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MMIRS Observers Manual

Contributors: B. McLeod, J. Bechtold, W. Brown, M. Conroy, F. DiMille, M. Hastie, V. Suc, A. Szentgyorgyi, D. Osip, J. Roll, Y. Beletsky, I. Chilingarian

Last update June 2013

Table of Contents

  1. Introduction.
  2. Description of MMIRS.
  3. What's ~NEW 2013A.
  4. Observing Instructions.
    1. Before your run.
    2. The Computers in the Control Room.
    3. Quick Start Up Procedure.
    4. Detailed Start Up Procedure.
    5. Problem Solving.
    6. Taking data with mmice.
    7. Displaying an image.
    8. In The Afternoon.
    9. Start of the Night.
    10. Long Slit Observing.
    11. Multi-Slit Mask Observing.
    12. Telluric Standards.
      1. Selecting Telluric Standards.
      2. Acquiring Telluric Standards.

    13. Imaging.
    14. Dark Frames at the End of the Night.

  5. Automatic Data Logging.
  6. Data Storage.
  7. Filters.
  8. General Comments and Information.
    1. Typical Count Levels.

  9. Problems.
  10. Data Reduction for MMIRS.
  11. Appendices.
    1. APPENDIX A: The Exposure Time Calculator, or ETC.
    2. APPENDIX B: How to plot the detector and guider footprint on an image in ds9.
    3. APPENDIX C: How to list guide stars available for your target.
    4. APPENDIX D: How to set up catalog files.

  1. Introduction.

    MMT and Magellan InfraRed Spectrograph (MMIRS) is a near infrared (NIR) imager and multi-object spectrograph with a 6.9'x 6.9' imaging field-of-view. The focal plane is a 2048x2048 pixel Hawaii2 detector with 18 micron pixels which subtend 0.2 arcsec on a F/5, 6.5m telescope. The instrument offers imaging, long-slit spectroscopy through a variety of slit widths, and multi-object spectroscopy over a 4' x 6.9' field of view. Grisms supporting spectroscopy at R=2400 and R=1200 are available. The dual guide-probe/wavefront sensor enables continuously updated wavefront sensing. The major subsystems of MMIRS are shown in Figure 1.

    Figure 1 Cut-away CAD drawing of the MMIRS cryotstat components. Major features not shown are the gatevalve and the mask section LN2 tank.

    The PI of the MMIRS program is Brian McLeod, CfA. He may be contacted at bmcleod@cfa.harvard.edu. The design, contruction and integration at the MMT and Magellan was the work of CfA scientists and engineers, especially from the SAO Central Engineering Department. MMIRS was constructed with funding from the National Science Foundation, Harvard College Observatory and the Smithsonian Astrophysical Observatory.

    Web pages with complementary information about MMIRS are:

    http://www.cfa.harvard.edu/mmti/mmirs.html Top level page

    http://www.cfa.harvard.edu/mmti/mmirs/instrstats.html This page contains a description of the available filters and grisms.

    See also McLeod, et al. (2012) MMT and Magellan Infrared Spectrograph, PASP, 124, 1318, d/PASP_MMIRS_2012.pdf Please cite this paper when publishing your MMIRS results.

    MMIRS has been operated at both the MMT and the Clay (Magellan 2) Telescope at Las Campanas. It is currently available at Magellan.

  2. Description of MMIRS.

    MMIRS is a near infrared (NIR) spectrograph and imager that has a passband that extends from Y to K band (0.9-2.4 microns). The science detector is a Teledyne Hawaii2, 2k x 2k, 18 micron pixel HgCdTe detector. The detector has four quadrants and each quadrant is read out through 8 channels. The full well is 230,000 e- & the gain is 5 e-/ADU (full well is 46,000 ADU). Detector response starts to become non-linear above approximately 40,000 ADU. The array is read out by a controller designed at CfA, based on a scalable architecture used in all CfA F/5 instrumentation at Magellan & the MMT.

    The various modes and functions of MMIRS are selected with a combination of five independent wheels - the Dekker (aperture selection) wheel, the slit/slit mask wheel, two filter wheels, and the grism wheel (see Figure 1.). The MMIRS mask wheel has a combination of 9 slots for custom masks, 7 fixed long slits and 1 imaging aperture. The grism wheel can hold up to 5 grisms with one clear slot for imaging. At this time there are three grisms: H+K @ R=1200, J @ R=2400 and H @ R=2400. This spectral resolution is achieved with a 0.4" slit. The available long slits are 1, 2, 3, 4, 6, 8 and 12 pixels in width (each pixel is 0.2") - See Figure 2. The filter wheels can hold up to 10 filters with one clear slot for imaging. The initial complement of filters are Y, J, H & Ks plus blocking filters of 1.25-2.5 microns and 0.95-1.5 microns.

    Figure 2 The MMIRS Mask Wheel

    MMIRS has two guide/wavefront sensing (GWFS) units. Typically one unit is used for standard guiding while the other probe does continuous WFS and provides guide information for rotator guiding. There is no slit viewing camera.

    The MMIRS cryostat is divided into two chambers - the slit mask (MOS) section and the camera section. The two dewar sections are separated by a gate valve. When the masks need to be changed out the gate valve is closed and the mask dewar is warmed up to room temperature using internal heaters The change over of slit masks will be completed by Observatory staff during the day and the MOS dewar will be returned to operating temperature before sunset. The gatevalve is operated by the Observatory staff. The second dewar, the camera dewar, remains at operating temperature through out the whole MMIRS run. Both dewars are cooled by LN2. The MOS dewar has a hold time of 36 hours when a MOS mask change is not done during the day and the camera dewar has a hold time of 48 hours. Observatory staff are responsible for keeping the dewars filled with LN2 - if you detect any change in operating temperature please inform the Observatory staff.

    The salient features of MMIRS are tabulated in Table 1.

