1. Spectral analysis of the LAT and GBM data
GRB tutorial
Spectral analysis of the
LAT and GBM data

2. All the software you need

3. The tools I used gtselect gtbin gtrspgen gtlikelihood DataServer
Select the ROI containing the bursts, in time, ra and dec
gtbin
Bin the LAT data in time -> obtain the light curve
Bin the LAT data in RA,DEC ->Obtaining a count map
Bin the GBM and LAT data in energy -> obtaining a spectrum PHA1 files
Bin the GBM and LAT data in time and energy->PHA2 files
gtrspgen
Compute the response for the LAT
gtlikelihood
Unbinned spectral analysis
DataServer
Hyppodraw, fv, ds9
visualization of LC and CMAP
Python as scripting tool
Xspec for performing the spectral analysis

4. Getting the data at http://glast.gsfc.nasa.gov/ssc/dev/databases/DC2/

5. The files you need: LAT livetime history (DC2_FT2.fits)
ftp://heasarc.gsfc.nasa.gov/FTP/glast/DC2/misc_data/DC2_FT2.fits
LAT photon data (all sky, first week): (LAT_allsky_ _V01.fits)
ftp://heasarc.gsfc.nasa.gov/FTP/glast/DC2/allsky/LAT_allsky_ _V01.fits
GRB GBM files:
ftp://heasarc.gsfc.nasa.gov/FTP/glast/DC2/burst/GRB tar.gz

6. Un-packaging the GBM files
dhcpvisitor216193:~/GLAST/GRB omodei$ l
-rw-r--r omodei omodei Feb 23 08:55 GLG_BCK_B0_BN _V01.BAK …
-rw-r--r omodei omodei Feb 23 08:55 GLG_CSPEC_B0_BN _V01.RSP
-rw-r--r omodei omodei Feb 23 08:55 GLG_CTIME_B0_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:42 GLG_CTIME_N0_ _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_NOTICE_ TXT
-rw-r--r omodei omodei Feb 23 08:55 GLG_TTE_B0_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:55 GLG_TTE_B1_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N0_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N1_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N2_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N3_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N6_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N7_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_N9_BN _V01.FIT
-rw-r--r omodei omodei Feb 23 08:52 GLG_TTE_NB_BN _V01.FIT

7. GCN-like notices: GLG_NOTICE_080104514.TXT
In DC2 we know (approximately) the position of the burst (GLG_NOTICE)
GRB can be displaced statistically and systematically…

GLAST BURST MONITOR BURST NOTIFICATION
**************************************
BURST Name = GRB
BURST Date =
BURST Time (Sec of Day) =
BURST RA (Deg) =
BURST DEC (Deg) =
BURST LOC ERR (Deg 1 sigma) =
Standard Intensity (cts/sec) =
(Standard Intensity is an angle-adjusted measure of the peak count rates in 2 NaI detectors closest t
o the source)
Closest detectors = N0 N6 B0

8. Quick look at the data: hippodraw
Open the LAT_allsky_ _V01.fits
Select EVENT extension
Do a color plot RA vs DEC
Set the axis bin width as you prefer (1 deg in the fig.)

9. Add a cut on TIME, reset the bin width (axis)…

10. Ra ~57
Dec ~14
Tmin :
Tmax:

11. GBM and LAT light curve
Lightcurves curves at LAT energy and GBM energy are different, as predicted from the model
This imply a spectral evolution!

12. Trick 2: open the header file of the TTE data!

13. Resolved in dataSubselector version v4r1p5 Alternatively…
1. Selecting the data
dhcpvisitor216193:~/GLAST/GRB omodei$ gtselect
Input FT1 file [] : ../DC2/LAT_allsky_ _V01.fits
Output FT1 file [] : GRB _select.fits
RA for new search center (degrees) < > [] : 59.34
Dec for new search center (degrees) < > [] : 14.35
radius of new search region (degrees) < > [] : 20
start time (MET in s) [] :
end time (MET in s) [] :
lower energy limit (MeV) [30] :
upper energy limit (MeV) [300000] :
Event classes (-1=all, 0=FrontA, 1=BackA, 2=FrontB, 3=BackB, 4=class A) <-1 - 4> [-1] :
There was a bug (in ST v6r4p1) related to insufficient precision of MET. (Resulting in empty files)
Resolved in dataSubselector version v4r1p5
Alternatively…

