ALFALFA Survey - Setup and Observing Cookbook
Current as of March 1, 2007
Disclaimer: CIMA changes, conditions change, and we have
to adapt to situations as they develop; this cookbook works today but may not
tomorrow! In particular, as of February 20, 2007, we are using the CIMA version
2.2.17, known as the Normal Version. Please read the documentation on the CIMA website. If you want to experiment with
CIMA offline, be careful not to overwrite or change the observing files!
Before Observing
The ALFA cover must have been removed. ALFA is covered during radar runs, so take a look
at the telescope schedule beforehand. For instance, if it looks like ALFA had to be covered
the day before your observations, make sure that time is allocated to remove the cover before
your run starts (this can be done during maintenance or system check time). In any case, it
is a good idea to double check with the telescope operator. Know the schedule a few days
ahead of time.
The ALFA motor must be switched on (this can be done from the control room!). If you have any doubts,
look for ALFA rotation using the dome video monitors (you should be able to see it move).
Also, the operator may need to turn on ALFA in software from the control room.
Ask the telescope operator to move to the appropriate azimuth and
approximate zenith angle for the night and, if necessary, to rotate
ALFA into place. Ask him/her to do this before starting
GALSPECT..
For the a2010 project, the telescope is fixed at AZ= 360 for Declinations < +16 degrees, and at AZ =180 for
Declinations > 20 degrees. The scenario is still be determined for
other values. (Note that we use azimuth=360 rather than azimuth=0 to
avoid wrap issues. Note also that Az=180 is equivalent to Az=540:
choose the value that has the smallest movement from the current position.) For Spring 2007, the azimuth should be set to
180 (or 540) most nights, since we are mostly observing north of
zenith, but some nights will require an azimuth
of 360 (NOT 0). Be sure to CHECK THE SCHEDULE. Be sure the
operator returns telescope control to you. Note that once you start up CIMA, you'll take over
control of the telescope motion and it will stop. So wait to start up CIMA. In the meantime, have
the operator start up GALSPECT (see below).
Set up the TOGS starting position. Open up the catalog file
/share/obs4/usr/a2010/a2010.cat and
edit the entry called galfasrc to the new right ascension and declination for
that night. As exact start times and slew times
can change, the observer needs to be ready to adjust the entry by estimating as the previous
observer is finishing, and again during setup if there are delays, when the telescope will
be on the meridian. This needs to be done as quickly as possible. We suggest also that you
take a look at the TOGS setup
document (provided by the TOGS group) to understand a bit about their setup.
TOGS GALFA setup - the operator will carry out this step.
Login to any machine in the control room to begin the GALFA startup.
Secure shell to the dataview machine: ssh -l guest dataview
Secure shell to the galfa machine: ssh -i galfa_key galfa@galfa1
Enter the command: /var/levels_togs. If you get the message
LO2: Set failed, got back: ERROR setting freq, then you need to start the gpib on the
wapp server. To do this, pull up another xterm, and ssh to the wappserver via
ssh
wapp@wappserv. Ask Brian for the password. Once logged on, type source
/share/wappsrc/bin/start_gpib. Go back to the xterm logged into galfa1 and again type
/var/levels_togs. This will run for the rest of the night, so minimize the windows.
Note: if the operator is not able to get GALSPECT to run, he/she should call the
TOGS contact for
the night.
Datataking
Quickly log into OBSERVER2 as "dtusr" (password taped to the monitor).
When ALFA is in place and you are close to the target position,
start CIMA by clicking with the right button of the mouse on the background. (When you start
CIMA, slewing will stop until you issue the observe command, and if you are not close
to target position, you will have to wait later.) Choose
"Cima Online GUI" from the menu. Select the version we are currently
using, the "normal" version 2.2.17 (effective 20Feb2007).
The Start New CIMA window will pop up in which you need to enter some
identifying information.
Start New Cima Session
Project number: a2010. This is important. Your settings and log files will be saved
(if you decide to do so) in the corresponding project directory, which for us is
/share/obs4/usr/a2010/. Note that if you enter captial "A"
it will be changed to small "a".
Observer: Your name for entry in operator's logbook.
Select Line observing mode.
Click Accept and CIMA will start up.
Now, several windows will pop up: the
CIMA Observation Status window, the CIMA Log Display window,
the CIMA Observer's Interface, the CIMA executive (
red font) and a widget
entitled Choose Receiver. The CIMA Observer's Interface
is the main window and should always be open. The buttons therein open new windows, which allow you
to control the telescope. These windows will be indicated with orange fonts
in this document; all the other ones will be red.