    Detector TypeTeledyne Hawaii2 HgCdTe
    Pixels2048 x 2048
    Pixel Size18 microns
    Field-of-View (imaging)6.8 x 6.8 arcmin
    Field-of-View (spec)4 x 6.8 arcmin
    Plate Scale at slit0.169 mm/arcsec
    Pixel Scale0.2 arcsec/pixel
    Readout Time0.7s for a single read
    Minimum Exposure time1s (must increase in integer seconds)
    Typical overhead per exposure7-17s (depending on size of file, dither size)
    Typical spectroscopic overheads 5-10 min for acquisition and mask alignment
    5 min for calibration frames (comps + flats)
    5-10 min for telluric setup and data taking
    Digitization 16 bit (65,536 ADU)
    Gain 5 e-/ADU
    Readnoise 16 e- per read
    Median Detector QEJ:69%, H:79%, K:73%
    Median Dark current0.06e-/pix/sec
    Full well ~230,000 e- (46,000 ADU) (non-linear above 40,000ADU)
    Fits File Sizeapprox 16804800 bytes per readout
    Imaging FiltersY, J, H, Ks
    Spectroscopic FiltersHK, zJ
    Grisms availableR=1200@HK, R=2400@H, R=2400@J
    Calibration lampsDim Incand, Bright Incand, Argon
    Table 1.

    The Hawaii2 science array is a HgCdTe device with 18 micron pixels and sensitive from 0.9 - 2.4microns. The detector is read out in 4 quadrants, 8 channels per quadrant. An SAO-built controller is used to read out the array in a time of 0.7 seconds. Digitization is done with a 16 bit ADC, so data values up to 65,536 are recorded. Non-linearity sets in above ~40,000 ADU. The median dark current is 0.06e-/pix/sec.

    There are two identical guide and wavefront sensing (GFWS) units mounted at the side of the instrument, external to the cryostat, which are fed by a fixed pick off mirror which surrounds the science beam. The field of the GWFS is shown in Figure 3. Each of the GWFS units is mounted on a 2-axis translation stage to allow it to probe one half of the available field and the cameras can be focussed individually. A stage allows switching between guiding and Shack-Hartmann mode; normal operation will have one of the units operating in guiding mode while the other is deriving continuous wavefront information. Slow-speed guiding information can also be derived from the Shack-Hartmann data which can be used to control the instrument rotation angle. In practice we have found it not to be necessary and is not part of the default operation. The guider optics operate from 600nm to 900nm as MMIRS will primarily be a bright-time instrument. The field of view of the guide camera is 80" with a pixel size of 0.16" (binned x2).

    Figure 3 MMIRS field of view and coordinate systems. Full resolution PDF: p/mmirs_coordinate_axes.pdf

    The origin of the instrument coordinate systems corresponds to pixel (1025,1037) on the science array. The center of the telescope rotator may differ from this instrument center by several arcseconds. The telescope rotation center will be determined at the start of each observing run by observatory personnel. When acquiring a new target, the telescope will first be pointed to place the target at the rotation center, and then offset to the instrument center.

    A schematic representation of the status of all the instrument mechanisms can be seen in the toppermmirs display.

    Figure 4 The toppermmirs display, showing the current status of the instrument. In this example the gatevalve is closed, as it would be during a slit mask exchange. The LEDs are used for calibrating the wavefront sensor and should normally be off, as they are shown here. Full resolution: p/toppermmirs.jpg

  3. What's ~NEW 2013A.

    1. 4-amplifier readout mode

      Prior to 2012B MMIRS has always been readout in 32-amp mode to achieve the fastest readout time (< 1 second). But at least 1 amplifier exhibits intermittent readout problems. MMIRS now supports a 4-amp readout mode that bypasses the problem amplifier - but also increases readout time to just under 7 seconds. See notes below about choosing the amp mode, appropriate exposure times and tables

    2. Improved box fitting within alignbox is now fully functional giving improved mask fitting performance and residuals

      The fitting algorithms underlying the alignbox application have been improved as follows:

      1. Hot pixels are clipped to 5 sigma of their 8 immediate neighbors
      2. New algorithm to determine the "top" level within slit or alignment box
      3. Dark subtraction done using a median filtered 10 second dark from the library.
      4. Initial mask measurement improved to reduce slit-to-slit interference in measurement
      5. Long slit angle fitting is more robust by rejecting boxes which fail to measure before computing rotation.

    3. Updated alignbox interface and fitting

      1. mask alignment - added a new status line labeled "slit positions for telluric" showing the number of slits that were fit successfully vs. the number of slits in the mask design. Failure to fit at least 90% will cause this status to be yellow.

    4. Clarification of Telluric Procedure

      1. Also, the Telescope telluric software procedure has been updated and allows telluric acquisition with either camera (whichever camera is acting as the guider). It allows the telescope to acquire the telluric using the guide camera, and then automatically moves the telluric back onto the science camera. Telluric exposures can then be acquired in the mask slits automatically using the telluric (mask) dither catalog.

  4. Observing Instructions.

    1. Before your run.

      1. Read this manual.
      2. Read the other documents on the main MMIRS page [1]
      3. Run the Exposure Time Calculator (ETC) if you need to (Appendix A).
      4. Prepare your target catalog in the correct format:

        For multi-slit mask users, a catalog will be automatically made for your mask targets and should be available on the operators computer once your masks have been loaded. For long slit users, you will need to specify a ROTATOR OFFSET angle in your Magellan format catalog. This angle should be your desired slit position angle times -1. For example for a slit aligned 20 degrees east of north, you would specify offset=-20. The rotator offset mode should be "OFF".

        At Magellan you can place catalogs in your assigned observer account on the two observer workstations (Guanaco or Zorro) and the telescope operator can then copy it to the Operator computer (Vicuna)

      5. Figure out how you will take home your data (see below for your options).
      6. If you are observing a multi-object spectroscopy program, follow the instructions in MMIRS Mask Making
      7. Set up dither files or other scripts. The observing sequence can be automated very easily, and you can set up scripts to dither the telescope, run through the filters at a standard star field, etc. automatically. See instructions on setting up dither files, Appendix D.

    2. The Computers in the Control Room.

      1. Magellan Computers

        The 3 MMIRS instrument computers are shack, wild, and hurley, but their consoles are located in the computer room. The observer will sit in front of the Magellan Mac computer guanaco and operate the instrument from the MMIRS computer wild from there. Data reduction can be carried out from the Magellan Mac zorro, by logging into shack or accessing the data directly on the cross-mounted disk at /Volumes/CRUNCH_MMIRS/. The hurley computer is dedicated to data acquisition and is not directly accessed by observers.

