Next Version ETA: 1 September 1995
Please send comments/corrections/typos to Dave Silva (silva@noao.edu) for incorporation in next version.
This is a user's guide for the IRAF based user interface to the Harcon and Arcon CCD controllers, hereafter referred to generically as the Arcon controllers. These controllers are currently in use at WIYN to control the Imager CCD (a.k.a. S2KB) and the Bench Spectrograph CCD (a.k.a. T2KC). The WIYN Arcon-IRAF interface is also used to control the Imager Filter Shutter Assembly (FSA) (a.k.a. the Imager "filter wheel").
This guide is maintained on-line as a HTML document. If you have a hard copy of this guide, it is strongly suggested that you verify that the hard copy version number and revision date matches the on-line version. The on-line URL is TBD.
This guide assumes a familiarity with basic IRAF usage and functionality.
Important: This manual covers operation of WIYN Imager CCD and the WIYN MOS Bench Spectrograph CCD.
The observer might find the following documents useful:
All three of this supplementary documents can be obtained by contacting Jeannette Barnes (jbarnes@noao.edu).
All data taking can be done by using a single command: observe. The observer will be prompted for all the information necessary for controlling the exposure. An Imager observe dialogue looks like this (with user input in bold):
cl> observe Exposure type (|zero|dark|object|dflat|sflat|focus) (zero): object Number of exposures to take (1:) (1): Exposure time (0.:) (0.): 1000 Title of picture (bias 16/07/93): HH80/81 [SII] Filter in wheel one (U): I Image obj107 written to disk Observation finished... [Running post processing command: postproc obj107]
Information requested includes:
Note that the FSA only holds one (1) filter wheel at a time, although three filter wheels exist. The FSA is "smart" enough to sense what filter wheel is physically in place and will warn the observer if the wrong filter wheel is requested. However, if the wrong wheel is requested during an observe setup, the error described in the next paragraph will occur.
Warning: If the filter fails to move to the correct position a warning message will be printed and the current observe command will abort.
Note that in each parameter query you will be supplied with a default value, which you can accept by simply hitting <RETURN>; these values are just the previous entries.
If you make a mistake, or change your mind, you can abort the
command during the parameter entry stage by typing CTRL-C;
having done so you should always enter the command flpr, to
clean up the hidden mess. Once the exposure has started it can be
terminated using the abort command (see Note that the observe command terminates as soon as the
exposure starts and you can enter other commands in the IRAF
Acquisition window. Additional Arcon commands entered at this
point can inadvertantly modify the current, active exposure. This
"feature" is a bug which will be corrected in later release of the
software. In the meantime, observers are urged not to issue
additional Arcon commands while an exposure is on-going.
In addition, we suggest that all data testing and reduction commands
be issued in the IRAF Data Reduction window, not the IRAF Data
Acquisition window.
When the exposure finishes the CCD will be read out. The first
line in the status window will change to "READING" and the
"buffers read" counter will indicate the number of buffers
of data successfully transferred to the Sun. The data is initially
written in the controllers internal format to a spool file on /tmp,
but it is automatically converted into an IRAF image within a few
seconds of the exposure finishing. The message "Image
...... written to disk" appears as soon as this process is
complete and shows you the name of the new IRAF image. This name is
derived from the exposure type by appending a running number
(controlled by the obspars parameter set described in section 3.2) which is automatically
incremented after each exposure. The image header will be in the
current directory (when the observe command completes) and the
pixel file will be located in your imdir. A temporary file
.Timage name.imh will be in your current directory until the
complete image is available. Then it is renamed to image
name.imh.
If you requested that observe take only a single exposure,
the message "observation finished ....." will appear in the
IRAF interface window as soon as the readout is complete; things are
then ready for you to start another exposure. If, instead, you
requested a sequence of several pictures, the next exposure will start
automatically. You may immediately examine or process the resulting
image even though the sequence is not complete. Note that the
"pictures remaining" counter in the status window shows how
many exposures remain in the sequence. Once the final picture has
been read out the message "sequence finished ......" will
appear in the IRAF interface window. Should you miss the end of
sequence or end of exposure message, note that the CCD is idle and
things are ready for you to initiate new exposures, whenever the top
line of the status display reads "CONTINUOUSLY_ERASING".
The MOS Bench Spectrograph CCD Arcon system behaves in nearly the
identical way to the Imager CCD Arcon system with two notable
exceptions:
2.1.2. The MOS Bench Spectrograph
Appendix C Section 2).
In addition to observe, there are specific commands to take one or more pictures of each type:
Except, of course, for the exposure type, these commands take the same parameters (and prompt for them in the same order) as does observe. Apart from saving you entering that one extra parameter, use of these commands allows one to set default parameter values, and also select which parameters are prompted for according to picture type.
Another useful command is:
If you type
cl> more
you will not be prompted for the number of exposures (as one might expect) but rather a single exposure will be taken (which more often than not is what you actually wanted to do). However, if you type
cl> more 10
ten more exposures will be acquired. Note to ICE users: mores does not work.
A very useful task when you want to take Imager calibration exposures, or exposures of the same object, in various filters is
For example, to take sequences of 10 dome flats each in R (60s exposures), U (10s), V (5s) and B (5s), type:
cl> doobs Exposure type (|object|dflat|sflat|): dflat Number of exposures to take in each filter (1:) (1): 10 wheel one, two or three (one): three list of filters in wheel3: R, U, V, B List of exposure times: 60,10,5 The following pictures will be taken: Pictures Filter3 Exposure 100 109 R 60 110 119 U 10 120 129 V 5 130 139 B 5 Title for pictures: Dome flats 21 June 95
The observe command (and its derivatives dark, dflat, etc.) have been purposely kept simple. Additional flexibility can be achieved by modifying the options listed in three key parameter sets (psets). Many observers will only modify these psets once, at the beginning of their run. These parameters sets are:
You should review these parameter files at the beginning of your run, and modify them as necessary. Many observers will never modify them again.
