update calibration in Chip.py (72f70d57) · Commits · csst-sims / csst_msc_sim

ObservationSim/Instrument/Chip/Chip.py

+140 −7

Original line number	Original line	Diff line number	Diff line
	@@ -529,12 +529,26 @@ class Chip(FocalPlane):
	print(" Applying Non-Linearity on the Bias image", flush=True)		print(" Applying Non-Linearity on the Bias image", flush=True)
	BiasCombImg = effects.NonLinearity(GSImage=BiasCombImg, beta1=5.e-7, beta2=0)		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		# Apply Bad lines
	if config["ins_effects"]["add_badcolumns"] == True:		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 = 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,		BiasCombImg, self.gain_channel = effects.ApplyGainNonUniform16(BiasCombImg, gain=self.gain,
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedGainNonuni+self.chipID,		seed=SeedGainNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)
	# BiasCombImg = effects.AddOverscan(		# BiasCombImg = effects.AddOverscan(
	@@ -606,8 +620,61 @@ class Chip(FocalPlane):
	print(" Applying Non-Linearity on the Flat image", flush=True)		print(" Applying Non-Linearity on the Flat image", flush=True)
	FlatCombImg = effects.NonLinearity(GSImage=FlatCombImg, beta1=5.e-7, beta2=0)		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:		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
			### 28 -> 116 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_ID30 + self.chipID16
			newimg.array[:, 0+ichanneldx:dx+ichanneldx] = CTI_sim(img_arr[:, 0+ichanneldx:dx+ichanneldx],dx,dy,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)
			newimg.wcs = FlatCombImg.wcs
			del FlatCombImg
			FlatCombImg = newimg

			### 116 -> 28 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		# Add Hot Pixels or/and Dead Pixels
	rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))		rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))
	@@ -627,7 +694,7 @@ class Chip(FocalPlane):
	# img += float(config["ins_effects"]["bias_level"])		# img += float(config["ins_effects"]["bias_level"])
	FlatCombImg = effects.AddBiasNonUniform16(FlatCombImg,		FlatCombImg = effects.AddBiasNonUniform16(FlatCombImg,
	bias_level=biaslevel,		bias_level=biaslevel,
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedBiasNonuni+self.chipID,		seed=SeedBiasNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)

	@@ -639,7 +706,7 @@ class Chip(FocalPlane):
	FlatCombImg.addNoise(readout_noise)		FlatCombImg.addNoise(readout_noise)

	FlatCombImg, self.gain_channel = effects.ApplyGainNonUniform16(FlatCombImg, gain=self.gain,		FlatCombImg, self.gain_channel = effects.ApplyGainNonUniform16(FlatCombImg, gain=self.gain,
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedGainNonuni+self.chipID,		seed=SeedGainNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)
	# FlatCombImg = effects.AddOverscan(FlatCombImg, overscan=overscan, gain=self.gain, widthl=27, widthr=27, widtht=8, widthb=8)		# 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		cr_map[cr_map < 0] = 0
	crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)		crmap_gsimg = galsim.Image(cr_map, dtype=np.uint16)
	del cr_map		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_utils.outputCal(
	chip=self,		chip=self,
	img=crmap_gsimg,		img=crmap_gsimg,
	@@ -725,8 +805,61 @@ class Chip(FocalPlane):
	print(" Applying Non-Linearity on the Dark image", flush=True)		print(" Applying Non-Linearity on the Dark image", flush=True)
	DarkCombImg = effects.NonLinearity(GSImage=DarkCombImg, beta1=5.e-7, beta2=0)		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
			### 28 -> 116 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_ID30 + self.chipID16
			newimg.array[:, 0+ichanneldx:dx+ichanneldx] = CTI_sim(img_arr[:, 0+ichanneldx:dx+ichanneldx],dx,dy,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)
			newimg.wcs = DarkCombImg.wcs
			del DarkCombImg
			DarkCombImg = newimg

			### 116 -> 28 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:		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		# Add Hot Pixels or/and Dead Pixels
	rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))		rgbadpix = Generator(PCG64(int(SeedDefective+self.chipID)))
	@@ -746,7 +879,7 @@ class Chip(FocalPlane):
	# img += float(config["ins_effects"]["bias_level"])		# img += float(config["ins_effects"]["bias_level"])
	DarkCombImg = effects.AddBiasNonUniform16(DarkCombImg,		DarkCombImg = effects.AddBiasNonUniform16(DarkCombImg,
	bias_level=biaslevel,		bias_level=biaslevel,
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedBiasNonuni+self.chipID,		seed=SeedBiasNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)

