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Commit 2c2dac03 authored by Fang Yuedong's avatar Fang Yuedong
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Catalog/C9_Catalog.py deleted 100644 → 0
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Catalog/Catalog_example.py deleted 100644 → 0
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import os
import numpy as np
import astropy.constants as cons
from astropy.table import Table
from scipy import interpolate
from ObservationSim.MockObject import CatalogBase, Star, Galaxy, Quasar
class Catalog(CatalogBase):
"""An user customizable class for reading in catalog(s) of objects and SEDs.
NOTE: must inherit the "CatalogBase" abstract class
...
Attributes
----------
cat_dir : str
a directory that contains the catalog file(s)
star_path : str
path to the star catalog file
star_SED_path : str
path to the star SED data
objs : list
a list of ObservationSim.MockObject (Star, Galaxy, or Quasar)
NOTE: must have "obj" list when implement your own Catalog
Methods
----------
load_sed(obj, **kwargs):
load the corresponding SED data for one object
load_norm_filt(obj):
load the filter throughput for the input catalog's photometric system.
"""
def __init__(self, config, chip, **kwargs):
"""Constructor method.
Parameters
----------
config : dict
configuration dictionary which is parsed from the input YAML file
chip: ObservationSim.Instrument.Chip
an ObservationSim.Instrument.Chip instance, can be used to identify the band etc.
**kwargs : dict
other needed input parameters (in key-value pairs), please modify corresponding
initialization call in "ObservationSim.py" as you need.
Returns
----------
None
"""
super().__init__()
self.cat_dir = os.path.join(config["data_dir"], config["catalog_options"]["input_path"]["cat_dir"])
self.chip = chip
if "star_cat" in config["catalog_options"]["input_path"] and config["catalog_options"]["input_path"]["star_cat"]:
star_file = config["catalog_options"]["input_path"]["star_cat"]
star_SED_file = config["catalog_options"]["SED_templates_path"]["star_SED"]
self.star_path = os.path.join(self.cat_dir, star_file)
self.star_SED_path = os.path.join(config["data_dir"], star_SED_file)
# NOTE: must call _load() method here to read in all objects
self.objs = []
self._load()
def _load(self, **kwargs):
"""Read in all objects in from the catalog file(s).
This is a must implemented method which is used to read in all objects, and
then convert them to ObservationSim.MockObject (Star, Galaxy, or Quasar).
Currently,
the model of ObservationSim.MockObject.Star class requires:
param["star"] : int
specify the object type: 0: galaxy, 1: star, 2: quasar
param["id"] : int
ID number of the object
param["ra"] : float
Right ascension (in degrees)
param["dec"] : float
Declination (in degrees)
param["mag_use_normal"]: float
the absolute magnitude in a particular filter
NOTE: if that filter is not the corresponding CSST filter, the
load_norm_filt(obj) function must be implemented to load the filter
throughput of that particular photometric system
the model of ObservationSim.MockObject.Galaxy class requires:
param["star"] : int
specify the object type: 0: galaxy, 1: star, 2: quasar
param["id"] : int
ID number of the object
param["ra"] : float
Right ascension (in degrees)
param["dec"] : float
Declination (in degrees)
param["mag_use_normal"]: float
the absolute magnitude in a particular filter
NOTE: if that filter is not the corresponding CSST filter, the
load_norm_filt(obj) function must be implemented to load the filter
throughput of that particular photometric system
param["bfrac"] : float
the bulge fraction
param["hlr_bulge"] : float
the half-light-radius of the bulge
param["hlr_disk"] : float
the half-light-radius of the disk
param["e1_bulge"], param["e2_bulge"] : float
the ellipticity of the bulge components
param["e1_disk"], param["e2_disk"] : float
the ellipticity of the disk components
(Optional parameters):
param['disk_sersic_idx']: float
Sersic index for galaxy disk component
param['bulge_sersic_idx']: float
Sersic index for galaxy bulge component
param['g1'], param['g2']: float
Reduced weak lensing shear components (valid for shear type: catalog)
the model of ObservationSim.MockObject.Galaxy class requires:
Currently a Quasar is modeled as a point source, just like a Star.
NOTE: To construct an object, according to its type, just call:
Star(param), Galaxy(param), or Quasar(param)
NOTE: All constructed objects should be appened to "self.objs".
NOTE: Any other parameters can also be set within "param" dict:
Used to calculate required quantities and/or SEDs etc.
Parameters
----------
**kwargs : dict
other needed input parameters (in key-value pairs), please modify corresponding
initialization call in "ObservationSim.py" as you need.
Returns
----------
None
"""
stars = Table.read(self.star_path)
nstars = stars['sourceID'].size
for istars in range(nstars):
param = self.initialize_param()
param['id'] = istars + 1
param['ra'] = stars['RA'][istars]
param['dec'] = stars['Dec'][istars]
param['sed_type'] = stars['sourceID'][istars]
param['model_tag'] = stars['model_tag'][istars]
param['z'] = 0.0
param['star'] = 1 # Star
param['mag_use_normal'] = stars['app_sdss_g'][istars]
obj = Star(param)
self.objs.append(obj)
def load_sed(self, obj, **kwargs):
"""Load the corresponding SED data for a particular obj.
Parameters
----------
obj : ObservationSim.MockObject
the object to get SED data for
**kwargs : dict
other needed input parameters (in key-value pairs), please modify corresponding
initialization call in "ObservationSim.py" as you need.
