create.par.file <-
function(
filename="Lambdar_default.par",
RootDirectory="./",
WorkingDirectory="./",
OutputDirectory="./",
Catalogue="catalogue.csv",
DataMap="image.fits",
BeamArea_SqAS=0,
PSFConvolve=0,
RadialTolerance=25,
MaxNumPSF=500,
PSFCheck=0,
PSFWeighted=1,
PSFMap='NONE',
Gauss_FWHM_AS=0,
PSFLabel='SEEING',
PSFLabelType='FWHM.ARCSEC',
SimGauss_AS=0,
RemoveContam=0,
CheckContam=0,
nNearestCheck=10,
NoContamImageFile='NoContamResidualImage.fits',
CatIDColumnLabel='CATAID',
RAColumnLabel='RAdeg',
DecColumnLabel='DECdeg',
ThetaColumnLabel='rotN2E',
SemiMajColumnLabel='radmajasec',
SemiMinColumnLabel='radminasec',
ContamColumnLabel='CONTAM',
FluxWgtColumnLabel='FLUXWEIGHT',
ErrorMap='NONE',
MaskMap='NONE',
WeightMap='NONE',
WeightMapZP=0,
Saturation=Inf,
SaturationLabel='SATUR',
GainLabel='GAIN',
DataExtn=0,
ErrorExtn=0,
MaskExtn=0,
WeightExtn=0,
ApertureType=1,
EFactor=1,
FluxCorr=1,
CropImage=0,
CropFitsName='croppedimage',
CropImRA0=-999,
CropImDec0=-999,
CropImRad=0.5,
Confusion_units=0,
nProcessors=1,
CarefulWithEdges=1,
AngularOffset=0,
MapUnitsPerBeam=0,
ResampleAper=0,
ResamplingRes=3,
ResamplingIters=2,
PSFConfidence=1,
ApStampWidth=1.05,
SourceMaskOnly=0,
WriteSourceMask=0,
WriteAAMask=0,
AllApersFile='AllApertures_Mask.fits',
WriteFAMask=0,
ConvApersFile='AllConvolvedApertures_Mask.fits',
WriteDFAMask=0,
DeblConvApersFile='AllDeblConvolvedApertures_Mask.fits',
WriteResidMap=0,
ResidImageFile='ResidualImage.fits',
WriteTable=1,
TableName='LAMBDAR_Results',
ShowTime=0,
Interactive=0,
UseMaskLim=0.2,
Diagnostic=0,
Verbose=0,
PlotDevice='png',
PlotSample=0,
PlotAll=0,
Magnitudes=1,
MagZPLabel='MagZP',
ABVegaFlux=1.0,
MagZeroPoint=8.9,
BlankCor=0,
nBlanks=10,
RanCor=0,
nRandoms=10,
DoSkyEst=0,
GetSkyRMS=0,
SkyEstIters=5,
SkyEstProbCut=3,
SkyCorrelNoise=1,
SkyDefault='median',
SourceMaskFile='SourceMask.fits',
TransmissionMap=0,
GetDeblFrac=0,
SourceMaskConfLim=0.95,
MinApRad=0,
MemorySafe=0,
ApertureConfLimit=0.9,
IterateFluxes=0,
nIterations=2,
FluxWgtType='scale',
UsePixelFluxWgts=0,
LDACBinary='ldactoasc',
PyFITSRead=0,
LogFile='LAMBDAR_Log.txt') {
#Sink Output to File {{{
sink(file=filename)
#}}}
#Write File {{{
cat(paste("#-------------------------------------------------------------------------------------
