integrated position calibration from Jundan Nie (c4de819d) · Commits · Bo Zhang / csst

csst/msc/astrometry.py

+444 −18

Original line number	Diff line number	Diff line
		from ..core.processor import CsstProcessor
		import os
		import time
		from functools import partial
		from multiprocessing import Pool
		from subprocess import Popen

		import healpy as hp
		import numpy as np
		from astropy import table
		from astropy import units as u
		from astropy.coordinates import SkyCoord
		from astropy.io import fits
		from astropy.wcs import WCS

		from .. import PACKAGE_PATH
		from ..core.processor import CsstProcessor

		CONFIG_SCAMP = PACKAGE_PATH + "/msc/config/test.txt"
		path_config = PACKAGE_PATH + "/msc/astrometry_config/"


		class CsstProcMscPositionCalibration(CsstProcessor):
		def prepare(self, **args):
		# prepare the environment
		# for example, if you make use of some third-party software like SEXTRACTOR,
		# do your preparation here.
		pass

		def run(self, data, args, *kwargs):
		# run your pipeline here
		# make sure that your input raw should be a child class instance of CsstData.
		pass

		def cleanup(self, **kwargs):
		# clean up environment
		pass

		def join_data(self, img_list, wht_list, flg_list, path_output):
		"""
		Prepare data for running scamp; Combine all image data, weight files, flag files to their one frame.

		Parameters
		----------
		img_list:
		image files to join together, e.g.,MSC_210304093000_0000000_06_img.fits
		wht_list:
		weith files to join together, e.g.,MSC_210304093000_0000000_06_img.fits
		flg_list:
		flag files to join together, e.g.,e.g.,MSC_210304093000_0000000_06_flg.fits
		path_output:
		the output dir for the joined file.

		Returns
		-------
		The joined multi-extension file(not stacked), weight, flag files.
		e.g., MSC_210304093000_0000000_img.fits,MSC_210304093000_0000000_wht.fits, MSC_210304093000_0000000_flg.fits.

		"""

		img_prefix = img_list[0][0].header['FILENAME'][0:-7]
		output_imgnm = path_output + img_prefix + '_img.fits'
		hdul_img = fits.HDUList()
		for i in range(0, len(img_list)):
		h0 = fits.PrimaryHDU(header=img_list[i][0].header)
		h1 = fits.ImageHDU(data=img_list[i][1].data, header=img_list[i][1].header)
		hdul_img.append(h0)
		hdul_img.append(h1)
		hdul_img.writeto(output_imgnm, overwrite=True)

		output_whtnm = path_output + img_prefix + '_wht.fits'
		hdul_wht = fits.HDUList()
		for i in range(0, len(wht_list)):
		h0 = fits.PrimaryHDU(header=wht_list[i][0].header)
		h1 = fits.ImageHDU(data=wht_list[i][1].data, header=wht_list[i][1].header)
		hdul_wht.append(h0)
		hdul_wht.append(h1)
		hdul_wht.writeto(output_whtnm, overwrite=True)

		output_flgnm = path_output + img_prefix + '_flg.fits'
		hdul_flg = fits.HDUList()
		for i in range(0, len(flg_list)):
		h0 = fits.PrimaryHDU(header=flg_list[i][0].header)
		h1 = fits.ImageHDU(data=flg_list[i][1].data, header=flg_list[i][1].header)
		hdul_flg.append(h0)
		hdul_flg.append(h1)
		hdul_flg.writeto(output_flgnm, overwrite=True)

		def run_sextractor(self, fn_list, path_output):
		"""
		Run sextractor

		Parameters
		----------
		fn_list:
		file name list, e.g.,MSC_210304093000_0000000_06_img.fits...
		config_sextractor:
		the path for sextractor configuration file.
		path_output:
		the current working dir