Returns
----------
sed : Astropy.Table
the SED Table with two columns (namely, "WAVELENGTH", "FLUX"):
sed["WAVELENGTH"] : wavelength in Angstroms
sed["FLUX"] : fluxes in photons/s/m^2/A
NOTE: the range of wavelengthes must at least cover [2450 - 11000] Angstorms
"""
if obj.type == 'star':
wave = Table.read(self.star_SED_path, path=f"/SED/wave_{obj.model_tag}")
flux = Table.read(self.star_SED_path, path=f"/SED/{obj.sed_type}")
wave, flux = wave['col0'].data, flux['col0'].data
else:
raise ValueError("Object type not known")
speci = interpolate.interp1d(wave, flux)
lamb = np.arange(2400, 11001 + 0.5, 0.5)
y = speci(lamb)
# erg/s/cm^2/A --> photons/s/m^2/A
all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))
return sed
def load_norm_filt(self, obj):
"""Load the corresponding thourghput for the input magnitude "param["mag_use_normal"]".
NOTE: if the input magnitude is already in CSST magnitude, simply return None
Parameters
----------
obj : ObservationSim.MockObject
the object to get thourghput data for
Returns
----------
norm_filt : Astropy.Table
the throughput Table with two columns (namely, "WAVELENGTH", "SENSITIVITY"):
norm_filt["WAVELENGTH"] : wavelengthes in Angstroms
norm_filt["SENSITIVITY"] : efficiencies
"""
return None
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import os
import galsim
import random
import numpy as np
import h5py as h5
import healpy as hp
import astropy.constants as cons
import traceback
from astropy.coordinates import spherical_to_cartesian
from astropy.table import Table
from scipy import interpolate
from datetime import datetime
from ObservationSim.MockObject import CatalogBase, Star, Galaxy, Quasar, Stamp
from ObservationSim.MockObject._util import tag_sed, getObservedSED, getABMAG, integrate_sed_bandpass, comoving_dist
from ObservationSim.Astrometry.Astrometry_util import on_orbit_obs_position
import astropy.io.fits as fitsio
from ObservationSim.MockObject._util import seds, sed_assign, extAv
# (TEST)
from astropy.cosmology import FlatLambdaCDM
from astropy import constants
from astropy import units as U
try:
import importlib.resources as pkg_resources
except ImportError:
# Try backported to PY<37 'importlib_resources'
import importlib_resources as pkg_resources
NSIDE = 128
class Catalog(CatalogBase):
def __init__(self, config, chip, pointing, chip_output, filt, **kwargs):
super().__init__()
self.cat_dir = config["catalog_options"]["input_path"]["cat_dir"]
self.seed_Av = 121212 #config["catalog_options"]["seed_Av"]
# (TEST)
self.cosmo = FlatLambdaCDM(H0=67.66, Om0=0.3111)
self.chip_output = chip_output
self.filt = filt
self.logger = chip_output.logger
with pkg_resources.path('Catalog.data', 'SLOAN_SDSS.g.fits') as filter_path:
self.normF_star = Table.read(str(filter_path))
with pkg_resources.path('Catalog.data', 'lsst_throuput_g.fits') as filter_path:
self.normF_galaxy = Table.read(str(filter_path))
self.config = config
self.chip = chip
self.pointing = pointing
self.max_size = 0.
if "stamp_cat" in config["catalog_options"]["input_path"] and config["catalog_options"]["input_path"]["stamp_cat"] and config["catalog_options"]["stamp_yes"]:
stamp_file = config["catalog_options"]["input_path"]["stamp_cat"]
self.stamp_path = os.path.join(self.cat_dir, stamp_file)
#self.stamp_SED_path = os.path.join(config["data_dir"], config["SED_templates_path"]["stamp_SED"]) ###shoule be stamp-SED
#self._load_SED_lib_stamps() ###shoule be stamp-SED
self.tempSed_gal, self.tempRed_gal = seds("galaxy.list", seddir="/public/home/chengliang/CSSOSDataProductsSims/testCats/Templates/Galaxy/") #only for test
self._add_output_columns_header()
self._get_healpix_list()
self._load()
def _add_output_columns_header(self):
self.add_hdr = " model_tag teff logg feh"
self.add_hdr += " bulgemass diskmass detA e1 e2 kappa g1 g2 size galType veldisp "
self.add_fmt = " %10s %8.4f %8.4f %8.4f"
self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
self.chip_output.update_output_header(additional_column_names=self.add_hdr)
def _get_healpix_list(self):
self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)
ra_min, ra_max, dec_min, dec_max = self.sky_coverage.xmin, self.sky_coverage.xmax, self.sky_coverage.ymin, self.sky_coverage.ymax
ra = np.deg2rad(np.array([ra_min, ra_max, ra_max, ra_min]))
dec = np.deg2rad(np.array([dec_max, dec_max, dec_min, dec_min]))
# vertices = spherical_to_cartesian(1., dec, ra)
self.pix_list = hp.query_polygon(
NSIDE,
hp.ang2vec(np.radians(90.) - dec, ra),
inclusive=True
)
# self.pix_list = hp.query_polygon(NSIDE, np.array(vertices).T, inclusive=True)
if self.logger is not None:
msg = str(("HEALPix List: ", self.pix_list))
self.logger.info(msg)
else:
print("HEALPix List: ", self.pix_list)
def load_norm_filt(self, obj):
if obj.type == "stamp":
return self.normF_galaxy ###normalize_filter for stamp
else:
return None
def _load_stamps(self, stamps, pix_id=None):
print("debug:: load_stamps")
nstamps = len(stamps['filename'])
self.rng_sedGal = random.Random()
