
Syntax: crush [[-option]...] scan-spec [[[-option]...] scan-spec] [...]

 Scan Specifications: 
  #             Scan number. E.g. 8293.
  #-#           Range of scan numbers. E.g. 8287-8291.
  <name>        Scan file name with or without path.

 Options to Crush: 

  -outpath=     Set the default output path. (../data/)
  -name=        Specify the name of the output file or 'auto'.
  -out=         Full path and name of the output or 'auto'. (auto)
  -MaiTau=      The Mai-Tau server address.. (fangorn.submm.caltech.edu)
  -default      Set the default values from 'crush.cfg'. 
  -bright       Set Bright Source overriders (bright.cfg). E.g. Jupiter.
  -faint        Set Faint Source overriders (faint.cfg).
  -deep         Set Deep Field Source overriders (deep.cfg).
  -point        Reduce in pointing mode (point.cfg). 
  -config=      Parse the specified configuration file. (/home/pumukli/.crush)
  -precess=     Precess coordinates to the epoch. (J2000.0)
  -info         Provide scan info on the console and exit. ()
  -log=         Log scan info to the specified file and exit. (off)
  -spectrum=    Write spectral info for specified model. (off)
  -skySpectrum= Write 2-D sky spectrum. (off)
  -scanMaps     Write maps for each scan too. 
  -help         Show this help screen.
  -version      Print version information.


 Scan Specific Options: 

 (These options apply to all subsequently listed scans on the command line.)

  -path=          The location of the SHARC-2 data. (/home/data/)
  -prefix=        The string preceding the scan serial no. (sharc2-)
  -tau=           Define how tau is obtained. (MaiTau:350um).
  -Jy=            Conversion factor from bolometer V to Jy/pixel. (6.4E-7)
  -directGains    Calculate gains directly from detector offsets. (*)
  -pixelData=     The way the pixel data is obtained. (fits:fwo)
  -pixelCoeffs=   Pixel Non-linearity coefficients file. (auto)
  -lookup=        Boolean or 'auto'. Whether to use lookups internally. (auto)
  -13Hz           Action on 13.4Hz noisy pixels. (filter)
  -width13Hz=     13.4Hz filter width in Hz. (0.3)
  -edge           Array edges to ignore. Single value, or l:r:t:b. (-1:-1:-1:-1)
  -minIntT=       Minimum required integration time in seconds. (30.0)
  -gapOK=         Tolerate timing gaps if found. (JSharc)
  -chopped=       Whether to use chopper information. (auto).
  -smear=         Maximum allowed chopper smear in arcsec. (4.0)
  -average=       Downsample data over the number of frames. (3)
  -flags=         Pixel flag pattern to exclude from reduction. (0x3)
  -hipass=        Time scale (s) for the high-pass filter or 'auto'. (off)
  -vclip=         Clip frames if scanning speed is below. (off)
  -aclip=         Clip frames if acceleration is above. (off)
  -scale=         Scaling factor to be applied to scan data. (1.0)
  -platescale=    The SHARC2 pixel plate scale. (auto)
  -pcenter=       Pointing Center from corner in pixels. (auto)
  -rcenter=       Rotation Axis from corner in pixels. (auto)
  -rotator=       Obtain/override instrument rotator value. (auto)
  -rot0=          Obtain/override the recorded rotator reference value. (auto)
  -FAZO=          Adjust the azymuthal pointing. (auto)
  -FZAO=          Adjust the zenith angle pointing. (auto)
  -excessLoad=    The excess load temperature in Kelvin. (0.00)


 Reduction Options: 

 (These are global settings affecting the reduction pipeline.)

  -map=         Where to insert the source model. (after:MUXOffsets)
  -reorder      Determine Pipeline Order based on preliminary solution. (*)
  -noreorder    Leave pipeline as is. 
  -radec        Reduce in RA/DEC coordinates. (*)
  -altaz        Reduce in Alt/Az coordinates. 
  -static       Assume source fixed on RA/DEC sky. Use absolute coordinates (*)
  -planetary    Use relative coordinates wrt tracking center - e.g. planets. 
  -linear       Use linear pixel response. 
  -nonlinear    Use non-linear pixel response. (*)
  -index        Create coordinate index file at end. 
  -noindex      Do not create coordinate index file. (*)
  -gains        Create standard pixel data file at end. 
  -nogains      Do not create standard pixel data file. (*)
  -models       Add model data to FITS. 
  -nomodels     Do not write model data. (*)
  -noflag       Disable all models that flag pixels. 
  -residuals    Dump unmodelled residuals to file. 
  -noresiduals  Do not write model residuals. (*)
  -covar=       [fits|scan|global|off|r:c] The way covariances are written. (off)
  -spacial      Write spacial correlations of residuals. 
  -nospacial    Do not write spacial correlations. (*)
  -histogram    Add residual pixel histogram data to FITS. (*)
  -nohist       Do not add pixel histograms to FITS. 
  -efficiency   Measure relative beam efficiencies on the array.
  -chi2=        If and how chi-squared is reported. (weight)
  -tauScale=    tau(id) = at + b as "id(a,b)". (350um,225GHz,Sharc2)
  -rounds=      Set the number of iterations in the solution. (6)
  -gainRounds=  Number of iterations for the initial gain solution. (auto)
  -gainGoal=    Gain convergence goal for 'auto' gain rounds. (1.0E-3)
  -TCscale=     Scaling factor for all model time constants. (1.0)
  -histbin=     The pixel histogram bin size in sigma units. (0.5)
  -histrange=   The pixel histogram range in sigma units. (20.0)
  -mask=        The source mask file used. (none)
  -model=       Specify an initial source model. (none)
  -aperture     Solve for sources inside the masked apertures. 
  -slice=       Chose a scan and frame to sample models. (off)
  -scramble     Scrable pixels (do not expect to see source!!!). 
  -debug        Look for anomalies in data. 