These parameter files can be listed by using the lpar command, e.g.,
cl> lpar obspars
and may be edited using the parameter editor, epar, or by simply typing the name of the parameter set e.g.,
cl> epar obspars -OR-
cl> obspars
To change a value, in either case, move the cursor up and down with the arrow keys until you are on the correct line and then simply type the new value followed by <RETURN>. When done editing the parameter file type :q. On the WIYN workstations, cntrl-Z works as well.
IRAF
(gain = 4) Gain setting
(preflash = 0.) Preflash time (seconds)
(xsum = 1) pixels summed in X direction
(ysum = 1) pixels summed in Y direction
(xstart = 1) Start of ROI in X
(ystart = 1) Start of ROI in Y
(xsize = 2048) Size of ROI in X
(ysize = 2048) Size of ROI in Y
(extend = "separate") Method of extending ROI to include overscan
(xskip1 = 0) X pixels to skip at start of overscan
(xskip2 = 0) X pixels to skip at end of overscan
(xtrim1 = 0) X pixels to trim at start of data
(xtrim2 = 5) X pixels to trim at end of data
(ytrim1 = 2) Y pixels to trim at start of data
(ytrim2 = 4) Y pixels to trim at end of data
(amplifiers = "lr") Readout amplifiers to be used
(pixsize = 21.) Pixel size in microns
(nxpixels = 2048) Detector size in X
(nypixels = 2048) Detector size in Y
(noverscan = 32) Number of overscan pixels
(detname = "S2KB") Detector identification
(mode = "ql")
Observers will wish to examine, and perhaps modify, the following parameters:
The next four parameters establish the CCD Region of Interest (ROI) to be read-out.
The ROI parameters shown in the example above correspond to reading out the entire CCD area.
MOS Bench Spectrograph note: there is no reason to ever readout less than the entire CCD during normal MOS Bench Spectrograph observations as it is beneficial to record the area beyond the spectra to monitor scattered light levels. This extended area is ultimately used to correct for scattered light (see the Hydra User's Manual for more details).
The preflash field is not relevant to WIYN applications. The extend, xskip1, xskip2, xtrim1, xtrim2, ytrim1, ytrim2, and amplifiers should be left set to their default values.
The fields pixsize, nxpixels, nypixels, noverscan, and detname are only informational. They can not (and should not) be changed.
The messages you will see when the waveforms are downloaded will look very similar to these:
Preflash time changed from 0.000000 to 0.000000 There are no regions of interest defined. There is one region of interest defined: ROI Lower Left Corner # of Pixels Upper Right Corner # x y x y x y --- ----- ----- ----- ----- ----- ----- 1 1 1 2048 2048 2048 2048 *** Regenerating waveforms *** /xp/run/waveforms/Harcon1.9 *** Recompiling waveforms *** /xp/run/waveforms/Harcon1.9 csh /xp/run/macro/wdl s2kb WDL revision 2.18 Binning factor 1: Pixel readtime = 15 us. Binning factor 2: Pixel readtime = 18 us. Binning factor 3: Pixel readtime = 22 us. Binning factor 4: Pixel readtime = 26 us. cp s2kb.nex /xp/run/macro/Harcon+Stis2048+Observe.nex *** Suspending the sequencer *** *** Reloading new waveforms ***
It is possible to change the slope time of the "Integrater" - usually erroneously referred to as the gain - which determines the number of e-/ADU, the readout noise, and the readout time. This can be changed by entering detpars and changing the gain entry to one of the possible options.
The recommended WIYN CCD gain values are:
For most Imager projects and all MOS projects, we strongly urge the observer to adopt the above gain values.
Nevertheless, the observer can determine the available gain options and current settings using:
cl> ccdinfo
(gain = 4) Gain setting
(preflash = 0.) Preflash time (seconds)
(xsum = 1) pixels summed in X direction
(ysum = 1) pixels summed in Y direction
(xstart = 1) Start of ROI in X
(ystart = 1) Start of ROI in Y
(xsize = 2048) Size of ROI in X
(ysize = 2048) Size of ROI in Y
(extend = "separate") Method of extending ROI to include overscan
(xskip1 = 0) X pixels to skip at start of overscan
(xskip2 = 0) X pixels to skip at end of overscan
(xtrim1 = 0) X pixels to trim at start of data
(xtrim2 = 5) X pixels to trim at end of data
(ytrim1 = 2) Y pixels to trim at start of data
(ytrim2 = 4) Y pixels to trim at end of data
(amplifiers = "lr") Readout amplifiers to be used
(pixsize = 21.) Pixel size in microns
(nxpixels = 2048) Detector size in X
(nypixels = 2048) Detector size in Y
(noverscan = 32) Number of overscan pixels
(detname = "S2KB") Detector identification
(mode = "ql")
*** Table of gain values ***
Detector = S2KB, 2048 x 2048, 21 um pixels
dcsT GAIN Read_Noise Gain Readout Time
(us) # (e-) (e-/ADU) (sec)
--- --- ----------- ----------- ------------
1: 3 1 14 7.5 88
2: 5 2 9 4.3 104
3: 8 3 8 2.8 129
4: 15 4 7 1.5 185
Full Well and Linearity to 200K e-
ADC Saturates before FW at Gain #'s 3-4
*** Select gain setting from the first column
*** The current gain setting is 4
cl>
When you enter detpars, you can edit the gain, and when you
enter :q it will download the waveforms and change the gain.
To see if it has changed, do another ccdinfo.