Choose Receiver
Select ALFA, disable quick Tsys, then click on
Select Receiver Now. Make sure that ALFA shows up in the AOSTATUS
monitor (to your left on top if you are in the control room).
Keep an eye on the CIMA Log Display and don't move to the next step until the
previous has completed; if you click too fast, you run the risk of getting an "executive busy" command.
Under Utilities in the CIMA Observers Interface window,
Restart the WAPPS.
When the output to log window is complete, dismiss the window.
If running TOGS, immediately click on Command File
Observing, and click on the Load button. Choose the file command_galfasrc.
The file should appear in the right hand box. Be sure that "Run Command File" is set to
Once and "Start From" is set to First line.
Click Run to run the file. The telescope will slew to the position you just set for 'galfasrc' in the
a2010.cat file, which should be very close to the meridian. As soon as it gets there it will load the
togs.gui file, their IFLO setup, and begin
about 6 minutes of frequency switching calibration. One only needs to
let it run. During this time, you can use the waterfall dataview application on the dataview machine to see that data is be
taken. You may also open the log files if you wish. Note: if the GALSPECT spectrometer is not set up within ten minutes of their allotted time (so that
the ~6 mins of calibration cannot be run before A2010 is scheduled to start), do not run the TOGS
calibration if the prime A2010 map LST range is reached. But, even if you don't run it at the beginning,
run the TOGS calibration at the end, if there is time and GALSPECT is running.
As soon as the TOGS calibration is done, Close the command file window and
proceed with the ALFALFA setup as usual.
Click on Load/Save State (from the CIMA
Observer's Interface).
Select Load a Saved State . The setup file depends on
the azimuth: a2010_az360.gui (Azimuth 360) or a2010_az180.gui (Azimuth 180/540).
It fires the cal at the end of each
scan ("loopend-OFF"), and adopts the topocentric reference frame. This will
set most of the parameters, but you must still apply the
configuration in each of the widgets described below. Select the
appropriate file and click Continue when loaded.
Dismiss the Load window.
Click on Pointing Control. Here we will set the ALFA parameters and point the
telescope. If you have run TOGS, ALFA should be in place and the
telescope should be close to the correct azimuth. If you have not run TOGS, double-check that ALFA is in place.
The telescope won't move until the receiver floor has
finished rotating (to ALFA, from some other receiver). Also note that the "Configure Wapps" will not work,
and you won't get data flowing from all the beams ( you can tell this from the alfadatawin program on the
dataview machine.)
For a2010, we maintain a source "catalog"
a2010.cat. Check at the top of the window if this file is
loaded, and, if not, load with the "Catalog" button (on the top
left).
Choose the appropriate drift***p* "source" corresponding to the
current observing block from the list of drifts.
You can also type the coordinates of the source (RA and Dec);
if you do so, be sure to use epoch J2000.
If necessary, update the RA to the current LST. This can be done
in a2010.cat before opening the Pointing
Control menu.
Click Point and continue with the following while the
telescope points.
Check that velocity is set to 0, reference frame to topocentric and type to optical.
Click ALFA Rotation Control Window. In the menu that
pops up, set Rotation angle to +19.0 (degrees) and hit Send.
You can actually see if ALFA is rotating by looking
at the TV camera in the control room (ask the telescope operator to show the appropriate camera).
The blue number next to the "Send" button should change to your entry once ALFA reaches that position.
(For drifts at 0 or 180 degrees azimuth, the correct angle to give equal Declination beam
spacing is thought to be 19 deg. At azimuth 90 deg, it is thought to be -14 deg.)
Once ALFA has rotated into position, click Close
. (Note that ALFA should be at 19 if you have run TOGS, but
that we do this step to make sure.)
Back in the Pointing Control window,
click on 0 to choose beam 0 as the ALFA center.
Note: if there are problems with ALFA not responding (e.g., it
doesn't rotate), click Restart ALFA under the
Utilities menu.
Restart the WAPPs under Utilities as above.
Click on Receiver IF/LO Control
Make sure that ALFA is selected, then click New Improved
IFLO Setup . This will open
the New Improved IFLO Control
window.
New Improved IFLO Control
Both "Choose Receiver" and "IFLO Path" should be set to ALFA. Note that this is another place where
you can select the receiver (several functions are redundant).
Check that the rest frequency is 1385.0 MHz for topocentric (as opposed to 1420.4058 if doppler
tracking is used), that the Destination is WAPP, and that the four bandwidths are all 100 MHz.
Hit Apply This Setup. It will take a few seconds to respond: watch the observation log display window.
Dismiss Receiver IF/LO Control and
New Improved IFLO Control windows.
