def test_apply_d2im():
from stwcs.updatewcs import apply_corrections as appc
acs_orig_file = get_filepath('j94f05bgq_flt.fits')
current_dir = os.path.abspath(os.path.curdir)
fname = get_filepath('j94f05bgq_flt.fits', current_dir)
d2imfile = get_filepath('new_wfc_d2i.fits')
try:
os.remove(fname)
except OSError:
pass
shutil.copyfile(acs_orig_file, fname)
fits.setval(fname, ext=0, keyword="D2IMFILE", value=d2imfile)
fits.setval(fname, ext=0, keyword="IDCTAB", value='N/A')
fits.setval(fname, ext=0, keyword="NPOLFILE", value='N/A')
# If D2IMEXT does not exist, the correction should be applied
assert appc.apply_d2im_correction(fname, d2imcorr=True)
updatewcs.updatewcs(fname)
# Test the case when D2IMFILE == D2IMEXT
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
assert not appc.apply_d2im_correction(fname, d2imcorr=False)
fits.setval(fname, ext=0, keyword='D2IMFILE', value="N/A")
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
# No D2IMFILE keyword in primary header
fits.delval(fname, ext=0, keyword='D2IMFILE')
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
def test_apply_d2im():
from stwcs.updatewcs import apply_corrections as appc
acs_orig_file = get_filepath('j94f05bgq_flt.fits')
current_dir = os.path.abspath(os.path.curdir)
fname = get_filepath('j94f05bgq_flt.fits', current_dir)
d2imfile = get_filepath('new_wfc_d2i.fits')
try:
os.remove(fname)
except OSError:
pass
shutil.copyfile(acs_orig_file, fname)
fits.setval(fname, ext=0, keyword="D2IMFILE", value=d2imfile)
fits.setval(fname, ext=0, keyword="IDCTAB", value='N/A')
fits.setval(fname, ext=0, keyword="NPOLFILE", value='N/A')
# If D2IMEXT does not exist, the correction should be applied
fileobj = fits.open(fname, mode='update')
assert appc.apply_d2im_correction(fileobj, d2imcorr=True)
updatewcs.updatewcs(fname)
# Test the case when D2IMFILE == D2IMEXT
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
assert not appc.apply_d2im_correction(fname, d2imcorr=False)
fits.setval(fname, ext=0, keyword='D2IMFILE', value="N/A")
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
# No D2IMFILE keyword in primary header
fits.delval(fname, ext=0, keyword='D2IMFILE')
assert not appc.apply_d2im_correction(fname, d2imcorr=True)
def headerRenameKey2(self, key, newkey):
for filename in self._matchingFiles:
print('rename %s: %s= %s' % (filename, key, newkey))
try:
value = fits.getval(filename, key)
fits.setval(filename, newkey, value)
fits.delval(filename, key)
except Exception as e:
print(str(e))
pass
def test_no_HDRNAME_no_WCSNAME(self):
"""
Test create_headerlet stepping through all
extensions in the science file
"""
newf = get_filepath('ncomp.fits', os.path.abspath(os.path.curdir))
shutil.copyfile(self.comp_file, newf)
#fits.delval(newf, 'HDRNAME', ext=1)
fits.delval(newf, 'WCSNAME', ext=1)
with pytest.raises(KeyError):
hlet = headerlet.create_headerlet(newf)
def test_no_HDRNAME_no_WCSNAME(self):
"""
Test create_headerlet stepping through all
extensions in the science file
"""
newf = get_filepath('ncomp.fits', os.path.abspath(os.path.curdir))
shutil.copyfile(self.comp_file, newf)
#fits.delval(newf, 'HDRNAME', ext=1)
fits.delval(newf, 'WCSNAME', ext=1)
with pytest.raises(KeyError):
hlet = headerlet.create_headerlet(newf)
def clear_comments(fits_file):
"""
Delete the COMMENTS in the FITS header
Parameters
----------
fits_file: str
Path to a FITS image file
"""
for comment_key in ['COMMENT', 'comment', 'Comment']:
try:
pyfits.delval(fits_file, comment_key)
except KeyError:
pass
def clear_comments(fits_file):
"""
Delete the COMMENTS in the FITS header
Parameters
----------
fits_file: str
Path to a FITS image file
"""
for comment_key in ['COMMENT', 'comment', 'Comment']:
try:
pyfits.delval(fits_file, comment_key)
except KeyError:
pass
def headerDeleteKey(self, key):
for filename in self._matchingFiles:
print('delete %s: %s' % (filename, key))
fits.delval(filename, key)
def add_keywds(fits_file, only_update, missing_keywds, specific_keys_dict):
'''
This function adds the missing keywords from the hdr_keywords_dictionary.py (hkwd) file and gives
the fake values taken from the dictionary sample_hdr_keywd_vals_dict.py (shkvd).
