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Commit 2c2dac03 authored by Fang Yuedong's avatar Fang Yuedong
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ObservationSim/Config/Header/global_header.header deleted 100644 → 0
View file @ 4afd1181
SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T NEXTEND = 1 / number of array dimensions GROUPS = F / ' ' DATE = '2021-03-04T09:30:00'/ the date on which this file was written FILENAME= 'MSC_MS_210304093000_100000000_06_raw' / file name FILETYPE= 'SCIE ' / observation type TELESCOP= 'CSST ' / telescope used to acquire data INSTRUME= 'MSC ' / instrument used to acquire data RADECSYS= 'ICRS ' / reference coordinates system EQUINOX = 2000.0 / FITSCREA= 'C6' / FITS create software version COMMENT ========================================================================COMMENT Object information COMMENT ========================================================================OBJECT = '00000000' / object name TARGET = '+000000000000' / target name (hhmmss+ddmmss) OBSID = '00000000' / observation ID OBJ_RA = 62.228226 / R.A. of the object (degrees) OBJ_DEC = -42.316932 / declination of the object (degrees) COMMENT ========================================================================COMMENT Telescope information COMMENT ========================================================================REFFRAME= 'CSSTGSC-1.0' / guide star catalog version DATE-OBS= '2021-03-04T09:30:00'/ date of the observation (yyyy-mm-dd hh:mm:ss) SATESWV = '0001' / software version in the satellite EXPSTART= 59130.5 / exposure start time (MJD) CABSTART= 59130.5 / (MJD) SUNANGL0= 50.0 / angle between sun and opt axis at CABSTART MOONANG0= 30.0 / angle between moon and opt axis at CABSTART TEL_ALT0= 20.0 / angle between opt axis and Elimb at CABSTART POS_ANG0= 20.0 / angle between y axis and NP at CABSTART POSI0_X = 0.0 / the orbital position in X at CABSTART POSI0_Y = 0.0 / the orbital position in Y at CABSTART POSI0_Z = 0.0 / the orbital position in Z at CABSTART VELO0_X = 0.0 / the orbital velocity in X at CABSTART VELO0_Y = 0.0 / the orbital velocity in Y at CABSTART VELO0_Z = 0.0 / the orbital velocity in Z at CABSTART EULER0_1= 0.0 / euler angle 1 at CABSTART EULER0_2= 0.0 / euler angle 2 at CABSTART EULER0_3= 0.0 / euler angle 3 at CABSTART RA_PNT0 = 0.0 / RA of the pointing (degrees) at CABSTART DEC_PNT0= 0.0 / DEC of the pointing (degrees) at CABSTART EXPEND = 0.0 / exposure end time (MJD) CABEND = 0.0 / (MJD) SUNANGL1= 50.0 / angle between sun and opt axis at CABEND MOONANG1= 30.0 / angle between moon and opt axis at CABEND TEL_ALT1= 20.0 / angle between opt axis and Elimb at CABEND POS_ANG1= 20.0 / angle between y axis and NP at CABEND POSI1_X = 0.0 / the orbital position in X at CABEND POSI1_Y = 0.0 / the orbital position in Y at CABEND POSI1_Z = 0.0 / the orbital position in Z at CABEND VELO1_X = 0.0 / the orbital velocity in X at CABEND VELO1_Y = 0.0 / the orbital velocity in Y at CABEND VELO1_Z = 0.0 / the orbital velocity in Z at CABEND EULER1_1= 0.0 / euler angle 1 at CABEND EULER1_2= 0.0 / euler angle 2 at CABEND EULER1_3= 0.0 / euler angle 3 at CABEND RA_PNT1 = 0.0 / RA of the pointing (degrees) at CABEND DEC_PNT1= 0.0 / DEC of the pointing (degrees) at CABEND EXPTIME = 150.0 / exposure duration EPOCH = 2000.0 / coordinate epoch COMMENT Other information COMMENT ========================================================================CHECKSUM= 'abcdefg ' / HDU checksum updated yyyy-mm-ddTHH:MM:SS DATASUM = 'abcdefg ' / data unit checksum updated yyyy-mm-ddTHH:MM:SS END
ObservationSim/Config/Header/global_header.param deleted 100644 → 0
View file @ 4afd1181
DATE|2020-01-01|Date this file was written
FILENAME|CSST_01_999999|Name of file
FILETYPE|zero|Type of data
EXPNUM|99999999|Exposure sequence number
TARGNAME|CSST_|Observation title
RADECSYS|FK5|Default coordinate system
