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Operating Phoenix

Start-of-night procedures
Focus and guiding
Observing scripts (abba, ab, slitscan, recenter...)
GCAL flats
Telluric standards
Thermal IR target acquisition
Image field and slit orientations - includes how to setup for observing at an arbitrary PA
Grating setup procedure
Quick look data reduction
End-of-night procedures
Troubleshooting

Troubleshooting procedures are partly based on the documentation written by Nigel Sharp for ABU/WildFire at Gemini South.

Start of the night procedures:

Starting from scratch: usually, the instrument will be left ready by the day crew before the first night of the run. However, if it is necessary to start from scratch, here are the instructions:

log in the Phoenix computer as aspp (contact someone on the staff for the password). This will bring up all the relevant windows. Instrument Control is in the top left, Instrument Status in the top right; an IRAF window is in the bottom left and the ximtool and a console window share the bottom right.
In the Instrument Control window type (the UNIX prompt should look something like phoenix1 <2:23pm> {77}):
- startwf
answer the questions carefully; this will start WildFire, the instrument control software. If everything works, the prompt should be now a '%'
From here on, just continue as for a normal start.
Do not type any command in the Instrument Status window unless instructed to do so (you don't want to upset WildFire).
See below for troubleshooting (instrument hangs, terminating an integration, not getting signal on the detectod, etc)

Normal start of night:

If WildFire is up and running and the instrument power is on, in the Instrument Control window type
- activate
  - this will turn on the array electronics. "activate" will ask for the bias setting - enter 0.32. It would return a number which should be 0.300+/-0.002
- setbias 0.32
  - to adjust the actual bias to 0.300
Check the instrument temperatures. The output will show in the Instrument Status window. The cold heads ("LN2") should read ~40K; the detector should read ~31K; and most of the dewar ~55K
- status t
Check the position of the instrument elements (filter wheels, grating, etc).
- status s
Create the data directories for the night. There are two data disks available (phx0 and phx1). At the beginning of the run, is a good idea to check the disk space.
- mkdir /phx0/yyyymmmdd
  - where yyyymmmdd corresponds to the UT date for the end of the night, using the standard three letter code for the month
Set the data directory.
- setdir /phx0/yyyymmmdd
Once the TCS and the VII are up, connect the instrument to the telescope. THIS IS VERY IMPORTANT - otherwise, you get mangled headers and no offset control!
- tcpon
Finally, if you want to change the parameters set, use:
- ped
On the IRAF display, frequency increases/wavelength decreases upwards (larger pixel values), and the slit is accurately aligned E-W, although it appears tilted on the array when seen in image mode.

Phoenix TV "guider": quite useful to see if you get the object in the right place

Turn ICCD all the way counter-clockwise
Turn on MAIN POWER
Turn on POWER (switch above the ICCD pot)
Push the INTEN ON button
With the current configuration (default instrument angle = 180deg and Phoenix on port 5), N is up and E is to the right on the TV
IMPORTANT:
- turn the ICCD down when slewing to avoid damage from bright stars
- use the neutral density filter (ND on) when observing bright targets
- turn the guider off at the end of the night

We are now using the OTR to select the observations, and all header updates for classical programmes are done after the fact. There is no e-obslog for Phoenix, classical observers can keep their own log or use the paper templates available in the Phoenix folder above the astronomer's workstation.

Use of QMon by classical observers is DISCOURAGED - blank headers are easier to update.

Typical overheads:

Readout single image	~25sec
Readout sequence of 10 images	~17sec
Each lnrs	1 sec

Focus and guiding:

Focus: if using the J9232 filter, remember to ask the SSA to use the Phoenix_J setup (works for both WFS). Otherwise, use Phoenix_P1 or Phoenix_P2 as appropriate.

Guiding: the telescope guiding system will compensate for differential refraction between the guiding wavelength and the instrument wavelength. Central wavelength and CassRot position angle are now read directly from the OT into the TCS. Just check as usual to see if they are correct.

Note that there is significant flexure/"flopsure" in the Phoenix imaging mode, which results in the image of the slit moving on the array. This effect has been measured to be 3.5pix perpendicular to the slit (up and down the array) between elevations of 85 and 30deg (~1pix/hour), suggesting that recentering at least once per hour may be advisable during a long observation. The flexure parallel to the slit is about 7pix between elevation 85 and 30deg.

Observing scripts:

Useful numbers:

Saturation on the array: 8000 counts
Plate scale

imaging mode: 0.055 "/pixel
spectroscopic mode: 0.085 "/pixel

Spectral coverage: ~1500 km/s or 0.005*(central wavelength or frequency)
Highest advisable exposure is 3000 counts.
At J, H, and K limit exposures to 1800sec.
At M limit exposures to 30sec, and use coadds (4 to 8, so the final exposure time is a compromise between accumulating signal and quality of the sky subtraction)
For long exposures (more than 10min) set the number of low noise reads to 8 (using the lnrs command or as one of the ask options).

