News
Download
Documentation
Instruments
About
Author: Attila Kovacs <attila[AT]sigmyne.com>
Last updated: 23 Sep 2018
Introduction
This document contains information specific to using CRUSH-2 with SOFIA/HAWC+. 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 and the main CRUSH-2 README (especially Section 1. Getting Started), which covers installation and basic usage.
The basic installation procedure for CRUSH is covered by both the SOFIA specific README (README.sofia) and the main CRUSH README. Here only the installation specific to HAWC+ is discussed.
Automatic pipeline reductions (such as in flight) should never hang if possible.
Unfortunately, there are two uncommon conditions that can cause CRUSH (Java, really) to hang indefinitely. First, while trying to render a PNG output if the X11 display connection had dropped unexpectedly. And second, while trying to check for updates if the network had disconnected unexpectedly.
Both of these scenarios can be preemted by specifying appropriate runtime options for running CRUSH reductions with limited scope.
Simply (create and) edit a file:
~/.crush2/startup/crush/autopipeline.conf(This will specify settings only for the crush executable, and will not affect other tools, like imagetool or show). Into this file add the following lines:
CRUSH_NO_UPDATE_CHECK="1"
EXTRAOPTS="$EXTRAOPTS -Djava.awt.headless=true"The first will disable update checking (which can hang if the network connection drops), while the second will run CRUSH in headless mode (assuming no X11 rendering functionality), in addition to any startup options defined for all programs, thereby avoiding hangs if and when PNG outputs are rendered.
Normal users, outside of the automatic pipeline, should probably not set these options. Update notification is a useful feature, letting users know if or when improved CRUSH releases become available. And, while CRUSH does not currently require on-screen rendering, it is possible that future releases may add graphical functionalities that users may want to access (but would not be available in headless mode!).
For SOFIA/HAWC+ CRUSH will be launched exclusively from the DRP pipeline. See the DRP documentation for details.
However, if you wish to run CRUSH manually, you may easily do so from the command-line with hawc+ as your instrument. E.g.:
./crush hawc+ [...]See the SOFIA specific README for using CRUSH with a SOFIA instrument, or consult the main README for more details on using CRUSH in general. This document discusses only the use of CRUSH specific to HAWC+.
The DRP interface to CRUSH allows manually specifying reduction options, which are passed to CRUSH verbetum as a single line. 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:
-faint -name="My HAWC+ image.fits" -projection=TANBelow is a brief guide to a few useful options, grouped by functionality.
-subarray=<list> Restrict imaging to specific subarrays only. The
argument is a comma separated list of subarray IDs
(R0, R1, T0, T1). E.g.:
> crush hawc+ -subarray=R0,T0 ...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.
polarrays Pixels of the the R and T polarization arrays, respectively.
subarrays Pixels of each of the 4 HAWC+ subarrays (40x32). Each subarray
may contain correlated signals to themselves, e.g. do to
correlated thermal fluctuations on their wafers.
bias Grouping of pixels by TES bias line. Each subarray has 20
bias lines, each applied to two consecutive detectors rows.
mux A grouping of pixels based on their SQUID multiplexing scheme
Each 4x8 pixel quadrant of the array is read out through the
same SQUID amplifier. Therefore, it is not suprizing that
correlated signals are present on these quadrants. The
decorrelating on `mux` groups is default in HAWC+ reductions
rows The HAWC+ multiplexing scheme is implemented in the time-domain
Thus, the first channels of each SQUID are read out at the same
time, followed by the second channel in each group etc. Thus,
if there is any pickup of high-frequency signals in the
multiplexing scheme, one could expect some correlated signals
to be present on these multiplexer address lines. There
is little evidence for these, but the reduction of very faint
compact sources may benefit from the additional decorrelation
on these groups.
For HAWC+, these SQUID address lines are effectively the
detectors rows, hence the naming.
series The grouping of pixels based on the series array through which
they are read out.band=X Set the observing band to A, B, C, D, or E. Normally,
the band setting is automatic through the SPECTEL1
fits keyword. However, setting the band manually may
be useful for polling band specific settings. E.g.