The parameter file obspars contains four distinct groups
of parameters as shown below:
The first group of parameters are used for all exposures. It is
not necessary to set the values of most of these, since they are
prompted for as needed. The values appearing in obspars are
simply the values entered the last time observe was run. The
parameter autopicnum determines whether observe will
prompt you for the running picture number, picture, which forms
part of the name of your images on disk. The value of picture
is always incremented after each exposure. If autopicnum=yes
(the default) the automatically derived value will always be used and
you will not be prompted. If autopicnum=no you will be prompted
for a new value of picture for every exposure, the
automatically derived value being supplied as the default. In either
case you can reset the sequence by just changing the value of
picture in obspars. Warning: Note that picture
will get out of step if you abort an exposure or sequence; the
value used will be the one which would have been appropriate if the
exposure or sequence had completed normally.
The second group of parameters controls what task or script is
run for postprocessing. One can chose a different script to
be executed after the entire sequence from the one that is run
after each exposure. The restart option determines whether a new
job is created after each exposure or not. If restart=yes
then a separate process will be created. This can cause too many
processes within the IRAF environoment. It can be controlled
by using a task call postkill. If restart=no, then
you must not change the postprocessing scripts and you must remain
in the current directory while taking data. If you want to change
either of these, you must restart Arcon.
The third group of parameters controls the positioning of the
Imager FSA filter wheel at the start of each exposure. For the
Imager FSA, setfilt can be "none" not to move
any wheel, "one" to move only wheel one, "two" to
move only wheel two, or three to move only the third wheel. You will
be prompted for the filter position when appropriate and the value you
enter will be saved in the image header, but you must wait several
seconds for the filter to engage. Remember that only one wheel is
physically mounted in the FSA at any one time.
For the MOS Bench Spectrograph, setfilt should be
set to "none".
Note that the filter position is never requested for exposures of
type "zero" or "dark". The parameter
filtype should always read "instrument".
The remaining parameters will be used in the future for improved
telescope/instrument focus interaction. For now, keep setfocus
= "no".
These parameter sets are not used with the MOS Bench
Spectrograph.
These parameter sets are used with the Imager FSA. The FSA has
three (3) different filter wheels but only one (1) filter wheel can be
inserted and used at a time. The FSA software can sense which wheel
is actually in use and will warn the observer if the observer
specifies the wrong filter wheel.
The wheel1/2/3 psets allow the observer to specify the name
and focus offset for each filter position in each wheel. This allows
filters to be referred to by name instead of having to remember which
filter is in which slot, in which wheel. They also contain the
corrections to the telescope focus which must be made when each filter
is used. In the future, these values will be used to automatically
adjust the telescope focus when filters are changed. For now, these
values are merely stored in the pset file for later reference.
When editing instrpars you can access these parameter sets
by using the arrow keys to move down to the correct line and then type
:e. Alternatively you can edit these parameter files by typing
e.g.
cl> epar wheel1 -OR-
cl> wheel1
Make certain that no extraneous characters appear in the value
field of wheel1, wheel2 or wheel3 after exiting;
if they do just enter a null string ("") as the value.
Whichever method you choose you will see something like this,
The focus# correction feature is not implemented in the
current version of the software. The corresponding filter focus
offset parameters should be set to zero for now.
If you want to say, move the filter wheel, without taking a CCD
exposure, use instrument. This task will prompt you for
positions for each motor and move it to that position, just as observe
does. However, instrument obeys the setfilters and
setfocus parameters in obspars and hence will only move
those motors you have enabled. More often than not it is precisely
those motors you have disabled in obspars that you want to
move. For instance you may normally have filter2 disabled
(setfilters=one), but want to switch to a filter on a different
wheel and switch back at the end. If you want to override
setfilters for a single invocation of instrument proceed
as follows:
The setfocus parameter can be overridden on the command
line in the same way.
The FSA (Filter/Shutter Assembly) Arcon/Iraf package allows the
user to enter commands through the IRAF interface to manipulate the
FSA. Most observers will never have to use these commands. The
following commands are available:
The observe command will automatically prompt the user for
the filter and will send the exposure time and the chosen filter to
the FSA.
Note: if the MPGrouter is down, these commands will not work
through the Iraf Acquisition Window. They will either timeout or
fail.
There are two ways to establish the current Imager focus:
wavefront curvature sensing and a manual focus exposure.
The former method is recommended for the start of the night or when
changing to a filter with an unknown filter offset. The latter method
is quicker during the night when the observer is trying to fine-tune
the focus in a sequence of exposures using the same filter or when
changing to a filter where the filter offset is known.
Wavefront curvature sensing is easy but time consuming - it takes
about 15 - 30 minutes. This is often time well-spent if you've become
really confused (often the case in these early days). Here's the easy
part: just ask the duty telescope operator to do this. Remember to
tell them what filter to use!
Manual focus exposures are a little more involved but often faster.
Some coordinating with the telescope operator is still needed. The
basic idea is to take obtain multiple images over a range of focus on
the same CCD frame. Note that 10 microns is about the right
minimal secondary movement amount. Here's a simple procedure:
This manual focus exposure procedure will be automated in the next
major Arcon software upgrade.
Because WIYN is a very lightweight telescope, it mechanically responds
quite rapidly to ambient temperature changes: a 1 deg C change
corresponds to about a 40 micron expansion or contraction. The
telescope often cools by 2-7 degrees C rapidly after sunset and then
about 1 deg per hour for the rest of the night. This corresponds to
focus changes of 80 - 320 microns after sunset and 40 microns per hour
after that. Since a 10 micron change significantly defocuses the
telescope, compensating for these large changes is very important in
maintaining focus.
To deal with this situation, the telescope trusses have been wired
with thermocouples which report the truss temperatures once every 10
secs. We have determined empirically that:
This calibration is preliminary and will be refined as soon as
possible.
The recommended procedure is to monitor the telescope temperature
and adjust the telescope focus by the appropriate amount when a
significant temperature change has occured. Please ask the operator
to show you how to monitor the telescope temperature.
One of the WIYN Project's highest engineering priorities is to
automate this process so that it is transparent to the user.
