def find_affine_transform(helper, band, obsids):
master_obsid = obsids[0]
caldb = helper.get_caldb()
orders = caldb.load_resource_for((band, master_obsid), "orders")["orders"]
ap = get_simple_aperture(helper, band, obsids, orders=orders)
item_path = caldb.query_item_path((band, master_obsid),
"IDENTIFIED_LINES_JSON")
from libs.identified_lines import IdentifiedLines
identified_lines_tgt = IdentifiedLines.load(item_path)
xy_list_tgt = identified_lines_tgt.get_xy_list_from_pixlist(ap)
from libs.echellogram import Echellogram
from libs.master_calib import load_ref_data
echellogram_data = load_ref_data(helper.config, band,
kind="ECHELLOGRAM_JSON")
echellogram = Echellogram.from_dict(echellogram_data)
xy_list_ref = identified_lines_tgt.get_xy_list_from_wvllist(echellogram)
assert len(xy_list_tgt) == len(xy_list_ref)
from libs.align_echellogram_thar import fit_affine_clip
affine_tr, mm = fit_affine_clip(np.array(xy_list_ref),
np.array(xy_list_tgt))
from libs.products import PipelineDict
d = PipelineDict(xy1f=xy_list_ref, xy2f=xy_list_tgt,
affine_tr_matrix=affine_tr.get_matrix(),
affine_tr_mask=mm)
caldb.store_dict((band, master_obsid),
item_type="ALIGNING_MATRIX_JSON",
data=d)
def identify_lines(helper, band, obsids):
from libs.master_calib import load_ref_data
ref_spec_key, ref_identified_lines_key = _get_ref_spec_name(helper)
ref_spec = load_ref_data(helper.config, band,
kind=ref_spec_key)
caldb = helper.get_caldb()
master_obsid = obsids[0]
tgt_spec_path = caldb.query_item_path((band, master_obsid),
"ONED_SPEC_JSON")
tgt_spec = caldb.load_item_from_path(tgt_spec_path)
from libs.process_thar import get_offset_treanform_between_2spec
intersected_orders, d = get_offset_treanform_between_2spec(ref_spec,
tgt_spec)
#REF_TYPE="OH"
#fn = "../%s_IGRINS_identified_%s_%s.json" % (REF_TYPE, band,
# helper.refdate)
l = load_ref_data(helper.config, band,
kind=ref_identified_lines_key)
#l = json.load(open(fn))
#ref_spectra = load_ref_data(helper.config, band, kind="SKY_REFSPEC_JSON")
offsetfunc_map = dict(zip(intersected_orders, d["sol_list"]))
from libs.identified_lines import IdentifiedLines
identified_lines_ref = IdentifiedLines(l)
ref_map = identified_lines_ref.get_dict()
identified_lines_tgt = IdentifiedLines(l)
identified_lines_tgt.update(dict(wvl_list=[], ref_indices_list=[],
pixpos_list=[], orders=[],
spec_path=tgt_spec_path))
from libs.line_identify_simple import match_lines1_pix
for o, s in zip(tgt_spec["orders"], tgt_spec["specs"]):
if (o not in ref_map) or (o not in offsetfunc_map):
wvl, indices, pixpos = [], [], []
else:
pixpos, indices, wvl = ref_map[o]
pixpos = np.array(pixpos)
msk = (pixpos >= 0)
ref_pix_list = offsetfunc_map[o](pixpos[msk])
pix_list, dist = match_lines1_pix(np.array(s), ref_pix_list)
pix_list[dist>1] = -1
pixpos[msk] = pix_list
identified_lines_tgt.append_order_info(o, wvl, indices, pixpos)
#REF_TYPE = "OH"
#fn = "%s_IGRINS_identified_%s_%s.json" % (REF_TYPE, band, helper.utdate)
# item_path = caldb.query_item_path((band, master_obsid),
# "IDENTIFIED_LINES")
# item_path = caldb.query_item_path((band, master_obsid),
# "IDENTIFIED_LINES")
caldb.store_dict((band, master_obsid),
"IDENTIFIED_LINES_JSON",
identified_lines_tgt.data)
