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GMOS OT Helpful Hints

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This page contains useful information for configuring GMOS observations which should help reduce the number of iterations on the Phase II file between the PI and the NGO. It also contains an overview of the required OT observations and components for programs of different types. Before submitting your Phase II program to Gemini, use the GMOS Phase II checklist to eliminate common mistakes. 

Contents


Templates

A detailed description of all features related to the use of the Observing Tool (OT) template observations is provided on the OT help pages.

Required OT observations and components

For each type of program, there are different requirements to which OT observations and components the user has to define in the Phase II. The table below gives an overview over the requirements. "Required" means that a Phase II will not be accepted without this type of observation or component being defined. "As needed" means that the user can add this type of observation or component as needed by the science goals of the program. Use the GMOS OT library as a source of template and example observations.

CuAr arcs mixed with the science data, i.e. taken at night, and any special standard stars are charged towards the program's allocated time. Baseline standard stars, GCAL flats, twilight flats, baseline CuAr arcs, and mask images are not charged. The time for the acquisition observations is already included in the science observation overhead. No additional time is charged. However, the acquisition observations have to be defined as separate observations in the Phase II.

Each "Observe" is given a Class (see more details about Classes).

The details of each of the required observations and components are explained in the sections below.

Observation or Component

Program Type Class
Imaging (details)
Pre-imaging for MOS
MOS (details) Longslit (details) IFU (details)
Science Obs. Required Required Required Required Science
Offset Comp. As needed As needed As needed As needed N/A
GCAL flats Do not add Required
Mix w/ science
Required
Mix w/ science
Required
Mix w/ science
Nighttime
Partner
Calibration
Twilight flats Do not add As needed
Separate observation
As needed
Separate observation
Required
Separate observation
Daytime
Calibration
CuAr arcs N/A Required
Baseline: Separate observation
Required
Baseline: Separate observation
Required
Baseline: Separate observation
Daytime
Calibration
Charged if mixed w/ science Charged if mixed w/ science Charged if mixed w/ science Nighttime
Program
Calibration
Acquisition Obs. N/A Required
Separate observation
Required
Separate observation
Required
Separate observation
Acquisition
If for baseline standard If for baseline standard If for baseline standard Acquisition
Calibration
Mask image N/A Required
Separate observation
N/A N/A Daytime
Calibration
Baseline standard stars Do not add Required
Separate observation
Required
Separate observation
Required
Separate observation
Nighttime
Partner
Calibration
Nod & Shuffle Darks N/A As needed (for
Nod & Shuffle only)
Separate observation
As needed (for
Nod & Shuffle only)
Separate observation
As needed (for
Nod & Shuffle only)
Separate observation
Daytime
Calibration
Special standard stars
Charged
As needed
Separate imaging observation
As needed
Separate longslit observation
Follow requirements for longslit
As needed
Separate longslit observation
Follow requirements for longslit
As needed
Separate IFU observation
Follow requirements for IFU
Nighttime
Program
Calibration

Calculation of overheads

Detailed information about overheads for acquisitions (and reacquisitions), as well as readout and configuration times can be found on the GMOS overheads page. PIs can now use the calculated planned execution times in the OT as reasonable approximations of the actual time that will be required, with the exception that reacquisitions must be included when integrations times are long. If you do not take this into consideration, it is likely that your Phase II will be overfull. Gemini queue observers will stop executing your program when the allocated time has been depleted, regardless of whether or not there are still unexecuted observations.

If your observation classes are set correctly, the OT will not add any planned time for GCAL flats, twilight flats, baseline CuAr arcs or other daytime calibrations (eg mask images or Nod & Shuffle Darks). The support staff from your National Gemini Office and/or your Gemini Support Scientist will work with you if you have questions about your OT calculated program execution time.

Grating choices

All of the gratings included in the OT are available for science use. Only three of the gratings can be mounted in GMOS simultaneously. Grating changes will not be done during the night.

