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Basic procedures

This page contains information on the setup of the computer account given to the observer, the available tools, etc.

The Guest Account

Upon arrival at La Serena, the observer should be given the password for a "guest observer" account (GuestA). This account provides restricted access to the same tools used by the staff observers without overloading the visitor with all the extra information required by the queue execution.

The account runs in the "astronomer" workstation, chamaeleon (, the double headed machine located at the right corner of the console in Cerro Pachon.

From Cerro Tololo, the account is accessible using one of the two WS in the Gemini offices located in the Round Building. However, one have to use the Login to Remote Host feature in the Solaris login screen (log into chamaeleon).

Be aware that none of these machines is visible from outside Gemini!

The first thing to start once logged into chamaeleon is mozilla. Use either the menu or just type 'mozilla' in a terminal. Use the default profile. Unless you are an experienced Gemini user, ignore the bookmarks that access the HelpDesk, Fault Report System, etc. A different password is needed for those, anyway. The Instruments bookmark give access to internal information about the instruments. The Weather bookmark points to useful things like the Seeing Monitor, satellite images, the Cloud Camera.

The Guest account contains a scratch disk, to be used for data processing at the summit, etc. This is /export/scratch/GuestA/

The observer can choose to keep an electronic log in whatever format he/she is more confortable with or use the paper obslog available in /home/GuestA/iraf/phoenix/

In either case, we would be grateful if a copy is e-mailed/left for us. If using the paper log, there is a copier at the back of the console room; the copy can be handed to the SSA at the end of the run - just tell him/her to pass it along to Claudia (the Gemini Phoenix Instrument Scientist).

Accessing a programme stored in the Observing Database (the OTR)

To execute the observations previously prepared during PhaseII and stored in the Observing Database, start the internal version of the Gemini Observing Tool (OTR). Start it under GEMINI -> OBSERVING -> OT. When started, it will ask for your program name and key  (the same key used for fetching your program). This is the only science program available to you. Selecting "Open" will give access to other library and calibration programs if needed. Observations (as defined by the PI) will be colored orange (For Activation) or green (Ready). To activate the "orange" ones, select one or more, then set to Ready (and click Save). Those observations are now ready to be queued for execution. There is no need to "store" the programme if modifications are done: the OTR is actually accessing the programme in the Observing Database, so be careful with the delete key!

If the programme does not contain Telluric Standards, a library with selected stars from the bright tellurics list (in the NOAO webpages) is available. From the File menu, select 'Open in new window', then scroll down the list until finding a programme with ID "GS-LIB-PHXCAL" (Phoenix Telluric Standards). Please do not queue the observations from this programme - copy the selected telluric to the classical programme window, add the Phoenix component, and queue from there (set it to 'Ready' first)

To see the observations in the queue, go to the File menu, and select the 'Display session queue' option. To execute an observation, just tell the SSA its number (eg, C-7-2). The SSA will slew the telescope to the target, acquire guiding and tell you when everything is ready.

No information is passed from the OT to Phoenix! All instrument setup has to be done from the Phoenix computer. The same applies for the offsets. There are simple scripts in the Phoenix computer to execute the most common dither patterns (abba, abc, abba perpendicular to the slit), but more complex dither patterns defined in the OT will have to be translated to N/S-E/W offsets and applied from the Phoenix computer - this will keep the header information consistent (offsets applied by the SSA will not appear in the headers). Remeber that offsets done this way are relative (the ones defined in the OT are absolute), so you will have to calculate the offset from one position to the next, not from the centre.

The seqexec (sequence executor, part of the Observatory Control System and used with the Gemini facility instruments) is not used with Phoenix.

Accessing GCAL (for flats)

To access the calibration unit GCAL, select it from the menu or open a terminal in any empty workspace and type 'gcal'. This will lauch the main GCAL window. Click the big "Mechanism control commands" button to open the control window. Ignore shutter (it applies only to the IR lamp), select the Visible diffuser, and the ND1.6 filter, then click Apply.

To take the flats, turn on the QH lamp (see the Instrument Operation and Procedures page), then ask the SSA to set the Science Fold to GCAL. Don't forget to turn the lamp off as soon as you are done.

Starting the data copier

The data taken with Phoenix are initially stored in the Phoenix computer, then automatically copied to the main data repository disk at the summit. In the process, the file name is changed. The observer can name the frames in any way he/she wants when observing (flatNNN for the flats, imageNNN for the acquisitions, etc), when transferred to the Gemini disk, the files will be renamed after the observing date (eg, 2005feb25_nnnn.fits, where nnnn is a running number).

The observer can choose to work with the data in the Phoenix computer or using the guest account. For the latter, it is necessary to transfer a copy of the files to the scratch disk. This is done using a TclTk "widget" called mmon_guest (open a terminal and just type it). The mmon GUI will appear.

Change "Original directory (prefix): " to "/net/reggie/staging/phoenix/yyyymmmdd/" where yyyymmmdd is the UT date at the end of the night (eg, for the night Feb 24-25 it would be 2005feb25). Don't forget the trailing "/"!

Change "Destination directory root: " to "/export/scratch/GuestA"  (for the GuestI account)

Change Instrument to Phoenix using the pull down menu

Set the "Directory date: " to the observation date (as above).

Select "Monitor"

That will copy the data to the /export/scratch/GuestA/phoenix/yyyymmmdd/ directory, where it can be processed.

At the end of the night, untoggle "Monitor"

Starting IRAF, processing observations

To start IRAF, first open the image display (eg, by typing 'ximtool-alt ;amp;' in a terminal).

Also in a terminal, type 'iterm' to open an xgterm IRAF window.

On that window, type 'gocl'

On the IRAF cl prompt, type 'cl <'

That will load the quicklook data reduction scripts described in the Procedures page (sntest2 and snflat), as well as put you in the scratch directory for the account and instrument (in this case, /scratch/GuestA/phoenix). Just cd to the night's subdirectory.

For a more complete processing, the same scripts used for data quality assessment during queue are available as well. An example processing script is available in /home/GuestA/iraf/phoenix/
Copy that file into the night's data directory, and edit as required.
Run at the cl prompt:

cl> <

Once a step is processed, comment it (put a # at the start of the line), so you can continue to process the subsequent observations.

In a nutshell:

pmkdark creates the combined dark to be used with the flats

pmkflat creates the combined flat. xwin,ywin are the sizes of the median box (the flat is created by dividing the combined image by its smoothed version).

psproc does all the rest (flatfields, combines, extracts). Run with fl_inter+ to do the extraction interactively.


The data will be available for download from the Gemini Science Archive as soon as the headers are fixed for compatibility with the GSA (it depends what else I have to do, can be from a few days to a couple of weeks after the Phoenix observing block is over; if you need your data sooner, drop me an e-mail)

The processed data in the /scratch/ disk will not be shipped or saved, so if the observer wants to keep a copy of that, there are two options:

1) ftp all frames to a laptop or home institution.

2) make a tape backup while at the summit. DAT (2s) are available, the tape drive is located in the computer room. Ask the SSA to point you to ANTU. Load the tape, then from chamaeleon

rsh antu -l GuestA

cd /net/chamaeleon/export/scratch/GuestA/phoenix/yyyymmmdd

tar -cvf /dev/rmt/0cn *

This will dump all files in that directory to the tape. Repeat as needed for other nights. Once done, eject the tape:

mt -f /dev/rmt/0cn offline

After your observing run is over, it is requested that an Observing Run Report be completed prior to your departure. Thanks!