RADECEQ|2000.0|Default equinox
RA|00:00:00.00|RA of observation (hr)
DEC|+00:00:00.00|Dec of observation (deg)
EQUINOX|2000|Epoch(year)
TIMESYS|UT|Time system
DATE-OBS|2020-01-01|UTC date of start of observation
TIME-OBS|00:00:00|UTC time of start of observation
EXPTIME|0.000|Exposure time (sec)
MJD-OBS|58849.00000|MJD of observation start
MJDSTART|58849.00000|MJD of observation start
MJDEND|58849.00000|MJD of observation end
ST|16:32:58|Sidereal time
TELESCOP|CSST|Telescope name
TELRADEC|ICRS|Telescope coordinate system
TELEQUIN|2000|Equinox of tel coords
TELRA|00:00:00.00|RA of telescope (hr)
TELDEC|00:00:00.00|Dec of telescope (deg)
TELFOCUS|-9999|Telescope focus
SUNANGLE|30.00|Angle between sun and direction
MOONANGL|30.00|Angle between moon and direction
SUN_ALT|30.00|Sun altitude
REFFRAME|GSC1|guide star catalog version
INSTRUME|MBI|Instrument used to acquire data
DETSIZE|[1:9232,1:9216]|Detector size
NUMDETE|1|Number of detectors
NUMAMPS|4|Number of amplifiers
PIXSCAL1|0.074|Pixel scale for axis 1 (arcsec/pixel)
PIXSCAL2|0.074|Pixel scale for axis 2 (arcsec/pixel)
SHUTSTAT|closed|Shutter status
DETETEMP|-100.00|Detector temperature
CHECHSUM|abcdefg|checksum of global headers
ITL-HEAD|OK|ITL Header flag
N-AMPS-X|2|Number of amplifiers in X
N-AMPS-Y|2|Number of amplifiers in Y
ObservationSim/Config/Pointing.py deleted 100644 → 0
View file @ 4afd1181
import os
import shutil
import yaml
import galsim
import numpy as np
from astropy.time import Time
from ObservationSim.Config._util import get_obs_id
import ObservationSim.Instrument._util as _util
class Pointing(object):
def __init__(self, id=0, ra=0., dec=0., img_pa=0., timestamp=1621915200, sat_x=0., sat_y=0., sat_z=0., sun_x=0., sun_y=0., sun_z=0., sat_vx=0., sat_vy=0., sat_vz=0., exp_time=150., pointing_type='SCI', pointing_type_code='101', pointing_id = '00000001', obs_config_file=None, t_shutter_open = 1.3, t_shutter_close = 1.3):
self.id = id
self.ra = ra
self.dec = dec
self.img_pa = img_pa * galsim.degrees
self.timestamp = timestamp
self.sat_x, self.sat_y, self.sat_z = sat_x, sat_y, sat_z
self.sun_x, self.sun_y, self.sun_z = sun_x, sun_y, sun_z
self.sat_vx, self.sat_vy, self.sat_vz = sat_vx, sat_vy, sat_vz
self.exp_time = exp_time
self.pointing_type = pointing_type
self.pointing_type_code = pointing_type_code
self.obs_id = pointing_id
self.survey_field_type = 'WIDE'
self.jdt = 0.
self.obs_config_file = obs_config_file
self.t_shutter_open = t_shutter_open
self.t_shutter_close = t_shutter_close
self.output_dir = "."
if self.obs_config_file is not None:
with open(self.obs_config_file, "r") as stream:
try:
self.obs_param = yaml.safe_load(stream)
except yaml.YAMLError as exc:
print(exc)
if self.obs_param["obs_type"]:
self.pointing_type = self.obs_param["obs_type"]
if self.obs_param["obs_type_code"]:
self.pointing_type_code = self.obs_param["obs_type_code"]
if self.obs_param["obs_id"]:
self.obs_id = str(self.obs_param["obs_id"])
def get_full_depth_exptime(self, filter_type):
if self.survey_field_type == 'WIDE':
if filter_type in _util.SPEC_FILTERS:
return 150. * 4
else:
if filter_type.lower() in ['nuv', 'y']:
return 150. * 4
elif filter_type.lower() in ['u', 'g', 'r', 'i', 'z']:
return 150. * 2
else:
return max(150., self.exp_time) # [TODO] for FGS
elif self.survey_field_type == 'DEEP':
if filter_type in _util.SPEC_FILTERS:
return 250. * 4 * 4
else:
if filter_type.lower() in ['nuv', 'y']:
return 250. * 4 * 4
elif filter_type.lower() in ['u', 'g', 'r', 'i', 'z']:
return 250. * 2 * 4
else:
return max(150., self.exp_time) # [TODO] for FGS
def read_pointing_columns(self, columns, id=0, t=1621915200, pointing_type='SCI'):
self.id = id
col_len = len(columns)
self.ra = float(columns[0])
self.dec = float(columns[1])
self.img_pa = float(columns[4]) * galsim.degrees
# self.pointing_type = pointing_type
if col_len > 5:
jdt = np.double(columns[5])
