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ISIS spectropolarimetry user guide

  1. Basic characteristics
  2. Polarization optics
  3. Preparation before a run
  4. Afternoon settings and calibrations
  5. Configuring the telescope
  6. Acquiring objects and taking data
  7. Data reduction
  8. Useful observing commands and information

  1. Basic characteristics

  2. ISIS is a modulation polarimeter with a double-beam analyzer (the calcite plate) and a rotating halfwave or quarterwave plate modulator, and linear and circular spectropolarimetry observations can be performed. In a standard configuration, where the halfwave plate is mounted on top of the quarterwave plate, the unvignetted field of view is about 130 and 35 arcsec for linear and circular spectropolarimetry observations, respectively. It is usually recommended to use only one arm of ISIS at a time to avoid the use of a dichroic which introduces reflected light from its rear into the polarization spectrum.

    The instrumental polarization measured from the zero-polarization standard star is p = 0.07 +/- 0.04 %.

    A polarization modulator (see picture below) consists of a waveplate and an analyzer. Rotation or periodic modification of a waveplate converts incident polarization in a time-varying manner, and the analyzer converts this into an intensity modulation which is then measured on CCD.

    A polarization modulator.

    A schematic plot of ISIS polarimeter with representative beam cross-sections and polarization ellipses can be found here (note that FOS is no longer in use). Physical dimensions of ISIS polarization modulator and slit area can be found on this picture.

    For a linear polarimetry, a standard sequence of exposures is:
    • exposure 1 with halfwave plate at 8.0 deg
    • exposure 2 with halfwave plate at 53.0 deg
    • exposure 3 with halfwave plate at 30.5 deg
    • exposure 4 with halfwave plate at 75.5 deg

    where exposures 1 and 2 yield Stokes Q, and exposures 3 and 4 Stokes U. A recipe how to derive the Stokes parameters can be found in the document ISIS Spectropolarimetry Users' Manual, section 3.2.

    A circular polarimetry measurement consists of:
    • exposure 1 with quarterwave plate at 95 deg
    • exposure 2 with quarterwave plate at 185 deg

    The angle of the halfwave (quarterwave) plate which provides the maximum brightness difference between the ordinary and extraordinary rays is the zero angle. Theoretical zero angles should be 0 (90) degrees for linear (circular) polarimetry measurements, but for ISIS an actual zero angle is around 8 (95) degrees. The exact value of a zero angle depends on a wavelength and a set-up and will be determined by a support astronomer.

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  3. Polarization optics

  4. The polarization optical elements, following the optical path from sky to detector, are:


    There are three different choices of polarizers (placed in the main colour-filter slide in the WHT A&G box):

    • MF-POL-PAR and MF-POL-PER: these are two linear polarizers (both transmit a linearly polarized beam perpendicular to each other). MF-POL-PAR is normally used to find zero angles during the set-up preparation. MF-POL-PER is not used much.
    • MF-POL-CIR: circular polarizer which is in fact elliptically polarized, and thus its use is not recommended.

    Retarder waveplates

    These are mounted above the slit. They are effective over the wavelength range 300-1100 nm. They can be inserted/retracted and set to any position angle or rotated continuously at a maximum speed of 1 Hz. The available retarder plates are:

    • Halfwave (λ/2) plate
    • Quarterwave (λ/4) plate

    Rotating the halfwave plate through n degrees results in a rotation of 2n degrees of the polarization vector of the light. The quarterwave plate converts circular into linear polarization, so that the calcite plate (linear beam-splitting polarizer) can detect its presence. Rotating the quarterwave plate rotates the linear polarization striking the calcite plate.

    A standard configuration is the halfwave plate mounted on top of the quarterwave plate, so that the quarterwave plate is closer to the slit. The table below lists the unvignetted field of view according to the plate position.

    Wave plate
    Unvigneted FoV (arcsec)
    Closer to the slit
    Further from the slit
    Closer to the slit
    Further from the slit

    Note that the quarterwave plate allows to observe only point sources due to its limited unvignetted field.

