def load_data(self, **kwargs): # if self.from_dict: q5file = self.data_file qpq5dict = CGMAbsSurvey.from_json(q5file) ism = LineList('ISM') qpq5dict.build_systems_from_dict(llist=ism) self.survey_data = qpq5dict #self.cgm_abs = qpq5dict.cgm_abs else: qpqdata = load_qpq(5) nmax = len(qpqdata) # max number of QSOs for i in range(nmax): # Instantiate the galaxy gal = Galaxy((qpqdata['RAD'][i], qpqdata['DECD'][i]), z=qpqdata['Z_FG'][i]) gal.L_BOL = qpqdata['L_BOL'][i] gal.L_912 = qpqdata['L_912'][i] gal.G_UV = qpqdata['G_UV'][i] gal.flg_BOSS = qpqdata['FLG_BOSS'][i] gal.zsig = qpqdata['Z_FSIG'][i] * u.km / u.s # Instantiate the IGM System igm_sys = IGMSystem( (qpqdata['RAD_BG'][i], qpqdata['DECD_BG'][i]), qpqdata['Z_FG'][i], [-5500, 5500.] * u.km / u.s, abs_type='CGM') igm_sys.zem = qpqdata['Z_BG'][i] igm_sys.NHI = qpqdata['NHI'][i] igm_sys.sig_NHI = qpqdata['SIG_NHI'][i] igm_sys.flag_NHI = qpqdata['FLG_NHI'][i] igm_sys.s2n_lya = qpqdata['S2N_LYA'][i] igm_sys.flg_othick = qpqdata['FLG_OTHICK'][i] igm_sys.z_lya = qpqdata['Z_LYA'][i] iname = qpqdata['QSO'][i] # Instantiate rho = qpqdata['R_PHYS'][i] * u.kpc cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs) aline = AbsLine(1215.67 * u.AA, closest=True, z=igm_sys.zabs, linelist=ism) aline.attrib['EW'] = qpqdata['EWLYA'][i] * u.AA # Rest EW aline.attrib['sig_EW'] = qpqdata['SIG_EWLYA'][i] * u.AA if aline.attrib['EW'] > 3. * aline.attrib['sig_EW']: aline.attrib['flag_EW'] = 1 else: aline.attrib['flag_EW'] = 3 aline.attrib['coord'] = igm_sys.coord #aline.limits._wvlim = qpqdata['WVMNX'][i]*u.AA ## (no data in QPQ7 file) #dv = ltu.rel_vel(aline.limits._wvlim, aline.wrest * (1 + qpqdata['Z_FG'][i])) #aline.limits._vlim = dv abslines = [] abslines.append(aline) comp = AbsComponent.from_abslines(abslines, chk_vel=False) cgabs.igm_sys.add_component(comp) # add metal lines for j in range(100): if qpqdata[i]['FLG_METAL_EW'][j] > 0: wave0 = qpqdata[i]['METAL_WREST'][j] iline = AbsLine(wave0 * u.AA, closest=True, z=igm_sys.zabs, linelist=ism) iline.attrib[ 'EW'] = qpqdata['METAL_EW'][i][j] * u.AA # Rest EW iline.attrib[ 'sig_EW'] = qpqdata['METAL_SIGEW'][i][j] * u.AA iline.attrib['flag_EW'] = qpqdata['FLG_METAL_EW'][i][j] iline.analy['flg_eye'] = qpqdata['FLG_METAL_EYE'][i][j] iline.attrib['coord'] = igm_sys.coord abslines = [] abslines.append(iline) comp = AbsComponent.from_abslines(abslines, chk_vel=False) cgabs.igm_sys.add_component(comp) # add ang_sep qsocoord = SkyCoord(ra=qpqdata['RAD'][i], dec=qpqdata['DECD'][i], unit='deg') bgcoord = SkyCoord(ra=qpqdata['RAD_BG'][i], dec=qpqdata['DECD_BG'][i], unit='deg') cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec') self.cgm_abs.append(cgabs)