t_temp = Time(jdt, format='jd')
self.jdt = jdt
self.timestamp = t_temp.unix
self.sat_x = float(columns[6])
self.sat_y = float(columns[7])
self.sat_z = float(columns[8])
self.sun_x = float(columns[9])
self.sun_y = float(columns[10])
self.sun_z = float(columns[11])
self.sat_vx = float(columns[15])
self.sat_vy = float(columns[16])
self.sat_vz = float(columns[17])
self.exp_time = float(columns[18])
is_deep = float(columns[19])
# [TODO] Can also define other survey types
if is_deep != -1.0:
self.survey_field_type = "DEEP"
if not self.obs_config_file:
self.obs_config_file = str(columns[20])
with open(self.obs_config_file, "r") as stream:
try:
self.obs_param = yaml.safe_load(stream)
except yaml.YAMLError as exc:
print(exc)
self.pointing_type_code = columns[21][0:3]
self.obs_id = columns[21][3:]
self.pointing_type = self.obs_param["obs_type"]
else:
self.timestamp = t
def make_output_pointing_dir(self, overall_config, copy_obs_config=False):
run_dir = os.path.join(overall_config["work_dir"], overall_config["run_name"])
if not os.path.exists(run_dir):
try:
os.makedirs(run_dir, exist_ok=True)
except OSError:
pass
self.output_prefix = get_obs_id(
img_type=self.pointing_type,
project_cycle=overall_config["project_cycle"],
run_counter=overall_config["run_counter"],
pointing_id=self.obs_id,
pointing_type_code = self.pointing_type_code)
self.output_dir = os.path.join(run_dir, self.output_prefix)
if not os.path.exists(self.output_dir):
try:
os.makedirs(self.output_dir, exist_ok=True)
except OSError:
pass
if copy_obs_config and self.obs_config_file:
obs_config_output_path = os.path.join(self.output_dir, os.path.basename(self.obs_config_file))
if not os.path.exists(obs_config_output_path):
try:
shutil.copy(self.obs_config_file, self.output_dir)
except OSError:
pass
ObservationSim/Config/__init__.py deleted 100644 → 0
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from .ChipOutput import ChipOutput
from .Pointing import Pointing
\ No newline at end of file
ObservationSim/Config/_util.py deleted 100644 → 0
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def get_obs_id(img_type='SCI', project_cycle=6, run_counter=0, pointing_id='00000001',pointing_type_code='101'):
# obs_type = {'SCI': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99'}
# obs_type = {'SCIE': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99', 'CAL': '01'}
obs_id = pointing_type_code + str(int(project_cycle)).rjust(2, '0') + str(int(run_counter)) + pointing_id
return obs_id
# def get_obs_id(img_type='SCI', project_cycle=6, run_counter=0, pointing_num=0):
# # obs_type = {'SCI': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99'}
# obs_type = {'SCIE': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99', 'CAL': '01'}
# obs_id = '1'+ obs_type[img_type] + str(int(project_cycle)).rjust(2, '0') + str(int(run_counter)) + str(pointing_num).rjust(8,'0')
# return obs_id
def get_file_type(img_type='SCI'):
file_type = {'SCI':'SCI', 'BIAS':'BIAS', 'DARK':'DARK', 'FLAT':'FLAT', 'CRS':'CRS', 'CRD':'CRD','CALS':'CALS','CALF':'CALF'}
return file_type[img_type]
\ No newline at end of file
ObservationSim/Instrument/Chip/Chip.py deleted 100755 → 0
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ObservationSim/Instrument/Chip/ChipUtils.py deleted 100644 → 0
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import os
import galsim
import ctypes
import numpy as np
from astropy.io import fits
from datetime import datetime
from ObservationSim.Instrument.Chip import Effects as effects
from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
try:
import importlib.resources as pkg_resources
except ImportError:
# Try backported to PY<37 'importlib_resources'
import importlib_resources as pkg_resources
def log_info(msg, logger=None):
if logger:
logger.info(msg)
else:
print(msg, flush=True)
def getChipSLSGratingID(chipID):
gratingID = ['','']