Program Organization

It is recommended that groups be used as much as possible to keep the Phase II organized.  Some recommended organizational practices are:

  1. Group science observations with their associated acquisition observation(s).
  2. Organize all the time for long observations (more than 2 hours) into a single observation.
  3. If a standard observation must be taken before or after a science observation (e.g. a telluric standard) then place the observations for the standard in the same group as the science observations.
  4. Place all daytime calibrations in a folder called Baseline.
  5. Place time constraints (dates/times, temporal spacing of observations) within the new Scheduling Note and within the Timing Windows under Observing Constraints.
  6. Group names within a program should be unique.

Imaging observations

If full-frame readout is being used then an offset iterator should be used to define at least two offset positions separated by at least 10 arcseconds in p in order to fill in the chip gaps. The first offset position should always have p=0, q=0.

Twilight flats are baseline calibration and are handled by Gemini staff. Twilight or GCAL imaging flat observations should not be included in the Phase II.

Observations in the z'- or Y-bands are susceptible to fringing (GN fringing, GS fringing). Ideally,  fringe frames can be derived from the science observations. If this is not possible or the baseline calibration (taken a few times per year) is not sufficient then blank sky observations need to be defined.  The class should be 'Nighttime Program Calibration' and the time will be charged to the program. These observations should be like the science observations but the target component should be blank or removed. Gemini staff will add the appropriate blank sky field.
 

MOS observations

Programs that contain MOS observations require masks designed either from GMOS pre-imaging taken for all separate fields or from object catalogs. PIs with MOS programs are encouraged to submit designs as soon as possible, either early in the semester if designed from object catalogs or shortly after pre-imaging has been taken.

MOS programs should contain the final Phase II information for the pre-imaging observations when it is first submitted. The MOS observations should also be included in the program. Small adjustments to the MOS observations are allowed when the mask design has been done. However, the pointing and PA of your target cannot be changed between the pre-imaging and the MOS observations. PIs with MOS programs will be contacted by Gemini when the pre-imaging data is available. Revised Phase II MOS programs and mask designs should be submitted asap. See GMOS mask deadlines (linked from the relevant semester's OT instructions page) for Classical runs. Mask designs should be submitted directly through the OT, instructions will be sent to you when your pre-imaging is available.

PIs with pre-imaging from previous semesters should use the mask naming scheme (below) for their current program. Upload the original pre-imaging through the OT so that masks can be checked. Please also include a note listing the previous program number.

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-2010B-Q-27 the mask names should be GN2010BQ027-01 and GN2010BQ027-02 for the first and the 2nd mask, respectively. Note the leading zero on the program ID and mask numbers.

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 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.

GCAL flats should be mixed with your science MOS observations. The baseline GCAL flats include one flat for each hour of open-shutter time, though a minimum of two flats is always taken. Make sure you get flats for all spectral configurations. GCAL flats within these guidelines have class 'Nighttime Partner Calibration' and are not charged to the program. Any additional GCAL flats should have class 'Nighttime Program Calibration' and will be charged to the program. The smartGCAL flats will automatically determine the best exposure times for the instrument configuration. 

CuAr arcs taken during the day are baseline calibrations. These calibrations are not charged to the program, but the PI has to define them in the Phase II. Define these observations as separate from the science observations and set the class to 'Daytime Calibration'. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the CuAr arc, make sure to remove the guide star from the target component, remove any science exposures, and change the class. Arcs taken as part of a science MOS observations should have class 'Nighttime Program Calibration' and will be charged to the program. The smartGCAL arcs will automatically determine the best exposure times for the instrument configuration.

Mask images are taken of all MOS masks before they are used for science. These calibrations are not charged to the program, but the PI has to define them in the Phase II. Define these observations as separate from the science observations. By applying the OT templates, a mask image observation is automatically created for each target.  For a complete example see the GMOS OT Library.

