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The ISIS user guide

  1. Preliminaries
  2. Starting the system
  3. Controlling ISIS mechanisms
  4. ISIS observing commands
  5. Afternoon settings and calibrations
  6. Observing with ISIS
  7. Copying data

1. Preliminaries

1.1 Instrument and telescope control system

As an ISIS observer you will use the following three computers:

  • taurus, on which we run the instrument control system (ICS) and which controls both the instrument and the A&G box mechanisms.
  • whticsdisplay1 (or whticsdisplay2 if whticsdisplay1 isn't available), as a front-end display computer interfaced to taurus to reduce processor overheads on the latter.
  • whtdrpc1, for miscellaneous tasks such as quick-look data reduction of scratch copies of data images.
In addition there is the telescope control system (TCS) computer.  As its name implies, this controls the telescope, which is operated solely by the Observing Support Assistant (OSA).

1.2 Preparing the catalogue file

If you are planning to observe many targets, it's recommended to create your own catalogue before your observing run, to save time on-sky. Please follow the instructions provided here.

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2. Starting the system

2.1 Starting the observing system

The observing system on taurus should be started in the afternoon, and is usually started prior to your run by the operations team. There are four monitors, and there should be several windows open on them:

  • An xterm pink window (labeled "WHTICS"). This is a Linux terminal to introduce the UltraDAS commands.
  • A window with the "mimic" display should be open in the left monitor, which by default usually shows a summary of the state of ISIS and A&G Box with a trace of the light path.
  • Several xterm orange windows. These terminals are for the DAS control of the cameras and usually you do not need to deal with them (it is better to minimize them). 
  • An "identify" window. Your Support Astronomer (SA) will enter your name and proposal identification at the begining of your run.
  • The observing log. The log is automatically updated each time a new file is written to disk. To put comments on a line click once with the mouse on the line and a box appears where you can type shorts comments.
  • Two detector information displays,  one for the blue and other for the red arm of ISIS (if other cameras are operative, typically the Aux Port, other displays will be open) and one summary detector information display.
  • The "talker" window (it displays messages from the observing system to the user). 
  • The "Instrument control" window where you can configure ISIS set-up (alternatively to commands from WHTICS). 
  • If you wish, you can also bring up a telescope info display window. Type:


If something goes wrong with the system ask for help from your SA or OSA.   Instructions for starting up and shutting down the observing system can be found here.

2.2 Starting a data reduction session

Log on to whtdrpc1, the Linux PC dedicated to data reduction (monitor to the right of the instrument control monitors):

  • LOGIN: whtguest
  • PASSWORD: provided by your support astronomer. 
  • Open a terminal window
  • Start iraf (type iraf). 
  • Change to the disk and directory where the data are going to be stored (e.g. cl>cd /obsdata/whta/20120814). 
  • Type: cl>ing to initialize ING specific packages (includes routines for checking focus, rotation and tilt of the detectors).
If you plan to reduce your data on-the-fly please don't work directly on the images stored in the /obsdata/whta/"date" directory (which is cross-mounted to whtdrpc1). Instead, copy the images to a directory in the /scratch filesystem, e.g. /scratch/whta/20120814, and run your analyses on the duplicated data.

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3. Controlling ISIS mechanisms 

3.1 The MIMIC display

The status of ISIS is displayed in the "mimic"  window.   There are 5 possible displays to select in this window; ISISP, ISISMechErrors, ISIS, ACAMINS and CAGBFilters. Choose the ISIS display to show the simplified view of the ISIS instrument components and their status, as well as a schematic of the light path through the instrument. The status flags are colour coded, red means there is a problem, blue means that a mechanism is moving, while white means that a mechanism is OK.

