add the function produce 1d sim spec by input image and sed (fb1989e6) · Commits · Zhang Xin / Sls 1d Spec

SpecGen/SpecGenerator.py

+202 −2

Original line number	Diff line number	Diff line
		@@ -2,8 +2,8 @@
		'''
		Author: zx
		Date: 2021-04-08 13:49:35
		LastEditTime: 2023-02-24 00:57:20
		LastEditors: xin zhangxinbjfu@gmail.com
		LastEditTime: 2024-08-28 16:45:32
		LastEditors: Zhang Xin zhangx@bao.ac.cn
		Description: In User Settings Edit
		FilePath: /undefined/Users/zhangxin/Work/SlitlessSim/sls_lit_demo/simDemo.py
		'''
		@@ -26,6 +26,7 @@ import time
		import mpi4py.MPI as MPI

		import os,sys
		import photutils

		from . import Config

		@@ -425,6 +426,205 @@ class SpecGenerator(object):
		# plt.show()
		return specTab, Aimg, stamp.array, saturePix

		def generateSpec1dforInputImg(self, img = None,img_pixel_scale = 0.06, limitfluxratio=0.9,deltLamb = 0.01, pixel_size = 0.074):

		specConfile = self.config.conFiles[self.grating]

		throughput_f = self.config.senFisle[self.grating] + self.config.orderIDs[self.beam] + '.fits'

		sed = self.generateSEDfromFiles(self.sedFile,2500,10000,deltLamb)

		x_nominal = int(np.floor(self.xcenter + 0.5))
		y_nominal = int(np.floor(self.ycenter + 0.5))
		dx = self.xcenter - x_nominal+0.5
		dy = self.ycenter - y_nominal+0.5
		offset = galsim.PositionD(dx, dy)

		folding_threshold=5.e-3
		if img is None:
		print("ERROR: input Image Error")
		return
		img = img/img.sum()
		gal_img = galsim.ImageF(img, scale=img_pixel_scale)
		gsp = galsim.GSParams(folding_threshold=folding_threshold)

		gal = galsim.InterpolatedImage(gal_img, gsparams=gsp)
		# if g_order in ['C','D','E']:
		# add_psf = galsim.Gaussian(sigma=contam_order_sigma[g_order], flux=1.0)
		# self.psf = galsim.Convolve(self.psf, add_psf)
		wcs_in = galsim.PixelScale(img_pixel_scale)
		wcs = galsim.PixelScale(pixel_size)
		gal = wcs.toWorld(wcs_in.toImage(gal))

		# print(skybg)
		# print(specConfile)
		# print(throughput_f)

		# plt.figure()
		# plt.plot(sed['WAVELENGTH'], sed['FLUX'])

		# gal = galsim.Sersic(s_n, half_light_radius=re)

		# gal_pa = pa * galsim.degrees
		# gal_ell = gal.shear(q=q_ell, beta=gal_pa)

		conv_gal = galsim.Convolve([gal,self.psf])


		stamp = conv_gal.drawImage(wcs=galsim.PixelScale(self.p_size), offset=offset)self.tself.expNummath.pi(self.aper/2)*(self.aper/2)
		stamp.setOrigin(0,0)
		t_center = photutils.centroids.centroid_1dg(stamp.array)
		stamp.setCenter(t_center[0],t_center[1])

		origin_star = [y_nominal - (stamp.center.y - stamp.ymin),
		x_nominal - (stamp.center.x - stamp.xmin)]


		origin_star = [y_nominal - (stamp.center.y - stamp.ymin),
		x_nominal - (stamp.center.x - stamp.xmin)]

		sdp = SpecDisperser.SpecDisperser(orig_img=stamp, xcenter=x_nominal,
		ycenter=y_nominal, origin=origin_star,
		tar_spec=sed,
		conf=specConfile,
		isAlongY=0, deltLamb = deltLamb/2.)

		spec_orders = sdp.compute_spec_orders()

		thp = Table.read(throughput_f)
		thp_i = interpolate.interp1d(thp['WAVELENGTH'], thp['SENSITIVITY'])

		Aimg_orig = spec_orders[self.beam][0]
		Aimg_ = Aimg_orig

		Aimg_ = Aimg_ + (self.skybg + self.dark)self.tself.expNum

		np.random.seed(int(time.time()))
		Aimg_ = np.random.poisson(Aimg_)
		for i in np.arange(self.expNum):
		Aimg_ = self.addReadoutNois(img = Aimg_, readout = self.readout)