Acquisition observations need to be defined for each MOS mask. No extra time is charged for these observations, as the overhead for setting up is already included in the science observation. However, the acquisition observations should be defined as separate observations in the Phase II. By applying the OT templates, an acquisition observation is automatically created for each target. The acquisition observation needs to have the same target, guide star, and PA as the science observation. Make sure that the exposure time (typically 30-90 sec) and filter match the setup required for the mask acqusition stars. Long-pass filters cannot be used for MOS acquisitions. Narrow band filters should in general not be used for MOS acquisitions.

The acquisition template "MOS: Acq starting with the mask in the beam" should only be used if the MOS mask was designed from pre-imaging obtained with the same GMOS instrument and using the same CCDs. MOS masks designed from other data (catalogs, pre-imaging using the previous GMOS CCDs, etc.) will need to be acquired using the "MOS: Acq starting with the mask out of the beam" template. The support staff from your National Gemini Office and/or your Gemini Support Scientist can provide further details regarding the use of the two different templates. See also the example in the GMOS OT Library.

Twilight flatfields are taken for each MOS mask if requested. No extra time is charged for these observations. However, the twilight flatfields should be defined as separate observations in the Phase II. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the twilight flatfield, make sure to remove the guide star from the target component, then edit the science exposures to have only one exposure with 30sec exposure time.  The class should be 'Daytime Calibration.'  If doing small wavelength dithers to fill in the chip gaps then only one wavelength setting will have a twilight flatfield taken, so you need to select the wavelength at which you want the twilight flatfield. If there are no twilight flats in the submitted Phase II for a MOS program, it will be assumed that they are not needed. See also the example in the GMOS OT Library.

Long-slit observations

GCAL flats should be mixed with your science observations. The baseline GCAL flats include one flat for each hour of open-shutter time, though a minimum of two flats is always taken. Make sure you get flats for all spectral configurations. GCAL flats within these guidelines have class 'Nighttime Partner Calibration' and are not charged to the program. Any additional GCAL flats should have class 'Nighttime Program Calibration' and will be charged to the program. The smartGCAL flats will automatically determine the best exposure times for the instrument configuration. 

CuAr arcs taken during the day as baseline calibrations. These calibrations are not charged to the program, but the PI has to define them in the Phase II. Define these observations as separate from the science observations and set the class to 'Daytime Calibration'. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the CuAr arc, make sure to remove the guide star from the target component, remove any science exposures, and change the class. Arcs taken as part of a science longslit observation should have class 'Nighttime Program Calibration' and will be charged to the program. The smartGCAL arcs will automatically determine the best exposure times for the instrument configuration. 

Acquisition observations need to be defined for each longslit target. No extra time is charged for these observations, as the overhead for setting up is already included in the science observation. However, the acquisition observations should be defined as separate observations in the Phase II. For Point Sources a ROI of Central Stamp (300x300 unbinned pixels) should be used to measure the slit center and to confirm if the science target is within the slit. For Extended Objects, Double Sources and Off-axis Sources a ROI of CCD2 should be used to measure the slit center and confirm if the object is within the slit. By applying the OT templates, an acquisition observation for each target will be automatically created. The acquisition observation needs to have the same target, guide star, and PA as the science observation. Make sure that the exposure time and filter match the setup required for the target. Long-pass filters cannot be used for longslit acquisitions. Narrow band filters should only be used if your target is an emission line source with no continuum. For a complete example see GMOS OT Library.

Twilight flatfields Twilight flats, which provide information about the slit function, are usually not taken for longslit programs, but can be provided if requested. No extra time is charged for these observations. However, the twilight flatfields should be defined as separate observations in the Phase II. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the twilight flatfield, make sure to remove the guide star from the target component, then edit the science exposures to have only one exposure with 30sec exposure time and class 'Daytime Calibration'. If doing small wavelength dithers to fill in the chip gaps then only one wavelength setting will have a twilight flatfield taken, so you need to select the wavelength at which you want the twilight flatfield. See also the example in the GMOS OT Library. If there are no twilight flats in the submitted Phase II for a longslit programs, it will be assumed that they are not needed.

