add pre/over-scan & format output (e13a656a) · Commits · csst-sims / csst_msc_sim

ObservationSim/Instrument/Chip/Chip.py

+18 −4

Original line number	Original line	Diff line number	Diff line
	@@ -358,7 +358,11 @@ class Chip(FocalPlane):
	# img.addNoise(dark_noise)		# img.addNoise(dark_noise)

	# Add dark current & Poisson noise		# Add dark current & Poisson noise
			InputDark = False
	if config["ins_effects"]["add_dark"] == True:		if config["ins_effects"]["add_dark"] == True:
			if InputDark:
			img = chip_utils.add_inputdark(img=img, chip=self, exptime=exptime)
			else:
	img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise)		img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise)
	else:		else:
	img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise, dark_noise=0.)		img, _ = chip_utils.add_poisson(img=img, chip=self, exptime=exptime, poisson_noise=poisson_noise, dark_noise=0.)
	@@ -391,13 +395,23 @@ class Chip(FocalPlane):
	chip_utils.log_info(msg=" Apply CTE Effect", logger=self.logger)		chip_utils.log_info(msg=" Apply CTE Effect", logger=self.logger)
	img = effects.CTE_Effect(GSImage=img, threshold=27)		img = effects.CTE_Effect(GSImage=img, threshold=27)

			### prescan & overscan
			if config["ins_effects"]["add_prescan"] == True:
			img = chip_utils.AddPreScan(GSImage=img, pre1=27, pre2=4, over1=71, over2=80)
			### 1*16 output
			if config["ins_effects"]["format_output"] == True:
			img = chip_utils.formatOutput(GSImage=img)
			self.nsecy = 1
			self.nsecx = 16


	# Add Bias level		# Add Bias level
	if config["ins_effects"]["add_bias"] == True:		if config["ins_effects"]["add_bias"] == True:
	chip_utils.log_info(msg=" Adding Bias level and 16-channel non-uniformity", logger=self.logger)		chip_utils.log_info(msg=" Adding Bias level and 16-channel non-uniformity", logger=self.logger)
	if config["ins_effects"]["bias_16channel"] == True:		if config["ins_effects"]["bias_16channel"] == True:
	img = effects.AddBiasNonUniform16(img,		img = effects.AddBiasNonUniform16(img,
	bias_level=float(self.bias_level),		bias_level=float(self.bias_level),
	nsecy = 2, nsecx=8,		nsecy = self.nsecy, nsecx=self.nsecx,
	seed=SeedBiasNonuni+self.chipID,		seed=SeedBiasNonuni+self.chipID,
	logger=self.logger)		logger=self.logger)
	elif config["ins_effects"]["bias_16channel"] == False:		elif config["ins_effects"]["bias_16channel"] == False:
	@@ -415,7 +429,7 @@ class Chip(FocalPlane):
	if config["ins_effects"]["gain_16channel"] == True:		if config["ins_effects"]["gain_16channel"] == True:
	img, self.gain_channel = effects.ApplyGainNonUniform16(		img, self.gain_channel = effects.ApplyGainNonUniform16(
	img, gain=self.gain,		img, 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)
	elif config["ins_effects"]["gain_16channel"] == False:		elif config["ins_effects"]["gain_16channel"] == False:

ObservationSim/Instrument/Chip/ChipUtils.py

+87 −3

Original line number	Original line	Diff line number	Diff line
	@@ -171,10 +171,11 @@ def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=Non
	def add_brighter_fatter(img):		def add_brighter_fatter(img):
	#Inital dynamic lib		#Inital dynamic lib
	try:		try:
	with pkg_resources.files('ObservationSim.Instrument.Chip.lib_bf').joinpath("libmoduleBF.so") as lib_path:		with pkg_resources.files('ObservationSim.Instrument.Chip.libBF').joinpath("libmoduleBF.so") as lib_path:
			print('--1', lib_path)
	lib_bf = ctypes.CDLL(lib_path)		lib_bf = ctypes.CDLL(lib_path)
	except AttributeError:		except AttributeError:
	with pkg_resources.path('ObservationSim.Instrument.Chip.lib_bf', "libmoduleBF.so") as lib_path:		with pkg_resources.path('ObservationSim.Instrument.Chip.libBF', "libmoduleBF.so") as lib_path:
	lib_bf = ctypes.CDLL(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]		lib_bf.addEffects.argtypes = [ctypes.c_int, ctypes.c_int, ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_float), ctypes.c_int]

