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Basic Information on cgslice


Task: cgslice
Purpose: Display an image and interactively extract 1-D slices
Categories: plotting

        CGSLICE displays an image via a contour plot or a pixel map
        representation on a PGPLOT device.  The cursor (or a text file
        with slice positions) is then used to define the end points of
        1-D slices which are marked on the image, and then plotted.
 
        After the image has been displayed, use the mouse (any button)
        or keyboard (enter any character) to define each end of the
        slice.  You can define many slices if you wish.  When you have
        marked all the slices you want, click the right button of the
        mouse (or enter 'X' from the keyboard).  You are then offered
        the choice to redo all the slices if you didn't like them (enter
        'R' from the keyboard) or to continue on and display the slices
        (click the right button or enter 'X' from the keyboard).
 
        Options to fit a Gaussian plus a baseline are available.  If
        you invoke the fitting, it is activated after each of all the
        slices defined is plotted.  With the cursor (any button of a
        mouse or any characer from the keyboard) you define the initial
        guesses for the Gaussian parameters.   The data, fitted model
        and residual are then plotted.   You can the redo the fitting if
        you wish (right button of mouse or entering 'X' from keyboard)
        before proceeding to fit the next slice that you defined.
 
        Options to save the slice values, slice positions and slice
        models are available.
 
        If you ask CGSLICE to display several sub-plots (e.g. each a
        different channel from a cube), the slicing is activated after
        each sub-plot is drawn.
 
        Blanked pixels are not displayed (or saved) and each slice is
        divided into segments with good points between blanked pixels.
 
        Manipulation of the device colour lookup table is available
        when you display with a pixel map representation (formerly
        called a "grey scale")
 

Key: in
        The input image.

Key: type
        Specifies the image type given, respectively, in the IN keyword.
        Minimum match is supported (note that "pixel" was formerly
        "grey" which is still supported).  Choose from:
 
        "contour"  (contour)
        "pixel"    (pixel map)
 
        Default is "pixel"

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
        3-D image, the slicing option is 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
        equal 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 planes 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
        IMAGE(10,20),IMAGE(22,30).
 
        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

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

Key: range
        4 values.  These are the image intensity range to display (min
        to max), the transfer function type and the colour lookup table
        for the displayed pixel map image.  The transfer function type
        can be one of "lin" (linear), "sqr" (square root), "log"
        (logarithmic), and "heq" (histogram equalization).  The colour
        lookup table is an integer from 1 to 8 specifying a lookup
        table.  Valid values are 1 (b&w), 2 (rainbow), 3 (linear pseudo
        colour), 4 (floating zero colour contours), 5 (fixed zero colour
        contours), 6 (rgb), 7 (background), 8 (heat) and 9 (absolute
        b&w).  If you enter a negative integer, then the reversed lookup
        table is displayed.
 
        The transfer function changes available with OPTIONS=FIDDLE are
        in addition (on top of) to the selections here, but the colour
        lookup table selections will replace those selected here.
 
        Default is linear between the image minimum and maximum with
        a b&w lookup table.   You can default the intensity range with
        zeros, viz. "range=0,0,log,-2" say.

Key: xrange
        The slice display x-axis range.  This may be useful if you use
        OPTIONS=accum (see below).  Default is autoscale.

Key: yrange
        The slice display y-axis range.  This may be useful if you use
        OPTIONS=accum (see below).  Default is autoscale.

Key: device
        The PGPLOT plot device, such as plot.plt/ps. No default.

Key: nxy
        Number of sub-plots in the x and y directions on the page.
        Defaults choose something sensible

Key: labtyp
        Up to three values.  The first two are the spatial label types
        of the x and y axes of the image. The third is the label type
        for the x-axis of the slice plot. 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
        "arcmas"    the label is in mas 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 natural coordinates as defined by
                    the header.
        "relnat"    the label is in offset natural coordinates
        "none"      no labels or ticks on the axes
 
        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).
 
        LABTYP(3) can only be "arcsec", "arcmin","arcmas", "reldeg" or
        "relpix". Default is "arcsec" for RA, DEC, LAT or LONG axes.
 
 
 

Key: options
        Task enrichment options.  Minimum match is active.
 
        "accumulate" means accumulate slices from different sub-plots on
          the same display.  By default, the slice display is cleared
          before the slices from the current sub-plot are displayed.
          The initial slice window extrema are defined from the first
          sub-plot so slices from succeeding sub-plots may not fit
          unless you use keywords XRANGE and YRANGE.
        "baseline" means fit a baseline (offset and slope) as well as
          a Gaussian when OPTIONS=fit.
        "fiddle" means enter a routine to allow you to interactively
          change the display lookup table.  You can cycle through a
          variety of colour lookup tables, as well as alter a linear
          transfer function by the cursor location, or by selecting
          predefined transfer functions (linear, square root,
          logarithmic, histogram equalization)
 
