1.2m Keplercam System Primer

Created: 08/02/05 by EF
Updated: 11/19/14 by EF

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This primer instructs users of the Keplercam CCD system on the 1.2-meter telescope. You should NOT operate the telescope and Keplercam from any account other than observer.

Click here for information on the Keplercam CCD Chip. For a (warm) QE curve, click here.

We keep the observer computer account unchanged, except for necessary updates. If you make minor changes in any observer directory, please advise us. The observer account is restored semi-periodically from a frozen disk version. If you don't like its setup, or wish to make lasting changes, please request your own account, but do not use it to observe.

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Getting Started

There are 2 monitors on the main desk in the control room. Log in to flwo48 (a Linux PC), with username observer. The password is printed near the top of the monitor. You will see several xterm windows appear and various window manager (currently Xfce) icons in the toolbar at the bottom of the display. The window manager allows you to drag windows from one screen to the other, but it's best not to fiddle in excess to avoid confusion. You also have 4 desktops you can use with the current windows manager.

We use a 3-button mouse with several functions. The location of the cursor driven by 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 once results in one of these actions:

Caution: clicking the left mouse button twice on the bar shrinks the whole window into the bar; repeating that on the shrunk bar restores the window.

  • The vertical bar on the left of each window is a scroll bar.

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    Taking Data

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

    To start the Keplercam system, mouse the cursor over to the Main Login window and type

    Three windows will appear:
    1. The Kep.err Window (small blue)
    2. The Telshell command Window (gray xterm)
    3. The Ntcs (Telescope Control System) Window (yellow)
    The Kep.err window is the error debugging output for all processes. It may be useful when problems occur, but you may iconify it for now.

    The Telshell window accepts all commands for system control of the CCD, telescope, filters and guider. It has the basic functions of tcsh (command line editing) as well as custom functions. It also has commands built-in to control the telescope, filter positions and guider functions, which duplicate many of the Ntcs GUI functions.

    The CCD is controlled with command "ccd" to which you pass different parameters. You only need a few of these, and there are aliases for the most frequently-used ones (see Taking Data).

    If you need to monitor the status of the CCD start a vncviewer session to the computer that controls the CCD, called kepccd. On any xterm, type:

    vncviewer kepccd.sao.arizona.edu:2

    You will be prompted for a password (same as for observer) and you may put the job in the background once it's running. A window like this snapshot will appear on your screen.

    The CCD temperature must always remain near -96.0C, as displayed in the ntcs window and saved in all image headers.
    Monitor the values in the Ntcs window.
    If you notice the temperature differs from -96.0C by about 2C or more, please contact staff as soon as possible.
    The percentage displayed next to the CCD temperature in the Ntcs window is the running time of the heater on the Lakeshore controller. If it is pegged at 0%, the heater is off. To check, read the heater setting on the display of the Lakeshore box attached to the topbox. If it shows it's off, press the "Heater Range" button (top, left) and use the arrows on the right to scroll to "Low," the normal setting, then press "Enter" (bottom, right). If the CCD warms up, you or the next observer may lose a night because the CCD will need to be pumped and cooled, a process of several hours. If the CCD temperature is displayed as +999.0C do not panic, this is an indication that communications between the CCD computer and the Lakeshore controller have failed; please inform the staff immediately! If you see a view similar to the snapshot, the system is behaving properly; otherwise you should restart the system, as described here .

  • Startup aliases and definitions for the system are in the file /home/observer/.kepccd.rtrc, which is executed when you type gokep. If you want different aliases or conditions at startup, create a file in your name, for example ted.cmd which contains the aliases you desire, and then from the Telshell window issue the command "source ted.cmd". You can always enter the binning commands in the Telshell window.
  • You must first decide what CCD format you want, binned 2x2 or unbinned. In the Telshell window, type small, which will result in 2x2 binning, or type large, which will result in full resolution. Small is the default on startup. If you desire large enter that in telshell now.

