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Author: Attila Kovacs <attila[AT]sigmyne.com>
Last updated: 27 Sep 2018
Introduction
This document contains information specific to using CRUSH-2 with SOFIA/HIRMES. It should be used in conjuction with the more generic README for SOFIA instruments (README.sofia), and with the master README for using CRUSH in general.
It is recommended that you also familiarize yourself with both the SOFIA specific README (README.sofia) and the main CRUSH-2 README (especially Section 1. Getting Started), which covers installation and basic usage.
You may specify reduction options as command-line arguments to CRUSH. Each option in the line begins with a dash -, and should not contain white spaces, unless these are enclosed in quotes. E.g. below is a valid option line, with three options, one of which contains a white-space characters:
crush hirmes -faint -name=“My HIRMES image.fits” -projection=TAN …
Spectral cubes can be quite large, and mostly empty, especially in mid-resolution mode. As such, you may want to produce compressed output. CRUSH has an option for that:
gzip Compress outputs (e.g. FITS) with gzip, if possible.
(The .gz extension will be added to the output name as
necessary.)The ‘gzip’ option is enabled, by default, for spectral cubes. To disable, use ‘-blacklist=gzip’ command-line option.
The SOFIA README offers is a brief guide to a few useful options for using CRUSH with any SOFIA instrument. Here only the options specific to HIRMES are discussed.
-spectral.unit=<spec> Set the spectral unit to use, e.g. to `GHz` or `um`.
All spectral inputs and outputs will be referred to in
the specified unit. (The default is `Hz`).
@See: `spectral.grid`
-spectral.grid=X Explcitly define the spectral bin (grid) size to X in
the specified `spectral.unit` (default is `Hz`).
@See: `spectral.unit`, `spectral.resolution`
-spectral.R=X Specify a spectral resolving power X (f/df) at the
center frequency of observation. This option is used
only if the spectral bin (grid) size is not explicitly
defined via `spectral.gid`.
@See: `spectral.grid`From this point on, the documentation is of more technical nature, intended for expert users only.
For a general overview of channel divisions, please consult Section 3. (Correlated Signals) in the main README document.
bias Grouping of pixels by TES bias line. Each subarray has 20
bias lines, each applied to two consecutive detectors rows.
cols Grouping of detector pixels by physical (geomtric) detector
columns.
mux A grouping of pixels based on their SQUID multiplexing scheme,
allowing to decorrelate pixels that share the same readout MUX.
pins A grouping of pixels among different MUXes that share the
same MUX address (i.e. pin).
rows Grouping of detector pixels by physical (geometric) detector
rows.
series The grouping of pixels based on the series array through which
they are read out.
subarrays Grouping of pixels by subarray.blinds @Expert
Use information from blind detectors (ones that are
not illuminated) when decorrelating groups of channels
The inclusion of blind detectors can be useful for
removing correlated thermal and/or electronic noise.
cols @Alias: 'correlated.cols'
@Expert
Decorrelate on physical (geometric) detector columns.
All correlated modality suboptions apply.
@See: 'correlated.<?>'
darkcorrect @Expert
Include the dark SQUIDs when decorrelating over SQUID
MUXes (`mux` option).
gyrocorrect @Since: 2.41
@Advanced
Correct for gyro drifts based on guide-star relock
data stored in the scan headers. This isn't normally
needed when the gyros funtion properly. But,
occasionally, they drift a fair bit, and this option
can activate the correction scheme on demand.
imaging.aperture=X[,Y] @Expert
Specifies the imaging aperture size, either as a square
of X arcseconds size, or a rectangle of X by Y arcsec.
los @Alias: 'correlated.los'
@Since: 2.41
@Expert
Remove correlations with the second-derivative to the
telescope line-of-sight (LOS) angle. It's a good proxy
for removing pitch-type acceleration response from the
detector timestreams.
@See: 'correlated.<?>'
mux @Alias: 'correlated.mux'
@Expert
Decorrelate on SQUID muxes. All correlated modality
suboptions apply.
@See: 'correlated.<?>'
offset.blue=dx,dy
offset.red=dx,dy
offset.hires=dx,dy @Expert
Specify the subarray offset (as dx,dy pixels in
the focal plane) from their nominal positions, for
the two lowres subarrays or the hires array.
pins @Alias: 'correlated.pins'
@Expert
Decorrelate on pixels that share MUX addresses (pins)
over different MUXes. All correlated modality
suboptions apply.
@See: 'correlated.<?>'
pixelsize=X[,Y] @Expert
Specify the size of the pixels for calculating pixel
positions based on a regular grid.