    3. Quick Start Up Procedure.

      1. Magellan Quick Start

        1. Log on to guanaco and zorro using the login and password listed on the posted Observer Setup Form.
        2. On BOTH guanaco and zorro, open a terminal or xterm and type


        3. On guanaco in any terminal, type


        This will start the mmice interface.

        • Click on the Quick Start tab.
        • Click on "Quick PowerAll". Wait for the button to turn green, indicating that all devices have been powered up.
        • Click on "Quick ServAll". Wait for all the server indicator lights in the top panel to turn green. ( Note: TELSCOPE may remain red, as this server is tarted by the telescope operator.)
        • Click on "Quick HomeAll". Wait for all the Homed indicator light in the top panel to turn green.
        • If any indicators are red go to the Problem Solving section below.

        Figure 5 MMice Quick Start tab.

    4. Detailed Start Up Procedure.

      A more deliberate startup sequence can be performed from the StartUp tab if QuickStart is unsuccessful. In general, this should only be necessary at the beginning of the run or after a power shutdown.

      Figure 6 MMice startup tab. Full size image: p/mmice-Startup.jpg

      On the mmice GUI in the Startup tab, press each of the following buttons and wait for the button to turn green.

      1. Power Up Racks This starts the Pulizzi servers which control all the power, and powers up all the devices:

      2. Start Thermal Vac Systems

      3. Start Instrument Motion Control Systems

      4. Home Dewar Stages Establishes the reference position for all the mechanisms inside the cryostat.

      5. Start Science Camera Software

      6. Start WFS/Guider Software

      7. Home WFS/Guider Stages

      8. Start Calibration Lamp Control Software

        Press Start Up MMIRS and the server status lights should turn green, as should the power status lights and all the device homed lights.

      When the Startup initializations have been completed, the ideal configuration for the mmice window is for all the boxes on the startup tab to be colored green. There may be some cases when some parts of the system will need to be restarted during the course of the run. Go to the "Problem Solving" section to see how to debug if any of the status indicators are red.

      In addition to mmice the following GUIs are used when observing with mmirs. They may be started or restarted from the Start/Stop page of mmice.

      1. toppermmirs - displays the status of the instrument mechanisms.
      2. alignbox - tool for aligning longslits and masks
      3. comment - allows the observer to add comments to the exposure log
      4. paddle - allows the observer to offset the telescope.
      5. expdisplay - displays the status of the observation, including the status of guiding

      To log into shack or wild, type mmirsshack or mmirswild in any terminal on the observer workstations.

    5. Problem Solving.

      The directions which follow indicate how to deal with servers & devices which do not start cleanly during a instrument setup. If any of the status indicator boxes on the Startup tab are red (failed) or yellow (hung) this is the first place to start.

      1. Server status. Go to the 'start/stop' tab. Check the 'Restart' radio button at the top right hand side of the tab. Locate the individual server which is red and click on that button to restart the server. If it does not turn green after a couple of attempts there could be a more serious problem. Pressing the "Log" button will show any error messages that arose when trying to start the server. Call for assistance if the problem persists. It is also possible from this page to individually kill or restart any of the GUIs (including mmice itself). This page cannot determine if a GUI is already running, but restarting a GUI generally does no harm with a single exception: if mmice is restarted during an exposure, the exposure will be lost.

      2. Power status. If any of these status indicators are red, try pushing that indicator. you may need to wait 30 sec for confirmation that the power is on. If power has failed to any of the devices said device will also be showing 'failed' homing.

      3. Homing status. If any device does not home successfully or needs to be re-homed during the night go to the Startup tab. Here each of the individual devices can be home independently. Locate the desired device and click on the button. If it does not home after a couple of attempts call for assistance.

      4. Telescope: Telescope operator needs to restart telserver

      5. ESTOP: Is the emergency stop button pushed? The Estop button is located on the instrument next to the mask exchange port. Ask a member of the staff to verify that the ESTOP has been released.

      6. Instrument Interlock: The rack doors must be closed and latched for the telescope to move. Verify (or ask a member of the staff to verify) that all rack doors are shut properly. The error indicator for this appears on the telescope operator's displays -- not on the MMIRS display.

      Figure 7 Mice Start/Stop tab. Full size image: p/mmice-StartStop.jpg

    6. Taking data with mmice.

      Data taking is done through the Config and ObserveOps tabs in mmice . The Config tab is used to set up the instrument as needed. The ObserveOps tab allows for traditional observing (one image at a time) or for performing sequences of exposures allowing for efficient observing. The sequences are defined by an ascii catalog file which can be generated with a text editor or by using the DitherTool tab of mmice . Details on how to make catalog files, with examples, are given in Appendix D.

      1. Check that all the subsystems are happy.

        In the previous section you should have gotten all the subsystems initialized. The status of each subsystem is indicated with color using the color convention of all the f/5 instruments; green means OK or RUNNING, yellow means HUNG (perhaps only temporarily), and red means NOT RUNNING. If any items are not green, go back to the Startup Procedures.

        The middle section (just above the tabs) is mostly informational. The first line displays the detector and MOS dewar temperatures. The detector temperature should be 78.00 and the MOS temperature should be 77K. The second line shows the status of the calibration lamps. The rest of the lines in this section display exposure status information including image type, exposure time, and exposure status, sequence, queue status, instrument configuration and telescope offsets.

        Figure 8 MMice status panel. Full size image: p/mmice-Status.jpg In this example we see that three servers are not running and two are hung. The recommended action would be to go to the Stop/Start page and restart them. Note that the telescope server will be started by the telescope operator at the beginning of the night.

      2. Next you'll go to the Config tab in mmice:

        Figure 9 MMice Config tab. Full size image: p/mmice-Config.jpg

      3. Check that TELNAME, INSTRNAME AND DETNAME are set correctly
              INSTRNAME = mmirs
              DETNAME = mmirs
        IMPORTANT: For Science observations, make sure none of these indicates Test . For calibrations during the day where the telescope is not to be commanded, set TELNAME to 'test'. INSTRNAME should only be set to 'test' if you do not wish to move MMIRS devices.

      4. Select the correct PI and Observing Program.

        The program number information is important to enter correctly in order to be able straight-forwardly retrieve data from SAO later on. If your observing program is not in the list, contact the MMIRS instrument specialist, who will get in contact with Maureen Conroy. If you switch programs during the night, don't forget to update the Observing Program and PI.

