SNID manual

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Contents: snid | logwave | plotlnw

This file discusses in turn the following three programs:

1. snid -- the SNID cross-correlation program
2. logwave -- program to create SNID spectral templates
3. plotlnw -- program to plot SNID spectral templates

1. snid

1.1. Syntax

	snid [options] spec1.dat[,spec2.dat,...] [templates.lnw]

spec1.dat is a file containing the input spectrum in two-column format. First column should be the wavelength (in Angstroms); second column can be flux, magnitudes, ADUs, etc. Lines starting with '#' are considered comments and are ignored. [See the file sn2003jo.dat in the examples/ directory for an example input spectrum]. The simplest use of SNID is then:

	snid spec1.dat

	snid spec1.dat,spec2.dat

	snid spec1.dat templates/*.lnw

1.2. Options

NOTE: The defaults for each option were chosen for a reason. Make sure you understand what each option does before overriding the default values when running SNID. A detailed description of each option is given below.

> snid
 S u p e r N o v a    I D e n t i f i c a t i o n (SNID v5.0, 24 Aug 2007)
 Copyright (C) 1999-2007 S. Blondin and J. L. Tonry

 Usage: snid [options] spec1.dat[,spec2.dat,...] [templates.lnw]

 options (default):
   INPUT SPECTRUM:
     wmin=               lower wavelength limit (data)
     wmax=               upper wavelength limit (data)
     wmask=              file containing wavelength mask (NA)
     fwmed=              median filtering width [Angstroms] (0.)
     medlen=             median filtering width [pixels] (1.)
     emclip=             clip emission at this redshift (NA)
     skyclip=0/1         clip sky emission lines (0)
     emwid=              emission clip width in Angstroms (40)
     aband=0/1           keep A band (1)
   TEMPLATE SPECTRA:
     agemin=             lower age limit (-90)
     agemax=             upper age limit (+1000)
     [age= dage=         alternate age range]
     deltamin=           lower delta limit (-9.99)
     deltamax=           upper delta limit (99.9)
     [delta= ddelta=     alternate delta range]
     nminspec=           minimum number of spectra per template (1)
     use=temp1,...       only use these templates (NA)
     usetype=type1,...   only use these (sub)types (NA)
     avoid=temp1,...     avoid these templates (NA)
     avoidtype=type1,... avoid these (sub)types (NA)
   REDSHIFT/CORRELATION:
     rlapmin=            minimum rlap listed (5.0)
     lapmin=             minimum overlap allowed (0.4)
     zmin=               lower redshift limit (-0.01)
     zmax=               upper redshift limit (1.2)
     [z= dz=             alternate z range]
     forcez=             forced initial redshift (NA)
     zfilter=            redshift filter for final median (0.02)
     k{1,2,3,4}=         bandpass filter range (1,4,85,102)
   OTHER:
     param=              get options from specified parameter file (NA)
     fout=(-1)-n         file output level (0)
     fluxout=n           write top n fluxed spectra to file
     flatout=n           write top n flattened spectra to file
     xcorout=n           write top n correlation functions to file
     tempdir=            template directory (see snidmore.f)
     plot=0/1            enable plotting (1)
     iquery=0/1          allow user to change initial redshift (1)
     inter=0/1           interactive (1)
     verbose=0-2         verbose level (2)

 [see file Howto.snid for more info]

INPUT SPECTRUM:

wmin= wmax= (data)
restrict wavelength range (in Angstroms) of input spectrum over which the correlation is computed. This option is often used to ignore noisy edges in the input spectrum. E.g.:

	snid wmin=4500 wmax=8500 spec1.dat

wmask= (NA)
specify a file containing wavelength ranges (one range per line) to mask out from the input spectrum. Lines starting with '#' are considered comments and are ignored. This option can be used to mask out chip gaps, bad columns etc. in the input spectrum. [See the file snid.wmask in the examples/ directory for an example mask file]. E.g.:

	snid wmask=examples/snid.wmask spec1.dat

fwmed= (0.)
specify a median filtering width (in Angstroms) to apply to the input spectrum. E.g.:

	snid fwmed=40 spec1.dat

medlen= (1.)
specify a median filtering width (in pixels) to apply to the input spectrum. E.g.:

	snid medlen=20 spec1.dat

emclip= (NA)
clip galaxy emission lines at the specified redshift. If strong emission lines dominated the input spectrum, use this option to avoid spurious correlation peaks. E.g.:

	snid emclip=0.357 spec1.dat

skyclip=0/1 (0)
set to 1 if you want to clip major sky lines from input spectrum. E.g.:

	snid skyclip=1 spec1.dat

emwid= (40)
set the emission clip width (in Angstroms; applies to both the emclip= and skyclip= options). E.g.:

	snid skyclip=1 emwid=20 spec1.dat
	snid emclip=0.357 emwid=20 spec1.dat

aband=0/1 (1)
set to 0 if you want to ignore the telluric A-band in the correlation. E.g.:

	snid aband=0 spec1.dat

TEMPLATE SPECTRA:

agemin= agemax= (-90,+1000)
[age= dage= (NA,3)]
restrict the ages (in days) of template spectra to use in the correlation. This option is useful when you have prior information on the supernova age (e.g. from a light curve). Note that this option does not apply to non-SN templates (AGN, galaxy, LBV, M-star), nor to SN for which the date of maximum is unknown (see tfirstlist file in the templates/ directory). This option can be alternatively specified using a central age and a +/- range using age= dage=. E.g.:

	snid agemin=-10 agemax=10 spec1.dat
  OR	snid age=0 dage=10 spec1.dat

deltamin= deltamax= (-9.99,99.9)
[delta= ddelta= (NA,0.2)]
restrict the decline rates (delta_m15) of template spectra to use in the correlation. Note that this option does not apply to non-SN templates (AGN, galaxy, LBV, M-star), nor to SN for which the date of maximum is unknown (see the tfirstlist file in the templates/ directory). This option can be alternatively specified using a central delta and a +/- range using delta= ddelta=. E.g.:

	snid deltamin=1.2 deltamax=1.4 spec1.dat
  OR	snid delta=1.3 ddelta=0.1 spec1.dat

nminspec= (1)
restrict the correlation to templates (within the age and delta limits) that have at least nminspec spectra. E.g.:

	snid nminspec=10 spec1.dat

use=temp1,... (NA)
use only these templates in the correlation. The value for this option is a comma-separated list of template names (without the '.lnw' suffix). E.g.:

	snid use=sn94D,sn98aq spec1.dat

usetype=type1,... (NA)
use only these template (sub)types in the correlation. The value for this option is a comma-separated list of template names. See the table below for the available (sub)type names (see also source/typeinfo.f). These names are case-sensitive!

