Examining Grating Spectra and Regions: PHA2 files

CIAO 4.0 Science Threads

Overview

Last Update: 6 Jun 2008 - added "opt=all" to dmcopy commands so all blocks are kept in the grating files

Synopsis:

An overview of displaying grating data Type II PHA files and the source and background extraction regions.

Related Links:

Analysis Guide for Chandra High Resolution Spectroscopy: an in-depth discussion of grating analysis.

Proceed to the HTML or hardcopy (PDF: A4 | letter) version of the thread.

A Type II PHA file is a standard FITS format in which each row contains array columns. The PHA file is a product of standard data processing and is identified by the pha2.fits extension; note that the "2" in the filename refers to the fact that it is a level=2 data product, not that it is a Type II file. In the case that the user has to manually reprocess an event file (e.g. when applying an updated order sorting table), the PHA2 spectrum file is obtained from the level 2 event file by tgextract; see the HETG/ACIS-S Grating Spectra for an example of this.

The SPECTRUM block of a PHA2 file has 13 columns of data:

     ColNo Name                  Description

     1     SPEC_NUM              Spectrum Number
     2     TG_M                  Diffraction order (m)
     3     TG_PART               Spectral component (HEG, MEG, LEG, HESF parts)
     4     TG_SRCID              Source ID, output by tgdetect
     5     X                     X sky coord of source
     6     Y                     Y sky coord of source
     7     CHANNEL[8192]         Vector of spectral bin numbers.
     8     COUNTS[8192]          Counts array (a spectrum)
     9     STAT_ERR[8192]        Statistical uncertainty (error) on counts colum
     10    BACKGROUND_UP[8192]   Upper Background count vector.
     11    BACKGROUND_DOWN[8192] Lower Background count vector.
     12    BIN_LO[8192]          Bin boundary, left edge
     13    BIN_HI[8192]          Bin boundary, right edge

There are two columns that are especially relevant when doing analysis:

TG_M indicates the order of the spectrum (+/- 1, +/-2, +/- 3)
TG_PART indicates the spectral component / grating arm (1 = HEG, 2 = MEG, 3 = LEG)

Examining the Files with Prism

Sample ObsIDs used: 459 (HETG/ACIS-S 3C 273); 460 (LETG/HRC-S, 3C 273); 1198 (LETG/ACIS-S, 3C 273); 1800 (LETG/HRC-I, PKS2155-304)

File types needed: evt2; pha2

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 hrcf00460N004_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.

Displaying the Spectrum

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)

For this example, the line style was set to "noline" and the "cross" symbol was used. As 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.). The Introduction to ChIPS thread (S-Lang or Python) has more information on plotting data.

With ChIPS

In order to display a spectrum with ChIPS, we need to specify which row in the file should be plotted. This example uses row 4, the +1 order HEG spectrum for the observation, chosen by the "[#row=4]" filter. Note that this example uses the Python interface to ChIPS:

unix% chips

chips> make_figure("acisf00459N002_pha2.fits[#row=4][cols bin_lo,counts]")

chips> set_curve("symbol.style=none")
chips> set_plot_title("ACIS+HEG order=+1")

These commands produce the plot shown in Figure 7 . Quit ChIPS before continuing:

chips> quit

With Sherpa

Sherpa can also be used to plot a PHA2 spectrum. 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 Package
-----------------------------------------------------
Version: CIAO 4.0

sherpa> load_pha("acisf00459N002_pha2.fits")
statistical errors were found in file 'acisf00459N002_pha2.fits'
but not used; to use them, re-read with use_errors=True
read background_up into a dataset from file acisf00459N002_pha2.fits
read background_down into a dataset from file acisf00459N002_pha2.fits
...

sherpa> plot_data(3)
sherpa> add_plot()
sherpa> grid_objects(1,2,0.18,0.18)
sherpa> plot_data(4, clearwindow=False)

sherpa> current_plot("all")
sherpa> limits(X_AXIS, AUTO, 5)

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 plot the data in CHANNEL vs. COUNTS:

sherpa> erase

sherpa> get_data(3).units="channel"
sherpa> get_data(4).units="channel"

sherpa> plot_data(3)
sherpa> add_plot()
sherpa> grid_objects(1,2,0.18,0.18)
sherpa> plot_data(4, clearwindow=False)

These commands create Figure 9 .

sherpa> exit
Goodbye.