  • By default, all 4 amps are read out. If you are interested in only one of the amps, say 1, you should issue the command:
    ccd selchan 1
    and to return to normal
    ccd selchan 0
    (the default). You only use less disk space this way, not readout time. The binned (unbinned) pixels are about 0.67" (0.34") on the sky.

  • The default centering is for the centers of the field and the CCD to coincide. You may change that from the TCS window. You may also select the amp from Telshell by typing:
    tele ampcen X
    where X=0-4 (0 being the center of the CCD). Once you select the amp center by either method, the centering persists until you change it again or you exit the system. If the telescope is tracking, the centering is applied immediately after you issue the command. You can find out which amp is selected by typing
    tele ampcen ?
    and Telshell will return the amp number in its window. The amp center is also shown in the "Tele Tasks" menu on the main TCS window.
  • The images are stored in a directory named /kep/yyyy.mmdd, for example /kep/2020.1221 for 2020 Dec 21. The directory changes and appears automatically at noon MST. About 3 months of data are kept on flwo48; older data are in the Keplercam archive in Cambridge. Data are stored as FITS EXTENSION files (see chip characteristics).

    NOTICE: commands are executed sequentially, including all CCD operations such as exposures and readouts, and all telescope operations such as slewing, offsets and filter changes. This means that one cannot command the telescope to slew before a readout is finished, for example.

    CCD commands may be called either interactively or from scripts. See the example scripts in the Telshell link for proper scripting syntax.
    The following are the interactive Telshell commands available (comment, object and setcom are exceptions that confirm the rule: they may be called from scripts):

    bias n
    Takes n zero-second exposures and names them ``BIAS''.
    total n
    Will do a fast clear of kepcam, open the shutter for time n, where n is seconds, reads out the CCD and store the data. No prompt will be made for comments - you must enter a name via "object" otherwise file is named after last object name, or seqno.kepccd.fits if no object has yet been set. If you loaded your object from a catalog through TCS, it will set theobject name as well. Total cannot be used to change the exposure time in the middle of one already in progress. To change an exposure time for an exposure already in progress see the extend and istore commands below.
    extend N
    Add N seconds to the current exposure time.
    Stop the current exposure immediately and store the file.
    dark [ n ]
    Same as total except the shutter isn't opened. The exposure is named ``DARK''. (Equivalent to the old "godark", which still exists for old-timers.)
    flat [ n ]
    Takes an exposure of length n, labels it ``FLAT'', and notes in the header that the exposure is a calibration flat field. (Equivalent to the old "goflat", which still exists for old-timers.)
    repeat n XX m
    Repeats n times CCD command XX. XX can only be one of these: total, dark or flat. Argument m is the desired exposure time for XX. For example: "repeat 7 flat 10" will acquire 7 10-second exposures labeled FLAT (see above). Notice that there is no feedback on the repetitions in the Telshell window, although Ntcs will show information about each exposure as usual.
    Prompts for a name and an exposure time (in seconds). Performs a fast CCD clear, opens the shutter for the specificed exposure time, reads out the CCD and stores a fits file with the data. Information contained in the comment block is automatically stored in the data header.
    go [ n ]
    Performs a fast CCD clear, opens the shutter for time n. The shutter will then close, BUT no storage occurs, so this command will work for multiple exposures in one frame.
    Stops the current exposure (no readout) or sequence of repeat commands.
    Reads out the CCD and stores the image on disk. Use after ccd gowait to store the exposure in a fits file.
    clear [ n ] (alias cc)
    Clear charge from the ccd n times
    puts you in the comment editor. If a change is made, the updated info is stored as comments in the next fits file header.
    object name
    gives the next file a name, puts that name in the FITS keyword OBJECT. This happens automatically if using catalogs.
    setcom kepccd Object name
    Puts the name in the comment file field Object, but does not set the File name or Object FITS keyword.

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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 a secondary object name, your name and the weather conditions.

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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 listing of all its features and for the use of this window, see the TCS manual .

