profoundMakeSegimExpand: Segmentation Map Expansion and Dilation
In ProFound: Photometry Tools

Description Usage Arguments Details Value Author(s) See Also Examples

A high level utility to achieve decent quality image segmentation based on the expansion of a pre-existing segmentation map. It uses smoothing and local flux weighted comparisons to grow the current segmentation map so as to better identify distinct objects for use in, e.g., profitSetupData.

profoundMakeSegimExpand(image = NULL, segim = NULL, mask = NULL, objects = NULL,
skycut = 1, SBlim = NULL, magzero = 0, gain = NULL, pixscale = 1, sigma = 1,
smooth = TRUE, expandsigma = 5, expand = "all", sky = NULL, skyRMS = NULL, header = NULL,
verbose = FALSE, plot = FALSE, stats = TRUE, rotstats = FALSE, boundstats = FALSE,
offset = 1, sortcol = "segID", decreasing = FALSE, ...)
profoundMakeSegimDilate(image = NULL, segim = NULL, mask = NULL, size = 9, shape = "disc",
expand = "all", magzero = 0, gain = NULL, pixscale = 1, sky = 0, skyRMS = 0,
header = NULL, verbose = FALSE, plot = FALSE, stats = TRUE, rotstats = FALSE,
boundstats = FALSE, offset = 1, sortcol = "segID", decreasing = FALSE, ...)

`image`	Numeric matrix; required, the image we want to analyse. Note, image NAs are treated as masked pixels.
`segim`	Integer matrix; required, the segmentation map of the image. This matrix must be the same dimensions as image.
`mask`	Boolean matrix; optional, parts of the image to mask out (i.e. ignore), where 1 means mask out and 0 means use for analysis. If provided, this matrix must be the same dimensions as image.
`objects`	Boolean matrix; optional, object mask where 1 is object and 0 is sky. If provided, this matrix must be the same dimensions as image.
`skycut`	Numeric scalar; the lowest threshold to make on the image in units of the skyRMS. Since we are restricted to expanding out pre-existing segmentation regions we can usually afford to make this value lower than the equivalent in `profoundMakeSegim`.
`SBlim`	Numeric scalar; the magnitude/arcsec^2 surface brightness threshold to apply. This is always used in conjunction with skycut, so set skycut to be very large (e.g. Inf) if you want a pure surface brightness threshold for the segmentation. magzero and pixscale must also be present for this to be used.
`magzero`	Numeric scalar; the magnitude zero point. What this implies depends on the magnitude system being used (e.g. AB or Vega). If provided along with pixscale then the flux and surface brightness outputs will represent magnitudes and mag/asec^2.
`gain`	Numeric scalar; the gain (in photo-electrons per ADU). This is only used to compute object shot-noise component of the flux error (else this is set to 0).
`pixscale`	Numeric scalar; the pixel scale, where pixscale=asec/pix (e.g. 0.4 for SDSS). If set to 1 (default), then the output is in terms of pixels, otherwise it is in arcseconds. If provided along with magzero then the flux and surface brightness outputs will represent magnitudes and mag/asec^2.
`sigma`	Numeric scalar; standard deviation of the blur used when smooth=TRUE.
`smooth`	Logical; should smoothing be done on the target image? If present, this will use the `imblur` function from the `imager` package. Otherwise it will use the `gblur` function from the `EBImage` package with a warning. These functions are very similar in output, but not strictly identical.
`expandsigma`	Numeric scalar; standard deviation of the blur used when expanding out the segim. Roughly speaking if skycut is set to a low number (say -5) then the expansion will not be prevented by the local sky level and it will grow by the number of pixels specified by expandsigma.
`expand`	Integer vector; specifies which segmentation regions should be expanded by the segID integer reference. If left with the default expand='all' then all segments will be expanded.
`size`	Integer scalar; the size (e.g. width/diameter) of the dilation kernel in pixels. Should be an odd number else will be rounded up to the nearest odd number. See `makeBrush`.
`shape`	Character scalar; the shape of the dilation kernel. See `makeBrush`.
`sky`	User provided estimate of the absolute sky level. Can be a scalar or a matrix matching the dimensions of image (allows values to vary per pixel). This will be subtracted off the image internally, so only provide this if the sky does need to be subtracted!
`skyRMS`	User provided estimate of the RMS of the sky. Can be a scalar or a matrix matching the dimensions of image (allows values to vary per pixel).
`header`	Full FITS header in table or vector format. If this is provided then the segmentations statistics table will gain RAcen and Decen coordinate outputs. Legal table format headers are provided by the `read.fitshdr` function or the hdr list output of `read.fits` in the astro package; the hdr output of `readFITS` in the `FITSio` package or the header output of `magcutoutWCS`. Missing header keywords are printed out and other header option arguments are used in these cases. See `magWCSxy2radec`.
`verbose`	Logical; should verbose output be displayed to the user? Since big image can take a long time to run, you might want to monitor progress.
`plot`	Logical; should a diagnostic plot be generated? This is useful when you only have a small number of sources (roughly a few hundred). With more than this it can start to take a long time to make the plot!
`stats`	Logical; should statistics on the segmented objects be returned?
`rotstats`	Logical; if TRUE then the asymm, flux_reflect and mag_reflect are computed, else they are set to NA. This is because they are very expensive to compute compared to other photometric properties.
`boundstats`	Logical; if TRUE then various pixel boundary statistics are computed (Nedge, Nsky, Nobject, Nborder, edge_frac, edge_excess and FlagBorder). If FALSE these return NA instead (saving computation time).
`offset`	Integer scalar; the distance to offset when searching for nearby segments (used in `profoundSegimStats`).
`sortcol`	Character; name of the output column that the returned segmentation statistics data.frame should be sorted by (the default is segID, i.e. segment order). See below for column names and contents.
`decreasing`	Logical; if FALSE (default) the segmentation statistics data.frame will be sorted in increasing order, if TRUE the data.frame will be sorted in decreasing order.
`...`	Further arguments to be passed to `magimage`. Only relevant is plot=TRUE.