if chipID == 1: gratingID = ['GI2', 'GI1']
if chipID == 2: gratingID = ['GV4', 'GV3']
if chipID == 3: gratingID = ['GU2', 'GU1']
if chipID == 4: gratingID = ['GU4', 'GU3']
if chipID == 5: gratingID = ['GV2', 'GV1']
if chipID == 10: gratingID = ['GI4', 'GI3']
if chipID == 21: gratingID = ['GI6', 'GI5']
if chipID == 26: gratingID = ['GV8', 'GV7']
if chipID == 27: gratingID = ['GU6', 'GU5']
if chipID == 28: gratingID = ['GU8', 'GU7']
if chipID == 29: gratingID = ['GV6', 'GV5']
if chipID == 30: gratingID = ['GI8', 'GI7']
return gratingID
def getChipSLSConf(chipID):
confFile = ''
if chipID == 1: confFile = ['CSST_GI2.conf', 'CSST_GI1.conf']
if chipID == 2: confFile = ['CSST_GV4.conf', 'CSST_GV3.conf']
if chipID == 3: confFile = ['CSST_GU2.conf', 'CSST_GU1.conf']
if chipID == 4: confFile = ['CSST_GU4.conf', 'CSST_GU3.conf']
if chipID == 5: confFile = ['CSST_GV2.conf', 'CSST_GV1.conf']
if chipID == 10: confFile = ['CSST_GI4.conf', 'CSST_GI3.conf']
if chipID == 21: confFile = ['CSST_GI6.conf', 'CSST_GI5.conf']
if chipID == 26: confFile = ['CSST_GV8.conf', 'CSST_GV7.conf']
if chipID == 27: confFile = ['CSST_GU6.conf', 'CSST_GU5.conf']
if chipID == 28: confFile = ['CSST_GU8.conf', 'CSST_GU7.conf']
if chipID == 29: confFile = ['CSST_GV6.conf', 'CSST_GV5.conf']
if chipID == 30: confFile = ['CSST_GI8.conf', 'CSST_GI7.conf']
return confFile
def generateHeader(chip, pointing, img_type=None, img_type_code=None, project_cycle='9', run_counter='1'):
if (img_type is None) or (img_type_code is None):
img_type = pointing.pointing_type
img_type_code = pointing.pointing_type_code
h_prim = generatePrimaryHeader(
xlen=chip.npix_x,
ylen=chip.npix_y,
pointing_id = pointing.obs_id,
pointing_type_code = img_type_code,
ra=pointing.ra,
dec=pointing.dec,
pixel_scale=chip.pix_scale,
time_pt = pointing.timestamp,
exptime=pointing.exp_time,
im_type=img_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=project_cycle,
run_counter=run_counter,
chip_name=str(chip.chipID).rjust(2, '0'))
h_ext = generateExtensionHeader(
chip=chip,
xlen=chip.npix_x,
ylen=chip.npix_y,
ra=pointing.ra,
dec=pointing.dec,
pa=pointing.img_pa.deg,
gain=chip.gain,
readout=chip.read_noise,
dark=chip.dark_noise,
saturation=90000,
pixel_scale=chip.pix_scale,
pixel_size=chip.pix_size,
xcen=chip.x_cen,
ycen=chip.y_cen,
extName=img_type,
timestamp=pointing.timestamp,
exptime=pointing.exp_time,
readoutTime=chip.readout_time,
t_shutter_open=pointing.t_shutter_open,
t_shutter_close=pointing.t_shutter_close)
return h_prim, h_ext
def output_fits_image(chip, pointing, img, output_dir, img_type=None, img_type_code=None, project_cycle='9', run_counter='1'):
h_prim, h_ext = generateHeader(
chip=chip,
pointing=pointing,
img_type=img_type,
img_type_code=img_type_code,
project_cycle=project_cycle,
run_counter=run_counter)
hdu1 = fits.PrimaryHDU(header=h_prim)
hdu1.add_checksum()
hdu1.header.comments['CHECKSUM'] = 'HDU checksum'
hdu1.header.comments['DATASUM'] = 'data unit checksum'
hdu2 = fits.ImageHDU(img.array, header=h_ext)
hdu2.add_checksum()
hdu2.header.comments['XTENSION'] = 'extension type'
hdu2.header.comments['CHECKSUM'] = 'HDU checksum'
hdu2.header.comments['DATASUM'] = 'data unit checksum'
hdu1 = fits.HDUList([hdu1, hdu2])
fname = os.path.join(output_dir, h_prim['FILENAME']+'.fits')
hdu1.writeto(fname, output_verify='ignore', overwrite=True)
def add_sky_background(img, filt, exptime, sky_map=None, tel=None):
# Add sky background
if sky_map is None:
sky_map = filt.getSkyNoise(exptime=exptime)
sky_map = sky_map * np.ones_like(img.array)
sky_map = galsim.Image(array=sky_map)
# Apply Poisson noise to the sky map
# # (NOTE): only for photometric chips if it utilizes the photon shooting to draw stamps
# if self.survey_type == "photometric":
# sky_map.addNoise(poisson_noise)
elif img.array.shape != sky_map.shape:
raise ValueError("The shape img and sky_map must be equal.")