	snid usetype=Ia spec1.dat	[use only SN Ia (all subtypes)]
	snid usetype=Ia-norm spec1.dat	[use only "normal" SN Ia]
	snid usetype=Ib,Ic		[use only SN Ib/c (all subtypes)]

avoid=temp1,... (NA)
avoid these templates in the correlation. The value for this option is a comma-separated list of template names (without the '.lnw' suffix). E.g.:

	snid avoid=sn94D,sn98aq spec1.dat

avoidtype=type1,... (NA)
avoid these template (sub)types in the correlation. The value for this option is a comma-separated list of template names. See the table below for the available (sub)type names (see also source/typeinfo.f). These names are case-sensitive!

	snid avoidtype=Ia spec1.dat	  [avoid SN Ia (all subtypes)]
	snid avoidtype=Ia-norm spec1.dat  [avoid "normal" SN Ia]
	snid avoidtype=Ib,Ic		  [avoid SN Ib/c (all subtypes)]

REDSHIFT/CORRELATION:

rlapmin= (5.0)
set the minimum rlap value. The rlap parameter is akin to a quality parameter: the higher the rlap, the better the correlation (see Blondin & Tonry 2007 [ADS, astro-ph] for a formal definition). Generally, correlations with rlap < 5.0 are not worth considering, but you may want to see what you get by increasing rlapmin. Make sure you know what you're doing before changing the value of rlapmin! Correlations with rlap < rlapmin are not used for type, redshift, and age statistics. E.g.:

	snid rlapmin=10 spec1.dat

lapmin= (0.4)
set the minimum lap value. The lap parameter measures the amount of overlap between the input and template spectra at the correlation redshift (see Blondin & Tonry 2007 [ADS] for a formal definition). Generally, correlations with lap < 0.4 are not worth considering, but you may want to see what you get by increasing lapmin. Make sure you know what you're doing before changing the value of lapmin! Correlations with lap < lapmin are not used for type, redshift, and age statistics. E.g.:

	snid lapmin=0.45 spec1.dat

zmin= zmax= (-0.01,1.2)
[z= dz= (NA,0.1)]
restrict the redshift range over which to compute the correlation. This option is useful when you have prior information on the supernova redshift (e.g. from a photo-z). This option can be alternatively specified using a central redshift and a +/- range using z= dz=. E.g.:

	snid zmin=0.2 zmax=0.4 spec1.dat
  OR	snid z=0.3 dz=0.1 spec1.dat

forcez= (NA)
force the initial redshift guess at this redshift. SNID normally runs a first set of correlations to estimate an initial redshift guess, then runs a second set of correlations with the input and template spectra trimmed to match at this redshift. Setting forcez= will skip the first round of correlations. This is useful when you know the redshift, e.g., from a galaxy spectrum. E.g.:

	snid forcez=0.357 spec1.dat

zfilter= (0.02)
redshift filter for final statistics. Correlation redshifts that differ from the initial redshift estimate by more than zfilter are tagged "bad" correlations and are not used for type, redshift, and age statistics. Make sure you know what you're doing before changing the value of zfilter! E.g.:

	snid zfilter=0.01 spec1.dat

k{1,2,3,4}= (1,4,85,102)
bandpass filter range, in bin indices (assuming the total number of bins is nw=1024). The (k1,k2,k3,k4) wavenumbers define the filter shape (a cosine bell). The filter is 0 for k ≤ k1 or k ≥ k4, rises from 0 to 1 for k1 < k < k2, is 1 for k2 ≤ k ≤ k3, and declines from 1 to 0 for k3 < k < k4. You will most certainly *never* want to change the default values of k{1,2,3,4}, but who knows. E.g.:

	snid k3=43 k4=51 spec1.dat 	[for a lower-pass filter]
	snid k1=21 k2=26 spec1.dat	[for a higher-pass filter]

OTHER:

param= (NA)
specify an input parameter file setting default values for various options. [See the file snid.param in the examples/ directory for an example parameter file]. Note that every time SNID is run, a snid.param file is created with all the option values for that run. This option is useful when running SNID on an entire data set with the same settings.

You can either edit the snid.param in the examples/ directory directly, or run SNID on one input spectrum with the appropriate settings, e.g.:

	snid agemin=-10 forcez=0.357 wmax=8500 spec1.dat

	cp snid.param mysnid.param		[rename snid.param]
  THEN	snid param=mysnid.param spec2.dat

fout=(-1)-n (0)
file output level. If -1 then no output is written (not recommended). If 0 then a generic output file called <ROOTSPEC>_snid.output is created, where <ROOTSPEC> is the root name of your input spectrum (e.g. spec1 for spec1.dat). [See the file sn2003jo_snid.output in the examples/ directory for an example output file]. This is the default setting. If fout > 1 then the same generic output file is created, AND fluxout=, flatout=, and xcorout= (see below) are set to that value. E.g.:

	snid fout=-1 spec1.dat 	[no output written-- not recommended]

	snid fout=2 spec1.dat	[this will create spec1_snid.output
				 and set fluxout=2, flatout=2, and
				 xcorout=2]

