Python AbsLine.analy['datafile']方法代码示例

# 需要导入模块: from linetools.spectralline import AbsLine [as 别名]
# 或者: from linetools.spectralline.AbsLine import analy['datafile'] [as 别名]
    def parse_absid_file(self, abs_fil):

        from xastropy import spec as xxspec 
        if self.linelist is None:
            self.linelist = LineList('ISM')
        # FITS binary table
        hdu = fits.open(abs_fil)
        table = hdu[1].data
        newz = table[0]['ZABS']
        if (self.zabs > 0.) & (np.abs(self.zabs-newz) > 1e-4):
            print('WARNING: Updating zabs from {:s}'.format(abs_fil))
        self.zabs = newz
        self.absid_file = abs_fil

        # Load up lines
        for row in table:
            aline = AbsLine(row['WREST']*u.AA, linelist=self.linelist,
                closest=True)
            # Velocity limits and flags
            try:
                aline.analy['vlim'] = row['VLIM'] * u.km/u.s
            except KeyError:
                aline.analy['vlim'] = row['DV'] * u.km/u.s
            try:
                aline.analy['do_analysis'] = row['do_analysis']
            except KeyError:
                aline.analy['do_analysis'] = row['FLG_ANLY']
            aline.analy['flg_eye'] = row['FLG_EYE']
            aline.analy['flg_limit'] = row['FLG_LIMIT']
            try:
                aline.analy['datafile'] = row['datafile']
            except KeyError:
                aline.analy['datafile'] = row['DATFIL']
            aline.analy['spec'] = None # Spectrum
            aline.attrib['z'] = self.zabs
            # Append
            self.lines.append(aline)
            ''' OLD FORMAT

# 需要导入模块: from linetools.spectralline import AbsLine [as 别名]
# 或者: from linetools.spectralline.AbsLine import analy['datafile'] [as 别名]
 def generate_line(self, inp):
     ''' Generate a new line, if it doesn't exist
     Parameters:
     ----------
     inp: tuple
       (z,wrest)
     '''
     # Generate?
     if self.grab_line(inp[1]) is None:
         #QtCore.pyqtRemoveInputHook()
         #xdb.set_trace()
         #QtCore.pyqtRestoreInputHook()
         newline = AbsLine(inp[1],linelist=self.llist[self.llist['List']])
         print('VelPlot: Generating line {:g}'.format(inp[1]))
         newline.analy['vlim'] = self.vmnx/2.
         newline.attrib['z'] = self.abs_sys.zabs
         newline.analy['do_analysis'] = 1 # Init to ok
         # Spec file
         if self.spec_fil is not None:
             newline.analy['datafile'] = self.spec_fil
         # Append
         self.abs_lines.append(newline)

# 需要导入模块: from linetools.spectralline import AbsLine [as 别名]
# 或者: from linetools.spectralline.AbsLine import analy['datafile'] [as 别名]
def jenkins2005():
    """Jenkins, E. et al. 2005, ApJ, 2005, 623, 767
    PHL 1811
    HST/STIS, FUSE
    Metals parsed from Table 1
      OI taken from text
      Had to input error on columns by hand (JXP)
    Total NHI from Lyman series. see Fig 3
    M/H from O/H
    """
    # Grab ASCII file from ApJ
    tab_fil = pyigm_path+"/data/LLS/Literature/jenkins2005.tb1.ascii"
    chk_fil = glob.glob(tab_fil)
    if len(chk_fil) > 0:
        tab_fil = chk_fil[0]
    else:
        url = 'http://iopscience.iop.org/0004-637X/623/2/767/fulltext/61520.tb1.txt'
        print('LLSSurvey: Grabbing table file from {:s}'.format(url))
        f = urllib2.urlopen(url)
        with open(tab_fil, "wb") as code:
            code.write(f.read())
    # Setup
    radec = '215501.5152-092224.688'  # SIMBAD
    lls = LLSSystem(name='PHL1811_z0.081', radec=radec, zem=0.192,
        zabs=0.080923, vlim=[-100., 100.]*u.km/u.s, NHI=17.98, ZH=-0.19,
        sig_NHI=np.array([0.05,0.05]))
    lls.lines = []  # Probably not used

    # AbsLines
    ism = LineList('ISM')
    Nsig = {'C IV': 0.4, 'N II': 0.4, 'Si II': 0.05, 'Si IV': 0.25, 
        'S II': 0.2, 'Fe II': 0.12, 'H I': 0.05, 'S III': 0.06}

    # Parse Table
    with open(tab_fil,'r') as f:
        flines = f.readlines()
    ion_dict = {}
    for iline in flines:
        iline = iline.strip()
        if (len(iline) == 0): 
            continue
        # Split on tabs
        isplit = iline.split('\t')
        # Offset?
        ioff = 0
        if isplit[0][0] in ['1','2']:
            ioff = -1
        # Catch bad lines
        if (isplit[1+ioff][0:6] in ['1442.0','1443.7','1120.9']): # Skip goofy CII line and CII*
            continue
        if len(isplit[2+ioff]) == 0: 
            continue
        # Ion
        if (len(isplit[0].strip()) > 0) & (isplit[0][0] not in ['1','2']):
            ionc = isplit[0].strip()
            try:
                Zion = ltai.name_ion(ionc)
            except KeyError:
                pdb.set_trace()
        # Generate the Line
        try:
            newline = AbsLine(float(isplit[2+ioff])*u.AA,linelist=ism, closest=True)
        except ValueError:
            pdb.set_trace()
        newline.attrib['z'] = lls.zabs
        # Spectrum
        newline.analy['datafile'] = 'STIS' if 'S' in isplit[1] else 'FUSE'
        # EW
        try:
            EWvals = isplit[4+ioff].split(' ')
        except IndexError:
            pdb.set_trace()
        newline.attrib['EW'] = float(EWvals[0])*u.AA/1e3
        newline.attrib['sig_EW'] = float(EWvals[2])*u.AA/1e3
        newline.attrib['flag_EW'] = 1
        if len(isplit) < (5+ioff+1):
            continue
        # Colm?
        #xdb.set_trace()
        newline.attrib['sig_logN'] = 0.
        if (len(isplit[5+ioff].strip()) > 0) & (isplit[5+ioff].strip() != '\\ldots'):
            if isplit[5+ioff][0] == '\\':
                ipos = isplit[5+ioff].find(' ')
                newline.attrib['logN'] = float(isplit[5+ioff][ipos+1:])
                newline.attrib['flag_N'] = 2
            elif isplit[5+ioff][0] == '<':
                ipos = 0
                newline.attrib['logN'] = float(isplit[5+ioff][ipos+1:])
                newline.attrib['flag_N'] = 3
            elif isplit[5+ioff][0] == '1':
                try:
                    newline.attrib['logN'] = float(isplit[5+ioff][0:5])
                except ValueError:
                    pdb.set_trace()
                newline.attrib['flag_N'] = 1
                try:
                    newline.attrib['sig_logN'] = Nsig[ionc]
                except KeyError:
                    print('No error for {:s}'.format(ionc))
            else:
#.........这里部分代码省略.........