The argument can be either X lateral size (in arcsec)
for square pixels, or two comma separated sizes for
rectangular pixels.
@See: 'platescale', 'rotation', 'pcenter'
platescale=X @Expert
Override the plate scale recorded in the FITS, and
set it manually to X arcsec/mm.
@See: 'pixelsize'
roll @Alias: 'correlated.roll'
@Since: 2.41
@Expert
Remove correlations with the second-derivative of the
aircraft roll angle (roll-type accelerations).
@See: 'correlated.<?>'
rotation=<deg> @Expert
Specify the focal-plane rotation (in degrees).
@See: 'pixelsize'
rotation.red=<deg>
rotation.blue=<deg>
rotation.hires=<deg> @Expert
Specify the relative rotation of each subarray in
the focal plane.
rows @Alias: 'correlated.rows'
@Expert
Decorrelate along the 'row' direction of the arrays,
the same as SQUID address lines. All correlated
modality sub-options apply.
@See: 'correlated.<?>'
rtoc @Expert
@Since: 2.33
Instruct crush to reference maps to Real-Time Object
Coordinates (RTOC) for sidereal and non-sidereal
sources alike. Otherwise, sidereal object coordinates
are determined via the header keywords OBSRA/OBSDEC or
OBJRA/OBJDEC.
series @Alias: 'correlated.series'
@Expert
Decorrelate on the series arrays. It seems that the
series array (at 4K) is sensitive to some level of
thermal fluctuation, and enabling decorrelation on
these can improve imaging quality.
spectral.grid=X Specify the bin spacing in the spectral dimension to
X, in the units set by 'spectral.unit'. When present
this option supercedes the 'spectral.R', which
is an elternative way to set the spectral bin size.
@See: 'spectral.unit'
spectral.obs Output spectra in the observing frame rather than the
default rest frame.
spectral.R=X Specify a spectral resolving power X at the
center frequency of observation. This option is used
only if the spectral bin (grid) size is not explicitly
defined via `spectral.grid`.
@See: `spectral.grid`
spectral.unit=<spec> Specify the unit of the spectral axis in the
output data. It can be a wavelength unit, such as 'um'
(micron) or a frequency unit, such as 'GHz'.
write.fieldspec Write the aggregate 1D field spectrum as and ASCII
table also. This data can also be readiliy plotted
using gnuplot if the '.eps' and/or '.png' sub-options
are set (see below). The plot can be customized via
a set of sub-options '.lt', '.lw', '.pt', '.ps' and
'.style' in accordance with gnuplot's capabilities.
@See: 'gnuplot'
write.fieldspec.eps Create an EPS plot from the aggregate 1D field
spectrum using gnuplot.
@See: 'gnuplot'
write.fieldspec.lt=N Set the plot line type to gnuplot's built-in type N.
write.fieldspec.lw=X Set the plot line with to X points wide, e.g. 2.5.
write.fieldspec.nodata=<string> Set how NaN (no data) values are reported
The specified string will be used verbetum where no
valid data is available.
write.fieldspec.png Create a PNG plot from the aggregate 1D field
spectrum using gnuplot. A set of sub-options can be
used to customize the appearance
write.fieldspec.png.bg=<color> Set the PNG background color to the
specified color (e.g. 'white' or '#FFFFFF', or
'transparent').
write.fieldspec.png.size=NxM Set the PNG output size to N by M pixels.
write.fieldspec.ps=X Set the plot point size scale factor to X, e.g. 1.5.
write.fieldspec.pt=N Set the plot point tyle to gnuplot built-in type N.
write.fieldspec.show Display the plot on screen right away.
write.fieldspec.style=<plotstyle> Set the gnuplot plotting style for 1D
data. E.g. 'histep', or 'points' or 'lines' or
'linespoints'.
write.flattened Write a flattened 2D (monochrome) FITS image also.
write.flattened.gzip Compress the flattened image with gzip.Here you will find only the log quantities specific to HIRMES. See also README.sofia for all SOFIA specific log quantities, and the main CRUSH README for an even more generic list of available log quantities.
gratingAngle (deg) Grating angle
gyro.max (arcsec) Maximum gyro drift during scan.
gyro.rms (arcsec) RMS gyro drift during scan.
FPIk (1/radian) FPI dispersion constant
mode HIRMES configuration mode.
ref.x (mm) Focal plane reference X position.
ref.y (mm) Focal plane reference Y position.
strip [0-7] Integer index of hires strip in used, if
applicableCopyright (C)2018 – Attila Kovacs <attila[AT]sigmyne.com>