def process_band(utdate, recipe_name, band, obsids, config_name):
helper = RecipeHelper(config_name, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
basename = (band, master_obsid)
multi_spec = caldb.load_item_from((band, master_obsid),
"multi_spec_fits")
# just to retrieve order information
wvlsol_v0 = caldb.load_resource_for(basename, "wvlsol_v0")
orders = wvlsol_v0["orders"]
wvlsol = wvlsol_v0["wvl_sol"]
#
from collections import namedtuple
Spec = namedtuple("Spec", ["s_map", "wvl_map"])
keys = []
fitted_pixels_list = []
from igrins.libs.ref_lines_db import SkyLinesDB, HitranSkyLinesDB
ref_lines_db = SkyLinesDB(config=config_name)
ref_lines_db_hitrans = HitranSkyLinesDB(config=config_name)
for hdu in multi_spec:
slit_center = hdu.header["FSLIT_CN"]
spec = Spec(dict(zip(orders, hdu.data)),
dict(zip(orders, wvlsol)))
fitted_pixels_list.append(ref_lines_db.identify(band, spec))
keys.append((slit_center, "OH"))
if band == "K":
fitted_pixels_hitran = ref_lines_db_hitrans.identify(band, spec)
fitted_pixels_list.append(fitted_pixels_hitran)
keys.append((slit_center, "Hitran"))
# concatenate collected list of fitted pixels.
fitted_pixels_master = pd.concat(fitted_pixels_list,
keys=keys,
names=["slit_center", "kind"],
axis=0)
if 0:
# storing multiindex seems broken. Enforce reindexing.
fitted_pixels_master.reset_index().to_json("test.json",
orient="split")
fitted_pixels_master.reset_index().to_csv("test.csv")
def process_band(utdate, recipe_name, band, obsids, config_name):
helper = RecipeHelper(config_name, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
basename = (band, master_obsid)
multi_spec = caldb.load_item_from((band, master_obsid), "multi_spec_fits")
# just to retrieve order information
wvlsol_v0 = caldb.load_resource_for(basename, "wvlsol_v0")
orders = wvlsol_v0["orders"]
wvlsol = wvlsol_v0["wvl_sol"]
#
from collections import namedtuple
Spec = namedtuple("Spec", ["s_map", "wvl_map"])
keys = []
fitted_pixels_list = []
from igrins.libs.ref_lines_db import SkyLinesDB, HitranSkyLinesDB
ref_lines_db = SkyLinesDB(config=config_name)
ref_lines_db_hitrans = HitranSkyLinesDB(config=config_name)
for hdu in multi_spec:
slit_center = hdu.header["FSLIT_CN"]
spec = Spec(dict(zip(orders, hdu.data)), dict(zip(orders, wvlsol)))
fitted_pixels_list.append(ref_lines_db.identify(band, spec))
keys.append((slit_center, "OH"))
if band == "K":
fitted_pixels_hitran = ref_lines_db_hitrans.identify(band, spec)
fitted_pixels_list.append(fitted_pixels_hitran)
keys.append((slit_center, "Hitran"))
# concatenate collected list of fitted pixels.
fitted_pixels_master = pd.concat(fitted_pixels_list,
keys=keys,
names=["slit_center", "kind"],
axis=0)
if 0:
