def f_add_aper_erm(input_path,
input_list,
sel_apertures,
dither_idx=0,
verbose=False):
'''
Utility function to add the apertures (e.g. slit, mos) of a component (e.g. background)
:param input_path:
:param list input_list: 2-dimensional list of filenames with indices [aperture][dither]
:param sel_apertures:
:param dither_idx:
:param verbose:
:return:
'''
#this function is only applicable to background
# and flatfield components, which depend on apertures
#add all aperture components to the erm file
#TODO: introduce logic to have always a full input component list and select by string, by checking the components in the global list
for aperture_idx in range(len(sel_apertures)):
filename = input_list[dither_idx][aperture_idx]
if aperture_idx == 0:
comp_erm = c_electronratemap.ElectronRateMap()
comp_erm.m_read_from_fits(os.path.join(input_path, filename))
if verbose:
print('Standard component: {:s}'.format(
sel_apertures[aperture_idx]))
else:
work_erm = c_electronratemap.ElectronRateMap()
work_erm.m_read_from_fits(os.path.join(input_path, filename))
comp_erm.m_add(work_erm)
if verbose:
print('Adding :{:s}'.format(
input_list[dither_idx][aperture_idx]))
return comp_erm
multiaccum.m_info()
# =======================================================================
# Generating the instances of the reference files (nrspydet.references)
# =======================================================================
print("# Generating the instances of the reference files (gain & IPC).")
gain = fpa106_toolbox.f_generate_gain('FULL-FRAME')
ctm = fpa106_toolbox.f_generate_ctm()
print("# Generating the count-rate maps.")
# Looping over dither pointings (all unity-maps)
count = 0
for i in range(len(mos_erm)):
t_map = mos_erm[i]
print('# Processing ' + t_map)
t_erm = c_electronratemap.ElectronRateMap()
t_erm.m_read_from_fits(os.path.join(input_path, t_map))
s_erm = c_electronratemap.ElectronRateMap()
s_erm.m_read_from_fits(os.path.join(input_path, fxs_erm[i]))
# Adding slit and mos flats together
t_erm.m_add(s_erm)
# -------------------------------------------------------------------
# Generating the exposure folders and the associated exposures - noiseless!
# -------------------------------------------------------------------
#Noiseless Unity - ** OLD ISP format **
unity_ctms = erm_to_sci.f_standard(t_erm,
multiaccum,
noise_category='noiseless',
print('ERROR - {}'.format(error.args))
raise ValueError
b_ctms = None
for dither_index in range(4):
# -------------------------------------------------------------------
# Name of the various files
# -------------------------------------------------------------------
g_ifs = list_galaxy[dither_index]
b_ifs = list_background[dither_index][0]
b_mos = list_background[dither_index][1]
b_slit = list_background[dither_index][2]
# -------------------------------------------------------------------
# Background ERM
# -------------------------------------------------------------------
b_erm = c_electronratemap.ElectronRateMap()
b_erm.m_read_from_fits(os.path.join(input_path, b_ifs))
# b_erm.m_display(491, display=False, filename=os.path.join(output_path, 'bsifs.pdf'))
work = c_electronratemap.ElectronRateMap()
work.m_read_from_fits(os.path.join(input_path, b_mos))
# work.m_display(491, display=False, filename=os.path.join(output_path, 'bsmos.pdf'))
b_erm.m_add(work, overwrite=False)
# b_erm.m_display(491, display=False, filename=os.path.join(output_path, 'bsifsmos.pdf'))
work = c_electronratemap.ElectronRateMap()
work.m_read_from_fits(os.path.join(input_path, b_slit))
# work.m_display(491, display=False, filename=os.path.join(output_path, 'bslit.pdf'))
b_erm.m_add(work)
# b_erm.m_display(491, display=False, filename=os.path.join(output_path, 'bsifsmosslit.pdf'))
# -------------------------------------------------------------------
# Galaxy ERM
# -------------------------------------------------------------------
def f_crm(input_path,
input_list,
FWA,
GWA,
sampling_grid,
components,
sel_apertures,
nexp,
multiaccum,
references,
output_path,
base_nid,
pipeline_id,
jlab_id,
base_obs_id,
datetime_start,
datetime_end,
datetime_file,
daily_folder,
save_background=True):
'''
Basic (for now NIPS centric and commissioning specific (nexp~=1)) function to take all basic ingredients and
perform