> crush hawc+ -band=A -poll=beam
The above line will report the Gaussian FWHM beam size
(in arcsec) used when reducing band A (53um) data.
biaslines @Alias: 'correlated.bias'
@Expert
Decorrelate TES bias lines. All correlated modality
suboptions apply.
@See: 'correlated.<?>'
filter=<wavelength> @Expert
Sets the filter band to one of:
53um, 62um, 89um, 155um, or 216um
Normally, the filter is set automatically to the
correct value based on the 'SPECTEL1' SOFIA header key.
For this reason, it is not recommended, nor trivial
for the user to override this automatic behaviour.
Rather, the setting of this option is useful for
setting conditional settings, which depend on the
HAWC+ waveband.
fixjumps @Expert
Enables ficing timestream blocks around flux jumps
in such a way that these will not cause problems.
@See: 'jumpdata'
gyrocorrect @Telescope: SOFIA
@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.
jumpdata=<path> @Expert
@Since: 2.40
Specify the file containing the residual pixel jump
counts when flux jumps occur. The input file follows
the format by Darren with 3 columns: (1) The character
'C' specifying that the value is per column, (2)
the column index (starting from 0), and (3) the
residual flux jump in readout counts.
@See: 'fixjumps'
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.R1=dx,dy
offset.R2=dx,dy
offset.T1=dx,dy
offset.T2=dx,dy @Expert
Specify the subarray offset (as dx,dy pixels in
the focal plane) from their nominal positions, for
both the first and second subarrays of the R and T
polarization arrays. For example, specifying zero
offsets for all (default) describes the focal plane
where R and T are perfectly aligned relative to
one another, and the two subarrays of each form a
single seamless polarization array.
peakflux @Since: 2.41
Switch to peak-flux calibration instead of the default
aperture flux calibration. Recommended for point
sources only.
pixelsize=<a>[,<b>] @Expert
Specify the size of the pixels for calculating pixel
positions based on a regular grid.
The argument can be either a lateral size (in arcsec)
for square pixels, or two comma separated sizes for
rectangular pixels.
@See: 'rotation', 'pcenter'
pols @Alias: 'correlated.polarrays'
@Expert
Decorrelate each polarization array separately. All
correlated modality sub-options apply.
@See: 'correlated.<?>'
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 array rotation (in degrees).
@See: 'rotation.T', 'pixelsize'
rotation.T=<deg> @Expert
Specify the rotation of the T polarization subarray
relative to the R subarray.
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. Normally, sidereal object coordinates
are determined via the header keywords OBSRA/OBSDEC or
OBJRA/OBJDEC. However, these were not always filled
correctly during the 2016 October flights, so this
option provides a workaround for those scans.
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.
subarray=<list> @Expert
Restrict the reduction only to the subarrays listed.
The argument is a comma-separated list of subarray
codes: R1, R2, T1, T2 or R (= R1,R2) or T (= T1,T2).
> crush hawc+ -subarray=R1,T1 [...]
write.flatfield[=path] @Expert
Write a DRP flatfield FITS file, to be used by
the chop-nod pipeline. The optional argument can
specify the FITS file's name. Otherwise, a default
name is used, containing the scan's ID, and placed in
the the directory specified by 'outpath'.
The file format is specified by Marc Berthoud.
@See: 'outpath'Here you will find only the log quantities specific to HAWC+. 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.
gyro.max (arcsec) Maximum gyro drift during scan.
gyro.rms (arcsec) RMS gyro drift during scan.
scan.Ax (arcsec) X amplitude
scan.Ay (arcsec) Y amplitude
scan.cross Is cross scanning?
scan.dY (arcsec) Raster scan step size
scan.frel Lissajous Y/X frequency ratio
scan.iters Number of iterations
scan.nsubs Number of subscans
scan.PA (deg) Current scan position angle
scan.pattern Scanning pattern
scan.phi0 (deg) Lissajous Y/X relative phase.
scan.strips Number of raster strips
scan.T (s) Scan duration
scan.t0 (s) Lissajous time shift.
scan.trk Is tracking enabled?
scan.X (arcsec) Raster scan lengthCopyright (C)2018 – Attila Kovacs <attila[AT]sigmyne.com>