--> Special Instructions 2001B | Gemini Observatory

Change page style: 

Special Instructions 2001B

You are here

Special Instructions for Completion of Phase II/OT Science Programs: Semester 2001B

This page provides instructions for completing Phase II Science Programs  for the 2001B NIRI and GMOS queues using the Observing Tool (OT) software. As 2001B is the first semester of queue and public OT use, certain aspects of the Phase II process differ from what is intended to be the normal routine. The instructions here take precedence!

General instructions

Distribution of Phase II Skeletons

Gemini staff will translate approved Phase I proposal into the Phase II format. In this process, the observations and other details entered in Phase I are used to construct a ("skeleton") framework of your Science Program. Due to the limited number of queue nights available, only PIs in the top two science ranking bands are being asked to complete their observation details at this time. PIs will be sent their the Phase II skeleton by e-mail.  

What to do Next

Read the introduction to the Observing Tool, download and install the software, look at the "getting started" information. Next, import your Phase II XML skeleton and define the observation details. There is extensive help regarding OT features on the web pages. 

If during detailed definition you find that the (ITAC- and Director-) approved observations need to be modified, please follow the change request process.

User Support

As this is the first public use of the Observing Tool, the Gemini staff are providing the first-point-of-contact support (and not, as is normal, the National Gemini Offices). To help us in the process of tracking user problems, questions and suggestions, and thereby improving the software and web pages, please continue to use the Gemini HelpDesk. Your query will be directed to your Contact Scientist and you are more likely to receive prompt attention! (It will also be copied to your National Office for training and information).

Deadlines and Mechanism for Return of Completed Science Programs

To return your completed Science Program, use the "export XML" file option and send by e-mail to your Contact Scientist. 

There are two scheduled deadlines for return of your completed Science Programs are:

  • 2 November at 5:59pm HST
  • 10 December at 5:59pm HST

Only those programs that have been received by these dates can be verified and made available for execution in the queue.

Verification and Confirmation of Observation Readiness

After receipt of your Science Program(s), your Contact Scientist will verify that all observation details have been completed correctly. You can help us and speed this process by checking the program yourself (see the OT/Phase II checklist). After verification, your Contact Scientist will confirm that the observations are in the queue (or need correction or further definition of details).

The Contact Scientist will verify each observation individually. It is not necessary for the entire Science Program to be verified before individual observations are released to the queue (for example, GMOS MOS observations cannot be put in the queue until after the pre-imaging).

Instructions Specific to GMOS


The current version of the OT assumes a setup time of 15 min for imaging and 30 min for all spectroscopic observations. Further, the overhead between each exposure is assumed to be 10sec. However, for unbinned slow readout of the full frame the real overhead is 2min. Fast readout cuts the time to 50sec, but gives higher readout noise.

Please take these overheads into account when you plan your observations i.e. add N*2min to your total time where N is the number of observations. Use the resulting number to assess whether your planned observations fit in the allocated time. Your Contact Scientist will work with you if you have questions about how to calculate the overheads.

Grating choices

Only the gratings R150, R400, and B600 are available for science use at this time. (Additional gratings are included in the OT for test purposes).

MOS observations

Programs that contain MOS observations need pre-imaging for all fields. The plan is to obtain the pre-imaging 3-4 weeks before the MOS observations. Thus, PIs with MOS programs are encouraged to meet the November deadline for submitting their programs.

MOS programs should contain the final Phase II information for the pre-imaging observations. The MOS observations should also be included in the program. However, small adjustments to the MOS observations are allowed when the mask design has been done.

The focal plane unit for the MOS observations should be specified as Custom Mask MDF, and the field for the name should contain your program ID and a running number for the mask within the program, e.g. for program GN-2001B-Q-27 the mask names should be GN-2001B-Q-27-1 and GN-2001B-Q-27-2 for the first and the 2nd mask, respectively.

The total time used for both pre-imaging and MOS observations must not exceed the allocated time.

It is recommended that pre-imaging observations are dithered by 5 arcsec in both directions, e.g. 4 exposures in a square pattern with size 5 arcsec will work ok.