      5. Type your name(s) into the OBSRVRS box.

      6. Next you'll go to the ObserveOps tab which allows you to take images one at a time or a sequence.

        Figure 10 MMice ObserveOps tab. Full size image: p/mmice-ObserveOps.jpg

        1. Manual/Catalog

          Manual means that all exposure parameters are directly set on this tab (although some software overrides may occur i.e. ObsType object will remove pickoff mirror). Catalog allows you to choose a catalog file that lists some or all of the parameters of a sequence of exposures. For example, you could have a list of dither positions to be observed in sequence. A full description of creating catalogs is provided in Appendix D. The file can be chosen by clicking on Menu.

        2. NAMPS

          Until the start of the 2012B MMIRS run, the MMIRS detector was always operated in the 32-amp mode giving the fastest readouts (less the 1 second). However, there have been persistent instabilities in one of the amplifiers. So to avoid this issue a new 4-amp readout mode as been added which doesn't use the problem amplifier. The trade-off is that the readout time is just under 7 seconds in 4-amp mode.

          Select the amplifier mode you wish to use:

          • 32-amp - the original default for 1 second readouts
          • 4-amp - new mode with 7 second readout

        3. ObsType

          Select the type of exposure from the following list:

          Table 2 MMIRS image types.

          objectA normal image containing an observing target. The file is named using the object name from the telescope catalog.
          setupLike object, but names the file "setup"
          skyflatA dark or twilight sky flat field image.
          compA comparison lamp Argon image.
          flat A continuum lamp image. The bright lamp is used for spectroscopic exposures, the dim lamp for imaging.
          darkA dark image.

        4. Exptime

          Exposure time in seconds. Must be an integer number of seconds.

        5. Slit/Mask

          Select which mask or long slit you want, or "Open" for imaging.

        6. Filter

          Select which filter you want.

        7. Grism

          Select which grism you want, or "Open" for imaging.

        8. ReadTab

          Unlike CCDs, infrared detectors can be read out without destroying the image already stored. This has three key advantages. 1) By reading out multiple times, the detector read noise can be averaged down. 2) By reading multiple time during the course of the exposure, pixels can be used even if they are saturated by the end of the exposure. 3) Cosmic rays can be identified by looking for discontinuities in the signal level of each pixel versus time. The 'ReadTab' button is used to select the readout mode for the IR detector. The recommended modes are ramp_1sec, and ramp_5sec, and fowler. The first two read out the detector once every 1 or 5 seconds. The data will be stored as a multi-extension FITS file with one readout per extension. The post processing script will display the different of the last readout minus the first readout. If you select Fowler, or click on Cancel, you will get a simple double correlated image saved as a standard FITS file. This mode can be used for setup exposures.

        9. Azoff/Eloff

          Allows for manual telescope Az & El instrument offsets to be set (e.g. for dither steps)

        10. GuideWait

          This drop down box allows the user to choose one of several guiding modes. It controls how mmice interacts with the guider, but does not control whether guiding is turned on -- that is controlled from the telescope operator's "guistarsmmirs" panel.

          Here is a description of these modes:

          • none : In this mode, the data acquisition process will continue independently of what the guider is doing. Dither commands will be sent directly to the telescope and the guider will not follow the telescope dither offsets. The data acquisition will not attempt to wait until the guider reports that it is locked on the stars. This should be used if you are doing calibrations or imaging programs without autoguiding.

          • autoguide : In this mode, the guide camera will dither with the telescope offsets and attempt to maintain the lock on the guider star. This should work fine in spectroscopic mode when the dithers are small. The telescope operator controls whether the dithers are handled by moving the guidebox on the guide camera or by moving the entire guide camera stage. For dithers less than 5 arcsec, box mode is recommended. For larger offsets, stage mode is recommended. In imaging mode it is more difficult to find a guide star that will remain in the guider field of view during the larger image offsets. When running in autoguide mode -mmice~ will also query the guider as to whether it has locked onto the guide stars at the start of each exposure. Data acquisition will begin only after the guider is locked on the stars. This is currently the only option for guiding.

          The Guiding row in the Exposure Status window will show YES or NO during "object" exposure, depending on whether the guide corrections are being sent. Flickers of a few seconds are common, but if the NO state persists it would be wise to consult with the telescope operator to verify that all is working well.

          • wfsonly : In this mode, coordinated offsets are sent to the guider and telescope (as in autoguide mode), but mmice does not wait for the guider to report that it has locked. This mode is useful when carrying out imaging programs with short exposure times where the overhead of guiding is not desired, with dithers small enough so that a single wavefront sensor star remains available.

          • autopick : THIS MODE IS NOT CURRENTLY AVAILABLE In this mode, offsets are sent directly to the telescope. The "guistarsmmirs" program is placed in "Auto" mode and watches the telescope position and automatically moves the guider to follow the current guide star or picks a new one if the old one is nolonger available. This mode is used in imaging programs when the dithers are too large to follow a single guide star. This mode works the same way that Megacam uses.

        11. Fileroot:

          Default has it set as object name from catalogue through the telstat or set by exposure type being done.

        12. Title By default mmice automatically queries the user for the title when the observer presses Go with a pop up window. This title goes into the data log and can be more descriptive than the fileroot. If the Prompt button is unchecked then no popup will appear and the user should enter the title in the entry box before pressing Go.

      7. Take an image by pressing Go . The number of images taken is controlled by first and last. If you are using a dither catalog, these numbers refer to the lines in the catalog.

        The Clear button is used to clear the camera in the event of an error. If the Go button remains red because of an error during observing the user must press Clear to reset the system.

        Pause. Abort, Resume.

        The bottom 2 lines of the "ObserveOps" tab allow the user to "PAUSE" an exposure or to pause the QUEUE of exposures. "Pause Expo" enables the options: ABORT, STOP, RESUME, or CHANGE the exposure time. ABORT will discard the current exposure, whereas STOP will read out the camera for the current truncated exposure time. Pause QUEUE has no effect on the current exposure, but it allows you to alter the automated exposure sequence, usually by changing the "last" requested exposure. Because MMIRS has no shutter, it is not possible to actually pause and resume an exposure as one would with a camera with a shutter.

