1.2m CCD Realtime System Primer

AndyCam Version

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Table Of Contents

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• Introduction
• Getting Started
• Taking Data
• Comment Editor
• Telescope and Top Box Control
• Displaying Images
• Focusing
• Scripts
• Data Archiving
• Purging Files
• Exiting
• Disasters
• Useful UNIX Commands
• Data Reduction in IRAF
• FITS Format
• Miscellaneous

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At this point, you need to learn how to use the mouse. It has three buttons: left, middle and center, which are almost always used in conjunction with the diamond key at the bottom left or right of the keyboard. The mouse serves many functions, only two of which will be described here.

First, the location of the mouse directs keyboard characters to the appropriate window. This is done simply by placing the mouse cursor (looks like a capital I) in the window you want to work in. Often if nothing happened after you typed a command, it is because the mouse was not in the right window. Second, when used with the diamond key, the mouse can be used to move or resize the window that the mouse is in. Here are some of the things you can do, although you should experiment around with the mouse in order to really understand it. The following are all done with the diamond key held down.

left mouse button

When clicked on and off while in the main part of the window, the window will be lowered.

center mouse button

Resize the window, also raises it

right mouse button

Move the window, also raises it.

• Any button on the cross at top left will iconify the window, placing it back in the Icon tablet. The window can be retrieved by clicking on the tablet.
• Any button on the square at the top right will resize the window.

• The left button when clicked in the barred area allows the window to be moved.
• The middle button raises or lowers the window.
• When pressed and held in the background area, the mouse buttons display various menus which offer things like opening a new window, a calculator, and most important, a way to kill one of the existent windows.
• The vertical bar area attached to the left of each window is the scroll bar, executed by the mouse buttons (try it). Cutting and pasting text in a window to the same window or another one is done using a button, first button to cut, second to paste.

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To start the ccd program, move the mouse to the Main Login window and type

gonccd

1. The Monitor Window (labeled tinst.setup)
2. The Rtshell Window
3. The TCS Window (Telescope Control System Window)

The Rtshell window accepts commands for the Realtime System control of the CCD. It has the functions of the tcsh (command line editing) as well as some custom functions. It also has commands built in to control the telescope, filter positions and guider functions, which duplicate many of the TCS functions.

Next, you should decide what ccd format you want, i.e. binned 2x2 or unbinned. The binned pixels are about .6" on the sky while the unbinned are of course half that. The telescope is capable of giving subarcsecond images, which would be degraded by the binned pixel size. However if good images are not essential, the smaller data size and quicker readout of the binned images may be appealing.

Click here for more info on the CCD Chip

In the rtshell window, type small, which is an alias for ccd program off, and will result in binned 2x2, Or type large, which is an alias for ccd program serial parallel and will result in full resolution. Small is executed by default on startup.

The next, decide what output data format you want for disk storage. The two choices are ccd filetype iraf or ccd filetype fits. One of these is also contained in the .ccd.rtrc file, and you should likewise make sure it is the command you want. With the installation of the FITS kernel in IRAF 2.11, there is no longer a need to use iraf type files (.imh)

There are thankfully only a few commands you need to know to take an exposure:

obs

Prompts for a title, and an exposure time (in seconds or sexagismal (mm:ss)). Will do a fast clear of the CCD, open the shutter, read out the CCD and store the data. Information contained in the comment block is automatically store in the data header.

total n

Will do a fast clear of the CCD, open the shutter for time n, where n can be seconds, or sexagismal (mm:ss), read out the CCD and store the data. No prompt will be made for comments - you must enter a name via "object" or "comments," otherwise file is named "unnamed". Total can not be used to change the exposure time in the middle of one already in progress. There is currently no way to change an exposure time for an exposure in progress, except by executing stop , and dstore , which will store the exposure as is.

bias n

Takes n zero-second exposures and names them ``BIAS''.

godark [ n ]

Same as total except the shutter isn't opened. The exposure is named ``DARK''.

goflat [ n ]

Takes an exposure of length n, calls it ``Flat'', and notes in the header that the exposure is a calibration flat field.

mtotal m

Like total, but for integer minute exposures.

go [ n ]

Does a fast camera clear, open the shutter for optional time n, or forever with no time. A total time may later be entered via the total n command. The shutter will close at the end of time, No storage occurs, so this works for multiple exposure frames.

stop

Closes the shutter; no readout.

dstore

Reads out the CCD and stores the image on disk. The comment field must have been edited.

repeat [ m ]

