Merge branch 'develop' into 'master'

release version 2.1.0 See merge request csst_sim/csst-simulation!17

Merge branch 'develop' into 'master'
release version 2.1.0 See merge request csst_sim/csst-simulation!17
959f0ebc · Zhang Xin · 81589f9d · f540664f · 959f0ebc · 959f0ebc
Commit 959f0ebc authored Jul 30, 2023 by Zhang Xin
--- a/ObservationSim/Straylight/data/sky/sky.dat
+++ b/ObservationSim/Straylight/data/sky/sky.dat
+2000 7.69E-22 7.94E-20 8.02E-20
+2500 1.53E-21 3.83E-19 3.84E-19
+3000 1.43E-19 1.63E-18 1.77E-18
+3500 8.33E-19 2.72E-18 3.55E-18
+4000 1.66E-18 3.12E-18 4.78E-18
+4500 2.59E-18 4.97E-18 7.57E-18
+5000 2.63E-18 5.07E-18 7.70E-18
+5500 2.55E-18 5.17E-18 7.72E-18
+6000 2.42E-18 5.14E-18 7.56E-18
+7000 1.95E-18 4.48E-18 6.42E-18
+8000 1.56E-18 3.82E-18 5.38E-18
+9000 1.23E-18 3.18E-18 4.40E-18
+10000 9.97E-19 2.70E-18 3.70E-18
+11000 8.02E-19 2.26E-18 3.06E-18
+12000 6.65E-19 1.94E-18 2.61E-18
+13000 5.58E-19 1.68E-18 2.24E-18
+14000 4.70E-19 1.46E-18 1.93E-18
+15000 3.97E-19 1.26E-18 1.66E-18
+16000 3.35E-19 1.09E-18 1.43E-18
+17000 2.79E-19 9.27E-19 1.21E-18
\ No newline at end of file
--- a/ObservationSim/MockObject/data/sky_emiss_hubble_50_50_A.dat
+++ b/ObservationSim/MockObject/data/sky_emiss_hubble_50_50_A.dat
--- a/ObservationSim/Straylight/data/sky/zodiacal.dat
+++ b/ObservationSim/Straylight/data/sky/zodiacal.dat
+2000  7.94E-20
+2500  3.83E-19
+3000  1.63E-18
+3500  2.72E-18
+4000  3.12E-18
+4500  4.97E-18
+5000  5.07E-18
+5500  5.17E-18
+6000  5.14E-18
+7000  4.48E-18
+8000  3.82E-18
+9000  3.18E-18
+10000  2.70E-18
+11000  2.26E-18
+12000  1.94E-18
+13000  1.68E-18
+14000  1.46E-18
+15000  1.26E-18
+16000  1.09E-18
+17000  9.27E-19
--- a/ObservationSim/Straylight/data/sky/zodiacal_.dat
+++ b/ObservationSim/Straylight/data/sky/zodiacal_.dat
+# A   erg/s/A/arcsec^2/cm^2
+1000 1.26e-28
+1100 1.02e-26
+1200 1.05e-25
+1400 2.5e-24
+1500 9.12e-24
+1600 2.3e-22
+1700 7.06e-21
+1800 1.5e-20
+1900 2.2e-20
+2000 3.49e-20
+2100 1.21e-19
+2200 2.16e-19
+2300 1.75e-19
+2400 1.79e-19
+2500 2.47e-19
+2600 2.93e-19
+2700 9.95e-19
+2800 2.82e-19
+2900 2.04e-18
+3000 1.2e-18
+3100 1.46e-18
+3200 2.25e-18
+3400 2.81e-18
+3500 2.73e-18
+3600 2.68e-18
+3700 3.25e-18
+3800 3.05e-18
+3900 3.27e-18
+4000 4.54e-18
+4250 4.48e-18
+4500 5.32e-18
+5000 4.92e-18
+5250 5.28e-18
+5500 5.2e-18
+5750 5.33e-18
+6000 5.11e-18
+6250 4.94e-18
+6500 4.88e-18
+6750 4.69e-18
+7000 4.4e-18
+7250 4.34e-18
+7500 4.13e-18
+7750 3.95e-18
+8000 3.85e-18
+8250 3.68e-18
+8500 3.46e-18
+8750 3.36e-18
+9000 3.23e-18
+9250 3.07e-18
+9500 2.98e-18
+9750 2.86e-18
+10000 2.78e-18
+10250 2.67e-18
+10500 2.56e-18
+10750 2.41e-18
+11000 2.31e-18
--- a/ObservationSim/Straylight/lib/BrightGaia_with_csst_mag
+++ b/ObservationSim/Straylight/lib/BrightGaia_with_csst_mag
--- a/ObservationSim/Straylight/lib/DE405
+++ b/ObservationSim/Straylight/lib/DE405
--- a/ObservationSim/Straylight/lib/PST
+++ b/ObservationSim/Straylight/lib/PST
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\ No newline at end of file
--- a/ObservationSim/Straylight/lib/R
+++ b/ObservationSim/Straylight/lib/R
--- a/ObservationSim/Straylight/lib/Zodiacal
+++ b/ObservationSim/Straylight/lib/Zodiacal
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+225.047501388876	221.834071897130	205.317724864488	176.849334282997	154.403178934298	136.681711201015	122.526540582659	112.212537983324	104.653215400233	98.4172276728472	92.4433471106159	87.1508159029366	83.3289937091939	81.3714666204164	80.0887264542075	77.8954914598142	73.2064798864838	64.4364099834633	50
+212	210	197	170	150	133	119	108.968150170540	101.799499174001	96	90.4505707007701	85.5319895790017	82	80.2295670263797	79.0725425099927	77	72.4830130455629	63.9926551958425	50
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+193.820004124204	191.992974204493	182.733799152023	158.374775391654	141.394751608534	127.177956024402	114.556469973086	104.869893480803	97.5423671128237	91.5486606096547	86.1255446666051	81.5577937981954	78.3921834737485	76.8539016661414	75.8817863624661	74.0930880533685	70.1050572294944	62.5349443814896	50