	@@ -194,3 +195,86 @@ def add_brighter_fatter(img):
	img.array[:, :] = np.reshape(arr_imc, [nx, ny])		img.array[:, :] = np.reshape(arr_imc, [nx, ny])
	del arr_ima, arr_imc		del arr_ima, arr_imc
	return img		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:-over2, pre1:-over1] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			imgt[chunkidx, :, :] = imgtemp
			if int(chunkidx/4) == 1:
			imgtemp[pre2:-over2, over1:-pre1] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			imgt[chunkidx, :, :] = imgtemp #[:, ::-1]
			if int(chunkidx/4) == 2:
			imgtemp[over2:-pre2, over1:-pre1] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			imgt[chunkidx, :, :] = imgtemp #[::-1, ::-1]
			if int(chunkidx/4) == 3:
			imgtemp[over2:-pre2, pre1:-over1] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			imgt[chunkidx, :, :] = imgtemp #[::-1, :]

			imgtx1 = np.hstack(imgt[:nsecx:, :, :])
			imgtx2 = np.hstack(imgt[:(nsecx-1):-1, :, :])

			newimg = galsim.Image(int(nx+(pre1+over1)nsecx), int(ny+(pre2+over2)nsecy), init_value=0)
			newimg.array[:, :] = np.concatenate([imgtx1, imgtx2])

			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[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			if int(chunkidx/4) == 1:
			imgt[chunkidx, :, :] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			if int(chunkidx/4) == 2:
			imgt[chunkidx, :, :] = img[iydy:(iy+1)dy, ixdx:(ix+1)dx]
			if int(chunkidx/4) == 3:
			imgt[chunkidx, :, :] = img[iydy:(iy+1)dy, ixdx:(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(dxnsecxnsecy), dy, init_value=0)
			newimg.array[:, :] = np.hstack([imgttx0, imgttx1, imgttx2, imgttx3])
			return newimg

config/config_50sqdeg.yaml

+7 −5

Original line number	Original line	Diff line number	Diff line
	@@ -9,13 +9,13 @@
	# 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: "/share/home/fangyuedong/new_sim/workplace/"		work_dir: "/share/home/weichengliang/CSST_git/test_new_sim/outputs/"
	data_dir: "/share/simudata/CSSOSDataProductsSims/data/"		data_dir: "/share/simudata/CSSOSDataProductsSims/data/"
	run_name: "test_new_sim"		run_name: "testRun0"

	# 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
	@@ -85,7 +85,7 @@ 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: "/share/home/fangyuedong/50sqdeg_pointings/"		pointing_dir: "/share/simudata/CSSOSDataProductsSims/data/"
	pointing_file: "pointing_50_combined.dat"		pointing_file: "pointing_50_combined.dat"

	# Number of calibration pointings		# Number of calibration pointings
	@@ -163,6 +163,7 @@ ins_effects:
	add_dark: ON # Whether to add dark noise		add_dark: ON # Whether to add dark noise
	add_readout: ON # Whether to add read-out (Gaussian) noise		add_readout: ON # Whether to add read-out (Gaussian) noise
	add_bias: ON # Whether to add bias-level to images		add_bias: ON # Whether to add bias-level to images
			add_prescan: OFF
	bias_16channel: ON # Whether to add different biases for 16 channels		bias_16channel: ON # Whether to add different biases for 16 channels
	gain_16channel: ON # Whether to make different gains for 16 channels		gain_16channel: ON # Whether to make different gains for 16 channels
	shutter_effect: ON # Whether to add shutter effect		shutter_effect: ON # Whether to add shutter effect
	@@ -177,6 +178,7 @@ ins_effects:
	add_hotpixels: ON # Whether to add hot pixels		add_hotpixels: ON # Whether to add hot pixels
	add_deadpixels: ON # Whether to add dead(dark) pixels		add_deadpixels: ON # Whether to add dead(dark) pixels
	bright_fatter: ON # Whether to simulate Brighter-Fatter (also diffusion) effect		bright_fatter: ON # Whether to simulate Brighter-Fatter (also diffusion) effect
			format_output: OFF

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