      8. Where's my data and what are the files called?

        The raw images are stored on a 1.5 Tb disk on hurley, in multi-extension FITS format. A copy of each file is automatically made available for immediate analysis on red. The analysis directories are called /data/crunch/MMIRS/yyyy.mmdd (e.g., /data/crunch/MMIRS/2009.1014). The files themselves will have names like target.0001.fits, where target is the catalog name supplied to the telescope. The /data/crunch/MMIRS disk from shack is also NFS mounted on the observer workstations as /Volumes/CRUNCH_MMIRS/. Since the instrument is operated from the observer workstation guanaco connected to the instrument computer wild, it is recommended that you do any additional data analysis from the observer workstation zorro; either directly using the cross-mounted /Volumes/CRUNCH_MMIRS/ or by logging into red.

    7. Displaying an image.

      After an exposure is finished, the postproc server will receive the incoming image and display it in ds9mmirs Frame1 on the console. It will also display the difference of the current image and the previous one in Frame2. The usual iraf programs such as imexamine will still work. In fact you can have imexamine running continuously as new images come in and they will be properly accessed. Note: the appropriate IRAF analysis window running remotely from Wild should be started from any terminal on Guanaco with the command mmirsiraf.

      The ds9mmirs window is intended to be dedicated to the near-realtime display. To look at previous images, we highly recommend working on shack and starting a local ds9 or running ds9 directly on zorro. To view previously displayed images, load them into ds9 using the File menu --> Open

    8. In The Afternoon.

      As soon as the instrument specialist has completed the slit mask exchange procedure, take a test exposure to verify that the instrument is working properly.

      • Go to the ObserveOps tab
      • Select exposure type dark
      • Select filter dark
      • Click on ReadTab and then click on Cancel. This will give you a basic double correlated sampled image.
      • Enter 1 for first and 3 for last
      • Press Go


      • In the Analysis IRAF window take the difference of the 2nd and 3rd images and compute statistics
         cd /data/crunch/MMIRS/YYYY.MMDD
         imarith dark.MMMM.fits - dark.NNNN.fits diff.MMMM.fits
         imstat diff.MMMM.fits nclip=2 lsigma=3 usigma=3

      The mean should be near zero. The stddev should be near 4.

    9. Start of the Night.

      • For Imaging programs, flats can be taken during twilight at the beginning (and end) of the night prior to the acquisition of any stars.

      • For initial pointing at the start of the night, ask the telescope operator to point to a 13th mag star near your first target.
      • In mmice, select the setup.cat dither file, and take two 5 sec exposures, the first offset by 30 arcsec from the nominal position. Note that in twilight conditions you may need to take a 1 sec exposure to avoid saturation.
      • Press "Draw Regions" in the paddlemmirs GUI.
      • Move the green "Star" region to the image of the star near the center of the frame. If you are unclear about which star is which, select in ds9 Analysis->Catalogs->Infrared->2MASS. Note that when the sky is still bright, the detector may saturate and you can end up with the star images being negative. The on-target stars will appear 150 pixels to the left of the offset position.
      • Press "Fix Pointing".
      • This will have moved the target to the center of rotation. You can now proceed with your first science target.
      • If you must check and confirm the position of the star, do the following:
      • Press "Reload" for the setup catalog.
      • Then press "Go" in mmice again. If the star is centered on the "rot" marker, you can move onto science target, otherwise do another iteration of centering the "Star" region and "Fix Pointing" followed by another CSET by the Telescope Operator.
      • Ask the telescope operator to slew to your first target and run Shack-Hartmann (wavefront sensing).

    10. Long Slit Observing.

      There are no slit viewing optics in mmirs so to get your target on the slit you must take images with the infrared detector to position your target in the correct place. You will use both mmice and alignbox to accomplish this.

      Ask the Telescope Operator to slew to your target from the observing catalog (and to offset to instrument center per normal operations)

      In the mmicemmirs window, tab ObserveOps, select the following:

      • Select Catalog button
      • Press "Menu" and select a dither catalog from the LongSlit submenu. Note that the offsets are applied in the "instrument" coordinate system so that the same offsets work no matter what position angle you are using.
      • NAMPS = 4 (or 32-amps for fast readout)
      • ObsType = object
      • Exptime = 300 (for typical exposures)
      • Slit/Mask = your choice of slit
      • Filter = your choice of filter
      • Grism = your choice of grism
      • ReadTab = ramp_7sec (required for 4-amp mode) or ramp_?sec for 32-amp mode
      • GuideWait = autoguide

      Figure 11 Longslit alignment tool. Full resolution image: p/alignbox-LongSlit.jpg

      In alignboxmmirs:

      • Select the LongSlit tab
      • Press "Start" to retrieve the configuration parameters from mmicemmirs
      • Press "Set LongSlit Dither" to select the dither catalog that you will use for your science target
      • Press "Offset to Slit" to move the telescope to the nominal slit position
      • Ask the telescope operator to ensure that "AUTO" is not selected on the guide setup interface.
      • Ask the telescope operator to start guiding.
      • ALWAYS WAIT until the gui shows a green "Guiding ON" and "Locked" status before proceeding with taking images In poor seeing or windy conditions the "Locked" status can be "twitchy" so you may have to settle for less than perfect locking.
      • NB: Be sure you have selected your dither catalog before aligning the slit. The dither catalogs will be correctly adjusted based on the alignment values.
      • press "Take Alignment Image". Three exposures will be taken, differenced, and displayed in ds9. The left panel shows the difference of the field minus an offset image. The right panel shows an image of the slit (minus the field). The software measures the location of the slit and the nearest object it can find and places markers on these positions in ds9mmirs.
      • If the "star" marker is not well centered on your target, carefully center the marker on the target (you may want to resize the circle by draging one corner)
      • Click on "Move to Slit" in alignboxmmirs.
      • This acquisition process can be repeated to improve the centering of the object in the slit by pressing "Take Alignment Image"
      • For all dithering, the default parameters that the Telescope operator selects should be Guider TweakType=Stage.
      • Notes:
        • Your guide stars should be selected carefully to allow for large range of stage motions. If proplems occur with long dithers, it is always possible to instead repeat the setup for each desired dither.
        • You can change the exposure time by entering a time in seconds in the "exptime" box
        • If the offset position puts another object on top of your target, you can change the offset position with the "azoff" and "eloff" boxes

      • If your target is too faint to see, and you are setting up using a nearby star, enter the offset from the star to the target in the "RA Off" and "Dec Off" boxes and press "Offset to Target"

      Now you are ready to take data.