- transform to count-rate-maps
- deal with dither, nods and (potentially) exposures
- create the archive structure, count-rate filenames and NID identifier
- generate background exposure (save_background=True/False is hardcoded)
- Include realistic dark flags
- Populate GWA information (current workaround IPS>4.0 should take care of this)
- Write the .fits files
Note: Currently NIPS-centric functions are embedded in code #TODO: extract into functions
:param input_path:
:param input_list:
:param FWA:
:param GWA:
:param sampling_grid:
:param components:
:param sel_apertures:
:param nexp:
:param multiaccum:
:param references:
:param output_path:
:param base_nid:
:param pipeline_id:
:param jlab_id:
:param base_obs_id:
:param datetime_start:
:param datetime_end:
:param datetime_file:
:param daily_folder:
:param save_background:
:return:
'''
#TODO: Idea, maybe promote this function upward to f_post_processing body, as it needs yet more parameters
# =======================================================================
# NIPS Archive structure: daily folder generation
# =======================================================================
work = os.path.join(output_path, daily_folder)
try:
os.makedirs(work)
except Exception as error:
if (error.args[0] != 17):
print(
'ERROR - Encountered an error when trying to create the daily folder:'
)
print('ERROR - {:s}'.format(work))
print('ERROR - {}'.format(error.args))
raise ValueError
# =======================================================================
# Generating the count-rate maps
# =======================================================================
print("# Generating the count-rate maps.")
dither_pts = sampling_grid['dither_pts']
nod_pts = sampling_grid['nod_pts']
target_list = input_list['target_erm']
if 'background' in components: bckg_list = input_list['bckg_erm']
for dither_idx in range(dither_pts):
if 'background' in components:
# -------------------------------------------------------------------
# Background ERM: we need to have a background to add, even if it is the same
# -------------------------------------------------------------------
b_erm = f_add_aper_erm(input_path,
bckg_list,
sel_apertures,
dither_idx=dither_idx,
verbose=True)
for nod_idx in range(nod_pts):
o_name = target_list[dither_idx][nod_idx]
# -------------------------------------------------------------------
# Target/object ERM
# -------------------------------------------------------------------
o_erm = c_electronratemap.ElectronRateMap()
o_erm.m_read_from_fits(os.path.join(input_path, o_name))
if 'background' in components:
# -------------------------------------------------------------------
# Obj ERM + Background ERM
# -------------------------------------------------------------------
o_erm.m_add(b_erm)
# -------------------------------------------------------------------
# Save first background ERM (mimmic off-source exposure for master background in IFS)
# -------------------------------------------------------------------
#TODO: boolean parameter save_background deeply buried in this function. Should be promoted to config file
if save_background and (dither_idx == 0) and (nod_idx == 0):
b_ctms = erm_to_sci.f_standard(
b_erm,
multiaccum,
noise_category='extended',
noise_model=references.noise_model,
scale=1.0,
nexp=nexp,
planes=None,
bias=None,
use_superbias=False,
dark=references.dark,
dark_sub=True,
readout=references.readout,
gain=references.gain,
ctm=references.ctm,
verbose=True,
seed=-1,
force_trimming=False,
old=True)
# -------------------------------------------------------------------
# Generating archive folders
# -------------------------------------------------------------------
nid, obs_id, folder_name, filenames = f_output_archive_structure(
output_path,
dither_idx,
nod_idx,
base_nid,
pipeline_id,
jlab_id,
base_obs_id,
datetime_start,
datetime_end,
datetime_file,
daily_folder,
is_background=True)
# -------------------------------------------------------------------
# Write out to archive folders
# -------------------------------------------------------------------
f_write_to_fits(b_ctms, output_path, daily_folder, folder_name,
filenames, obs_id)