elif tel is not None: # If sky_map is given in flux
sky_map = sky_map * tel.pupil_area * exptime
img += sky_map
return img, sky_map
def get_flat(img, seed):
flat_img = effects.MakeFlatSmooth(
GSBounds=img.bounds,
seed=seed)
flat_normal = flat_img / np.mean(flat_img.array)
return flat_img, flat_normal
def add_cosmic_rays(img, chip, exptime=150, seed=0):
cr_map, cr_event_num = effects.produceCR_Map(
xLen=chip.npix_x, yLen=chip.npix_y,
exTime=exptime+0.5*chip.readout_time,
cr_pixelRatio=0.003*(exptime+0.5*chip.readout_time)/600.,
gain=chip.gain,
attachedSizes=chip.attachedSizes,
seed=seed) # seed: obj-imaging:+0; bias:+1; dark:+2; flat:+3;
img += cr_map
cr_map[cr_map > 65535] = 65535
cr_map[cr_map < 0] = 0
crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
del cr_map
return img, crmap_gsimg, cr_event_num
def add_PRNU(img, chip, seed=0):
prnu_img = effects.PRNU_Img(
xsize=chip.npix_x,
ysize=chip.npix_y,
sigma=0.01,
seed=seed)
img *= prnu_img
return img, prnu_img
def get_poisson(seed=0, sky_level=0.):
rng_poisson = galsim.BaseDeviate(seed)
poisson_noise = galsim.PoissonNoise(rng_poisson, sky_level=sky_level)
return rng_poisson, poisson_noise
def get_base_img(img, chip, read_noise, readout_time, dark_noise, exptime=150., InputDark=None):
if InputDark == None:
# base_level = read_noise**2 + dark_noise*(exptime+0.5*readout_time)
## base_level = dark_noise*(exptime+0.5*readout_time)
base_level = dark_noise*(exptime)
base_img1 = base_level * np.ones_like(img.array)
else:
base_img1 = np.zeros_like(img.array)
ny = int(chip.npix_y/2)
nx = chip.npix_x
arr = np.arange(ny).reshape(ny, 1)
arr = np.broadcast_to(arr, (ny, nx))
base_img2 = np.zeros_like(img.array)
base_img2[:ny, :] = arr
base_img2[ny:, :] = arr[::-1,:]
base_img2[:,:] = base_img2[:,:]*(readout_time/ny)*dark_noise
return base_img1+base_img2
def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=None, dark_noise=None, InputDark=None):
if poisson_noise is None:
_, poisson_noise = get_poisson(seed=seed, sky_level=sky_level)
read_noise = chip.read_noise
if dark_noise is None:
dark_noise = chip.dark_noise
base_img = get_base_img(img=img, chip=chip, read_noise=read_noise, readout_time=chip.readout_time, dark_noise=dark_noise, exptime=exptime, InputDark=InputDark)
img += base_img
img.addNoise(poisson_noise)
# img -= read_noise**2
if InputDark != None:
hdu = fits.open(InputDark) ##"Instrument/data/dark/dark_1000s_example_0.fits"
img += hdu[0].data/hdu[0].header['exptime']*exptime
hdu.close()
return img, base_img
def add_brighter_fatter(img):
#Inital dynamic lib
try:
with pkg_resources.files('ObservationSim.Instrument.Chip.libBF').joinpath("libmoduleBF.so") as lib_path:
lib_bf = ctypes.CDLL(lib_path)
except AttributeError:
with pkg_resources.path('ObservationSim.Instrument.Chip.libBF', "libmoduleBF.so") as lib_path:
lib_bf = ctypes.CDLL(lib_path)
lib_bf.addEffects.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_float), ctypes.c_int]
# Set bit flag
bit_flag = 1
bit_flag = bit_flag | (1 << 2)
nx, ny = img.array.shape
nn = nx * ny
arr_ima= (ctypes.c_float*nn)()
arr_imc= (ctypes.c_float*nn)()
arr_ima[:]= img.array.reshape(nn)
arr_imc[:]= np.zeros(nn)
lib_bf.addEffects(nx, ny, arr_ima, arr_imc, bit_flag)
img.array[:, :] = np.reshape(arr_imc, [nx, ny])
del arr_ima, arr_imc
return img
"""
def add_inputdark(img, chip, exptime):
fname = "/share/home/weichengliang/CSST_git/test_new_sim/csst-simulation/ObservationSim/Instrument/data/dark/dark_1000s_example_0.fits"
hdu = fits.open(fname)
#ny, nx = img.array.shape
#inputdark = np.zeros([ny, nx])
img.array[:, :] += hdu[0].data/hdu[0].header['exptime']*exptime
hdu.close()
del inputdark
return img
"""
def AddPreScan(GSImage, pre1=27, pre2=4, over1=71, over2=80, nsecy = 2, nsecx=8):
img= GSImage.array
ny, nx = img.shape
dx = int(nx/nsecx)
dy = int(ny/nsecy)
imgt=np.zeros([int(nsecy*nsecx), int(ny/nsecy+pre2+over2), int(nx/nsecx+pre1+over1)])
for iy in range(nsecy):
for ix in range(nsecx):
if iy % 2 == 0:
tx = ix
else:
tx = (nsecx-1)-ix
ty = iy