+188	186	177	154	138	125	113	103.472133032474	96.0903350126002	90	84.5712734023673	80.0733060196831	77	75.5390696543528	74.6534779457045	73	69.2354109431844	62.0164859012028	50
+183.842837044530	182.024159108189	172.344533420539	150.807353418120	135.768869174150	123.346387286385	111.525364984557	102.194863876581	95.0804127903208	89.2261952892916	83.9273482154446	79.4828215244692	76.4425184504893	75.0392867782103	74.2377524946620	72.6854861374556	69.0300582442024	61.9190393525135	50
+180.968778410604	179.564401655269	168.710041490384	148.577490076315	134.536333150083	122.310168405082	110.395727673146	101.298913319835	94.6606644919416	89.2399817403860	84.1171019637652	79.6572074513917	76.5467168402564	75.1263973841518	74.3544108040747	72.8432674378230	69.2054776231947	62.0535516979877	50
+179	178	166	147	134	122	110	101.161848147921	95.0155655993437	90	84.9567367232255	80.3383120527731	77	75.4186123665846	74.5571121154899	73	69.3317767733990	62.1369431889709	50
+177.716192339462	176.914980078633	164.212279700143	145.946781747252	133.985466739967	122.542599304634	110.686153375186	102.107114286080	96.2902104428977	91.4521554519937	86.2753467707504	81.3049172606660	77.5516836342678	75.6227629219776	74.5104734257943	72.8034337656115	69.0902625613226	61.9595784328209	50
+177.527104455602	176.712382137394	163.722331182737	146.018968006791	134.830286161505	124.136925910825	112.638397112107	104.241674217759	98.4721687469323	93.4914124288013	87.9535951873799	82.4835397260425	78.1987269430036	75.8001614550468	74.3229427532328	72.3856940471913	68.6070385465521	61.6055994609451	50
+179	178	165	148	137	127	116	107.618369565958	101.509629084266	96	89.8850372551827	83.8376297796048	79	76.1007406725702	74.2139258713895	72	68.1194074619438	61.2325926607631	50
+182.588689893918	181.204809466168	168.324866297409	152.368482555836	140.770745347464	131.186919198783	120.730021514699	112.131318192577	105.251463102523	98.8170347545853	91.9445480061505	85.3102631039541	79.9803766420691	76.6271017220435	74.3467174753257	71.8415195408390	67.8138035575069	60.9658651642528	50
+188.293174137357	186.030514239601	173.215448593483	158.383674933557	145.661040722416	136.105090914582	126.050683878426	117.039742915109	109.149274748558	101.609183359224	93.9322814719671	86.7630167892887	81.0287457580997	77.2925195138329	74.6601679460091	71.8732156326712	67.6731871518618	60.8016070816238	50
+196	192	179	165	151	141	131	121.444142789946	112.555351044031	104	95.6297114342393	88.0370932777062	82	77.9629373990224	75.0370165858846	72	67.6296500807821	60.7037292676442	50
+205.595714751532	198.636152427066	185.006773628739	171.171880621998	156.116737055362	145.117131307640	134.615982788241	124.445016873482	114.821979010604	105.613038862998	96.8183116745740	88.9736950113039	82.7490320196781	78.5042987286960	75.3600026973967	72.1267843673288	67.6152841800409	60.6361425770818	50
+216.966865661637	205.461857200499	190.564022591480	175.853739666387	160.340365763647	147.701969690105	135.936645151968	125.142864222108	115.301445669936	106.071854134304	97.2795559745780	89.4140244321794	83.1307344690420	78.7825468539377	75.5118655829902	72.1584804591610	67.5621812854119	60.5627578647043	50
+230	212	195	178	163	148	134	122.638183892218	113.346038043688	105	96.7949181158581	89.1992839824302	83	78.6636251258314	75.3753445451096	72	67.4024332326682	60.4474859852797	50
\ No newline at end of file
--- a/ObservationSim/Straylight/lib/__init__.py
+++ b/ObservationSim/Straylight/lib/__init__.py
--- a/ObservationSim/Straylight/lib/libstraylight.dylib
+++ b/ObservationSim/Straylight/lib/libstraylight.dylib
--- a/ObservationSim/Straylight/lib/libstraylight.so
+++ b/ObservationSim/Straylight/lib/libstraylight.so
--- a/ObservationSim/_util.py
+++ b/ObservationSim/_util.py
@@ -144,8 +144,8 @@ def makeSubDir_PointingList(path_dict, config, pointing_ID=0):
            pass
    return subImgdir, prefix