To first order, the focus offsets between the broad-band filters
typically used at WIYN are determined by the filter thicknesses.
Thus, these focus offsets are fixed with time.
We have not determined reliable filter focus offsets at this
writing. For now, observers should pick a filter to be their baseline
filter and then determine offsets to their other filters. Such
offsets should be reported to Dave Sawyer (dsawyer@noao.edu) and Dave
Silva (silva@noao.edu) so we can begin to compile an offset database.
The MPGrouter is the source of all information from other
WIYN specific instruments. Special clients are written for each
instrument. These clients send out status and instrument specific
information and subscribe to other instrument information that has
been made available. The maximum frequency of updates to this
information is on a per second basis. The information should be
within a 2 second range of accuracy, unless messages have been
dropped. Dropped messages are generally due to a CPU being too busy
to read them.
The MPG MSG icon contains the most recent detected status
of the MPGrouter. It is only noticed during the picture taking phase,
where the process of getting and reformatting header information is
done. The process is called icsInfo. It subscribes to
FSA information as well as the TCS data streams.
The warnings that it issues are:
You can iconify this message by clicking on the CONTINUE
button.
You can collect data if the MPGrouter is not running, but you will
not get TCS, FSA, Hydra, or Bench Spectrograph headers. Furthermore,
FSA commands entered through the IRAF interface will not be executed.
This causes long delays, waiting for commands to timeout.
3.2 obspars
I R A F
Image Reduction and Analysis Facility
PACKAGE = fsa
TASK = obspars
ccdtype = zero Exposure type
npics = 1 Number of exposures to take
picture = 1 Picture number of first exposure
exposure = 0. Exposure time
title = Test frame Title of picture
(autopic = yes) Generate picture number automatically ?
# POST PROCESSING PARAMETERS
(postpic = display $image) Post processing command for single picture
(postseq = ) Post processing command for sequences
(restart = no) Restart the server on every command?
# SELECTING FILTER FOR EACH EXPOSURE
(setfilt = one) Query and set filters?
(filtype = instrument) Type of filters to use
# SETTING FOCUS FOR EACH EXPOSURE
(setfocus = yes) Query and set focus?
(foctype = telescope) Type of focus to use
(tempera = 0.) Telescope temperature
(basefoc = INDEF) Focus base value
(reftemp = 0.) Telescope temperature for base focus value
(tfrcoef = ) Coefficients of Temperature Focus relationship
# PARAMETERS FOR FOCUS EXPOSURES
nfexpo = 7 Number of focus exposures
(refis = middle) Reference is first, middle or last exposure?
freferen = 5000 Focus value
fdelta = 30 Focus increment
(focmode = auto) Focus mode
(shtype = detector) Shift type
(f_stepsize = 0.) Focus stepsize in arc seconds
(f_direction = north) Focus direction for telescope
(fnrows = 30) Focus number of rows to shift
(mode = ql)
($nargs = 0)
3.3 wheel1/2/3
I R A F
Image Reduction and Analysis Facility
PACKAGE = fsa
TASK = wheel1
(id1 = u) Short identifier for filter in position 1
(name1 = Harris_U) Full name of filter in position 1
(focus1 = 40) Focus value for filter 1
(id2 = B) Short identifier for filter in position 2
(name2 = Harris_B) Full name of filter in position 2
(focus2 = 10) Focus value for filter 2
(id3 = V) Short identifier for filter in position 3
(name3 = Harris_V) Full name of filter in position 3
(focus3 = 0) Focus value for filter 3
....
(id8 = drk) Short identifier for filter in position 8
(name8 = Dark) Full name of filter in position 8
(focus8 = 0) Focus value for filter 8
Each group of three parameters corresponds to one slot in the
filter wheel. The parameter id# is the short identification
for the filter that you should type when prompted for a filter
position by observe. It should be short, should be unique
amongst the filters in the wheel and must not contain any white
space or other weird characters. One exception to the uniqueness
requirement is that any empty positions may be given the same
name e.g. "clear" (but not a null ""
or blank " " name ) provided you don't care which one
is actually used. The value of name# is what will be
recorded in the image header. It can not contain the special
character "~" and blanks will appear as underscores in
the header.
3.3.1 Setting Up the Imager FSA Without Taking an Exposure
- Instrument
cl> instrument setfilters=two
Filter in wheel two (u): cb
4.0 FSA Package
5.0. Focusing the Imager
5.1. Establishing the Initial Imager Focus
5.2. Maintaining the Imager Focus
5.3. Filter Focus Offsets
6.0 Router Related Issues
Appendix A: Arcon Software Task Cribsheet Summary
Data taking commands
Exposure Control Commands
Parameter Sets
FSA Setup Control
Loaded packages
Appendix B: Logging in and Logging Out
B.1. Computers and Peripherals
Figure 1 shows the control room at WIYN. Sam Barden, the
Hydra Project Scientist, is sitting in front of the monitor for
oatmeal, the Hydra Sun workstation. The Imager Sun workstation
pearl is in the far corner near the empty blue chair to Sam's
right. Sam is using Oatmeal and next to him on his left is
Vanilla another data acquisition computer used with the Bench
Spectograph and Hydra.
B.2. A Guided Tour of the Arcon Windows
The Imager Harcon system is run from the pearl workstation while the Bench Spectrograph CCD is run from the vanilla workstation. The current observer logins and passwords are posted on the machines.
When the observer logs in, an OpenWindows environment is loaded and the Arcon-IRAF interface software is executed automatically.
Several windows will come up including a IRAF Data Acquisition and a IRAF Reduction window. The controller software will automatically be down-loaded as well as any appropriate CCD controller parameters specific to the installed chip. Also, the FSA IRAF package will be loaded into the IRAF Acquisition window CL.