		Aimg = Aimg_ - (self.skybg + self.dark)self.tself.expNum


		wave_pix = spec_orders[self.beam][5]
		wave_pos = spec_orders[self.beam][3]

		wave_pos_y=spec_orders[self.beam][4]

		sh = Aimg.shape
		spec_pix = np.zeros(sh[1])
		err2_pix = np.zeros(sh[1])

		# print(spec_orders[beamOrder][4])
		# print(sh)
		# plt.figure()
		# plt.imshow(Aimg)
		y_cent_pos = int(np.round(np.mean(wave_pos_y)))

		tFlux = np.sum(spec_orders[self.beam][0])
		# print(tFlux)
		fluxRatio = 0
		for i in range(int(sh[0]/2)):
		pFlux = np.sum(spec_orders[self.beam][0][y_cent_pos-i:y_cent_pos+i+1])

		fluxRatio = pFlux/tFlux
		if fluxRatio>limitfluxratio:
		break

		f1 = spec_orders[self.beam][0][y_cent_pos-i:y_cent_pos+i+1].sum(0)
		f2 = spec_orders[self.beam][0].sum(0)
		ratio_vec = np.zeros_like(f1)
		nozero_flag = f2 != 0

		ratio_vec[nozero_flag] = f1[nozero_flag]/f2[nozero_flag]
		# ratio_vec = spec_orders[self.beam][0][y_cent_pos-i:y_cent_pos+i+1].sum(0)/spec_orders[self.beam][0].sum(0)
		y_range = i
		# print(y_range, fluxRatio)
		y_len_pix = 2 * y_range + 1
		for i in range(sh[1]):
		spec_pix[i] = sum(Aimg[y_cent_pos-y_range:y_cent_pos+y_range+1, i])
		err2_pix[i] = sum(Aimg_orig[y_cent_pos-y_range:y_cent_pos+y_range+1, i]) + (self.skybg + self.dark)self.t y_len_pix * self.expNum + self.readoutself.readout y_len_pix * self.expNum

		bRange = self.config.bandRanges[self.grating]
		wave_flux = np.zeros(wave_pix.shape[0])
		err_flux = np.zeros(wave_pix.shape[0])
		specRangeImg = []

		true_center = stamp.center + galsim.PositionD(self.xcenter-x_nominal, self.ycenter-y_nominal)
		wavePos_x = true_center.x + wave_pos - wave_pos[0]

		wavePos_x_interp = np.arange(int(wavePos_x[0]), int(wavePos_x[-1]))
		lam_trace = np.interp(wavePos_x_interp,wavePos_x,wave_pix)

		wave_flux = np.zeros(lam_trace.shape[0])
		err_flux = np.zeros(lam_trace.shape[0])



		for i in np.arange(1, lam_trace.shape[0] - 1):
		w = lam_trace[i]
		wave2pix_pos=wavePos_x_interp[i]

		if (bRange[0] <= w <= bRange[1]):
		thp_w = thp_i(w)
		deltW = np.abs(w - lam_trace[i - 1]) / 2 + np.abs(lam_trace[i + 1] - w) / 2
		f = spec_pix[wave2pix_pos]
		f_ratio = ratio_vec[wave2pix_pos]
		if f_ratio==0:
		f_ratio=1
		f = f / self.t / thp_w / deltW /self.expNum/f_ratio
		err = err2_pix[wave2pix_pos]
		# err = err/ t / deltW
		err = np.sqrt(err)/ self.t / deltW/ thp_w /self.expNum/f_ratio
		specRangeImg.append(wave2pix_pos)
		# err = err / thp_w
		else:
		f = 0
		err = 0

		wave_flux[i] = f
		err_flux[i] = err

		Aimg_cal = Aimg_[y_cent_pos-y_range:y_cent_pos+y_range+1, specRangeImg]
		ids = Aimg_cal > self.saturation

