update calibration in Chip.py

ObservationSim/Instrument/Chip/Chip.py

@@ -529,12 +529,26 @@ class Chip(FocalPlane):
                         print("  Applying Non-Linearity on the Bias image", flush=True)
                     BiasCombImg = effects.NonLinearity(GSImage=BiasCombImg, beta1=5.e-7, beta2=0)
 
+                ###########################START
+                ### prescan & overscan
+                if config["ins_effects"]["add_prescan"] == True:
+                    chip_utils.log_info(msg="  Apply pre/over-scan", logger=self.logger)
+                    BiasCombImg = chip_utils.AddPreScan(GSImage=BiasCombImg, pre1=pre1, pre2=pre2, over1=over1, over2=over2)
+
+                ### 1*16 output
+                if config["ins_effects"]["format_output"] == True:
+                    chip_utils.log_info(msg="  Apply 1*16 format", logger=self.logger)
+                    BiasCombImg = chip_utils.formatOutput(GSImage=BiasCombImg)
+                    self.nsecy = 1
+                    self.nsecx = 16
+                ###########################END
+
                 # Apply Bad lines 
                 if config["ins_effects"]["add_badcolumns"] == True:
                     BiasCombImg = effects.BadColumns(BiasCombImg-float(self.bias_level)+5, seed=SeedBadColumns, chipid=self.chipID, logger=self.logger) + float(self.bias_level)-5
 
                 BiasCombImg, self.gain_channel = effects.ApplyGainNonUniform16(BiasCombImg, gain=self.gain,
-                    nsecy = 2, nsecx=8, 
+                    nsecy = self.nsecy, nsecx=self.nsecx, 
                     seed=SeedGainNonuni+self.chipID,
                     logger=self.logger)
                 # BiasCombImg = effects.AddOverscan(
@@ -606,8 +620,61 @@ class Chip(FocalPlane):
                         print("  Applying Non-Linearity on the Flat image", flush=True)
                     FlatCombImg = effects.NonLinearity(GSImage=FlatCombImg, beta1=5.e-7, beta2=0)
 
+                ###if config["ins_effects"]["cte_trail"] == True:
+                ###    FlatCombImg = effects.CTE_Effect(GSImage=FlatCombImg, threshold=3)
+                ###########################START
+                pre1 = self.prescan_x  #27
+                over1= self.overscan_x #71
+                pre2 = self.prescan_y  #0 #4
+                over2= self.overscan_y #84 #80
                 if config["ins_effects"]["cte_trail"] == True:
-                    FlatCombImg = effects.CTE_Effect(GSImage=FlatCombImg, threshold=3)
+                    chip_utils.log_info(msg="  Apply CTE Effect", logger=self.logger)
+                    ###img = effects.CTE_Effect(GSImage=img, threshold=27)
+                    ###CTI_modeling
+                    ### 2*8 -> 1*16 img-layout
+                    FlatCombImg = chip_utils.formatOutput(GSImage=FlatCombImg)
+                    self.nsecy = 1
+                    self.nsecx = 16
+
+                    img_arr = FlatCombImg.array
+                    ny, nx = img_arr.shape
+                    dx = int(nx/self.nsecx)
+                    dy = int(ny/self.nsecy)
+                    newimg = galsim.Image(nx, int(ny+over2), init_value=0)
+                    for ichannel in range(16):
+                        print('\n***add CTI effects: pointing-{:} chip-{:} channel-{:}***'.format(pointing_ID, self.chipID, ichannel+1))
+                        #nx,ny,noverscan,nsp,nmax = 4608,4616,84,3,10
+                        noverscan,nsp,nmax = over2,3,10
+                        beta,w,c = 0.478,84700,0
+                        t = np.array([0.74,7.7,37],dtype=np.float32)
+                        rho_trap = np.array([0.6,1.6,1.4],dtype=np.float32)
+                        trap_seeds = np.array([0,1000,10000],dtype=np.int32) + ichannel + self.chipID*16
+                        release_seed = 50 + ichannel + pointing_ID*30  + self.chipID*16
+                        newimg.array[:, 0+ichannel*dx:dx+ichannel*dx] = CTI_sim(img_arr[:, 0+ichannel*dx:dx+ichannel*dx],dx,dy,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)
+                    newimg.wcs = FlatCombImg.wcs
+                    del FlatCombImg
+                    FlatCombImg = newimg
+
+                    ### 1*16 -> 2*8 img-layout
+                    img = chip_utils.formatRevert(GSImage=FlatCombImg)
+                    self.nsecy = 2
+                    self.nsecx = 8
+
+                ### prescan & overscan
+                if config["ins_effects"]["add_prescan"] == True:
+                    chip_utils.log_info(msg="  Apply pre/over-scan", logger=self.logger)
+                    if config["ins_effects"]["cte_trail"] == False:
+                        FlatCombImg = chip_utils.AddPreScan(GSImage=FlatCombImg, pre1=pre1, pre2=pre2, over1=over1, over2=over2)
+                    if config["ins_effects"]["cte_trail"] == True:
+                        FlatCombImg = chip_utils.AddPreScan(GSImage=FlatCombImg, pre1=pre1, pre2=pre2, over1=over1, over2=0)
+
+                ### 1*16 output
+                if config["ins_effects"]["format_output"] == True:
+                    chip_utils.log_info(msg="  Apply 1*16 format", logger=self.logger)
+                    FlatCombImg = chip_utils.formatOutput(GSImage=FlatCombImg)
+                    self.nsecy = 1
+                    self.nsecx = 16
+                ###########################END
 
