def test_lev3_FUV(self):
"""
This test is for level 3 FUV data
"""
# Prepare input files.
self.get_input_file("input", "o5in01tnq_raw.fits")
outroot = "calstis_lev3_FUV"
# Run test
calstis("o5in01tnq_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot + "_flt.fits", outroot + "_flt_ref.fits"),
(outroot + "_x2d.fits", outroot + "_x2d_ref.fits")]
self.compare_outputs(outputs)
def test_lev3_FUV(self):
"""
This test is for level 3 FUV data
"""
# Prepare input files.
self.get_input_file("input", "o5in01tnq_raw.fits")
outroot = "calstis_lev3_FUV"
# Run test
calstis("o5in01tnq_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot + "_flt.fits", outroot + "_flt_ref.fits"),
(outroot + "_x2d.fits", outroot + "_x2d_ref.fits")]
self.compare_outputs(outputs)
def test2_lev1_FUV(self):
"""
This test is for level 1? FUV data
"""
# Prepare input files.
self.get_input_file("input", "odj102010_raw.fits")
self.get_input_file("input", "odj102010_wav.fits")
outroot = "calstis_1lev1_FUVspec"
# Run test
calstis("odj102010_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot+"_flt.fits", outroot+"_flt_ref.fits"),
(outroot+"_x1d.fits", outroot+"_x1d_ref.fits")]
self.compare_outputs(outputs)
def test2_lev1_FUV(self):
"""
This test is for level 1? FUV data
"""
# Prepare input files.
self.get_input_file("input", "odj102010_raw.fits")
self.get_input_file("input", "odj102010_wav.fits")
outroot = "calstis_1lev1_FUVspec"
# Run test
calstis("odj102010_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot + "_flt.fits", outroot + "_flt_ref.fits"),
(outroot + "_x1d.fits", outroot + "_x1d_ref.fits")]
self.compare_outputs(outputs)
def test_lev2_CCD(self):
"""
This test is for level 2 CCD data
"""
# Prepare input files.
self.get_input_file("input", "o3wd01060_raw.fits")
self.get_input_file("input", "o3wd01060_wav.fits")
self.get_data("input", "o3wd01060_spt.fits")
outroot = "calstis_lev2_CCD"
# Run test
calstis("o3wd01060_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot + "_flt.fits", outroot + "_flt_ref.fits"),
(outroot + "_crj.fits", outroot + "_crj_ref.fits"),
(outroot + "_sx1.fits", outroot + "_sx1_ref.fits"),
(outroot + "_sx2.fits", outroot + "_sx2_ref.fits")]
self.compare_outputs(outputs)
def test_lev2_CCD(self):
"""
This test is for level 2 CCD data
"""
# Prepare input files.
self.get_input_file("input", "o3wd01060_raw.fits")
self.get_input_file("input", "o3wd01060_wav.fits")
self.get_data("input", "o3wd01060_spt.fits")
outroot = "calstis_lev2_CCD"
# Run test
calstis("o3wd01060_raw.fits", outroot=outroot)
# Compare results
outputs = [(outroot + "_flt.fits", outroot + "_flt_ref.fits"),
(outroot + "_crj.fits", outroot + "_crj_ref.fits"),
(outroot + "_sx1.fits", outroot + "_sx1_ref.fits"),
(outroot + "_sx2.fits", outroot + "_sx2_ref.fits")]
self.compare_outputs(outputs)
def test_ccd_imaging(self):
"""
This test is for calstis on CCD imaging data
"""
# Prepare input files.
self.get_input_file("input", "oci402010_raw.fits")
self.get_data("input", "oci402dnj_epc.fits")
self.get_data("input", "oci402doj_epc.fits")
outroot = "stis_test1"
outfile = outroot + "_flt.fits"
outcrj = outroot + "_crj.fits"
outsx2 = outroot + "_sx2.fits"
reffile_flt = 'reference_stis_01_flt.fits'
reffile_crj = 'reference_stis_01_crj.fits'
reffile_sx2 = 'reference_stis_01_sx2.fits'
calstis("oci402010_raw.fits", outroot=outroot)
# Compare results
outputs = [(outfile, reffile_flt), (outcrj, reffile_crj),
(outsx2, reffile_sx2)]
self.compare_outputs(outputs)
def test_ccd_imaging(self):
"""
This test is for calstis on CCD imaging data
"""