Confirm in CIMA log window that IFLO parameters are set before moving. (Make sure you wait until
the frequency is set before proceeding!)
Click Backend Control
The WAPP ALFA window should pop up.
Check that the configuration is "2 chan, 3-level auto." If not,
choose it from the pull-down menu (click on the displayed configuration
[in red] with the left
button of the mouse).
Here, you can leave cal to "nocal" and Secs to "5" because we don't use this.
The number of seconds for its duration is only relevant if you
choose to test the cal by pressing the "Start Cal" button.
Check that the integration time (i.e., how often the data are written to file) is 1 sec.
Ignore the "Piggyback GALFA" button, and leave the radar blanker OFF.
Hit Configure WAPP ALFA to apply your setup, ONLY AFTER ALFA is in place. Make sure the log
display window indicates that the WAPP configuration is finished.
Adjust power, and look at the numbers on the Backend Control window:
1+/- 0.2 is ok. If the numbers are zeros (or close to zeros), trying redoing the startup sequence:
This appears to depend on the order in which you do things. If that doesn't work, probably
the ALFA amplifiers have
not been turned on. If this is the case, you can ask the telescope operator to turn them on
for you, or you can do it yourself by typing "/home/aoui/bin/alfaon" on an xterm (FYI:
"/home/aoui/bin/alfasafe" turns the ALFA amplifiers off).
If the power is now back, but the numbers look wrong, try adjusting the power a few times.
The bottom part of the window is the "Monitor Control". Do not worry about it (it is meant to
display the signal from one beam and one polarization at a time on the monitors sitting on the
top shelf of the wall to your right, in the control room). Just make sure that the control
is set to "Remote" and not to "Local".
Click Spectral Line Observing. This opens Spectral Line Observer's Widget you'll be using most of the night. Note it also has buttons that allow you to "start a new fits file" and "adjust power".
Choose your observing mode from the "Mode" pull-down menu.
For all a2010 observations, use the "Fixed Azimuth Drift Map" mode.
In this mode, the name of the drift and the starting RA are taken from
the Pointing Control window.
Make sure that the starting RA is sufficiently later than current RAJ from the right most view screen, so
that the telescope can be in position before that RA drifts into the beam, but not so much
that you waste a lot of time. (A typical value is ~60 secs from now, but it depends on how close
the telescope is now positioned.)
Check the azimuth value to confirm that it is correctly set to
180 or 360. (Note 180 is equivalent to 540 and telescope will know to
go to the closer angle, so you do not need to change to 540.)
The remaining values should be loaded from the configuration
files. Be sure that they are set properly (you can do this after
hitting Observe (see below) and abort if you see an
error.) The proper values are:
Source is the appropriate driftMMMpN (from the a2010.cat).
Epoch should be J
RA is set to ~60 seconds from now.
Declination should correspond to that given in a2010.cat
ALFA rotation angle is correct, usually 19 degrees.
Drift type is set to Follow Dec J2000
Scan length is set to 600 seconds
Number of loops is set to cover length of run. Easiest to leave
it at the default 99.
New FITS (each loop) is set to 1.
Calmode is set to loopend=ON
Caltype is set to hcal. We do not use an "extra" cal.
Cal Secs is set to 1 and Async secs to 0
Adjust power to first loop only; ignore Cal Only.
These settings allow for a 600 second scan and 1 sec cal scan to be placed in a single FITS file of about 212 MB.
If you have moved at all since the last time, hit Adjust Power Again.
Otherwise, hit Observe and make sure that the slew time is less than the wait time displayed
in the AO Observer Display.
If not, hit "Abort" and set a slightly later RA. Start a new FITS
file just in case and hit Observe again.
Monitor your data: watch
particularly for power dips, GPS, birdies, and gaps in the data.
Be vigilant for new sources of RFI; carefully check the waterfall plots and/or quicklook.
Know the expected locations in the band of the "usual suspects". The
FAA radar is usually at
1350 MHz (although they sometimes use 1330 MHz, out of our bandpass!)
For example, strong RFI at 1367 and 1382 MHz is due to the
Punta Salinas naval base radar, which should not be on during
ALFALFA run.
(see this link).
Maintain a log file, with an entry for each new fits
file that is written. The file should be in /share/obs4/usr/a2010/ ;
if it's not there, make one using the format logYYMMDD. More instructions below.
Check the declination on the monpnt window to confirm that it
remains near the J2000 value (within a few arcseconds).
If you abort a scan during the night with the "Abort" command
in the Spectral Line Observing
widget, be sure to start a new fits file before observing again; if you don't, the two scans (the one you aborted and the new one) will be in the same fits file, complicating the data reduction.
