Configuration Parameters
A number of reduction parameters can be changed using entries in the configuration file.
If you installed the pipeline with pip
, the configuration file will not be
easy to find, since it will be stored with installed pip
packages. We recommend
editing a copy of the config instead. You can create a copy of the config file
by invoking the pipeline with the --write_config
option:
reduce_kcwi --write_config
This will create an editable file wherever you run the command from. You can
make whatever changes you need to this file, and then run the pipeline with the
-c
option (see main reduction script)
pointing to that file. For example,
reduce_kcwi -r -c PATH/TO/CONFIG/kcwi.cfg -f kb0001.fits
The configuration file contains a number of parameters connected to the structure of the files and to the specifications of the instrument, e.g., the number of continuum bars. There is usually no reason to modify these parameters, and they are not described here.
Note
If a parameter in the kcwi.cfg
file is not described here, then you can
assume that it should not be modified.
The remaining parameters are used to control the processing algorithms and are described here.
Blue and Red sections of the configuration file
Now that the Red channel has been installed, there is a need to specify
different default parameters for each channel. These are delineated in the
config file with [BLUE]
and [RED]
section headers. For example, to
deal with cosmic rays, the Red channel uses a median stack of three continuum
bars images and a median stack of three arc lamp images, while the Blue channel
only requires one each of those images.
Processing parameters
bias_min_nframes = 7
flat_min_nframes = 6
dome_min_nframes = 3
twiflat_min_nframes = 1
dark_min_nframes = 3
arc_min_nframes = 1 # = 3 for [RED]
contbars_min_nframes = 1 # = 3 for [RED]
minoscanpix = 75 # = 20 for [RED]
oscanbuf = 20 # = 5 for [RED]
These parameters control the minimum number of bias, internal/dome/twilight flats and darks that the DRP expects before producing a master calibration. The arcs and contbars minimum numbers are different for the Blue and Red channels as described above. The values shown here are synchronized with the calibration scripts that are used at WMKO for afternoon calibrations.
The overscan parameters are based on the configuration of the Blue and Red detectors and we do not recommend altering these parameters, but show them here to illustrate that they differ between channels.
skipscat = False # Skip subtracting scattered light?
skipsky = False # Skip sky subtraction?
These control scattered light subtraction and sky subtraction. Setting either
of these to True
will skip the subtraction for all subsequent runs of the
pipeline. Skipping sky subtraction globally can also be invoked by using
-k
on the command line.
plot_pause = 1 # Pause time for each plot in seconds
saveintims = False # Save intermediate images during basic reduction
verbose = 1 # Verbosity of output
These control various aspects of how the DRP runs: how long to pause at each
plot if not in interactive mode (see plot_level
below), whether to save
intermediate images for diagnosis, and the verbosity level of text output.
TAPERFRAC = 0.2 # Adjusts edge taper for Atlas cross-correlation
TUKEYALPHA = 0.2 # Tukey alpha value for cross-correlating bars
FRACMAX = 0.5 # How much of line peak to use for fitting
MIDFRAC = -1.0 # Middle fraction or -1 to use default calculation
ATOFF = 0 # Atlas offset or 0 to use default calculation
LINELIST = "" # Optional line list to use instead of generated
LINETHRESH = 100. # Line threshold for fitting
These adjust the way in which arc line fitting is performed. Most of these parameters are also available on the command line.
In most cases, you will not have to adjust these. For the Red channel, we use these default values:
TUKEYALPHA = 0.7
FRACMAX = 0.25
LINETHRESH = 10.
See the [RED]
section to make changes for Red channel data.
default_arc_lamp = 'ThAr'
KCWI has two calibration lamps, Thorium/Argon (ThAr) and Iron/Argon (FeAr). This parameter specifies which of the two lamps should be used by the DRP. The default is to use the ThAr lamp.
Wavelength correction parameters:
radial_velocity_correction = "heliocentric"
air_to_vacuum = True # Defaults to vacuum wavelengths
These control the refinement of the wavelength solution. You can specify if you
want air wavelengths by setting air_to_vacuum
to False
. You can
specify the type of radial velocity correct as one of:
heliocentric
barycentric
none
Plotting parameters
# BOKEH SERVER
enable_bokeh = True
plot_level = 1
These parameters control the plotting features of the DRP. Plotting is performed using a combination of a Bokeh server running in the background and a browser front end.
To activate the plotting features, set enable_bokeh = True
. When the DRP
starts, it will check if there is an instance of the Bokeh server running or
start one. A browser window will be opened automatically when needed.
The plot_level
parameter controls the level of interactivity. Setting it 0
will disable plotting. Setting it to 1 will enable plotting, but the DRP will
not interact with the user. A higher level will increase both the verbosity and
the interactivity of the plots. The highest level is 3. At this level, the user
will be provided with a plot of every arc line, for example, with a graphic
representation of the fitting used to determine the central position.
For general use, it is advisable to leave the plot level to 1.
The size of the plotting window can be specified using plot_width
and
plot_height
.
Cosmic rays rejection parameters
CRR_MINEXPTIME = 60.0
CRR_PSSL = 0.0
CRR_GAIN = 1.0
CRR_READNOISE = 3.2
CRR_SIGCLIP = 4.5
CRR_SIGFRAC = 0.3
CRR_OBJLIM = 4.0
CRR_PSFFWHM = 2.5
CRR_FSMODE = "median"
CRR_PSFMODEL = "gauss"
CRR_SATLEVEL = 60000.0
CRR_VERBOSE = False
CRR_SEPMED = False
CRR_CLEANTYPE = "meanmask"
CRR_NITER = 4
These parameters are used to control the CRR algorithms. See the documentation in astroscrappy for details.
Combining science images
The following parameter controls what is done with science frames, including
standard star observations. There is one in each of the [BLUE]
and [RED]
sections of the parameter file, so you can specify a non-default value for one
channel at a time.
object_min_nframes = 1
If you wish to combine images (to mitigate CRs, e.g.), you can set this to the
number of identically positioned science images that you want to combine. There
is an additional step required. The FITS header keyword GROUPID for the images
to be combined must be identical. This can be achieved with any FITS header
keyword editor. It is recommended that you combine at least three images to
have a good chance of mitigating CRs. In the case that three images are
combined, the routine kcwidrp.primitives.MakeMasterObject
will use the
median
method for combining the images. If there are more than three, it
will use the average
method. In both cases, it does a 2-sigma high clip.
A master object file will be output using the base name of the first file in the group. For example:
kr230605_00119_mobj.fits
This file will then be processed through the rest of the pipeline and result in a combined, calibrated data cube:
kr230605_00119_icubes.fits
which should have fewer CRs than an individual frame. Be aware, however, that if
you have only three images and use the median
combine method, the S/N ratio
will be equivalent to a single exposure. The other frames in the group will not
be processed beyond the point where they are combined (currently just after
illumination correction: _intf.fits
creation).