    The quarterwave and halfwave plates can be interchanged, to optimize a particular application. This has to be done when ISIS is off the telescope, hence you should communicate this change to your support astronomer well in advance.

    The dekker masks

    The dekker masks on the polarization dekker are placed above the slit to avoid overlap between the two sets of spectra produced by the calcite slab analyzer.
    Polarization dekker set
    Polarization dekker slide. The numbers on top denote the dekker position in the dekker slide, and they correspond with the column "Dekker slide position" in the table below.
    The choice of the dekker position will depend on the nature of targets which will be observed. The table below describes the characteristics of each dekker mask.

    Dekker slide position
    ICS command
    Aperture (arcsec)
    Separation (arcsec)
    dekker 1
    dekker 2
    dekker 3
    dekker 4
    dekker 5
    dekker 6
    dekker 7
    dekker 8
    dekker 9

    For point sources a dekker with three apertures, one for the source and two for the sky, can be used. Each aperture generates two beams. In the polarization dekker slide, positions 1-3 have three apertures. The default option is the dekker in position 2 (ICS command "dekker 3") in which the ordinary and extraordinary beams of the target and sky are aligned next to each other so that the CCD can be windowed to reduce the readout time.

    The default dekker (ICS command "dekker 3") has three apertures of 5 arcsec width, separated by 18 arcsec. Therefore the total width is 41 arcsec. The unilluminated space between slots is 13 arcsec. The separation of o and e rays is 8 arcsec.

    Dekker positions 1 and 3 are not usually used. The dekker position 1 is specially designed sky compensation dekker (see page 23, section 5.3 of the Users' manual for more details). The dekker position 3 was designed originally for the FOS (Faint Object Spectrograph), which is no longer in operation, and introduces vignetting when used along with the quarterwave plate.

    For extended sources the comb dekkers (dekkers at positions 4-6) are used. They have different duty ratios, thus one has to plan in advance the size and number of position offsets along the slit to allow the observation of the full slit. There are few more choices of comb dekkers on a different dekker slide, although they are almost never used.

    The analyzer

    • Calcite slab: is located immediately below the slit. It is a Savart plate which equalizes focus for both polarizations and reduces polarization anomalies within ISIS. It produces two beams, the ordinary (o) and extraordinary (e) beam, which are both 100% polarized but orthogonally. The o and e beams are separated from each other between 2.1 and 2.6 mm. The relative intensity of these beams depends on the percentage of polarized light in the incoming beam. It is effective over the wavelength range 330-1100 nm.

    • Polaroid: in principle, it could be used for occasions when full spatial detail is mandatory, without interruptions by the Dekker structure. Although it is hardly used.

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  5. Preparation before a run

    • Choose a dekker position according to the nature of targets which will be observed.

    • Using a dichroic is not recommended for spectropolarimetric observations due to the reflected light from its rear. The reflected light is displaced along the slit, partly into the spectrum of the other polarization, which may compromise the polarimetry measurements. If observations are requested using the red and blue arms it is usually recommended to alternate between the two arms and not use them simultaneously. If one is interested in the polarization of emission lines and not too worried about continuum contamination from the reflection in the dichroic the simultaneous observations in the two arms can be considered.

    • Using GG495 order-sorting filter in the red arm should not introduce any extra polarization or problems (see e.g. Harries et al., 2002, MNRAS 337, 341, who used GG495 with R1200R grating centered at 6560 Å).

    • Q and U, hence also the polarization angle, are defined relative to some instrumental coordinate system. It is convenient to keep the orientation of the instrument fixed relative to the sky (set Cassegrain rotator tracking), but equally it is important to keep the relative orientations of the telescope and ISIS constant (this will mean there is only one global system to calibrate for polarization zero-point). Our compromise recommendation is to track in angle during the entire observation, but to aim at having the slit vertical halfway through the observation. You can plan this using ING's Object Visibility web-page, selecting 'Parallactic angle' in Options.