self.rng_sedGal.seed(float(pix_id)) # Use healpix index as the random seed
self.ud = galsim.UniformDeviate(pix_id)
for istamp in range(nstamps):
print("debug::", istamp)
fitsfile = os.path.join(self.cat_dir, "stampCats/"+stamps['filename'][istamp].decode('utf-8'))
print("debug::", istamp, fitsfile)
hdu=fitsio.open(fitsfile)
param = self.initialize_param()
param['id'] = hdu[0].header['index'] #istamp
param['star'] = 3 # Stamp type in .cat file
param['ra'] = hdu[0].header['ra']
param['dec']= hdu[0].header['dec']
param['pixScale']= hdu[0].header['pixScale']
#param['srcGalaxyID'] = hdu[0].header['srcGID']
#param['mu']= hdu[0].header['mu']
#param['PA']= hdu[0].header['PA']
#param['bfrac']= hdu[0].header['bfrac']
#param['z']= hdu[0].header['z']
param['mag_use_normal'] = hdu[0].header['mag_g'] #gals['mag_true_g_lsst']
# Apply astrometric modeling
# in C3 case only aberration
param['ra_orig'] = param['ra']
param['dec_orig']= param['dec']
if self.config["obs_setting"]["enable_astrometric_model"]:
ra_list = [param['ra']] #ra_arr.tolist()
dec_list= [param['dec']] #dec_arr.tolist()
pmra_list = np.zeros(1).tolist()
pmdec_list = np.zeros(1).tolist()
rv_list = np.zeros(1).tolist()
parallax_list = [1e-9] * 1
dt = datetime.fromtimestamp(self.pointing.timestamp)
date_str = dt.date().isoformat()
time_str = dt.time().isoformat()
ra_arr, dec_arr = on_orbit_obs_position(
input_ra_list=ra_list,
input_dec_list=dec_list,
input_pmra_list=pmra_list,
input_pmdec_list=pmdec_list,
input_rv_list=rv_list,
input_parallax_list=parallax_list,
input_nstars=1,
input_x=self.pointing.sat_x,
input_y=self.pointing.sat_y,
input_z=self.pointing.sat_z,
input_vx=self.pointing.sat_vx,
input_vy=self.pointing.sat_vy,
input_vz=self.pointing.sat_vz,
input_epoch="J2015.5",
input_date_str=date_str,
input_time_str=time_str
)
param['ra'] = ra_arr[0]
param['dec']= dec_arr[0]
# Assign each galaxy a template SED
param['sed_type'] = sed_assign(phz=param['z'], btt=param['bfrac'], rng=self.rng_sedGal)
param['redden'] = self.tempRed_gal[param['sed_type']]
param['av'] = 0.0
param['redden'] = 0
param['mu'] = 1
#param["CSSTmag"]= True
#param["mag_r"] = 20.
#param['']
###more keywords for stamp###
param['image'] = hdu[0].data
param['image'] = param['image']/(np.sum(param['image']))
obj = Stamp(param)
self.objs.append(obj)
def _load(self, **kwargs):
self.objs = []
self.ids = 0
if "stamp_cat" in self.config["catalog_options"]["input_path"] and self.config["catalog_options"]["input_path"]["stamp_cat"] and self.config["catalog_options"]["stamp_yes"]:
stamps_cat = h5.File(self.stamp_path, 'r')['Stamps']
print("debug::",stamps_cat.keys())
for pix in self.pix_list:
try:
stamps = stamps_cat[str(pix)]
print("debug::",stamps.keys())
self._load_stamps(stamps, pix_id=pix)
del stamps
except Exception as e:
self.logger.error(str(e))
print(e)
if self.logger is not None:
self.logger.info("maximum galaxy size: %.4f"%(self.max_size))
self.logger.info("number of objects in catalog: %d"%(len(self.objs)))
else:
print("number of objects in catalog: ", len(self.objs))
def load_sed(self, obj, **kwargs):
if obj.type == 'stamp':
sed_data = getObservedSED(
sedCat=self.tempSed_gal[obj.sed_type],
redshift=obj.z,
av=obj.param["av"],
redden=obj.param["redden"]
)
wave, flux = sed_data[0], sed_data[1]
else:
raise ValueError("Object type not known")
speci = interpolate.interp1d(wave, flux)
lamb = np.arange(2000, 11001+0.5, 0.5)
y = speci(lamb)
# erg/s/cm2/A --> photon/s/m2/A
all_sed = y * lamb / (cons.h.value * cons.c.value) * 1e-13
sed = Table(np.array([lamb, all_sed]).T, names=('WAVELENGTH', 'FLUX'))
del wave
del flux
return sed
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from ctypes import *
import numpy as np
try:
import importlib.resources as pkg_resources
except ImportError:
# Try backported to PY<37 'importlib_resources'
import importlib_resources as pkg_resources
def checkInputList(input_list, n):
if not isinstance(input_list, list):
raise TypeError("Input type is not list!", input_list)
for i in input_list:
if type(i) != type(1.1):
if type(i) != type(1):
raise TypeError("Input list's element is not float or int!", input_list)
if len(input_list) != n:
raise RuntimeError("Length of input list is not equal to stars' number!", input_list)
def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_pmdec_list, input_rv_list, input_parallax_list, input_nstars, input_x, input_y, input_z, input_vx, input_vy, input_vz, input_epoch, input_date_str, input_time_str, lib_path=None):
#Check input parameters
if not isinstance(input_nstars, int):
raise TypeError("Parameter 7 is not int!", input_nstars)
checkInputList(input_ra_list, input_nstars)
checkInputList(input_dec_list, input_nstars)
checkInputList(input_pmra_list, input_nstars)
checkInputList(input_pmdec_list, input_nstars)
checkInputList(input_rv_list, input_nstars)
checkInputList(input_parallax_list, input_nstars)
if not isinstance(input_x, float):
raise TypeError("Parameter 8 is not double!", input_x)