# storing multiindex seems broken. Enforce reindexing.
fitted_pixels_master.reset_index().to_json("test.json", orient="split")
fitted_pixels_master.reset_index().to_csv("test.csv")
def process_band_make_offset_map(utdate, recipe_name, band,
obsids, config_name):
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config_name, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
basename = (band, master_obsid)
ordermap_fits = caldb.load_resource_for(basename,
("sky", "ordermap_fits"))
slitposmap_fits = caldb.load_resource_for(basename,
("sky", "slitposmap_fits"))
# slitoffset_fits = caldb.load_resource_for(basename,
# ("sky", "slitoffset_fits"))
yy, xx = np.indices(ordermap_fits[0].data.shape)
msk = np.isfinite(ordermap_fits[0].data) & (ordermap_fits[0].data > 0)
pixels, orders, slit_pos = (xx[msk], ordermap_fits[0].data[msk],
slitposmap_fits[0].data[msk])
# load coeffs
# This needs to be fixed
names = ["pixel", "order", "slit"]
in_df = pd.read_json("coeffs.json", orient="split")
in_df = in_df.set_index(names)
poly, coeffs = NdPolyNamed.from_pandas(in_df)
cc0 = slit_pos - 0.5
values = dict(zip(names, [pixels, orders, cc0]))
offsets = poly.multiply(values, coeffs) # * cc0
offset_map = np.empty(ordermap_fits[0].data.shape, dtype=np.float64)
offset_map.fill(np.nan)
offset_map[msk] = offsets * cc0 # dd["offsets"]
if 0:
slitoffset_fits = caldb.load_resource_for(basename,
("sky", "slitoffset_fits"))
offset_map_orig = slitoffset_fits[0].data
def process_band(utdate,
recipe_name,
band,
groupname,
obsids,
frame_types,
aux_infos,
config_name,
a0v=None,
a0v_obsid=None,
basename_postfix=None,
outname_postfix=None):
a0v = filter_a0v(a0v, a0v_obsid, aux_infos["GROUP2"])
# print master_obsid, a0v_obsid
groupname = aux_infos["GROUP1"]
helper = RecipeHelper(config_name, utdate, recipe_name)
generate_a0v_divided(helper,
band,
groupname,
obsids,
a0v,
basename_postfix=basename_postfix,
outname_postfix=outname_postfix)
def process_band(utdate,
recipe_name,
band,
groupname,
obsids,
config,
interactive=True):
# utdate, recipe_name, band, obsids, config = "20150525", "A0V", "H", [63, 64], "recipe.config"
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
desc = "SPEC_FITS_FLATTENED"
blaze_corrected = True
src_filename = caldb.query_item_path((band, groupname), desc)
if not os.path.exists(src_filename):
desc = "SPEC_FITS"
blaze_corrected = False
src_filename = caldb.query_item_path((band, groupname), desc)
out_filename = caldb.query_item_path((band, groupname),
"SPEC_FITS_WAVELENGTH")
from igrins.libs.master_calib import get_ref_data_path
tell_file = get_ref_data_path(helper.config,
band,
kind="TELL_WVLSOL_MODEL")
if not interactive:
tgt_basename = helper.get_basename(band, groupname)
figout_dir = helper._igr_path.get_section_filename_base(
"QA_PATH", "", "tell_wvsol_" + tgt_basename)
from igrins.libs.path_info import ensure_dir
ensure_dir(figout_dir)
else:
figout_dir = None
#print src_filename, out_filename, figout_dir, tell_file
run(src_filename,
out_filename,
plot_dir=figout_dir,
tell_file=tell_file,
blaze_corrected=blaze_corrected)
def process_band_make_offset_map(utdate, recipe_name, band, obsids,
config_name):
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config_name, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
basename = (band, master_obsid)
ordermap_fits = caldb.load_resource_for(basename, ("sky", "ordermap_fits"))