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  6. Afternoon settings and calibrations

  7. As you proceed to set-up ISIS for spectropolarimetric observations, various components specific to this mode of ISIS will appear on the ISIS Mimic window (see picture here).

    1. Set the dekker position

    2. To set the default position of the dekker (called POL18ARCSEC, which has a gap of 18 arcsec between the centre of the central dekker slot and the centre of the left or right dekker slot), type:

      SYS@taurus> dekker 3

      Other dekker positions are listed here.

    3. Put the retarder plate in the beam

    4. Deploy the halfwave plate (for linear spectropolarimetry) or the quarterwave plate (for circular spectropolarimetry) in the light path:

      SYS@taurus> hwin (for linear) or qwin (for circular)

      To take halfwave or quarterwave plate out of the beam, type:

      SYS@taurus> hwout or qwout

    5. Put the Savart plate in the beam

    6. To move the Savart plate to the light path, type:

      SYS@taurus> fcp calcite

      To move the Savart plate out of the beam, type:

      SYS@taurus> fcp_out

    7. Setup the detector

    8. Set the appropriate window and readout speed of the detector as usual.

      The windows below can be used as a reference but need to be checked.

      SYS@taurus> window red 1 "[840:1190,1:4200]"

      SYS@taurus> window blue 1 "[890:1240,1:4200]"

    9. Take calibrations

    10. Take usual set of calibrations described in ISIS cookbook.

      For the flat fields use the same polarimetry components in the light path as for your observations, except for the dekker, for which it is recommended to take two sets of flat fields. First set should be taken with the dekker position clear (type SYS@taurus> dekker 9). Once you insert the dekker for observations, take another set of flat fields. Note that roughly double the exposure time will be needed compared to flat fields taken at dekker position clear. This is because in the case of dekker out each pixel is illuminated by both ordinary and extraordinary rays.

      To take flat fields, set the halfwave (quarterwave) plate to the angle where the contrast between the ordinary and extraordinary rays is minimized. For ISIS this is around 30.5 or 75.5 deg for linear, and around 185 deg for circular spectropolarimetry.

      If you want to take sky flat fields in addition to the tungsten lamp flat fields, ask the telescope operator to point the telescope to the Arago point (telescope azimuth = Sun azimuth - 180 deg and elevation ~ 20 deg at sunset), where the degree of the sky polarization is close to zero. This point lies about 20 deg above the antisolar point when the sun is close to (or below) the horizon.

      It is important not to change any sensitivity parameters of the system between calibrations and science observations. This applies particularly to gratings, grating settings and filters.

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  8. Configuring the telescope

    1. Focusing the telescope

    2. To find the focus of the telescope with ISIS for spectropolarimetric observations, follow the usual focusing procedure. Choose some bright star (brighter star is needed than for the normal ISIS observations), e.g. V ~ 6-8 mag. The usual telescope focus is 0.2 (0.1) mm lower when using a halfwave (quarterwave) plate compared to the ISIS focus without a wave plate. This means that the telescope focus will be around 97.65 and 97.75 mm for the linear and circular spectropolarimetry, respectively.

      Once the value of the focus is determined, set the value by

      SYS@taurus> focus 97.65

      If you are doing both linear and circular spectropolarimetry, it is recommended that you add all necessary focus changes to your observing scripts, or automate focus changes using a GUI hwp (qwp) "Dfocus" setting of -0.2 (-0.1) mm for linear (circular) spectropolarimetry observations.

      Make sure you determine the telescope focus well. An out-of-focus image can lead to polarization effects if one samples it asymmetrically with the spectrograph slit. To some extent, one samples a certain part of the primary mirror and will see the polarization due to oblique incidence on that part of the mirror. With accurate focusing, all parts of the primary contribute equally and the average is zero.

    3. TV and autoguider focus

    4. It may be necessary to decrease the TV focus by 1500 and the autoguider focus by a few hundred. The telescope operator will take care of this.