if not isinstance(input_y, float):
raise TypeError("Parameter 9 is not double!", input_y)
if not isinstance(input_z, float):
raise TypeError("Parameter 10 is not double!", input_z)
if not isinstance(input_vx, float):
raise TypeError("Parameter 11 is not double!", input_vx)
if not isinstance(input_vy, float):
raise TypeError("Parameter 12 is not double!", input_vy)
if not isinstance(input_vz, float):
raise TypeError("Parameter 13 is not double!", input_vz)
#Convert km -> m
input_x = input_x*1000.0
input_y = input_y*1000.0
input_z = input_z*1000.0
input_vx = input_vx*1000.0
input_vy = input_vy*1000.0
input_vz = input_vz*1000.0
if not isinstance(input_date_str, str):
raise TypeError("Parameter 15 is not string!", input_date_str)
else:
input_date_str = input_date_str.strip()
if not (input_date_str[4]=="-" and input_date_str[7]=="-"):
raise TypeError("Parameter 15 format error (1)!", input_date_str)
else:
tmp = input_date_str.split("-")
if len(tmp) != 3:
raise TypeError("Parameter 15 format error (2)!", input_date_str)
input_year = int(tmp[0])
input_month = int(tmp[1])
input_day = int(tmp[2])
if not (input_year>=1900 and input_year<=2100):
raise TypeError("Parameter 15 year range error [1900 ~ 2100]!", input_year)
if not (input_month>=1 and input_month<=12):
raise TypeError("Parameter 15 month range error [1 ~ 12]!", input_month)
if not (input_day>=1 and input_day<=31):
raise TypeError("Parameter 15 day range error [1 ~ 31]!", input_day)
if not isinstance(input_time_str, str):
raise TypeError("Parameter 16 is not string!", input_time_str)
else:
input_time_str = input_time_str.strip()
if not (input_time_str[2]==":" and input_time_str[5]==":"):
raise TypeError("Parameter 16 format error (1)!", input_time_str)
else:
tmp = input_time_str.split(":")
if len(tmp) != 3:
raise TypeError("Parameter 16 format error (2)!", input_time_str)
input_hour = int(tmp[0])
input_minute = int(tmp[1])
input_second = float(tmp[2])
if not (input_hour>=0 and input_hour<=23):
raise TypeError("Parameter 16 hour range error [0 ~ 23]!", input_hour)
if not (input_minute>=0 and input_minute<=59):
raise TypeError("Parameter 16 minute range error [0 ~ 59]!", input_minute)
if not (input_second>=0 and input_second<60.0):
raise TypeError("Parameter 16 second range error [0 ~ 60)!", input_second)
#Inital dynamic lib
try:
with pkg_resources.files('ObservationSim.Astrometry.lib').joinpath("libshao.so") as lib_path:
shao = cdll.LoadLibrary(lib_path)
except AttributeError:
with pkg_resources.path('ObservationSim.Astrometry.lib', "libshao.so") as lib_path:
shao = cdll.LoadLibrary(lib_path)
shao.onOrbitObs.restype = c_int
d3 = c_double * 3
shao.onOrbitObs.argtypes = [c_double, c_double, c_double, c_double, c_double, c_double, \
c_int, c_int, c_int, c_int, c_int, c_double, \
c_double, POINTER(d3), POINTER(d3), \
c_int, c_int, c_int, c_int, c_int, c_double, \
POINTER(c_double), POINTER(c_double) ]
output_ra_list = list()
output_dec_list = list()
for i in range(input_nstars):
input_ra = c_double(input_ra_list[i])
input_dec = c_double(input_dec_list[i])
input_pmra = c_double(input_pmra_list[i])
input_pmdec = c_double(input_pmdec_list[i])
# input_rv = c_double(input_rv_list[i] * 3600.) # Convert from km/s to km/h
input_rv = c_double(input_rv_list[i])
input_parallax = c_double(input_parallax_list[i])
p3 = d3(input_x, input_y, input_z)
v3 = d3(input_vx, input_vy, input_vz)
input_year_c = c_int(input_year)
input_month_c = c_int(input_month)
input_day_c = c_int(input_day)
input_hour_c = c_int(input_hour)
input_minute_c = c_int(input_minute)
input_second_c = c_double(input_second)
DAT = c_double(37.0)
output_ra = c_double(0.0)
output_dec = c_double(0.0)
rs = shao.onOrbitObs(input_ra, input_dec, input_parallax, input_pmra, input_pmdec, input_rv, \
input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c, \
DAT, byref(p3), byref(v3), \
input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c, \
byref(output_ra), byref(output_dec))
if rs != 0:
raise RuntimeError("Calculate error!")
output_ra_list.append(output_ra.value)
output_dec_list.append(output_dec.value)
return np.array(output_ra_list), np.array(output_dec_list)
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ObservationSim/Config/ChipOutput.py deleted 100755 → 0
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import os
import logging
import ObservationSim.Config._util as _util
from ObservationSim.Config.Header import generatePrimaryHeader
class ChipOutput(object):
def __init__(self, config, chip, filt, pointing, logger_filename=None):
self.config = config
self.chip = chip
self.filt = filt
self.pointing_type = pointing.pointing_type
self.chip_label = str(chip.chipID).rjust(2, '0')
# Get primary header based on chip and pointing
self.h_prim = generatePrimaryHeader(
xlen=chip.npix_x,
ylen=chip.npix_y,
pointing_id=pointing.obs_id,
pointing_type_code=pointing.pointing_type_code,
ra=pointing.ra,
dec=pointing.dec,
pixel_scale=chip.pix_scale,