#
# Default Parameter File for use by LAMBDAR
#
# NB: All Parameters are provided here.
# In some cases, certain parameters will not be required.
#
# Written by: A.H. Wright
#
#-------------------------------------------------------------------------------------
# #---------Working Directory Path-----------#
RootDirectory ",paste(RootDirectory ,collapse=' '),"
WorkingDirectory ",paste(WorkingDirectory ,collapse=' '),"
# #-------File Paths: Relative to Root-------#
Catalogue ",paste(Catalogue ,collapse=' ')," #Catalogue Filename and Path
PSFMap ",paste(PSFMap ,collapse=' ')," #PSF Filename and Path (use 'NONE' if not wanted)
DataMap ",paste(DataMap ,collapse=' ')," #Image Filename and Path
ErrorMap ",paste(ErrorMap ,collapse=' ')," #Error Map Filename and Path (use 'NONE' if not wanted)
MaskMap ",paste(MaskMap ,collapse=' ')," #Mask Filename and Path (use 'NONE' if not wanted)
WeightMap ",paste(WeightMap ,collapse=' ')," #Weight Map Filename and Path (use 'NONE' if not wanted)
# #-------Catalogue Specific Variables-------#
CatIDColumnLabel ",paste(CatIDColumnLabel ,collapse=' ')," #Label for designating the Catalogue ID Column of the supplied catalogue
RAColumnLabel ",paste(RAColumnLabel ,collapse=' ')," #Label for designating the RA Column of the supplied catalogue
DecColumnLabel ",paste(DecColumnLabel ,collapse=' ')," #Label for designating the Dec Column of the supplied catalogue
ThetaColumnLabel ",paste(ThetaColumnLabel ,collapse=' ')," #Label for designating the Theta (on-sky aperture angle) Column of the supplied catalogue
SemiMajColumnLabel ",paste(SemiMajColumnLabel ,collapse=' ')," #Label for designating the SemiMajor Axis Column of the supplied catalogue
SemiMinColumnLabel ",paste(SemiMinColumnLabel ,collapse=' ')," #Label for designating the SemiMinor Axis Column of the supplied catalogue
ContamColumnLabel ",paste(ContamColumnLabel ,collapse=' ')," #Label for designating the Contaminants ID Column of the supplied catalogue
FluxWgtColumnLabel ",paste(FluxWgtColumnLabel ,collapse=' ')," #Label for designating the FluxWeights Column of the supplied catalogue
# #-------Telescope Specific Variables-------#
MapUnitsPerBeam ",paste(as.numeric(MapUnitsPerBeam),collapse=' ')," #Is the Image in units per beam (as opposed to UnitsPerPixel)? [1/0]
Confusion_units ",paste(Confusion_units ,collapse=' ')," #Image Confusion in units
Gauss_FWHM_AS ",paste(Gauss_FWHM_AS ,collapse=' ')," #Gaussian FWHM of Seeing in ArcSec
PSFLabel ",paste(PSFLabel ,collapse=' ')," #If Gaussian FWHM above is -ve, look for the PSF Sigma/FWHM in header with this keyword
PSFLabelType ",paste(PSFLabelType ,collapse=' ')," #Is the PSFLabel keyword a Sigma or FWHM [SIGMA/FWHM] and in Pixels or Arcsec [PIX/AS]
SimGauss_AS ",paste(SimGauss_AS ,collapse=' ')," #Gaussian FWHM of Gaussianisation Kernel (used for convolution of Simulation Image Noise), in ArcSec
BeamArea_SqAS ",paste(BeamArea_SqAS ,collapse=' ')," #Beam area in Square Arcsec
FluxCorr ",paste(FluxCorr ,collapse=' ')," #Flux Correction Factor
EFactor ",paste(EFactor ,collapse=' ')," #Error Map Scale Factor
WeightMapZP ",paste(WeightMapZP ,collapse=' ')," #Zero Point of the Weight Map - used for masking Data if no mask is supplied
Saturation ",paste(Saturation ,collapse=' ')," #Saturation value of the Map - used for Flagging bad fluxes. If unknown, use Inf
SaturationLabel ",paste(SaturationLabel ,collapse=' ')," #Saturation Label in FITS header - used for reading saturation value if none supplied
GainLabel ",paste(GainLabel ,collapse=' ')," #Gain Label in FITS header - used for generating error map if no error.map/gain supplied
# #-------Fits Extension Values--------------#
DataExtn ",paste(DataExtn ,collapse=' ')," #Fits header extension of Data in Image File
ErrorExtn ",paste(ErrorExtn ,collapse=' ')," #Fits header extension of Data in Error File
MaskExtn ",paste(MaskExtn ,collapse=' ')," #Fits header extension of Data in Mask File
WeightExtn ",paste(WeightExtn ,collapse=' ')," #Fits header extension of Data in Weight Map File
# #--------Image Cropping Options------------#
CropImage ",paste(as.numeric(CropImage) ,collapse=' ')," #Do we want to crop the input image to a particular subsection? [1/0]
CropImRA0 ",paste(CropImRA0 ,collapse=' ')," #RA that crop will centre around (deg; -999 will focus crop on image centre)
CropImDec0 ",paste(CropImDec0 ,collapse=' ')," #Dec that crop will centre around (deg; -999 will focus crop on image centre)
CropImRad ",paste(CropImRad ,collapse=' ')," #Radius of crop (deg; Negative will default to 1deg radius)
CropFitsName ",paste(CropFitsName ,collapse=' ')," #Name of the output cropped image (without '.fits' extension)
# #--------Additional Options----------------#
RemoveContam ",paste(as.numeric(RemoveContam) ,collapse=' ')," #Remove Contaminants from the image? [1/0]
