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Basic Information on sfind

Task: sfind
Purpose: Automatically or interactively find sources in images
Categories: plotting

        SFIND has been updated to incorporate a new statistically
        robust method for detecting source pixels, called FDR (which
        stands for "False Discovery Rate"), as an alternative to
        simple sigma-clipping, which formed the basis of the original
        implementation. Details of the FDR method can be found in
        Hopkins et al 2001, (astro-ph/0110570) and references
        therein. The original implementation of sfind has been
        preserved, and can be applied by specifying the option
        "oldsfind".  In addition, when using SFIND in the new 'FDR'
        mode, several new features are available. SFIND now provides the
        option of outputing
          1: a 'normalised' image (options=normimg) created by
             subtracting a background and dividing by sigma (the
             standard deviation),
          2: a 'sigma' image (options=sigmaimg), created by sigma-
             clipping the normalised image at a user-specified sigma
          3: an 'fdr' image (options=fdrimg) created similarly to the
             sigma-image by clipping the normalised image at the FDR-
             defined threshold.
        In 'FDR' mode (the default), no interactive source detection
        is possible, as is the case with the original version.  Instead,
        the detected sources are drawn from a distribution of pixels
        with a robustly known chance of being falsely drawn from the
        background, thus more reliably characterising the fraction of
        expected false sources than is possible with a sigma-clipping
        The process of source detection and measurement is slightly
        different in 'FDR' mode compared to the original SFIND
        implementation (see below).  In 'FDR' mode, the following steps
        are performed:
          1: The image is first normalised by estimating the background
             (mean) and standard deviation (sigma) for the whole image
             in uniformly distributed regions of size 'rmsbox' (a user
             input).  This is done by fitting a gaussian to the pixel
             histogram, (as is done in the task 'imsad') - if the fit is
             poor, an interative method is used instead.  With these
             values known, the image has the mean subtracted and is
             divided by sigma to create a normalised image.  This is the
             same as saying the normalised image has a gaussian mean of
             0 and sigma of 1.  The normalised image is output as a
             Miriad image called sfind.norm if 'options=normimg' is set.
             The rms noise measured over the image can also be output as
             sfind.rms if 'options=rmsimg' is set.
          2: From the normalised image a sigma-clipped image (called
             sfind.sig) may be output (if 'options=sigmaimg').  This is
             simply an image with pixel values set to 100 if the pixel
             value in the normalised image is greater than the user
             specified value of 'xrms,' or 0 otherwise.
          3: The FDR method is implemented using the normalised image.
             Each pixel is assigned a p-value, a probability that it was
             drawn from the background, and a cutoff p-value is
             established based on the percentage of false rejections
             (source pixels) that the user specifies with the parameter
             'alpha'.  If 'options=fdrimg' is set, this cutoff p-value
             threshold is used to create an 'fdr' image (called
             sfind.fdr) in the same way as the sigma image above is
          4: With the FDR cutoff threshold established, sources may now
             be detected and measured. Each pixel with a p-value lying
             *below* the cutoff p-value (i.e. a low chance of being
             drawn from the background) may be part of a source.  For
             each such 'FDR-detected' pixel, a hill-climbing routine
             finds a local peak from adjacent FDR-selected pixels.  This
             is then used as the starting point for a routine that
             selects contiguous monotonically decreasing adjacent pixels
             from the FDR-selected ones, and to which a 2-D elliptical
             gaussian is fit in the same way as the original SFIND (see
             below).  The same parameters are returned as in the
             original implementation, and the logfile has the same
             format (see below).
        Also, in FDR mode 'option=auto' from the original implementation
        is assumed automatically, regardless of user input. This means
        the inputs for 'type,' 'range,' 'device' etc are not relevant
        and are ignored.
        In the original implementation, SFIND displays an image via a
        contour plot or a pixel map representation on a PGPLOT device.
        The user is then provided with the opportunity to interactively
        flag sources as real or not (indicated by a Y or N flag in a
        log file).
        Source positions are calculated by an algorithm which searches
        for pixels brighter than the surrounding 24 pixels and then bi-
        parabolically fitting positions and flux densities.  Once a
        source such as this is detected, SFIND checks to see whether it
        is brighter than the user set multiple of the background rms.
        If so, a 2D elliptical gaussian fit is performed (using the same
        routine as IMFIT) and the source parameters are displayed on the
        terminal (and written to a log file after user input to
        determine a flag, Y or N, to attach). The source parameters are
        (in order):
                  Quantity                        Notes
               --------------                  -----------
        Position                       RA and Dec. in standard Miriad
                                       hms,dms format
        Formal errors in RA and Dec.   (arcsec; treat judiciously)
        Peak flux density              (mJy)
        Formal error in peak flux      in mJy (generally not a good
        density                        estimate of the true error)
        Integrated flux density        (mJy)
        Major and minor axes and       (arcseconds for axes, degrees for
        position angle of source       Warning: these are not
                                       deconvolved from the synthesized
        Local background rms (sigma)   (mJy) calculated from a Gaussian
                                       fit to the pixel histogram, as
                                       per imsad
        rms of gaussian fit
        Manipulation of the device colour lookup table is available
        when you display with a pixel map representation.