The basic behaviour of profoundMakeSegimExpand and profoundMakeSegimDilate is to intelligently expand out image segments already identified by, e.g., profoundMakeSegim.

The profoundMakeSegimExpand defaults should work reasonably well on modern survey data (see Examples), but should the solution not be ideal try modifying these parameters (in order of impact priority): skycut (or SBlim), expandsigma, sigma.

profoundMakeSegimDilate is similar in nature to the pixel growing objmask routine in IRAF (see the ngrow and agrow description at http://iraf.noao.edu/projects/ccdmosaic/objmasks/objmasks.html). This similarity was discovered after implementation, but it is worth noting that the higher level curve of growth function profoundProFound is not trivially replicated by other astronomy tools.

The main difference between profoundMakeSegimExpand and profoundMakeSegimDilate is the former grows the expansion a bit more organically, whereas the latter always gives new pixels to the brighter object if in doubt. That said, profoundMakeSegimDilate often gives very similar solutions and runs about 10+ times faster, so might be the only option for larger images.

A list containing:

`segim`	Integer matrix; the segmentation map matched pixel by pixel to image.
`objects`	Logical matrix; the object map matched pixel by pixel to image. 1 means there is an object at this pixel, 0 means it is a sky pixel. Can be used as a mask in various other functions that require objects to be masked out.
`sky`	The estimated sky level of the image. `profoundMakeSegimExpand` only).
`skyRMS`	The estimated sky RMS of the image. `profoundMakeSegimExpand` only).
`segstats`	If stats=TRUE this is a data.frame (see below), otherwise NULL.
`header`	The header provided, if missing this is NULL.
`SBlim`	The surface brightness limit of detected objects. Requires at least magzero to be provided and skycut>0, else NULL. `profoundMakeSegimExpand` only.
`call`	The original function call.

If stats=TRUE then the function profoundSegimStats is called and the segstats part of the returned list will contain a data.frame with columns (else NULL):