CheckContam ",paste(as.numeric(CheckContam) ,collapse=' ')," #Check Contaminants for ones that are irrelevant (do not overlap with main galaxies)? [1/0]
nNearestCheck ",paste(nNearestCheck ,collapse=' ')," #Number of Nearest Neighbours to check when looking for Contaminant-Galaxy Overlaps
RadialTolerance ",paste(as.numeric(RadialTolerance),collapse=' ')," #Radial tolerance (in pixels) for accepting sources in PSF estimation (default: 25pix)
MaxNumPSF ",paste(as.numeric(MaxNumPSF) ,collapse=' ')," #Maximum Number of Point Sources used in PSF estimation. Lower numbers allow iterative cleaning of sources
PSFCheck ",paste(as.numeric(PSFCheck) ,collapse=' ')," #Check PSF by comparing to a stacked PSF made from the image? [1/0]
PSFConvolve ",paste(as.numeric(PSFConvolve) ,collapse=' ')," #Convolve the Aperture with a PSF? [1/0]
ApertureConfLimit ",paste(ApertureConfLimit ,collapse=' ')," #Confidence limit used when converting PSF convolved apertures to binary apertures
PSFWeighted ",paste(as.numeric(PSFWeighted) ,collapse=' ')," #Do you want PSFWeighted Photometry [1]? or Aperture Photometry [0]? [1/0]
AngularOffset ",paste(as.numeric(AngularOffset) ,collapse=' ')," #0 if the catalogue is in N0E90 angular coords, 1 if it is in N90E0 coords
ApertureType ",paste(ApertureType ,collapse=' ')," #Choice of initial aperture type: 0 - all as point sources; 1 - boxcar aps; 2 - gaussian aps
MinApRad ",paste(MinApRad ,collapse=' ')," #State minimum aperture to use for sources
ResampleAper ",paste(as.numeric(ResampleAper) ,collapse=' ')," #Smooth Boxcar Apertures by resampling? (Improves aperture surface integral accuracy) [1/0]
ResamplingRes ",paste(ResamplingRes ,collapse=' ')," #Rate of Upscaling in Resolution during Aperture Resampling (final res is n^[nIters] higher)
ResamplingIters ",paste(ResamplingIters ,collapse=' ')," #Number of iterations to perform in resampling
UseMaskLim ",paste(UseMaskLim ,collapse=' ')," #Limit for determining whether or not to use an object overlapping the mask edge
Verbose ",paste(as.numeric(Verbose) ,collapse=' ')," #Verbose Output?
ShowTime ",paste(as.numeric(ShowTime) ,collapse=' ')," #Display execution & total elapsed time during run?
PlotSample ",paste(as.numeric(PlotSample) ,collapse=' ')," #Plot a sample of the Object Apertures & Fluxes for Inspection? Includes Aperture Images and object COGs
PlotAll ",paste(as.numeric(PlotAll) ,collapse=' ')," #Plot All of the Object Apertures & Fluxes for Inspection? [1] Or just the non-contaminant sources? [2] Includes Aperture Images and object COGs
Diagnostic ",paste(as.numeric(Diagnostic) ,collapse=' ')," #Diagnostic Output of Variable Values During Computation - Helpful in Understanding Code
Interactive ",paste(as.numeric(Interactive) ,collapse=' ')," #Interactive Mode - Allows user access to entire parameter-space after final calculations
Magnitudes ",paste(as.numeric(Magnitudes) ,collapse=' ')," #Output Fluxes as magnitudes
ABVegaFlux ",paste(ABVegaFlux ,collapse=' ')," #Flux of ABVega in this band - only used if outputting magnitudes
MagZeroPoint ",paste(MagZeroPoint ,collapse=' ')," #Magnitude of the Image Zero Point. If -999, ZP will be read from FITS header
MagZPLabel ",paste(MagZPLabel ,collapse=' ')," #Label used for the Zero Point Keyword in the FITS header
DoSkyEst ",paste(as.numeric(DoSkyEst) ,collapse=' ')," #Perform estimate of local sky-background for each object, and subtract it from the flux
SkyEstIters ",paste(SkyEstIters ,collapse=' ')," #Number of iterations of sigma-cutting used in sky estimation
SkyEstProbCut ",paste(SkyEstProbCut ,collapse=' ')," #Sigma Level used in sigma-cutting of sky pixels
SkyDefault ",paste(SkyDefault ,collapse=' ')," #Default Value to use for local sky if estimation fails. May be numeric, 'median', or 'mean'. Otherwise will be NA.
SkyCorrelNoise ",paste(SkyCorrelNoise ,collapse=' ')," #Level of Correlated noise in the image, if known (factor is multiplicative - 1 == no correlated noise)
GetSkyRMS ",paste(as.numeric(GetSkyRMS) ,collapse=' ')," #As above without subtraction, and output the local sky RMS (if doing sky estimate, this happens automatically)
RanCor ",paste(as.numeric(RanCor) ,collapse=' ')," #Do you want to calculate mean & median sky-flux using randoms around every aperture? [1/0]
nRandoms ",paste(nRandoms ,collapse=' ')," #Number of randoms calculated *per aperture*
BlankCor ",paste(as.numeric(BlankCor) ,collapse=' ')," #Do you want to calculate mean & median confusion using blanks around every aperture? [1/0]
nBlanks ",paste(nBlanks ,collapse=' ')," #Number of blanks calculated *per aperture*
UsePixelFluxWgts ",paste(UsePixelFluxWgts ,collapse=' ')," #Do you want the pixel flux at the object RA DEC to be used for relative flux.weighting? [1/0]
FluxWgtType ",paste(FluxWgtType ,collapse=' ')," #What is the form of the input flux.weights ('flux', 'mag', or 'scale')?