-def get_shear_field(config, shear_cat_file=None):
-    if not config["shear_setting"]["shear_type"] in ["constant", "extra", "catalog"]:
+def get_shear_field(config):
+    if not config["shear_setting"]["shear_type"] in ["constant", "catalog"]:
        raise ValueError("Please set a right 'shear_method' parameter.")

    if config["shear_setting"]["shear_type"] == "constant":
@@ -153,18 +153,6 @@ def get_shear_field(config, shear_cat_file=None):
        g2 = config["shear_setting"]["reduced_g2"]
        nshear = 1
        # TODO logging
-    elif config["shear_setting"]["shear_type"] == "extra":
-        # TODO logging
-        if not os.path.exists(shear_cat_file):
-            raise ValueError("Cannot find external shear catalog file.")
-        try:
-            shearCat = np.loadtxt(shear_cat_file)
-            nshear = shearCat.shape[0]
-            g1, g2 = shearCat[:, 0], shearCat[:, 1]
-        except:
-            print("Failed to read the shear catalog file.")
-            print("Setting to no shear.")
-            g1, g2 = 0., 0.
    else:
        g1, g2 = 0., 0.
        nshear = 0

--- a/README.md
+++ b/README.md
 # CSST主巡天仿真软件

 ## 重要更新或问题修复：
-
+* 2023.07.29: 更新至v2.1版本，内容包括：
+    * 加入杂散光模块，config文件中添加开关：enable_straylight_model: True/False
+    * 调整WCS定义：x：E, y：-N
+    * 头文件关键字调整
+    * 适配C6-50平方度仿真星表
+    * Bug修复：修复像场畸变导致形变的方向错误等bug
 * 2023.05.01: 更新至v2.0版本，新功能包含：
    * C6仿真实现
    * fits贴图功能
@@ -11,7 +16,7 @@
    * 导星探测器仿真
    * 仪器参数更新，bug修复等
 * 2022.08.23: 更新至最新的透过率曲线，在图像头文件中加入版本号。仿真软件版本号进行重新标记，当前版本为1.0.4
-* 2022.06.20: 版本v0.5上线，请于release_v0.5 branch中进行clone操作(注：目前已重新设置为v1.0，release_v1.0.0)
+* 2022.06.20: 版本v0.5上线，release_v0.5 branch(注：目前已重新设置为v1.0，release_v1.0.0)
 * 2022.04.13: 修复了天测模块中的调用错误
 * 2022.04.08: 修复了仅输出星表选项("out_cat_only")存在的问题