Args:
only_update: If false a copy of the original fits file will be created with the
updated header.
missing_keywds: list, missing keywords will be appended here
specific_keys_dict: dictionary with specific keys and values that need to be changed
'''
missing_keywds = list(OrderedDict.fromkeys(missing_keywds))
#print ("specific_keys_dict = ", specific_keys_dict)
# create name for updated fits file
updated_fitsfile = fits_file
if not only_update:
updated_fitsfile = fits_file.replace('.fits', '_updatedHDR.fits')
subprocess.run(["cp", fits_file, updated_fitsfile])
# add missimg keywords
wcs_keywds_from_main_hdr = {}
print('Saving keyword values in file: ', updated_fitsfile)
ext = 0
for i, key in enumerate(missing_keywds):
if key in specific_keys_dict:
#print ("found it in the dict: ", key, specific_keys_dict[key])
if specific_keys_dict[key] == 'remove':
# keyword to be deleted
try:
fits.delval(updated_fitsfile, key, ext)
except:
KeyError
else:
# change the keyword to specified value
fits.setval(updated_fitsfile,
key,
value=specific_keys_dict[key])
continue
# get the index of the keyword previous to the one you want to add
prev_key_idx = list(shkvd.keywd_dict.keys()).index(key) - 1
# add the keyword in the right place from the right dictionary
new_value = shkvd.keywd_dict[key]
after_key = list(shkvd.keywd_dict.keys())[prev_key_idx]
if after_key == 'wcsinfo':
after_key = list(shkvd.keywd_dict.keys())[prev_key_idx - 1]
if key != 'wcsinfo':
print("adding keyword: ", key, " in extension: primary after: ",
after_key)
# choose right value for GWA_XTIL according to the grating
if key == "GWA_XTIL":
grating = fits.getval(fits_file, "GRATING", 0)
new_value = get_gwa_Xtil_val(grating, path_to_tilt_files)
print("Replacing value of keyword ", key,
" corresponding to GRATING=", grating, "and value ",
new_value)
# choose right value for GWA_YTIL according to the grating
if key == "GWA_YTIL":
grating = fits.getval(fits_file, "GRATING", 0)
new_value = get_gwa_Ytil_val(grating, path_to_tilt_files)
print("Replacing value of keyword ", key,
" corresponding to GRATING=", grating, "and value ",
new_value)
fits.setval(updated_fitsfile,
key,
0,
value=new_value,
after=after_key)
else:
# go into the subdictionary for WCS keywords
extname = 'sci'
sci_hdr = fits.getheader(updated_fitsfile, extname)
main_hdr = fits.getheader(updated_fitsfile, 0)
for subkey, new_value in shkvd.keywd_dict["wcsinfo"].items():
# first remove these keywords from the main header
if subkey in main_hdr:
#val = fits.getval(updated_fitsfile, subkey, 0)
#wcs_keywds_from_main_hdr[subkey] = val
fits.delval(updated_fitsfile, subkey, 0)
# following commented lines are not working
# uncomment this line if wanting to use the original keyword value given by create_data
#new_value = wcs_keywds_from_main_hdr[subkey]
if subkey not in sci_hdr:
print("adding keyword: ", subkey, " in extension: ",
extname, " with value: ", new_value)
fits.setval(updated_fitsfile,
subkey,
1,
value=new_value,
after='EXTNAME')
print("Science header has been updated.")
def add_keywds(fits_file, only_update, missing_keywds, specific_keys_dict, mode_used):
'''
This function adds the missing keywords from the hdr_keywords_dictionary.py (hkwd) file and gives
the fake values taken from the dictionary sample_hdr_keywd_vals_dict.py (shkvd).