 Options to PixelOffsets:

  -Ioffset=     Activate model at iteration. (auto)
  -Eoffset=     Estimator to use. (default)


 Options to CorrelatedNoise:

  -Icorr=       Activate model at iteration. (auto)
  -Ecorr=       Estimator to use (default)
  -ItauAdjust   Adjust transmission based on total power variation. (auto)


 Options to PixelWeighting:

  -Ipweight=     Activate model at iteration. (auto)
  -pwRange=      Relative spectral interval for pixel weighting. (0.7-0.9)
  -mindof=       Minimum degrees of freedom required for weighting. (1.0)
  -flagFraction= Flag noisies fraction of pixels. (off)
  -maxNoise=     Maximum tolerated noise over median pixel noise. (off)


 Options to ResidualSpikeRemoval:

  -Ispike=      Activate model at iteration. (auto)
  -spikelevel=  Level (in sigmas) above which to remove residual spikes. (10.0)
  -spikeratio=  Maximum fraction of pixel spikes before flagging. (0.0010)


 Options to PixelGains:

  -Igain=       Activate model at iteration. (auto)


 Options to PixelNonlinearities:

  -Inonlinear=  Activate model at iteration. (off)


 Options to TemporalPixelAnalysis:

  -Itemporal=   Activate model at iteration. (auto)
  -temporalT=   Minimum feature size (frames). (5)
  -maxTemporal= Maximum tolerated spectral feature before flagging. (10.0)


 Options to ChopResiduals:

  -Ichop=        Activate model at iteration. (auto)


 Options to SkyPolynomials:

  -Isky=      Activate model at iteration. (auto)
  -skyT=      Number of frames per sky polynomial fit. (1)
  -skyorder=  The polynomial order to fit for the sky. (1). 

 Options to TimeWeighting:

  -Itweight=    Activate model at iteration. (auto)
  -weightT=     Number of frames per weight value. (100)


 Options to RowBiasDrifts:

  -IrowDrift=   Activate model at iteration. (auto)
  -rowDriftT=   Number of frames per row bias drift value. (32)


 Options to MUXOffsets:

  -Imux=        Activate model at iteration. (off)
  -Emux=        Estimator to use. (default)
  -muxT=        Number of frames per multiplexer offset value. (1)


 Options to SourceMap:

  -Imap=        Activate model at iteration. (auto)
  -Emap=        Source map estimator (default)
  -Ifidel=      Faithful source removal from iteration. (3)
  -Iextended=   Source generations preserving all extended structure. (2)
  -cutoff=      S/N below which to clip when not faithful. (5.0)
  -unit=        The mapping units. ("Jy/beam")
  -mapJy=       Conversion factor from bolometer V to Jy/pixel. (3.53E-7)
  -minExp=      Clip positions with smaller relative exposure. (output:0.1)
  -maxRMS=      Clip positions with higher relative RMS. (none:3.0)
  -show         Display source map while reducing. 
  -noshow       Do not display source on-the-fly. (*)
  -atm          Apply atmospheric flux correction. (*)
  -noatm        No atmospheric correction.
  -compact      Cleaner maps but extended structures may be missing. 
  -extended     Retain extended structures in map. (*)
  -extFilter=   Filter extended structures over scale. (off)
  -fftFilter=   Filter extended structures over scale. (off)
  -extBlank=    The S/N level that is used for blanking the extended filter.6.0)
  -beam=        The SHARC2 beam FWHM in arcsec. (8.5)
  -grid=        The map pixelization in arcsec. (1.62)
  -projection=  The spherical projection method used (GLS)
  -smooth=      Smooth map to beam size in arcsec. (initial:0.0,faithful:0.0,final:4.0)
  -lambda=      The MEM lambda parameter (0.1)
  -positivity=  The MEM positivity (absolute)
  -diameter=    The assumed source diameter in arcsec. (15.0)
  -minPixels=   Minimum number of active pixels for mapping. (100)
  -mapWeight=   Derive robust map weights for each scan. (true)
  -reweight=    Robust reweighting of the final map. (true)
  -correct=     Flux correcting FWHM or 'point' or 'none', (none)


 Options to BeamEfficiency:

  -Ibeam=        Activate model at iteration. (off)


 Options to PixelDrifts:

  -Idrift=      Activate model at iteration. (auto)
  -driftT=      Number of frames per drift offset value. (512)


 Options to SpectralPixelAnalysis:

  -Ispectral=   Activate model at iteration. (auto)
  -maxSpectral= Maximum tolerated spectral feature before flagging. (6.0)


 Options to RegionalCorrelations:

  -Iregion=      Activate model at iteration. (off)
  -regionalT=    Temporal resolution in frames. (8)
  -regionType=   Form of the regional correlations. (Gaussian)
  -regionSize=   Scale or FWHM (in arcsec) of the regions. (30.0)


 Options to BlockCorrelations:

  -Iblock=     Activate model at iteration. (off)
  -Eblock=     Estimator to use. (default)
  -blockT=     Number of frames per blockal offset value. (8)
  -blocksize=  Lateral size(s) in pixels.of initial blocks. (6x6)


 Options to AccelerationResponse:

  -Iaccel=       Activate model at iteration. (off)