IFU observations

IFU observations can be done either in "two-slit mode" or "one-slit mode". For GMOS observations in "one-slit mode" the "IFU Right slit (red)" must be chosen. (The Blue slit is not offered due to a larger number of broken fibers). 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. GMOS is used for blocks of time in either mode, and changes between the modes are done infrequently.

The OT visualization of the GMOS IFU shows the larger of the two IFU fields at the target position. Thus, if switching between fpu=none and the IFU, the user will see the OIWFS field patrol field move -- this is as expected, since the larger of the two IFU fields is approximately 30 arcsec from the center of the imaging field of view.

In one-slit mode the central wavelength you specify will be interpreted as the desired wavelength at the center of the detector array. In two-slit mode, the central wavelength you specify will be the wavelength at the location of the two pseudo-slits.

In two-slit mode you will have to use one of the color filters in order to avoid overlap between the spectra, see the grating/filter combinations page for details. In 1-slit mode you may have to use a filter to avoid 2nd order contamination.

GCAL flats should be mixed with your science observations. For IFU observations it is particularly important to take GCALflats frequently as flexure can impact the fiber tracing. The baseline GCAL flats include one flat for each hour of open-shutter time, though a minimum of two flats is always taken. Make sure you get flats for all spectral configurations. GCAL flats within these guidelines have class 'Nighttime Partner Calibration' and are not charged to the program. Any additional GCAL flats should have class 'Nighttime Program Calibration' and will be charged to the program. The smartGCAL flats will automatically determine the best exposure times for the instrument configuration. 

CuAr arcs taken during the day as baseline calibrations. These calibrations are not charged to the program, but the PI has to define them in the Phase II. Define these observations as separate from the science observations and set the class to 'Daytime Calibration'. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the CuAr arc, make sure to remove the guide star from the target component, remove any science exposures, and change the class. Arcs taken as part of of a science IFU observation should have class 'Nighttime Program Calibration' and will be charged to the program. As flexure can have a noticeable impact on IFU observations, it is recommended to include arcs in the science IFU observation, especially if the wavelength coverage does not include any sky lines. The smartGCAL arcs will automatically determine the best exposure times for the instrument configuration. 

Acquisition observations need to be defined for each IFU target. No extra time is charged for these observations, as the overhead for setting up is already included in the science observation. However, the acquisition observations should be defined as separate observations in the Phase II. By applying the OT templates, an acquisition observation for each target will be automatically created. The acquisition observation needs to have the same target, guide star, and PA as the science observation. Make sure that the exposure time (typically 2-5 min.) and filter match the setup required for the target. Longpass filters cannot be used for IFU acquisitions. Narrow band filters should only be used if your target is an emission line source with no continuum. See also the example in the GMOS OT Library.

Twilight flatfields are taken for IFU observations. No extra time is charged for these observations. However, the twilight flatfields should be defined as separate observations in the Phase II. Make sure the instrument configuration matches the science observation. If you copy the science observation in order to edit it for the twilight flatfield, make sure to remove the guide star from the target component, then edit the science exposures to have only one exposure with 90sec exposure time with class 'Daytime Calibration'. For small spectral dithers, twilight flats are typically only taken for one wavelength setting. See also the example in the GMOS OT Library.

Standard Stars

Imaging standards sufficient to obtain flux calibration at the 5% level are base calibrations and are taken by Gemini staff. If better calibration is needed then observations for additional standards must be included in the Phase II. The class should be 'Nighttime Program Calibration' and the time will be charged to the program.