16. It is useful to rename the file! (GRB080104514_select.fits)

17. 2. Binning the LAT data in spatial coordinates CMAP
dhcpvisitor216193:~/GLAST/GRB omodei$ gtbin
This is gtbin version v0r16p3
Type of output file <CMAP|LC|PHA1|PHA2> [] : CMAP
Event data file name [] : GRB _select.fits
Output file name [] : GRB _lat.cmap
Spacecraft data file name[] : ../DC2/DC2_FT2.fits
Size of the X axis in pixels [] : 360
Size of the Y axis in pixels [] : 180
Image scale (in degrees/pixel) [1] :
Coordinate system (CEL - celestial, GAL -galactic) <CEL|GAL> [GAL] :
First coordinate of image center in degrees (RA or galactic l) [0] :
Second coordinate of image center in degrees (DEC or galactic b) [0] :
Rotation angle of image axis, in degrees [0] :
ds9 -bin factor cmap b -scale sqrt "GRB _select.fits[bin=RA,DEC]"

18. 3. Binning the LAT data in time
Obtaining the LAT light curve
dhcpvisitor216193:~/GLAST/GRB omodei$ gtbin
This is gtbin version v0r16p3
Type of output file <CMAP|LC|PHA1|PHA2> [PHA1] : LC
Event data file name [] : GRB _select.fits
Output file name [] : GRB _lat.lc
Spacecraft data file name[] : ../DC2/DC2_FT2.fits
Algorithm for defining time bins <FILE|LIN|SNR> [LIN] :
Start value for first time bin [] :
Stop value for last time bin [] :
Width of linearly uniform time bins [] : 0.1

19. 3. Binning the LAT data in energy
Obtaining a spectrum (PHA1) file
dhcpvisitor216193:~/GLAST/GRB omodei$ gtbin
This is gtbin version v0r16p3
Type of output file <CMAP|LC|PHA1|PHA2> [PHA1] :
Event data file name [GRB _select.fits] :
Output file name [] : GRB _lat.pha
Spacecraft data file name [../DC2/DC2_FT2.fits] :
Algorithm for defining energy bins <FILE|LIN|LOG> [LIN] : LOG
Start value for first energy bin [30] :
Stop value for last energy bin [300000] :
Number of logarithmically uniform energy bins [15] :
gtbin evfile=GRB _select.fits scfile=../DC2/DC2_FT2.fits outfile=GRB _lat.pha algorithm=PHA1 energybinalg=LOG emin=30 emax= enumbins=15
This is gtbin version v0r16p3
Done!

20. 4. Binning the GBM data in energy
dhcpvisitor216193:~/GLAST/GRB omodei$ gtbin
This is gtbin version v0r16p3
Type of output file <CMAP|LC|PHA1|PHA2> [PHA1] :
Event data file name [] : GLG_TTE_N0_BN _V01.FIT
Output file name [] : GRB _N0.pha
Spacecraft data file name [NONE] :
This has to be done for each bright detectors in the GBM:
<12 NaI, <2 BGO.
Notice: in DC2 one can use all the GBM detectors due to the fact that the background used to build the data is the same of the .bak files.
In reality things are different!

21. Compute the response function for the LAT
dhcpvisitor216193:~/GLAST/GRB omodei$ gtrspgen
This is gtrspgen version v1r2
Response calculation method (GRB, PS) <GRB|PS> [GRB] :
Spectrum file name [] : GRB _lat.pha
Spacecraft data file name [] : ../DC2/DC2_FT2.fits
Output file name [] : GRB _lat.rsp
Time of GRB (s) [] :
Response function to use, e.g. DC1F/DC1B, G25F/G25B, TestF/TestB [DC2] :
Algorithm for defining true energy bins <FILE|LIN|LOG> [] : LOG
Start value for first energy bin [30] :
Stop value for last energy bin [300000] :
Number of logarithmically uniform energy bins [100] : !
I renamed GBM files to match my “convention” GRBYYMMDDFFF_det.*
GLG_CSPEC_B0_BN _V01.RSP =>GRB _B0.rsp
GLG_CSPEC_B1_BN _V01.RSP => GRB _B1.rsp
GLG_CSPEC_N0_BN _V01.RSP => GRB _N0.rsp
GLG_CSPEC_N1_BN _V01.RSP => GRB _N1.rsp
GLG_CSPEC_N2_BN _V01.RSP => GRB _N2.rsp
GLG_CSPEC_N3_BN _V01.RSP => GRB _N3.rsp
GLG_CSPEC_N6_BN _V01.RSP => GRB _N6.rsp
GLG_CSPEC_N7_BN _V01.RSP => GRB _N7.rsp
GLG_CSPEC_N9_BN _V01.RSP => GRB _N9.rsp
GLG_CSPEC_NB_BN _V01.RSP => GRB _NB.rsp

