def print_elemvar_table(table,outname):
    # Write the table
    elems= ['C','N','O','Na','Mg','Al','Si','S','K','Ca','Ti','V','Mn','Fe',
            'Ni']
    with open(outname,'w') as outfile:
        cnt= 0
        for elemc in elems:
            # First write total
            tline= '%s ' % elemc
            ref= table[elems.index(elemc)][cnt]
            for ii,elem in enumerate(elems):
                if elem == elemc:
                    tline+= '& %.3f' % (table[ii][cnt])
                else:
                    tline+= '& %i' % (int(round(100.*table[ii][cnt]/ref)))
            outfile.write(tline+'\\\\\n')
            cnt+= 1
            if _NO_INDIV_WINDOWS: continue
            # Now do each individual window
            for jj in range(apwindow.num(elemc,pad=0)):
                tline= '%s%i ' % (elemc,jj+1)
                ref= table[elems.index(elemc)][cnt]
                for ii,elem in enumerate(elems):
                    if elem == elemc:
                        tline+= '& %.3f' % (table[ii][cnt])
                    else:
                        tline+= '& %i' % (100.*table[ii][cnt]/ref)
                outfile.write(tline+'\\\\\n')
                cnt+= 1
    return None
Exemple #2
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def parse_elemvar():
    table= calc_elemvar_table.calc_elemvar_table('elemVariations_DR12_M67.sav')
    # Parse the table for easier use
    out1= {}
    out2= {}
    cnt= 0
    for elemc in elems:
        ref= {}
        others= {}
        cnt+= 1
        for jj in range(apwindow.num(elemc,pad=0)):
            ref[jj]= table[elems.index(elemc)][cnt]
            tothers= []
            for ii,elem in enumerate(elems):
                if elem == elemc:
                    continue
                else:
                    tothers.append(100.*table[ii][cnt]/ref[jj])
            others[jj]= tothers
            cnt+= 1
        out1[elemc]= ref
        out2[elemc]= others
    return (out1,out2)
Exemple #3
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def windows(*args, **kwargs):
    """
    NAME:
       windows
    PURPOSE:
       plot the spectral windows for a given element
    INPUT:
       Either:
          (a) wavelength, spectrum (\AA,spectrum units)
          (b) spectrum (assumed on standard APOGEE re-sampled wavelength grid)
          (c) location ID, APOGEE ID (default loads aspcapStar, loads extension ext(=1); apStar=True loads apStar spectrum)
          +element string (e.g., 'Al'); Adding 1 and 2 splits the windows into two
    KEYWORDS:
       plot_weights= (False) if True, also plot the weights for the windows (assumes that the spectrum is on the apStarWavegrid)
       markLines= mark the location of 'lines' (see apogee.spec.window.lines)
       apogee.spec.plot.waveregions keywords
    OUTPUT:
       plot to output
       The final axes allow one to put additional labels on the plot, e.g., for adding the APOGEE ID:
       bovy_plot.bovy_text(r'$\mathrm{%s}$' % '2M02420597+0837017',top_left=True)       
       Note that an ID (e.g., the apogee ID) and Teff, logg, metallicity, and alpha-enhancement labels can be added using the keywords label* above
    HISTORY:
       2015-01-26 - Written (based on older code) - Bovy (IAS)
    """
    pad = kwargs.pop('pad', 3)
    try:
        si, ei = apwindow.waveregions(args[2], pad=pad, asIndex=True)
    except IOError:
        try:
            si, ei = apwindow.waveregions(args[2][:-1], pad=pad, asIndex=True)
        except IOError:
            raise IOError(
                "Windows for element %s could not be loaded, please specify an existing APOGEE element"
                % ((args[2].lower().capitalize())))
        if args[2][-1] == '1':
            si = si[:len(si) // 2]
            ei = ei[:len(ei) // 2]
        else:
            si = si[len(si) // 2:]
            ei = ei[len(ei) // 2:]
        # Remove the number from the element
        newargs = (args[0], args[1], args[2][:-1])
        for ii in range(len(args) - 3):
            newargs = newargs + (args[ii + 3], )
        args = newargs
    # Also get the number and total width of all of the windows
    dlam = apwindow.total_dlambda(args[2], pad=pad)
    numw = apwindow.num(args[2])
    # Set spacing between windows
    if numw > 20:
        kwargs['skipdx'] = 0.003
        kwargs['_noskipdiags'] = True
    elif numw > 15:
        kwargs['skipdx'] = 0.01
    # Set initial space to zero
    kwargs['_startendskip'] = 0
    # Set initial figure width
    if not kwargs.get('overplot', False) and not 'fig_width' in kwargs:
        if dlam > 150.:
            kwargs['fig_width'] = 8.4
        else:
            kwargs['fig_width'] = 4.2
    # Don't tick x
    kwargs['_noxticks'] = True
    # Label the largest wavelength in angstrom
    kwargs['_labelwav'] = True