Sometimes the WAPPS are left in an uncertain state if a scan is aborted abruptly. Be sure
to restart the WAPPs after aborting a scan-in-progress (i.e. after data taking starts), and then make
sure to reconfigure them. Unfortunately this means that you have to readjust the power, so you
really want to be careful not to abort needlessly.
When finished, abort the last scan, after a few seconds of
integration time.
If running TOGS (if not, skip to next step),
Restart the WAPPS using that option under Utilities.
Note any error messages; if there are any, try again.
Click on Command File Observing, and click the Load
button. Choose and run the script command_galfacurpos. This will again load the togs.gui
file and IFLO setup, and begin the TOGS calibration at the current telescope position. Let the
calibration finish (about 6 minutes) and then follow the exit procedure as normal.
Select Exit normally to exit
CIMA.
Exit data monitoring programs.
Log out of observer2.
The operator will end the galspect process. (The procedure is
to pull up the window running GALSPECT, and hit CTRL-C to exit. Logout of
the galfa1 machine and then exit dataview.)
Recovering from WAPP errors
The only sign of WAPP errors in CIMA is that messages appear in red in the
CIMA log window. WAPP error messages include: WAPPs confused
or WAPP (3) ERROR - Counts don't match for chip 1. The latter indicates
a hardware problem on WAPP3. Occasionally there is no warning message from CIMA, but the countdown
time on the aostatus window stops, meaning that the WAPPs are no longer taking data.
Sometimes the problems go away, so try to restart
the WAPPs and then the observing again. To do this:
Abort Observation in, e.g., the Spectral
Line Observing Widget
Restart ALL WAPPS under
Utilities
Adjust power in the Spectral
Line Observing Widget
Configure WAPP ALFA in
Backend Control
Start a New Fits File in
Backend Control
Adjust RA for new observation in the Spectral
Line Observing Widget
Hit Observe in the Spectral
Line Observing Widget
Once drift starts, confirm coordinates. (Sometimes
control returns to telescope operator rather than observer.)
If this does not work, try again, up to a few times. If this still does not help,
exit CIMA and start again.
If the error messages keep appearing, it will be necessary to have the operator call an engineer to
look into the problem. Currently, the WAPP experts are Giacomo Comes, Arun and Ryan Seal.
If you abort a scan during the night with the "Abort" command in the Spectral Line Observing widget, be sure to start a new fits file before observing again; if you don't, the two scans (the one you aborted and the new one) will be in the same fits file, complicating the data reduction.
Sometimes the WAPPS are left in an uncertain state if a scan is aborted abruptly. Be sure
to restart the WAPPs after aborting a scan-in-progress (i.e. after data taking starts), and then make
sure to reconfigure them. Unfortunately this means that you have to readjust the power, so you
really want to be careful not to abort needlessly.
Data Monitoring
Mikael has developed a great package for telescope monitoring and data
display.
These programs read the data that are being broadcasted to the FITS files, and not
the FITS files themselves. The screens are updated every 10 seconds.
On Dataview, click on the background and select from the menu:
Quicklook Data Display -- launches the ALFA on-line display. Click 'ALFA Pattern' and 'Diagrams - Waterfall' to
see all 7 beams
Observers Monitor -- opens a widget that gives the power levels. Normal power levels are coded in blue.
Array Rotation -- shows ALFA rotation
angle - check at beginning of night.
ALFA Beam Position -- shows approximate positions of each beam; can set to RA,Dec (note:
currently, the positions aren't quite perfect but still helpful.) Check at beginning of night.
Frontend Monitor -- launches the ALFA instrument monitor,
showing voltages, currents, and temperatures
in all beams (same display as to the right of the operator's station)..
You can open the same widgets by typing on an xterm on a linux machine:
/home/cima/bin/alfadatawin -- waterfall plots in your color of choice. Too cool. Enough said.
The program alfadatawin is currently only available on Linux machines. The other commands are available
on other machines, too. Notice that you will not be able to start alfadatawin if the process
is already running on dataview (started by one of the previous observers). If this happens, ask the
telescope operator to contact Mikael, Arun, or Phil to kill the previous process(es).
Notes
In particular, use these displays to monitor the power levels. Notice that after hitting
"Observe" the CIMA monitor WAPP power levels do not update, whereas the monitoring windows
show the current levels.
After a cal, the WAPP power levels will spike and so the
displays will momentarily change scale.
If you reset the WAPPs, you will have to exit and restart alfadatawin to get it to grab
the online data again.
To log out of dataview at the end of the observing run, close the windows "politely" by hitting
exit in each display window before logging out. This will make sure that the processes terminate.