22. Everything is here: Notice: no background for the LAT
~/GLAST/GRB omodei$ l *pha
GRB _B0.pha
GRB _B1.pha
GRB _N0.pha
GRB _N1.pha
GRB _N2.pha
GRB _N3.pha
GRB _N6.pha
GRB _N7.pha
GRB _N9.pha
GRB _NB.pha
GRB _lat.pha
~/GLAST/GRB omodei$ l *rsp
GRB _B0.rsp
GRB _B1.rsp
GRB _N0.rsp
GRB _N1.rsp
GRB _N2.rsp
GRB _N3.rsp
GRB _N6.rsp
GRB _N7.rsp
GRB _N9.rsp
GRB _NB.rsp
GRB _lat.rsp
~/GLAST/GRB omodei$ l *bak
GRB _B0.bak
GRB _B1.bak
GRB _N0.bak
GRB _N1.bak
GRB _N2.bak
GRB _N3.bak
GRB _N6.bak
GRB _N7.bak
GRB _N9.bak
GRB _NB.bak
Notice: no background for the LAT

23. Running XSPEC NaI < 1 MeV 150 keV < BGO< 30MeV
dhcpvisitor216193:~/GLAST/GRB omodei$ xspec
XSPEC version:
Build Date/Time: Tue Nov 22 20:13:
!XSPEC12>cpd /xw;
!XSPEC12>data GRB _N0.pha, GRB _N6.pha, GRB _B0.pha, GRB _LAT.pha
!XSPEC12>response GRB _N0.rsp, GRB _N6.rsp, GRB _B0.rsp, GRB _LAT.rsp
!XSPEC12>backgrnd GRB _N0.bak, GRB _N6.bak ,GRB _B0.bak
Net count rate (cts/s) for Spectrum: e+01 +/ e+00 (30.7 % total )
Net count rate (cts/s) for Spectrum: e+01 +/ e+00 (28.8 % total )
Net count rate (cts/s) for Spectrum: e+01 +/ e+00 (9.4 % total )
!XSPEC12>setplot energy;
!XSPEC12>ignore 1: **;
!XSPEC12>ignore 2: **;
!XSPEC12>ignore 3:**-150.0;
!XSPEC12>ignore 3:3e4-**;
!XSPEC12>setplot rebin ;
!XSPEC12>setplot rebin ;
!XSPEC12>setplot rebin ;
!XSPEC12>setplot rebin 1 1 4;
!XSPEC12>model grbm
Input parameter value, delta, min, bot, top, and max values for ...
grbm:alpha>
grbm:beta>
grbm:tem>
e e+24
grbm:norm>
!XSPEC12> renorm
!XSPEC12>fit
!XSPEC12>plot ldata
NaI < 1 MeV
150 keV < BGO< 30MeV

24. The result (2NaI, 1BGO + LAT)
========================================================================
Model grbm<1> Source No.: 1 Active/On
Model Model Component Parameter Unit Value
par comp
grbm alpha / E-02
grbm beta / E-02
grbm tem keV /
grbm norm E-03 +/ E-04
________________________________________________________________________
Chi-Squared = using 344 PHA bins.
Reduced chi-squared = for degrees of freedom
Null hypothesis probability = e+00

25. With all the detectors (8NaI, 1BGO + LAT)
========================================================================
Model grbm<1> Source No.: 1 Active/On
Model Model Component Parameter Unit Value
par comp
grbm alpha / E-02
grbm beta / E-02
grbm tem keV /
grbm norm E-03 +/ E-04
________________________________________________________________________
Chi-Squared = using 980 PHA bins.
Reduced chi-squared = for degrees of freedom
Null hypothesis probability = e+00

26. Scripting xspec set PREFIX GRB set GRBNAME 080104514
set GRBNAME $PREFIX$GRBNAME
echo $GRBNAME
cpd /xw
dat ${GRBNAME}_N0.pha, ${GRBNAME}_N6.pha, ${GRBNAME}_B0.pha, ${GRBNAME}_LAT.pha;
respon ${GRBNAME}_N0.rsp, ${GRBNAME}_N6.rsp, ${GRBNAME}_B0.rsp, ${GRBNAME}_LAT.rsp;
back ${GRBNAME}_N0.bak, ${GRBNAME}_N6.bak ,${GRBNAME}_B0.bak;
setplot energy;
ignore 1: **
ignore 2: **
ignore 3:**-150.0
ignore 3:3e4-**
#ignore 8:**-3e4
setplot rebin 5 5 1
setplot rebin 5 5 2
setplot rebin
setplot rebin 1 1 4
mod grbm;
renorm
fit
plot ldata;

