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Special Instructions 2002A

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Special Instructions for Completion of Phase II/OT Science Programs: Semester 2002A

This page provides instructions for completing Phase II Science Programs  for the 2002A NIRI, GMOS and T-ReCS queues using the Observing Tool (OT) software. 

General instructions

Distribution of Phase II Skeletons

Gemini staff will translate approved Phase I proposals 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. 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 (the current OT release is the same as in 2001B so no need to do this again if you have it already), 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 for all queries, staff at the National Gemini Offices are the first point of contact. 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 NGO and, if they are unable to resolve the questions, it will be redirected to Gemini Observatory staff and your Contact Scientist.

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. 

The scheduled deadlines for return of your completed Science Programs depends on the Science Ranking Band (SRB) and instrument mode. (See the 2002A queue status page for an explanation of the SRBs). The deadlines are at 5:59pm HST on:

  • 22 January for Science Ranking Bands 1 and 2 (GMOS all modes and NIRI J-K f/6 imaging only) and GMOS MOS pre-imaging (all Bands).
  • 10 February for SRBs 1, 2 and 3 (including other NIRI modes).
  • 10 March for SRBs 1-4.

Note that only the observation descriptions received by these dates can be verified and made available for execution in the queue. Hence if you have a program in SRB1 with early RA targets, the earlier deadline you can make the better. 

These deadlines also apply to pre-imaging for GMOS MOS observations. The subsequent deadline for return of the MOS observation descriptions will be communicated to the PI by their Contact Scientist once the pre-imaging data are ready.

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 or binning cuts the time to 50sec. Fast readout is not recommended for observations of faint sources, as it gives significantly 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. The support staff from your National Gemini Office and your Contact Scientist will work with you if you have questions about how to calculate the overheads.

The current version of the OT cannot sequence GMOS. This means that if you want to observe one target in several instrument configuration, e.g. several filters, you will need to define one observation for each. If you want the observations to be taken the same night you need to group them together. This should only be done if either the science requires the observations to be taken together, of if the total time to take the observations is less than about 2 hours. You will save a bit of time on the overheads by doing this since the overhead for changing from one instrument configuration to the next is only 1-5 min (depending on the change).

Grating choices

Only the gratings R150, R400, B600, and R831 are available for science use at this time. (Additional gratings are included in the OT for test purposes).

Three of the gratings can be mounted in GMOS simultaneously. Grating changes will not be done during the night.

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 first deadline of the semester 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. PIs with MOS programs will be contacted by Gemini when the pre-imaging data is available and information will be given on deadlines for submission of mask designs and revised Phase II information.

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-2002A-Q-27 the mask names should be GN2002A-Q-27-1 and GN2002A-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. (Examples are available for download in the GMOS OT library).

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

IFU observations

IFU observations can be done either in "two-slit mode" or "one-slit mode". The change between the two modes is a manual process that involves taking the IFU out of the instrument. This will not be done during the night. The plan is to operate for blocks of time in either mode, and change between the modes only infrequently.

Instructions Specific to NIRI


Although significant progress has been made with NIRI commissioning, regular science observations will not begin until January 2002. Broad-band near-IR wide-field imaging projects are likely to be executed initially and the information currently available on the web pages is sufficient to prepare for those programs. Additional commissioning information will likely be needed to prepare for spectroscopic and thermal-IR observing programs. Additional information on these modes will not be available until after the first Phase II deadline in mid-January. We request that Phase II proposals be completed by the January 17 deadline only for wide-field imaging (f/6 J through K) programs in scientific ranking bands (SRBs) 1 and 2. The remaining programs in SRB 1 and 2 should ideally be prepared by the second deadline. We will be providing updates to the PIs based on the results of additional commissioning work as it becomes available.

System Verification Data

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.

Modification of the IRAF scripts, along with the addition of the spectroscopic tasks, is on-going.

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

The NIRI Aladdin array is continuous across the quadrant boundaries, but sometimes a mismatch in the background level is seen in exposures that are not background-dominated. It may be 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. This is usually not important in long exposures that are background limited, but can be for standard star observations (for example).

Filter availability

Please check to make sure that any narrow band filters you require have been installed in NIRI. All NIRI filters listed on the web pages as "arrived" (including methane filters) are now installed in the camera. No other filters are anticipated to be installed before the end of the semester.

Choice of Wavefront Sensors

Wide-field imaging with the f/6 camera requires the use of peripheral wavefront sensors for guiding. If your program uses the f/14 or f/32 cameras, the on-instrument wavefront sensor can be used. Construct your dither pattern and select the appropriate wavefront sensor guide stars to avoid vignetting, if possible. Please keep the following considerations in mind:

  • OIWFS can only be used with the f/14 or f/32 cameras. (The f/6 camera can be used with the f/14 beamsplitter at some loss of field of view to maintain the f/6 spectral coverage while using the OIWFS for guiding).
  • Since OIWFS provides tip-tilt guiding only, image quality with PWFS1 or PWFS2 may be just as good.
  • 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. Large offsets will probably not be possible using OIWFS, so it should also be "frozen" if the guide star leaves the available field of view.

Ensure that only one guide star and one wavefront sensor 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, filter, and slit have 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 with the normal slits. Please note that many of the slits are only 50 arcsec long, even though they are meant for use at f/6.

The f/14 beamsplitter can be used with the f/6 camera to allow for use of the OIWFS. In this mode the spectral coverage is that of the f/6 camera while the spatial coverage is limited to the f/14 field of view. As stated above, most of the slits are limited to 50 arcsec anyway, so there is no loss of spatial coverage using this mode for the shorter slits. The user can then choose either OIWFS or PWFS guide stars.

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 are subject to change.

Instructions Specific to T-ReCS

T-ReCS is due to be delivered to Gemini Observatory early in 2002. The current schedule has T-ReCS on-telescope commissioning in April/May and science use in June/July. If this schedule is held, PIs of T-ReCS queue programs will be contacted in ~April to prepare their Phase II programs using a new release of the Observing  Tool.

Last update January 6, 2002; Phil Puxley, Inger Jorgensen and Joe Jensen

Gemini Observatory Participants