fluxout=n (0)
write the top n fluxed (i.e. non-flattened-- see the example run section below) template spectra, as well as the fluxed input spectrum, to files. By 'top n' we mean the template spectra with the highest rlap value. The input fluxed spectrum is written to an output file named <ROOTSPEC>_snidflux.dat, where <ROOTSPEC> is the root name of your input spectrum (e.g. spec1 for spec1.dat). The top n template spectra are written to output files named <ROOTSPEC>_comp[000]n_snidflux.dat, where [000]n is the rank of the template spectrum (i.e. '0001' for the template spectrum with the highest rlap value). [See the files named sn2003jo_*snidflux.dat in the examples/ directory for example output fluxed spectra]. E.g.:

	snid fluxout=3 spec1.dat

flatout=n (0)
write the top n flattened (see the example run section below) template spectra, as well as the flattened input spectrum, to files. By 'top n' we mean the template spectra with the highest rlap value. The input flattened spectrum is written to an output file named <ROOTSPEC>_snidflat.dat, where <ROOTSPEC> is the root name of your input spectrum (e.g. spec1 for spec1.dat). The top n template spectra are written to output files named <ROOTSPEC>_comp[000]n_snidflat.dat, where [000]n is the rank of the template spectrum (i.e. '0001' for the template spectrum with the highest rlap value). [See the files named sn2003jo_*snidflat.dat in the examples/ directory for example output flattened spectra]. E.g.:

	snid flatout=3 spec1.dat

xcorout=n (0)
write the top n cross-correlation functions (untrimmed and trimmed-- see the example run section below) to files. By 'top n' we mean the cross-correlation functions corresponding to the templates with the highest rlap value. The untrimmed cross-correlation function are written to output files named <ROOTSPEC>_comp[000]n_snidxcor.dat, where <ROOTSPEC> is the root name of your input spectrum (e.g. spec1 for spec1.dat), and [000]n is the rank of the template spectrum (i.e. '0001' for the template spectrum with the highest rlap value). The correlation functions trimmed at the initial redshift, or 'trimmed' correlation functions, are written to output files named <ROOTSPEC>_comp[000]n_snidxcor_trim.dat [See the files named sn2003jo_*snidxcor*.dat in the examples/ directory for example output cross-correlation functions]. E.g.:

	snid xcorout=3 spec1.dat

tempdir= (see snidmore.f)
Specify a directory containing the SNID spectral templates other than the one specified in snidmore.f at installation [see the Installation instructions]. E.g.:

	snid tempdir=/home/username/more_templates/ spec1.dat

	ls *.lnw > templist

plot=0/1 (1)
set to 0 to disable interactive plotting. This can be useful when running SNID on a large data set in batch-processing mode. E.g.:

	snid plot=0 spec1.dat

iquery=0/1 (1)
set to 0 to skip the user query to change the initial redshift estimate (i.e. Do you want to enter a new redshift? (y/n) [n]: -- see the example run section below). Since the time it takes to type 'iquery=0' is longer than hitting the <CR> key when prompted to enter a new redshift, you probably will not be using this option often. Nevertheless:

	snid iquery=0 spec1.dat

inter=0/1 (1)
set to 0 to turn interactive mode off. In this case the user will not be prompted for any input.

	snid inter=0 spec1.dat

verbose=0-2 (2)
set the verbose level. If 0 then no output is written to the screen, which can be useful for processing large datasets. In this case then inter is set to 0 also (see above). E,g.:

	snid verbose=0 plot=0 spec1.dat		[no output to screen
						 or interactive plotting]

	snid verbose=1 spec1.dat		[slightly less verbose
                                                 output]

1.3. Example run

In what follows we will go through an example run. If this is the first time you use SNID then read this carefully, as all the important aspects are covered.

First you need to go to the test/ directory, which contains an example input spectrum, sn2003jo.dat. Then simply run snid with no options by typing:

	snid sn2003jo.dat

 S u p e r N o v a    I D e n t i f i c a t i o n (SNID v5.0, 24 Aug 2007)

 Searching in redshift range: -0.010  1.200 ; rlapmin =  5.00
 Restricting to age range:  -90.0 1000.0
 Restricting to delta range:  -10.0   99.9
 Reading data file: sn2003jo.dat
 Restricting to wavelength range:    4335.2   8915.3
 Reading template files...agn kcE kcS0 kcSB1 kcSB2 kcSB3 kcSB4 kcSB5
 kcSB6 kcSa kcSb kcSc lbv01ac lbv03hy lbv99bw mstar sn00E sn00H sn00cx
 sn01el sn02ap sn02bo sn02cx sn02er sn02ic sn03cg sn03du sn03fg sn04S
 sn04aw sn04dj sn04eo sn04et sn05bf sn05cs sn05gj sn05hj sn05hk sn05kl
 sn06aj sn06bp sn06gz sn79C sn80K sn81B sn83N sn83V sn84L sn86G sn87A
 sn88L sn89B sn90B sn90I sn90K sn90N sn90O sn90U sn90aa sn91A sn91M
 sn91N sn91T sn91ar sn91bg sn92A sn92H sn92ar sn93J sn93ac sn94D sn94I
 sn94M sn94Q sn94S sn94T sn94ae sn95D sn95E sn95F sn95ac sn95al sn95bd
 sn96C sn96L sn96X sn96cb sn97br sn97cn sn97cy sn97dc sn97dd sn97dq
 sn97ef sn97ei sn98S sn98T sn98aq sn98bu sn98bw sn98dt sn99aa sn99ac
 sn99aw sn99by sn99di sn99dn sn99ee sn99em sn99ex sn99gi  done 
 Loaded  1515 spectra out of  111 templates
 Searching all correlation peaks... done
 Initial redshift estimate: z = 0.532
 Do you want to enter a new redshift? (y/n) [n]: 

The next five lines of text report on various parameter settings. Here for instance SNID will consider correlations in the redshift interval 0.1 ≤ z ≤ 1.2, and only use correlations with rlap ≥ 5.0 to compute type, redshift, and age statistics. Only templates in the age range -90 ≤ age ≤ +1000 [days] and with -10 ≤ dm15 ≤ 99.9 will be used (i.e. all templates in this case). The input file is sn2003jo.dat, and the wavelength range is restricted by default to be that of the input spectrum, or 4335.2 ≤ lambda ≤ 8915.3 in this case.