Repeats the last command m times. To take m+1 exposures, use the sequence total n; repeat m, all on one line. A more frequently used sequence might be goflat 3; repeat 24 to obtain 25 flat fields. The comment field should be edited beforehand, or fresh should be used. To end a sequence, type ccd norepeat.

abort

Kills an exposure, but does not clear the CCD.

kill or sac

Kills an exposure, clears the CCD. Dead.

clear

Resets status, often needed after an abort.

cc [ n ]

clears the camera (fast read) n times.

comment

puts you in the comment editor. If a change is made, the comment block is stored as comments in the disk fits header, and object goes into the fits keyword OBJECT.

fresh

uses the most recent comments for the next image

object name

gives the next file a name, puts that name in the FITS keyword OBJECT, but does not put that name in the comment field, nor does the comment field get stored in the next file, unless the comment command is also explicitly invoked.

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The stored frame will use the object name as a name, if one has been provided via the comment block, the command object, or by using the command obs. An object name will also be entered into the frame header if the catalog option in the TCS window has been invoked (see below and the TCS manual). If neither option has been chosen, the frame will be named unnamed, and the comment field in the header will be blank. Iraf format files can be renamed (from inside IRAF) with imrename and FITS format files can be renamed with the oldcom command in the rtshell window. The obs command automatically stores the comment block, even if hasn't been edited recently.

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Here is a sample TCS window:

Filters

Filters can only be loaded by Bas, Ted or other qualified people. To move to a particular filter, simply click the left mouse button on that filter button. The longest time required move to a filter is 15 seconds, for a 4 position move. The filter currently over detector is displayed in the TCS window. You should blow the dust off the filters using a canister of dry air before your run begins, or perhaps even every afternoon. There is an access port that makes this easy.

We have UBVRI filters . Note that 2" filters will vignette at the edges of the CCD field, in a curious way that causes astigmatic star images.

Telescope Focus

Please try using the experimental findfwhm to measure and set the focus. This script is fully automatic, estimates the seeing, and records its results along with mirror temperatures to a file we are using to monitor the seeing.

Telescope focus is one of the functions of the hexapod, which is controlled from the Sun computer by the TCS program. To change the focus, click the left mouse button on the TCS Focus Move button. A smaller window will popup with buttons for movement in or out. The movement step size can be changed with the Focus Set button. Movement to larger numbers is against gravity. Always come to the final focus position from the same direction that you used to determine that position. The focus position is displayed in the TCS window, and is stored in the data header. A good script for automatically focusing the telescope is nfoc, which calls the script testfoc with arguments 8 2 15 (numframes exptime stepsize).

The telescope focus shows changes with outside air temperature in a fairly uniform way. After slewing to extreme hour angles, the focus may also change. If you see unusual changes in focus values, please report that in detail, in the nightly logs.

Slewing

Use the TCS New Coords button to enter your next position, using spaces or colons to separate h:m:s and d:m:s. The epoch may be omitted, in which case 1950.0 will be used. The coordinates may also be selected from a catalog (see the TCS manual). Once coordinates are loaded, then click on the Slew Enable button. The STOP button will abort a move or a new coords command, but hitting the cancel button on the DFM rack is faster.

Other Features:

One can also offset the telescope from the present position an arbitrary number of arcsecs, change the track rates, set the time, and basically do all of the TCS functions from the rtshell window as well as the TCS window via special commands. See the TCS manual) for details. Rtshell also allows script control of the system, see the Rtshell Users Guide and the Rtshell Script Writers Bible for further information.

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There are help files in the directory ~observer/saoimage.help which describe the various features. Click on saoimage's Color menu button and you will enable the lookup table, altered by holding a mouse key down and then moving the mouse. Of particular note is the n key, which will load an image in standalone mode (IRAF won't know about it), which occurs much faster than displaying through IRAF, plus the pixel values aren't truncated. The complete path name of the .imh file must be entered.

The most useful iraf package for analyzing your image is imexamine which places a cross shaped cursor on the image, allowing line and column plots (l or c keys), and radial profile plots of stars (r key). These graphs will come up in a separate graphics window. Use q to exit imexamine. The implot package also comes in handy.

Hardcopies can be made by going to the etc menu, and clicking on print.

If for some reason another saoimage is running, IRAF will not display in the new saoimage. If you suspect this has occurred, i.e. disp doesn't seem to do anything, go to the main login window and type ps aex | grep image. Kill any processes named saoimage or ximage with command kill -9 procnumber, then try saoimage again. If it won't let you kill them (not owner), use godown to reboot.

If you are not running iraf, there are two aliases for using saoiaage, view and iview . View is for use with fits files, and is used with view [filenumber], iview is used the same way for iraf files.