Key: in
        The input image.

Key: type
        Specifies the type of the image in the IN keyword. Minimum match
        is supported.   Choose from:
        "contour"   (contour plot)
        "pixel"     (pixel map)
        It is strongly suggested that pixel maps be used for source
        finding, as contour plots may be deceiving.  Default is "pixel".
        Ignored in 'FDR' mode (the default).

Key: region
        Region of interest.  Choose only one spatial region (bounding
        box only supported), but as many spectral regions (i.e.,
        multiple IMAGE specifications) as you like.  If you display a
        3-D image, the cursor options are activated after each sub-plot
        (channel or group of channels; see CHAN below) is drawn.
        Default is full image.

Key: xybin
        Upto 4 values.  These give the spatial increment and binning
        size in pixels for the x and y axes to be applied to the
        selected region.   If the binning size is not unity, it must be
        equal to the increment.  For example, to bin up the image by 4
        pixels in the x direction and to pick out every third pixel in
        the y direction, set XYBIN=4,4,3,1.
        Defaults are 1,XYBIN(1),XYBIN(1),XYBIN(3)

Key: chan
        2 values. The first is the channel increment, the second is
        the number of channels to average, for each sub-plot.  Thus
        CHAN=5,3  would average groups of 3 channels together, starting
        5 channels apart such as: 1:3, 6:8, 11:13 ...   The channels
        available are those designated by the REGION keyword.  A new
        group of channels (sub-plot) is started if there is a
        discontinuity in the REGION selected channels (such as
        Defaults are 1,1

Key: slev
        2 values.   First value is the type of contour level scale
        factor.  "p" for percentage and "a" for absolute.   Second
        value is the level to scale LEVS by.  Thus  SLEV=p,1  would
        contour levels at LEVS * 1% of the image peak intensity.
        Similarly, SLEV=a,1.4e-2   would contour levels at LEVS * 1.4E-2
        Default is no additional scaling of LEVS.
        Ignored in 'FDR' mode (the default).

Key: levs
        Levels to contour for first image, are LEVS times SLEV
        (either percentage of the image peak or absolute).
        Defaults try to choose something sensible
        Ignored in 'FDR' mode (the default).

Key: range
        3 values. The pixel map range (background to foreground), and
        transfer function type.  The transfer function type can be one
        of "lin" (linear), "log" (logarithmic), "heq" (histogram equal-
        ization), and "sqr" (square root).  See also OPTIONS=FIDDLE
        which is in addition to the selections here.
        Default is linear between the image minimum and maximum
        If you wish to just give a transfer function type, set
        range=0,0,heq   say.
        Ignored in 'FDR' mode (the default).

Key: cutoff
        Flux density below which possible sources are ignored.
        Default is zero.
        Ignored in 'FDR' mode (the default).