3.2  ISIS & AG box common commands

ISIS mechanisms can be controlled from "WHTICS" terminal window or from the GUI (next section). WHTICS is a Linux window, and so commands can run in the background, and can be combined with Ultra-DAS commands to write scripts. The most usual operations the observer will do are:

Select which arm(s) to observe with

    SYS@taurus> bfold 0      (to observe in the red arm only, dichroic and mirror out of the beam)
    SYS@taurus> bfold 1      (to observe in the blue arm only, mirror in the beam)
    SYS@taurus> bfold 2       (to observe in both arms simultaneously, dichroic in the beam)

Set the gratings to the correct central wavelengths as in the following example
    SYS@taurus> cenwave blue 4500          (sets the central wavelength in the blue arm to 4500 Å)
    SYS@taurus> cenwave red 6500            (sets the central wavelength in the red arm to 6500 Å)

Select the slit width

    SYS@taurus> slitarc 1.0    (sets slit width to 1.0 arcsecond.  Maximum possible width is 22.0 arcseconds, and the minimum slit width is 0.32 arcsecond.)

Slit width temperature correction is implemented; more details about this correction can be found here.

Select the dekker mask. Note that the long slit module of ISIS has a slit length of 4.0 arcminutes. This is curtailed to 3.2 arcmin (blue) and 3.5 arcmin (red) with the default CCD windows.

Whilst observing the dekker slide is normally inserted above the slit to mask off the slit ends.  This reduces ghosting in ISIS and it is therefore recommended that the dekker is used. To check if the dekker is in place ask your support astronomer or, looking at the mimic display, check that the dekker status is CLEAR and not OUT. If the dekker is OUT you may move the dekker slide into the beam at the correct position using the command

    SYS@taurus> dekker 8

Here are images of the available dekkers; the one used for long-slit mode (Obs) is on the extreme left of this image.

Introduce a blue blocking filter in the red arm of ISIS. Your support astronomer will advise if one is needed to prevent contamination of the red spectrum by second order light.  The status of below slit filter slides which contain these filters can be checked on the mimic display.

    SYS@taurus> rfilta 3  (introduce the GG495 blocking filter)

Select slit mode to observe (remove the comparison mirror in case it is in)

    SYS@taurus> agslit

Select comparison mode to take lamps (introduce a mirror in the beam to drive the light from the lamps into the spectrograph)

    SYS@taurus> agcomp

3.3  Controlling ISIS mechanisms from the GUI

The ISIS mechanisms can also be controlled from a GUI. Manuals of the new ISIS Control System and the A&G Control System explaining how to use the GUIs can be found here and here.

The use of the GUI is very simple. A number of icons buttons are used throughout the GUI in order to perform specific tasks.
buttons 1

button 2

The GUI has several windows, those relevant for the ISIS user are here.

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Note that UltraDAS commands run under Linux ("WHTICS"), and therfore they can be executed in background mode (by appending & at the end of the command line). This enables one to take images simultaneously with both red and blue arms, for example run red 900 & run blue 900 takes a 900s exposure in each arm, and returns the command-line prompt when the blue-arm exposure completes. Note that the red-arm exposure (in this example) won't necessarily be complete when the prompt is returned; don't e.g., turn on calibration lamps until exposures in both arms are complete.

Furthermore, UltraDAS commands can be combined with ISIS commands to create scripts to execute observing sequences.  A complete list and description of the commands can be found in the command dictionary of the UltraDas Software manual. A summary of the most commonly used commands is given here for a quick reference:

  • Data acquisition commands
    Some of the most important commands related to data acquisition are listed below (arguments are denoted by <>):

    • run <camera> <int time> <"title">
      Takes a run and saves it in:
      E.g. run blue 600 "N157 B", takes a 600s exposure with the blue arm and stores it in the output file (e.g. The title of the fits file is set to "N157 B". If you do not specify a title, the name in a header will be the same as in your catalogue.

    • multrun <camera> <m> <int time> <"title">
      Same as run but repeats the run sequence m times and generates m output files.

    • flat <camera> <int time> <"title">
      Takes a run and set the OBSTYPE header parameter to FLAT.

    • multflat <camera> <m> <int time> <"title">
      Same as flat but repeats the run sequence m times and generates m output files.

