr_scale=driz_cr_scale,
+                         driz_separate=False,
+                         driz_sep_wcs=False,
+                         median=False,
+                         blot=False,
+                         driz_cr=False,
+                         driz_cr_corr=False,
+                         build=False,
+                         final_wht_type='IVM',
+                         gain=_gain,
+                         rdnoise=_rdnoise,
                          static=False,
                          **drizzle_params)
         else:
@@ -4799,12 +4816,19 @@ def process_direct_grism_visit(direct={},
             AstroDrizzle(direct['files'], output=direct['product'],
                          clean=True, final_pixfrac=pixfrac,
                          context=(isACS | isWFPC2),
-                         skysub=True, skymethod=skymethod,
-                         resetbits=4096, final_bits=bits, driz_sep_bits=bits,
-                         preserve=False, driz_cr_snr=driz_cr_snr,
-                         driz_cr_scale=driz_cr_scale, build=False,
+                         skysub=True,
+                         skymethod=skymethod,
+                         resetbits=4096,
+                         final_bits=bits,
+                         driz_sep_bits=bits,
+                         preserve=False,
+                         driz_cr_snr=driz_cr_snr,
+                         driz_cr_scale=driz_cr_scale,
+                         driz_cr_grow=driz_cr_grow,
+                         build=False,
                          final_wht_type='IVM',
-                         gain=_gain, rdnoise=_rdnoise,
+                         gain=_gain,
+                         rdnoise=_rdnoise,
                          static=static_mask,
                          **drizzle_params)
 

grizli/utils.py

@@ -6267,8 +6267,6 @@ def drizzle_from_visit(visit, output=None, pixfrac=1., kernel='point',
 
                 wcs_rows.append(row)
 
-                sci_list.append((flt[('SCI', ext)].data - sky)*phot_scale)
-
                 err = flt[('ERR', ext)].data*phot_scale
 
                 # JWST: just 1,1024,4096 bits
@@ -6340,9 +6338,10 @@ def drizzle_from_visit(visit, output=None, pixfrac=1., kernel='point',
                                 log_comment(LOGFILE, msg, verbose=verbose)
 
                 wht_list.append(wht)
+                sci_i = (flt[('SCI', ext)].data - sky)*phot_scale
+                sci_i[wht <= 0] = 0
+                sci_list.append(sci_i)
 
-                # wcs_i = HSTWCS(fobj=flt, ext=('SCI',ext), minerr=0.0,
-                #                wcskey=' ')
                 if not hasattr(wcs_i, 'pixel_shape'):
                     wcs_i.pixel_shape = wcs_i._naxis1, wcs_i._naxis2
 
@@ -9117,7 +9116,7 @@ def log_function_arguments(LOGFILE, frame, func='func', ignore=[], verbose=True)
     logstr = logstr.format(func, args)
     msg = log_comment(LOGFILE, logstr, verbose=verbose, show_date=True)
 
-    return msg
+    return args
 
 
 def ctime_to_iso(mtime, format='%a %b %d %H:%M:%S %Y', strip_decimal=True, verbose=True):
@@ -9581,7 +9580,7 @@ def N(self):
         return len(self.values)
 
 
-    def info(self, sort_counts=-1):
+    def info(self, sort_counts=0):
         """
         Print a summary
         """