--- a/config/config_50sqdeg.yaml
+++ b/config/config_50sqdeg.yaml
+---
+###############################################
+#
+#  Configuration file for CSST simulation
+#  CSST-Sim Group, 2023/04/25
+#
+###############################################
+
+# Base diretories and naming setup
+# Can add some of the command-line arguments here as well;
+# OK to pass either way or both, as long as they are consistent
+work_dir: "/share/home/fangyuedong/csst-simulation/workplace/"
+data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
+run_name: "rotate_0"
+
+# Whether to use MPI
+run_option:
+  use_mpi: NO
+  # NOTE: "n_threads" paramters is currently not used in the backend
+  # simulation codes. It should be implemented later in the web frontend
+  # in order to config the number of threads to request from NAOC cluster
+  n_threads: 80
+
+  # Output catalog only?
+  # If yes, no imaging simulation will run
+  out_cat_only: NO
+
+###############################################
+# Catalog setting
+###############################################
+# Configure your catalog: options to be implemented 
+# in the corresponding (user defined) 'Catalog' class
+catalog_options:
+  input_path:
+    cat_dir: ""
+    # star_cat: "C6_MMW_GGC_Astrometry_healpix.hdf5"
+    star_cat: "starcat/"
+    galaxy_cat: "qsocat/cat2CSSTSim_bundle-50sqDeg/"
+    # AGN_cat: "AGN_C6_ross13_rand_pos_rmax-1.3.fits"
+
+  SED_templates_path:
+    star_SED: "Catalog_20210126/SpecLib.hdf5"
+    galaxy_SED: "Catalog_C6_20221212/sedlibs/"
+    AGN_SED: "qsocat/qsosed/"
+    # AGN_SED_WAVE: "wave_ross13.npy"
+
+  # Only simulate stars?
+  star_only: NO
+
+  # Only simulate galaxies?
+  galaxy_only: YES
+
+  # rotate galaxy ellipticity
+  rotateEll: 0. # [degree]
+
+  seed_Av: 121212    # Seed for generating random intrinsic extinction
+
+###############################################
+# Observation setting
+###############################################
+obs_setting:
+
+  # Options for survey types:
+  # "Photometric": simulate photometric chips only
+  # "Spectroscopic": simulate slitless spectroscopic chips only
+  # "FGS": simulate FGS chips only (31-42)
+  # "All": simulate full focal plane
+  survey_type: "Photometric"
+  
+  # Exposure time [seconds]
+  exp_time: 150.
+
+  # Observation starting date & time
+  date_obs: "210525" # [yymmdd]
+  time_obs: "120000" # [hhmmss]
+
+  # Default Pointing [degrees]
+  # Note: NOT valid when a pointing list file is specified
+  ra_center: 192.8595
+  dec_center:  27.1283
+  # Image rotation [degree]
+  image_rot: -113.4333
+
+  # (Optional) a file of point list 
+  # if you just want to run default pointing:
+  # - pointing_dir: null
+  # - pointing_file: null
+  pointing_dir: "/share/home/fangyuedong/50sqdeg_pointings/"
+  pointing_file: "pointing_50_combined.dat"
+
+  # Number of calibration pointings
+  np_cal: 0
+
+  # Run specific pointing(s):
+  # - give a list of indexes of pointings: [ip_1, ip_2...]
+  # - run all pointings: null
+  # Note: only valid when a pointing list is specified
+  run_pointings: [0]
+  
+  # Run specific chip(s):
+  # - give a list of indexes of chips: [ip_1, ip_2...]
+  # - run all chips: null
+  # Note: for all pointings
+  run_chips: [8]
+
+  # Whether to enable astrometric modeling
+  enable_astrometric_model: True
+
+  # Whether to enable straylight model
+  enable_straylight_model: True
+
+  # Cut by saturation magnitude in which band?
+  cut_in_band: "z"
+
+  # saturation magnitude margin
+  mag_sat_margin: -2.5
+
+  # limiting magnitude margin
+  mag_lim_margin: +1.0
+
+###############################################
+# PSF setting
+###############################################
+psf_setting:
+  
+  # Which PSF model to use:
+  # "Gauss": simple gaussian profile
+  # "Interp": Interpolated PSF from sampled ray-tracing data
+  psf_model: "Interp"
+
+  # PSF size [arcseconds]
+  # radius of 80% energy encircled
+  # NOTE: only valid for "Gauss" PSF
+  psf_rcont: 0.15
+
+  # path to PSF data
+  # NOTE: only valid for "Interp" PSF
+  psf_dir: "/share/simudata/CSSOSDataProductsSims/data/psfCube1"
+
+###############################################
+# Shear setting
+###############################################
+
+shear_setting:
+  # Options to generate mock shear field:
+  # "constant": all galaxies are assigned a constant reduced shear
+  # "catalog": from catalog