chunkidx = int(tx+ty*nsecx) #chunk1-[1,2,3,4], chunk2-[5,6,7,8], chunk3-[9,10,11,12], chunk4-[13,14,15,16]
imgtemp = np.zeros([int(ny/nsecy+pre2+over2), int(nx/nsecx+pre1+over1)])
if int(chunkidx/4) == 0:
imgtemp[pre2:pre2+dy, pre1:pre1+dx] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
imgt[chunkidx, :, :] = imgtemp
if int(chunkidx/4) == 1:
imgtemp[pre2:pre2+dy, over1:over1+dx] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
imgt[chunkidx, :, :] = imgtemp #[:, ::-1]
if int(chunkidx/4) == 2:
imgtemp[over2:over2+dy, over1:over1+dx] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
imgt[chunkidx, :, :] = imgtemp #[::-1, ::-1]
if int(chunkidx/4) == 3:
imgtemp[over2:over2+dy, pre1:pre1+dx] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
imgt[chunkidx, :, :] = imgtemp #[::-1, :]
imgtx1 = np.hstack(imgt[:nsecx:, :, :]) #hstack chunk(1,2)-[1,2,3,4,5,6,7,8]
imgtx2 = np.hstack(imgt[:(nsecx-1):-1, :, :]) #hstack chunk(4,3)-[16,15,14,13,12,11,,10,9]
newimg = galsim.Image(int(nx+(pre1+over1)*nsecx), int(ny+(pre2+over2)*nsecy), init_value=0)
newimg.array[:, :] = np.concatenate([imgtx1, imgtx2]) #vstack chunk(1,2) & chunk(4,3)
newimg.wcs = GSImage.wcs
return newimg
def AddPreScanFO(GSImage, pre1=27, pre2=4, over1=71, over2=80, nsecy = 1, nsecx=16):
img= GSImage.array
ny, nx = img.shape
dx = int(nx/nsecx)
dy = int(ny/nsecy)
newimg = galsim.Image(int(nx+(pre1+over1)*nsecx), int(ny+(pre2+over2)*nsecy), init_value=0)
for ix in range(nsecx):
newimg.array[pre2:pre2+dy, pre1+ix*(dx+pre1+over1):pre1+dx+ix*(dx+pre1+over1)] = img[0:dy, 0+ix*dx:dx+ix*dx]
newimg.wcs = GSImage.wcs
return newimg
def formatOutput(GSImage, nsecy = 2, nsecx=8):
img = GSImage.array
ny, nx = img.shape
dx = int(nx/nsecx)
dy = int(ny/nsecy)
imgt = np.zeros([int(nsecx*nsecy), dy, dx])
for iy in range(nsecy):
for ix in range(nsecx):
if iy % 2 == 0:
tx = ix
else:
tx = (nsecx-1)-ix
ty = iy
chunkidx = int(tx+ty*nsecx)
if int(chunkidx/4) == 0:
imgt[chunkidx, :, :] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
if int(chunkidx/4) == 1:
imgt[chunkidx, :, :] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
if int(chunkidx/4) == 2:
imgt[chunkidx, :, :] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
if int(chunkidx/4) == 3:
imgt[chunkidx, :, :] = img[iy*dy:(iy+1)*dy, ix*dx:(ix+1)*dx]
imgttx0 = np.hstack(imgt[ 0:4:, :, :])
imgttx1 = np.hstack(imgt[ 4:8:, :, ::-1])
imgttx2 = np.hstack(imgt[8:12:, ::-1, ::-1])
imgttx3 = np.hstack(imgt[12:16:,::-1, :])
newimg = galsim.Image(int(dx*nsecx*nsecy), dy, init_value=0)
newimg.array[:, :] = np.hstack([imgttx0, imgttx1, imgttx2, imgttx3])
return newimg
def formatRevert(GSImage, nsecy = 1, nsecx=16):
img = GSImage.array
ny, nx = img.shape
dx = int(nx/nsecx)
dy = int(ny/nsecy)
newimg = galsim.Image(int(dx*8), int(dy*2), init_value=0)
for ix in range(0,4):
tx = ix
newimg.array[0:dy, 0+tx*dx:dx+tx*dx] = img[:, 0+ix*dx:dx+ix*dx]
for ix in range(4,8):
tx = ix
newimg.array[0:dy, 0+tx*dx:dx+tx*dx] = img[:, 0+ix*dx:dx+ix*dx][:, ::-1]
for ix in range(8,12):
tx = 7-(ix-8)
newimg.array[0+dy:dy+dy, 0+tx*dx:dx+tx*dx] = img[:, 0+ix*dx:dx+ix*dx][::-1, ::-1]
for ix in range(12,16):
tx = 7-(ix-8)
newimg.array[0+dy:dy+dy, 0+tx*dx:dx+tx*dx] = img[:, 0+ix*dx:dx+ix*dx][::-1, :]
return newimg
ObservationSim/Instrument/Chip/Effects.py deleted 100644 → 0
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ObservationSim/Instrument/Chip/libBF/diffusion_X1.c deleted 100644 → 0
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#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nrutil.h"
#define ISSETBITFLAG(x,b) ((x) & (1 << (b)))
#define ADD_DIFFUSION 1
#define ADD_BF_FILTER 2
float linearInterp(float xp, float x0, float y0, float x1, float y1);
void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bit_flag)
{
int nx, ny, i,j,k,ks;
int it,jt,itt,jtt;
int diffuidx[26][2],diffuN,ilow,ih,im,dim[3];
float diffua[5][5],cdiffu[26],**bfa;
double mvar,mcov,tmp,ma,mb,mc;
char fname[100];
nx = ngx_ima; //input-image size
ny = ngy_ima;
//0. init. original image with an input array (arr_ima)
//1. Adding diffusion effect.
