4shooter Realtime System Primer

Created: 07/22/93 by NC
Updated: 10/06/05 by EF

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Warning! This document is obsolete and no longer maintained. Several commands have changed for Keplercam.

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Introduction

 This primer is intended to instruct new users of the CCD system on the 1.2-meter telescope. As such, many of the features of both the Realtime system and the Unix operating system itself will not be discussed unless they are essential to the taking or archiving of data. There are other manuals for the operation of the telescope itself and of the irarray. Be advised that this system is subject to change, and many changes might have occurred since you last used it. This primer will concentrate on what can be done by one particular user, namely "4obs". We try to keep this one computer account unchanged. If you make minor changes please advise us. The 4obs account is restored periodically from a frozen disk version. (To restore, type restore.4sh and log out and then back in.) If you don't like its setup, or wish to make lasting changes, please ask for your own account (we STRONGLY discourage operating the telescope from accounts other than 4obs or observer).

Note: flwo48 was upgraded after the summer 2003 shutdown. One of the visible changes is a much-improved GUI for your screens. One obvious new feature is the existence of 2 desktops per screen, as you can find out by clicking on the "Desktops" in the Icon Manager at the lower right (see below for details). Another feature is that the left (right) screen is a 24-bit (8-bit) display. Please explore, and if you run into difficulties, please tell us about them in detail.

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Getting Started

 Log in to the Sun computer named flwo48, using the name 4obs. The password should be printed on the monitor. You will soon see several windows appear, including a blue one called Main Login, a maroon (according to some X geek) one called Iraf, a clock, and the FVWM Icon Manager (lower right of each screen). The blue and maroon windows are simply unix xterm windows. You might use the second monitor to display the images (it is called flwo48:0.1)

At this point, you need to learn how to use the mouse. It has 3 buttons: left, middle and right. The mouse serves many functions, only a few of which will be described here.

The location of the mouse brings focus, i.e. directs keyboard characters to the appropriate window. You simply place the mouse cursor (looks like a capital I) on the window you want to work in. Often, if nothing happened after you typed a command, it was because the mouse was not in the right window. A simple action you can achieve is to click with the left button on a window just about anywhere on it, except on the little boxes at top right: that brings it to the foreground. Other actions, such as clicking, dragging to select, and inserting, are standard X. At the top margin of each window is a bar; clicking a mouse button there results in one of these actions:

  • The vertical bar area attached to the left of each window is the scroll bar.

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    Taking Data

    First, the telescope PC must be working, as well as the guide PC. To start these up, go to     Startup and TCS.

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

    go4
    Three windows will appear:
    1. The Monitor Window (blue, labeled inst.go)
    2. The Rtshell Window (blue xterm)
    3. The TCS (Telescope Control System) Window
    You only need the monitor window for debug output when problems occur, so you might iconify it.

    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.

    The basic parameters of the CCDs are changed with command "ccd" with several different parameters. You only need a few of these, and there are aliases for the most frequently-used ones:

  • You must first decide what CCD format you want, i.e. binned 2x2 or unbinned. The binned (unbinned) pixels are about 0.66" (0.33") on the sky. The telescope is capable of giving subarcsecond images (a rare occurrence in recent times), which would be degraded by the binned pixel size. However if good images are not essential, the smaller data size and quicker readout (about 30 sec) of the binned images should be appealing.

    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.

    One of these commands is contained in a file called ``.4shooter.rtrc'' in the 4obs home directory an is executed when you typed go4. If you want a different size at startup, edit that file and change commands. This will insure that every time you exit and return to the system the size will be the same. You can always enter the binning commands in the Rtshell window.

  • Normally, all 4 CCDs are read out. If you are interested in only one of the chips, say chip 3, you should issue the command "ccd selchan 3" and to return to normal "ccd selchan" (the default). You only save disk space this way, not readout time unfortunately. If in doubt, typing "ccd selchan ?" in the rtshell will return the status, 0 being the default, all 4 CCDs.

    Click here for more info on the CCD Chip

    You may also want to change the number of channels that are read out. You can choose between 4 and 8 channels. split will result in 8 channels (2 per chip), while nosplit results in 4 channels (1 per chip). You are strongly DISCOURAGED to use split , see the staff if you have any questions.
    The frames are stored in a directory named like /4sh/flwo2/year/month/day, for example /4sh/flwo2/2000/01/03 for 2000 Jan 3. The directory changes at noon MST. Data are stored in FITS EXTENSION files, so a command has been issued as ccd filetype extfits in the rtshell (do not change under any circumstance!).