          For hard copy devices (e.g. postscript), a keyboard driven
          fiddle is offered; you can cycle through different colour
          tables and invoke the predefined transfer functions, but the
          linear fiddler is not available.  In this way you can make
          colour hardcopy plots.
        "fit" means fit a Gaussian to each slice.  The cursor is used
          to make the initial estimates of the Gaussian parameters.
        "grid" means overlay a  coordinate grid on the display
        "noerase"  Don't erase a snugly fitting rectangle into which the
          "3-axis" value string is written.
        "noimage"  means do not generate the pixel map or contour plot
          display of the image.   Useful if you have specified the slice
          locations with a text file via the POSIN keyword and you don't
          want to see the slice locations displayed on the image.  The
          region of the viewsurface used for the slice display is larger
          with this option active.
        "unequal"  means display image with unequal scales in x and y.
          The default is that the scales are equal.
        "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.
        "xrange" means when OPTIONS=fit, use the cursor to define an
          x-range outside of which pixels will be excluded from the fit.
        "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 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 2.
          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).

Key: 3format
        If you ask for "3value" labelling, this keyword allows you
        specify the FORTRAN format of the labelling.  I have given
        up trying to invent a decent algorithm to choose this. Examples
        are "1pe12.6", or "f5.2" etc   If you leave this blank cgdisp
        will try something that you probably won't like.

Key: csize
        Three values.  Character sizes in units of the PGPLOT default
        (which is ~ 1/40 of the view surface height) for the plot axis
        labels, the velocity/channel labels and the slice plot labels
        Defaults choose something sensible.

Key: posin
        The BLC and TRC of the slices can be defined in this text file
        rather than being defined interactively with the cursor. The
        slices defined in this file will be marked on the 2-D image
        (unless you set OPTIONS=noimage) display and then the slices
        extracted, displayed and optionally fitted and saved.
 
        Entries in this file can be white space or comma delimitered or
        both.  All lines beginning with # are ignored.
 
                        **** DO NOT USE TABS ****
 
        Double quotes " are used below to indicate a string.  The "
        should not be put in the file.   For the string parameters
        discussed below, you can abbreviate them with minimum match.
 
        Each line describes a slice and should be as follows:
 
         ##### The columns in each line must be
 
            1       2     3   4    5   6   7   8       Logical column
        -----------------------------------------
         XOTYPE  YOTYPE   X1  Y1   X2  Y2  CS  CE      where
 
 
        XOTYPE and YOTYPE  give the coordinate types of the slice BLC
        and TRC in the file for the x- and y-directions, respectively.
        Choose from:
 
         "hms", "dms", "arcsec", "arcmin", "absdeg", "reldeg", "abspix",
         "relpix", "absnat", "relnat", "absghz", "relghz", "abskms", &
         "relkms"  as described in the keyword LABTYP.
        Note that %OTYPE does not depend upon what you specified for
        LABTYP.
 
        X1,Y1 defines the BLC of the slice in the nominated OTYPE
        coordinate system (X- and Y-OTYPE can be different).
        X2,Y2 defines the TRC of the slice in the nominated OTYPE
        coordinate system (X- and Y-OTYPE can be different).
 
          For %OTYPE = "abspix ", "relpix", "arcsec", "arcmin",
                       "absdeg", "reldeg", "absghz", "relghz", "abskms",
                       "relkms", "absnat" and "relnat"   X1,Y1 and X2,Y2
                       are all single numbers.
 
          For %OTYPE = "hms" or "dms", the X and/or Y location is/are
          replaced by three numbers such as  HH MM SS.S or DD MM SS.S.
          Thus if XOTYPE=hms & YOTYPE=dms then the line should be
          structured like
 
           hms  dms  HH MM SS.S DD MM SS.S  HH MM SS.S DD MM SS.S  CS CE
              or perhaps
           hms  relpix HH MM SS.S Y1  HH MM SS.S Y2  CS CE
 
        CS to CE is the channel range (image planes) from which the
        slice is to be extracted.  If you specify only CS than the slice
        is extracted from that channel.  If CS=0 then the slice is
        extracted from all channels.  If CS and CE are both omitted, the
        default is to extract the slice from all channels.
 

Key: posout
        An ascii file into which the BLC and TRC for each slice are
        saved.  The columns are in the same format as is needed for the
        POSIN keyword.

Key: valout
        An ascii file into which the slices are saved.  If the file
        already exists, new slices are appended to it.  The columns of
        the file are the slice number, the slice segment number, the
        slice segment point number, the slice abcissa and the slice
        value.

Key: modout
        An ascii file into which the Gaussian models for the slices are
        saved (OPTIONS=fit or OPTIONS=fit,baseline).  If the file
        already exists, new models are appended to it.  The columns of
        the file are the slice number, the model peak, centre, FWHM,
        baseline offset and baseline slope.
 
Revision: 1.14, 2012/03/02 00:55:01 UTC

Generated by miriad@atnf.csiro.au on 21 Jun 2016