slitposmap_fits = caldb.load_resource_for(basename,
("sky", "slitposmap_fits"))
# slitoffset_fits = caldb.load_resource_for(basename,
# ("sky", "slitoffset_fits"))
yy, xx = np.indices(ordermap_fits[0].data.shape)
msk = np.isfinite(ordermap_fits[0].data) & (ordermap_fits[0].data > 0)
pixels, orders, slit_pos = (xx[msk], ordermap_fits[0].data[msk],
slitposmap_fits[0].data[msk])
# load coeffs
# This needs to be fixed
names = ["pixel", "order", "slit"]
in_df = pd.read_json("coeffs.json", orient="split")
in_df = in_df.set_index(names)
poly, coeffs = NdPolyNamed.from_pandas(in_df)
cc0 = slit_pos - 0.5
values = dict(zip(names, [pixels, orders, cc0]))
offsets = poly.multiply(values, coeffs) # * cc0
offset_map = np.empty(ordermap_fits[0].data.shape, dtype=np.float64)
offset_map.fill(np.nan)
offset_map[msk] = offsets * cc0 # dd["offsets"]
if 0:
slitoffset_fits = caldb.load_resource_for(basename,
("sky", "slitoffset_fits"))
offset_map_orig = slitoffset_fits[0].data
def process_band(utdate, recipe_name, band,
groupname, obsids, config,
interactive=True):
# utdate, recipe_name, band, obsids, config = "20150525", "A0V", "H", [63, 64], "recipe.config"
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config, utdate, recipe_name)
caldb = helper.get_caldb()
master_obsid = obsids[0]
desc = "SPEC_FITS_FLATTENED"
blaze_corrected=True
src_filename = caldb.query_item_path((band, groupname),
desc)
if not os.path.exists(src_filename):
desc = "SPEC_FITS"
blaze_corrected=False
src_filename = caldb.query_item_path((band, groupname),
desc)
out_filename = caldb.query_item_path((band, groupname),
"SPEC_FITS_WAVELENGTH")
from igrins.libs.master_calib import get_ref_data_path
tell_file = get_ref_data_path(helper.config, band,
kind="TELL_WVLSOL_MODEL")
if not interactive:
tgt_basename = helper.get_basename(band, groupname)
figout_dir = helper._igr_path.get_section_filename_base("QA_PATH",
"",
"tell_wvsol_"+tgt_basename)
from igrins.libs.path_info import ensure_dir
ensure_dir(figout_dir)
else:
figout_dir = None
#print src_filename, out_filename, figout_dir, tell_file
run(src_filename, out_filename,
plot_dir=figout_dir, tell_file=tell_file,
blaze_corrected=blaze_corrected)
def load_aperture_wvlsol(extractor, band):
"""
for orders that wvlsols are derived.
"""
config, utdate = extractor.pr.config, extractor.pr.utdate
bottomup_solutions = get_bottomup_solutions(extractor, band)
recipe_name = ""
helper = RecipeHelper(config, utdate, recipe_name)
caldb = helper.get_caldb()
#def load_resource_for(self, basename, resource_type):
basename = caldb.db_query_basename("flat_on",
(band, extractor.pr.master_obsid))
wvlsol_v0 = caldb.load_resource_for(basename, "wvlsol_v0")
orders = wvlsol_v0["orders"]
ap = Apertures(orders, bottomup_solutions)
return ap
def get_calibs(band):
config_name = os.path.join("/home/jjlee/work/igrins/plp_jjlee",
"recipe.config")
from igrins.libs.recipe_helper import RecipeHelper
utdate = "20170314"
recipe_name = ""
helper = RecipeHelper(config_name, utdate, recipe_name)
caldb = helper.get_caldb()
basename = (band, "1")
ap = load_aperture(caldb, basename)
ordermap = caldb.load_resource_for(basename, "ordermap")
slitposmap = caldb.load_resource_for(basename, "slitposmap")
return ap, ordermap, slitposmap
def load_aperture_wvlsol(extractor, band):
"""
for orders that wvlsols are derived.