Displaying ACIS and HRC Extraction Regions

Each pha2 file has a second block, named REGION, which stores the regions used by tgextract to extract the source and background spectra.

There are three regions associated with each order: source, upper background, and lower background. For an ACIS/HETG observation, this gives 36 regions: 12 spectral components (+/- 3, +/- 2, and +/- 1 for HEG and MEG) times 3 regions apiece (source and two backgrounds).

To look at the columns of a REGION block:

unix% dmlist "acisf00459N002_pha2.fits[REGION]" cols

--------------------------------------------------------------------------------
Columns for Table Block REGION
--------------------------------------------------------------------------------
 
ColNo  Name                 Unit        Type             Range
   1   SPEC_NUM                          Int2           1:32767              Spectrum number
   2   ROWID                             String[64]                          Source or a background
   3   SHAPE                             String[16]                          Shape of region
   4   TG_LAM               angstrom     Real4          0:      400.0        Dispersion coordinate 
   5   TG_D                 degrees      Real4          -2.0:        2.0     Cross-dispersion coordinate 
   6   R[2]                 (angstrom , degrees) Real4(2)       -Inf:+Inf    Raduis vector for SHAPE
   7   ROTANG               degrees      Real4          -360.0:      360.0   Rotation angle for SHAPE
   8   TG_PART                           Int2           0:9                  Grating part index (HEG=1, MEG=2, LEG=3)
   9   TG_SRCID                          Int2           1:32767              Source identification number
  10   TG_M                              Int2           -62:62               Diffraction order
  11   COMPONENT                         Int2           -                    Component number

ds9 cannot display these regions as they are written in the pha2 file. In order to view them, we need to rename the (TG_LAM,TG_D) columns to (X,Y) so that ds9 knows how to interpret them. We will also need to create images in (TG_LAM,TG_D) coordinates, on which we can display the regions.

The following dmcopy commands create image and region files for the 1st and 3rd orders of the MEG arm:

unix% dmcopy \
      "acisf00459N002_evt2.fits[bin tg_lam=0:30:0.08,tg_d=-0.01:0.01:0.00008][tg_m=-1,1,tg_part=2]" \
      459_order1.fits opt=all

unix% dmcopy \
      "acisf00459N002_evt2.fits[bin tg_lam=0:15:0.08,tg_d=-0.01:0.01:0.00008][tg_m=-3,3,tg_part=2]" \
      459_order3.fits opt=all

unix% dmcopy \
      "acisf00459N002_pha2.fits[region][tg_m=1,tg_part=2][cols x=tg_lam,y=tg_d,*]" \
      region_order1.fits opt=all

unix% dmcopy \
      "acisf00459N002_pha2.fits[region][tg_m=3,tg_part=2][cols x=tg_lam,y=tg_d,*]" \
      region_order3.fits opt=all

In creating the images, the filter includes + and - orders to obtain more events in the image. Since the regions are the same for +/- orders, it is only necessary to copy one (the + orders were used here). The image limits are typical for ACIS/HETG observations, but will need to be adjusted for other configurations.

To display the event files with the regions overlaid:

unix% ds9 -tile 459_order1.fits -region region_order1.fits -cmap a\
      459_order3.fits -region region_order3.fits -cmap a

which produces Figure 10 . We can see that all events are contained within at least one extraction region.

For HRC/LETG data, a bow-tie extraction region is used. Using similar dmcopy commands as for the ACIS data:

unix% dmcopy \
      "hrcf00460N004_evt2.fits[bin tg_lam=0:210:0.25,tg_d=-2:2:0.0008][tg_m=-1,1,tg_part=3]" \
      hrc_order1_img.fits opt=all

unix% dmcopy \
      "hrcf00460N004_pha2.fits[REGION][tg_m=1,tg_part=3][cols x=tg_lam,y=tg_d,*]" \
      hrc_region_order1.fits  opt=all

To display the file and regions:

unix% ds9 hrc_order1_img.fits -region hrc_region_order1.fits -cmap b &

which produces Figure 11 .

History

01 Jun 2004	reviewed for CIAO 3.2: no changes
06 Dec 2005	updated for CIAO 3.3: version numbers
01 Dec 2006	updated for CIAO 3.4: ChIPS and Sherpa versions
24 Jan 2008	updated for CIAO 4.0: updated ChIPS and Sherpa syntax
06 Jun 2008	added "opt=all" to `dmcopy` commands so all blocks are kept in the grating files