    • arc <camera> <int time> <"title">
      Takes a run and set the OBSTYPE header parameter to ARC.

    • multarc <camera> <m> <int time> <"title">
      Same as arc but repeats the run sequence m times and generates m output files.

    • bias <camera> <"title">
      Takes a run and set the OBSTYPE header parameter to BIAS.

    • multbias <camera> <m>  <"title">
      Same as run but repeats the bias sequence m times and generates m output files.

    • glance <camera> <int time>
      Takes an exposure and saves it in This file is overwritten when a new glance is taken. If you want to have a permanent copy of a given glance image, type promote

    • scratch <camera> <k> < int time> <"title">
      Takes a run and saves it in: k is an integer within the range 1-99. The scratch file is overwritten when a new scratch<k> is taken.

    • abort <camera>
      Aborts an exposure which is running in the backgroud. The data are not saved to disk.

    • finish <camera>
      Terminates an exposure which is running in the background, and saves the data to disk.

    • newtime <camera> <int time>
      Changes the length of an exposure which is running in the background (e.g. newtime red 900 for the red arm)

    • Ctrl_z followed by bg suspends the current process which is running in the foreground and starts it running in the background. Therefore if you executed a pair of integrations as run red 900 & run blue 900; bell, so that the red integration is running in the background and the blue integration is running in the foreground (with an audio alarm queued to sound when the blue-arm integration completes in this instance), typing Ctrl_z then bg would cause the blue integration to also run in the background, making the command line prompt available to issue, e.g., a pair of finish commands. Note that the bell command would execute immediately on typing Ctrl_z in this example.

    The arguments above stand for

       < camera>    Indicates which CCD you want to use, the red or blue one. Enter red or blue.

       < int time>    Integration time in seconds.

       < "title">        Title of the exposure recorded in the image header (optional argument).

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5. Afternoon settings and calibrations

Setting the CCDs from the observing system (WHTICS)

Before starting the calibration images in the afternoon you should set the readout speed and the windowing of the CCD camera.

- Set the detector readout speed to slow or fast (as desired) by typing for example:

    SYS@taurus> rspeed <camera> slow

Have a look at the blue-arm and red-arm pages for details on the operational characteristics for each readout speed.  Normal observations are usually using the slow readout speed. Be careful as the default read speed on e.g., resetting the controllers is fast, so you should check that it is in slow mode before starting to take your calibrations in the afternoon (if you plan to observe in slow read mode).

- Windowing the CCDs. Note that the ISIS detectors cover more than 4 arcminutes in the spatial direction. It is therefore desirable to window each CCD to an appropriate length by defining an effective slit length

    SYS@taurus> window red 1 "[555:1520,1:4200]"   (3.5 arcminutes for red arm+REDPLUS)

    SYS@taurus> window blue 1 "[585:1550,1:4200]"   (3.2 arcminutes for blue arm+EEV12).

- Binning the CCDs.

    SYS@taurus> bin red 1 2   will bin x2 in the dispersion direction.

Currently, it is not recommended to use 4x1 or 4x2 binning while windowing, because the CCD controller times out and/or the observing system hangs for a short time, one or other of which occurs for more than 50% of the time. All images are read-out and saved correctly, but it is not possible to take multiple (multrun) exposures. This problem occurs for both red and blue CCDs, and slow and fast read-out speeds. The current workaround is not to use the combination of binning 4x1 or 4x2 with windowing. This problem is caused by a controller internal error.

Once the CCD windows have been defined, the system will automatically create and save two files, one for each CCD, which contain the window, bin and readout speed parameters. The default file names are udas_REDPLUS.cfg and udas_EEV12.cfg. Different names can be used with:

    SYS@taurus> saveccd <camera> <filename>

To load the CCD parameters use:

    SYS@taurus> setccd <camera> <filename>

To load the default CCD configuration files just omit the field <filename>.