27. Time resolved temporal analysis1 2 3 4

28. Creating Pha2 files… LAT All the GBM detectors I want to analyze …
dhcpvisitor216193:~/GLAST/GRB omodei$ gtbin
This is gtbin version v0r16p3
Type of output file <CMAP|LC|PHA1|PHA2> [] : PHA2
Event data file name [GRB _select.fits] :
Output file name [] : GRB _lat.pha2
Spacecraft data file name [NONE] :
Algorithm for defining energy bins <FILE|LIN|LOG> [LOG] :
Start value for first energy bin [30] :
Stop value for last energy bin [300000] :
Number of logarithmically uniform energy bins [15] :
Algorithm for defining time bins <FILE|LIN|SNR> [] : FILE
Name of the file containing the time bin definition [] : timebins.fits
Type of output file <CMAP|LC|PHA1|PHA2> [PHA2] :
Event data file name [] : GLG_TTE_B1_BN _V01.FIT
Output file name [] : GRB _B1.pha2
Algorithm for defining time bins <FILE|LIN|SNR> [FILE] :
Name of the file containing the time bin definition [timebins.fits] :
LAT
All the GBM detectors
I want to analyze …

29. grbm alpha /
grbm beta /
grbm tem keV /
grbm norm E-05 +/ E-04

30. grbm alpha / E-02
grbm beta / E-02
grbm tem keV /
grbm norm E-03 +/ E-03

31. grbm alpha /
grbm beta / E-02
grbm tem keV /
grbm norm E-03 +/ E-04

32. grbm alpha /
grbm beta / E-02
grbm tem keV /
grbm norm E-03 +/ E-03

33. Conclusions
Have fun !!

35. hcpvisitor216193:~/GLAST/GRB080104514 omodei$ gtlikelihood
Statistic to use <BINNED|UNBINNED> [UNBINNED] :
Spacecraft file [../DC2/DC2_FT2.fits] :
Event file [GRB _select.fits] :
Unbinned exposure map [none] :
Exposure hypercube file [none] :
Source model file [myGRBmod.xml] :
Response functions to use [DC2] :
Optimizer <LBFGS|MINUIT|DRMNGB> [DRMNGB] :
Computing exposure at (57, 14) !
myGRB:
Prefactor: /
Index: /
Scale: 100
Npred:
ROI distance: 0
TS value:
Total number of observed counts: 108
Total number of model events:
-log(Likelihood):
Elapsed CPU time:

36. Scripts:
Python tcl

37. Trick 1: How to get MET out of a GLG_NOOTICE
import time
import datetime
refdate=datetime.date(2001, 1, 1)
grbdate=datetime.date(2008, 1, 4)
tstart=(grbdate - refdate).days*
print ‘Burst Time in MET is:’,tstart
Burst Time in MET is:
Many other tools can do this, even excel…
But, the triggertime in the notice is not the Montecarlo starting time of the burst…

38. Python… running the ScienceTools
import os
import time
import datetime
refdate=datetime.date(2001, 1, 1)
grbnumber=" "
grbprefix="GRB"
infile="../DC2/LAT_allsky_ _V01.fits"
scfile="../DC2/DC2_FT2.fits"
grbdate=datetime.date(2008, 1, 4)
tstart=(grbdate - refdate).days*
tmin=str(tstart-5)
tmax=str(tstar+60)
deltatime=".1"
ra="57"
dec="14"
rad="15"
emin="30"
emax="300000"
enumbins="15"
eventClass="-1"

39. Flags to decide the steps to do…
…again python…
select=0
lc=1
cmap=1
pha=1
pha2=1
rsp=1
gbm=1
gbm2=1
grbname=grbprefix+grbnumber;
grbfile=grbname+"_select.fits"
lat_lc=grbname+"_lat.lc"
lat_cmap=grbname+"_lat.cmap"
lat_pha=grbname+"_lat.pha"
lat_pha2=grbname+"_lat.pha2"
lat_rsp=grbname+"_lat.rsp"
timebinfile="timebins.fits"
numxpix="360"
numypix="180"
pixscale="1"
coordsys="GAL"
Flags to decide the steps to do…
…my naming convention…