It will take several minutes for the hardware and software to be ready. When it finishes the message "Connecting to the controller..." will appear, followed by "Data reader restarting ...." and several messages associated with the downloading of the detpars waveform. Wait until you see the "cl> prompt" in the data acquisition screen before continuing.
abort focus pictitle setshutter
ccdinfo initfilter postarch sflat
comp initshutter postkill shutter
connect instrpars@ preview stop
dark instrument rebootfilter tchange
detcomp more rebootshutter teloffset
detparm@ movie recover telpars@
detpars object resume wheel1@
dflat observe rtdpars@ wheel2@
disconnect obspars@ setdetector wheel3@
doobs pause setfilter zero
expshutter pflat setrtd
cl>
Loading the instrument package automatically establishes the connection to the controller, as indicated by the "Connecting to the Controller...." message hidden amongst the package menus. Exiting from the package with bye or (usually inadvertently!) CTRL-Z breaks the connection.
NOTE:You can not take data if the connection is broken.
Once the initialization procedure has been completed, your screen should appear somewhat like Figure 2.
The key windows for taking data with Arcon, identified by the names given in their title bars, are as follows:
Arcon CONSOLE - As its name implies this window serves as a console for Arcon. While you are observing you will see many messages appear here, only some of which will be repeated in the IRAF acquisition window. This window is hidden behind the Data Acquisition screen and if it is distracting, you can close it. But don't quit from it. In the event that something goes wrong, the diagnostic messages appearing in this window may tell you (or at least us) what happened.
Arcon STATUS - This very important window gives several lines of information summarizing the status of the controller, the instrument, and any ongoing exposures (see Figure 2). The first line shows what the controller is currently doing. if you have just brought the system up, it should read "CONTINUOUSLY_ERASING" indicating that the CCD is idle and is continuously running the erase cycle; if it doesn't, chances are something went wrong in the initialization and you should seek help. During exposures this line should read "INTEGRATING", and should change to "READING" as the CCD is read out. Other messages which may occur will be described later as appropriate. Just below the status line are counters showing the number of seconds left in the current exposure, the number of exposures left in the current sequence, and, during read out, the number of buffers of data successfully transferred to the Sun. Also shown are parameters of the current exposure such as the title, picture name etc. Finally, for the Harcon the bottom line contains some important telemetry information. This includes the temperatures and voltages of the Dewar and CCD as well as the CHIP ID number.
COUNTDOWN -This is the very small window with the very large font. It provides a copy of the exposure time counter for the visually handicapped.
IRAF Acquisition - This black colored window is one of two running the IRAF cl. We recommend you type all data taking commands here, so that your data taking and data reduction activities are well separated and don't interfere with one another.
IRAF Reductions - This window (colored an off-white) is the other IRAF window. We suggest that normal IRAF commands, used to examine or reduce your data are entered in this window. The parameters used in this IRAF environment are NOT the same as those used when taking data in the Data Acquisition window.
IRAF Display Window - "Ximtool" window will be used when displaying your images from IRAF. This resides on the 2nd monitor.
The following 3 windows display messages associated with MPGrouter messages.
A further word about image directories is in order at this point.
Your data acquisition machines has roughly 9 Gb bulk data storage. On
each of these there will be a directory, /data1, where this space is
mounted. At the start of your run all these disks will be cleared.
However, you may have no trouble filling the available space in a few
nights of typical observing. From time to time you should use the
command disks to see how much space is free on each disk.
Arcon uses the value of the IRAF environment variable imdir
in order to decide where to write the pixel files for newly
created images.
B.3. Shutting Down and Logging Out
Before you log out, for whatever reason, you must first stop the Arcon related processes. To do this, bring up the background menu and follow the Arcon submenu. Release the mouse button on Arcon Exit. The processes that will be removed are all transputer, arcon/iraf and router executables and their corresponding windows. " IRAF Acquisition" is setup to automatically disconnect upon exit or logout. This allows for a clean download of transputer code when the Arcon is used again.
If you have a suspicion that the system is somewhat flakey you can verify that everything is cleaned up after exiting Arcon by typing:
pearl% NexUp No match. No match. No match.
If you get "No match." three times in a row, as above, all is well. If instead you see something like
pearl% NexUp root 2227 0.0 3.0 2664 844 p6 S 17:32 0:05 muxnex arcon 2229 0.0 .6 172 160 p2 S 17:32 0:00 arsh c0e2 arcon 2228 0.0 .0 144 0 p2 IW 17:32 0:00 arsh c0e2 /dev/nexc0 Nomatch. rwrw 1 arcon 0 Jul 13 17:32 /tmp/xpim2229.1 rwrwrw 1 arcon 0 Jul 13 17:33 /tmp/xpim2245.1
then there are some leftover processes which you must kill by hand as follows,
pear1% kill -9 2227 2229 2228
In this command the list of numbers after the -9 are the pid's of the leftover processes as displayed by NexUp. The files with names like /tmp/xpim2229.1 are the spool files used by Arcon to transfer data to the Sun. If any of these are owned by you and have a size other than zero (the number just before that date), then they may contain your missing data! See Appendix C section 3 for information on how to retrieve this. It is common to see a few zero length files as shown in the example, but these can be ignored.
Now you can exit from the windowing system and log out completely,
by moving the mouse to a blank area of the screen, then hold down the
right mouse button, and select "exit" from the menu
which will appear.
C.2. Warm Starts
Rather more often than we would like, something or other happens which causes the system to hang requiring that the software be reloaded.
Before doing so it is worth testing to see if the problem is confined to the IRAF interface layer, by proceeding as follows:
cl> flpr
This flushes out any brain-damaged executables locked into the IRAF process cache. Having done this, test to see if the problem has gone away by taking a "zero" frame.
If this fails, or if the status window has stopped functioning, then the problem is probably in Arcon itself and it is best to reload the software from scratch. This takes very little time. There are 2 options for restarting Arcon.