time_pt=pointing.timestamp,
exptime=pointing.exp_time,
im_type=pointing.pointing_type,
sat_pos=[pointing.sat_x, pointing.sat_y, pointing.sat_z],
sat_vel=[pointing.sat_vx, pointing.sat_vy, pointing.sat_vz],
project_cycle=self.config["project_cycle"],
run_counter=self.config["run_counter"],
chip_name=self.chip_label)
obs_id = _util.get_obs_id(img_type=self.pointing_type, project_cycle=config["project_cycle"], run_counter=config[
"run_counter"], pointing_id=pointing.obs_id, pointing_type_code=pointing.pointing_type_code)
self.subdir = pointing.output_dir
self.cat_name = self.h_prim['FILENAME'] + '.cat'
if logger_filename is None:
logger_filename = self.h_prim['FILENAME'] + '.log'
self.logger = logging.getLogger()
fh = logging.FileHandler(os.path.join(
self.subdir, logger_filename), mode='w+', encoding='utf-8')
fh.setLevel(logging.DEBUG)
self.logger.setLevel(logging.DEBUG)
logging.getLogger('numba').setLevel(logging.WARNING)
formatter = logging.Formatter(
'%(asctime)s - %(msecs)d - %(levelname)-8s - [%(filename)s:%(lineno)d] - %(message)s')
fh.setFormatter(formatter)
self.logger.addHandler(fh)
hdr1 = "# obj_ID ID_chip filter xImage yImage ra dec ra_orig dec_orig z mag obj_type "
hdr2 = "pm_ra pm_dec RV parallax"
fmt1 = "%20s %4d %5s %10.3f %10.3f %15.8f %15.8f %15.8f %15.8f %7.4f %8.4f %15s "
fmt2 = "%15.8f %15.8f %15.8f %15.8f"
self.hdr = hdr1 + hdr2
self.fmt = fmt1 + fmt2
self.logger.info("pointing_type = %s\n" % (self.pointing_type))
def Log_info(self, message):
print(message)
self.logger.info(message)
def Log_error(self, message):
print(message)
self.logger.error(message)
def update_output_header(self, additional_column_names=""):
self.hdr += additional_column_names
def create_output_file(self):
if self.pointing_type == 'SCI':
self.cat = open(os.path.join(self.subdir, self.cat_name), "w")
self.logger.info("Creating catalog file %s ...\n" %
(os.path.join(self.subdir, self.cat_name)))
if not self.hdr.endswith("\n"):
self.hdr += "\n"
self.cat.write(self.hdr)
def cat_add_obj(self, obj, pos_img, pos_shear):
ximg = obj.real_pos.x + 1.0
yimg = obj.real_pos.y + 1.0
line = self.fmt % (
obj.id, int(self.chip_label), self.filt.filter_type, ximg, yimg, obj.ra, obj.dec, obj.ra_orig, obj.dec_orig, obj.z, obj.getMagFilter(
self.filt), obj.type,
obj.pmra, obj.pmdec, obj.rv, obj.parallax)
line += obj.additional_output_str
if not line.endswith("\n"):
line += "\n"
self.cat.write(line)
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"""
generate image header
"""
import numpy as np
from astropy.io import fits
import astropy.wcs as pywcs
from scipy import math
import random
import os
import sys
def chara2digit(char):
""" Function to judge and convert characters to digitals
Parameters
----------
"""
try:
float(char) # for int, long and float
except ValueError:
pass
return char
else:
data = float(char)
return data
def read_header_parameter(filename='global_header.param'):
""" Function to read the header parameters
Parameters
----------
"""
name = []
value = []
description = []
for line in open(filename):
line = line.strip("\n")
arr = line.split('|')
# csvReader = csv.reader(csvDataFile)
# for arr in csvReader:
name.append(arr[0])
value.append(chara2digit(arr[1]))
description.append(arr[2])
# print(value)
return name, value, description
def rotate_CD_matrix(cd, pa_aper):
"""Rotate CD matrix
Parameters
----------
cd: (2,2) array
CD matrix
pa_aper: float
Position angle, in degrees E from N, of y axis of the detector
Returns
-------
cd_rot: (2,2) array
Rotated CD matrix
Comments
--------
`astropy.wcs.WCS.rotateCD` doesn't work for non-square pixels in that it
doesn't preserve the pixel scale! The bug seems to come from the fact
that `rotateCD` assumes a transposed version of its own CD matrix.
"""
rad = np.deg2rad(-pa_aper)
mat = np.zeros((2,2))
mat[0,:] = np.array([np.cos(rad),-np.sin(rad)])
mat[1,:] = np.array([np.sin(rad),np.cos(rad)])
cd_rot = np.dot(mat, cd)
return cd_rot
def Header_extention(xlen = 9232, ylen = 9216, gain = 1.0, readout = 5.0, dark = 0.02,saturation=90000, row_num = 1, col_num = 1):
""" Creat an image frame for CCST with multiple extensions
Parameters
----------
"""
flag_ltm_x = [0,1,-1,1,-1]
flag_ltm_y = [0,1,1,-1,-1]
flag_ltv_x = [0,0,1,0,1]
flag_ltv_y = [0,0,0,1,1]
detector_size_x = int(xlen)
detector_size_y = int(ylen)
data_x = str(int(detector_size_x))
data_y = str(int(detector_size_y))
data_sec = '[1:'+data_x+',1:'+data_y+']'
name = []
value = []
description = []
for k in range(1,2):
# f = open("extension"+str(k)+"_image.param","w")
j = row_num
i = col_num
ccdnum = str((j-1)*5+i)
name = ['EXTNAME',
'BSCALE',
'BZERO',
'OBSID',
'CCDNAME',
'AMPNAME',
'GAIN',
'RDNOISE',
'DARK',
'SATURATE',
'RSPEED',
'CHIPTEMP',
'CCDCHIP',
'DATASEC',
'CCDSUM',
'NSUM',
'LTM1_1',
'LTM2_2',
'LTV1',
'LTV2',
'ATM1_1',
'ATM2_2',
'ATV1',
'ATV2',
'DTV1',
'DTV2',
'DTM1_1',
'DTM2_2']
value = ['IM'+str(k),
1.0,
0.0,
'CSST.20200101T000000',
'ccd' + ccdnum.rjust(2,'0'),
'ccd' + ccdnum.rjust(2,'0') + ':'+str(k),