IterateFluxes ",paste(as.numeric(IterateFluxes) ,collapse=' ')," #Do you want to iterate the flux determination to improve deblending?
nIterations ",paste(nIterations ,collapse=' ')," #How many iterations do you want to do?
# #---------------Outputs--------------------#
OutputDirectory ",paste(OutputDirectory ,collapse=' ')," #Output directory Name and Path
LogFile ",paste(LogFile ,collapse=' ')," #Filename for Log
PlotDevice ",paste(PlotDevice ,collapse=' ')," #The device to use for plotting: can be one of: PNG, PDF, or X11
GetDeblFrac ",paste(as.numeric(GetDeblFrac) ,collapse=' ')," #Only Output Deblend Fractions for each aperture to file? (Overrules all other Flags) [1/0]
SourceMaskOnly ",paste(as.numeric(SourceMaskOnly) ,collapse=' ')," #Only Output Source Mask image to file? (Overrules all other Flags except the above) [1/0]
WriteTable ",paste(as.numeric(WriteTable) ,collapse=' ')," #Output Results Table?
TableName ",paste(TableName ,collapse=' ')," #Filename for Results Table
WriteAAMask ",paste(as.numeric(WriteAAMask) ,collapse=' ')," #Write the All Apertures Mask image to file? [1/0]
AllApersFile ",paste(AllApersFile ,collapse=' ')," #Filename for All Apertures Mask
WriteFAMask ",paste(as.numeric(WriteFAMask) ,collapse=' ')," #Write the Convolved Apertures Mask image to file? [1/0]
ConvApersFile ",paste(ConvApersFile ,collapse=' ')," #Filename for All Convolved Apertures Mask
WriteDFAMask ",paste(as.numeric(WriteDFAMask) ,collapse=' ')," #Write the Deblended Convolved Apertures Mask image to file? [1/0]
DeblConvApersFile ",paste(DeblConvApersFile ,collapse=' ')," #Filename for Deblended Convolved Apertures Mask
WriteSourceMask ",paste(as.numeric(WriteSourceMask),collapse=' ')," #Write the Source Mask image to file? [1/0]
SourceMaskConfLim ",paste(SourceMaskConfLim ,collapse=' ')," #When convolving with PSF, to what confidence should the Sourcemask extend when masking Apertures?
SourceMaskFile ",paste(SourceMaskFile ,collapse=' ')," #Filename for Source Mask
TransmissionMap ",paste(as.numeric(TransmissionMap),collapse=' ')," #Do you want to produce a Transmission Map instead of a Sourcemask (transparent over sources instead of opaque)? [0/1]
WriteResidMap ",paste(as.numeric(WriteResidMap) ,collapse=' ')," #Write the Residual Image Map to file? [1/0]
ResidImageFile ",paste(ResidImageFile ,collapse=' ')," #Filename for Residual Image
NoContamImageFile ",paste(NoContamImageFile ,collapse=' ')," #Filename for Contaminant Subtracted Residual Image
# #-------Computational Management-----------#
MemorySafe ",paste(as.numeric(MemorySafe) ,collapse=' ')," #Do we want to perform checks to ensure the program does not use more memory than is available? [1/0]
nProcessors ",paste(nProcessors ,collapse=' ')," #Number of Processors Available for Use in Computations
CarefulWithEdges ",paste(as.numeric(CarefulWithEdges),collapse=' ')," #Do we want to be careful with sources at the edge of the image? Things too close to image edges are removed
ApStampWidth ",paste(ApStampWidth ,collapse=' ')," #Width of the Aperture stamps in multiples of aperture major axis; Can be changed with caution if memory issues arise.
PSFConfidence ",paste(PSFConfidence ,collapse=' ')," #PSF Confidence Value used in buffering the Aperture Stamp Widths; PSF integrated out to this width, and that radii is added.
LDACBinary ",paste(LDACBinary ,collapse=' ')," #If using LDAC catalogue format, specify here the absolute path to the LDAC-to-ASCII conversion binary.
PyFITSRead ",paste(PyFITSRead ,collapse=' ')," #Do you want to read images via PyFITS instead of via the FITSio package (with large images can be ~2x faster."))
#}}}
#Close Sink and return NULL {{{
sink()
return=NULL
#}}}
}
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