def load_data(self, **kwargs): # #q8file = resource_filename('pyigm', 'data/CGM/QPQ/qpq8_all_measured.dat') q8file = self.data_file if self.from_dict: q8file = self.data_file qpq8dict = CGMAbsSurvey.from_json(q8file) ism = LineList('ISM') qpq8dict.build_systems_from_dict(llist=ism) self.survey_data = qpq8dict #self.cgm_abs = qpq8dict.cgm_abs else: qpqdata = Table.read(q8file, format='ascii') #nmax = len(qpqdata) # max number of QSOs q8filecoord = resource_filename('pyigm', 'data/CGM/QPQ/qpq8_pairs.fits') qpqdatacoord = Table.read(q8filecoord) if self.nmax is not None: nmax = self.nmax else: nmax = len(qpqdatacoord) #(qpqdata) # match names with qpqdatacoord qnames = [] for i in range(len(qpqdatacoord)): qname = qpqdatacoord['QSO'][i].strip() qnames.append(qname[-10:]) qnames2 = [] for i in range(len(qpqdata)): qname = qpqdata['Pair'][i] qnames2.append(qname) for j in range(nmax): # i,j # match names with qpqdatacoord i = np.where(np.asarray(qnames2) == qnames[j])[0] # Instantiate the galaxy gal = Galaxy((qpqdatacoord['RAD'][j], qpqdatacoord['DECD'][j]), z=qpqdatacoord['Z_FG'][j]) gal.L_BOL = qpqdatacoord['L_BOL'][j] gal.L_912 = qpqdatacoord['L_912'][j] gal.G_UV = qpqdatacoord['G_UV'][j] gal.zsig = qpqdatacoord['Z_FSIG'][j] * u.km / u.s # Instantiate the IGM System igm_sys = IGMSystem( (qpqdatacoord['RAD_BG'][j], qpqdatacoord['DECD_BG'][j]), qpqdatacoord['Z_FG'][j], [-5500, 5500.] * u.km / u.s, abs_type='CGM') # Redshifts: QSO emission redshifts igm_sys.zem = qpqdatacoord['Z_BG'][j] igm_sys.NHI = qpqdata['HIcol'][i] igm_sys.sig_NHI = [ qpqdata['HIcolhierr'][i], qpqdata['HIcolloerr'][i] ] igm_sys.s2n_lya = qpqdatacoord['S2N_LYA'][j] iname = qpqdata['Pair'][i][0] #+'_'+qpqdata['subsys'][i] # Instantiate rho = qpqdatacoord['R_PHYS'][j] * u.kpc cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs) ### add metal lines ### not included CII*, SiII* lines = [ ['CII 1334'], ## ['CII* 1335'], ['CIV 1548', 'CIV 1550'], ['NI 1134', 'NI 1199'], ['NII 1083'], ['NV 1238', 'NV 1242'], ['OI 1302'], ['OVI 1037'], ['MgI 2852'], ['MgII 2796', 'MgII 2803'], ['AlII 1670'], ['AlIII 1854', 'AlIII 1862'], [ 'SiII 1190', 'SiII 1193', 'SiII 1304', 'SiII 1260', 'SiII 1526', 'SiII 1808' ], ## ['SiII* 1264'], ['SiIII 1206'], ['SiIV 1393', 'SiIV 1402'], [ 'FeII 1608', 'FeII 2344', 'FeII 2374', 'FeII 2382', 'FeII 2586', 'FeII 2600' ], ['FeIII 1122'] ] for kk in i: for icmp in range(len(lines)): abslines = [] for ii in range(len(lines[icmp])): wave0 = float(lines[icmp][ii].split(' ')[1]) ewstr = str(lines[icmp][ii].split(' ')[1]) + 'EW' ewerrstr = str( lines[icmp][ii].split(' ')[1]) + 'EWerr' if ewstr == '1808EW': ewstr = '1808E' if ewerrstr == '1122EWerr': ewerrstr = '122EWerr' if qpqdata[ewstr][kk] != '/': # find z v0 = 0.5 * ( qpqdata['v_lobound'][kk] + qpqdata['v_upbound'][kk]) * u.km / u.s dv = v0 zref = igm_sys.zabs z_cmp = ltu.z_from_dv(dv, zref) ## vlim v1 = qpqdata['v_lobound'][kk] * u.km / u.s z1 = ltu.z_from_dv(v1, zref) v1_cmp = ltu.dv_from_z(z1, z_cmp) v2 = qpqdata['v_upbound'][kk] * u.km / u.s z2 = ltu.z_from_dv(v2, zref) v2_cmp = ltu.dv_from_z(z2, z_cmp) # iline iline = AbsLine(wave0 * u.AA, closest=True, z=z_cmp) iline.attrib['coord'] = igm_sys.coord ## EW iline.attrib['EW'] = float( qpqdata[ewstr][kk]) * u.AA # Rest EW iline.attrib['sig_EW'] = float( qpqdata[ewerrstr][kk]) * u.AA