Log files
It is very important to keep an accurate log of what happens, even to note "an uneventful night". To do so:
ssh to another machine as a2010
open a new file logYYMMDD in /share/obs4/usr/a2010 using your favorite
text editor. Use a posted log file as the template.
record **anything** of note, especially
(1) the CIMA version number and the saved state (a2010_az360.gui or a2010_az180.gui)
(2) any bad files,
(3) any power adjustments,
(4) unusual rfi etc. (see observational troubleshooting list to check
To quote Brian: I cannot stress the importance of keeping accurate logs.
While the file conversion software works automatically, it is good to have a backup to check against when
comparing scan numbers. Sometimes CIMA squeezes in extra scans at the beginning or end of the run, or
has some other unpredictable behavior. It is also important to note "empty" files, as IDL will hiccup on these.
The folks who calibrate/process the drifts you take will thank you for your carefully note-taking (and will be entirely
justified in saying unkind things about you otherwise).
After Observing
After the run has finished, do the following things to keep the rest of the a2010 group informed about how the run is
going.
Check with the scheduling team about other mods that they or you should make.
If anything important happened, send a message to RG and MH.
Reading Data into IDL and saving to Disk
Once a observing session is complete, all the FITS files can be converted into a set of IDL structures for
future use; ask Brian about any details about this. It is probably best to do this at your "office" workstation
at AO, and run the job on one of the fusion machines. Below, IDL> means "inside idl".
Login as user a2010. The ".idlstartup" file in ~a2010 is configured with the proper routines, which are
located in /share/a2010/idl and its subdirectories.
Change to the data directory /share/a2010/data/{run_directory} (ie /share/a2010/data/07.02.17/
Filecreator needs as input a list of the FITS files with full path names that you wish to process. The
best way to do this is
ls /share/pserverf.sda2/wappdata/wapp.YYYYMMDD.a2010.* > filesYYYYMMDD.txt
This will put all the a2010 files from that date into the text
file. Check your log to confirm the directory.
This next step is very, very, VERY important. You MUST consult the log to see what files should be
removed from this list. If there are files that have no data (ie the files at the end of the run), they
will cause the filecreator program to hiccup, and therefore should be removed from the list. If there are
files you KNOW contain junk, remove them from the list. ALSO, if you run crossed over midnight, you may
need to add or delete files. You can ls, grep, do whatever you want to make the list, just make sure that
the list contains all the viable files you wish to process for a
single observing run. Make sure that there is no blank line at the end
of the list, or filecreator will crash.
Start up IDL in /share/a2010/data/{run_directory} by typing idl
Make sure that you are on
a fast machine (fusion01, fusion02, aolc1,2,3,4,6,g,h,j,k,m,o,p), and
that someone
else isn't using up all the cpu (do a
"top" to check that).
IDL>@wasinit2 (If this doesn't work, check that your idl account is set up properly)
IDL> .com filecreator
You are now ready to process a run's data. There are five different file types that will be created:
sssssssss.sav - A 600 second d structure *.sav IDL file
ssssssssCALOFbegin - The first record of a drift used as a cal off
ssssssssCALOFend - The last record of a drift used as a cal off
ssssssssCALON - A 1 second CALON
ssssssssCALOF - A 1 second CAL off
IDL> filecreator, filelist
filelist is a string of the filename you created
above, ie 'files20070223.txt'.
The files being created will be reported on screen as the job is done. In addition, the names of the CAL
files will be written to the file 2007-MM-DD.CALlist. This list is important, as it will form the calibration structures from the procedures
calib1 and calib2.
Example from February 23, 2007: There were 26 files made that night, so I created a list in the
/share/a2010/data/07.02.23/ directory with ls
/share/pserverf.sda2/wappdata/wapp.20070223.a2010.*.fits >
files20070223.txt and ls /share/pserverf.sda2/wappdata/wapp.20070224.a2010.*.fits >>
files20070223.txt, because the run crossed midnight. However, upon
examining the log I see that files 15 and 11 were aborted. I removed
these files from the list, as they contain no data. I then start IDL
with idl while on one of the fast machines listed above. I compile
filecreator as above, and then invoke the command:
IDL> filecreator, 'files20070223.txt'
IDL goes to work. When the job is done there will be many IDL save files, CALON files, and CALOFbegin and CALOFend files, the
filesYYYMMDD.txt you created, and a new CALlist file.
Page created and maintained by the members of the
Cornell ExtraGalactic Group
and their ALFALFA team friends
Last modified: Thurs Mar 01 17:40 EST 2007 by becky