Examining Grating Spectra and Regions: PHA2 files

ACIS-S HETG/LETG Observations

We can use prism to examine the PHA2 file for ObsID 459:

unix% prism acisf00459N002_pha2.fits &

which will give you something like Figure 1 . In this example, there are twelve rows - all the +/- orders for both HEG and MEG - for the observation. The columns CHANNEL, COUNTS, BIN_LO, etc. are all so-called "vector columns"; each contains a vector of elements which, in this example, is 8192 elements long.

An ACIS-S/LETG observation (ObsID 1198) looks similar in Prism  but only contains 6 rows (+/- orders for the LEG).

Each vector column can be viewed as follows:

unix% prism acisf00459N002_pha2.fits &

left-click on column of interest (to select column)
Navigate menu -> Expand Column (to expand column)

Figure 3  shows the (partial) result of the expansion of column BIN_LO.

HRC-S/HRC-I LETG Observations

Examining an HRC-S/LETG observation (ObsID 460) is done in the same way as an ACIS grating observation:

unix% prism hrcf00460N002_pha2.fits &

but there is an important difference in the results. As seen in the Prism display , there are only two rows for the LEG observation. HRC-S cannot resolve orders and the COUNTS in the +/- 1 order are in fact the total counts of all orders combined. Also, the BIN_LO and BIN_HI columns should be considered for reference only; they actually represent the boundary wavelength of the +/- 1 order alone, while photons from all orders are included in the spectra.

The same holds true for HRC-I/LETG observations, as seen Figure 5  in the example of ObsID 1800.

With Prism

The quickest way to display one of the spectra of a PHA2 file is with Prism. For example a user who wants to take a quick look at BIN_LO vs. COUNTS for the order +1 (TG_M=1) of the HEG spectrum (TG_PART=1) should do the following (ObsId 459):

unix% prism acisf00459N002_pha2.fits &

middle-click on row #4  (to select spectrum)
left-click on BIN_LO column  (to select X-axis column)
left-click on COUNTS column  (to select Y-axis column)
Vizualization menu -> Interactive plot (to view the plot)
Vizualization menu -> Print plot (to print the plot)

As clearly visible from the output in Figure 6 , the plot is good for a general overview only (are there enough counts, are there striking features, etc.). At the same time as the plot was created, a ChIPS session was launched by Prism in an xterm window. This window can be used to customize the plot; see the Introduction to ChIPS thread for more information on plotting with ChIPS.

With ChIPS

In order to display a spectrum with ChIPS, we need to separate it out from the PHA2 file (keep in mind that each row of the PHA2 file corresponds to one spectrum):

unix% dmtype2split "acisf00459N002_pha2.fits[#row=4]" acisf00459N002_heg_p1.pha

The newly created file, which is the +1 order HEG spectrum for this observation, can be used as input to ChIPS:

unix% chips

Welcome to ChIPS, version CIAO 3.4
Copyright (C) 1999-2003, Smithsonian Astrophysical Observatory

chips> plot "acisf00459N002_heg_p1.pha[cols bin_lo,counts]"
chips> symbol none
chips> step
chips> xlabel "Wavelength (\AA)"
chips> ylabel Counts
chips> title "ACIS+HEG order=+1"

These commands produce the plot shown in Figure 7 .

An alternative way to read and display a PHA2 spectrum is through S-Lang variables. In this case the PHA2 does not need to be split first. To produce the plot above using S-Lang syntax:

chips> clear
chips> pha2 = readbintab("acisf00459N002_pha2.fits")
chips> print(pha2)                                  
_filename        =  acisf00459N002_pha2.fits
_path            =  /data/ciao/threads/
_filter          =  NULL
_filetype        =  4
_header          =  String_Type[190]
_ncols           =  13
_nrows           =  12
SPEC_NUM         =  Short_Type[12]
TG_M             =  Short_Type[12]
TG_PART          =  Short_Type[12]
TG_SRCID         =  Short_Type[12]
X                =  Float_Type[12]
Y                =  Float_Type[12]
CHANNEL          =  Short_Type[12,8192]
COUNTS           =  Short_Type[12,8192]
STAT_ERR         =  Float_Type[12,8192]
BACKGROUND_UP    =  Short_Type[12,8192]
BACKGROUND_DOWN  =  Short_Type[12,8192]
BIN_LO           =  Double_Type[12,8192]
BIN_HI           =  Double_Type[12,8192]

chips> bin_lo_heg_p1 = pha2.BIN_LO[3,*] 
chips> counts_heg_p1 = pha2.COUNTS[3,*]
chips> curve(bin_lo_heg_p1,counts_heg_p1)
0
chips> symbol none
chips> step
chips> xlabel "Wavelength (\AA)"
chips> ylabel Counts
chips> title "ACIS+HEG order=+1"

Note that S-Lang follows C conventions by numbering array indexes from 0, rather than 1. Therefore the 4th row (HEG, +1 order) in the PHA2 file is the 3rd row within the pha2 data arrays (hence the syntax "bin_lo_heg_p1 = pha2.BIN_LO[3,*]" and "counts_heg_p1 = pha2.COUNTS[3,*])".

With Sherpa

Sherpa can also be used to plot a PHA2 spectrum. In this case, the spectra do not need to be split first; Sherpa reads all the rows and allows you to specify individual ones for plotting or fitting purposes:

unix% sherpa

-----------------------------------------------------
Welcome to Sherpa: CXC's Modeling and Fitting Program
-----------------------------------------------------
Version: CIAO 3.4

Type AHELP SHERPA for overview.
Type EXIT, QUIT, or BYE to leave the program.

Notes:
    Temporary files for visualization will be written to the directory: 
    /tmp
    To change this so that these files are not deleted when you exit Sherpa,
    edit $ASCDS_WORK_PATH in your 'ciao' setup script.

    Abundances set to Anders & Grevesse

sherpa> data acisf00459N002_pha2.fits
The inferred file type is PHA Type II.  If this is not what you want, please 
specify the type explicitly in the data command.
Warning: could not find SYS_ERR column
WARNING: statistical errors specified in the PHA file.
         These are currently IGNORED.  To use them, type:
         READ ERRORS "<filename>[cols CHANNEL,STAT_ERR]" fitsbin
WARNING: backgrounds UP and DOWN are being read from this file,
         and are being combined into a single background dataset.
WARNING: multiple datasets have been input.
         The next available dataset number is 13.

sherpa> sherpa.dataplot.curvestyle="histo"     
sherpa> sherpa.dataplot.symbolstyle="none"  
sherpa> analysis channel
sherpa> lp 2 data 3 data 4

Figure 8  shows the plot of the HEG -1 order (row 3, upper drawing area) and +1 order (row 4, lower drawing area) that is created. To change the axes to CHANNEL vs. COUNTS:

sherpa> ploty 3 counts
sherpa> ploty 4 counts
sherpa> lp 2 data 3 data 4

These commands alter the plots to look like Figure 9 . ChIPS commands (within Sherpa) can be used at this point to customize the plot.

sherpa> exit
Goodbye.