Documentation 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
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 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).
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: 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.
Generated by rsault@atnf.csiro.au on 11 Jul 1996