if(ISSETBITFLAG(bit_flag, ADD_DIFFUSION))
{
printf("adding diffusion.....\n");
printf("ERR: no diffusion filter ...");
exit(0);
}
//2. Adding BF effect
if(ISSETBITFLAG(bit_flag, ADD_BF_FILTER))
{
printf("Adding BF effect...\n");
//setup BF correlation fliter
float neX;
float neP1 = 50000;
float bfaP1[9]={0.9707182, 0.002143905, 0.004131103, 0.001149542, 0.0005501739, 0.0005469659, 0.0003726081, 0.0003795207, 0.0001633302};
float neP2 = 10000;
float bfaP2[9]={0.9945288, 0.0003041936, 0.0007539311, 0.0002424675, 0.0001226098, 0.00009308617, 0.00008027447, 0.00006309676, 0.00006400052};
bfa=matrix(-2,2,-2,2);
// smooth with the BF filter
for(i=0;i<nx;i++)for(j=0;j<ny;j++) arr_imc[j+i*ny]=0;
for(i=0;i<nx;i++)
{
for(j=0;j<ny;j++)
{
//rescale BF filter with the local pix value
neX = arr_ima[j+i*ny];
if(neX >= 10000)
{
bfa[0][0]=0; //linearInterp(neX, neP1, bfaP1[0], neP2, bfaP2[0]); //0;
bfa[0][1]=bfa[0][-1]=linearInterp(neX, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
bfa[-1][0]=bfa[1][0]=linearInterp(neX, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neX, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
bfa[0][-2]=bfa[0][2]=linearInterp(neX, neP1, bfaP1[4], neP2, bfaP2[4]);
bfa[-2][0]=bfa[2][0]=linearInterp(neX, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neX, neP1, bfaP1[6], neP2, bfaP2[6]);
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neX, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neX, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
}
else
{
neX=10000;
bfa[0][0]=0;
bfa[0][1]=bfa[0][-1]=bfaP2[1];
bfa[-1][0]=bfa[1][0]=bfaP2[2];
bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=bfaP2[3];
bfa[0][-2]=bfa[0][2]=bfaP2[4];
bfa[-2][0]=bfa[2][0]=bfaP2[5];
bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=bfaP2[6];
bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=bfaP2[7];
bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=bfaP2[8];
}
tmp = 0;
for(it=-2;it<=2;it++)
for(jt=-2;jt<=2;jt++)
{
bfa[it][jt] = bfa[it][jt]/neX*arr_ima[j+i*ny];
tmp += bfa[it][jt];
}
bfa[0][0]=1.-tmp;
// assign electrons according to the BF filter bfat
for(it=-2;it<=2;it++)
{
for(jt=-2;jt<=2;jt++)
{
itt=i+it;
jtt=j+jt;
if(itt>=0 && jtt>=0 && itt<nx && jtt<ny)
//c0[itt][jtt]+=bfa[it][jt]*b[i][j];
arr_imc[jtt+itt*ny] += bfa[it][jt]*arr_ima[j+i*ny];
}
}
}
}
free_matrix(bfa,-2,2,-2,2);
}
else
{
for(i=0;i<nx;i++) for(j=0;j<ny;j++) arr_imc[j+i*ny]=arr_ima[j+i*ny]; ////for ADD_BF False
}
}
float linearInterp(float xp, float x0, float y0, float x1, float y1)
{
float yp;
yp = y0 + ((y1-y0)/(x1-x0)) * (xp - x0);
return yp;
}
ObservationSim/Instrument/Chip/libBF/nrutil.c deleted 100644 → 0
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ObservationSim/Instrument/Chip/libBF/nrutil.h deleted 100644 → 0
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/* CAUTION: This is the ANSI C (only) version of the Numerical Recipes
utility file nrutil.h. Do not confuse this file with the same-named
file nrutil.h that may be supplied in a 'misc' subdirectory.