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  9. Acquiring objects and taking data
    1. Acquiring objects

    2. Point the telescope to the source and type:

      SYS@taurus> agslit

      Due to the thickness and field vignetting of wave plates they have to be retracted from the optical path to acquire a target:

      SYS@taurus> hwout or qwout

      After the acquisition is finished and auto-guiding is on, the wave plate can be inserted back into the beam:

      SYS@taurus> hwin or qwin

      In the acquisition camera you should see something like the image below, where the vertical thick apertures are the dekker slots. Inside the dekker slots, towards the lower extreme, it is possible to distinguish a shadowed area which are edges of the dekker which can be seen due to 7.5 deg tilt of the dekker with respect to the slit-view camera. On the upper extreme of the dekker slots there are thin horizontal lines which are the joints of the metal plates of two adjacent dekkers. Finally, the dekker selected for observing has in the upper part of the slots another shadowed area which is the ISIS slit. The source should be placed in the intersection between the central dekker slot and the ISIS slit.

      Sometimes, particularly for bright targets, it is necessary to move the source out of ISIS slit to be able to see the dekker shape.

      Polarization dekker set
      Example of an image of the slit-view camera for ISIS in spectropolarimetry mode using the polarization dekker.

    3. Taking data

    4. Once the acquisition is finished, the telescope operator should start guiding if necessary and you can start the science observations.

      Take data using spectropolarimetry scripts in /home/whtobs/isis_scripts:

      SYS@taurus> linpolscript <camera> <int time> <title> [nloop] for lin. polarimetry,

      SYS@taurus> cirpolscript <camera> <int time> <title> [nloop] for circ. polarimetry,

      where arguments are denoted by <> and nloop is a number of loops which equals to one if not specified.

      This is an example of scripts for a linear and a circular spectropolarimetry which will take 4 and 2 images, respectively, at zero angles determined by your support astronomer. Zero angles are different for the red and the blue arm of ISIS, and also vary with other spectrograph settings like the central wavelength. Your support astronomer will modify the scripts to contain correct zero angles for your run.

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  10. Data reduction
  11. The observers can use the TSP (Time Series/Polarimetry Package) in Figaro, which is installed on ING computers as part of Starlink.

    In the terminal in the directory where your data are load packages:

    convert (this package is needed for fit/fits input files)

    Now you can use a function CCD2POL which reduces CCD spectropolarimetry data. This function expects in each frame four spectra corresponding to the ordinary and extraordinary rays for each of two apertures (A and B). These spectra are combined to derive a polarization spectrum in TSP format. ISIS data have usually six spectra for three apertures B (sky), A (target), and B (sky). Choose two apertures, one containing the target spectrum and one for the sky. The input data are expected to have Y axis as the dispersion direction (which is the case of ISIS data).

    To run the function CCD2POL, type:


    Here is an example of ccd2pol input parameters:

    FIGARO Input file for 0.0 degrees[1]
    FIGARO Input file for 45.0 degrees[1]
    FIGARO Input file for 22.5 degrees[1]
    FIGARO Input file for 67.5 degrees[1]
    Start column for the A aperture data
    Start column for the B aperture data
    Separation of ordinary and extraordinary spectra
    Number of columns to include in each extracted spectrum
    Aperture containing star (A or B)
    Bias level to be subtracted from data
    CCD readout noise (electrons/pixel)
    CCD gain (photons per ADU)
    Data reduction algorithm (OLD or RATIO)
    Output Dataset

    In the example above the spectra are laid out in columns with the aperture A spectrum in columns 147 to 156 (ordinary) and columns 183 to 192 (extraordinary) and the aperture B spectrum in columns 228 to 237 (ordinary) and columns 264 to 273 (extraordinary).

    The two algorithms (OLD or RATIO) differ in the method used to compensate for transparency variations between the observations at two plate positions. The RATIO algorithm works very well on bright stars, but can fail on faint objects (or on 100% polarized calibration sources) through attempting to take the square root of a negative number. Under these circumstances the OLD algorithm should be used.

    The variances on the polarization data are calculated from photon statistics plus readout noise.