      • If the field contains bright stars saturating the detector during the alignment (usually it is the case) it is highly recommended to execute a 10-sec long "object" exposure with ramp=1sec in the 32-amp mode before starting your science observations. This will clear the detector from the persistence effect caused by saturated stars which may spoil your first science exposure.
      • Ask the telescope operator to continue guiding and start Wave Front Sensing (WFS).
      • Press "Go" in mmicemmirs to start observations

      After the exposure sequence on the target is complete, take a comp and flat

      • Load the dither file "Calibrations/compflat_GG_FF", where GG and FF are the grism and filter you are using.
      • Press "Go"

      Follow the directions below for telluric standards.

    11. Multi-Slit Mask Observing.

      An observing catalog generated from the mask design files is automatically generated on the day of a mask change. It can be found on shack as /data/archive/MMIRS/Masks-YYYY.MMDD.cat. It can also be found on guanaco in /Volumes/ARCHIVE_MMIRS, so that the telescope operator can copy it, although it should already be available on the operator computer in the catalogs folder.

      Ask the Telescope Operator to slew to your target from the observing catalog (and to offset to instrument center per normal operations)

      In the mmicemmirs window, tab ObserveOps, select the following:

      • Press "Menu" and select a dither catalog from the Standard submenu. Note that the offsets are applied in the "instrument" coordinate system so that the same offsets work no matter what position angle you are using.
      • NAmps = 4 (or 32-amps for fast readout)
      • ObsType = object
      • Exptime = 300 (for typical exposures)
      • Slit/Mask = your choice of mask
      • Filter = your choice of filter
      • Grism = your choice of grism
      • ReadTab = ramp_7sec (required for 4-amp mode) or ramp_?sec for 32-amp mode
      • GuideWait = autoguide

      Figure 12 Mask alignment tool. Full resolution: p/alignbox-MaskAlignment.jpg

      In alignboxmmirs:

      • Select the Mask Alignment tab
      • Verify you have selected the correct mask catalog in mmicemmirs - it will be corrected during the mask alignment procedure - but only if it is selected BEFORE you press start next.
      • Press "Start" to retrieve the configuration parameters from mmicemmirs

        If the mask file and mask image file do not appear - please notify the Instrument Specialist. You may generate them now using the Measure Mask button - but they should have been generated during the afternoon.

      • Ask the telescope operator to start guiding.
      • Ask the telescope operator to ensure that "AUTO" is not selected on the guide setup interface.
      • ALWAYS WAIT until the gui shows a green "Guiding ON" and "Locked" status before proceeding with taking images In poor seeing or windy conditions the "Locked" status can be "twitchy" so you may have to settle for less than perfect locking
      • Press "Take Alignment Image" to take a dithered pair of images without the mask in. The difference image will be displayed automatically in ds9mmirs. The nominal positions of the slits and measured positions of the alignment stars will displayed as ds9 regions.
        • *NOTE*: The mask catalog used for telluric dithers to various slits will be recreated each time an alignment image is taken.
        • The recommended default EXPTIME is 10 seconds, which should give optimum alignment images. If the alignment stars are saturated, the exposure time can be set as low as 3 seconds.
        • Successful alignment is not guaranteed with exposure times below 3 seconds. A shorter exposure time may result in not all slits being successfully measured, in which case they will not appear in the telluric dither catalog.
        • The recommended alignment star magnitude range is 13.5 < H < 16 to avoid saturation.

      • You can zoom in on the alignment boxes in ds9mmirs by clicking on the "Next Box" button. Choose one of these two options depending on how close you are to the desired alignment:

        • OPTION 1, crude initial alignment. If the red circles are not on the stars, move the green "star" region onto its corresponding star, verify that "Fix to Nearest" is selected, and press "Fix Pointing". You only need to do this to ONE of the star/box pairs.

        • OPTION 2, accurate least square fit. If the red circles are on top of the stars, select the "Box and Star Alignment" tab. Examine the sx_Res and sy_Res columns and deselect any rows with residuals larger than 1 pixel. Then press "Apply Offset" to correct the alignment in both translation and rotation.

      • Select "mask" and press "Take Alignment Image" to take an image with the mask in. The alignment stars should now be visible in the boxes and the red markers should be on the stars.
      • Follow OPTION 2 above.
      • Repeat "Take Alignment Image" until the recommended offsets reported in the "az", "el" boxes are less than 0.1" and "dr" is less than 100" in rotation. In general this will take 2-3 iterations.

      Now you are ready to take data.

      • Ask the telescope operator to continue guiding and start Wave Front Sensing (WFS).
      • Press "Go" in mmicemmirs to start observations

      After the exposure sequence on the target is complete, take a comp and flat

      • Load the dither file "Calibrations/compflat_GG_FF", where GG and FF are the grism and filter you are using.
      • Press "Go"

      Follow the directions below for telluric standards.

    12. Telluric Standards.

      Because the atmosphere has many strong absorption bands in the near IR it is necessary to observe standard stars at an airmass close to the airmass of your observations. An excellent description of telluric standards, can be found at http://www.gemini.edu/?q=node/10165 . A typical observing sequence would be to start by observing the telluric standard. Then observe your object till it transits, and go back to the telluric, and then resume your observations. Telluric standards with K=9 are appropriately bright.

      1. Selecting Telluric Standards.

        The process for selecting telluric standards was developed by the FIRE spectrograph team, and is adapted here from the FIRE manual:

        It is best practice to observe A0V telluric standard stars between science objects, to calibrate atmospheric absorption features. These observations are also used to perform flux calibration by the reduction software. There is a tool installed on guanaco and zorro which assists users in selecting tellurics from a large list of A0V standards. For each field required, run the following:

        find_tellurics --RA 14:47:17 --DEC +04:01:12 --UO 08:50 --UT 09:25

        The program, find_tellurics, takes the following inputs:

        -RA, DEC - The right ascension and declination of your science target
        -UO - The central UT time of your science target observation (note this is the letter "O", not a zero)
        -UT - The expected UT central time of observation for the telluric standard

        The software will output a list of stars which are the closest match in airmass and sky angle:

