Configuration file

The default configuration file is given below:

[Pre-processing options]

run_pre_processing     = True
remove_data_products   = True
split_observing_blocks = True
y_pixel_range          = [0,1024]


[Sky-subtraction]

sky_subtraction_method     = dithering-offset
sky_subtraction_min_offset = 100
remove_horizontal_stripes  = True

[Centering]

centering_method = single-Moffat
tied_offset      = False


[PDI options]

size_to_crop         = [120,120]
r_inner_IPS          = [0,3,6,9,12]
r_outer_IPS          = [3,6,9,12,15]
crosstalk_correction = True
minimise_U_phi       = True
r_crosstalk          = [7,17]


[Object information]

object_name      =
disk_pos_angle   = 0.0
disk_inclination = 0.0

The input parameters are divided into five groups:

Each parameter in the configuration file is explained below.

Pre-processing options

run_pre_processing:

True, False (default = True)

If True, perform the pre-processing reduction on the SCIENCE data. run_pre_processing should bet True the first time PIPPIN is run, but can be changed to False if you wish to tweak the input parameters of the PDI.

remove_data_products:

True, False (default = True)

If True, remove the intermediate data products (_reduced.fits and _skysub.fits files) once the pre-processing reduction is finished.

split_observing_blocks:

True, False (default = True)

If True, split the observing-blocks by ID. split_observing_blocks can be set to False if concurrent observations have altering OBS IDs.

y_pixel_range:

list (default = [0, 1024])

Vertical pixel indices to crop the intermediate data products between. Changing y_pixel_range can help to save time or memory with large data-cubes.

Sky-subtraction

sky_subtraction_method:

dithering-offset, box-median (default = dithering-offset)

If dithering-offset, PIPPIN uses observations at different dithering positions to subtract the sky background. The minimum separation of the dithering-positions is indicated with sky_subtraction_min_offset. If sky_subtraction_method is set to box-median, the sky contribution is estimated with the median in two boxes left and right of the beams. The boxes are drawn at a separation indicated by sky_subtraction_min_offset and continue to the edge of the detector.

sky_subtraction_min_offset:

integer (default = 100)

The minimum horizontal pixel-offset PIPPIN uses when carrying out the sky-subtraction via dithering-offset or box-median.

remove_horizontal_stripes:

True, False (default = False)

If True, PIPPIN attempts to remove the horizontal stripe pattern found as a read-out artefact in certain observations by fitting polynomials to each row of pixels.

Centering

centering_method:

single-Moffat, double-Moffat, maximum (default = single-Moffat)

Method to use for fitting the beam-centres. If centering_method is set to single-Moffat, PIPPIN uses a Moffat function for each beam to locate the ordinary and extra-ordinary beam-centres. If centering_method is set to double-Moffat, PIPPIN utilises two Moffat functions, one subtracted from the other, to replicate the flat top of saturated beams. If centering_method is set to maximum, PIPPIN locates the beam-centres as the brightest pixel in a median-filtered image (using a 3 \(\times\) 3 box). In general, the single-Moffat option should give a sufficiently accurate assessment of the beam-centres.

tied_offset:

True, False (default = False)

If True, PIPPIN will tie the offset between the two beams based on the used detector and fit for both beams at the same time. tied_offset is only supported by the single-Moffat and double-Moffat options of the centering_method parameter.

PDI options

size_to_crop:

list (default = [120,120])

The image-size of the ordinary and extra-ordinary beams (_beams.fits files). The final data products will inherit this image-size.

r_inner_IPS:

list or integer (default = [0,3,6,9,12])

Inner radii of the annuli that PIPPIN uses to equalise the flux in the ordinary and extra-ordinary beams following Avenhaus et al. (2014). These annuli are also used to perform the IP-subtraction under the assumption that the stellar light in the annulus is unpolarised (see Instrumental polarisation).

r_outer_IPS:

list or integer (default = [3,6,9,12,15])

Outer radii of the annuli that PIPPIN uses to equalise the flux in the ordinary and extra-ordinary beams. These annuli are also used to perform the IP-subtraction under the assumption that the stellar light in the annulus is unpolarised (see Instrumental polarisation).

crosstalk_correction:

True, False (default = False)

If True, PIPPIN corrects for the instrumental crosstalk between the linear and circular Stokes parameters following Avenhaus et al. (2014). The reduced efficiency of the Stokes \(U\) parameter is assessed in the annulus provided by r_crosstalk.

Attention

The crosstalk correction is made to function with non-symmetric disks as it employs a counting method of pixels with higher \(Q\)- than \(U\)-signal (Avenhaus et al. 2014). However, this method is not expected to work well with high-inclination disks due to the un-equal distribution of (any) signal-producing pixels over the \(Q\)- and \(U\)-quadrants.

minimise_U_phi:

True, False (default = False)

If True, PIPPIN minimises the \(U_\phi\)-signal in the r_crosstalk annulus following Avenhaus et al. (2014). If True, PIPPIN fits for an offset-angle when computing \(U_\phi\) (and \(Q_\phi\)).

Attention

Minimising the \(U_\phi\)-signal should be done with caution as it can lead to the removal of real \(Q_\phi\)-signal in high-inclination disks or in cases where crosstalk and IP have not been sufficiently corrected.

r_crosstalk:

list (default = [7,17])

Inner and outer radius of the annulus used in correcting for crosstalk with the crosstalk_correction and minimise_U_phi options.

Attention

Performing a crosstalk correction via crosstalk_correction = True or minimise_U_phi = True requires sufficient \(Q\)- and \(U\)-signal to be present in the r_crosstalk annulus. In cases where the signal is found only in specific quadrants of the \(Q\) or \(U\) images (e.g. a high-inclination or asymmetric disk), we recommend against using the crosstalk_correction and minimise_U_phi corrections.

Object information

object_name:

str (default = file_path)

Object name to query the SIMBAD archive for target coordinates. These coordinates are subsequently used to set up a world-coordinate system. If this parameter is not provided, PIPPIN will attempt to infer the object name from the directory in which it is run. If the object_name is not recognised by SIMBAD, the pipeline will exit with an error.

disk_pos_angle:

float (default = 0.0)

Disk position angle in degrees. This parameter is used to determine the de-projected radius.However, t

disk_inclination:

float (default = 0.0)

Disk inclination in degrees. This parameter is used to determine the de-projected radius.