"""
config, utdate = extractor.pr.config, extractor.pr.utdate
bottomup_solutions = get_bottomup_solutions(extractor, band)
recipe_name = ""
helper = RecipeHelper(config, utdate, recipe_name)
caldb = helper.get_caldb()
#def load_resource_for(self, basename, resource_type):
basename = caldb.db_query_basename("flat_on",
(band, extractor.pr.master_obsid))
wvlsol_v0 = caldb.load_resource_for(basename, "wvlsol_v0")
orders = wvlsol_v0["orders"]
ap = Apertures(orders, bottomup_solutions)
return ap
def process_band(utdate, recipe_name, band,
obsids, frametypes,
config, interactive=True):
# utdate, recipe_name, band, obsids, config = "20150525", "A0V", "H", [63, 64], "recipe.config"
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config, utdate, recipe_name)
caldb = helper.get_caldb()
from igrins.libs.load_fits import get_hdus, get_combined_image
hdus = get_hdus(helper, band, obsids)
a_and_b = dict()
for frame, hdu in zip(frametypes, hdus):
a_and_b.setdefault(frame.upper(), []).append(hdu)
# print a_and_b.keys()
a = get_combined_image(a_and_b["A"]) / len(a_and_b["A"])
b = get_combined_image(a_and_b["B"]) / len(a_and_b["B"])
sky_data_ = a+b - abs(a-b)
from igrins.libs.get_destripe_mask import get_destripe_mask
destripe_mask = get_destripe_mask(helper, band, obsids)
from igrins.libs.image_combine import destripe_sky
sky_data = destripe_sky(sky_data_, destripe_mask, subtract_bg=False)
# from igrins.libs.destriper import destriper
# sky_data = destriper.get_destriped(sky_data_)
basename = helper.get_basename(band, obsids[0])
store_output(caldb, basename, hdus[0], sky_data)
def process_band(utdate, recipe_name, band, obsids, config_name):
helper = RecipeHelper(config_name, utdate, recipe_name)
# STEP 1 :
## make combined image
make_combined_image(helper, band, obsids, mode=None)
# Step 2
## load simple-aperture (no order info; depends on
extract_spectra(helper, band, obsids)
fit_wvl_sol(helper, band, obsids)
def process_thar_band(utdate, refdate, band, obsids, config):
helper = RecipeHelper(utdate, refdate, config)
# STEP 1 :
## load simple-aperture (no order info; depends on
## aperture trace from Flat)
# Step 2
## extract 1-d spectra from ThAr
thar_products = get_thar_products(helper, band, obsids)
# Step 3:
## compare to reference ThAr data to figure out orders of each strip
## - simple correlation w/ clipping
new_orders = get_orders_matching_ref_spec(helper, band, obsids,
thar_products)
# Step 4:
# step 5:
## - For each strip, measure x-displacement from the reference
## spec. Fit the displacement as a function of orders.
## - Using the estimated displacement, identify lines from the spectra.
thar_reidentified_products = identify_lines(helper, band, obsids,
thar_products)
# Step 6:
## load the reference echellogram, and find the transform using
## the identified lines.
find_initial_wvlsol(helper, band, obsids, thar_products,
thar_reidentified_products, new_orders)
# Step 8:
## make order_map and auxilary files.
save_figures(helper, band, obsids, thar_products, new_orders)
save_db(helper, band, obsids)
from find_affine_transform import find_affine_transform
find_affine_transform(helper, band, obsids)
from igrins.libs.transform_wvlsol import transform_wavelength_solutions
transform_wavelength_solutions(helper, band, obsids)
# Step 8:
## make order_map and auxilary files.
save_figures(helper, band, obsids)
save_db(helper, band, obsids)
if __name__ == "__main__":
utdate = "20160226"
obsids_off = range(11, 21)
obsids_on = range(583, 593)
recipe_name = "FLAT"
band = "H"
config_name = "../recipe.config"
helper = RecipeHelper(config_name, utdate)
process_band(utdate, recipe_name, band, obsids_off, obsids_on, config_name)
def main(utdate, band, obsids, config_name):
helper = RecipeHelper(config_name, utdate)
find_affine_transform(helper, band, obsids)
def process_band_make_offset_map(utdate, recipe_name, band,
obsids, config_name):
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config_name, utdate, recipe_name)
def process_band(utdate, recipe_name, band, obsids, config_name):
helper = RecipeHelper(config_name, utdate, recipe_name)
identify_multiline(helper, band, obsids)
def process_band(utdate, recipe_name, band, obsids, config_name):
from igrins.libs.recipe_helper import RecipeHelper
helper = RecipeHelper(config_name, utdate, recipe_name)
derive_wvlsol(helper, band, obsids)