	@@ -759,7 +892,7 @@ class Chip(FocalPlane):

	DarkCombImg, self.gain_channel = effects.ApplyGainNonUniform16(		DarkCombImg, self.gain_channel = effects.ApplyGainNonUniform16(
	DarkCombImg, gain=self.gain,		DarkCombImg, gain=self.gain,
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedGainNonuni+self.chipID,		seed=SeedGainNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)
	# DarkCombImg = effects.AddOverscan(		# DarkCombImg = effects.AddOverscan(

config/config_C6_dev.yaml

+12 −12

Original line number	Original line	Diff line number	Diff line
	@@ -9,15 +9,15 @@
	# Base diretories and naming setup		# Base diretories and naming setup
	# Can add some of the command-line arguments here as well;		# Can add some of the command-line arguments here as well;
	# OK to pass either way or both, as long as they are consistent		# 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/"		work_dir: "/share/simudata/CSSOSDataProductsSims/data/CSSTSimImage_C8/"
	data_dir: "/Volumes/EAGET/C6_data/inputData/"		data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
	run_name: "C6_new_sim_2sq_run1"		run_name: "testRun_cal"
	project_cycle: 6		project_cycle: 6
	run_counter: 1		run_counter: 1

	# Whether to use MPI		# Whether to use MPI
	run_option:		run_option:
	use_mpi: NO		use_mpi: YES
	# NOTE: "n_threads" paramters is currently not used in the backend		# NOTE: "n_threads" paramters is currently not used in the backend
	# simulation codes. It should be implemented later in the web frontend		# simulation codes. It should be implemented later in the web frontend
	# in order to config the number of threads to request from NAOC cluster		# 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)		# "FGS": simulate FGS chips only (31-42)
	# "All": simulate full focal plane		# "All": simulate full focal plane
	# "CALIBRATION": falt, bias, dark with or without postflash		# "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		#"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',		#'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'		#'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:		# if you just want to run default pointing:
	# - pointing_dir: null		# - pointing_dir: null
	# - pointing_file: 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"		pointing_file: "pointing_radec_246.5_40.dat"

	# Number of calibration pointings		# Number of calibration pointings
	np_cal: 0		np_cal: 3

	# Run specific pointing(s):		# Run specific pointing(s):
	# - give a list of indexes of pointings: [ip_1, ip_2...]		# - 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...]		# - give a list of indexes of chips: [ip_1, ip_2...]
	# - run all chips: null		# - run all chips: null
	# Note: for all pointings		# Note: for all pointings
	run_chips: [5]		run_chips: null

	# Whether to enable astrometric modeling		# Whether to enable astrometric modeling
	enable_astrometric_model: False		enable_astrometric_model: True

	# Whether to enable straylight model		# Whether to enable straylight model
	enable_straylight_model: True		enable_straylight_model: True
	@@ -137,7 +137,7 @@ psf_setting:
	# Which PSF model to use:		# Which PSF model to use:
	# "Gauss": simple gaussian profile		# "Gauss": simple gaussian profile
	# "Interp": Interpolated PSF from sampled ray-tracing data		# "Interp": Interpolated PSF from sampled ray-tracing data
	psf_model: "Gauss"		psf_model: "Interp"

	# PSF size [arcseconds]		# PSF size [arcseconds]
	# radius of 80% energy encircled		# radius of 80% energy encircled
	@@ -169,12 +169,12 @@ ins_effects:
	# switches		# switches
	# Note: bias_16channel, gain_16channel, and shutter_effect		# Note: bias_16channel, gain_16channel, and shutter_effect
	# is currently not applicable to "FGS" observations		# 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_back: YES # Whether to add sky background
	add_dark: YES # Whether to add dark noise		add_dark: YES # Whether to add dark noise
	add_readout: YES # Whether to add read-out (Gaussian) noise		add_readout: YES # Whether to add read-out (Gaussian) noise
	add_bias: YES # Whether to add bias-level to images		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		bias_16channel: YES # Whether to add different biases for 16 channels
	gain_16channel: YES # Whether to make different gains for 16 channels		gain_16channel: YES # Whether to make different gains for 16 channels
	shutter_effect: YES # Whether to add shutter effect		shutter_effect: YES # Whether to add shutter effect