Bring up the background menu, follow the Arcon submenu and release the mouse on Arcon ReStart.
Bring up the background menu, follow the Arcon submenu, and follow the CPU Pegged Options:
Release the mouse on Iraf/Arcon Kill. After all processes disappear, follow the CPU Pegged Options menu again and release on Iraf/Arcon Start. This will start new Arcon and Iraf processes.
If the CPU is still pegged, then follow the instructions for logging out and then log back in.
C.3. What to do if Your Picture Doesn't Show Up: Recover
Sometimes Arcon will successfully transfer your data to the spool file on /tmp but the picread program which converts this to an IRAF image will fail. Usually there is an error message, but you should be suspicious that this has happened if the exposure completes normally, but you can't find the output image. The command recover will help you to retrieve your valuable images in such cases. It searches /tmp for any spool files owned by you and for any of these that are complete will show the FITS header and ask if you want to recover the image or not. If you reply yes then picread will be run to convert the xpim file to an IRAF image. A single spool file occasionally contains more than one image. In this case recover will list how many images are present, but will only show you the header of the first. All images will be recovered if you tell the program to go ahead. Spool files are not removed from /tmp until successfully converted by picread. However, we suggest you run recover immediately if you encounter this problem, so that you don't forget later, and so that /tmp doesn't get filled with unprocessed raw data files.
Sometimes a failure occurs during the transfer of the data from the controller to the Sun. In this case a partial spool file results, and there is no way to resurrect the data. Recover will give you the option of deleting any such files, and you should do so to avoid filling /tmp with debris.
You can change where your image data is stored "on the fly" with the command
cl> reset imdir = /data1/whatever/
Note that the trailing "/" character is necessary. This variable will be restored to its original default value when you log out of IRAF. Also the values in the acquisition and reduction windows are independent and must be set separately. To change imdir permanently and insure the two windows use the same value, you must edit your .login file as follows,
cl> edit home$.login
# PEARL IMAGE .LOGIN DEFAULT FILE
..........
# Image pixel directory definition. This is the ONLY place where this
# variable should be defined and changed.
setenv imdir "/data1/whatever/" <----- Change this line as required
You must then log out of Arcon and log back in, for the change to take effect.
It is common practice at KPNO to set the IRAF image (pixel) directory to "HDR$pixels/", i.e.
cl> reset imdir = /data1/whatever/
This option assures that your pixels files will appear in a sub-directory named pixels below the directory where the IRAF header files are created. We urge the observer to adopt this directory structure style.
There is an option to automatically perform a IRAF process on the newly created image. This is fondly known as postproc. To choose this option, set obspars.postpic (see Section 3.2) to postproc $image . If you have chosen this option via the obspars parameters, at the end of the picture creation, you will see the message "[Running post processing command: ....]" and the picture will automatically be displayed in the ximtool window.
There is another option to run a process after the entire sequence. It works in a similar fashion and is activated by setting the obspars.postseq parameter to the script you want executed.
Note: if you want a special task to be executed, it must be defined as an IRAF task in the usual way. See the appropriate IRAF documentation for further assistance. You will then have to set the obspars.postpic or obspars.postseq parameters as desired.
Examples of setting the obspars parameters:
(postpic = "display $image 1" ) Post processing command for single exposures
(postseq = "imcombine $sequence") Post processing command for sequences
In the above example, for a single exposure both the postpic and postseq
scripts will be run. The postseq script is always run.
The possible substitution strings are:
$image -replaced by name of last image readout
$sequence -replaced by list of images in sequence
$picture -replacec by picture number of last image readout
$npics -replaced by number of pictures in sequence
$type -replaced by exposure type
$title -replaced by exposure title
examples:
display $image 1 - display last image
imcombine $sequence - combine all images in sequence
hedit $image i_title \"$title - $type\" - change image title to include type
(quotes must be \ escaped)
postproc $image - the nominal default KPNO
postproc script
Warning: no check is made of the command syntax or it's validity, or that the necessary packages are loaded until it is executed by the cl. Errors in the execution may produce incomprehensible error messages from IRAF. To clear this out type flpr
An information sideline, from within IRAF, if you cd to the directory containing your headers you can do the following types of commands:
imexamine @lastpic - display and examine the last exposure imcombine @lastseq - combine last sequence
These are special functions that accept @file input. The lastpic has the last exposure name in it. Similarly, the lastseq has a list of the last sequence taken in it.
The restart parameter in obspars will determine how the postprocess is run. If it is set to "yes", then a new postprocessing job is created for each new image. This can create too many IRAF background processes. If too many jobs are active, the task postkill can be used to clear them out. If you do run out of batch slots, you will be warned that it was not possible to execute the postprocess command.
If restart is set to "no" then you need to remain
in the directory that you started in, when using postprocessing.
Also, the postprocessing script can not be changed unless you restart
Arcon after the change is made. This option loads in the script
initially and uses the files lastseq and lastpic in the
current directory to perform the desired script(s).
Appendix F: Writing Your Data To Tape
So now that you have some data, you probably want to save it to tape using the IRAF command wfits.
First, you must allocate a tape drive. At WIYN, there are both Exabyte and DAT tape drives. The Exabytes are known as mtb and the DAT drives are known as mtc. (You can find these names printed on each drive unit; you can also run the IRAF command devices to list both the IRAF and Unix names of all the I/O devices on the mountain.) Do an
cl> allocate mtb
to allocate the Exabyte tape drive at WIYN (use mtc for the DAT drives).
Since all of the KPNO IRAF data acquisition systems subscribe to IRAF networking, you can in fact use any tape drive in any dome, although you need to check with the appropriate astronomer if you want to use someone else's tape drive---be nice!. To allocate a drive elsewhere you might do something like a
cl> allocate lapis!mtb
The parameters for wfits are:
iraf_files = "@savethisstuff" IRAF images
fits_files = "mtb" FITS filename
newtape = yes Blank tape?
bscale = 1. FITS bscale
bzero = 0. FITS bzero
(make_image = yes) Create a FITS image?