The next line starting with:

	Reading template files...agn kcE kcS0 kcSB1 kcSB2 kcSB3 kcSB4 kcSB5

SNID then correlates the input spectrum (sn2003jo.dat) with each of the 1515 template spectra. The 10 best peaks in each correlation function (i.e. a total of 15150 peaks here) are fitted and the corresponding redshift is determined. The input and template spectra are then trimmed to match at that redshift and the corresponding lap parameter is calculated. If lap ≥ lapmin, the redshift is saved.

	Searching all correlation peaks... done	

SNID then computes an initial redshift estimate as an rlap-weighted median of all the correlations redshifts with lap ≥ lapmin (up to a maximum of 15150 here), and reports this value to the screen:

	Initial redshift estimate: z = 0.532

	No peaks are good, setting z = 0.000

If forcez= is set, SNID skips the initial redshift estimate and does not prompt the user for a new redshift (see below). Instead, it simply displays the message below: (E.g., if forcez=.524)

	Forcing initial redshift: 0.524

	Do you want to enter a new redshift? (y/n) [n]:

	 Enter a new redshift:

SNID then runs a second round of correlations, trimming the input and template spectra such that they overlap at the initial redshift estimate (or user-input redshift):

 	Trimming spectra to match at z = 0.532

NOTE: if none of the 'lap' values exceed the minimum set by lapmin, the user is prompted for a new redshift or a new value of lapmin:

 	No template meets lap >= lapmin at redshift z = redshift
 	Enter a new (1) redshift; (2) lapmin; or (q)uit:

Otherwise, SNID looks for all templates that satisfy the following conditions:

1. |z - z_initial| < zfilter
2. rlap ≥ rlapmin,

 	No template meets |z-0.532| < zfilter and rlap >= rlapmin
 	Enter a new (1) redshift; (2) zfilter; (3) rlapmin; (4) lapmin; or (q)uit:

Otherwise, SNID attempts to classify the input spectrum and outputs the following table:

                                SNID RESULTS

 No.  Temp/Misc     Type        Subtype      Redshift         Age
==========================================================================
 Best-match template(s):
   1  sn99ee        Ia          Ia-norm      0.528 (0.005)     7.1
 NOTE: the top  65 ( 1) templates have same type (subtype)
--------------------------------------------------------------------------
 Best type(s):
 [fraction]
   1  100.0%        Ia          ---          0.531 (0.008)     0.8 (  4.6)
 [slope]
 NOTE: all null slopes
--------------------------------------------------------------------------
 Best subtype(s):
 [fraction]
   1   92.3%        Ia          Ia-norm      0.530 (0.008)     0.6 (  4.8)
 [slope]
   1   0.040        Ia          Ia-91T       0.536 (0.005)     1.9 (  1.9)
==========================================================================

 NOTE: Favoured type is: Ia, but there is no favoured subtype

 Hit <CR> to view template listings, or (q)uit listings and move on:

SNID classifies the templates according to their 'rlap' value (akin to a quality parameter: the higher the rlap, the better the correlation; see Blondin & Tonry 2007 [ADS, astro-ph] for a formal definition), and displays the templates with the highest rlap value:

 	No.  Temp/Misc     Type        Subtype      Redshift         Age
       ==========================================================================
 	Best-match template(s):
 	  1  sn99ee        Ia          Ia-norm      0.528 (0.005)     7.1
 	NOTE: the top  65 ( 1) templates have same type (subtype)

The next section of the table displays some statistics on the type (not subtype) determination: i.e. one of Ia, Ib, Ic, II, or NotSN:

 	No.  Temp/Misc     Type        Subtype      Redshift         Age
       ==========================================================================
 	Best type(s):
 	[fraction]
 	  1  100.0%        Ia          ---          0.531 (0.008)     0.8 (  4.6)
 	[slope]
 	NOTE: all null slopes

1. [fraction] the highest fraction of templates of a given type with rlap ≥ rlapmin
2. [slope] the highest increase of fraction with increasing rlap

The results in the [slope] section will become clearer with the graphical interface, so we will return to it later. In the meantime, note that SNID reports all of the fraction vs. rlap curves to have null slope, so the type determination is not affected by this.

NOTE: sometimes there are several best types (e.g. 50% Ia and 50% Ic), in which case a WARNING! is issued.

The next section of the table displays some statistics on the subtype determination:

 	No.  Temp/Misc     Type        Subtype      Redshift         Age
       ==========================================================================
 	Best subtype(s):
 	[fraction]
 	  1   92.3%        Ia          Ia-norm      0.530 (0.008)     0.6 (  4.8)
 	[slope]
 	  1   0.040        Ia          Ia-91T       0.536 (0.005)     1.9 (  1.9)

Here we see that the best subtype is 'Ia-norm', with 92.3% of templates with rlap ≥ rlapmin corresponding to this subtype. The median redshift for all these Ia-norm templates is 0.530 with a standard deviation of 0.008, and the median age is 0.6 days past maximum with a standard deviation of 4.8 days.

Note that the results in the [slope] section are somewhat different, with the best subtype being 'Ia-91T' with a slope of 0.040. The median redshift for all these Ia-91T templates is 0.536 with a standard deviation of 0.005, and the median age is 1.9 days past maximum with a standard deviation of 1.9 days.