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Please try using the experimental findfwhm to measure and set the focus. This script is fully automatic, estimates the seeing, and records its results along with mirror temperatures to a file we are using to monitor the seeing.

If your roots are very deep, follow the old method and take manual focus frames thusly:

1. Determine the appropriate exposure time for the star and place the star in the middle of the CCD.
2. Move the focus up to 60 units larger than the suspected true focus position.
3. In the Rtshell window, type go n, where n is the exposure time.
4. After the beep, offset the telescope about 15" west, and move the focus outward about 20 units (positive direction).
5. type go n again. repeat 4 & 5 about six times, leave a double offset for the last exposure.
6. for the last exposure type total m*n, where m*n is the total exposure you expect (the TCS will tell you this). If you don't want any more exposures, make m*n equal or less than the current exposure time.
7. The chip will now be read out. You have created a multiple exposure of the star at different focus settings, which can be inspected via the imexamine routine for the best focus. Come back up to correct focus.

The telescope focus appears to change with temperature.

Guider Focusing

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It is not easy to kill a script, for the shell is occupied during the script and will not accept commands like "kill". Typing CNTRL-C during readout will sometimes kill each exposure individually, and thus is useful if there are only a few exposures left. Otherwise, you must kill the rtshell window (using the 3rd mouse button to bring up "Destroy Window"), and then restart the Realtime system. This problem may be avoided by putting in 5 second delays between each sequenced exposure in the script used, during which time one can type a CNTRL-C which will kill the sequence. The sample scripts listed here have such a feature.

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1. To use IRAF:

   To write to a new DAT tape use wfits *.fits mta newtape+

   To write on a tape containing files use wfits *.fits mta newtape-

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   Purging Files

   Eventually, you will need to remove your files from disk, either because you are running out of room, or your run is over. To check the data disk space, in the login window type ls -l /ccd, which whill produce an output like:

   lrwxrwxrwx 1 root 13 Jun 8 1998 /ccd -> /data/ccd/ccd

   This shows that the /data disk holds the ccd data. Now type df /data which will produce output like:

   Filesystem            kbytes    used   avail capacity  Mounted on
   /dev/dsk/c0t2d0s2    8749013 3488159 5173364    41%    /data
   

   and note the space available on data disk, for this example 5 gigabytes of storage remains.

   The Iraf command to delete files is imdelete. Please use it for IRAF or FITS files. You may wish to edit the parameter file for imdelete (via epar imdelete) to turn on the safety measures.

   Your data will be subject to deletion the afternoon following your last night of observing. You may want to check the data disk to see what garbage is left over from the previous observer.

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   Exiting (gracefully and otherwise)

   You don't have to logout, but if you want to, first kill the Realtime system. Type exit twice in the Rtshell window, or use the alias bye. The windows will go away after a while. If you accidentally get out of the Realtime system (by typing a lot of CTRL-C's for instance), you can re-enter by typing gonccd . in the login window, which is the official way to bring up the system.

   After exiting Realtime system, you can exit the computer by typing exit in the Main Login window

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   Disasters

   If you get into bad trouble, for example the screen locks up on you and you get no response for several minutes, you will have to reboot the system. You may also have to do this to restart after being shutdown because of maintenance work or power problems.

   There are three possible wyas to reboot:

   1. If you can still type commands into some window somewhere (ON FLWO48!) , type godown -r, which is a link into shutdown, and will flush all disk buffers to disk and shutdown as gracefully as possible.
   2. On the Sun console keyboard, press the `Stop' key in the upper left corner (also marked `L1') while simultaneously pressing the `a' key. This is also called `pressing L1/A' in some documentation. Possible file system corruption may occur, as disk buffers are NOT flushed.
   3. Turn Flwo48's power off, wait 5 seconds, switch back on. The power switch is located on the back of flwo48's pizza box. Possible file system corruption may occur, as disk buffers are NOT flushed.

   The number 1 method should always be attempted first, but if it won't work try 2, then 3.

   After shutting down the machine via either of the first two methods, you reboot by typing a `b' at the `<' prompt. In the third case, the computer should reboot automatically without user intervention.

   Within a few minutes, after a lot of messages, the login window should be back.