		Returns
		-------
		The photometric catalog, with position and flux, e.g.,MSC_210304093000_0000000_06_img.acat
		"""
		fn = fn_list
		config_sextractor = path_config + "new_csst_realtime.no.weight.sex"
		sex_comd1 = 'sex -c ' + config_sextractor + ' '
		sex_comd2 = fn + ' -CATALOG_NAME ' + fn[0:-5] + '.acat'
		sex_comd3 = ' -PARAMETERS_NAME ' + path_config + 'csst_realtime.param' + ' -FILTER_NAME ' + path_config + 'csst_realtime.conv' + ' -STARNNW_NAME ' + path_config + 'csst_realtime.nnw'
		sex_comd = sex_comd1 + sex_comd2 + sex_comd3
		print(sex_comd)
		p = Popen(sex_comd, shell=True)
		p.wait()

		def combine_catalog(self, img_list, path_output):
		"""
		Combine the sextractor catalog together

		Parameters
		-----------
		img_list:
		image list, in table format
		path_output:
		the output dir

		Returns
		-------
		The combined catalog,e.g., MSC_210304093000_0000000.acat.fits
		"""
		fn = path_output + img_list[0][0].header['FILENAME'][0:-7]
		output_catnm = str(fn + '.acat.fits')
		hdul = fits.HDUList()
		if len(img_list) == 18:
		for i in range(0, len(img_list)):
		image_prefix = img_list[i][0].header['FILENAME']
		cat_nm = path_output + image_prefix + '.acat'
		cat_i = fits.open(cat_nm)
		hdul.append(cat_i[0])
		hdul.append(cat_i[1])
		hdul.append(cat_i[2])
		hdul.writeto(output_catnm, overwrite=True)
		else:
		print('the length of file list in not equal to 18, needs to check')

		def run_scamp(self, img_list, path_output):
		"""
		Run scamp

		Parameters
		---------
		img_list:
		to join a file 'image_prefix+.acat.fits', e.g.,MSC_210304093000_0000000.acat.fits
		config_scamp:
		the config file path for scamp

		Returns
		-------
		Image header updated with WCS keywords, MSC_210304093000_0000000.acat.head.
		"""
		image_prefix = (img_list[0][0].header)['FILENAME'][0:-7]
		config_scamp = path_config + "default2.scamp"
		scamp_comd = 'scamp ' + image_prefix + '.acat.fits -ASTREFCAT_NAME= ' + 'ref.cat\
		-MERGEDOUTCAT_NAME ' + 'merged.cat -FULLOUTCAT_NAME ' + 'full.cat\
		-c ' + config_scamp
		print(scamp_comd)
		p = Popen(scamp_comd, shell=True)
		p.wait()

		def convert_hdu_to_ldac(self, hdu):
		"""
		Convert an hdu table to a fits_ldac table (format used by astromatic suite)

		def test_dir():
		print(CONFIG_SCAMP)
		No newline at end of file
		Parameters
		----------
		hdu:
		`astropy.io.fits.BinTableHDU` or `astropy.io.fits.TableHDU`
		HDUList to convert to fits_ldac HDUList

		Returns
		-------
		tbl1:
		`astropy.io.fits.BinTableHDU`
		Header info for fits table (LDAC_IMHEAD)
		tbl2:
		`astropy.io.fits.BinTableHDU`
		Data table (LDAC_OBJECTS)
		"""
		tblhdr = np.array([hdu[1].header.tostring()])
		col1 = fits.Column(name='Field Header Card', array=tblhdr, format='13200A')
		cols = fits.ColDefs([col1])
		tbl1 = fits.BinTableHDU.from_columns(cols)
		tbl1.header['TDIM1'] = '(80, {0})'.format(len(hdu[1].header))
		tbl1.header['EXTNAME'] = 'LDAC_IMHEAD'

		dcol = fits.ColDefs(hdu[1].data)
		tbl2 = fits.BinTableHDU.from_columns(dcol)
		tbl2.header['EXTNAME'] = 'LDAC_OBJECTS'
		return tbl1, tbl2

		def get_refcat(self, img_list, path_gaia, search_radius, silent=True):
		"""
		Get reference catalog for scamp. The reference cat is GAIA EDR3.