(long_header = no) Print FITS header cards?
(short_header = yes) Print short header?
(bitpix = 0 ) FITS bits per pixel
(blocking_fac = 0) FITS tape blocking factor
(scale = yes) Scale data?
(autoscale = yes) Auto_scaling?
(mode = "ql")
The crucial parameters are:
In order to check to see what is on the tape, you can list the titles quite easily. Simply do a
cl> rfits mtb 1-999 make- short+ old+
to see what's there. To direct this output into a file, you can add a tapelist to the end, and then you can print that list on the printer by a simple lprint tapelist. Alternatively, you could choose to read a single file back onto disk to examine:
cl> rfits mtb 15 junk make+ old+
will create an image with the original name. (Note that even if you specify old+ you must still give the name of a legal temporary file in the output file position, i.e. junk in this example.) If the same image name already exists on disk, you should instead use old- to create an image named junk , or whatever you wish.
As you write your tape, you will get a file-by-file account of what is going on the tape. When you come to the end of the tape, you will find that there is a message saying that the file was NOT completely written to tape. An easy way to continue at this point is to edit your "at" file to remove the names of the files that were successfully written to tape. Rewind the tape with rew mtb , mount the new tape, and then re-run wfits , remembering to set newtape=yes.
NOTE: If you do write additional files to an ``old tape" (one containing useful data but which had previously been removed from the drive), make certain that the software (IRAF and Unix) is aware that the tape has been rewound before starting to write to the tape----or your old data may be overwritten! To safegaurd against this possibility we suggest that you ALWAYS swap tapes by first:
cl> deallocate mtb (or mtc or ...)
Physically swap tapes
cl> allocate mtb (or mtc or ...)
We remind the observer that s/he, and s/he alone, is responsible for keeping one's bits safe. We recommend the following before deleting any data from disk:
This section has no pretensions of being a tutorial to IRAF, but it is our intention to call your attention to or remind you of some of the more useful IRAF commands for examining your data. Use the IRAF help command and/or poke around to become familiar with these commands.
The IRAF image display window is ``ximtool", and combines the best features of Sunview/IMTOOL with SAOIMAGE. To load an image into the display, simply type display image 1 , where the ``1" denotes display frame number 1. (Up to 4 images can be loaded in frames 1-4.) This command uses many defaults that sometimes need to be changed, depending on the data and your needs.
Since the largest image that physically fits on the screen contains only about 1000 pixels on a side, and since the WIYN CCDs are considerably bigger than this, there is some trickiness to how you might want to display your data. Basically you have two options:
Phil Massey recommends option (1) for spectroscopic applications but (2) for direct imaging. One of the other authors prefers to do both, using (2) [see the full frame] in the ``Data Acquisition" window, so that images will be automatically displayed showing the full field, but setting the defaults in the ``Data Reduction" window using (1) so that each pixel can be cherished by redisplaying an image from there.
Once the image is loaded, you can adjust the brightness and contrast parameters by moving the mouse in the window while holding down the right-hand button. Negative contrast (black stars on white background) is realized by moving the mouse to the upper half of the ximtool window; positive contrast is obtained by moving the mouse to the lower half of the window. Higher contrast is achieved by moving the mouse vertically away from the center. The image is made darker (blacker) by moving the mouse to the upper left (negative contrast) or lower right (positive contrast). The most extreme displays are usually obtained when the mouse is in one of these two corners.
You can learn the approximate pixel location of the mouse by reading the value in the box at lower right. The intensity is also displayed there. If the intensity read-out has a "+" or "-" next to it, the pixel is either brighter or fainter than the display command has scaled the data. To change the scaling from the default, use the display command as follows:
cl> display image 1 zscale- zrange- z1=0 z2=2000
to set the scaling is now set to 0-2000 rather than the automatic scaling printed out previously when display was executed.
You may also zoom the picture using the middle mouse button. Press the button once and the image will move in an attempt to center up on the mouse cursor. Press it again without moving the cursor and the image will zoom up a factor of 2. Pressing the middle button 3 more times will zoom the picture up to a factor of 4, 8, and back to 1 (normal). If you move the cursor while zoomed and then press the middle button, the picture will pan to center up on the cursor.
You can also pan by simply grabbing the green outline in the panner box using the left mouse button, and moving it to outline the part of the image you would like.
The controls on the upper right allow one to flip the image left and right, up or down, change frames (the frame number is displayed between the two fat arrows), and, best of all, open a control pannel (left most icon). The control pannel allows you to turn the coordinates box and panners on and off, flip, blink, and much, much more.
If you find that you have somehow mysteriously added little green
boxes on your image, you can get rid of these by placing the cursor in
such an extraneous box, holding down the right-most mouse button, and
selecting ``Destroy".
Appendix G: Using imexamine
The imexamine task provides some of the most powerful
diagnostic quick-look tools within IRAF. If an image that you wish to
examine is already displayed in the ximtool window, simply type
imexamine. Wait patiently without moving the mouse and
a blinking, round cursor will appear on the display. (If you lose
patience, try pressing the ``L5" key without moving the cursor.) Place
the cursor over a star, and strike the r key, and you will be
presented with a radial plot of the star, along with the values of a
fit to the stellar profile. The last number displayed is the FWHM in
pixels, quite useful for determining the best focus. Other very useful
commands include l for making a line plot at the position of
the cursor, and c for making a column plot at the position of
the cursor. Other useful cursor strokes are shown below.
Analyzing direct imaging focus frames has now been made fun and easy thanks to the new kpnofocus routine. Simply run kpnofocus, giving as input the name of the focus frame. Next, mark the top image in a multiple focus exposure using the ``g" key. You will have to wait a few seconds, but you will then be presented with a plot of FWHM vs. focus value. Do this for a few stars and then exit using ``q". This routine must be loaded from the nmisc package.