		#1. saturation pixel number, 2. total pixel number, 3 saturation ratio, 4.flux ratio in photo aperture,5.max value,6.min value
		saturePix = np.zeros(6)

		saturePix[0] = Aimg_cal[ids].shape[0]
		saturePix[1] = Aimg_cal.shape[0]*Aimg_cal.shape[1]
		saturePix[2] = saturePix[0]/saturePix[1]
		saturePix[3] = 1
		saturePix[4] = np.amax(Aimg_cal)
		saturePix[5] = np.amin(Aimg_cal)


		idx = (lam_trace >= bRange[0]-100)
		idx1 = (lam_trace[idx] <= bRange[1]+100)

		w_select = lam_trace[idx][idx1]
		f_select = wave_flux[idx][idx1]
		e_select = err_flux[idx][idx1]
		lam_index = np.argsort(w_select)

		specTab = Table(np.array([w_select[lam_index], f_select[lam_index], e_select[lam_index]]).T,names=('WAVELENGTH', 'FLUX','ERR'))

		# spec_orig = np.loadtxt(sedFile)

		# plt.figure()
		# plt.plot(spec_orig[:,0], spec_orig[:,1])

		# plt.figure()
		# plt.errorbar(wave_pix[idx][idx1], wave_flux[idx][idx1],err_flux[idx][idx1])
		# plt.legend([self.sedFile])
		# # plt.plot(wave_pix[idx][idx1], wave_flux[idx][idx1])
		# plt.show()
		return specTab, Aimg, stamp.array, saturePix




		def addReadoutNois(self, img = None, readout = 5):
		random.seed(time.time())
		for i in range(img.shape[0]):

data/galImg/gal.fits

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data/galImg/gal1.fits

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data/galImg/gal2.fits

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example/sim_demo1.py

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		'''
		Author: xin zhangxinbjfu@gmail.com
		Date: 2022-08-18 23:13:26
		LastEditors: xin zhangxinbjfu@gmail.com
		LastEditTime: 2023-02-24 01:05:33
		LastEditors: Zhang Xin zhangx@bao.ac.cn
		LastEditTime: 2024-08-28 16:50:24
		FilePath: /undefined/Users/zhangxin/Work/SlitlessSim/sls_1d_sim/sls_1d_gitlab/sls_1d_spec/example/sim_demo1.py
		Description: 这是默认设置,请设置`customMade`, 打开koroFileHeader查看配置进行设置: https://github.com/OBKoro1/koro1FileHeader/wiki/%E9%85%8D%E7%BD%AE
		'''
		@@ -23,12 +23,21 @@ if __name__ == '__main__':
		config = Config(dataDir = dataDir)
		sedFn = dataDir + 'sed/sed_44575.txt'
		psf = galsim.Gaussian(fwhm=0.39)
		specG = SpecGenerator(sedFn = sedFn, grating = 'GI', beam = 'A', aper = 2.0, xcenter = 2000.,ycenter = 5000., p_size = 0.074, psf = psf, skybg = 0.3, dark = 0.02, readout = 5, t = 150., expNum = 1,config = config)
		specTab, specImg, img, satPix=specG.generateSpec1dforStar()

		# galaxy sersic model
		# specG = SpecGenerator(sedFn = sedFn, grating = 'GI', beam = 'A', aper = 2.0, xcenter = 2000.,ycenter = 5000., p_size = 0.074, psf = psf, skybg = 0.3, dark = 0.02, readout = 5, t = 150., expNum = 1,config = config)
		# specTab, specImg, img, satPix=specG.generateSpec1dforStar()

		#star
		# specG = SpecGenerator(sedFn = sedFn, grating = 'GI', beam = 'A', aper = 2.0, xcenter = 2000.,ycenter = 5000, p_size = 0.074, psf = psf, skybg = 0.3, dark = 0.02, readout = 5, t = 150., expNum = 1,config = config)
		# specTab, specImg, img, satPix=specG.generateSpec1dforGal(s_n = 1.0, re = 0.5, pa = 90,q_ell = 1.0,limitfluxratio=0.8)

		# galaxy input image
		galfn = dataDir + "galImg/gal2.fits"
		galimg = fits.getdata(galfn)
		specG = SpecGenerator(sedFn = sedFn, grating = 'GV', beam = 'A', aper = 2.0, xcenter = 2000.,ycenter = 5000., p_size = 0.074, psf = psf, skybg = 0.3, dark = 0.02, readout = 5, t = 1500., expNum = 1,config = config)
		specTab, specImg, img, satPix=specG.generateSpec1dforInputImg(img = galimg,img_pixel_scale = 0.06, limitfluxratio=0.9,deltLamb = 0.01, pixel_size = 0.074)

		fits.writeto("specImg.fits",specImg,overwrite=True)
		fits.writeto("DImg.fits",img,overwrite=True)
		specTab.write("specTab.fits",overwrite=True)