Here we can explain how the 'slope' is calculated. We first make an array of integer rlap values ranging from rlapmin to the highest rlap value. Here rlapmin = 5.0, and the highest rlap value is 10.8 (see below), so the rlap array will look like:

	rlap_i = 5, 6, 7, 8, 9, 10

	           rlap_i =    5    6    7    8    9   10
fraction(Ia-91T) ≥ rlap_i = 0.06 0.06 0.14 0.18 0.33 0.00 

Going back to the NOTE: all null slopes for the type determination, the fraction values for the same rlap array are:

	           rlap_i =    5    6    7    8    9   10
    fraction(Ia) ≥ rlap_i = 1.00  1.00 1.00 1.00 1.00 1.00 
 fraction(other) ≥ rlap_i = 0.00  0.00 0.00 0.00 0.00 0.00 

The line below the table states:

 	NOTE: Favoured type is: Ia, but there is no favoured subtype

One can then look at the template list (ordered by rlap value), or skip that and go directly to interactive plotting:

	Hit <CR> to view template listings, or (q)uit listings and move on:

                          TEMPLATE LISTINGS

   No.  Name          Type        lap    rlap    z    zerr    Age   NOTES
     1  sn99ee        Ia-norm     0.542  10.8  0.528  0.005    7.1
     2  sn99ac        Ia-91T      0.559   9.4  0.534  0.007    0.8
     3  sn02er        Ia-norm     0.547   9.3  0.540  0.006   -6.4
     4  sn99ac        Ia-91T      0.575   8.7  0.534  0.008    3.1
     5  sn81B         Ia-norm     0.639   8.7  0.542  0.007    0.0
     6  sn04eo        Ia-norm     0.566   8.6  0.530  0.007   -6.4
     7  sn81B         Ia-norm     0.634   8.6  0.542  0.007   -0.9
     8  sn03du        Ia-norm     0.582   8.3  0.526  0.007    5.0
     9  sn02bo        Ia-norm     0.563   8.1  0.539  0.008   -1.4
    10  sn02er        Ia-norm     0.540   8.1  0.533  0.007   -3.5
    11  sn95D         Ia-norm     0.544   8.1  0.525  0.007    4.2
    12  sn02er        Ia-norm     0.519   7.9  0.531  0.007   -0.5
    13  sn02bo        Ia-norm     0.604   7.2  0.546  0.009   -4.5
    14  sn89B         Ia-norm     0.611   7.1  0.527  0.008   -0.5
    15  sn94ae        Ia-norm     0.508   6.9  0.525  0.009    6.4
    16  sn95D         Ia-norm     0.544   6.8  0.522  0.009    6.1
    17  sn02er        Ia-norm     0.598   6.8  0.538  0.009   -2.5
X   18  sn94D         Ia-norm     0.643   6.7  0.567  0.010  -10.7  WARNING! |z-  0.532 | > 0.020
    19  sn02er        Ia-norm     0.563   6.7  0.546  0.009   -8.4

 Hit <CR> to view next set of templates or (q)uit listings:

X   18  sn94D         Ia-norm     0.643   6.7  0.567  0.010  -10.7  WARNING! |z-  0.532 | > 0.020

	WARNING! |z-  0.532 | > 0.020

        Name          Type         Age   NOTES
	sn97cy        IIn    (...) 29.4  Age from 1st spectrum (1997-07-23)

In some cases the date of explosion is also known (for some of the core-collapse supernovae-- see the file texplist in the templates/ directory). In these cases the 'Age' column is still in days from maximum light, but the age in days from explosion is given in the 'NOTES' column:

        Name          Type         Age   NOTES
	sn05bf        Ib-pec (...) 2.2   Age from explosion =  42.6

For the NotSN type (which includes AGN, Gal, LBV, M-star), the 'Age' column is obviously not in days from maximum light. For the AGN, Gal, and LBV subtypes, the age is given as -99.9 and a 'Age N/A' note appears in the last column:

        Name          Type         Age   NOTES
	lbv03hy       LBV   (...) -99.9  Age N/A

        Name          Type         Age   NOTES
	mstar         M-star (...) 5.0   Age is MK type

Hitting <CR> again will output the next 20 best-match templates, and so on until all templates with rlap ≥ rlapmin (5.0 here) are listed. At any time the user can quit these listings and go directly to interactive plotting.

   No.  Name          Type        lap    rlap    z    zerr    Age   NOTES
    20  sn02er        Ia-norm     0.592   6.5  0.537  0.009   -1.5
    21  sn02bo        Ia-norm     0.536   6.5  0.533  0.009   -0.3
    22  sn02bo        Ia-norm     0.509   6.5  0.538  0.009   -3.4
    23  sn04S         Ia-norm     0.632   6.4  0.535  0.010    1.7
    24  sn03du        Ia-norm     0.527   6.3  0.528  0.008   -1.1
    25  sn94ae        Ia-norm     0.472   6.3  0.530  0.008    3.3
    26  sn95D         Ia-norm     0.550   6.3  0.522  0.010    8.1
    27  sn99ee        Ia-norm     0.574   6.3  0.533  0.010    2.2
    28  sn92A         Ia-norm     0.718   6.2  0.550  0.009   -5.0
    29  sn02bo        Ia-norm     0.509   6.2  0.537  0.010   -2.5
    30  sn99ee        Ia-norm     0.573   6.2  0.537  0.010    0.3
    31  sn94ae        Ia-norm     0.661   6.2  0.518  0.010    9.4
    32  sn89B         Ia-norm     0.514   6.2  0.522  0.008    3.5
    33  sn04eo        Ia-norm     0.514   6.1  0.522  0.009    2.2
    34  sn02er        Ia-norm     0.596   6.0  0.542  0.010   -5.4
    35  sn02bo        Ia-norm     0.631   6.0  0.529  0.010    5.5
    36  sn03du        Ia-norm     0.510   5.9  0.528  0.009    0.8
    37  sn03du        Ia-norm     0.510   5.9  0.524  0.009    3.9
    38  sn03du        Ia-norm     0.531   5.8  0.548  0.010  -10.1
    39  sn02bo        Ia-norm     0.508   5.8  0.535  0.010   -1.2

 Hit <CR> to view next set of templates or (q)uit listings:

   No.  Name          Type        lap    rlap    z    zerr    Age   NOTES
    40  sn02bo        Ia-norm     0.509   5.7  0.535  0.010   -1.5
    41  sn92A         Ia-norm     0.718   5.7  0.540  0.009   -0.4
    42  sn90O         Ia-norm     0.627   5.7  0.551  0.012   -6.1
    43  sn89B         Ia-norm     0.510   5.6  0.522  0.009    5.5
    44  sn94D         Ia-norm     0.531   5.6  0.522  0.009    2.9
    45  sn95E         Ia-norm     0.470   5.5  0.531  0.009    0.1
    46  sn98aq        Ia-norm     0.447   5.5  0.529  0.008    5.9
    47  sn98aq        Ia-norm     0.447   5.5  0.528  0.008    6.9
    48  sn90O         Ia-norm     0.625   5.4  0.547  0.012   -5.1
    49  sn02er        Ia-norm     0.598   5.3  0.531  0.011    3.4
    50  sn03cg        Ia-norm     0.506   5.3  0.526  0.010    4.5
    51  sn94ae        Ia-norm     0.500   5.3  0.526  0.011    4.4
    52  sn96C         Ia-norm     0.535   5.3  0.519  0.012    8.3
    53  sn01el        Ia-norm     0.560   5.3  0.536  0.010    9.2
    54  sn98aq        Ia-norm     0.447   5.2  0.529  0.008    4.9
    55  sn94ae        Ia-norm     0.512   5.2  0.526  0.011    3.3
    56  sn99ee        Ia-norm     0.573   5.2  0.526  0.011   11.1
    57  sn99aw        Ia-91T      0.508   5.2  0.537  0.011    3.2
    58  sn99aa        Ia-91T      0.559   5.2  0.545  0.011   -0.6
    59  sn03du        Ia-norm     0.509   5.2  0.527  0.010    1.9

 Hit <CR> to view next set of templates or (q)uit listings:

   No.  Name          Type        lap    rlap    z    zerr    Age   NOTES
    60  sn92A         Ia-norm     0.498   5.1  0.538  0.009    3.3
    61  sn03du        Ia-norm     0.527   5.1  0.546  0.011   -6.2
    62  sn03cg        Ia-norm     0.467   5.1  0.528  0.009    1.5
    63  sn02er        Ia-norm     0.588   5.0  0.543  0.012   -4.4
    64  sn94D         Ia-norm     0.528   5.0  0.529  0.009   -1.8
    65  sn86G         Ia-91bg     0.490   5.0  0.525  0.010    1.6
    66  sn03du        Ia-norm     0.510   5.0  0.528  0.011   -0.2

 Created output file: sn2003jo_snid.output

 On to interactive plotting...

Notice that an output file named sn2003jo_snid.output is created (since fout ≥ 0; see description of options). Below is a description of the contents of this file:

lines 4-28: summary info (input spectrum and options)

	# Input spectrum                 : sn2003jo.dat
	# Parameter file                 : NA
	# Wavelength range               :    4335.19   8915.26
	(etc.)

	zinit       0.5315
	zuser       0.5315

	zmed        0.5308    0.0082
	agem          0.80      4.62

	#type ntemp fraction slope redshift redshift_error age age_error
	Ia             65      1.00    0.0000    0.5308    0.0082     0.800     4.625
	Ia-norm        60      0.92   -0.0330    0.5304    0.0083     0.550     4.795
	Ia-91T          4      0.06    0.0404    0.5356    0.0051     1.950     1.852
	(etc.)

	#no. sn type lap rlap z zerr age age_flag grade
	   1  sn99ee        Ia-norm    0.5415  10.82   0.5276   0.0054     7.10  0   good
	   2  sn99ac        Ia-91T     0.5591   9.40   0.5342   0.0071     0.80  0   good
	   3  sn02er        Ia-norm    0.5469   9.29   0.5402   0.0062    -6.40  0   good
	(etc.)

	age_flag = 0	means the age is in days from maximum light
	age_flag = 1	means the age is in days from the 1st spectrum
	age_flag = 2	means the age is N/A (i.e. for the 'NotSN' type)
		
	grade = good	means that |z - zuser| < zfilter (0.02 here)
	grade = bad	means that |z - zuser| ≥ zfilter (0.02 here)
	grade = cut	means the template has an rlap < rlapmin

	#--- rlap cutoff

Now on to interactive plotting! You should see a window with a top section comprising various buttons, and a lower panel for plotting output:

By default, the best-match template spectrum is shown (red line) overplotted on the input spectrum (white line), and you can see the 'flux' button is pressed. This simply means we are seeing a plot of relative flux vs. wavelength. The labels give us the name of the input spectrum and info on the template spectrum:

	Input: sn2003jo.dat
	No. 1: sn99ee (Ia-norm; +7) ; z = 0.528 +/- 0.005

To see a similar plot for other template spectra, simply use the 'template navigation' buttons:

Button	Description
	This prompts you (in the terminal from which you ran SNID) to enter a template number, between 1 and the lowest-ranked template with rlap >= rlapmin: Enter template No. [1 - 66]:
	Sets the template number to 1
	Decreases the template number by 1
	Increases the template number by 1
	Sets the template number to the lowest-ranked template with rlap ≥ rlapmin (66 in this case)

Button	Description
	plots the relative flux vs. wavelength input and template spectra [default] (see the figure above)
	plots the 'flattened' flux vs. wavelength input and template spectra. This is what SNID actually 'sees' when computing the correlation. A pseudo-continuum is removed from the input and template spectra, such that they appear 'flattened'. It's always good to look at this plot to see what SNID did to your input spectrum, and help you judge whether you need to trim noisy edges (with the wmin= wmax= options). (see the figure below)
	plots the correlation function between the input spectrum and a given template spectrum. The solid white line is the initial correlation function, while the dashed red line is the correlation function computed when the input and template spectra are trimmed to match at the correlation redshift. The labels give us the name of the input spectrum and info on the template spectrum: No. 1: sn2003jo x sn99ee (Ia-norm; +7) Trimmed at z= 0.532 ; r= 20.0 Here the correlation is between sn2003jo and the best-match template (No. 1): sn99ee (a 'Ia-norm' SN at age +7). The dashed red line is the correlation function trimmed at z= 0.532, and the corresponding r-value (multiplied by the 'lap' parameter to give the rlap quality parameter; see Blondin & Tonry 2007 [ADS, astro-ph] for a formal definition) is r= 20.0. The higher the r-value, the better the correlation (i.e. the higher the correlation peak, simply put). (see the figure below)

