create.par.file: Create Parameter File

In AngusWright/LAMBDAR: Measure galaxy fluxes from an arbitrary FITS image using input aperture locations and dimensions

Create Parameter File

Description

Generate the parameter file for use in the measure.fluxes procedure. All Parameter file values can be sent to the procedure, or the default file can be generated by simply invoking the routine with no parameters specified.

Usage

   create.par.file(filename='Lambdar_default.par',
       RootDirectory = "./", WorkingDirectory = "./",
       OutputDirectory = "./", Catalogue = "catalogue.csv",
       DataMap = "image.fits", BeamArea_SqAS = 0, PSFConvolve
       = 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, 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, PlotSample = 0, PlotAll = 0, Magnitudes =
       1, MagZPLabel = "MagZP", ABVegaFlux = 1, 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, LogFile = "LAMBDAR_Log.txt")

Arguments

filename	string; Filename to use for outputting Lambdar Parameter File
RootDirectory	string; Path to Root Directory for program execution. Default is ‘./’; i.e. the current R working directory
WorkingDirectory	string; Path of Working Directory, relative to the Root Directory, for program execution.
Catalogue	string; Catalogue Filename and Path from Root. Accepted formats are ‘.csv’, ‘.fits’, ‘.Rdata’
PSFMap	string; PSF Filename and Path from Root (use ‘NONE’ if not wanted)
DataMap	string; Image Filename and Path from Root
ErrorMap	string; Error Map Filename and Path from Root (use ‘NONE’ if not wanted)
MaskMap	string; Mask Filename and Path from Root (use ‘NONE’ if not wanted)
WeightMap	string; Weightmap Filename and Path from Root (used if generating a mask from weightmap - use ‘NONE’ if not wanted)
CatIDColumnLabel	string; Label for ‘Catalogue ID’ Column in input catalogue
RAColumnLabel	string; Label for ‘Right Ascension’ Column in input catalogue
DecColumnLabel	string; Label for ‘Declination’ Column in input catalogue
ThetaColumnLabel	string; Label for ‘Aperture Angle’ Column in input catalogue (column may not be needed)
SemiMinColumnLabel	string; Label for ‘SemiMinor Axis’ Column in input catalogue (column may not be needed)
SemiMajColumnLabel	string; Label for ‘SemiMajor Axis’ Column in input catalogue (column may not be needed)
ContamColumnLabel	string; Label for ‘Contaminant Flag’ Column in input catalogue (column may not be needed)
FluxWgtColumnLabel	string; Label for ‘Flux Weights’ Column in input catalogue (column may not be needed)
FluxWgtType	string; What form do the flux.weights take? magnitudes ‘mag’, Fluxes ‘flux’, or scales ‘scale’.
MapUnitsPerBeam	boolean 0/1; Is the Image Flux measured in Unitsperbeam (as opposed to UnitsPerPixel)? [1/0]
Confusion_units	float; Confusion Correction in Units
Saturation	float; image saturation in ADU
SaturationLabel	string; saturation fits keyword
GainLabel	string; gain fits keyword. Used to determine gain if no weightmap or error.map is provided
Gauss_FWHM_AS	float; Gaussian FWHM of Seeing in ArcSec (used if generating a PSF)
PSFLabel	string; what is the header keyword for the PSF size (used if generating a PSF and Gauss_FWHM_AS is negative)
PSFLabelType	string; is the PSF size in the header specified a FWHM [FWHM] or StDev [SD], and is it in units of arcsec [ARCSEC] or Pixels [PIX].
SimGauss_AS	float; FWHM of Gaussian used when performing Gaussianisation of the input image. Used when generating a Simulated Image, to accurately reproduce the background correlations.
BeamArea_SqAS	float; Beam area in Square Arcsec (used if MapUnitsPerBeam=1)
FluxCorr	float; Flux Correction Factor (multiplicative)
EFactor	float; Error Map Scale Factor (multiplicative)
DataExtn	integer; Fits header extension of Data in Image File
ErrorExtn	integer; Fits header extension of Data in Errormap File (used if reading error.map from file)
MaskExtn	integer; Fits header extension of Data in Maskmap File (used if reading mask from file)
WeightExtn	integer; Fits header extension of Data in Weightmap File (used if generating mask from weightmap)
WeightMapZP	float; Zero Point of the Weight Map. i.e. the value that corresponds to ‘No Data’ (used if generating mask)
CropImage	boolean 0/1; Do we want to crop the input image to a particular subsection? [1/0]
CropImRA0	float; RA that crop will centre around (deg; -999 will focus crop around the centre of the input image)
CropImDec0	float; Dec that crop will centre around (deg; -999 will focus crop around the centre of the input image)
CropImRad	float; Radius of crop (deg; NA will default to 1deg radius)
CropFitsName	string; Name of the output cropped images (without ‘.fits’ extension)
RemoveContam	boolean 0/1; Remove Contaminants (Catalogue must contain contaminant flag column) from the image? [1/0]
CheckContam	boolean 0/1; Check for relevant Contaminants? Contaminants deemed not needed (not overlapping science targets) will not be measured. [1/0]
nNearestCheck	integer; number of nearest neighbours to check when discarding contaminant
MinApRad	flaot; Minimum Aperture Radius
PSFConvolve	boolean 0/1; Convolve the Aperture with a PSF? [1/0]