Key: rmsbox
        In 'FDR' mode (the default) this is the size of the 'smoothing'
        box used when estimating the background and standard deviation
        of the image. It is suggested that this be several to many times
        the beam size to prevent sources from artificially skewing the
        background estimates. This may require some experimentation,
        and 'options=normimg' may be useful in determining the
        effectiveness of a particular rmsbox size.
        In the original implementation (options=oldsfind), it is the
        size (in pixels) of a box centred on each source within which
        the background rms is calculated.  Only pixels outside the "beam
        exclusion radius" (1.5 x BMAJ) are used in this calculation.
        Default is 20 pixels.

Key: alpha
        This (real) number is the *percentage* of false *pixels* which
        can be accepted when applying the FDR method.  Alpha determines
        the threshold set in selecting pixels which belong to sources
        (as an alternative to a simple sigma-cut), prior to the source-
        fitting and measuring step.  Must be a positive number.
        Default is 2.0 percent.  Ignored if options=oldsfind.

Key: xrms
        In 'FDR' mode (the default) this parameter defines the sigma-
        cutoff for the creation of the image sfind.sig if
        'options=sigmaimg' is set.  If not, it is ignored.  It has no
        role in the detection or measurement of sources.  No default.
        In the original implementation (options=oldsfind), it is the
        multiple of the background rms value above which a source must
        be before the user is given the choice of verifying it.
        No default.

Key: device
        The PGPLOT plot device, such as plot.plt/ps. No default.
        Ignored in 'FDR' mode (the default).

Key: nxy
        Number of sub-plots in the x and y directions on the page.
        Defaults choose something sensible
        Ignored in 'FDR' mode (the default).

Key: labtyp
        Two values.  The spatial label type of the x and y axes.
        Minimum match is active.  Select from:
        "hms"       the label is in H M S (e.g. for RA)
        "dms"       the label is in D M S (e.g. for DEC)
        "arcsec"    the label is in arcsecond offsets
        "arcmin"    the label is in arcminute offsets
        "absdeg"    the label is in degrees
        "reldeg"    the label is in degree offsets
             The above assume the  pixel increment is in radians.
        "abspix"    the label is in pixels
        "relpix"    the label is in pixel offsets
        "abskms"    the label is in Km/s
        "relkms"    the label is in Km/s offsets
        "absghz"    the label is in GHz
        "relghz"    the label is in GHz offsets
        "absnat"    the label is in linear coordinates as defined by
                    the header.  You might call this the natural axis
        "relnat"    the label is in offset natural coordinates
        All offsets are from the reference pixel.
        Defaults are "abspix", LABTYP(1) unless LABTYP(1)="hms"
        whereupon LABTYP(2) defaults to "dms" (for RA and DEC).
        Ignored in 'FDR' mode (the default).

Key: logfile
        Log file name, default 'sfind.log'.