gain,
readout,
dark,
saturation,
10.0,
-100.0,
'ccd' + ccdnum.rjust(2,'0'),
data_sec,
'1 1',
'1 1',
flag_ltm_x[k],
flag_ltm_y[k],
flag_ltv_x[k]*(detector_size_x-20*2+1),
flag_ltv_y[k]*(detector_size_y+1),
flag_ltm_x[k],
flag_ltm_y[k],
flag_ltv_x[k]*(detector_size_x-20*2+1),
flag_ltv_y[k]*(detector_size_y+1),
0,
0,
1,
1]
description = ['Extension name',
' ',
' ',
'Observation ID',
'CCD name',
'Amplifier name',
'Gain (e-/ADU)',
'Readout noise (e-/pixel)',
'Dark noise (e-/pixel/s)',
'Saturation (e-)',
'Read speed',
'Chip temperature',
'CCD chip ID',
'Data section',
'CCD pixel summing',
'CCD pixel summing',
'CCD to image transformation',
'CCD to image transformation',
'CCD to image transformation',
'CCD to image transformation',
'CCD to amplifier transformation',
'CCD to amplifier transformation',
'CCD to amplifier transformation',
'CCD to amplifier transformation',
'CCD to detector transformatio',
'CCD to detector transformatio',
'CCD to detector transformatio',
'CCD to detector transformatio']
return name, value, description
##9232 9216 898 534 1309 60 -40 -23.4333
def WCS_def(xlen = 9232, ylen = 9216, gapx = 898.0, gapy1 = 534, gapy2 = 1309, ra = 60, dec = -40, pa = -23.433,psize = 0.074, row_num = 1, col_num = 1):
""" Creat a wcs frame for CCST with multiple extensions
Parameters
----------
"""
flag_x = [0, 1, -1, 1, -1]
flag_y = [0, 1, 1, -1, -1]
flag_ext_x = [0,-1,1,-1,1]
flag_ext_y = [0,-1,-1,1,1]
x_num = 5
y_num = 6
detector_num = x_num*y_num
detector_size_x = xlen
detector_size_y = ylen
gap_x = gapx
gap_y = [gapy1,gapy2]
ra_ref = ra
dec_ref = dec
pa_aper = pa
pixel_size = psize
gap_y1_num = 3
gap_y2_num = 2
x_center = (detector_size_x*x_num+gap_x*(x_num-1))/2
y_center = (detector_size_y*y_num+gap_y[0]*gap_y1_num+gap_y[1]*gap_y2_num)/2
gap_y_map = np.array([[0,0,0,0,0],[gap_y[0],gap_y[1],gap_y[1],gap_y[1],gap_y[1]],[gap_y[1],gap_y[0],gap_y[0],gap_y[0],gap_y[0]],[gap_y[0],gap_y[0],gap_y[0],gap_y[0],gap_y[0]],[gap_y[0],gap_y[0],gap_y[0],gap_y[0],gap_y[1]],[gap_y[1],gap_y[1],gap_y[1],gap_y[1],gap_y[0]]])
frame_array = np.empty((5,6),dtype=np.float64)
# print(x_center,y_center)
j = row_num
i = col_num
ccdnum = str((j-1)*5+i)
x_ref, y_ref = (detector_size_x+gap_x)*i-gap_x-detector_size_x/2, detector_size_y*j + sum(gap_y_map[0:j,i-1]) - detector_size_y/2
# print(i,j,x_ref,y_ref,ra_ref,dec_ref)
name = []
value = []
description = []
for k in range(1,2):
cd = np.array([[ pixel_size, 0], [0, pixel_size]])/3600.*flag_x[k]
cd_rot = rotate_CD_matrix(cd, pa_aper)
# f = open("CCD"+ccdnum.rjust(2,'0')+"_extension"+str(k)+"_wcs.param","w")
name = ['EQUINOX',
'WCSDIM',
'CTYPE1',
'CTYPE2',
'CRVAL1',
'CRVAL2',
'CRPIX1',
'CRPIX2',
'CD1_1',
'CD1_2',
'CD2_1',
'CD2_2']
value = [2000.0,
2.0,
'RA---TAN',
'DEC--TAN',
ra_ref,
dec_ref,
flag_ext_x[k]*((x_ref+flag_ext_x[k]*detector_size_x/2)-x_center),
flag_ext_y[k]*((y_ref+flag_ext_y[k]*detector_size_y/2)-y_center),
cd_rot[0,0],
cd_rot[0,1],
cd_rot[1,0],
cd_rot[1,1]]
description = ['Equinox of WCS',
'WCS Dimensionality',
'Coordinate type',
'Coordinate typ',
'Coordinate reference value',
'Coordinate reference value',
'Coordinate reference pixel',
'Coordinate reference pixel',
'Coordinate matrix',
'Coordinate matrix',
'Coordinate matrix',
'Coordinate matrix']
return name, value, description
def generatePrimaryHeader(xlen = 9232, ylen = 9216,pointNum = '1', ra = 60, dec = -40, psize = 0.074, row_num = 1, col_num = 1):
# array_size1, array_size2, flux, sigma = int(argv[1]), int(argv[2]), 1000.0, 5.0
filerParm_fn = os.path.split(os.path.realpath(__file__))[0] + '/filter.lst'
f = open(filerParm_fn)
s = f.readline()
s = s.strip("\n")
filter = s.split(' ')
k = (row_num-1)*5+col_num
ccdnum = str(k)
g_header_fn = os.path.split(os.path.realpath(__file__))[0] + '/global_header.param'
name, value, description = read_header_parameter(g_header_fn)
h_prim = fits.Header()
date = '200930'
time_obs = '120000'
for i in range(len(name)):
if(name[i]=='FILTER'):
value[i] = filter[k-1]
if(name[i]=='FILENAME'):
value[i] = 'CSST_' + date + '_' +time_obs + '_' + pointNum.rjust(6,'0') + '_' +ccdnum.rjust(2,'0')+'_raw'
if(name[i]=='DETSIZE'):
value[i] = '[1:' + str(int(xlen)) + ',1:'+ str(int(ylen)) + ']'
if(name[i]=='PIXSCAL1'):
value[i] = str(psize)
if(name[i]=='PIXSCAL2'):
value[i] = str(psize)
h_prim[name[i]] = (value[i],description[i])
h_prim.add_comment('==================================================================',after='FILETYPE')
h_prim.add_comment('Target information')
h_prim.add_comment('==================================================================')
h_prim.add_comment('==================================================================',after='EQUINOX')
h_prim.add_comment('Exposure information')
h_prim.add_comment('==================================================================')
h_prim.add_comment('==================================================================',after='MJDEND')
h_prim.add_comment('Telescope information')
