Content-type: text/html Manpage of cgslice


Section: User Commands (1)
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cgslice - Display an image and interactively extract 1-D slices  






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 (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")  


The input image.
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"

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
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)
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

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
Levels to contour for first image, are LEVS times SLEV (either percentage of the image peak or absolute). Defaults try to choose something sensible
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.

The slice display x-axis range. This may be useful if you use OPTIONS=accum (see below). Default is autoscale.
The slice display y-axis range. This may be useful if you use OPTIONS=accum (see below). Default is autoscale.
The PGPLOT plot device, such as plot.plt/ps. No default.
Number of sub-plots in the x and y directions on the page. Defaults choose something sensible
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.

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).
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.
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.
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.

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.
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.
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.




This document was created by man2html, using the manual pages.
Time: 18:35:38 GMT, July 05, 2011