+  shear_type: "catalog"
+
+  # For constant shear filed
+  reduced_g1: 0.
+  reduced_g2: 0.
+
+###############################################
+# Instrumental effects setting
+###############################################
+ins_effects:
+  # switches
+  # Note: bias_16channel, gain_16channel, and shutter_effect
+  # is currently not applicable to "FGS" observations
+  field_dist:     ON  # Whether to add field distortions
+  add_back:       ON  # Whether to add sky background
+  add_dark:       ON  # Whether to add dark noise
+  add_readout:    ON  # Whether to add read-out (Gaussian) noise
+  add_bias:       ON  # Whether to add bias-level to images
+  bias_16channel: ON  # Whether to add different biases for 16 channels
+  gain_16channel: ON  # Whether to make different gains for 16 channels
+  shutter_effect: ON  # Whether to add shutter effect
+  flat_fielding:  ON  # Whether to add flat-fielding effect
+  prnu_effect:    ON  # Whether to add PRNU effect
+  non_linear:     ON  # Whether to add non-linearity
+  cosmic_ray:     ON  # Whether to add cosmic-ray
+  cray_differ:    ON  # Whether to generate different cosmic ray maps CAL and MS output
+  cte_trail:      ON  # Whether to simulate CTE trails
+  saturbloom:     ON  # Whether to simulate Saturation & Blooming
+  add_badcolumns: ON  # Whether to add bad columns
+  add_hotpixels:  ON  # Whether to add hot pixels
+  add_deadpixels: ON  # Whether to add dead(dark) pixels
+  bright_fatter:  ON  # Whether to simulate Brighter-Fatter (also diffusion) effect
+
+  # Values: 
+  # default values have been defined individually for each chip in:
+  # ObservationSim/Instrument/data/ccd/chip_definition.json
+  # Set them here will override the default values
+  # dark_exptime:   300   # Exposure time for dark current frames [seconds]
+  # flat_exptime:   150   # Exposure time for flat-fielding frames [seconds]
+  # readout_time:   40    # The read-out time for each channel [seconds]
+  # df_strength:    2.3   # Sillicon sensor diffusion strength
+  # bias_level:     500   # bias level [e-/pixel]
+  # gain:           1.1   # Gain
+  # full_well:      90000 # Full well depth [e-]
+
+###############################################
+# Output options (for calibration pointings only)
+###############################################
+output_setting:
+  readout16:      OFF # Whether to export as 16 channels (subimages) with pre- and over-scan
+  shutter_output: OFF # Whether to export shutter effect 16-bit image
+  bias_output:    ON  # Whether to export bias frames
+  dark_output:    ON  # Whether to export the combined dark current files
+  flat_output:    ON  # Whether to export the combined flat-fielding files
+  prnu_output:    OFF # Whether to export the PRNU (pixel-to-pixel flat-fielding) files
+  NBias:          1     # Number of bias frames to be exported for each exposure
+  NDark:          1     # Number of dark frames to be exported for each exposure
+  NFlat:          1     # Number of flat frames to be exported for each exposure
+
+###############################################
+# Random seeds
+###############################################
+random_seeds:
+  seed_poisson:         20210601  # Seed for Poisson noise
+  seed_CR:              20210317  # Seed for generating random cosmic ray maps
+  seed_flat:            20210101  # Seed for generating random flat fields
+  seed_prnu:            20210102  # Seed for photo-response non-uniformity
+  seed_gainNonUniform:  20210202  # Seed for gain nonuniformity
+  seed_biasNonUniform:  20210203  # Seed for bias nonuniformity
+  seed_rnNonUniform:    20210204  # Seed for readout-noise nonuniformity
+  seed_badcolumns:      20240309  # Seed for bad columns
+  seed_defective:       20210304  # Seed for defective (bad) pixels
+  seed_readout:         20210601  # Seed for read-out gaussian noise
+...
\ No newline at end of file
--- a/config/config_C6.yaml
+++ b/config/config_C6.yaml
@@ -9,13 +9,13 @@
 # Base diretories and naming setup
 # Can add some of the command-line arguments here as well;
 # OK to pass either way or both, as long as they are consistent
-work_dir: "/share/home/fangyuedong/fgs_sim/csst-simulation/workplace/"
+work_dir: "/share/home/fangyuedong/csst-simulation/workplace/"
 data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
-run_name: "C6_spectroscopic_20230225"
+run_name: "profile_C6"