                 # Add Hot Pixels or/and Dead Pixels
                 rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))
@@ -627,7 +694,7 @@ class Chip(FocalPlane):
                     # img += float(config["ins_effects"]["bias_level"])
                     FlatCombImg = effects.AddBiasNonUniform16(FlatCombImg, 
                         bias_level=biaslevel, 
-                        nsecy = 2, nsecx=8, 
+                        nsecy = self.nsecy, nsecx=self.nsecx, 
                         seed=SeedBiasNonuni+self.chipID,
                         logger=self.logger)
                 
@@ -639,7 +706,7 @@ class Chip(FocalPlane):
                     FlatCombImg.addNoise(readout_noise)
 
                 FlatCombImg, self.gain_channel = effects.ApplyGainNonUniform16(FlatCombImg, gain=self.gain,
-                    nsecy = 2, nsecx=8, 
+                    nsecy = self.nsecy, nsecx=self.nsecx, 
                     seed=SeedGainNonuni+self.chipID,
                     logger=self.logger)
                 # FlatCombImg = effects.AddOverscan(FlatCombImg, overscan=overscan, gain=self.gain, widthl=27, widthr=27, widtht=8, widthb=8)
@@ -702,6 +769,19 @@ class Chip(FocalPlane):
                     cr_map[cr_map < 0] = 0
                     crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
                     del cr_map
+                    ###########################START
+                    ### prescan & overscan
+                    if config["ins_effects"]["add_prescan"] == True:
+                        chip_utils.log_info(msg="  Apply pre/over-scan", logger=self.logger)
+                        crmap_gsimg = chip_utils.AddPreScan(GSImage=crmap_gsimg, pre1=pre1, pre2=pre2, over1=over1, over2=over2)
+
+                    ### 1*16 output
+                    if config["ins_effects"]["format_output"] == True:
+                        chip_utils.log_info(msg="  Apply 1*16 format", logger=self.logger)
+                        crmap_gsimg = chip_utils.formatOutput(GSImage=crmap_gsimg)
+                        self.nsecy = 1
+                        self.nsecx = 16
+                    ###########################END
                     chip_utils.outputCal(
                         chip=self,
                         img=crmap_gsimg,
@@ -725,8 +805,61 @@ class Chip(FocalPlane):
                         print("  Applying Non-Linearity on the Dark image", flush=True)
                     DarkCombImg = effects.NonLinearity(GSImage=DarkCombImg, beta1=5.e-7, beta2=0)
 