The setccd command is especially useful after issuing a dasreset. This command resets the software and hardware of a CCD camera (e.g. when one camera stops working):

    SYS@taurus> dasreset <camera>

After a dasreset, binning, windows and readout speed revert to their defaults, 1x1, no window and fast respectively.

5.2 Taking arcs

    SYS@taurus> agcomp

    SYS@taurus> complamps cuar+cune

and take a test exposure:

    SYS@taurus> arc red 5 test

This exposure will allow you to compute the exposure time to obtain a reasonably intense arc. Follow the same procedure with the blue arm. Take into account that usually long exposure times of > 40 s are needed in the blue.

5.3 Taking lamp flats

Before taking flats turn off all the dome lights and close the curtains in the control room.

    SYS@taurus> agcomp

    SYS@taurus> complamps w

and take a test exposure:

    SYS@taurus> flat red 1 test

This exposure will allow you to compute the exposure time to obtain a reasonable intense flat. Flats should not be brighter than 42000 ADUs. When using low resolution gratings in the red arm, the use of a neutral density filter is needed. ND filters can be put in place with e.g.

    SYS@taurus> compnd 0.8  

To remove the ND filters type

    SYS@taurus> compnd 0

Once the proper neutral density filter and exposure time is set, do a multflat:

    SYS@taurus> multflat red 11 5 "good flat"&

5.4 Taking biases

Before taking bias frames turn off all the dome lights and close the blinds in the control room. It's also good practice to configure the comparison mirror in the beam. As an example, to take 11 bias frames in the red and blue arms

    SYS@taurus> agcomp

    SYS@taurus> complamps off

    SYS@taurus> multbias red 11 & multbias blue 11 &

In principle, one can also take biases on ACAM simultaneously with those in the ISIS red and blue arms (by simply concatenating multbias acam 11 & to the above line). However, it's been noted that taking biases simultaneously on ACAM and the ISIS red arm causes additional noise in the form of horizontal lines on ACAM and the ISIS red arm, which are not present if biases are taken separately. Taking biases on ACAM and ISIS simultaneously is therefore discouraged.

5.5 Taking sky flats

We suggest that observers take twilight sky flats in order to determine the slit illumination function. Knowledge of this is desirable when observing extended targets or two (or more) targets simultaneously in the slit, and is useful for accurate sky subtraction. The internal-lamp flats, being free of lines, are of course used for determining the CCD's pixel-to-pixel response.

To take sky flats with ISIS leave the telescope at Zenith in engineering mode (i.e. no tracking). No offsets between individual flats are needed.

For the higher resolution gratings (R1200R, R1200B, H2400B), you should start 10-15 minutes before a sunset. For lower resolution gratings start around a sunset.

    SYS@taurus> agslit

take a test exposure to decide the exposure time:

    SYS@taurus> sky red 1 test

Once the counts level is good, take sky flats with the following command

    SYS@taurus>sky red <exp_time> & sky blue <exp_time>

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6. Observing with ISIS

6.1 Target acquisition

Acquisition of targets in the slit will be carried out by the telescope operator. Briefly, the slit is polished and aluminised, and is inclined to the optical axis of the telescope at an angle of 7.5 degrees to allow the reflected image of the sky to be viewed by the A&G box TV camera, currently ag4. To configure the A&G box for acquisition and observing, issue the command


The default orientation of the slit will be set to the parallalctic angle at the mid-point of your integration by the OSA, but inform the telescope operator if you prefer a different angle, for example, in order to place multiple targets in the slit. If you want to save an acquisition image, ask the telescope operator to stop ag4 running in TV framing mode and execute the command

    SYS@taurus> run ag4 <exp> <"comment">

Remember to ask the telecope operator to switch ag4 back to TV framing mode, so that the centering in the slit can be monitored throughout your subsequent science integrations.

6.2 Focusing the telescope

To focus the telescope point to a bright star (V=9-11), it can be one of your standards) at low airmass. Use fast readout speed and take a test image with one of the arms (usually red, because the seeing is better in red than in blue).