Button	Description
	shows a plot of rlap value vs. redshift used for the initial redshift estimate. As a reminder, SNID correlates the input spectrum (here sn2003jo.dat) with each of the 1515 template spectra. The 10 best peaks in each correlation function (i.e. a total of 15150 peaks here) are fitted and the corresponding redshift is determined. The input and template spectra are then trimmed to match at that redshift and the corresponding lap parameter is calculated. If lap ≥ lapmin, the redshift is saved. In the present example, 9200 redshifts were saved, and the plot shows these 9200 points. The initial redshift estimate is an rlap-weighted median of these 9200 redshifts. (see the figure below)
	shows a plot of age vs. redshift for all templates with rlap ≥ rlapmin. The white squares correspond to templates whose redshift does not differ from the initial redshift estimate by more than zfilter (0.02 here), while the red squares correspond to templates whose redshift differ from the initial redshift estimate by more than zfilter (0.02 here). The green dot shows the redshift/age of the best-match template. The dashed lines show the median redshift/age of all templates (the zmed and agem values reported in sn2003jo_snid.output). NOTE: points that correspond to templates with unknown ages or NotSN types do not show up on this plot. (see the figure below)

Button	Description
	fraction of templates with rlap ≥ rlap_i as a function of rlap_i (where rlap_i runs from 0 to the integer part of the highest rlap value) for the 'Ia' type and all associated subtypes (Ia-norm, Ia-91T, Ia-91bg, Ia-csm, Ia-pec). The vertical dotted line shows the value of rlapmin. (see the figure below)
	see description of 'Ia' button above but for the 'Ib' type.
	see description of 'Ia' button above but for the 'Ic' type.
	see description of 'Ia' button above but for the 'II' type.
	see description of 'Ia' button above but for the 'NotSN' type.
	see description of 'Ia' button above but for all template types (excluding subtypes, i.e.: Ia, Ib, Ic, II, and NotSN).

Button	Description
	quit the interactive plotting. This will also end the SNID run: Thank you for using SNID! Goodbye. will appear on the terminal from which you ran SNID.
	produce postscript output of the graph currently shown in the graphics output window. For an input spectrum named sn2003jo.dat the output .ps files will be named as follows: sn2003jo_comp[000]n_snidflux.ps for the 'flux' button sn2003jo_comp[000]n_snidflat.ps for the 'flat' button sn2003jo_comp[000]n_snidxcor.ps for the 'xcor' button where n is the template number (e.g. 0001 for No. 1 template); sn2003jo_snidpeaks.ps for the 'peaks' button sn2003jo_snidzt.ps for the 'z/t' button and, finally: sn2003jo_snidfrac_<TYPENAME>.ps for any of the 'Fraction' buttons, where <TYPENAME> is one of the template types (Ia, Ib, Ic, II, or NotSN). NOTE: in all cases a message is displayed on the terminal screen stating which files have been created.
	produce ascii output of the graph currently shown in the graphics output window. For an input spectrum named sn2003jo.dat the output .dat files will be named as follows. The template spectra are written to files named: sn2003jo_comp[000]n_snidflux.dat for the 'flux' button sn2003jo_comp[000]n_snidflat.dat for the 'flat' button while the input spectrum is written to files named: sn2003jo_snidflux.dat for the 'flux' button sn2003jo_snidflat.dat for the 'flat' button also: sn2003jo_comp[000]n_snidxcor.dat for the 'xcor' button where n is the template number (e.g. 0001 for No. 1 template); sn2003jo_snidpeaks.dat for the 'peaks' button sn2003jo_snidzt.dat for the 'z/t' button and, finally: sn2003jo_snidfrac_<TYPENAME>.dat for any of the 'Fraction' buttons, where <TYPENAME> is one of the template types (Ia, Ib, Ic, II, or NotSN). NOTE: in all cases a message is displayed on the terminal screen stating which files have been created. NOTE: each output .dat file contains header information (lines starting with '#') similar to the labels that appear in the graphics output window.

1.4. Other examples

In what follows we illustrate the use of the more common options for a typical SNID run. The input spectrum is assumed to be called 'spec1.dat'.

Example 1. The input spectrum is noisy blueward of 4500 Angstroms and redward of 8500 Angstroms. You can then restrict the correlation to the [4500,8500] wavelength interval using the wmin and wmax options:

	snid wmin=4500 wmax=8500 spec1.dat 

Example 2. You know the host galaxy redshift (e.g. z=0.357), but the input spectrum is not contaminated by galaxy emission lines. You can then force the intial redshift estimate with the forcez option:

	snid forcez=.357 spec1.dat

Example 3. Same as above, except the input spectrum is heavily contaminated by galaxy emission lines. You can then clip these emission lines using the emclip option:

	snid forcez=.357 emclip=.357 spec1.dat

Example 4. If you only have a rough idea of the redshift (e.g. z=0.3 +/- 0.1), you can restrict the redshift interval using the z and dz options:

	snid z=.3 dz=.1 spec1.dat

Example 5. Suppose you know the input spectrum is that of a supernova well past maximum light. You can then restrict the correlation to templates with positive ages using the agemin option:

	snid agemin=0 spec1.dat

	snid age=0 dage=10 spec1.dat

Example 6. For high-S/N spectra (e.g. for nearby supernovae) you will get better results by restricting the correlation to higher values of rlap using the rlapmin option:

	snid rlapmin=10 spec1.dat

Example 7. Assume you know the input spectrum is that of an SN Ia, you can restrict correlations to Ia templates only with the usetype option:

	snid usetype=Ia spec1.dat

Example 8. If you want to run SNID non-interactively on a large number of spectra (spec1.dat, spec2.dat, ... , specn.dat). You would then turn the interactive mode off with the inter option, disable plotting with the plot option, and (possibly) set the verbose level to null with the verbose option. You can run the whole data set through SNID as follows:

[in (t)csh]
	foreach file (`ls spec*.dat`)
	snid inter=0 plot=0 verbose=0 $file
	end

[in bash]
	for file in spec*.dat ; do snid inter=0 plot=0 verbose=0 $file ; done

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2. logwave

2.1. Syntax

	logwave [options] list

The 'list' file is a table with the following columns [see the snid_list file in the test/ directory for an example]:

#Object  Type      Filename                        Age Age_flag Delta AB? Wave_range   Redshift
sn98aq   Ia-norm   spectra/sn1998aq-19980418.flm    -9.0   0   1.15   0   3720  7419   0.00395
sn90aa   Ic-norm   spectra/sn1990aa-19900927-oi.flm  0.0   1  -9.99   0   3900  9850   0.01647
kcS0     Gal       spectra/s0_template.dat         -99.9   2  -9.99   0   1235  9940   0.