    # Don't label the lines unless explicitly asked for
    kwargs['labelLines'] = kwargs.get('labelLines', False)
    # Plot the weights as well
    if kwargs.pop('plot_weights', False):
        kwargs['_plotw'] = apwindow.read(args[2], apStarWavegrid=True)
        if kwargs.get('apStar', False):
            kwargs['yrange'] = kwargs.get('yrange',
                                          [0., 1.1 * numpy.nanmax(args[1])])
        else:
            kwargs['yrange'] = kwargs.get('yrange', [0., 1.2])
    # mark the 'lines'
    markLines = kwargs.get('markLines', not 'overplot' in kwargs)
    if markLines and not '_markwav' in kwargs:
        kwargs['_markwav'] = apwindow.lines(args[2])
    # Plot
    waveregions(args[0],
                args[1],
                startindxs=si,
                endindxs=ei,
                *args[3:],
                **kwargs)
    # Add label
    bovy_plot.bovy_text(r'$\mathrm{%s}$' % ((args[2].lower().capitalize())),
                        top_left=True,
                        fontsize=10,
                        backgroundcolor='w')
    return None
Exemple #4
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def windows(*args,**kwargs):
    """
    NAME:
       windows
    PURPOSE:
       plot the spectral windows for a given element
    INPUT:
       Either:
          (a) wavelength, spectrum (\AA,spectrum units)
          (b) spectrum (assumed on standard APOGEE re-sampled wavelength grid)
          (c) location ID, APOGEE ID (default loads aspcapStar, loads extension ext(=1); apStar=True loads apStar spectrum)
          +element string (e.g., 'Al'); Adding 1 and 2 splits the windows into two
    KEYWORDS:
       plot_weights= (False) if True, also plot the weights for the windows (assumes that the spectrum is on the apStarWavegrid)
       markLines= mark the location of 'lines' (see apogee.spec.window.lines)
       apogee.spec.plot.waveregions keywords
    OUTPUT:
       plot to output
       The final axes allow one to put additional labels on the plot, e.g., for adding the APOGEE ID:
       bovy_plot.bovy_text(r'$\mathrm{%s}$' % '2M02420597+0837017',top_left=True)       
       Note that an ID (e.g., the apogee ID) and Teff, logg, metallicity, and alpha-enhancement labels can be added using the keywords label* above
    HISTORY:
       2015-01-26 - Written (based on older code) - Bovy (IAS)
    """
    pad= kwargs.pop('pad',3)
    try:
        si,ei= apwindow.waveregions(args[2],pad=pad,asIndex=True)
    except IOError:
        try:
            si, ei= apwindow.waveregions(args[2][:-1],pad=pad,asIndex=True)
        except IOError:
            raise IOError("Windows for element %s could not be loaded, please specify an existing APOGEE element" % ((args[2].lower().capitalize())))
        if args[2][-1] == '1':
            si= si[:len(si)//2]
            ei= ei[:len(ei)//2]
        else:
            si= si[len(si)//2:]
            ei= ei[len(ei)//2:]
        # Remove the number from the element
        newargs= (args[0],args[1],args[2][:-1])
        for ii in range(len(args)-3):
            newargs= newargs+(args[ii+3],)
        args= newargs
    # Also get the number and total width of all of the windows
    dlam= apwindow.total_dlambda(args[2],pad=pad)
    numw= apwindow.num(args[2])
    # Set spacing between windows
    if numw > 20:
        kwargs['skipdx']= 0.003
        kwargs['_noskipdiags']= True
    elif numw > 15:
        kwargs['skipdx']= 0.01
    # Set initial space to zero
    kwargs['_startendskip']= 0
    # Set initial figure width
    if not kwargs.get('overplot',False) and not 'fig_width' in kwargs:
        if dlam > 150.:
            kwargs['fig_width']= 8.4
        else:
            kwargs['fig_width']= 4.2
    # Don't tick x
    kwargs['_noxticks']= True
    # Label the largest wavelength in angstrom
    kwargs['_labelwav']= True
    # Don't label the lines unless explicitly asked for
    kwargs['labelLines']= kwargs.get('labelLines',False)
    # Plot the weights as well
    if kwargs.pop('plot_weights',False):
        kwargs['_plotw']= apwindow.read(args[2],apStarWavegrid=True)
        if kwargs.get('apStar',False):
            kwargs['yrange']= kwargs.get('yrange',
                                         [0.,1.1*numpy.nanmax(args[1])])
        else:
            kwargs['yrange']= kwargs.get('yrange',[0.,1.2])
    # mark the 'lines'
    markLines= kwargs.get('markLines',not 'overplot' in kwargs)
    if markLines and not '_markwav' in kwargs:
        kwargs['_markwav']= apwindow.lines(args[2])
    # Plot
    waveregions(args[0],args[1],startindxs=si,endindxs=ei,
                *args[3:],**kwargs)
    # Add label
    bovy_plot.bovy_text(r'$\mathrm{%s}$' % ((args[2].lower().capitalize())),
                        top_left=True,fontsize=10,backgroundcolor='w')
    return None