Frank Valdes has provided a very useful routine to aid us in determining the best focus of a spectrograph using a series of exposures of comparison lines. The assumption is that the collimator or camera focus has been changed between each of the exposures. The routine works by cross-correlation, and provides an easy measure of the full-width-at-half-maximum (fwhm) of the images. In addition, one can specify that the dispersion axis be broken into multiple samples to determine if the best focus is wavelength dependent, and/or the spatial axis can be broken into multiple samples to determine if the best focus varies across the spatial axis.
The simplest session of this program looks like this:
nl> lpar specfocus
images = "d*.imh" List of images
(focus = "1430x10") Focus values
(corwidth = 20) Correlation width
(level = 0.5) Percent or fraction of peak for width measureme
(shifts = yes) Compute shifts across the dispersion?\n
(dispaxis = 2) Dispersion axis (long slit only)
(nspectra = 1) Number of spectral samples (long slit only)
(ndisp = 1) Number of dispersion samples
(slit1 = 5) Lower slit edge
(slit2 = 50) Upper slit edge\n
(logfile = "logfile") Logfile
(mode = "ql")
SPECFOCUS: NOAO/IRAF V2.10EXPORT feed@indigo Sat 19:37:35 19-Sep-92
Best average focus at 1465. with average width of 1.41 at 50% of peak
-- Average Over All Samples
Image Focus Width
d0001.imh 1430. 2.86
d0002.imh 1440. 2.23
d0003.imh 1450. 1.66
d0004.imh 1460. 1.44
d0005.imh 1470. 1.44
d0006.imh 1480. 1.89
d0007.imh 1490. 2.54
-- Image d0004.imh at Focus 1460. --
The dispersion axis goes along columns (dispaxis=2), and the slit covers columns 5 through 50. In addition, there is a very sophisticated graphical display that helps in interpreting the results in the case of multiple sampling along the dispersion/spatial axis; read the help page for specfocus. Currently specfocus may be loaded from the nlocal package.
At CTIO it is common to measure the CCD gain and read-noise whenever a CCD is installed on the telescope. Rob Seaman has provided a useful script called findgain that will provide good estimates of the gain and read-noise using two flat-field exposures and two bias frames. The frames should not have been processed or combined in any manner. The astronomer should specify a section of the image over which the flat-field is relatively constant. Additional details can be found by reading the help page for findgain . The routine currently lives in the nproto package.
The actual exposure time of your image may differ by some fraction of a second from the requested exposure time due to the fact that no shutter can open or close instantaneously.
If you are attempting absolute photometry or spectrophotometry, and plan short enough exposure times that you are worried about the shutter correction, there is a simple routine in IRAF called findshutcor which will help you evaluate the correction. Written by Rob Seaman, the routine determines the shutter correction from a series of flat-field exposures of varying lengths (1 sec - 20 sec, say). You must be careful not to have saturated on the longest exposures, of course, and the frames must have been processed for removing the overscan level, but not flat-fielded. In taking the data one must also carefully take into account the possibility that the flat-field lamps intensity may drift slightly with time; i.e., a good exposure sequence might be 1sec, 20 sec, 2 sec, 2 sec, 20 sec, 1 sec. The findshutcorr routine currently lives in the nlocal package.
Are you wondering how likely it is going to remain clear, or are you considering packing it in for the night? The wdisplay task in the nlocal package may help you decide what to do. Three times an hour, 24 hours a day, a new GOES weather satellite picture in one of three wavelength bands (visible, IR, and a water-vapor narrow-IR band) is downloaded. It is fun, easy, and informative to display the last four images, and quickly blink between to see what's coming your way, or leaving you alone. Simply run
cl> wdisplay ir four+
to load the last four images into your ximtool window. (You may have to select the menu item "FitFrame".) Hit CNTL-F repeatedly to make a little movie. Further information can be gleaned from the help page.
If you would like to compare your guessimate with that of an
expert, you can also easily retrieve the most recent weather
prediction. Put the mouse in a blank area of the screen and select
``Weather Forecast" under ``Astronomer Tools". You'll be presented
with a map of the US with little dots on it; place the cursor near
Tucson, and click. You can check the weather back home the same way,
of course.
Appendix J: Other Nifty Things
There is a prototype automatic logging routine that constructs a TeX version of the observing log. Instructions may be obtained via anonymous ftp to ``ftp.noao.edu", cd kpno/manuals, binary, get ccdlogs2.ps.Z. Comments should be directed to tlauer@noao.edu.
Under ``Astronomer tools" in the root menu, there is an ephemeris program (``xephem"), provided by Elwood Downey, that will tell you the Julian date and times of sunrise, sunset, and twilight, and many more wonderful things. (Do a Unix level ``man xephem" for more information.)
Version Date Author Comment ------- ---- ------ ------- 0.0 ??? CTIO original CTIO Arcon User's Manual 0.1 6/1/95 Kennedy programmer pass 1 0.2 6/15/95 Kennedy programmer pass 2 0.3 7/2/95 Silva drs pass 1 - shipped to Armandroff 0.4 7/12/95 Silva drs pass 2 - incorp Armandroff comments, shipped to Massey 0.5 7/21/95 Silva incorp Massey comments, issued as beta 0.5 0.6 8/2/95 Silva incorp von Hippel comments, fixed HTML refs, added new appendices with misc IRAF information, issued as beta 0.6 TODO: (1) Add "focus" command information when available (mid-September). (2) Beef up HTML internal referencing (3) Add "active" Table of Contents at top of document (4) Add "obsinit" information when it becomes available (5) Investigate/document how to write observing scripts (if possible). (6) Investigate/document Arcon/CLI interface (if possible). (7) Add xtapemon stuff. (8) Re-review ICE manual for other tidbits to include.