2nd column is the template subtype, which must be one of the subtypes listed in typeinfo.f (in the source/ directory), namely:

Third column is the spectrum filename (which should have two columns: wavelength in Angstroms and Flux in arbitrary units; lines starting with '#' are considered comments and are ignored.);

4th column is the template age (usually in days from maximum light);

5th column is an age flag, which takes the following values:

	age_flag = 0	means the age is in days from maximum light
	age_flag = 1	means the age is in days from the 1st spectrum
	age_flag = 2	means the age is N/A (i.e. for the 'NotSN' type)

2.2. Options

NOTE: The defaults for each option were chosen for a reason. Make sure you understand what each option does before overriding the default values when running logwave. A detailed description of each option is given below.

> logwave
 Logwave (v2.0, 31 July 2007)
 Copyright (C) 1999-2007 S. Blondin and J. L. Tonry

 Usage: logwave [options] list

 list format:
     Object Type Filename Age Age_flag Delta AB? Wave_range [Redshift]
 creates output files: Object.lnw

 options (default):
     w0= w1=  wavelength range (2500,10000)
     nw=      number of log bins (1024)

 [see file Howto.snid for more info]

w0= w1= (2500,10000)
this is the wavelength range of the output template, *not* the wavelength range of each individual spectrum listed in the 'list' file!

nw= (1024)
number of logarithmic wavelength bins between w0 and w1. The wavelength bin edges are then defined as:

	wlog(i) = w0 * exp{(i-1)*dwlog}	for i=1 to nw+1,

IMPORTANT! All templates used in a given SNID run must have the same (w0,w1,nw) parameters! Again, do not change these default values unless you know what you're doing!

2.3. Example run

In what follows we will go through an example run. If this is the first time you use logwave then read this carefully, as all the important aspects are covered.

First you need to go to the test/ directory, which contains an example input list, snid_list. Then simply run logwave with no options by typing:

	logwave snid_list

 Reading data files from: snid_list
 nfile =  34 ; nsn =  6
 Max epochs = 27 for sn98aq
 Total spectra =  34
 sn98aq.lnw processed, with  27 epochs
 sn90aa.lnw processed, with   3 epochs
 kcS0.lnw processed, with   1 epochs
 kcSa.lnw processed, with   1 epochs
 kcSb.lnw processed, with   1 epochs
 kcSc.lnw processed, with   1 epochs

	plotlnw sn98aq.lnw

	ls *.lnw > templist

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3. plotlnw

3.1. Syntax

	plotlnw [options] template.lnw

3.2. Options

NOTE: The defaults for each option were chosen for a reason. Make sure you understand what each option does before overriding the default values when running plotlnw. A detailed description of each option is given below.

> plotlnw
 Plotlnw (v1.0, 20 July 2007)
 Copyright (C) 2007 S. Blondin

 Usage: plotlnw [options] template.lnw

 options (default):
     filter=0/1        apply bandpass filter (0)
     k{1,2,3,4}=       bandpass filter range (1,4,85,102)
     x{min,max}=       abscissa range (template)
     yoff=             vertical offset between spectra (1)
     ps=0/1            create postscript output (0)

 [see file Howto.snid for more info]

filter=0/1
set to 1 if you want to apply a bandpass filter to the template spectra.

k{1,2,3,4}= (1,4,85,102)
bandpass filter range, in bin indices (assuming the total number of bins is nw=1024). The (k1,k2,k3,k4) wavenumbers define the filter shape (a cosine bell). The filter is 0 for k ≤ k1 or k ≥ k4, rises from 0 to 1 for k1 < k < k2, is 1 for k2 ≤ k ≤ k3, and declines from 1 to 0 for k3 < k < k4. You will most certainly never want to change the default values of k{1,2,3,4}, but who knows. E.g.:

	plotlnw filter=1 k3=43 k4=51 template.lnw 	[for a lower-pass filter]
	plotlnw filter=1 k1=21 k2=26 template.lnw 	[for a higher-pass filter]

x{min,max}= (template)
specify an abscissa range (in Angstroms) for the output plot. The default corresponds to the (w0,w1) values used by logwave to generate the template, and is usually (2500,10000) Angstroms. E.g.:

	plotlnw xmin=3500 xmax=8000 template.lnw

yoff= (1)
specify the vertical offset between each template spectrum. E.g.:

	plotlnw yoff=.5 template.lnw

ps=0/1 (0)
set to 1 to create postscript output. The output file is named template.lnw.ps. E.g.:

	plotlnw ps=1 template.lnw

3.3. Example runs

In what follows we will go through several example runs. We will use the sn98aq.lnw template in the templates/ directory [in what follows we assume that we are still in the test/ directory]:

To simply plot the template:

	plotlnw ../templates/sn98aq.lnw

	plotlnw filter=1 ../templates/sn98aq.lnw		[default bandpass filter]
	plotlnw filter=1 k3=43 k4=51 ../templates/sn98aq.lnw 	[for a lower-pass filter]
	plotlnw filter=1 k1=21 k2=26 ../templates/sn98aq.lnw 	[for a higher-pass filter]

	plotlnw xmin=3500 xmax=8000 ../templates/sn98aq.lnw

	plotlnw yoff=.5 ../templates/sn98aq.lnw

	plotlnw ps=1 filter=1 xmin=3500 xmax=8000 yoff=.5 ../templates/sn98aq.lnw

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