Key: options
        Task enrichment options.  Minimum match is active.
        "fiddle" means enter a routine to allow you to interactively
          change the display lookup table.  You can cycle through b&w
          and colour displays, as well as alter the transfer function by
          the cursor location, or by selecting predefined transfer
          functions such as histogram equalization, logarithmic, &
          square root.
        "wedge" means that if you are drawing a pixel map, also draw
          and label a wedge to the right of the plot, showing the map
          of intensity to colour
        "3value"  means label each sub-plot with the appropriate value
          of the third axis (e.g. velocity or frequency for an xyv
          ordered cube, position for a vxy ordered cube).
        "3pixel"  means label each sub-plot with the pixel value of the
          the third axis.   Both "3pixel" and "3value" can appear, and
          both will be written on the plot.  They are the average values
          when the third axis is binned up with CHAN.  If the third axis
          is not velocity or frequency, the units type for "3VALUE" will
          be chosen to be the complement of any like axis in the first
          two.  E.g., the cube is in vxy order and LABTYP=ABSKMS,ARCSEC
          the units for the "3VALUE" label will be arcsec.  If
          LABTYP=ABSKMS,HMS the "3VALUE" label will be DMS (if the third
          [y] axis is declination).
        "grid" means draw a coordinate grid on the plot rather than just
        "noerase"  Don't erase a snugly fitting rectangle into which the
         "3-axis" value string is written.
        "unequal" means draw plots with unequal scales in x and y. The
         default is that the scales are equal.
        "mark" When source has been found, and user has agreed that it
          is real, mark it with a cross.
        "nofit" Prevents the program from fitting elliptical gaussians
          to each source.  The data given on each source will be that
          from a bi-parabolic fit, as per the earlier version of sfind.
          Note that flux densities from this fit are bi-parabolically
          fitted *peak* flux densities, and the positions are to the
          peak flux density position (which will always be within 1
          pixel of the brightest pixel in the source).  This option is
          useful for providing a starting point for groups of sources
          which the gaussian fitting procedure hasn't taken a liking to.
        "asciiart" During the interactive section of the program, an
          ascii picture of each source is displayed, showing which
          pixels have been used in the gaussian fitting procedure.  The
          brightest pixel in the source is symbolised by a "O", the rest
          by asterisks.  This option is ignored if "nofit" is being
        "auto" The interactive section of the program is bypassed, and
          all detected sources are flagged as real. The image is not
          This is set automatically in 'FDR' mode (the default) and it
          is only necessary to select it manually if using
          'options=oldsfind' (see below).
        "negative" The map is inverted before source detection and
          fitting, i.e., positive pixels become negative and vice versa.
          This is to enable detection of negative sources without
          recourse to MATHS.  This feature may be used for detecting
          sources in polarisation maps.
        "pbcorr" Corrects the flux density value calculated for each
          source for the effect of the primary beam attenuation.  This
          is dealt with correctly for mosaics as well as single
        "oldsfind" Use this to run SFIND as the original implementation
          for the interactive interface, or just consistency with
          earlier measurements.
        "fdrimage" An output image called sfind.fdr will be created
          with pixel values of 100, if their p-values are below the FDR
          threshold, or 0 otherwise.
          Ignored if 'oldsfind' is present.
        "sigmaimg" An output image called sfind.sig will be created
          with pixel values of 100, if their sigma-values are above
          the user specified threshold from 'xrms,' or 0 otherwise.
          Ignored if 'oldsfind' is present.
        "rmsimg" An output image called sfind.rms will be created
          where the pixel values correspond to the rms noise level
          calculated when normalising the image.
          Ignored if 'oldsfind' is present.
        "normimg" An output image called sfind.norm will be created
          by subtracting a background mean from the input image and
          dividing by the standard deviation. The mean and sigma are
          calculated in regions of size 'rmsbox' tiled over the image.
          Ignored if 'oldsfind' is present.
        "kvannot" As well as the regular log file (always written)
          create a kview format annotation file, called 'sfind.ann'
          containing one ellipse per object, with the appropriate
          location, size, and position angle.
        "fdrpeak" The default for source measurement is to use only
          pixels above the FDR threshold in measuring the properties of
          sources. (This is analogous, in SExtractor, for example,
          to having the detect and analyse thresholds at the same
          level.) In some cases it may be desirable to allow fitting of
          sources where the peak pixel is above the FDR threshold, but
          other source pixels are not required to be. This is the case
          for obtaining reasonable measurements of sources close to the
          threshold. Selecting 'fdrpeak' allows this. If 'fdrpeak'
          is selected, source pixels are still required to be contiguous
          and monotonically decreasing from the peak pixel, but not
          necessarily to be above the FDR threshold.
        "allpix" Rather than selecting pixels for the gaussian fitting
          by requiring they be monotonically decreasing away from the
          peak pixel, this option allows all FDR-selected pixels
          contiguous with the peak pixel to be fit for a source.
          If this option is selected, the fdrpeak option is ignored.
        "psfsize" Restricts the minimum fitted size of a detected source
          to the size of the sythesised beam, i.e., the PSF.  Any source
          fitted to have a smaller size than this has its FWHM and PA
          set to those of the synthesised beam, and is refit for the
          position and amplitude only.
        "bright" If your sources are too bright for the default format
          using this option will shift the decimal point right one digit
        Some common combinations of options I have used (for examples):