		Parameters
		----------
		image_prefix:
		a image to get its reference catalog, e.g.,MSC_210304093000_0000000_img.fits.
		Usually the center of the image is the wcs parameters CRVAL1,CRVAL1.
		search_radius:
		circle radius for searching, units: degree. e.g., 2 degree for a 1x1 deg^2 image.
		For large ccd size, use larger radius. csst, r=3 deg.
		path_gaia: directory of the reference catalog.

		Returns
		-------
		outcat:
		filename of the cross matched catalog.
		This catalog is used as a reference catalog for running scamp.
		e.g.,MSC_210304093000_0000000.gaialac.fits

		"""
		image_prefix = (img_list[0][0].header)['FILENAME'][0:-7]
		fname = image_prefix + '_img.fits'
		gaianame = image_prefix + '.gaia.fits'
		gaialacnm = image_prefix + '.gaialac.fits'
		outcat = gaianame
		hdu = fits.open(fname)
		header1 = hdu[0].header
		header2 = hdu[1].header
		deltatime = 0.00
		ra = float(header2['CRVAL1'])
		dec = float(header2['CRVAL2'])
		c = SkyCoord(ra, dec, unit=(u.deg, u.deg))
		print('ra, dec ra.deg dec.deg= ', ra, dec, c.ra.deg, c.dec.deg)
		ra = c.ra.deg
		dec = c.dec.deg
		c = SkyCoord(ra, dec, unit=(u.deg, u.deg))
		phi = c.ra.deg / (180. / np.pi)
		theta = (90. - c.dec.deg) / (180 / np.pi)
		vec = hp.ang2vec(theta, phi)
		list1 = hp.query_disc(nside=32, vec=vec, radius=np.radians(search_radius))
		if -1 in list1:
		list1.remove(-1)
		ipring = np.array(list1)
		pix = np.unique(ipring)
		npix = pix.size
		print(ipring, 'ipring', pix, 'pix', npix, 'npix')
		dt = np.dtype(
		[('ra', '>f8'), ('dec', '>f8'), ('ra_error', '>f8'), ('dec_error', '>f8'), ('phot_g_mean_mag', '>f8'),
		('pmra', '>f8'), ('pmra_error', '>f8'), ('pmdec', '>f8'), ('pmdec_error', '>f8')])
		refcat = table.Table(dtype=dt)
		for i in pix:
		print('i= %5.5d' % i, path_gaia)
		fname = path_gaia + 'healpix-' + '%5.5d' % i + '.fits'
		print('fname=', fname)
		if not silent: print('Reading ', fname)
		d = table.Table.read(fname)
		refcat = [refcat, d]
		refcat = table.vstack(refcat, join_type='inner')
		refcat.rename_column('ra', 'X_WORLD')
		refcat.rename_column('dec', 'Y_WORLD')
		print('delta_time between obs_cat and ref_cat:', deltatime)

		mask = (refcat['pmdec'] != refcat['pmdec'])
		refcat['pmdec'][mask] = 0
		mask = (refcat['pmra'] != refcat['pmra'])
		refcat['pmra'][mask] = 0
		refcat['X_WORLD'] = refcat['X_WORLD'] + deltatime * refcat['pmra'] / np.cos(
		refcat['Y_WORLD'] / 180. * np.pi) / 3600.0 / 1000.0
		refcat['Y_WORLD'] = refcat['Y_WORLD'] + deltatime * refcat['pmdec'] / 3600.0 / 1000.0
		refcat['ra_error'] = refcat['ra_error'] / 1000.0 / 3600.0
		refcat['dec_error'] = refcat['dec_error'] / 1000.0 / 3600.0
		refcat.rename_column('ra_error', 'ERRA_WORLD')
		refcat.rename_column('dec_error', 'ERRB_WORLD')
		refcat.rename_column('phot_g_mean_mag', 'MAG')
		if outcat: refcat.write(outcat, format='fits', overwrite=True)

		if os.path.isfile(gaianame):
		print('exist')
		hdu = fits.open(gaianame)
		hdu1 = self.convert_hdu_to_ldac(hdu)
		hdup = fits.PrimaryHDU()
		hdu = hdu1[0]
		tbhdu = hdu1[1]
		thdulist = fits.HDUList([hdup, hdu, tbhdu])
		if os.path.isfile(gaialacnm): os.remove(gaialacnm)
		thdulist.writeto(gaialacnm)

		print('##################### end #####################')
		return gaialacnm

		def rewrite_wcs_head(self, head):
		"""
		Rewrite the WCS head from Scamp to the standard fits header