    Here is a sample TCS window, captured while idling:

    Filters can only be loaded by Wayne, Ted, or other qualified staff. 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 4-inch UBVRI, Sloan and narrow-band filters. Note that our 2-inch filters vignette at the edges of the CCD field, in a curious way that causes astigmatic star images. NOT recommended with Keplercam, not used for years.

    Telescope Focus
    Telescope focus uses the hexapod under control of the TCS program on 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. Larger numbers increase the separation between the primary and secondary mirrors. The focus position is displayed in the TCS window, and is stored in the data header. The rate for focus changes is about 0.02 mm/sec (a typical change is about 0.02 mm).

    For instructions on how to measure and set the focus with Keplercam, please follow this link.

    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 arcsec, change the track rates, set the time, and basically do all of the TCS functions from the Telshell window as well as the TCS window via special commands. See the TCS manual) for details. The Telshell window also allows script control of the system, see the Telshell Users Guide for further information.

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    Telescope Focusing

    To measure and set the focus, use the kfindfwhm script. It is fully automatic, estimates the focus, sets it, estimates the seeing, and records its results along with mirror temperatures to a file we use to monitor the seeing.

    The telescope focus changes with outside air temperature in a predictable way (more at the seeing link). 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.

    You may also use the ancient, manual style of focusing the telescope, as we describe here.

    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 the guider focus while on-axis, and store this to calculate off-axis focus. If the telescope focus was correctly set, you only need to change the on-axis guider focus once. When the telescope goes out of focus, just refocus the telescope, and the guider will be back in focus. Note that changing the guider focus while guiding will stop the guiding.

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    The Telshell window 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 observer directory for sample scripts. For details on writing your own scripts, go to the Telshell Users Guide 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 Telshell 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.

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    Dome or twilight flats

    Click here for instructions.

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    Data Archiving

    Use unix tar in the data directory. The data are also archived automatically via ftp to CfA in Cambridge. However, the CF does not back up the archive in Cambridge to tape; only "snapshot" short-term disk backups are available. To preserve your data, you may also want to backup your files to tape at the CF. Please ask the staff for the name of the directory.
      To write to a new DLT tape (and rewind when done) use: tar cvf *.fits /dev/st1
      To write to a DLT containing files (positioned at the end of the tape) use:tar cvf *.fits /dev/nst1
      To find the status of the DLT without rewinding it, use: mt -f /dev/nst1 status
      To advance the DLT to the end of recorded data, use: mt -f /dev/nst1 eom
      To use a DDS4 DAT, substitute st0 for st1 above.

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    Purging Files

    Eventually, you may 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 available, in an xterm window enter the command df /rdata (/rdata is the remotely mounted disk from kepccd), which will produce the output:
    Filesystem           1K-blocks      Used Available Use% Mounted on
    kepccd:/data         307663800 166030328 126005040  57% /rdata
    and note the space available on the data disk, about 120 gigabytes in this example.

    The Iraf command to delete FITS files is imdelete. You may wish to edit the parameter file for imdelete (epar imdelete) to turn on its safety measures against accidental deletion.

    You can also use delete or rm for most files including FITS files, and unix rmdir for directories. 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 request postponing such deletion until it becomes absolutely necessary (especially on weekends). You may want to check the data disk to see what volume of data may be 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 exit the Realtime system. Type exit in the Telshell 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 gokep (after all windows are gone!). in the login window, which is the official way to bring up the system.

    After exiting Realtime system, you can exit the computer by pulling up selecting Logout from the windows manager menu in the toolbar at the bottom.

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    If the CCD is stuck in the readout, or it produces unusually noisy or incomplete images you may need to restart the CCD system on the PC that controls Keplercam (kepccd).

    First, however, if INST STAT in the Ntcs GUI says "Partial" and nothing else happens but you still have a response in the Telshell, try typing "dstore" there, which may complete the stuck readout and clear the problem.