 # Whether to use MPI
 run_option:
-  use_mpi: YES
+  use_mpi: NO
  # NOTE: "n_threads" paramters is currently not used in the backend
  # simulation codes. It should be implemented later in the web frontend
  # in order to config the number of threads to request from NAOC cluster
@@ -100,11 +100,14 @@ obs_setting:
  # - give a list of indexes of chips: [ip_1, ip_2...]
  # - run all chips: null
  # Note: for all pointings
-  run_chips: [24]
+  run_chips: [8]

  # Whether to enable astrometric modeling
  enable_astrometric_model: True

+  # Whether to enable straylight model
+  enable_straylight_model: True
+
  # Cut by saturation magnitude in which band?
  cut_in_band: "z"

@@ -141,17 +144,12 @@ shear_setting:
  # Options to generate mock shear field:
  # "constant": all galaxies are assigned a constant reduced shear
  # "catalog": from catalog
-  # "extra": from seprate file
  shear_type: "catalog"

  # For constant shear filed
  reduced_g1: 0.
  reduced_g2: 0.

-  # Extra shear catalog
-  # (currently not used)
-  # shear_cat: "mockShear.cat"
-
 ###############################################
 # Instrumental effects setting
 ###############################################
@@ -159,25 +157,25 @@ ins_effects:
  # switches
  # Note: bias_16channel, gain_16channel, and shutter_effect
  # is currently not applicable to "FGS" observations
-  field_dist:     ON  # Whether to add field distortions
-  add_back:       ON  # Whether to add sky background
-  add_dark:       ON  # Whether to add dark noise
-  add_readout:    ON  # Whether to add read-out (Gaussian) noise
-  add_bias:       ON  # Whether to add bias-level to images
-  bias_16channel: ON  # Whether to add different biases for 16 channels
-  gain_16channel: ON  # Whether to make different gains for 16 channels
-  shutter_effect: ON  # Whether to add shutter effect
-  flat_fielding:  ON  # Whether to add flat-fielding effect
-  prnu_effect:    ON  # Whether to add PRNU effect
-  non_linear:     ON  # Whether to add non-linearity
-  cosmic_ray:     ON  # Whether to add cosmic-ray
-  cray_differ:    ON  # Whether to generate different cosmic ray maps CAL and MS output
-  cte_trail:      ON  # Whether to simulate CTE trails
-  saturbloom:     ON  # Whether to simulate Saturation & Blooming
-  add_badcolumns: ON  # Whether to add bad columns
-  add_hotpixels:  ON  # Whether to add hot pixels
-  add_deadpixels: ON  # Whether to add dead(dark) pixels
-  bright_fatter:  ON  # Whether to simulate Brighter-Fatter (also diffusion) effect
+  field_dist:     YES  # Whether to add field distortions
+  add_back:       YES  # Whether to add sky background
+  add_dark:       YES  # Whether to add dark noise
+  add_readout:    YES  # Whether to add read-out (Gaussian) noise
+  add_bias:       YES  # Whether to add bias-level to images
+  bias_16channel: YES  # Whether to add different biases for 16 channels
+  gain_16channel: YES  # Whether to make different gains for 16 channels
+  shutter_effect: YES  # Whether to add shutter effect
+  flat_fielding:  YES  # Whether to add flat-fielding effect
+  prnu_effect:    YES  # Whether to add PRNU effect
+  non_linear:     YES  # Whether to add non-linearity
+  cosmic_ray:     YES  # Whether to add cosmic-ray
+  cray_differ:    YES  # Whether to generate different cosmic ray maps CAL and MS output
+  cte_trail:      YES  # Whether to simulate CTE trails
+  saturbloom:     YES  # Whether to simulate Saturation & Blooming
+  add_badcolumns: YES  # Whether to add bad columns
+  add_hotpixels:  YES  # Whether to add hot pixels
+  add_deadpixels: YES  # Whether to add dead(dark) pixels
+  bright_fatter:  YES  # Whether to simulate Brighter-Fatter (also diffusion) effect

  # Values: 
  # default values have been defined individually for each chip in:

--- a/config/config_C6_fits.yaml
+++ b/config/config_C6_fits.yaml
@@ -147,17 +147,12 @@ shear_setting:
  # Options to generate mock shear field:
  # "constant": all galaxies are assigned a constant reduced shear
  # "catalog": from catalog
-  # "extra": from seprate file
  shear_type: "catalog"

  # For constant shear filed
  reduced_g1: 0.
  reduced_g2: 0.

-  # Extra shear catalog
-  # (currently not used)
-  # shear_cat: "mockShear.cat"
-
 ###############################################
 # Instrumental effects setting
 ###############################################