40. …be patient… if select:
cmd="gtselect infile="+infile+" outfile="+grbfile+" ra="+ra+" dec="+dec+" rad="+rad+" tmin="+tmin+" tmax="+tmax+" emin="+emin+" emax="+emax+" eventClass="+eventClass
print cmd
os.system(cmd)
if lc:
cmd="gtbin evfile="+grbfile+" scfile="+scfile+" outfile="+lat_lc+" algorithm=LC timebinalg=LIN"+" tstart="+tmin+" tstop="+tmax+" deltatime="+deltatime+" energybinalg=LOG"
if cmap:
cmd="gtbin evfile="+grbfile+" scfile="+scfile+" outfile="+lat_cmap+" algorithm=CMAP numxpix=360 numypix=180 pixscale=1 coordsys="+coordsys+" xref=0 yref=0 axisrot=0"
if pha:
cmd="gtbin evfile="+grbfile+" scfile="+scfile+" outfile="+lat_pha+" algorithm=PHA1 energybinalg=LOG"+" emin="+emin+" emax="+emax+" enumbins="+enumbins
if pha2:
cmd="gtbin evfile="+grbfile+" scfile="+scfile+" outfile="+lat_pha2+" algorithm=PHA2 energybinalg=LOG"+" emin="+emin+" emax="+emax+" enumbins="+enumbins+" timebinalg=FILE timebinfile="+timebinfile
if rsp:
cmd="gtrspgen respalg=GRB specfile="+lat_pha+" scfile="+scfile+" outfile="+lat_rsp+" time="+tmin+" resptype=DC2"+" energybinalg=LOG"+" emin="+emin+" emax="+emax+" enumbins=100"

41. …done!
if gbm:
detectorList=["N0","N1","N2","N3","N4","N5","N6","N7","N8","N9","NA","NB","B0","B1"]
for det in detectorList:
gbm_file_in="GLG_TTE_"+det+"_BN"+grbnumber+"_V01.FIT"
gbm_file_out=grbname+"_"+det+".pha"
cmd="gtbin evfile="+gbm_file_in+" scfile=NONE outfile="+gbm_file_out+" PHA1"
os.system(cmd)
cmd="cp GLG_CSPEC_"+det+"_BN"+grbnumber+"_V01.RSP "+grbname+"_"+det+".rsp"
cmd="cp GLG_BCK_"+det+"_BN"+grbnumber+"_V01.BAK "+grbname+"_"+det+".bak"
if gbm2:
gbm_file_out=grbname+"_"+det+".pha2"
cmd="gtbin evfile="+gbm_file_in+" scfile=NONE outfile="+gbm_file_out+" PHA2 timebinalg=FILE timebinfile="+timebinfile
print "Done!"

42. PlotWithHippo import sys import os import hippo
import hippoplotter as plot
from hippo import FitsController
from hippo import Display
def CM(grbnumber):
my_file='GRB'+grbnumber+'_lat.cmap'
plot.fitsImage(my_file, zlog=1, aspect=2)
def LAT_SELECTION(grbnumber):
my_file='GRB'+grbnumber+'_select.fits'
ntc = FitsController.instance()
hdus = ntc.getNTupleNames(my_file)
events = ntc.createNTuple ( my_file, hdus[1] )
lc=plot.Histogram(events,'TIME')
lc.setBinWidth('x',.1)
sm = plot.XYHist(events,'RA','DEC')
sm.setBinWidth ( 'x', .5 )
sm.setBinWidth ( 'y', .5 )
str = raw_input("Type return to quit. ")
def LAT_LC(grbnumber):
my_file='GRB'+grbnumber+'_lat.lc'
plot.Scatter(events,'TIME','COUNTS',pointRep='Line')

43. PlotWithHippo def LAT_GBM_LC(grbnumber): lc=range(15) events=range(15)
ntc = FitsController.instance()
lat_file='GRB'+grbnumber+'_select.fits'
hdus = ntc.getNTupleNames(lat_file)
events[0]= ntc.createNTuple ( lat_file, hdus[1] )
lc[0]=plot.Histogram(events[0],'TIME')
lc[0].setBinWidth('x',.1)
detectorList=["N0","N1","N2","N3","N4","N5","N6","N7","N8","N9","NA","NB","B0","B1"]
i=0
for det in detectorList:
i=i+1
gbm_file = "GLG_TTE_"+det+"_BN"+grbnumber+"_V01.FIT"
if os.path.exists(gbm_file):
print "file "+gbm_file+" exists:"
hdus = ntc.getNTupleNames(gbm_file)
events[i] = ntc.createNTuple ( gbm_file, hdus[2] )
lc[i] = plot.Histogram(events[i],'TIME')
lc[i].setBinWidth ( 'x', .1 )
lc[i].setTitle(det)
tstart=lc[1].getRange('x')[0]+5
tend=lc[1].getRange('x')[1]-5
print 'Tstart=',tstart,', Tend=',tend
lc[i].setRange('x',tstart,tend)
str = raw_input("Type return to quit/continue. ")