Pre-imaging exposures should be taken in the broad band filter closest to the central wavelength coverage of the MOS observations.

Instructions Specific to NIRI


As you already know, significant progress was made recently with the NIRI flexure problems. We anticipate excellent performance when we begin observations again. NIRI has not yet passed all its acceptance tests, however, and there is still some uncertainty about when NIRI acceptance testing and commissioning will be complete. Queue observations will not begin until all systems are working together reliably and commissioning is complete.

Because of the uncertainty in when queue observations will start, we request that Phase II proposals be completed by the November 2 deadline only for wide-field imaging (f/6 J through K) programs in scientific ranking band (SRB) 1. The remaining programs in SRB 1 and 2 should be prepared by the second deadline, December 10. We will be providing updates to the PIs based on the results of additional commissioning work scheduled for November.

Data from the first System Verification programs executed in May have now been released, along with the first release of the NIRI IRAF imaging reduction scripts. You may wish to download some of the SV data and become familiar with the data structure and reduction scripts. For more information, please see the NIRI SV data page.

First Frame

The first exposure of a given sequence or dither pattern is usually badly affected by a pattern in the background due to changes in the detector readout mode or configuration. For this reason, please add an additional step at the beginning of each sequence (or repeat the first position at the end of the dither sequence). Short exposures that are not background limited (e.g., standard star measurements) are usually OK.

Quadrant Boundaries

It is a good idea to avoid placing your target directly on the boundaries between quadrants (center row and column). To avoid having the target fall on the boundaries, you can either offset the target coordinates slightly to place the target off-center, or you can construct the dither sequence to avoid positions with x=0 or y=0.

Filter availability

Please check to make sure that any narrow band filters you require have been installed in NIRI. All filters listed on the NIRI web pages as "arrived" (including methane filters) are now installed in the camera.

Choice of Wavefront Sensors

Construct your dither pattern and select peripheral wavefront sensor (PWFS) guide stars to avoid vignetting, if possible. Please keep the following considerations in mind:

  • PWFS1 will vignette slightly more than PWFS2, so if the only guide stars available are close to the science target, PWFS2 may be the better choice.
  • PWFS2 can work on fainter stars. If the star is fainter than V=13.5, choose PWFS2 instead of PWFS1.
  • PWFS1 can provide closed-loop active optics (aO) correction of the primary mirror, while PWFS2 is generally used only for tip-tilt and focus correction. You may get better image quality using PWFS1 if the guide star is brighter than V=13.5 mag.
  • PWFS guide stars are required for f/6 observations.

If the science target it extended and large offsets to empty sky fields are necessary, you have two choices. If the offset can be arranged so that the PWFS can follow to the new position, then you may guide at both positions. If the guide star leaves the field of view available to the PWFS, then you should set the status of the PWFS to "freeze". This will keep the PWFS at a fixed location relative to the science field and will allow rapid recovery of the guide star when returning to the science target. Note that if the science field is vignetted by the PWFS probe arm, the sky field will be as well.

Ensure that only one guide star and one WFS are specified for an observation. The ability to use multiple guide stars will be added in the future.

Thermal IR Observations

For thermal IR observations, please ensure that the f/14 camera is selected for L band and f/32 for M band. The OIWFS can be used for f/14 and f/32 observations.


For spectroscopic observations, confirm that the proper grism and slit has been selected. Note that the selection of grisms and slit sizes has been optimized for the f/6 camera. At f/6 you will probably get the best combination of spatial and spectral coverage. The "blue" slits should be selected if the spectral features being observed are near the blue end of the spectral window, which in some cases falls off the detector. Please note that many of the slits are only 50 arcsec long, even though they are meant for use at f/6.

Please remember that the spectroscopic and thermal-IR observing modes have not yet been commissioned and verified, and the instructions for use of these modes is subject to change.

Last update October 22, 2001; Phil Puxley, Inger Jorgensen and Joe Jensen

Gemini Observatory Participants