--- a/config/config_C6_test_wcs.yaml
+++ b/config/config_C6_test_wcs.yaml
+---
+###############################################
+#
+#  Configuration file for CSST simulation
+#  CSST-Sim Group, 2023/04/25
+#
+###############################################
+
+# Base diretories and naming setup
+# Can add some of the command-line arguments here as well;
+# OK to pass either way or both, as long as they are consistent
+work_dir: "/share/home/fangyuedong/csst-simulation/workplace/"
+data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
+run_name: "fd_shear_g2m"
+
+# Whether to use MPI
+run_option:
+  use_mpi: YES
+  # NOTE: "n_threads" paramters is currently not used in the backend
+  # simulation codes. It should be implemented later in the web frontend
+  # in order to config the number of threads to request from NAOC cluster
+  n_threads: 80
+
+  # Output catalog only?
+  # If yes, no imaging simulation will run
+  out_cat_only: NO
+
+###############################################
+# Catalog setting
+###############################################
+# Configure your catalog: options to be implemented 
+# in the corresponding (user defined) 'Catalog' class
+catalog_options:
+  input_path:
+    cat_dir: "Catalog_C6_20221212"
+    star_cat: "C6_MMW_GGC_Astrometry_healpix.hdf5"
+    galaxy_cat: "cat2CSSTSim_bundle/"
+    AGN_cat: "AGN_C6_ross13_rand_pos_rmax-1.3.fits"
+
+  SED_templates_path:
+    star_SED: "Catalog_20210126/SpecLib.hdf5"
+    galaxy_SED: "Catalog_C6_20221212/sedlibs/"
+    AGN_SED: "quickspeclib_ross13.fits"
+    AGN_SED_WAVE: "wave_ross13.npy"
+
+  # Only simulate stars?
+  star_only: NO
+
+  # Only simulate galaxies?
+  galaxy_only: YES
+
+  # rotate galaxy ellipticity
+  rotateEll: 0. # [degree]
+
+  seed_Av: 121212    # Seed for generating random intrinsic extinction
+
+###############################################
+# Observation setting
+###############################################
+obs_setting:
+
+  # Options for survey types:
+  # "Photometric": simulate photometric chips only
+  # "Spectroscopic": simulate slitless spectroscopic chips only
+  # "FGS": simulate FGS chips only (31-42)
+  # "All": simulate full focal plane
+  survey_type: "All"
+  
+  # Exposure time [seconds]
+  exp_time: 150.
+
+  # Observation starting date & time
+  date_obs: "210525" # [yymmdd]
+  time_obs: "120000" # [hhmmss]
+
+  # Default Pointing [degrees]
+  # Note: NOT valid when a pointing list file is specified
+  ra_center: 192.8595
+  dec_center:  27.1283
+  # Image rotation [degree]
+  image_rot: -113.4333
+
+  # (Optional) a file of point list 
+  # if you just want to run default pointing:
+  # - pointing_dir: null
+  # - pointing_file: null
+  pointing_dir: "/share/simudata/CSSOSDataProductsSims/data/"
+  pointing_file: "pointing_radec_246.5_40.dat"
+
+  # Number of calibration pointings
+  np_cal: 0
+
+  # Run specific pointing(s):
+  # - give a list of indexes of pointings: [ip_1, ip_2...]
+  # - run all pointings: null
+  # Note: only valid when a pointing list is specified
+  run_pointings: [0]
+  
+  # Run specific chip(s):
+  # - give a list of indexes of chips: [ip_1, ip_2...]
+  # - run all chips: null
+  # Note: for all pointings
+  run_chips: [9]
+
+  # Whether to enable astrometric modeling
+  enable_astrometric_model: False
+
+  # Whether to enable straylight model
+  enable_straylight_model: False
+
+  # Cut by saturation magnitude in which band?
+  cut_in_band: "z"
+
+  # saturation magnitude margin
+  mag_sat_margin: -2.5
+
+  # limiting magnitude margin
+  mag_lim_margin: +1.0
+
+###############################################
+# PSF setting
+###############################################
+psf_setting:
+  
+  # Which PSF model to use:
+  # "Gauss": simple gaussian profile
+  # "Interp": Interpolated PSF from sampled ray-tracing data
+  psf_model: "Interp"
+
+  # PSF size [arcseconds]
+  # radius of 80% energy encircled
+  # NOTE: only valid for "Gauss" PSF
+  psf_rcont: 0.15
+
+  # path to PSF data
+  # NOTE: only valid for "Interp" PSF
+  psf_dir: "/share/simudata/CSSOSDataProductsSims/data/psfCube1"
+
+###############################################
+# Shear setting
+###############################################
+
+shear_setting:
+  # Options to generate mock shear field:
+  # "constant": all galaxies are assigned a constant reduced shear
+  # "catalog": from catalog
+  shear_type: "catalog"
+
+  # For constant shear filed
+  reduced_g1: 0.
+  reduced_g2: 0.
+
+###############################################
+# Instrumental effects setting
+###############################################
+ins_effects:
+  # switches
+  # Note: bias_16channel, gain_16channel, and shutter_effect
+  # is currently not applicable to "FGS" observations