Generic observing caveats:

There is NO CLEAN WAY to stop an exposure. Therefore if you set a long exposure time, be VERY sure that the instrument configuration is correct. Be VERY sure you have not set a long exposure/many coadds if that is not what you want.
If by any reason you need to terminate a long integration, refer to the troubleshooting procedures below before hiting the dreaded CTRL-C.
There are three different positions for 2- and 3-pix slits, depending on the wavelength of the observations. Check here for the list or type help slit in the WildFire window. Note that the flats must be taken with the correct slit in position!
The minimum exposure time is 1sec. Use the ND filter when imaging bright stars to avoid saturating the array. Heavy saturation will leave an afterimage that takes quite a long time to disappear (there has been much debate where taking a series of short darks helps with the persistence, but for all that is worth it does seem that it goes away with time, not with exposures).

IMPORTANT NOTE ABOUT OFFSETS: the offsets defined in the OT are NOT passed to the telescope. Dither patterns other than the default observing sequences below must be manually executed FROM THE PHOENIX COMPUTER (if you ask the SSA to apply them, there will be NO indication in the image header of the updated telescope position). Offsets are also relative to the last position, and done in N-E orientation (not p and q as for the facility instruments).

The following scripts are in /home/aspp/OBSERVERS/blum/

The source_phx.tcl script (usage: source_phx) will source all the scripts. It has to be sourced first (usage: source_phx) will source all the scripts. It has to be sourced first (usage: source /home/aspp/OBSERVERS/blum/source_phx.tcl).

The individual scripts can also be sourced independently. If you add new scripts, put them into source_phx.tcl so when starting/restarting wildfire, a minimum of work is needed to source the observing scripts.

gcal.tcl

zcenter.tcl

recenter.tcl

abba.tcl

abbaperp.tcl

slitscan.tcl

immode.tcl

spmode.tcl

mgo.tcl

Useful observing setup commands:

*cover*	*open*: light path to the Science Fold mirror,
	*close*: light path to the Phoenix internal hollow cathod lamp
*viewer*	*dark, open* (grating), image, lyot
*slit*	*open*: for imaging
	an integer number to select the corresponding slit
*help*	*filt*: lists filters in filter wheel
	*cvf*: lists filters in CVF wheel (there are no CVF filters)
	*slit*: lists slits in slit wheel
	*grat*: explans the grating parameters
	*lyot*: lists the various lyot stops
*filt*	an integer number to select the corresponding filter in the filter wheel
	open to select the open position in the filter wheel (used with a filter in CVF)
*cvf*	an integer number to select the corresponding filter in the CVF wheel (note that although cvf 7 is listed as a blank, it actually contains the L2870 filter)
	nd to select the neutral density filter in the CVF whell (attenuates by 100x)
	*open* to select the open position in CVF wheel (used with a filter in filter wheel)
*grat*	*(number) (units) (offset)*: sets the grating position; see below for an explanation
*settime*	a real number to set the exposure time
*eask*	edits the list of parameters that are queried by ask before an observation; la = list/ask; l = lists only
*ask*	enter the new values for the observation parameters
*toffset*	*X Y*; moves the telescope X arcsec E, Y arcsec N
*north*	X ; moves the telescope X arcsec north (or south, east, west)
kick	increases the voltage in the motor to coach a "sticky" mechanism to move. USE WITH CARE! If repeated issues of kick do not work, it may indicate a more serious problem. kick should NOT be used as "normal operational procedure" (i.e., whole night long).

Observing commands:

zcenter	set the fiducial position of the slit. Required at least once at the start of the night or every time the PA of the slit is changed. Reccomended when changing filters (particularly to the L and M bands)
recenter	given the X,Y coordinates of a target, will offset it to the fiducial slit position as defined by zcenter.
go	start the integration with the current setup (set by *ask*
*observe*	equivalent to an ask followed by a go with an option to abort the operation after the ask.

GCAL flats:

Flats are taken with the facility calibration unit GCAL and the following (approximate) configurations:
Note: use these values as indicative only.

Filter	Lamp	Diffuser	ND filter	Exptime
M2030 M2150	QH	optical	open	10sec
L3100	QH	optical	open	7sec
J7799	QH	optical	ND1.0	2sec
K4667	QH	optical	ND1.0	1sec
K4578	QH	optical	ND1.0	1sec
H6420	QH	optical	ND1.0	1sec

Note that depending on the grating setting, it may be necessary to increase the exposure time/remove the ND filter (e.g, if too close to the edge of the filter). If in doubt, start with an 1 second exposure, ND=1.0mag, and work your way towards ~2000-2500 counts average.