+                ###if config["ins_effects"]["cte_trail"] == True:
+                ###    DarkCombImg = effects.CTE_Effect(GSImage=DarkCombImg, threshold=3)
+                ###########################START
+                pre1 = self.prescan_x  #27
+                over1= self.overscan_x #71
+                pre2 = self.prescan_y  #0 #4
+                over2= self.overscan_y #84 #80
+                if config["ins_effects"]["cte_trail"] == True:
+                    chip_utils.log_info(msg="  Apply CTE Effect", logger=self.logger)
+                    ###img = effects.CTE_Effect(GSImage=img, threshold=27)
+                    ###CTI_modeling
+                    ### 2*8 -> 1*16 img-layout
+                    DarkCombImg = chip_utils.formatOutput(GSImage=DarkCombImg)
+                    self.nsecy = 1
+                    self.nsecx = 16
+
+                    img_arr = DarkCombImg.array
+                    ny, nx = img_arr.shape
+                    dx = int(nx/self.nsecx)
+                    dy = int(ny/self.nsecy)
+                    newimg = galsim.Image(nx, int(ny+over2), init_value=0)
+                    for ichannel in range(16):
+                        print('\n***add CTI effects: pointing-{:} chip-{:} channel-{:}***'.format(pointing_ID, self.chipID, ichannel+1))
+                        #nx,ny,noverscan,nsp,nmax = 4608,4616,84,3,10
+                        noverscan,nsp,nmax = over2,3,10
+                        beta,w,c = 0.478,84700,0
+                        t = np.array([0.74,7.7,37],dtype=np.float32)
+                        rho_trap = np.array([0.6,1.6,1.4],dtype=np.float32)
+                        trap_seeds = np.array([0,1000,10000],dtype=np.int32) + ichannel + self.chipID*16
+                        release_seed = 50 + ichannel + pointing_ID*30  + self.chipID*16
+                        newimg.array[:, 0+ichannel*dx:dx+ichannel*dx] = CTI_sim(img_arr[:, 0+ichannel*dx:dx+ichannel*dx],dx,dy,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)
+                    newimg.wcs = DarkCombImg.wcs
+                    del DarkCombImg
+                    DarkCombImg = newimg
+
+                    ### 1*16 -> 2*8 img-layout
+                    DarkCombImg = chip_utils.formatRevert(GSImage=DarkCombImg)
+                    self.nsecy = 2
+                    self.nsecx = 8
+
+                ### prescan & overscan
+                if config["ins_effects"]["add_prescan"] == True:
+                    chip_utils.log_info(msg="  Apply pre/over-scan", logger=self.logger)
+                    if config["ins_effects"]["cte_trail"] == False:
+                        DarkCombImg = chip_utils.AddPreScan(GSImage=DarkCombImg, pre1=pre1, pre2=pre2, over1=over1, over2=over2)
                     if config["ins_effects"]["cte_trail"] == True:
-                    DarkCombImg = effects.CTE_Effect(GSImage=DarkCombImg, threshold=3)
+                        DarkCombImg = chip_utils.AddPreScan(GSImage=DarkCombImg, pre1=pre1, pre2=pre2, over1=over1, over2=0)
+
+                ### 1*16 output
+                if config["ins_effects"]["format_output"] == True:
+                    chip_utils.log_info(msg="  Apply 1*16 format", logger=self.logger)
+                    DarkCombImg = chip_utils.formatOutput(GSImage=DarkCombImg)
+                    self.nsecy = 1
+                    self.nsecx = 16
+                ###########################END
 