    If that fails or the problem is different, you do need to take the following steps to restart the CCD:

    If the Telshell window on flwo48 echoes gobbledygook when you type something sensible, the cause is likely to be an attempt to stop a script while it is still exposing by typing CONTROL-C at least once. Another possibility is that tcs just becomes unresponsive on flwo48. Click here for instructions to recover from either event.

    If you get into bad trouble, for example the complete 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 two possible ways to reboot:

    1. If you can still move the mouse (ON FLWO48!) , access the Logout button by clicking the "Applications Menu" bottom left of the toolbar, and select Restart from the logout menu. This 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. As a last resort ONLY, turn the power off on flwo48, wait 5 seconds, then back on. The power switch is located on the top of flwo48's case. 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.

    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
      xpp 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 Telshell window, but in general it is better to execute them in the login or other windows.

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

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    Using IRAF

    Warning: avoid reducing images on flwo48, especially if you are not experienced, and least of all during observations. To learn about processing Keplercam CCD images, visit the NOAO IRAF FAQ, search for the keyword "Massey" and select "A user's guide to CCD reductions with IRAF."

    Once you have taken an image, move over to the IRAF window to look at the data. In that window, type cd; ecl as usual. You will need to cd to the data directory, for example cd /kep/2020.0101. Type dimtool for ds9, *the preferred display method*, simtool or ximtool, then type flwo48:0 at the IRAF prompt to display on the monitor. If you are displaying unbinned images, you may need to change the stdimage in IRAF if you have changed the default at login: 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 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 to the prompt. You can now display images from either that IRAF window, or one on the right monitor.

    You may use mscdisplay (in the mscred package) to display images, e.g., type "mscdispl 0004.M31 1." You must first start ds9 or equivalent from the IRAF prompt, as above. The task mscexamine supposedly allows one to examine them (like imexamine but for mosaics). Unfortunately, mscexamine appears to be unreliable: it reports wild x,y pixel coordinates and erratically dies with the message "ERROR: invalid floating point operation." Another approach is to use imexamine on individual frames (see below for an example). If you use ds9 you also have the option of loading the array directly into it (use "File" menu, then "Open Other" then "Open Mosaic IRAF..."), imexamine will work on the full array. Make sure you have set stdimage=imt2048 (the default). Note: this all works only if you have started up ds9 from IRAF, not standalone.

    Other mosaic commands can be found in the package "mscred" (loaded at startup). Warning. A "feature" of mscred is that pixel coordinates are always displayed in detector units, in this case one unbinned pixel. Thus, if you take binned data, and use mscdisplay or mscexamine, the pixel values shown in your imtool (ds9, saoimage, ximtool) and in your fwhm from radial profile fits will seem to be twice as big as they actually are. Note: in ds9, the WCS values are absent when the images are displayed from IRAF. To avoid this annoyance and those above, you should load your images directly from ds9, as described above. Single frames can be displayed thus: "display 0001.M31[1] 1", for example. This method is sometimes more useful since the pixel coordinates displayed do reflect reality. Many other commands can be executed on these files by using the image extension value [1]-[4].

    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 printed by going to the etc menu, and clicking on print.

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    Reducing your data with mscred in IRAF

    It is best to perform the necessary debiasing and flatfielding of the Keplercam data with IRAF. You should use tasks in the IRAF package mscred. Within IRAF, type "help mscred" and "help mscguide" for detailed instructions on the tasks you'll need to master.

    The data archive of Kepler images is located on CF machines at /data/kepler/Archive/rawdata/kepcam. For further information about the archive please contact Bill Wyatt at CFA.

    Once you've settled in your office with a nice thermos of piping hot water for your mate, inside IRAF you should type a sequence like this one:

    cl> cd your.data.directory
    cl> mscred
    mscred> zerocombine *BIAS.fits
    mscred> flatcombine *FLAT*.fits
    mscred> ccdproc *your.object*.fits
    Some examples of parameter values for the 3 tasks to use for reductions are here. You may need to tweak some of these for your version of IRAF.

    Once you have reduced your data, you will undoubtedly wish to analyze it. A complete discussion is beyond the scope of this document, but you may find the following items useful:

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