Key: csize
        Two values.  Character sizes in units of the PGPLOT default
        (which is ~ 1/40 of the view surface height) for the plot axis
        labels and the velocity/channel labels.
        Defaults choose something sensible.
        Ignored in 'FDR' mode (the default).
   Known Bugs:
        In FDR mode the code has problems with very large images.  I
        think this is dependent on the available memory of the machine
        running Sfind, but need to do more testing to be certain.  I
        have confirmed that on a machine with 256MB of memory and 256MB
        swap space, an image of 3600x3600 pixels will be analysed
        correctly.  For larger images, the code will halt
        unceremoniously at the first call to memfree in subroutine fdr.
        I don't understand why this happens, although I am guessing it
        may have to do with the call to memfree trying to free more
        memory than is available.
        The output is designed to print source fluxes in FORTRAN format
        f8.3 and f9.3 for peak and integrated flux densities
        respectively.  This means that if your source's peak flux
        is > 9999.999 mJy, (i.e. 10 Jy) or its integrated flux
        is > 99999.999 mJy (i.e., 100 Jy), then it will not be
        displayed properly. For people detecting very bright sources -
        use options=bright to use f8.2 and f9.2 instead.
        If 'options=fdrimg', 'sigmaimg', or 'normimg' are used with a
        subregion of the image (specified by the 'region' keyword), the
        output images are made the size of the *full* input image.  This
        retains the original masking information, has zeroes outside the
        regular bounding box of the selected region of interest, and the
        relevant output within.  This does not affect the analysis
        (which is all performed within the bounding box of the regular
        region of interest), only the output images.
        The following comments refer to the original SFIND
        implementation.  The FDR implementation is much more robust to
        finding faint sources close to bright sources, however since the
        gaussian fitting process is the same, the comments about noise
        or morphology are still relevant.
        The gaussian fitting procedure can at times be temperamental.
        If the source lies in a noisy region of the map, or close to
        another bright source, or is simply of a morphology poorly
        suited to being fit by gaussians, firstly the source may not be
        detected at all, and if it is, the quoted errors on position and
        flux density can be extremely high (often displayed in the
        output as a row of asterisks due to the vagaries of FORTRAN).
        In many of these cases, the given values of flux density and
        position are still quite reasonable, (perhaps with errors an
        order of magnitude larger than would otherwise be typical), but
        user discretion is advised.  No responsibility is taken by the
        programmer(s) for loss of life or property caused by taking the
        results of this program under these conditions too seriously, or
        by frustration generated by the use of this program under any
        Additionally, for unresolved sources, the "integrated" flux
        density quoted may be less than the peak flux density.  (This
        occurs if the fitted size of the source, proportional to
        bmaj x bmin, is a smaller gaussian volume than that of the
        beam.)  In this situation it is suggested that the peak flux
        density be used.
      Suggestions for believing in a source or not:
        If a source is close to being indistinguishable by eye from the
        background there are a few rules of thumb to help determine
        whether the gaussian fit is telling the truth about a source, or
        whether the source is even real.
        1) If the pixels used in the fit are widely scattered (as
           opposed to comprising a nice contiguous group) the fit will
           probably not be very good and/or will not be a good
           description of the source.
        2) Check the fwhms and the position angle, and compare it to the
           pixels used in the fit.  (Remember these values are in arcsec
           for the FWHM and degrees for the PA, while the ascii picture
           is in pixels).  If these obviously do not agree, then the fit
           was poor and the source is probably not real.
        3) Check the rms of the background. If this is high then firstly
           the fit may not be good (as per 1), and secondly the source
           is in a noisy area and should be treated with caution anyway.
Revision: 1.20, 2017/03/09 01:37:11 UTC

Generated by miriad@atnf.csiro.au on 09 Mar 2017