    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 sexagesimal (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 (also, see kill command below).
    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
    Stops the current exposure; 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 6; 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 (stop+abort+clear)
    Kills an exposure, clears the CCD. No readout.
    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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    Comment Editor

     The comment block can be edited by typing the command comment. Here's how the comment-editing window appears:

    When the window appears, move the cursor to the right side of the window where the changeable parameters are. On the 1.2m, the coordinates, airmass, times and filter are transferred from the telescope computer, so the only things you might want to enter are the object name, your name and the weather conditions.

    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. The obs command automatically stores the comment block, even if it hasn't been edited recently.

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    Telescope and Top Box Control

     The TCS window allows control of the movement of the telescope, telescope focus, top box filter wheel and guider functions. It also displays the current telescope position, focus and filter position, and telescope times if the PC communication is on (set by clicking on the PC Comm button). For a more detailed listing of the use of this window, see the TCS manual .

    Here is a sample TCS window:

    Filters
    Filters can only be loaded by Wayne, Ted, Bob 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, Sloan and narrow-band filters. Note that 2" filters will vignette at the edges of the CCD field, in a curious way that causes astigmatic star images. NOT recommended with 4shooter.

    Telescope Focus
    Telescope focus uses the hexapod under control of the TCS program on the Sun computer (flwo48). To change the focus manually, click the left mouse button on the TCS Focus Move button. A smaller window will pop up 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. The focus position is displayed in the TCS window, and is stored in the data header.

    To actually measure and set the focus, please try the findfwhm script. This script is fully automatic; it estimates the focus and sets it, estimates the seeing, and records its results along with mirror temperatures in a file we are using to monitor the seeing. If you prefer to use the old methods to focus, click here.

    The telescope focus shows changes with position in an erratic way, and with outside air temperature, in a more uniform way. After slewing through large angles, the focus may change, but not always. If you are observing a single object for a long time, you will notice the focus position increase as the temperature drops during the night.

    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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    Telescope Focusing (old style)

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

    1. Determine the appropriate exposure time for a star in your favorite field and place the star in the middle of the CCD. Make sure the star is NOT one of the entries in the bright star catalog!
    2. Move the focus 60 units lower than the suspected true focus. Please visit the HEXAPOD description.
    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 up about 20 units.
    5. type go n again. repeat 3 & 4 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 multiple exposures of the star at different focus settings, which can be inspected via the imexamine routine for the best focus.
    You might also use a script called testfoc which takes 3 arguments, numframes, exptime and stepsize. For example, testfoc 8 2 15 will produce a frame name 0002.FineFoc.fits which contains eight exposures of two seconds each, with a focus offset of 15 steps between each frame, and will then prompt the user for the number of the in-focus image and set the focus to the correct value. The command nfoc is equivalent to testfoc 8 2 15.

    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.

    Once you've tried the old way, please try using findfwhm to measure and set the focus. This script is fully automatic, estimates the focus, sets it, estimates the seeing, and records its results along with mirror temperatures to a file we are using to monitor the seeing.

    Guider Focusing

    After focusing the telescope, put the guider on-axis, then in the guider's acquire window adjust the focus value. The guider will remember ANY change to guider focus while on-axis, and store this for use in the future. If the telescope focus was correctly set, you only need to change the on-axis guider focus once. When the telescope comes out of focus, just refocus the telescope, and the guider will be back to focus.

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    Scripts

     The rtshell allows many manual commands to be automated. For instance, scripts have been written that will execute a sequence of commands that will take flat field exposures in various filters. Likewise, scripts can be written to move to a standard star and take exposures in several filters. Check the scripts subdirectory in the 4obs directory for sample scripts. For details on writing your own scripts, go to the Rtshell Script Writers Bible for further information.

    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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    Twilight flats

     The script dotwilight.script allows you to create sky flats automatically. The script determines the date of observation and calculates the appropriate exposure times, given the readout time of the 4shooter. It also determines which filter is in place, and uses it to expose. Follow the link above for a detailed explanation and instructions.