PSFWeighted	boolean 0/1; Use PSF Weighted Apertures [1] or convert all apertures to boxcar prior to measurement [0]?
ApertureConfLimit	float; when not using PSF Weighted Apertures, this is the integral point at which the boxcar boundary occurs
AngularOffset	boolean 0/1; 0 if the catalogue is in N90E0 angular coords, 1 if it is in N0E90 coords [0/1]
ApertureType	integer; What type of aperture do we want? Force point sources [0], BoxCar Apertures [1], Gaussian Apertures [2], or Segmentation Apertures [3]?
ResampleAper	boolean 0/1; Smooth Apertures by resampling? (Improves aperture surface integral accuracy) [1/0]
ResamplingRes	integer; Rate of Upscaling in Resolution during Aperture Resampling (final res is ResamplingRes^[nIters] higher)
ResamplingIters	integer; Number of iterations to perform in resampling
UseMaskLim	float in {0,1}; fraction of aperture stamp that must be within the mask. If less, aperture is discarded.
Verbose	boolean 0/1; Verbose Output? [1/0]
ShowTime	boolean 0/1; Display execution times & total elapsed time during run? [1/0]
PlotSample	boolean 0/1; Plot a random sample of the Apertures to file, during various procedures, for Inspection? [1/0]
PlotAll	integer 0/1/2; Plot all of the Apertures to file, during various procedures, for Inspection? [1] Or if removing contaminants (RemoveContam parameter), just plot the non-contaminant sources? [2]
Diagnostic	boolean 0/1; Diagnostic Output of Variable Values During Computation - Helpful in Understanding Code & debugging [1/0]
Interactive	boolean 0/1; Interactive Mode - Allows user access to entire parameter-space after final calculations [1/0]
Magnitudes	boolean 0/1; Output Flux magnitudes? [1/0]
ABVegaFlux	float; Flux of Vega in this band (used for calculation of AB magnitudes)
MagZeroPoint	float; Magnitude of the Image Zero Point. If -999, ZP will be read from FITS header
MagZPLabel	string; Label used for the Zero Point Keyword in the FITS header, if reading from FITS
DoSkyEst	boolean 0/1; Perform a subtraction of the local background for each aperture? [1/0]
SkyEstIters	integer; Number of iterative clips performed during sky estimation
SkyEstProbCut	float; Probability limit (specified as a sigma value) used in iterative clipping of sky-pixels during sky estimation
SkyDefault	character/float; The default value to use if sky estimation fails; can be a value (numeric), ‘mean’, or ‘median’
SkyCorrelNoise	float; Multiplicative factor describing the amount of correlated noise in the data.map
GetSkyRMS	boolean 0/1; Perform an estimation of the local sky background, without doing subtraction
RanCor	boolean 0/1; Perform a randoms measurement for each aperture? [1/0]
nRandoms	integer; number of randoms to measure, per aperture.
BlankCor	boolean 0/1; Perform a randoms measurement for each aperture? [1/0]
nBlanks	integer; number of Blanks to attempt to measure, per aperture. Actual number successfully measured is output by blanks function
UsePixelFluxWgts	boolean 0/1; Do we want to weight initialise deblends by object central pixel fluxes? [0/1]
IterateFluxes	boolean 0/1; Perform an iteration of the flux measurements, to create improve photometric accuracy (generally, not always)
nIterations	integer; Number of iterations we would like to perform when refining fluxes
GetDeblFrac	boolean 0/1; Do we just want to return the deblend solutions? No flux measurement will be output [0/1]
OutputDirectory	string; Output directory Name and Path
LogFile	string; Filename for Log
SourceMaskOnly	boolean 0/1; Only Output Source Mask image to file, and stop (without calculating fluxes)? (Overrules all other Flags) [1/0]
TransmissionMap	boolean 0/1; Do we want to output a transmission map rather than a sourcemask? [1/0]
WriteTable	boolean 0/1; Output Results Table? [1/0]
TableName	string; Filename for Results Table
WriteAAMask	boolean 0/1; Write the All Apertures Mask image to file? [1/0]
AllApersFile	string; Filename for All Apertures Mask
WriteSourceMask	boolean 0/1; Write the Source Mask image to file? [1/0]
SourceMaskConfLim	float in {0,1}; Confidence Limit used when making sourcemask of convolved apertures
SourceMaskFile	string; Filename for Source Mask
WriteDFAMask	boolean 0/1; Write the Convolved Apertures Mask image to file? [1/0]
DeblConvApersFile	string; Filename for All Convolved Apertures Mask
WriteFAMask	boolean 0/1; Write the Convolved Apertures Mask image to file? [1/0]
ConvApersFile	string; Filename for All Convolved Apertures Mask
WriteResidMap	boolean 0/1; Write the Residual Image Map to file? [1/0]
ResidImageFile	string; Filename for Residual Image
NoContamImageFile	string; Filename for Contaminant Subtracted Residual Image
nProcessors	integer; Number of Processors Available for Use in Computations
MemorySafe	boolean 0/1; do we want to check that memory usage will be less than system limits? [0/1]
ApStampWidth	float in {1,Inf}; Width of the Aperture stamps in multiples of aperture major axis; Can be changed *with caution* if memory issues arise.
PSFConfidence	float in {0,1}; Confidence level to which the PSF is generated, or to which aperture stamps are padded if reading PSF from File