                 # Add Hot Pixels or/and Dead Pixels
                 rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))
@@ -746,7 +879,7 @@ class Chip(FocalPlane):
                     # img += float(config["ins_effects"]["bias_level"])
                     DarkCombImg = effects.AddBiasNonUniform16(DarkCombImg, 
                         bias_level=biaslevel, 
-                        nsecy = 2, nsecx=8, 
+                        nsecy = self.nsecy, nsecx=self.nsecx, 
                         seed=SeedBiasNonuni+self.chipID,
                         logger=self.logger)
 
@@ -759,7 +892,7 @@ class Chip(FocalPlane):
 
                 DarkCombImg, self.gain_channel = effects.ApplyGainNonUniform16(
                     DarkCombImg, gain=self.gain, 
-                    nsecy = 2, nsecx=8, 
+                    nsecy = self.nsecy, nsecx=self.nsecx, 
                     seed=SeedGainNonuni+self.chipID,
                     logger=self.logger)
                 # DarkCombImg = effects.AddOverscan(

config/config_C6_dev.yaml

@@ -9,15 +9,15 @@
 # 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: "/Users/zhangxin/Work/SlitlessSim/CSST_SIM/CSST_new_sim/csst-simulation/"
-data_dir: "/Volumes/EAGET/C6_data/inputData/"
-run_name: "C6_new_sim_2sq_run1"
+work_dir: "/share/simudata/CSSOSDataProductsSims/data/CSSTSimImage_C8/"
+data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
+run_name: "testRun_cal"
 project_cycle: 6
 run_counter: 1
 
 # Whether to use MPI
 run_option:
-  use_mpi: NO
+  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
@@ -67,7 +67,7 @@ obs_setting:
   # "FGS": simulate FGS chips only (31-42)
   # "All": simulate full focal plane
   # "CALIBRATION": falt, bias, dark with or without postflash
-  survey_type: "CALIBRATION"
+  survey_type: "Photometric"
   #"LED": ['LED1','LED2','LED3','LED4','LED5','LED6','LED7','LED8','LED9','LED10','LED11','LED12','LED13','LED14'] or null
   #'LED1': '275', 'LED2': '310', 'LED3': '430', 'LED4': '505', 'LED5': '545', 'LED6': '590', 'LED7': '670',
   #'LED8': '760', 'LED9': '940', 'LED10': '940', 'LED11': '1050', 'LED12': '1050','LED13': '340', 'LED14': '365'
@@ -95,11 +95,11 @@ obs_setting:
   # if you just want to run default pointing:
   # - pointing_dir: null
   # - pointing_file: null
-  pointing_dir: "/Volumes/EAGET/C6_data/inputData/"
+  pointing_dir: "/share/simudata/CSSOSDataProductsSims/data/"
   pointing_file: "pointing_radec_246.5_40.dat"
 
   # Number of calibration pointings
-  np_cal: 0
+  np_cal: 3
 
   # Run specific pointing(s):
   # - give a list of indexes of pointings: [ip_1, ip_2...]
@@ -111,10 +111,10 @@ obs_setting:
   # - give a list of indexes of chips: [ip_1, ip_2...]
   # - run all chips: null
   # Note: for all pointings
-  run_chips: [5]
+  run_chips: null
 
   # Whether to enable astrometric modeling
-  enable_astrometric_model: False
+  enable_astrometric_model: True
 
   # Whether to enable straylight model
   enable_straylight_model: True
@@ -137,7 +137,7 @@ psf_setting:
   # Which PSF model to use:
   # "Gauss": simple gaussian profile
   # "Interp": Interpolated PSF from sampled ray-tracing data
-  psf_model: "Gauss"
+  psf_model: "Interp"
 
   # PSF size [arcseconds]
   # radius of 80% energy encircled
@@ -169,12 +169,12 @@ ins_effects:
   # switches
   # Note: bias_16channel, gain_16channel, and shutter_effect
   # is currently not applicable to "FGS" observations
-  field_dist:     NO  # Whether to add field distortions
+  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
-  add_prescan:    OFF
+  add_prescan:    YES
   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