To bring up the GCAl window, select it from the Gemini menu in the GuestA account. Click the Mechanism Control Commands button and select the appropriate setup. Don't forget to hit APPLY. It may be necessary to datum all mechanisms at the start of the night.

To reach S/N ~400 you need 15 images with the above level (2.0-2.5k).

Very important: turn off the QH lamp as soon as the flats are done. The average life for those lamps is about 40hrs and, although the spares are not hard to come by, changing the bulb in the middle of the night will imply in substantial time lost!

The GCAL spare bulbs are in the Instrument Lab, in a cabinet located against the wall to the right of the door, at the back of the room. Remember to use the cloth gloves to manipulate the bulbs. To change any of the lamps, the telescope has to be taken to the zenith and the GCAL bottom cover unscrewed. The lamp positions are clearly identified (here is a picture).

Telluric standards:

The rule here is simple: the brightest, the better. My usual procedure has been to obtain the telluric standard after the target, matching in airmass, and using the list of bright OBA+early F stars provided at the NOAO Phoenix webpage. Select the appropriate sidereal time bin and choose a star that is off by ~0.1 airmass (higher or lower depending if the star is rising or setting) from the matching value (that will compensate for the acquisition overhead). There is an OTR library (GS-LIB-PHXCAL) that contains the subset of stars in that list that can be used (a few were doubles or had no good guide star). Select the appropriate star, copy the observation to the programme, then copy and paste the instrument configuration from the science target. Please do not queue directly from the LIB programme (this will leave an instrument configuration component there that the next observer will have to remove).

Some programmes may require a KIII spectrum for wavelength calibration (some spectral regions do not have enough atmosphere absorption lines to provide the calibration). A list of bright KIII stars is available at the telescope (in the Phoenix - a green paper - folder, in the shelf above chamaeleon).

Acquiring the target in the thermal IR:

The usual procedure is to position the star in the slit using the same filter as used for taking spectra. However, the Phoenix filters have different indices of refraction and are individually wedged to avoid fringing, so the telescope must be positioned slightly differently for different filters in order to get starlight through the slit. Another problem is that the slit position does not reproduce accurately. In the thermal IR, one often cannot see the target on a Phoenix image, because the background is too high, so the best procedure appears to be

put the target in the slit using a short wavelength filter (usually K4308)
change to the thermal IR filter and offset the telescope.

The offsets determined so far are (for cass rotator at 90deg; i.e., EW slit):

K4308 --> M2150: offset -0.10", -3.80" (0.10 W, 3.80 S)
K4308 --> M2030: offset -1.25", +3.40" (1.25 W, 3.40 N)
K4308 --> L3290: offset +0.9", -3.20" (0.9 E, 3.20 S)
K4308 --> L2734: offset -0.35", +2.78" (0.35 W, 2.78 N)

For arbitrary rotation angles, the offsets are

dra = x cos(theta-90) + y sin(theta-90)
ddec = -x sin(theta-90) + y cos(theta-90)

where theta is the Slit PA, and the x's and y's are as given above (i.e., -1.25 and +3.40 for K4308-->M2030)

To detect the object in the thermal IR image, one must use the neutral density filter (nd) in the cvf wheel, and one usually must take pairs of offset images and difference them. If the object is brigth enough in the optical, it is useful to mark the position on the TV monitor at which the starlight goes through the slit using a grease pencil. Remember that positions will be different for different filters. The observer can then move the telescope so that the (visible) object is at the marked location, and if desired touch up the position in the slit by examining pairs of subtracted images.

Another procedure, when the target is bright enough in L and M, is to use the Lyot central mask to cut the background. Set the lyot to position lyot16, configure the instrument to image the slit, measure the slit centre at column 128, then issue the zcenter command to define the fiducial position for that filter. After that, set the slit to open to directly image the field and use the recenter command to obtain the offsets to move the star into the slit position. Don't forget to set the viewer and lyot to the correct position once ready to start taking the spectra.

Image field and slit orientations:

The default Cass rotator position (shown in the TSD as IPA) is 90deg. At this position and Phoenix on port 4, the field orientations are as follows:

TV monitor	if using the old monitor flipped on its side, N is up and E to the right if using the new (white TV set) one, N is to the right and E is down
Phoenix image	N is up and E to the left
Phoenix spectrum	slit is E-W, E to the right Wavelength increases towards smaller pixels

The IPA (field orientation) is now set when the observation is selected from the queue. If other than 90degrees, don't forget to run zcenter with the appropriate parameters, otherwise the observing scripts will not work.