Args:
only_update: If false a copy of the original fits file will be created with the
updated header.
missing_keywds: list, missing keywords will be appended here
specific_keys_dict: dictionary with specific keys and values that need to be changed
mode_used: str or None, observation mode used FS, MOS, or IFU (if None then a configuration file
is expected to exist and contain a variable named mode_used)
'''
missing_keywds = list(OrderedDict.fromkeys(missing_keywds))
# create name for updated fits file
updated_fitsfile = fits_file
if not only_update:
updated_fitsfile = fits_file.replace('.fits', '_updatedHDR.fits')
subprocess.run(["cp", fits_file, updated_fitsfile])
# add missimg keywords
print ('Saving keyword values in file: ', updated_fitsfile)
ext = 0
for i, key in enumerate(missing_keywds):
if key in specific_keys_dict:
#print ("found it in the dict: ", key, specific_keys_dict[key])
if specific_keys_dict[key] == 'remove':
# keyword to be deleted
try:
fits.delval(updated_fitsfile, key, ext)
except:
KeyError
else:
# change the keyword to specified value
fits.setval(updated_fitsfile, key, value=specific_keys_dict[key])
continue
# get the index of the keyword previous to the one you want to add
prev_key_idx = list(lev2bdict.keywd_dict.keys()).index(key) - 1
# add the keyword in the right place from the right dictionary
new_value = lev2bdict.keywd_dict[key]
after_key = list(lev2bdict.keywd_dict.keys())[prev_key_idx]
if after_key == 'wcsinfo':
after_key = list(lev2bdict.keywd_dict.keys())[prev_key_idx-1]
if key != 'wcsinfo':
# the DATAMODL keyword will only be modified if mode is IFU
if key == 'DATAMODL':
if 'IFU' in mode_used:
new_value = 'IFUImageModel'
else:
new_value = 'ImageModel'
if key == 'GRATING':
new_value = fits.getval(updated_fitsfile, 'GWA_POS', 0)
grating = new_value
if key == 'FILTER':
new_value = fits.getval(updated_fitsfile, 'FWA_POS', 0)
# choose right value for GWA_XTIL according to the grating
if key == "GWA_XTIL":
new_value = get_gwa_Xtil_val(grating, path_to_tilt_files)
print("Replacing value of keyword ", key, " corresponding to GRATING=", grating, "and value ", new_value)
# choose right value for GWA_YTIL according to the grating
if key == "GWA_YTIL":
new_value = get_gwa_Ytil_val(grating, path_to_tilt_files)
print("Replacing value of keyword ", key, " corresponding to GRATING=", grating, "and value ", new_value)
if key == "EXP_TYPE":
new_value = set_exp_type_value(mode_used)
fits.setval(updated_fitsfile, key, 0, value=new_value, after=after_key)
print("adding keyword: ", key, " in extension: PRIMARY after: ", after_key, " value: ", new_value)
else:
# go into the sub-dictionary for WCS keywords
extname = 'sci'
sci_hdr = fits.getheader(updated_fitsfile, extname)
main_hdr = fits.getheader(updated_fitsfile, 0)
for subkey, new_value in lev2bdict.keywd_dict["wcsinfo"].items():
# first remove these keywords from the main header
if subkey in main_hdr:
#val = fits.getval(updated_fitsfile, subkey, 0)
#wcs_keywds_from_main_hdr[subkey] = val
try:
fits.delval(updated_fitsfile, subkey, 0)
except:
KeyError
# following commented lines are not working
# uncomment this line if wanting to use the original keyword value given by create_data
#new_value = wcs_keywds_from_main_hdr[subkey]
if subkey not in sci_hdr:
print("adding keyword: ", subkey, " in extension: ", extname, " with value: ", new_value)
fits.setval(updated_fitsfile, subkey, 1, value=new_value, after='EXTNAME')
# if the keyword is not in the sample dictionary then remove it
for key in lev2bdict.keywd_dict:
if key != 'wcsinfo':
try:
fits.delval(updated_fitsfile, key, 1)
except:
KeyError
print ("Main and science headers have been updated.")
return updated_fitsfile
MEX = str(input('Is MEX "true" or "false"? '))
if MEX == 'false':
filepath = Path(input('what directory are the images in? '))
filename = input('what are the image filenames? ')
hdus = sorted(filepath.glob(filename))
for hdu in hdus:
print(hdu)
fits.setval(
hdu,
'RADESYS',
value=coords,
comment='Coordinate System (keyword changed by SCantu)',
before='RADECSYS')
fits.delval(hdu, 'RADECSYS')
elif MEX == 'true':
filepath = Path(input('where are the MEX files? '))
filename = input('what is the image filename? ')
hdus = sorted(filepath.glob(filename))
for hdu in hdus:
print(hdu)
for i in range(len(fits.info(hdu, output=False)) - 1):
fits.setval(
hdu,
'RADESYS',
value=coords,
comment='Coordinate System (keyword changed by SCantu)',
before='RADECSYS',
def delhdrkey(im, kwds=kwds):
h = fits.getheader(im)
for k in kwds:
if k in list(h.keys()):
print('removing', k, h[k])
fits.delval(im, k)
def add_keywds(fits_file, only_update, missing_keywds, specific_keys_dict):
'''
This function adds the missing keywords from the hdr_keywords_dictionary.py (hkwd) file and gives
the fake values taken from the dictionary sample_hdr_keywd_vals_dict.py (shkvd).