*That* file is the one from the book, and contains both ANSI and
traditional K&R versions, along with #ifdef macros to select the
correct version. *This* file contains only ANSI C. */
#ifndef _NR_UTILS_H_
#define _NR_UTILS_H_
static float sqrarg;
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
static double dsqrarg;
#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
static double dmaxarg1,dmaxarg2;
#define DMAX(a,b) (dmaxarg1=(a),dmaxarg2=(b),(dmaxarg1) > (dmaxarg2) ?\
(dmaxarg1) : (dmaxarg2))
static double dminarg1,dminarg2;
#define DMIN(a,b) (dminarg1=(a),dminarg2=(b),(dminarg1) < (dminarg2) ?\
(dminarg1) : (dminarg2))
static float maxarg1,maxarg2;
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?\
(maxarg1) : (maxarg2))
static float minarg1,minarg2;
#define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?\
(minarg1) : (minarg2))
static long lmaxarg1,lmaxarg2;
#define LMAX(a,b) (lmaxarg1=(a),lmaxarg2=(b),(lmaxarg1) > (lmaxarg2) ?\
(lmaxarg1) : (lmaxarg2))
static long lminarg1,lminarg2;
#define LMIN(a,b) (lminarg1=(a),lminarg2=(b),(lminarg1) < (lminarg2) ?\
(lminarg1) : (lminarg2))
static int imaxarg1,imaxarg2;
#define IMAX(a,b) (imaxarg1=(a),imaxarg2=(b),(imaxarg1) > (imaxarg2) ?\
(imaxarg1) : (imaxarg2))
static int iminarg1,iminarg2;
#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ?\
(iminarg1) : (iminarg2))
#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
void nrerror(char error_text[]);
float *vector(long nl, long nh);
int *ivector(long nl, long nh);
unsigned char *cvector(long nl, long nh);
long *lvector(long nl, long nh);
double *dvector(long nl, long nh);
float **matrix(long nrl, long nrh, long ncl, long nch);
double **dmatrix(long nrl, long nrh, long ncl, long nch);
int **imatrix(long nrl, long nrh, long ncl, long nch);
float **submatrix(float **a, long oldrl, long oldrh, long oldcl, long oldch,
long newrl, long newcl);
float **convert_matrix(float *a, long nrl, long nrh, long ncl, long nch);
float ***f3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_vector(float *v, long nl, long nh);
void free_ivector(int *v, long nl, long nh);
void free_cvector(unsigned char *v, long nl, long nh);
void free_lvector(long *v, long nl, long nh);
void free_dvector(double *v, long nl, long nh);
void free_matrix(float **m, long nrl, long nrh, long ncl, long nch);
void free_dmatrix(double **m, long nrl, long nrh, long ncl, long nch);
void free_imatrix(int **m, long nrl, long nrh, long ncl, long nch);
void free_submatrix(float **b, long nrl, long nrh, long ncl, long nch);
void free_convert_matrix(float **b, long nrl, long nrh, long ncl, long nch);
void free_f3tensor(float ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
int ***i3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_i3tensor(int ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
unsigned char ***b3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_b3tensor(unsigned char ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
double ***d3tensor(long nrl, long nrh, long ncl, long nch, long ndl, long ndh);
void free_d3tensor(double ***t, long nrl, long nrh, long ncl, long nch,
long ndl, long ndh);
char **cmatrix(long nrl, long nrh, long ncl, long nch);
void free_cmatrix(char **m, long nrl, long nrh, long ncl, long nch);
#endif /* _NR_UTILS_H_ */
ObservationSim/Instrument/Chip/libCTI/CTI_modeling.py deleted 100644 → 0
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ObservationSim/Instrument/Chip/libCTI/Makefile deleted 100755 → 0
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#include objects here:
objects = src/add_CTI1.o src/nrutil.o src/ran1.o src/ran2.o src/poidev.o src/gammln.o src/gasdev.o src/sort.o src/creattraps.o
add_CTI.so: $(objects)
gcc -shared -fPIC -std=c99 -o $@ $(objects) -lm
# general compilation rules
.SUFFIXES: .c .o
.c.o:
cc -c $< -O3 -shared -fPIC -std=c99 -o $@
.PHONY : clean
clean:
rm -f src/*.o add_CTI.so
ObservationSim/Instrument/Chip/libCTI/readme deleted 100644 → 0
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CTI_lgl_v0.3/
add_CTIfinal.c >> add_CTI.c
ObservationSim/Instrument/Chip/libCTI/src/add_CTI.c deleted 100644 → 0
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ObservationSim/Instrument/Chip/libCTI/src/creattraps.c deleted 100644 → 0
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#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "nrutil.h"
void creattraps(long *seed,int ntrap,int ny,int nmax,float c,float beta,float **sp)
{
//creat ntrap traps along one column
//sp[i][0] the number of trap in the ith pixle;
//sp[i][j] (c,1+c) the height of the jth trap in the ith pixle;
float ran1(long *idum);
void sort(unsigned long n, float arr[]);
float tmp,betare,height;
int i,nyt,ntmp,j;
float *tmpv;
tmpv = vector(1,100);
if(nmax>50){printf(" the upper limite of trap in each pixe is too large, nmax=%d\n",nmax); getchar();}
betare=1./beta;
for(i=0;i<ny;i++)sp[i][0]=0;
for(i=0;i<ntrap;i++){
nyt=ran1(seed)*ny;
sp[nyt][0]++;
}
for(i=0;i<ny;i++){
ntmp=sp[i][0];
if(ntmp==1){
height=ran1(seed)-c;
if(height<=0){sp[i][1]=0;}
else{
sp[i][1]=pow(height,betare);
}
}
if(ntmp>1){
if(ntmp>nmax)sp[i][0]=ntmp=nmax; // upper limite of trap in each pixel is nmax
for(j=1;j<=ntmp;j++)tmpv[j]=ran1(seed)-c;
sort(ntmp, tmpv);
for(j=1;j<=ntmp;j++){
height=tmpv[j];
if(height<=0){sp[i][j]=0;}
else{sp[i][j]=pow(height,betare);}
}
}
sp[i][ntmp+1]=999999;
}
free_vector(tmpv,1,100);
}
ObservationSim/Instrument/Chip/libCTI/src/gammln.c deleted 100644 → 0
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