# Prepare input files.
self.get_input_file("input", "oci402010_raw.fits")
self.get_data("input", "oci402dnj_epc.fits")
self.get_data("input", "oci402doj_epc.fits")
outroot = "stis_test1"
outfile = outroot + "_flt.fits"
outcrj = outroot + "_crj.fits"
outsx2 = outroot + "_sx2.fits"
reffile_flt = 'reference_stis_01_flt.fits'
reffile_crj = 'reference_stis_01_crj.fits'
reffile_sx2 = 'reference_stis_01_sx2.fits'
calstis("oci402010_raw.fits", outroot=outroot)
# Compare results
outputs = [(outfile, reffile_flt), (outcrj, reffile_crj),
(outsx2, reffile_sx2)]
self.compare_outputs(outputs)
def regress(folder):
""" Run *drk and *bia files in folder through CalSTIS to check
for errors in processing
"""
start_dir = os.getcwd()
print('#------------------#')
print('Running regression for')
print(folder)
print('#------------------#')
monitor_dir = '/grp/hst/stis/darks_biases'
test_suite = os.path.join(monitor_dir, 'test_suite')
test_dark = os.path.join(monitor_dir, 'test_dark')
print((glob.glob(os.path.join(folder, '*bia.fits'))))
reference_files = glob.glob(os.path.join(folder, '*bia.fits')) + \
glob.glob(os.path.join(folder, '*drk.fits'))
print(reference_files)
assert len(reference_files) >= 1, 'No reference files in folder'
print('Copying files and removing old files')
for testing_dir in [test_suite, test_dark]:
for oldfile in glob.glob(os.path.join(testing_dir, '*_drk.fits')) + \
glob.glob(os.path.join(testing_dir, '*_bia.fits')):
print(('removing', oldfile))
os.remove(os.path.join(testing_dir, oldfile))
for newfile in reference_files:
print(('moving', newfile, '-->', testing_dir))
shutil.copy(newfile, testing_dir)
#######################################
# Run checks in the test_suite folder #
#######################################
os.chdir(test_suite)
print((os.getcwd()))
bias_biwk_refs = glob.glob('*bias*_bi*.fits')
bias_biwk_refs.sort()
biasrefs = glob.glob('*bias*_wk*.fits')
biasrefs.sort()
darkrefs = glob.glob('*dark*.fits')
darkrefs.sort()
raws = glob.glob('*raw.fits')
print('Setting IMPHTTAB in datasets')
for dark, bias in zip(darkrefs, biasrefs):
remove_products()
print('#-------------------------------------------#')
print(('Running CalSTIS with %s %s ' % (dark, bias)))
print('#-------------------------------------------#')
for rawfile in raws:
if os.path.exists( rawfile.replace('raw.fits', 'wav.fits') ):
wavefile = rawfile.replace('raw.fits', 'wav.fits')
else:
wavefile = ''
pyfits.setval(rawfile, 'DARKFILE', value=dark, ext=0)
pyfits.setval(rawfile, 'BIASFILE', value=bias, ext=0)
pyfits.setval(rawfile, 'IMPHTTAB', value='oref$x9r1607mo_imp.fits', ext=0)
if wavefile:
pyfits.setval(wavefile, 'DARKFILE', value=dark, ext=0)
pyfits.setval(wavefile, 'BIASFILE', value=bias, ext=0)
pyfits.setval(wavefile, 'IMPHTTAB', value='oref$x9r1607mo_imp.fits', ext=0)
status = calstis(rawfile, wavecal=wavefile)
if status: sys.exit('Calstis Error detected for %s' % (dark[5:9]))
######################################
# Run checks in the test_dark folder #
######################################
os.chdir(test_dark)
print((os.getcwd()))
raws = glob.glob('*raw.fits')
print('Setting IMPHTTAB in datasets')
for item in raws:
pyfits.setval(item, 'IMPHTTAB', value='oref$x9r1607mo_imp.fits', ext=0)
for bias in bias_biwk_refs:
remove_products()
print('#------------------------------------------#')
print(('Running CalSTIS with %s' % (bias)))