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   Useful UNIX Commands

   (aliases are put in parentheses) (arguments inside [] are optional)

     ls -l[dirname]    (dir)   - lists the contents of a directory
     rm file          (del)   - deletes file
     mv file1 file2             - renames file1 to file2
     cp file1 file2              - copies file1 into file2
     cat file                  - lists the contents of a file
     lpr filename              - prints file named filename
     xterm &                 - creates another window 
     vi[filename]             - an editor
     emacs[filename]          - another editor
     cd directory             - change to directory directory
     mail                   - To read your mail
     mail name[@host.domain]  - To send mail to user 
     telnet [hostname]        - Connect to hostname
     rlogin hostname          - A better connect to hostname 
     ftp [hostname]          - remote file transfer program
   

   Unix device names:

   • 4mm DAT tape drive - /dev/nrst0
   • 8mm EXABYTE tape drive - /dev/nrst1
   • 2nd 4mm DAT tape drive - /dev/nrst2
   • Postscript Laser printer - lp

   Unix commands can be executed in the Rtshell window, but in general it is better to execute them in the login or other windows.

   Remote logins and transfers via rlogin, telnet, or ftp can be done via the microwave link to Tucson. It is wise not to use the login window for these transactions.

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   Data Reduction in IRAF

   It is possible to do the necessary debiasing and flatfielding of the CCD data in IRAF. The packages needed to do this (imred, ccdred) have to be loaded. A "translation" file called instru is in the observer directory, which is needed by ccdproc. You'll almost certainly want to check the parameter files of ccdred (do you want real output?), ccdproc (what do you want to do, check the bias overscan sizes, trim sizes), and the combining tasks (flatcombine etc.).

   The pixel directory must be set by you, because the default directory (on the user disk) doesn't have room for an entire night's data. The simplest thing is to put the data in a subdirectory of the night's data, e.g., in IRAF do this:

   cd /ccd/flwo2/1992/01/03

   mkdir reduced

   set imdir=/ccd/flwo2/1992/01/03/reduced/

   Don't forget the final slash in the imdir command!

   For accurate data reduction, it is recommended that you take 5 bias exposures, and more than 20 flatfield exposures in each filter with exposure times such that the level obtained is close to what the sky level will be for your object exposures (probably less than 1000 counts). For an example exposure time of 2 seconds, the latter is easily done via

   goflat 2; repeat 19

   Two header items need to be correct for the IRAF ccdred package to work properly. These are the keywords IMAGETYP and FILTER. For the bias frames, the IMAGETYP should be "zero". For the flatfield frames, the IMAGETYP should be "flat" and the FILTER keyword should be whatever is appropriate. For the object exposures, IMAGETYP should be "object" and the FILTER keyword should also be whatever is correct. These items can be checked via:

   ccdlist *.fits

   Any necessary changes can be made via:

   hedit

   You will first be prompted for a file name, which can be a wildcard name (e.g., data* will use all the frames named data001, data002 etc.).

   Moving along now, do lpar ccdred, and make sure the file looks like this :

      (pixeltype = "real real")    Output and calc pixel datatypes
        (verbose = yes)            Print log info to the stdout?
        (logfile = "logfile")      Text log file
       (plotfile = "")             Log metacode plot file
         (backup = " ")            Backup directory or prefix
     (instrument = "ccddb$flwo/ccd.dat") CCD instrument file
         (ssfile = "subsets")      Subset translation file
       (graphics = "stdgraph")     Interactive graphics device
         (cursor = "")             Graphics cursor input
        (version = "2: October 1987")
          (flpar = no)             flush pfile on assign?
           (mode = "ql")
   

   You have the option of making the output file pixeltype real if you are worried about precision. All Parameter files can be changed via epar filename. The editor is exited with CTRL-D.

   If you have a number of flats or biases, you should use flatcombine or zerocombine on these. Enter epar flatcombine. I suggest you use the avsigclip technique on the flats, and maxreject on the biases to combine them, so as to get rid of cosmic rays. Leave the imagetyp equal to ``flat'', or ``zero'' as the case may be. For flatcombine, subsets should be used ("yes"). The great advantage of using IRAF is found here: To combine the flats, for instance, you need only type:

   flatcombine data*.fits

   for the case where "data" is the prefix for ALL of your files. The program will sort out the flats from the biases and objects, and then sort out the different filters among the flats. You will be left with combined flats with names like ``FlatV'', ``FlatR'', if the filters in the headers were V and R, for example.

   The command

   zerocombine data*.fits

   does something similar to the bias frames, only combining those frames with IMAGETYP of ``zero''. The output file will be called ``Zero''.

