INSTRUCTIONS FOR CREATING AXF FILES FOR CNOC2 -- Pat Hall, August 27 1998
chooyu.astro.utoronto.ca!/d/palung/hall/cnoc/howto_axf

The .axf file contains information about the positions of the spectra in an
image.  It is crucial for the extraction step, and is done separately for A&B.


1. Copy each spectral mask image, the r-band image (optional but useful),
and *.cat and *.puma (not *arr.puma) files to a directory.

2. Start saoimage or saotng and examine the mask images to make sure there's
<1 pixel offset between spectra in them.  Hint for saotng: kill magnifier
(panner) after the first image is loaded; this'll speed it up.

3. Coadd both images, offseting first if necessary.  There should be about
2350 counts in non-spectra regions.

4. Within gca (/d/makalu/hyee/ngca/gca):

> rca 1 name	(read catalog, into 1, supply "name" without suffix)

> colr
> 2 1		(may have problems if not all colors and/or mags exist)
> 3 2
> 

> macro setmaskcnoc2	(unnecessary if pvel not used; see below)

> rdpu name.puma	(read puma file, supply name.puma)

> pvel		(optional; displays catalog and masks graphically.
			   An alternative is axfchk; see #18 below.)

	field 1
	filter 2
	mag limit of 22.0 works ok

	Shift-S gets you into slit mode; r to go to cursor mode
	m displays masks
	n displays mask numbers
	r gets you out of slit mode
	l and r are lower left & upper right limits for enlarging
	o zooms back to original size
	h gets you back to gca

Compare the picture in pvel with the coadded image displayed using gca.

Now make the initial, temporary .axf file:

- iaxf 1	(field number 1)
- start with 2 -2 for additional objects outside the slit (pixel units)
- use mag limits of 23.5 21.5 for starters
- no delta correction
- save to .axf file (must specify extension; use .axf.temp here)
- comment: 1447a6A may98, e.g.

When iaxf is run, a list of extra objects gets produced by gca.  As described
below, you'll go through this list and make sure the spectra show up in the
real image.  Also you'll check that there are no extra spectra in the image
that gca did not catch.  If either of the above is amiss then re-run iaxf with 
different paramters or edit the .axf file.  If you edit the .axf file then 
re-number the spectra so that they are all cardinal numbers.  In detail:


5. Convert the .axf file to saoimage display file using 
/d/baobab/lin/saotng/axftoreg

6. saoimage -min 2250 -max 4000 (e.g.) the coadded mask with log scaling
and inverted color.  Read in the *.saoreg file with cursor/region/read.

7. Create .axf.notes file and edit as you go, with e.g.
   "deleted original slit X.  Y slits remaining."

8. Compare the catalog and the image making sure that all the slits were cut.
   DELETE any slits not cut from the .puma file, and repeat rdpu & iaxf.
   Serendipitous objects are automatically added in to the .axf file, and 
   should be added to the .axf.notes file by hand.  These objects have 
   negative slit numbers, and stars have numbers in the -1000s.

9. Repeat axftoreg and display.  Saoimage hint: type 'n' for new display
   ... you can browse the history of displays, too.

10. cp *.saoreg check.saoreg  (working copy)
    When check.saoreg is read in to saoimage, it is labelled by real-slit#.

11. Delete serendipitous objects whose spectra are invisible.
	Don't be too eager -- make really sure it's invisible, e.g.
	potentially interesting single emission line objects missed now
	but noticed later will require time-consuming re-extractions.

12. After checking each slit, delete red box and write out *.reg file.
    Edit the .axf.notes file as you go about what has been added/deleted.

13. To add in an object with PPP position within the x range of the slit:
	--rerun iaxf w/xy and mag limits set to catch the object
	--output *.add
	--cut & paste desired object IN CORRECT X-COORD POSITION in .axf file
	--if there is >3-4 pixel offset in y:  change y-coord and delta-y
	  to match the original object (that object which the slit targeted?)

14. To add in an object with PPP position NOT within the x range of the slit:
	--get its PPP number
	--add it in to the .axf file by hand
	--edit its position to be at the extreme L/R edge of the slit

15. /d/baobab/lin/progs/reorder ... moves *.axf.temp to *.axf
	NOTE that this program ONLY RENUMBERS the objects sequentially;
	it does NOT reorder the objects in their correct x-coord position

16. Repeat axftoreg and 'cp *.saoreg check.saoreg' and read in to saoimage
    for a final check with the new running numbers.

17. When done, put files in archive as follows:

	cat/*.axf
	specred/extr/*.puma (edited)
	specred/extr/*.notes


18. axfchk -- alternative to pvel for checking .cat file to determine the
		reality of objects seen in slits.

Add to loginuser.cl:
	task axfchk="/d/cnoc2/lin/temp/axfchk.cl"
	task $readcat = "$!/d/cnoc2/lin/temp/readcat.e"

Cursor commands:
i: slit info
n: object info and marker; gives ppp# etc., and colors as follows:
	star=orange plus, ft.object=blue dot, galaxy=blue square
d: delete marker
p...p: cross section in x, averaged in y 
	(move cursor between p's to define region)
q: quit

Run saotng as follows (note frame* must match stdimage):
	saotng -fifo /dev/imt1 -winwidth 512 -winheight 512 -framewidth 2048 
	-frameheight 2048 -maxsize 10000000 -flip y 
optionally: -accel /d/baobab/lin/saotng/accel.cmds