        Object: RA= 14:47:17, Dec= +04:01:12 airmass= 1.372 at lst 16:43:14
        Best telluric matches:
        (1): HD123309 ----- Magellan Catalog Number: 10215
        Mag= 9.40 (Band= V) RA= 14:07:24 Dec= -23:28:29 Anguler Offset= 29.16 deg
        This telluric: airmass = 1.364 at lst 17:18:14 airmass diff from source = 0.007. Match rating = 54.18
        (2): HD125062 ----- Magellan Catalog Number: 10249
        Mag= 9.98 (Band= V) RA= 14:17:29 Dec= -19:29:07 Anguler Offset= 24.62 deg
        This telluric: airmass = 1.346 at lst 17:18:14 airmass diff from source = 0.025. Match rating = 30.37
        (3): HD123426 ----- Magellan Catalog Number: 10217
        Mag= 9.66 (Band= V) RA= 14:08:10 Dec= -24:33:51 Anguler Offset= 30.12 deg
        This telluric: airmass = 1.354 at lst 17:18:14 airmass diff from source = 0.018. Match rating = 27.47

        The "Match rating" field is a figure of merit for the quality of telluric match, and should be as large as possible with maximum 100. Once you've selected from the list presented, the telescope operators have the catalog file of all MMIRS A0V calibrators available in MMIRS_tellurics.cat. It is a long list, so you should specify the star by its catalog object number rather than name. The object number is listed above in the field "Magellan Catalog Number." Note that the catalog orients the slit at the parallactic angle.

      2. Acquiring Telluric Standards.

        It is possible to acquire the telluric standard without removing the mask by using the guider.

        The mask alignment process will generate a mask dither catalog that will offset the telescope to put the telluric standard on each slit of a mask if you follow this procedure.

        • Masks

        If you are observing the telluric standard before observing with the mask you must first take an image of the mask using alignboxmmirs before continuing. This will measure the exact location of the mask.

        • Select the desired mask using mmicemmirs.
        • Select the Mask tab in alignboxmmirs.
        • Press "Start"
        • Press "Take alignment image" ( with "mask" checked, if using a mask).

        Once the mask has been measured, or if you've just finished your science observations, then

        • Ask the telescope operator to "Follow the telluric acquisition procedure, por favor". You will need to tell the operator which target to use. The operator will tell you when the telescope is pointed at the the telluric standard.
        • In mmicemmirs, change the following settings,
          • Press "Menu" to select the dither catalog. For mask observations choose the catalog appropriate for you mask from the "Masks" submenu". The first 5 entries in the mask catalog put the star in the center, and top, bottom, left and rightmost slits.
          • NAmps = 32 or 4
          • ObsType = object
          • ExpTime = typically 20 for mag=8, or 60 for mag=10
          • ReadTab = ramp_1sec (for 32-amp) or ramp_7sec (for 4 amp)
          • GuideWait = none

        • Press "Go"

        After taking the telluric spectra, you can return to the target you were just observing without realigning by asking the telescope operator to "Return to the science target, and restore the offsets, por favor". Reset the mmicemmirs parameters:

        • ExpTime = ?? your desired exposure
        • ReadTab = whatever you were using
        • GuideWait = autoguide

        Backup plan: If the telluric spectra do not appear, you may need to align the telluric manually.

        • Follow the Start of the Night. procedure using the telluric standard instead of the pointing star.
        • After you have successfully placed the telluric star on the center of rotation, ask the telescope operator to offset to the instrument center.
        • Take spectra with the settings given above.
        • If you have aligned manually, the slit will have been moved and you must take another set of compflats.

        • LongSlit

          Please follow the standard longslit alignment procedure using either the same dither catalog as for your science target or a simple longslit_2.cat

    13. Imaging.

      It is recommended to use guiding and wavefront sensing for imaging projects. The main role of guiding is to keep the wavefront sensor star going into the wavefront sensor.

      The recommended maximum single exposure times for imaging are 45 sec for H and K and 300 sec for Y and J. At a minmum, you must remain at the same dither position for at least 15 seconds longer than the wavefront sensor exposure time (typically 30 seconds and not less than 15 seconds).

      Using the ramp_5sec readout mode is also recommended for imaging as it will give you increased dynamic range on bright stars and reduced noise in Y and J imaging.

      The best deep images are obtained if the dither pattern is random, rather than a square or line. You can read all about dither patterns on the Spitzer Science Center web site, here [2]. A set of random dither patterns can be found on wild in /home/mmirs/Dither/Random. For example, random30.cat contains a set of dither patterns that fill a 30" box. To observer the same posiiton sequentially at each position in a 120" box, you would use random2x_120.cat.

    14. Dark Frames at the End of the Night.

      At the end of the night you should take dark frames of every length of exposure that you took during the night. Fortunately you don't have to keep track of this yourself. Login into wild from guanaco by typing "mmirswild".

      cd /data/ccd/MMIRS/YYYY.MMDD
      darkscript 5
      Checking exposure times on all      379 files
      Please wait...
      1.  Go to Config page and set telescope to TEST
      2.  Go to the ObserveOps page and press Menu-->Darks-->darks-2011.1201
      3.  Press GO and watch the darks go!

      On the morning of a mask change procedure, please do not start the dark script until the GateValve has been closed and the mask change procedure has been begun by the instrument specialist.

  5. Automatic Data Logging.

    Please keep observing notes using the comment GUI which is started with mmirs. This will bring up a panel showing the fits files in the current data directory. You can highlight any one of the files and add comments to that log entry. To produce a nice postscript output click on View Log . The comments are archived along with the data and provide a valuable future reference.

    Figure 13 Comment GUI.

  6. Data Storage.

    1. External USB/FireWire Disk. (Magellan)

    At Magellan the data is cross-mounted onto Zorro for easy access. A USB/FireWire disk can be plugged into Zorro. The data can be copied directly using the Finder or from a unix shell. At the end of your run, Eject your disk using the Finder, and unplug it. NB: Data CANNOT be copied during observing operations. The additional load on network and disks will cause detector readouts to fail!

    From zorro the archive data (updated the morning following the run) can be found in:


    and the crunch data (where you may have some processed files) can be found in:


  7. Filters.

    The filter transmission data in text format are available at http://www.cfa.harvard.edu/mmti/mmirs/instrstats.html MMIRS has two filter wheels, one top and one bottom, which can accommodate 5 filters each. Installing a new filter in MMIRS requires disassembly of the cryostat -- a major operation -- and cannot be done without advance planning. Contact Brian McLeod for more information.