+  field_dist:     YES  # Whether to add field distortions
+  add_back:       YES  # Whether to add sky background
+  add_dark:       YES  # Whether to add dark noise
+  add_readout:    YES  # Whether to add read-out (Gaussian) noise
+  add_bias:       YES  # Whether to add bias-level to images
+  bias_16channel: OFF  # Whether to add different biases for 16 channels
+  gain_16channel: OFF  # Whether to make different gains for 16 channels
+  shutter_effect: OFF  # Whether to add shutter effect
+  flat_fielding:  OFF  # Whether to add flat-fielding effect
+  prnu_effect:    OFF  # Whether to add PRNU effect
+  non_linear:     OFF  # Whether to add non-linearity
+  cosmic_ray:     OFF  # Whether to add cosmic-ray
+  cray_differ:    OFF  # Whether to generate different cosmic ray maps CAL and MS output
+  cte_trail:      OFF  # Whether to simulate CTE trails
+  saturbloom:     OFF  # Whether to simulate Saturation & Blooming
+  add_badcolumns: OFF  # Whether to add bad columns
+  add_hotpixels:  OFF  # Whether to add hot pixels
+  add_deadpixels: OFF  # Whether to add dead(dark) pixels
+  bright_fatter:  OFF  # Whether to simulate Brighter-Fatter (also diffusion) effect
+
+  # Values: 
+  # default values have been defined individually for each chip in:
+  # ObservationSim/Instrument/data/ccd/chip_definition.json
+  # Set them here will override the default values
+  # dark_exptime:   300   # Exposure time for dark current frames [seconds]
+  # flat_exptime:   150   # Exposure time for flat-fielding frames [seconds]
+  # readout_time:   40    # The read-out time for each channel [seconds]
+  # df_strength:    2.3   # Sillicon sensor diffusion strength
+  # bias_level:     500   # bias level [e-/pixel]
+  # gain:           1.1   # Gain
+  # full_well:      90000 # Full well depth [e-]
+
+###############################################
+# Output options (for calibration pointings only)
+###############################################
+output_setting:
+  readout16:      OFF # Whether to export as 16 channels (subimages) with pre- and over-scan
+  shutter_output: OFF # Whether to export shutter effect 16-bit image
+  bias_output:    ON  # Whether to export bias frames
+  dark_output:    ON  # Whether to export the combined dark current files
+  flat_output:    ON  # Whether to export the combined flat-fielding files
+  prnu_output:    OFF # Whether to export the PRNU (pixel-to-pixel flat-fielding) files
+  NBias:          1     # Number of bias frames to be exported for each exposure
+  NDark:          1     # Number of dark frames to be exported for each exposure
+  NFlat:          1     # Number of flat frames to be exported for each exposure
+
+###############################################
+# Random seeds
+###############################################
+random_seeds:
+  seed_poisson:         20210601  # Seed for Poisson noise
+  seed_CR:              20210317  # Seed for generating random cosmic ray maps
+  seed_flat:            20210101  # Seed for generating random flat fields
+  seed_prnu:            20210102  # Seed for photo-response non-uniformity
+  seed_gainNonUniform:  20210202  # Seed for gain nonuniformity
+  seed_biasNonUniform:  20210203  # Seed for bias nonuniformity
+  seed_rnNonUniform:    20210204  # Seed for readout-noise nonuniformity
+  seed_badcolumns:      20240309  # Seed for bad columns
+  seed_defective:       20210304  # Seed for defective (bad) pixels
+  seed_readout:         20210601  # Seed for read-out gaussian noise
+...
\ No newline at end of file
--- a/config/config_NGP.yaml
+++ b/config/config_NGP.yaml
@@ -138,17 +138,12 @@ shear_setting:
  # Options to generate mock shear field:
  # "constant": all galaxies are assigned a constant reduced shear
  # "catalog": from catalog
-  # "extra": from seprate file
  shear_type: "constant"

  # For constant shear filed
  reduced_g1: 0.026
  reduced_g2: 0.015

-  # Extra shear catalog
-  # (currently not used)
-  # shear_cat: "mockShear.cat"
-
 ###############################################
 # Instrumental effects setting
 ###############################################

--- a/config/config_example.yaml
+++ b/config/config_example.yaml
@@ -131,17 +131,12 @@ shear_setting:
  # Options to generate mock shear field:
  # "constant": all galaxies are assigned a constant reduced shear
  # "catalog": from catalog
-  # "extra": from seprate file
  shear_type: "constant"

  # For constant shear filed
  reduced_g1: 0.026
  reduced_g2: 0.015

-  # Extra shear catalog
-  # (currently not used)
-  # shear_cat: "mockShear.cat"
-
 ###############################################
 # Instrumental effects setting
 ###############################################