    SYS@taurus>rspeed red fast

    SYS@taurus>glance red 10 &

Exposure times of ~10s should be used to adequately sample the seeing. Look at the image to check that the spectrum isn't saturated and has SNR of at least ∼50 per pixel, and then execute the focusrun script:

   SYS@taurus>focusrun <camera> <num_exp> <exp_time> <focus_start> <focus_increment>

Typical values are

   SYS@taurus>focusrun red 9 10 97.7 0.05

This will take 9 images of 10s each, changing the focus of the telescope from 97.7 mm in increments of 0.05 mm between the images. All images are saved and you can determine the best focus by analyzing "manually" the spatial profile in each image, or running the iraf focus script in the directory where your data are being written (/obsdata/whta/"date"):

   ecl> ! isis_focus

Note that usage of an exclamation mark at the beginning of this command is necessary. The script prompts for the run number of the first image and number of images taken in the focus sequence. The run number should be given without the "fit" extension, and with r at the beginning (e.g. r1234567). The first image will be opened in ds9 and you can now position the cursor on the spectrum and press any key on the keyboard to measure the spatial profile at that position. All images are displayed one by one and a spatial-profile fit is shown for each image in the sequence. Eventually, a window opens showing measured values of FWHM versus the telescope focus, with a parabolic fit over-plotted. At the same time, the best empirical and fitted telescope focus values are printed in the iraf terminal. Closing the opened graphical window will give you a prompt back in iraf session.

Once the value of the focus is determined (e.g. 97.85) set the value of the focus by

   SYS@taurus> focus 97.85

NB Don't forget to change the readout speed back to slow.

Warning: If changes are made to the configuration of ACAM when ISIS is the selected instrument the corresponding focus offset for the ACAM optical element configured will be applied to the telescope. An ISIS focus run performed with a focus offset applied will compensate for it. However, if the telescope focus is set to the ISIS nominal focus with a focus offset applied, but an explicit focus run isn't performed (e.g. due to time constraints), the telescope will be defocused by an amount commensurate with the offset. In this case, if you notice that the dF parameter in the TCS window is non-zero, ask the TO to remove it. Check at the start of the night that a focus offset isn't applied, and never change the configuration of ACAM while observing with ISIS.

    SYS@taurus>rspeed red slow

6.3 Taking spectra of an object

First select the slit mode and slit width 

   SYS@taurus> slitarc 1.0

   SYS@taurus> agslit

Ask the OSA to point to your target (you can provide a catalogue of targets with the coordinates of the targets you plan to observe during your run). Also state the position angle you want for the slit. If you will observe with the slit at parallactic angle (i.e. oriented in the vertical direction) to minimise differential slit losses sue to differential chromatic refraction), it's advisable to adjust this at least every 1.5-2 hours because the slit doesn't actively track the parallactic angle. The change of parallactic angle with time can be determined using the Staralt software (select Option=Parallactic Angle). Note that it's as important to adjust the slit orientation every ~1.5-2 hours near zenith as it is at higher air mass; although differential chromatic refraction is smaller near zenith, the rate of change of parallactic angle is higher. These two effects combine to make the relative movement of blue and red images across the slit only weakly dependent on air mass.

If you change the slit PA to better track the vertical, always check the acquisition, and re-centre as necessary. In the case of a target acquired in a blind offset, repeat the blind offset acquisition if you change the slit orientation.

The OSA will take an image of the slit with the TV camera and will use it to centre your object in slit. If your objects are faint (V>20) it is a good practice to acquire a brighter object in the field close to the target (less than 20 arcminutes, but preferably less than 2 arcminutes) and do a blind offset to your target. In bright time and/or when the seeing is not good then you'll likely need to use blind offset stars for brighter targets (V>18). In such cases prepare blind offset stars in advance to save time. For accurate blind offsets, both target and offset star should be in the same coordinate system and have at least two decimal places in seconds of RA and one decimal place in arcseconds of Dec. Always check if the offset star has an appreciable proper motion. Once your object is in the slit do

   SYS@taurus> run red <exp_time> "<comment>" & run blue <exp_time> "<comments>"; bell

An audio alarm will sound when the blue-arm exposure completes,.