  8. General Comments and Information.

    1. Typical Count Levels.

      The bias level in up-the-ramp data is typically 16000 ADU.

      Please refer to the Exposure Time Calculator below for more estimates of background and counts expected at a given magnitude.

  9. Problems.

    1. Problems with mmice.

      Many problems can be diagnosed using the mmice Status display. The top section shows the status of all the servers in the MMIRS client/server system. Green indicates that the server is up. Red indicates that the server is not running. Yellow indicates that the server is up but not responding. Sometimes servers will go yellow briefly if they are very busy. The servers are as follows:

      • Detector

        This is the data acquisition server. If mmice fails to take an image, press the ccdmmirs button on the Start/Stop page. Problems with the array readout (weird patterns, all zeros), are also best dealt with by restarting the detector server.

      • Telescope

        This server provides information about the status of the telescope. Image header information comes from this server. If observe complains about no telescope information, set TELESCOPE=TEST on the Config tab. Don't forget to reset to the telname to mmt_f5 when the telescope is turned on or else your image headers will be missing information, dithering will fail, skyflats will fail!

      • Guidecam

        The detector server for the guider camera.

      • Guidserv

        Does the calculations for the guider.

      The remaining items indicate the status of the instrument

      • Homed indicates that the topbox has been initialized. If the indicator is red, which it will be following a full power-up, press the Home button.

      • ESTOP indicates that the emergency stop button on MMIRS has been pressed. The ESTOP buttons is normally engaged when exchanging slit masks. If the power to the rack is turned off, the light will also turn red.

      • LOAD turns red when the mask load switch on the instrument has been turned on. This switch is used to engage the manual advance button and lock out the computer during slit mask changes.

    2. dooldmice.

      If you are still having problems with mmice , and you can't get Mo or Brian on the phone, AND you are really REALLY desperate, it may be that someone changed something in the dommice code and now it won't work. As a last resort, you can invoke the previous version of mmice by typing "dooldmmice".

    3. All problems.

      All problems (weather not withstanding), comments and suggestions should be reported. The best way to do this is to fill out the Astronomers section of the Daily Report, or in your Run Report, accessible under Forms at www.lco.cl. You can update the Daily Report any time during the night. Remember, if you don't report it, it can't be fixed!

  10. Data Reduction for MMIRS.

    For more information on MMIRS data reduction see:

    MMIRS Pipeline

  11. Appendices.

    1. APPENDIX A: The Exposure Time Calculator, or ETC.

      Exposure Time Calculator

      This calculator uses the information contained in the previous section.


    2. APPENDIX B: How to plot the detector and guider footprint on an image in ds9.

      DS9 templates for MMIRS are available in /home/mmirs/ds9templates, or can be downloaded here:

      Save the downloaded files to a convenient location. Then in ds9 go to the Regions menu and select Template-->Load. Then just click in your image to put the template region on your image. To edit the center position and position angle, double click on the region. In the Composite window, select Coordinate-->WCS, and optionally Coordinate-->Sexagesimal. Then you can edit the position angle and center position.

    3. APPENDIX C: How to list guide stars available for your target.

      Guide star availability can be checked by installing the MMIRS Mask Making software. Create a TAB DELIMITED file with a single ra/dec pair, e.g. tester.targets

      ra dec
      -- ---
      12:00:00 -37:00:00
      Then invoke the program as follows:
      xfitmask tester tester.targets -check_boxes no -start_date XXXX
      The GUI will appear and list all valid rotation angles. Note that a Magellan catalog file needs to have the sign of this position angle changed in the ROTATOR OFFSET column.

    4. APPENDIX D: How to set up catalog files (Note: NOT TELESCOPE TARGET CATALOG) .


Rather than entering separate, time-consuming commands to do things such as change the filter, enter an exposure time, and type in an object name, the Catalog Ops refers to an established catalog to perform all those functions, and more. A series of exposures for a given target can be planned in advance and executed without astronomer intervention, in principle. Dither catalogs can be generated manually or with the DitherTool tab of mice.

The catalog can be very versatile as it allows you to offset the telescope, specify filters for each image, and specify exposure times for each image.

The catalogs are TAB delimited tables. Columns in the table are delimited by the TAB character. The first line contains the column names. The second contains dashes separated by tabs. See [3] for information on manipulating tables of this format. The available column names are

exptime    The exposure time
filts      The filter name
grism	   The grism name
exptype    object, comp, flat, or dark
azoff      The azimuth instrument offset
eloff      The elevation instrument offset
readmode   e.g. /home/mmirs/ReadMode/ramp_5sec.cat

  1. Examples.

    Example dither files are located on (shack or wild) at:

    /home/mmirs/Dither/XXX/*.cat in the following subdirectories: User Mask, Standard, Dark.

    The following are commonly used dither files:

    line3.cat 3 position diagonal dither that gets rid of the gaps

    line5.cat 5 position diagonal dither that gets rid of the gaps

    xyphotom.cat used for making photometric illumination correction

    3x3.cat 3x3 pattern with 10 arcsec spacing

    standards.cat run through filters and get standards in each; 1sec, 10sec and 100sec exposures

    To list the offsets for a catalog use the following command:

    column < line5.cat azoff eloff


    You can of course create your own cat files in a text editor. However, the Dither Tool allows you to create cat files easily.

    To use the dither tool, bring up the dithertool tab:

    Figure 14 mice DitherTool tab. Full size image: p/mmice-DitherTool.jpg

    The output of the dither tool is saved to a tab delimited text file which can be viewed or modified with any editor. Some examples of the output of the dither tool are shown below.

  3. Check your cat files.

    If you create your own dither file it is important to verify that the formatting, especially the white space, is correct before using it. To verify the formatting type:

     justify < filename.cat

    which should produce the output neatly aligned in columns. Remember columns in the table must be separated by tabs.

  1. Archives.

Picture/Image Archive: p

Document Archive: d

Attachment Author Date Size Actions
MMIRS.ObsManual.2010Sep.txt maginst 05-09-2011 54K Delete
mmirs_image.tpl amatthew 09-16-2010 2.6K Delete
mmirs_longslit.tpl amatthew 09-16-2010 2.6K Delete
mmirs_mask.tpl amatthew 09-16-2010 2.6K Delete