Spectroscopic flux standards sufficient to determine the spectral response function, not absolute flux calibration, are baseline calibration and are not charged to the program. Observations for the baseline flux standard need to be defined in the Phase II. All MOS flux standards are taken in longslit mode (using the longslit closest in width to the width of the MOS slitlets in MOS mode). All standard star observations should have the observing conditions set to 'Any' and should have the target component deleted and the PA set to 'average parallactic'. The observer will fill in the target and align the PA to the parallactic angle when taking the standard. Baseline standard observations consist of the following components:

  1. Acquisition with class 'Acquisition Calibration': The longslit acquisition sequence for all standard stars (flux standard, velocity standards, etc) uses an ROI of Central Stamp (300x300 unbinned pixels) to image the field, measure the slit center, and to confirm if the target is within the slit. (For GMOS-N, the IFU acquisition sequence for standard stars includes a ROI of Central Stamp to image the field. For an IFU acquisition, the offsets from the center of the CCD2 to the IFU-1 and IFU-2 fields are well known by the telescope observers and do not need to be defined.) See the examples included in the GMOS OT Library.
  2. Spectroscopic observation with class 'Nighttime Partner Calibration': Please select an exposure time long enough to obtain good signal-to-noise (i.e., 120 seconds). The instrument configuration should match the science observations (using the longslit closest in width to the width of the MOS slitlets in MOS mode). For longslit and MOS programs, the spectroscopic observations should have the ROI defined as central spectrum. For MOS mode, if the grating is not the R150, then a GMOS sequence should be used to define three wavelength settings that will bracket the expected wavelengths of the MOS observations. The three recommended wavelength settings for each grating are shown in the table below. GCAL flats at each wavelength setting should be included. Examples can be found in the GMOS OT Library.

  3. Daytime arcs with class 'Daytime Calibration'.  All wavelength settings used by the nighttime observation should be included.  All other guidelines for daytime arcs apply.

Grating First Setting Second Setting Third Setting
R400  central wavelength - 150 nm  central wavelength  central wavelength + 150 nm
B/R600 central wavelength - 100 nm central wavelength central wavelength + 100 nm
R831 central wavelength - 80 nm central wavelength central wavelength + 80 nm
B1200 central wavelength - 30 nm central wavelength central wavelength + 30 nm

Recommended wavelength settings for standard star observations obtained for MOS programs

Additional spectroscopic standards --- absolute flux standards, velocity standards, line-strength standards,  telluric standards, etc.--- must also be defined. If absolute flux calibration is desired then the 5arcsec-wide longslit should be used and at least three wavelength settings should be used, as in the MOS spectral response calibration above, to cover the full wavelength ranges of most gratings.  Recommended settings are the same as the ones given in the table above.

The guidelines are the same as for normal longslit observations except that the classes for the on-sky observes should be 'Nighttime Program Calibration' and the time will be charged to the program. The associated acquisition observations should have class 'Acquisition' and any GCAL flats are still 'Nighttime Partner Calibration'. Daytime arcs are always 'Daytime Calibration' and are not charged. 

Observations that will be split over several nights

Some observations cannot be completed within one night and therefore will require multiple acquisitions. Exactly how such an observation will be split in several observations over several nights will normally be determined by the Gemini Staff at the time of scheduling the night's observations (see the overheads page for guidelines). The user should define such observations as one observation, and add a comment to explain which assumptions were made about the number of reacquisitions and the resulting overheads.

Observing conditions

The observing conditions are specified as percentiles in image quality, cloud cover, sky background (and water vapor). Refer to the observing conditions page for details about the meaning of these percentiles. If the percentiles do not give sufficient information to the queue observer about the observing conditions required for a given observation, the user should add a comment to the observation detailing the observing conditions, e.g. "Need fwhm better than 0.75 arcsec in r". Such comments cannot be used to request better observing conditions than approved by the time allocation process.

Baseline calibrations

GMOS Baseline calibrations that are not specifically mentioned above should not be included in the Phase II programs prepared by the users.


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