h_prim.add_comment('==================================================================')
h_prim.add_comment('==================================================================',after='REFFRAME')
h_prim.add_comment('Detector information')
h_prim.add_comment('==================================================================')
h_prim.add_comment('==================================================================',after='FILTER')
h_prim.add_comment('Other information')
h_prim.add_comment('==================================================================')
return h_prim
def generateExtensionHeader(xlen = 9232, ylen = 9216,ra = 60, dec = -40, pa = -23.433, gain = 1.0, readout = 5.0, dark = 0.02, saturation=90000, psize = 0.074, row_num = 1, col_num = 1):
h_ext = fits.Header()
for i in range(1,2):
# NAXIS1:Number of pixels per row; NAXIS2:Number of rows
h_ext['NAXIS1'] = xlen
h_ext['NAXIS2'] = ylen
name, value, description = Header_extention(xlen = xlen, ylen = ylen, gain = gain, readout = readout, dark = dark, saturation=saturation, row_num = row_num, col_num = col_num)
for j in range(len(name)):
h_ext[name[j]] = (value[j],description[j])
name, value, description = WCS_def(xlen = xlen, ylen = ylen, gapx = 898.0, gapy1 = 534, gapy2 = 1309, ra = ra, dec = dec, pa = pa ,psize = psize, row_num = row_num, col_num = col_num)
for j in range(len(name)):
h_ext[name[j]] = (value[j],description[j])
h_ext.add_comment('==================================================================',after='OBSID')
h_ext.add_comment('Readout information')
h_ext.add_comment('==================================================================')
h_ext.add_comment('==================================================================',after='CHIPTEMP')
h_ext.add_comment('Chip information')
h_ext.add_comment('==================================================================')
h_ext.add_comment('==================================================================',after='DTM2_2')
h_ext.add_comment('WCS information')
h_ext.add_comment('==================================================================')
return h_ext
def main(argv):
xlen = int(argv[1])
ylen = int(argv[2])
pointingNum = argv[3]
ra = float(argv[4])
dec = float(argv[5])
pSize = float(argv[6])
ccd_row_num = int(argv[7])
ccd_col_num = int(argv[8])
pa_aper = float(argv[9])
gain = float(argv[10])
readout = float(argv[11])
dark = float(argv[12])
fw = float(argv[13])
h_prim = generatePrimaryHeader(xlen = xlen, ylen = ylen,ra = ra, dec = dec, psize = pSize, row_num = ccd_row_num, col_num = ccd_col_num, pointNum = pointingNum)
h_ext = generateExtensionHeader(xlen = xlen, ylen = ylen,ra = ra, dec = dec, pa = pa_aper, gain = gain, readout = readout, dark = dark, saturation=fw, psize = pSize, row_num = ccd_row_num, col_num = ccd_col_num)
hdu1 = fits.PrimaryHDU(header=h_prim)
hdu2 = fits.ImageHDU(np.zeros([ylen,xlen]),header = h_ext)
hdul = fits.HDUList([hdu1,hdu2])
hdul.writeto(h_prim['FILENAME']+'.fits',output_verify='ignore')
# if __name__ == "__main__":
# main(sys.argv)
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from .ImageHeader import generatePrimaryHeader
from .ImageHeader import generateExtensionHeader
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XTENSION= 'IMAGE ' / extension type BITPIX = 16 / bits per data value NAXIS = 2 / number of data axes NAXIS1 = 9216 / length of first array axis NAXIS2 = 9232 / length of second array axis PCOUNT = 0 GCOUNT = 1 EXTNAME = 'SCI ' EXTVER = 1 BSCALE = 1 BZERO = 32768 BUNIT = 'ADU ' / physical unit of array values COMMENT ========================================================================COMMENT Detector information COMMENT ========================================================================CAMERA = 'MS' / camera of main survey DETSN = '12345678' / detector serial number DETNAME = 'CCD' / detector type DETTEMP1= 173.0 / detector temperature at EXPSTART(in Kelvin) DETTEMP2= 173.0 / detector temperature at EXPEND(in Kelvin) DETTEMP3= 173.0 / detector temperature at READT1(in Kelvin) DETSIZE = '9560x9264' / detector size DATASECT= '9216x9232' / data section PIXSCAL1= 0.074 / pixel scale for axis 1 PIXSCAL2= 0.074 / pixel scale for axis 2 PIXSIZE1= 10 / pixel size for axis 1 (in um) PIXSIZE2= 10 / pixel size for axis 2 (in um) COMMENT ========================================================================COMMENT CCD chip information COMMENT ========================================================================CHIPID = '08' / chip ID CHIPLAB = 'y-1' / chip label FILTER = 'y' / filter name NCHAN = 16 / number of readout channels PSCAN1 = 27 / horizontal prescan width, per readout channel PSCAN2 = 8 / vertical prescan width, per readout channel OSCAN1 = 16 / horizontal overscan width,per readout channel OSCAN2 = 16 / vertical overscan width,per readout channel COMMENT ========================================================================COMMENT WORLD COORDINATE SYSTEM AND RELATED PARAMETERS COMMENT ========================================================================WCSAXES = 2 / number of World Coordinate System axes CRPIX1 = -10017.0 / x-coordinate of reference pixel CRPIX2 = 24876.0 / y-coordinate of reference pixel CRVAL1 = 62.228226 / first axis value at reference pixel CRVAL2 = -42.316932 / second axis value at reference pixel CTYPE1 = 'RA---TAN' / the coordinate type for the first axis CTYPE2 = 'DEC--TAN' / the coordinate type for the second axis CD1_1 = 1.88602083707394E-05 / partial of first axis coordinate w.r.t.x CD1_2 = 8.17455836176000E-06 / partial of first axis coordinate w.r.t.y CD2_1 = -8.1745583617600E-06 / partial of second axis coordinate w.r.t.x CD2_2 = 1.88602083707394E-05 / partial of second axis coordinate w.r.t.y OTHERS = '' / COMMENT ========================================================================COMMENT Readout information COMMENT ========================================================================GAINLVL = '01' / gain level GAIN01 = 1.1 / gain (channel 01) GAIN02 = 1.1 / gain (channel 02) GAIN03 = 1.1 / gain (channel 03) GAIN04 = 1.1 / gain (channel 04) GAIN05 = 1.1 / gain (channel 05) GAIN06 = 1.1 / gain (channel 06) GAIN07 = 1.1 / gain (channel 07) GAIN08 = 1.1 / gain (channel 08) GAIN09 = 1.1 / gain (channel 09) GAIN10 = 1.1 / gain (channel 10) GAIN11 = 1.1 / gain (channel 11) GAIN12 = 1.1 / gain (channel 12) GAIN13 = 1.1 / gain (channel 13) GAIN14 = 1.1 / gain (channel 14) GAIN15 = 1.1 / gain (channel 15) GAIN16 = 1.1 / gain (channel 16) RON01 = 5.0 / read noise (channel 01) RON02 = 5.0 / read noise (channel 02) RON03 = 5.0 / read noise (channel 03) RON04 = 5.0 / read noise (channel 04) RON05 = 5.0 / read noise (channel 05) RON06 = 5.0 / read noise (channel 06) RON07 = 5.0 / read noise (channel 07) RON08 = 5.0 / read noise (channel 08) RON09 = 5.0 / read noise (channel 09) RON10 = 5.0 / read noise (channel 10) RON11 = 5.0 / read noise (channel 11) RON12 = 5.0 / read noise (channel 12) RON13 = 5.0 / read noise (channel 13) RON14 = 5.0 / read noise (channel 14) RON15 = 5.0 / read noise (channel 15) RON16 = 5.0 / read noise (channel 16) READT0 = '2024-00-00T00:00:00'/ readout start time(UTC) READT1 = '2024-00-00T00:00:00'/ readout end time(UTC) ROSPEED = 10.0 / readout speed (in MHz) EXPTIME = 150.0 / exposure duration DARKTIME= 150.0 / dark current time COMMENT ========================================================================COMMENT Shutter information COMMENT ========================================================================SHTSTAT = T / shutter status SHTOPEN0= 0.0 / shutter open time (begin) SHTOPEN1= 0.0 / shutter open time (end) SHTCLOS0= 0.0 / shutter close time (begin) SHTCLOS1= 0.0 / shutter close time (end) COMMENT ========================================================================COMMENT LED information COMMENT ========================================================================LEDFLAG = 0 / main/backup LED LEDSTAT = '00000000000000' / LED status LEDEXPT = 0.0 / LED flash time (s) LEDTEMP = 173.0 / LED temperature (in K) COMMENT ========================================================================COMMENT Other information COMMENT ========================================================================CHECKSUM= '''abcde''' / HDU checksum updated yyyy-mm-ddTHH:MM:SS DATASUM = '''abcde''' / data unit checksum updated yyyy-mm-ddTHH:MM:SS END
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EXTNAME|IM1|Extension name
EXTVER|1|The ID number
BSCALE|1|
BZERO|8|
OBSID|CSST.20200101T000000|Observation ID
CCDNAME|CCD02|CCD name
AMPNAME|ccd02:B|Amplifier name
GAIN|1.00|Gain (e/ADU)
RDNOISE|5.00|Readout noise (e)
SATURATE|90000.0|Saturation (ADU)
RSPEED|10.0|Read speed (in MHz)
CHIPTEMP|-100.0|Chip temperature (in K)
CCDCHIP|1|CCD chip ID
CCDLABEL|GI-1|CCD chip label
HOSCAN|2000|Horizontal overscan width, per readout channel
VOSCAN|2000|Virtical overscan height, per readout channel
CCDSUM|1 1|CCD pixel summing
CCDSEC|[1:9216:9232]|CCD section
AMPSEC|[1:9216:9232]|Amplifier section
DATASEC|[1:9216,1: 9232]|Data section
DETSEC|[1:9216,1:9232]|Detector section
BIASSEC|[9216:9217,9232:9234]|Bias section
TRIMSEC|[1:9216,1:9232]|Trim section
WCSDIM|2|WCS dimensionality
EQUINOX|2000|Epoch (year)
CTYPE1|RA---TPV|Coordinate type
CTYPE2|DEC---TPV|Coordinate type
CRVAL1|1.00|Coordinate reference value
CRVAL2|1.00|Coordinate reference value
CRPIX1|1.00|Coordinate reference pixel
CRPIX2|1.00|Coordinate reference pixel
CD1_1|1|Coordinate matrix
CD2_1|0|Coordinate matrix
CD1_2|0|Coordinate matrix
CD2_2|1|Coordinate matrix
CHECKSUM|C65|SHA256 checksum of global headers
\ No newline at end of file
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GV GI y z y GI GU r u NUV i GV GU g NUV NUV g GU GV i NUV u r GU GI y z y GI GV
3 3 3 1 1 1 3 2 2 1 1 1 4 2 3 2 1 1 4 2 4 1 1 2 4 2 2 4 2 2
26 21 16 11 6 1 27 22 17 12 7 2 28 23 18 13 8 3 29 24 19 14 9 4 30 25 20 15 10 5
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