flgew = 1 if iline.attrib[ 'EW'] < 3. * iline.attrib['sig_EW']: flgew = 3 iline.attrib['flag_EW'] = flgew ## column densities colstr = str( lines[icmp][ii].split(' ')[0]) + 'col' colerrstr = str( lines[icmp][ii].split(' ')[0]) + 'colerr' iline.attrib['logN'] = qpqdata[colstr][kk] iline.attrib['sig_logN'] = qpqdata[colerrstr][ kk] abslines.append(iline) if len(abslines) > 0: comp = AbsComponent.from_abslines(abslines, chk_vel=False) comp.limits._vlim = [v1_cmp.value, v2_cmp.value ] * u.km / u.s cgabs.igm_sys.add_component(comp) # add ang_sep qsocoord = SkyCoord(ra=qpqdatacoord['RAD'][j], dec=qpqdatacoord['DECD'][j], unit='deg') bgcoord = SkyCoord(ra=qpqdatacoord['RAD_BG'][j], dec=qpqdatacoord['DECD_BG'][j], unit='deg') cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec') self.cgm_abs.append(cgabs)
def load_data(self, **kwargs): # q6file = self.data_file if self.from_dict: qpq6dict = CGMAbsSurvey.from_json(q6file) ism = LineList('ISM') qpq6dict.build_systems_from_dict(llist=ism) self.survey_data = qpq6dict #self.cgm_abs = qpq6dict.cgm_abs else: qpqdata = Table.read(q6file) if self.nmax is not None: nmax = self.nmax else: nmax = len(qpqdata) for i in range(nmax): # Instantiate the galaxy gal = Galaxy((qpqdata['RAD'][i], qpqdata['DECD'][i]), z=qpqdata['Z_FG'][i]) gal.L_BOL = qpqdata['L_BOL'][i] gal.L_912 = qpqdata['L_912'][i] gal.G_UV = qpqdata['G_UV'][i] gal.flg_BOSS = qpqdata['FLG_BOSS'][i] gal.zsig = qpqdata['Z_FSIG'][i] * u.km / u.s # Instantiate the IGM System igm_sys = IGMSystem( (qpqdata['RAD_BG'][i], qpqdata['DECD_BG'][i]), qpqdata['Z_FG'][i], [-5500, 5500.] * u.km / u.s, abs_type='CGM' ) ## if velocity range lower - does not load all abslines igm_sys.zem = qpqdata['Z_BG'][i] igm_sys.NHI = qpqdata['NHI'][i] igm_sys.sig_NHI = qpqdata['SIG_NHI'][i] igm_sys.flag_NHI = qpqdata['FLG_NHI'][i] igm_sys.s2n_lya = qpqdata['S2N_LYA'][i] igm_sys.flg_othick = qpqdata['FLG_OTHICK'][i] igm_sys.z_lya = qpqdata['Z_LYA'][i] iname = qpqdata['QSO'][i] # Instantiate rho = qpqdata['R_PHYS'][i] * u.kpc cgabs = CGMAbsSys(gal, igm_sys, name=iname, rho=rho, **kwargs) aline = AbsLine(1215.67 * u.AA, closest=True, z=igm_sys.zabs) aline.attrib['EW'] = qpqdata['EWLYA'][i] * u.AA # Rest EW aline.attrib['sig_EW'] = qpqdata['SIG_EWLYA'][i] * u.AA if aline.attrib['EW'] > 3. * aline.attrib['sig_EW']: aline.attrib['flag_EW'] = 1 else: aline.attrib['flag_EW'] = 3 aline.attrib['coord'] = igm_sys.coord aline.limits._wvlim = qpqdata['WVMNX'][i] * u.AA dv = ltu.rel_vel(aline.limits._wvlim, aline.wrest * (1 + qpqdata['Z_FG'][i])) aline.limits._vlim = dv abslines = [] abslines.append(aline) ### comp = AbsComponent.from_abslines(abslines, chk_vel=False) # add ang_sep qsocoord = SkyCoord(ra=qpqdata['RAD'][i], dec=qpqdata['DECD'][i], unit='deg') bgcoord = SkyCoord(ra=qpqdata['RAD_BG'][i], dec=qpqdata['DECD_BG'][i], unit='deg') cgabs.ang_sep = qsocoord.separation(bgcoord).to('arcsec') cgabs.igm_sys.add_component(comp) self.cgm_abs.append(cgabs)