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    Data Archiving

     You can either create a fits tape using iraf, or use unix tar in the data directory. The csh command backup is a user friendly version of tar.
    1. To use IRAF:
      To write to a new DAT tape use mscwfits *.fits mta newtape+
      To write on a tape containing files use mscwfits *.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 df /4sh (/4sh is linked to /data/ccd/4shooter), which will produce the output: 
    Filesystem            kbytes    used   avail capacity  Mounted on
/dev/dsk/c0t2d0s2    8749013 4167071 4494452    49%    /data
    and note the space available on the data disk, about 4.5 gigabytes in this example.

    The Iraf command to delete files is imdelete. You can 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.

    You can also use delete for fits files. Unix rm can also be used, as can rmdir. Your data will be subject to deletion the afternoon following your last night of observing. However, if there is ample space to start your run, you might consider postponing such deletion until it becomes necessary (especially on weekends). 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 go4 . 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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    Problems

     If the CCDs are slow or unresponsive, click here for instructions to recover.

    If tcs becomes unresponsive on flwo48, click here for instructions to recover.

    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 ways 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. If the computer has been crashing on its own, you may want to power down the computer at this point (in the computer room), to reset various modules.
    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 the power off on flwo48, wait 5 seconds, then 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 2 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 
  ssh [user@hostname]        - Connect securely to hostname
  sftp [user@hostname]     - secure file transfer program
    Unix device names: Unix commands can be executed in the Rtshell window, but in general it is better to execute them in the login or other windows.

    It is wise not to use the login window for remote logins or transfers via ssh or sftp.

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    Using IRAF

     Once you have taken an image, move over to the IRAF window to look at the data. In that window, type cd; cl as usual. You will need to cd to the data directory, for example cd /4sh/flwo2/2003/01/03. Type dimtool for ds9, *the preferred display method*, simtool or ximtool, then type flwo48:0.0 (flwo48:0.1) at the IRAF prompt to display on the right (left) monitor. If you are displaying unbinned images, you will need to change the stdimage in IRAF: type set stdimage=imt2048 to view your full images.

    If you want to use the left monitor to display images, there are a few tricks. To use saoimage (ds9), type simtool (dimtool) as above, but type flwo48:0.1 to the IRAF prompt. This will place the saoimage (ds9) window on the left monitor. To use ximtool, you must find an xterm in the left monitor (to open an xterm, move the cursor there, and click on the left button). Start up IRAF, type ximtool, and answer flwo48:0.1 to the prompt. You can now display images from either that IRAF window, or one on the right monitor.

    Use mscdisplay (in the mscred package) to display images (ex. mscdispl 0004.M31 1); mscexamine to examine them (like imexamine but for mosaics). Caveat: although mscexamine appears to work to some degree, imexamine on individual frames (see below for an example) is the only reliable approach. Make sure you have set stdimage=imt1024. Other mosaic commands can be found in the package "mscred" (loaded at startup). Warning. A "feature" of the mscred package is that coords are always in detector units, in this case one unbinned pixel. So, if you take binned data, and use mscdisplay or mscexamine, the pixel values shown in your imtool (saoimage, ximtool etc) and in your fwhm as gotten from radial profile fits will seem to be twice as big as they should be. Single frames can be displayed thus: "display 0001.M31[1] 1", for example. This method is sometimes more useful since the coordinates are more easily understood. Many other commands can be executed on these files by using the image extension value [1]-[4] for nosplit mode, [1]-[8] for split mode (so rare, you'll never see it).

    Help can be found in the TDC web page in its "Data Analysis Software" section. 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. The most useful iraf packages for analyzing your image are imexamine or mscexamine which place 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.

    If for some reason another saoimage, ds9 or ximtool is still running, IRAF will not display in the new one. If you suspect this has occurred, as evidenced by display not doing anything, go to the main login window and type ps auxw |grep -i saoimage, ps auxw |grep -i ximtool or ps auxw |grep -i ds9. Kill any processes named saoimage, ds9 or ximtool with command kill -9 procnumber, then try simtool, dimtool or ximtool again. If it won't let you kill them (not owner), use godown to reboot.

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

    It is possible to do the necessary debiasing and flatfielding of the 4shooter CCD data in IRAF. The package usually needed to do this is mscred

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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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