Args:
only_update: If false a copy of the original fits file will be created with the
updated header.
missing_keywds: list, missing keywords will be appended here
specific_keys_dict: dictionary with specific keys and values that need to be changed
'''
missing_keywds = list(OrderedDict.fromkeys(missing_keywds))
#print ("specific_keys_dict = ", specific_keys_dict)
# create name for updated fits file
updated_fitsfile = fits_file
if not only_update:
updated_fitsfile = fits_file.replace('.fits', '_updatedHDR.fits')
subprocess.run(["cp", fits_file, updated_fitsfile])
# add missimg keywords
wcs_keywds_from_main_hdr = {}
print('Saving keyword values in file: ', updated_fitsfile)
ext = 0
for i, key in enumerate(missing_keywds):
if key in specific_keys_dict:
#print ("found it in the dict: ", key, specific_keys_dict[key])
if specific_keys_dict[key] == 'remove':
# keyword to be deleted
try:
fits.delval(updated_fitsfile, key, ext)
except:
KeyError
else:
# change the keyword to specified value
fits.setval(updated_fitsfile,
key,
value=specific_keys_dict[key])
continue
# get the index of the keyword previous to the one you want to add
prev_key_idx = list(lev2bdict.keywd_dict.keys()).index(key) - 1
# add the keyword in the right place from the right dictionary
new_value = lev2bdict.keywd_dict[key]
after_key = list(lev2bdict.keywd_dict.keys())[prev_key_idx]
if after_key == 'wcsinfo':
after_key = list(lev2bdict.keywd_dict.keys())[prev_key_idx - 1]
if key != 'wcsinfo':
print("adding keyword: ", key, " in extension: primary after: ",
after_key)
# the DATAMODL keyword will only be modified if mode is IFU
if key == 'DATAMODL' and lev2bdict.keywd_dict[
'EXP_TYPE'] == 'NRS_IFU':
new_value = 'IFUImageModel'
fits.setval(updated_fitsfile,
key,
0,
value=new_value,
after=after_key)
else:
# go into the subdictionary for WCS keywords
extname = 'sci'
sci_hdr = fits.getheader(updated_fitsfile, extname)
main_hdr = fits.getheader(updated_fitsfile, 0)
for subkey, new_value in lev2bdict.keywd_dict["wcsinfo"].items():
# first remove these keywords from the main header
if subkey in main_hdr:
#val = fits.getval(updated_fitsfile, subkey, 0)
#wcs_keywds_from_main_hdr[subkey] = val
try:
fits.delval(updated_fitsfile, subkey, 0)
except:
KeyError
# following commented lines are not working
# uncomment this line if wanting to use the original keyword value given by create_data
#new_value = wcs_keywds_from_main_hdr[subkey]
if subkey not in sci_hdr:
print("adding keyword: ", subkey, " in extension: ",
extname, " with value: ", new_value)
fits.setval(updated_fitsfile,
subkey,
1,
value=new_value,
after='EXTNAME')
# if the keyword is not in the sample dictionary then remove it
for key in lev2bdict.keywd_dict:
if key != 'wcsinfo':
try:
fits.delval(updated_fitsfile, subkey, 1)
except:
KeyError
print("Main and science headers have been updated.")
"""
Edit header
Usage:
python edit_header.py T2m3wb-20190826.143357-0072.fits KEYWORD value
IMAGETYP: arc, object
"""
from astropy.io import fits
import sys
if len(sys.argv)!=4:
print('Usage: filename keyword value')
filename = sys.argv[1]
keyword = sys.argv[2]
value = sys.argv[3].replace(' ', '')
print "'%s' '%s'"%(keyword, value)
fits.delval(filename, keyword)
if keyword=='IMAGETYP':
fits.setval(filename, keyword, value=value, after='OBJECT')
else:
fits.setval(filename, keyword, value=value)