Grating setup procedure:

To set the grating positions, use the grat command in WildFire. The following syntaxes are equivalent:

*grat 2154.5 K 2000*	drives the grating to 2154.5 Kaysers (cm-1) with an offset of 2000 encoder units
same as above, but in microns
*grat -14567*	drives the grating to the encoder number (no offset given)

The encoder values are relative, and therefore may change between runs if the instrument is warmed up or if the mechanism is datumed by any other reason. However, using encoder units allow for a much more precise repositioning of the grating than the other two. Also, if the mechanism is datumed the difference between old and new encoder values should be a constant: find it for one setting and just add to the remaining.

2004Dec19: Bob Blum wrote a script which uses a fit to the encoder/wavenumber values obtained for the last three semesters of queue and that seems to work fairly well. It lives in the usual place in the Phoenix computer and can be run as

enc XXXX.X

where XXXX.X is the desired central wavenumber. The script will return the corresponding encoder number. There may be an offset to be added, which has to be checked on the sky, but will be valid to all subsequent grating positions.

Obtaining the grating setting for an observation can be tedious and is time consuming. Best strategy seems to be do it for as many settings as possible in the first night of a run or if the weather is too bad for anything else.

Acquire a bright star, center it on the slit as usual.
Set the grating to an approximate position using any of the first two forms of the grat command above. The offset value may change from run to run, but it is usually around +1400;nbsp; to +1800.
Obtain one spectrum, extract (see below) and plot. Frequency increases/wavelength decreases towards higher pixel values. Now compare your spectrum with the appropriate section in the Infrared Arcturus Atlas to determine the approximate central wavelength. The atlas contains both a K star spectrum and a spectrum of the transmission of the Earth's atmosphere (which is what is detected by looking at an A star).
Type status s. The current encoder position will be listed on the Instrument Status window.
Determine how many microns/wavenumbers you want to shift to get the correct wavelength centered on the array. The full spectral range corresponds to about 2000 encoder units. Increasing encoder units drives the grating to higher frequencies.
Don't forget to write down the final encoder value!
The grating can never be moved back to precisely the same spot. Always take flats before moving to a new grating position!

Quick look data reduction (in the Phoenix computer):

Start IRAF on the IRAF window that comes up automatically when login in.
Load twod and apextract
If the target is bright enough compared to the background, a single file may be used. In this case skip irdiff and go directly to apall. Otherwise you need a pair of offset observations.
epar irdiff

exten = 3
prefix = the root filename (e.g., if the files are data123, data124 and so on, prefix=data)
pic = the name of the difference file to be created. The default (junk9999) is good enough.

irdiff p1 p2, where p1 and p2 are the beginning and ending image index.
appal junk9999 - all questions probably are answerable as the default. This will create the 1D file (junk9999.ms) with the sky subtracted positive spectrum in junk9999.
splot junk9999.ms to examine the resulting spectrum.

Quick look data reduction (from the Guest account):

Start IRAF as described in the Observer Setup page.
display the first spectrum for the target and measure the approximate background value (just put the cursor somewhere away from the spectrum and/or atmospheric lines)
epar sntest2
the parameters are the root filename (eg, 2004dec19), the file numbers for a pair of spectra (eg, 181 and 182), the path for the files (the easiest way is to cd to the night's directory in the scratch disk), and the background level measured above. The size of the aperture for extraction can also be changed if needed.
the script will subtract the spectra one for the other, displaying the result (fl_display=yes); then extract the spectra interactively or not (fl_inter=yes). It calculates the signal by extracting the mean counts in the spectrum (it gets the mean and the stddev, then recalculates the mean excluding values at more than 3sigma - this eliminates the atmospheric lines); and gets the noise from the variance plane of the extracted spectrum (which is why it needs the background added back). The S/N computation uses the correct values for coadds, gain and read noise and tends to be quite accurate as long as there is a decent continuum to start with.
So, a typical command line would be:

sntest2 2004dec19 181 182 bglev=5. fl_inter-

A quick look script to evaluate the signal on flats is also available. Given a single flat, the script will return the mean counts and estimate the number of flats required to reach S/N=400. It will also warn if the counts are too low or too high. Just type

snflat 2004dec19_0103

End of the night procedures:

Phoenix:

To do all at once. Very important! Please don't forget
- end_of_night

This script will:
- Turn off the array electronics.
  - deactivate
- Protect the dewar window from dust and contamination
  - cover closed
- Physically shield the detector from light. A deactivated array remains sensitive to light (the resulting image is negative).
  - viewer dark
Database:
- Toggle off "Monitor" in mmon
- There is no need to exit the OT during a run (or to exit the Guest session), but I usually minimize all the windows to avoid any extraneous typing during the day.
GCAL:
- Double check if all lamps are off, and the shutter closed.
Troubleshooting: What to do if...

Gemini Observatory: Exploring The Universe From Both Hemispheres