    If you want to plot results, you can use a function PPLOT, which plots a polarization spectrum:


    Here is an example of pplot input parameters:

    Stokes Data to Plot
    Error per bin (per cent)
    Autoscale Plot
    Label for plot
    Plot Device

    Finally, if you want to calculate the polarization P and the position angle Theta for a polarization spectrum, use PTHETA function:


    Here is an example of ptheta input parameters:

    Polarization Spectrum
    First Wavelength to Use
    Last Wavelength to Use

    The input in this example is in pixels. The idea is that observers can quickly reduce the data immediately at the telescope, to confirm that the polarization and position angle are consistent with expectation from the literature. For a proper data reduction, observers can extract ordinary and extraordinary rays for target and sky apertures, and make a cube of these extracted spectra which will be then an input for CCD2POL.

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  12. Useful observing commands and information
  13. Commands to move halfwave (quarterwave) plate

    SYS@taurus> hwin (qwin), moves retarder plate in

    SYS@taurus> hwout (qwout), moves retarder plate out

    SYS@taurus> hwp <angle> (qwp <angle>), moves retarder plate to requested angle (0-360 deg)

    SYS@taurus> hwprot <rate> (qwprot <rate>), rotates retarder plate at requested rate (0 - 1 Hz)

    SYS@taurus> hwstop (qwstop), stops the rotation of retarder plate

    A continuous rotation for both quarter and halfwave plates has time-out of 12 hours in case the observer would forget to stop it.

    Other useful commands

    SYS@taurus> fcp calcite, moves the Savart plate into beam

    SYS@taurus> fcp_out, moves the Savart plate out of beam

    SYS@taurus> dekker 3, chooses the standard position of the polarization dekker

    SYS@taurus> mainfiltnd MF-POL-PAR, selects polarizer in the main colour filter unit

    SYS@taurus> mainfiltnd 1, removes polarizer in the main colour filter unit

    In case retarder plates do not move, type:

    SYS@taurus> inhw (inqw), which initializes halfwave (quarterwave) plate.

    Reference system

    The angle of the halfwave and quarterwave plate is relative to the instrumental reference. The orientation of the calcite block and the slit are fixed with respect to ISIS. So if the ISIS slit is at the parallactic angle, the angle of the retarder plate relative to north will depend on where on the sky the telescope points.

    A note on circular polarimetry

    Because the quarterwave plate is not exactly quarterwave for all wavelengths, the circular polarimeter is partly sensitive to linear polarization. If you suspect linear polarization in your source, you can depolarize it by continuous rotation of the halfwave plate ahead of the quarterwave plate (which is default configuration). This should eliminate systematic errors due to linear polarization, and invert but leave otherwise intact, the true circular polarization.

    If linear polarization of your source is strong, you must determine to what extent the telescope converts linear to circular. The way to do this is to set up ISIS for circular polarization, but observe a strongly linearly polarized star. Obtain 2 complete observations, with a rotator angle difference of 90 degrees. External circular polarization is constant, but converted linear will be inverted in the two observations.

    Instrumental polarization zeropoint

    To 'depolarize' a zero-polarization star completely, observe it twice, with a difference of about 90 degrees in rotator angle. In the Alt-Az frame, the average of the two observations represents pure instrumental zeropoint. The converse holds for a representation in the equatorial coordinate frame: the average is purely the stellar polarization.

    Photon noise calculation

    An absolute error in the Stokes parameter ~ 1/√ N_total , where N_total is a number of photons per resolution element. So for example, in order to determine one Stokes parameter to a degree-of-polarization accuracy of 0.005, 4x104 photons per resolution element are required. To obtain both linear Stokes parameters with that accuracy, we need two such observations. See more details in the section 3.8.1 of ISIS Spectropolarimetry Users' Manual.

    More information

    Some more information about ISIS spectropolarimetry can be found in the document ISIS Spectropolarimetry Users' Manual. Bear in mind that this is an old document that contains some information which is not valid anymore.

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Contact:  (ISIS Polarisation Specialist)
Last modified: 26 February 2018