# -------------------------------------------------------------------
# Note: Just for NIPS2.0 and commissioning; otherwise introduce the
# following for loop and change the f_standard parameter to nexp=1
# GG: Generating the exposure folders and the associated exposures - 4 exposures for pointing
# -------------------------------------------------------------------
#for iexp in range(nexp):
# GG: Note nexp in this function is only used to scale noise -> nexp=1
o_ctms = erm_to_sci.f_standard(o_erm,
multiaccum,
noise_category='extended',
noise_model=references.noise_model,
scale=1.0,
nexp=nexp,
planes=None,
bias=None,
use_superbias=False,
dark=references.dark,
dark_sub=True,
readout=references.readout,
gain=references.gain,
ctm=references.ctm,
verbose=True,
seed=-1,
force_trimming=False,
old=True)
# -------------------------------------------------------------------
# Generating archive folders
# -------------------------------------------------------------------
nid, obs_id, folder_name, filenames = f_output_archive_structure(
output_path,
dither_idx,
nod_idx,
base_nid,
pipeline_id,
jlab_id,
base_obs_id,
datetime_start,
datetime_end,
datetime_file,
daily_folder,
is_background=False)
#TODO: Extract all below code into a NIPS specific function and include switch parameter in config file to branch off
# -------------------------------------------------------------------
# Populate header keywords: (specific to NIPS2.0)
# - dark flags
# - GWA information
# -------------------------------------------------------------------
flag_arrays = []
# Reading in quality flags from one of our darks
hdu = fits.open(_dark491fname)
flag_arrays.append(hdu[3].data)
print('# Reading in FLAG array 1')
hdu = fits.open(_dark492fname)
flag_arrays.append(hdu[3].data)
print('# Reading in FLAG array 2')
hdu.close()
# Before writing out the cont-rate maps (new format for NIPS2.0) we need to update the GWA keywords because
# the version of the IPS with which they were created did not populated the GWA keyword with the correct value
# Therefore opening the model gtp file:
#TODO: insert a try catch to skip this if IPS already populates it (not sure on which attribute)
filename = _model_path + _model_name + '/Description/disperser_' + GWA + '_TiltY.gtp'
poly = tiltpoly.TiltPoly()
poly.m_readFromFile(filename)
GWA_XTIL = poly.zeroreadings[0] # dispersion direction
filename = _model_path + _model_name + '/Description/disperser_' + GWA + '_TiltX.gtp'
poly = tiltpoly.TiltPoly()
poly.m_readFromFile(filename)
GWA_YTIL = poly.zeroreadings[0] # spatial direction
mode_gg = 'unknown'
slit_gg = 'unknown'
aperture_gg = 'unknown'
sca_ids = ['NRS1', 'NRS2']
read_out = 'NRSRAPID'
#TODO: Hardcoding warning: create a function of (readout_mode, nf) that spits out the cooked readout
for o_idx in range(1, len(filenames) + 1):
o_ctms[o_idx].fits_header['GWA_XTIL'] = GWA_XTIL
o_ctms[o_idx].fits_header['GWA_YTIL'] = GWA_YTIL
o_ctms[o_idx].m_set_keywords(nid, 'IPS', sca_ids[o_idx - 1],
mode_gg, slit_gg, aperture_gg,
FWA, GWA, read_out, False)
#o_ctms[o_idx].quality = flag_arrays[o_idx-1]
# -------------------------------------------------------------------
# Write out to archive folders
# We keep the old count-rate for NIPS 2.7 compatibility and plotting
# -------------------------------------------------------------------
f_write_to_fits(o_ctms, output_path, daily_folder, folder_name,
filenames, obs_id)
return None
raise ValueError
print("# Generating the count-rate maps.")
b_ctms = None
# Looping over dither pointings
for idither in range(3):
# Reading in background maps
b_mos = bkg_mos_erm[idither]
b_slit = bkg_slit_erm[idither]
# -------------------------------------------------------------------
# Background ERM
# -------------------------------------------------------------------
b_erm = c_electronratemap.ElectronRateMap()
b_erm.m_read_from_fits(os.path.join(input_path, b_mos))
b_erm1 = c_electronratemap.ElectronRateMap()
b_erm1.m_read_from_fits(os.path.join(input_path, b_slit))
b_erm.m_add(b_erm1)
# Looping over nodding positions
for inod in range(3):
# -------------------------------------------------------------------
# Name of the various files
# -------------------------------------------------------------------
g_mos = target_erm[idither][inod]
# Reading in targets e-/rate maps
g_erm = c_electronratemap.ElectronRateMap()
g_erm.m_read_from_fits(os.path.join(input_path, g_mos))