		Parameters
		----------
		head: scamp head file names

		Returns
		-------
		wcshead: a new head file in fits format

		"""
		wcshead = head + '.fits'
		f = open(head, 'r')
		f1 = open(wcshead, 'w')
		a = ''
		i = 0
		for v in f.readlines():
		sp = ''
		asp = ''
		i += 1
		if len(v) <= 81:
		sp = ' ' * (81 - len(v))
		if 'END' in v:
		asp = ' ' * 80 * (36 - i % 36)
		i = i + (36 - i % 36)
		# print(i)
		a = a + v + sp + asp
		f1.write(a.replace('\n', ''))
		f1.close()
		f.close()
		return wcshead

		def check_astrometry(self, img_list, path_output):
		"""
		Check position calibration quality

		Parameters
		------------
		img_list:
		list of images, in table format
		path_output:
		work dir

		Returns
		-------
		ccdraoff:
		ra difference between observed catalog and reference catalog
		ccddecoff:
		dec difference between observed catalog and reference catalog
		ccdraoff_med,ccddecoff_med:
		median of the ra or dec difference
		ccdraoff_rms,ccddecoff_rms:
		rms of the ra or dec difference
		"""
		print('############## check the astrometry quality and save files ################')
		r1 = []
		d1 = []
		image_prefix = (img_list[0][0].header)['FILENAME'][0:-7]
		fn = path_output + image_prefix
		wcshead = self.rewrite_wcs_head(fn + '.acat.head')
		acat = fits.open(fn + '.acat.fits')
		acat_change = str(fn + '.acat.change.fits')
		cat_suffix = '.acat'
		hdul = fits.HDUList()
		if len(img_list) == 18:
		for i in range(0, len(img_list)):
		wcshdr = fits.getheader(wcshead, i, ignore_missing_simple=True) # read headers and change to RA---TPV,DEC--TPV for wcs_transfer package
		wcshdr['CTYPE1'] = 'RA---TPV'
		wcshdr['CTYPE2'] = 'DEC--TPV'
		w = WCS(wcshdr)
		# print(wcshdr)
		cat_nm = path_output + (img_list[i][0].header)['FILENAME'] + cat_suffix
		cat_i = fits.open(cat_nm)
		sexcat = cat_i[2].data
		ra_sex = sexcat['ALPHA_J2000']
		dec_sex = sexcat['DELTA_J2000']
		x = sexcat['XWIN_IMAGE']
		y = sexcat['YWIN_IMAGE']
		r, d = w.all_pix2world(x, y, 0) # convert xwin,ywin to ra,de
		sexcat['ALPHA_J2000'] = r
		sexcat['DELTA_J2000'] = d
		cat_i[2].data = sexcat
		hdul.append(cat_i[0])
		hdul.append(cat_i[1])
		hdul.append(cat_i[2])
		r1 = np.hstack((r1, r))
		d1 = np.hstack((d1, d))
		obsc = SkyCoord(ra=r1 * u.degree, dec=d1 * u.degree)
		tmp_cat = np.zeros((len(obsc), 2))
		tmp_cat[:, 0] = obsc.ra
		tmp_cat[:, 1] = obsc.dec
		np.savetxt(path_output + 'scamp_coord.txt', tmp_cat, fmt="%.10f %.10f", delimiter="\n")
		hdul.writeto(acat_change, overwrite=True) # update the cat with new ra,dec (from 1st scamp wcs.)
		else:
		print('the length of fitslist is not equal to 18,needs to check')

