Examining Grating Spectra and Regions: PHA2 files
[CIAO 3.4 Science Threads]
OverviewLast Update: 1 Dec 2006 - updated for CIAO 3.4: ChIPS and Sherpa versions Synopsis: An overview of displaying grating data Type II PHA files and the source and background extraction regions. Related Links:
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Contents
- What is a PHA2 File?
- Examining the Files with Prism
- Displaying the Spectrum
- Displaying the Extraction Regions
- History
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Images
- Prism view of ACIS-S HETG dataset
- Prism view of ACIS-S LETG dataset
- Expanded view of BIN_LO column
- Prism view of HRC-S LETG dataset
- Prism view of HRC-I LETG dataset
- View of order +1 spectrum with Prism
- View of order +1 spectrum with ChIPS
- View of order +/-1 spectrum with Sherpa: count rate
- View of order +/-1 spectrum with Sherpa: counts
- Data with source and background regions overlaid
What is a PHA2 File?
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 Obtain Grating Spectra from HETG/ACIS-S Data 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 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.
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) 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.
Displaying the 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 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 unix% dmcopy \ "acisf00459N002_pha2.fits[region][tg_m=1,tg_part=2][cols x=tg_lam,y=tg_d,*]" \ region_order1.fits unix% dmcopy \ "acisf00459N002_pha2.fits[region][tg_m=3,tg_part=2][cols x=tg_lam,y=tg_d,*]" \ region_order3.fits
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 ovelaid:
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.
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 |