`segID`	Segmentation ID, which can be matched against values in segim
`uniqueID`	Unique ID, which is fairly static and based on the xmax and ymax position
`xcen`	Flux weighted x centre
`ycen`	Flux weighted y centre
`xmax`	x position of maximum flux
`ymax`	y position of maximum flux
`RAcen`	Flux weighted degrees Right Ascension centre (only present if a header is provided)
`Deccen`	Flux weighted degrees Declination centre (only present if a header is provided)
`RAmax`	Right Ascension of maximum flux (only present if a header is provided)
`Decmax`	Declination of maximum flux (only present if a header is provided)
`sep`	Radial offset between the cen and max definition of the centre (units of pixscale, so if pixscale represents the standard asec/pix this will be asec)
`flux`	Total flux (calculated using image-sky) in ADUs
`mag`	Total flux converted to mag using magzero
`cenfrac`	Fraction of flux in the brightest pixel
`N50`	Number of brightest pixels containing 50% of the flux
`N90`	Number of brightest pixels containing 90% of the flux
`N100`	Total number of pixels in this segment, i.e. contains 100% of the flux
`R50`	Approximate elliptical semi-major axis containing 50% of the flux (units of pixscale, so if pixscale represents the standard asec/pix this will be asec)
`R90`	Approximate elliptical semi-major axis containing 90% of the flux (units of pixscale, so if pixscale represents the standard asec/pix this will be asec)
`R100`	Approximate elliptical semi-major axis containing 100% of the flux (units of pixscale, so if pixscale represents the standard asec/pix this will be asec)
`SB_N50`	Mean surface brightness containing brightest 50% of the flux, calculated as flux*0.5/N50 (if pixscale has been set correctly then this column will represent mag/asec^2. Otherwise it will be mag/pix^2)
`SB_N90`	Mean surface brightness containing brightest 90% of the flux, calculated as flux*0.9/N90 (if pixscale has been set correctly then this column will represent mag/asec^2. Otherwise it will be mag/pix^2)
`SB_N100`	Mean surface brightness containing all of the flux, calculated as flux/N100 (if pixscale has been set correctly then this column will represent mag/asec^2. Otherwise it will be mag/pix^2)
`xsd`	Weighted standard deviation in x (always in units of pix)
`ysd`	Weighted standard deviation in y (always in units of pix)
`covxy`	Weighted covariance in xy (always in units of pix)
`corxy`	Weighted correlation in xy (always in units of pix)
`con`	Concentration, R50/R90
`asymm`	180 degree flux asymmetry (0-1, where 0 is perfect symmetry and 1 complete asymmetry)
`flux_reflect`	Flux corrected for asymmetry by doubling the contribution of flux for asymmetric pixels (defined as no matching segment pixel found when the segment is rotated through 180 degrees)
`mag_reflect`	flux_reflect converted to mag using magzero
`semimaj`	Weighted standard deviation along the major axis, i.e. the semi-major first moment, so ~2 times this would be a typical major axis Kron radius (always in units of pix)
`semimin`	Weighted standard deviation along the minor axis, i.e. the semi-minor first moment, so ~2 times this would be a typical minor axis Kron radius (always in units of pix)
`axrat`	Axial ratio as given by min/maj
`ang`	Orientation of the semi-major axis in degrees. This has the convention that 0= \| (vertical), 45= \, 90= - (horizontal), 135= /, 180= \| (vertical)
`signif`	Approximate singificance of the detection using the Chi-Square distribution
`FPlim`	Approximate false-positive significance limit below which one such source might appear spuriously on an image this large
`flux_err`	Estimated total error in the flux for the segment
`mag_err`	Estimated total error in the magnitude for the segment
`flux_err_sky`	Sky subtraction component of the flux error
`flux_err_skyRMS`	Sky RMS component of the flux error
`flux_err_shot`	Object shot-noise component of the flux error (only if gain is provided)
`sky_mean`	Mean flux of the sky over all segment pixels
`sky_sum`	Total flux of the sky over all segment pixels
`skyRMS_mean`	Mean value of the sky RMS over all segment pixels
`Nedge`	Number of edge segment pixels that make up the outer edge of the segment
`Nsky`	Number of edge segment pixels that are touching sky
`Nobject`	Number of edge segment pixels that are touching another object segment
`Nborder`	Number of edge segment pixels that are touching the image border
`Nmask`	Number of edge segment pixels that are touching a masked pixel (note NAs in image are also treated as masked pixels)
`edge_frac`	Fraction of edge segment pixels that are touching the sky i.e. NskyNedge, higher generally meaning more robust segmentation statistics
`edge_excess`	Ratio of the number of edge pixels to the expected number given the elliptical geometry measurements of the segment. If this is larger than 1 then it is a sign that the segment geometry is irregular, and is likely a flag for compromised photometry
`flag_border`	A binary flag telling the user which image borders the segment touches. The bottom of the image is flagged 1, left=2, top=4 and right=8. A summed combination of these flags indicate the segment is in a corner touching two borders: bottom-left=3, top-left=6, top-right=12, bottom-right=9.

Aaron Robotham

profoundMakeSegim, profoundProFound, profoundSegimStats, profoundSegimPlot

## Not run: 
image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits',
package="ProFound"))$imDat
segim=profoundMakeSegim(image, plot=TRUE, skycut=2)
profoundMakeSegimExpand(image, segim$segim, plot=TRUE, skycut=1)
profoundMakeSegimDilate(image, segim$segim, plot=TRUE)

#Some other examples:

profoundMakeSegimExpand(image, segim$segim, plot=TRUE, skycut=0)
profoundMakeSegimExpand(image, segim$segim, plot=TRUE, skycut=-Inf, sigma=3)

profoundMakeSegimDilate(image, segim$segim, plot=TRUE, size = 15)
profoundMakeSegimDilate(image, segim$segim, plot=TRUE, size = 21)

#This expansion process is a *much* better idea then simply setting the original skycut
#to a low value like 1/0:
profoundMakeSegim(image, plot=TRUE, skycut = 1)
profoundMakeSegim(image, plot=TRUE, skycut = 0)

## End(Not run)