		def write_headers(self, img_list):
		"""
		Wrtie history to header
		"""
		head_suffix = img_list[0][0].header['FILENAME'][0:-7] + '.acat.head.fits'
		hdul2 = fits.open(head_suffix, ignore_missing_simple=True)
		if len(img_list) == 18:
		for i in range(0, len(img_list)):
		fits_nm = img_list[i][0].header['FILENAME'] + '.head'
		hdul1 = fits.open(fits_nm, mode='update', ignore_missing_simple=True)
		hdr = hdul1[0].header
		hdr2 = hdul2[i].header
		hdr.extend(hdr2, unique=True, update=True)
		WCS_S = 0
		WCS_V = '2.0.4'
		WCS_P = 'default.scamp'
		WCS_TOL = time.strftime('%Y-%m-%d %H:%M:%S %p')
		hdr.set('WCS_S', '0', '0=done')
		hdr.set('WCS_V', WCS_V, 'Version of WCS calibration')
		hdr.set('WCS_P', WCS_P, 'Configure file name of WCS')
		hdr.set('WCS_TOL', WCS_TOL, 'Time of last wcs calibration')
		# hdul1.flush()
		# hdul1.close()
		else:
		print('The total number of the fits files is not 18.')

		def prepare(self, path_gaia, path_output, search_radius=2.0):
		self.path_gaia = path_gaia
		self.path_output = path_output
		self.search_radius = search_radius

		def run(self, img_list, wht_list, flg_list, fn_list, path_gaia, path_output, search_radius):
		print('preparing files for position calibration....')
		self.join_data(img_list, wht_list, flg_list, path_output=path_output)
		print('################## run sextractor ###################')
		p = Pool()
		prod_x = partial(self.run_sextractor, path_output=path_output)
		result = p.map(prod_x, fn_list)
		p.close()
		p.join()
		print('################## sextractor done ###################')
		print('############### combine sextractor catalog ###############')
		self.combine_catalog(img_list, path_output)
		print('############### get reference catalog ###############3')
		refcat = self.get_refcat(img_list, path_gaia=path_gaia, search_radius=search_radius, silent=True)
		Popen('cp ' + refcat + ' ref.cat', shell=True)
		print('############### run scamp ##################')
		self.run_scamp(img_list, path_output=path_output)
		print('################ scamp done #################')
		print('Checking astrometry quality....')
		self.check_astrometry(img_list, path_output)
		print('################ updating headers.... #############')
		self.write_headers(img_list)
		print('#### Position calibration process done ####')

		def cleanup(self, img_list, path_output):
		# clean up environment
		image_prefix = img_list[0][0].header['FILENAME'][0:-7]
		for i in range(0, len(img_list)):
		fn = img_list[i][0].header['FILENAME'] + '.acat'
		if os.path.isfile(path_output + fn): os.remove(path_output + fn)
		if os.path.isfile(path_output + image_prefix + '.gaia.fits'):
		os.remove(path_output + image_prefix + '.gaia.fits')
		if os.path.isfile(path_output + image_prefix + '.gaialac.fits'):
		os.remove(path_output + image_prefix + '.gaialac.fits')
		if os.path.isfile(path_output + 'scamp.xml'):
		os.remove(path_output + 'scamp.xml')
		if os.path.isfile(path_output + 'full_1.cat'):
		os.remove(path_output + 'full_1.cat')
		if os.path.isfile(path_output + 'merged_1.cat'):
		os.remove(path_output + 'merged_1.cat')
		if os.path.isfile(path_output + image_prefix + '_img.fits.back'):
		os.remove( path_output + image_prefix + '_img.fits.back')
		if os.path.isfile(path_output + image_prefix + '_wht.fits'):
		os.remove(path_output + image_prefix + '_wht.fits')
		if os.path.isfile(path_output + image_prefix + '_flg.fits'):
		os.remove(path_output + image_prefix + '_flg.fits')