6.3.1 Blind offset acquisition

In the blind offset procedure, the accumulated handset corrections applied to locate the reference object in the slit from its initial "gocat" location are converted to tangent-plane coordinates, and these are added to the pointing model's collimation terms in elevation and azimuth. This creates a localised, incremental correction to the pointing model, and this localised pointing model is adopted in the blind offset procedure to position the faint target in the slit once the reference target has been acquired accurately. However, closing the loop on the reference star discards this localised pointing model, and if the loop is subsquently opened and a blind_offset applied, the rms offset accuracy will be degraded to at least 0.5-arcsec. A blind offset should not be executed if the loop has been closed on the reference object. For example, if a bright target in a galaxy or cluster is observed closed-loop, followed immediately by a blind offset to a faint target in the same galaxy or cluster, the acquisition of the faint target will be compromised.

The correct procedure for a blind offset acquisition is

(i) gocat "target" and identify a suitable guide star
(ii) gocat "reference"
(iii) centre the reference object
(iv) quickly apply blind_offset "target"
(v) close the loop quickly

The rms accuracy of this procedure is <~0.2-arcsec. Open-loop tracking error (~0.1-arcsec/minute) in the acquisition is minimised by identifying a guide star in advance of the blind offset, allowing the loop to be closed quickly after the blind offset to the target completes, and of course by quickly applying the blind offset once the reference target has been centred in the slit.

6.4 Night calibrations

If you need arcs of lamp flats during the night proceed as in section 5.2.

6.5 Observing bright targets

If you need to observe bright targets you can use the main neutral density filters in the light path, common for both red and blue arm. Take into account that these neutral density filters are not uniform, mostly outside the useful area of the chip. The table below indicates the area of the chip in pixels where the filters were observed to be "gray". In addition to the non-uniformity all these filters have small-scale structures, difficult to be removed by flat-field correction. If there is a need to use these filters, flat-fields should be taken to mask regions with small-scale structures out. To insert the main neutral density filter, use the command:

   SYS@taurus> mainfiltnd 2

to insert 0.3 neutral density filter (see the table below). The available options are the following:
mainfiltnd ND useful window
1 0 -
2 0.3 [500:1600,1400:2800]
3 0.9 [500:1600,1900:3000]
4 1.3 [600:1600,1400:3000]
5 1.8 [500:1600,1400:2800]
6 3.0 [1050:1550,1900:3000]

6.6 Quick-look spectrum extraction

Run the ISIS quick-look script at IRAF with e.g.:

   ecl> ing

   ing> isis

   isis> isis_ql r1234567 252

where the image name is given without the '.fit' extension, and the last number on the line is the approximate x position of the spectrum on the CCD. The script carries out an optimal extraction (takes ~ 1 sec) and displays the spectrum in the iraf graphics window using splot, so all the usual keystrokes are available. No wavelength calibration is provided. We strongly recommend that to use the isis_ql package you first copy the required data to a scratch area, e.g. /scratch/whta/"directory".

Note that if the detector is binned, e.g., x2, in the dispersion direction, isis_ql still plots the extracted spectrum in unbinned pixels. Therefore a line expected to fall e.g., 300 binned pixels redward of the central pixel will fall 600 plotted pixels redward of the central pixel.

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7. Copying data 

You can copy your data to your laptop or an external disk when connected to the ingext WiFi network:
  • rsync -avuz .
Or, you can copy the data to the FTP area, and subsequently retrieve it over the Internet:
  • follow these instructions
Or, you can write your data to a DVD (~4 GB capacity)
  • get a DVD from your SA or OSA and put the DVD in the DVD burner (located in the computer room)
  • follow the instructions here

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Contact:  (ISIS Instrument Specialist)
Last modified: 16 October 2018