print('#------------------------------------------#')
for rawfile in raws:
pyfits.setval(rawfile, 'BIASFILE', value=bias, ext=0)
pyfits.setval(rawfile, 'DARKFILE', value=darkrefs[0], ext=0)
status = calstis(input=rawfile)
if status: sys.exit('Calstis Error detected for %s' % (dark[5:9]))
os.chdir(start_dir)
def bd_calstis(joinedfile, thebiasfile=None):
""" Run CalSTIS on the joined file
Header keywords will be set for ocrreject to work correctly and not
flag regions outside the original aperture:
APERTURE --> 50CCD
APER_FOV --> '50x50'
DARKCORR --> 'OMIT'
FLATCORR --> 'OMIT'
Parameters
----------
joinedfile : str
join of multiple input darks
thebiasfile : str, bool
the biasfile to be subtracted by basic2d
"""
with pyfits.open(joinedfile, 'update') as hdu:
hdu[0].header['CRCORR'] = 'PERFORM'
hdu[0].header['APERTURE'] = '50CCD'
hdu[0].header['APER_FOV'] = '50x50'
hdu[0].header['DARKCORR'] = 'OMIT'
hdu[0].header['FLATCORR'] = 'OMIT'
if thebiasfile:
hdu[0].header['BIASFILE'] = thebiasfile
crj_file = joinedfile.replace('.fits', '_crj.fits')
path, name = os.path.split(joinedfile)
name, ext = os.path.splitext(name)
trailerfile = os.path.join(path, name+'_bd_calstis_log.txt')
if os.path.exists(crj_file):
print('Deleting old file: %s' % crj_file)
os.remove(crj_file)
if os.path.exists(trailerfile):
print('Deleting old file: %s' % trailerfile)
os.remove(trailerfile)
print('Running CalSTIS on %s' % joinedfile)
print('to create: %s' % crj_file)
status = calstis(joinedfile,
wavecal="",
outroot="",
savetmp=False,
verbose=False,
trailer=trailerfile)
if status != 0:
try:
print()
with open(trailerfile) as tr:
for line in tr.readlines():
print(' {}'.format(line.strip()))
finally:
raise Exception('CalSTIS failed to properly reduce {}'.format(joinedfile))
pyfits.setval(crj_file, 'FILENAME', value=os.path.split(crj_file)[1])
def bd_calstis(joinedfile, thebiasfile=None):
""" Run CalSTIS on the joined file
Header keywords will be set for ocrreject to work correctly and not
flag regions outside the original aperture:
APERTURE --> 50CCD
APER_FOV --> '50x50'
DARKCORR --> 'OMIT'
FLATCORR --> 'OMIT'
Parameters
----------
joinedfile : str
join of multiple input darks
thebiasfile : str, bool
the biasfile to be subtracted by basic2d
"""
with pyfits.open(joinedfile, 'update') as hdu:
hdu[0].header['CRCORR'] = 'PERFORM'
hdu[0].header['APERTURE'] = '50CCD'
hdu[0].header['APER_FOV'] = '50x50'
hdu[0].header['DARKCORR'] = 'OMIT'
hdu[0].header['FLATCORR'] = 'OMIT'
if thebiasfile:
hdu[0].header['BIASFILE'] = thebiasfile
crj_file = joinedfile.replace('.fits', '_crj.fits')
path, name = os.path.split(joinedfile)
name, ext = os.path.splitext(name)
trailerfile = os.path.join(path, name + '_bd_calstis_log.txt')
if os.path.exists(crj_file):
print('Deleting old file: %s' % crj_file)
os.remove(crj_file)
if os.path.exists(trailerfile):
print('Deleting old file: %s' % trailerfile)
os.remove(trailerfile)
print('Running CalSTIS on %s' % joinedfile)
print('to create: %s' % crj_file)
status = calstis(joinedfile,
wavecal="",
outroot="",
savetmp=False,
verbose=False,
trailer=trailerfile)
if status != 0:
try:
print()
with open(trailerfile) as tr:
for line in tr.readlines():
print(' {}'.format(line.strip()))
finally:
raise Exception(
'CalSTIS failed to properly reduce {}'.format(joinedfile))
pyfits.setval(crj_file, 'FILENAME', value=os.path.split(crj_file)[1])