csst/msc/astrometry_config/csst_realtime.conv

0 → 100644

+7 −0

Original line number	Diff line number	Diff line
		CONV NORM
		# 5x5 convolution mask of a gaussian PSF with FWHM = 2.5 pixels.
		0.034673 0.119131 0.179633 0.119131 0.034673
		0.119131 0.409323 0.617200 0.409323 0.119131
		0.179633 0.617200 0.930649 0.617200 0.179633
		0.119131 0.409323 0.617200 0.409323 0.119131
		0.034673 0.119131 0.179633 0.119131 0.034673

csst/msc/astrometry_config/csst_realtime.nnw

0 → 100644

+28 −0

Original line number	Diff line number	Diff line
		NNW
		# Neural Network Weights for the SExtractor star/galaxy classifier (V1.3)
		# inputs: 9 for profile parameters + 1 for seeing.
		# outputs: ``Stellarity index'' (0.0 to 1.0)
		# Seeing FWHM range: from 0.025 to 5.5'' (images must have 1.5 < FWHM < 5 pixels)
		# Optimized for Moffat profiles with 2<= beta <= 4.

		3 10 10 1

		-1.56604e+00 -2.48265e+00 -1.44564e+00 -1.24675e+00 -9.44913e-01 -5.22453e-01 4.61342e-02 8.31957e-01 2.15505e+00 2.64769e-01
		3.03477e+00 2.69561e+00 3.16188e+00 3.34497e+00 3.51885e+00 3.65570e+00 3.74856e+00 3.84541e+00 4.22811e+00 3.27734e+00

		-3.22480e-01 -2.12804e+00 6.50750e-01 -1.11242e+00 -1.40683e+00 -1.55944e+00 -1.84558e+00 -1.18946e-01 5.52395e-01 -4.36564e-01 -5.30052e+00
		4.62594e-01 -3.29127e+00 1.10950e+00 -6.01857e-01 1.29492e-01 1.42290e+00 2.90741e+00 2.44058e+00 -9.19118e-01 8.42851e-01 -4.69824e+00
		-2.57424e+00 8.96469e-01 8.34775e-01 2.18845e+00 2.46526e+00 8.60878e-02 -6.88080e-01 -1.33623e-02 9.30403e-02 1.64942e+00 -1.01231e+00
		4.81041e+00 1.53747e+00 -1.12216e+00 -3.16008e+00 -1.67404e+00 -1.75767e+00 -1.29310e+00 5.59549e-01 8.08468e-01 -1.01592e-02 -7.54052e+00
		1.01933e+01 -2.09484e+01 -1.07426e+00 9.87912e-01 6.05210e-01 -6.04535e-02 -5.87826e-01 -7.94117e-01 -4.89190e-01 -8.12710e-02 -2.07067e+01
		-5.31793e+00 7.94240e+00 -4.64165e+00 -4.37436e+00 -1.55417e+00 7.54368e-01 1.09608e+00 1.45967e+00 1.62946e+00 -1.01301e+00 1.13514e-01
		2.20336e-01 1.70056e+00 -5.20105e-01 -4.28330e-01 1.57258e-03 -3.36502e-01 -8.18568e-02 -7.16163e+00 8.23195e+00 -1.71561e-02 -1.13749e+01
		3.75075e+00 7.25399e+00 -1.75325e+00 -2.68814e+00 -3.71128e+00 -4.62933e+00 -2.13747e+00 -1.89186e-01 1.29122e+00 -7.49380e-01 6.71712e-01
		-8.41923e-01 4.64997e+00 5.65808e-01 -3.08277e-01 -1.01687e+00 1.73127e-01 -8.92130e-01 1.89044e+00 -2.75543e-01 -7.72828e-01 5.36745e-01
		-3.65598e+00 7.56997e+00 -3.76373e+00 -1.74542e+00 -1.37540e-01 -5.55400e-01 -1.59195e-01 1.27910e-01 1.91906e+00 1.42119e+00 -4.35502e+00

		-1.70059e+00 -3.65695e+00 1.22367e+00 -5.74367e-01 -3.29571e+00 2.46316e+00 5.22353e+00 2.42038e+00 1.22919e+00 -9.22250e-01 -2.32028e+00


		0.00000e+00
		1.00000e+00

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csst/msc/astrometry_config/csst_realtime.sex

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