Details

This function reads the various inputs from the LAMBDAR parameter file. Generally, if a particular parameter isn't found during parameter file read then the program will warn the user in the log file, and will continue on using the default values for that parameter. In this way a user that wishes to use all default values, and specify only one or two parameters explicitly, can provide a simply file containing only those parameters that they wish to modify. Exceptions to this rule are those parameters that are considered vital to the correct running of the program. These are: > The Root Path (can be simply set to "./") > The Working Directory Path (can be simply set to "./") > The Input Image File > The Input Catalogue

Details of what is expected in the input catalogue are given in the open.catalogue manual page

Value

NULL; Procedure outputs the parameter file to ‘LAMBDAR_default.par’

Author(s)

Angus H Wright ICRAR [e-mail]

References

Wright et al. 2015 (in prep)

See Also

measure.fluxes

Examples

#Load LAMBDAR
library(LAMBDAR)
#To output the default parameter file to 'Lambdar_default.par', simply call:
create.par.file()

#To specify the output file as 'Lambdar_Custom.par':
create.par.file(file="Lambdar_Custom.par")

#Finally, all parameters can be set as they are output:
create.par.file(file="Lambdar_Custom.par", Catalogue="MyCat.csv",
DataMap="SampleImage.fits",nProcessors=10)

AngusWright/LAMBDAR documentation built on May 12, 2022, 1:49 a.m.