   There is also a command to combine dark images, obviously called

   darkcombine data*.fits

   Now do lpar ccdproc. The file should look like:

         images = " "        List of CCD images to correct
       (ccdtype = " ")       CCD image type to correct
     (max_cache = 0)         Max image cache mem (in Mbytes)
        (noproc = no)        List processing steps only?n
        (fixpix = no)        Fix bad CCD lines and columns?
      (overscan = yes)       Apply overscan strip correction?
          (trim = yes)       Trim the image?
       (zerocor =  no)       Apply zero level correction?
       (darkcor = no)        Apply dark count correction?
       (flatcor = yes)       Apply flat field correction?
      (illumcor = no)        Apply illumination correction?
     (fringecor = no)        Apply fringe correction?
       (readcor = no)        Convert ZERO to readout correction?
       (scancor = no)        Convert FLAT to scan correction?
      (readaxis = "line")    Read out axis (column|line)
       (fixfile = )          File for bad lines and columns
       (biassec = "[1030:1038,2:1023]") Overscan strip section
       (trimsec = "[1:1024,1:1024]") Trim data section
          (zero = "")        Zero level calibration image
          (dark = "")        Dark count calibration image
          (flat = "FlatB,FlatV,FlatR ")       Flat field images
         (illum = "")        Illumination correction images
        (fringe = "")        Fringe correction images
      (scantype = "shortscan")    Scan type (shortscan|longscan)
         (nscan = )          Number of short scan lines
   (interactive = no)        Fit overscan interactively?
      (function = "legendre")     Fitting function
         (order = 1)         Num of polynomial terms/spline pieces
        (sample = "*")       Sample points to fit
      (naverage = 1)         Number of sample points to combine
      (niterate = 1)         Number of rejection iterations
     low_reject = 3.)        Low sigma rejection factor
   (high_reject = 3.)        High sigma rejection factor
          (grow = 0.)        Rejection growing radius
          (mode = "ql")      
   

   Pay particular attention to the biassec and trimsec, as these will obviously need to be changed for 2048x2048 images. darkcor should be turned on if you want to subtract darks, and the dark frame should be given in the appropriate row.

   The combined bias frame for the thinned chip shows no structure, but if you still want to subtract off the bias frame change zerocor in the parameter file to ``yes'', and enter ``Zero'' (or whatever) for the zero file.

   You may want to change the input files now for zero and flat in the ccdproc parameter file to be what you actually wound up with. These can also be entered on the IRAF command line.

   You are now ready to process all of the flats. Type:

   ccdproc Flat*.fits

   This will first debias the flat frame(s) by calculating the overscan value, subtracting that value from the entire image, and then subtracting the ZeroS frame from the result. If the flats have zeroes anywhere, an error in division will occur when processing the object frames. In that case, correct the flats for the zeros by loading the IRAF package prototype, and using the command:

   imreplace upper=n

   where n is some value below the mean (found by imstat). You will be prompted for the file name and the replacement value, which could be anything but zero, but might as well be the mean value.

   The file called subsets should have been modified or created and will look something like:

         'B'     B
         'V'     V
         'R'     R
   

   This file is used to distinguish between the choices of flat fields to be used to flatten the object frames.

   You are now ready to process all of the object data. Type ccdproc objects. You can also enter the bias and flatfield frames at this time via: ccdproc data.fits zero=zero flat=flat. If the bias or flats have not been processed, they will be at this time. One can also use files that contain the file names here, like: ccdproc @data zero=zero flat=@flats, where @data and @flats are text files with the actual file names to be used listed, one to a line.

   NOTE: The reduced images are written over the raw images. Processing can be checked by:

   ccdlist filenames

   A useful command is flpr, which clears the processor should any errors have occurred along the line.

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   FITS Format

   To record data in FITS format, issue the command ccd filetype fits in the Rtshell window. Using this format makes available other commands in the Rtshell window (basically duplicating what exists in IRAF). These are described in the Realtime manual of Bill Wyatt. Some of the more commonly used commands are:

   dlink now moves you to the current data directory

   dlink date moves you to the data directory of date

   info n displays header of picture number n

   dir lists data files in current data directory

   view n brings up saoimage, with picture n. Also kills any previous saoimage.

   To archive data, see the archive section on data storage.

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   Miscellaneous

   The Rtshell window has an extensive help command, describing all of the commands listed above, plus those dealing with driftscanning, changing the readout pattern of the CCD and other things.

   Several aliases have been written which readout the chip in popular ways; execute them in the Rtshell window:

   ccd2048 - (size = 2048x2048 = full res) alias ``large''

   ccd2048c - (full res, but only reads central 1024x1024; this speeds up the readout)

   ccd1024 - (2x2 binning) alias ``small''

   ccd512 - (4x4 binning)

   ccd512c - (2x2 binning, but only read out central 512x512)

   ccd256 - (8x8 binning)

   ccd128 - (16x16 binning)

   These last two are readout very fast, good for snapshots of fields.

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