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+\{\
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+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "funregions 7"
+.TH funregions 7 "April 14, 2011" "version 1.4.5" "SAORD Documentation"
+.SH "NAME"
+FunRegions \- Spatial Region Filtering
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+This document contains a summary of the user interface for spatial
+region filtering images and tables.
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+Spatial region filtering allows a program to select regions of an
+image or rows of a table (e.g., X\-ray events) to process using
+simple geometric shapes and boolean combinations of shapes. When an
+image is filtered, only pixels found within these shapes are
+processed. When a table is filtered, only rows found within these
+shapes are processed.
+.PP
+Spatial region filtering for images and tables is accomplished by
+means of \fBregion specifications\fR. A region specification
+consists of one or more \fBregion expressions\fR, which are geometric
+shapes,combined according to the rules of boolean algebra. Region
+specifications also can contain comments and local/global processing
+directives.
+.PP
+Typically, region specifications are specified using bracket notation
+appended to the filename of the data being processed:
+.PP
+.Vb 1
+\& foo.fits[circle(512,512,100)]
+.Ve
+.PP
+It is also possible to put region specification inside a file and
+then pass the filename in bracket notation:
+.PP
+.Vb 1
+\& foo.fits[@my.reg]
+.Ve
+.PP
+When region filters are passed in bracket notation in this manner, the
+filtering is set up automatically when the file is opened and all
+processing occurs through the filter. Programs also can use the filter
+library \s-1API\s0 to open filters explicitly.
+.PP
+\&\fBRegion Expressions\fR
+.PP
+More specifically, region specifications consist of one or more lines
+containing:
+.PP
+.Vb 9
+\& # comment until end of line
+\& global keyword=value keyword=value ... # set global value(s)
+\& # include the following file in the region descriptor
+\& @file
+\& # use the FITS image as a mask (cannot be used with other regions)
+\& @fitsimage
+\& # each region expression contains shapes separated by operators
+\& [region_expression1], [region_expression2], ...
+\& [region_expression], [region_expression], ...
+.Ve
+.PP
+A single region expression consists of:
+.PP
+.Vb 2
+\& # parens and commas are optional, as is the + sign
+\& [+-]shape(num , num , ...) OP1 shape num num num OP2 shape ...
+.Ve
+.PP
+e.g.:
+.PP
+.Vb 3
+\& ([+-]shape(num , num , ...) && shape num num || shape(num, num)
+\& # a comment can come after a region -- reserved for local properties
+\& [+-]shape(num , num , ...) # local properties go here, e.g. color=red
+.Ve
+.PP
+Thus, a region descriptor consists of one or more region
+expressions or \fBregions\fR, separated by comas, new\-lines, or
+semi\-colons. Each \fBregion\fR consists of one or more geometric
+shapes combined using standard boolean operation. Several types
+of shapes are supported, including:
+.PP
+.Vb 11
+\& shape: arguments:
+\& ----- ----------------------------------------
+\& ANNULUS xcenter ycenter inner_radius outer_radius
+\& BOX xcenter ycenter xwidth yheight (angle)
+\& CIRCLE xcenter ycenter radius
+\& ELLIPSE xcenter ycenter xwidth yheight (angle)
+\& FIELD none
+\& LINE x1 y1 x2 y2
+\& PIE xcenter ycenter angle1 angle2
+\& POINT x1 y1
+\& POLYGON x1 y1 x2 y2 ... xn yn
+.Ve
+.PP
+In addition, the following regions accept \fBaccelerator\fR syntax:
+.PP
+.Vb 13
+\& shape arguments
+\& ----- ------------------------------------------
+\& ANNULUS xcenter ycenter radius1 radius2 ... radiusn
+\& ANNULUS xcenter ycenter inner_radius outer_radius n=[number]
+\& BOX xcenter ycenter xw1 yh1 xw2 yh2 ... xwn yhn (angle)
+\& BOX xcenter ycenter xwlo yhlo xwhi yhhi n=[number] (angle)
+\& CIRCLE xcenter ycenter r1 r2 ... rn # same as annulus
+\& CIRCLE xcenter ycenter rinner router n=[number] # same as annulus
+\& ELLIPSE xcenter ycenter xw1 yh1 xw2 yh2 ... xwn yhn (angle)
+\& ELLIPSE xcenter ycenter xwlo yhlo xwhi yhhi n=[number] (angle)
+\& PIE xcenter ycenter angle1 angle2 (angle3) (angle4) (angle5) ...
+\& PIE xcenter ycenter angle1 angle2 (n=[number])
+\& POINT x1 y1 x2 y2 ... xn yn
+.Ve
+.PP
+Note that the circle accelerators are simply aliases for the annulus
+accelerators. See region geometry
+for more information about accelerators.
+.PP
+Finally, the following are combinations of pie with different shapes
+(called \*(L"panda\*(R" for \*(L"Pie \s-1AND\s0 Annulus\*(R") allow for easy specification of
+radial sections:
+.PP
+.Vb 6
+\& shape: arguments:
+\& ----- ---------
+\& PANDA xcen ycen ang1 ang2 nang irad orad nrad # circular
+\& CPANDA xcen ycen ang1 ang2 nang irad orad nrad # circular
+\& BPANDA xcen ycen ang1 ang2 nang xwlo yhlo xwhi yhhi nrad (ang) # box
+\& EPANDA xcen ycen ang1 ang2 nang xwlo yhlo xwhi yhhi nrad (ang) # ellipse
+.Ve
+.PP
+The panda and cpanda specify combinations of annulus and circle with pie,
+respectively and give identical results. The bpanda combines box and pie,
+while epanda combines ellipse and pie.
+See region geometry
+for more information about pandas.
+.PP
+The following \*(L"shapes\*(R" are ignored by funtools (generated by ds9):
+.PP
+.Vb 8
+\& shape: arguments:
+\& ----- ---------
+\& PROJECTION x1 y1 x2 y2 width # NB: ignored by funtools
+\& RULER x1 y1 x2 y2 # NB: ignored by funtools
+\& TEXT x y # NB: ignored by funtools
+\& GRID # NB: ignored by funtools
+\& TILE # NB: ignored by funtools
+\& COMPASS # NB: ignored by funtools
+.Ve
+.PP
+All arguments to regions are real values; integer values are
+automatically converted to real where necessary. All angles are in
+degrees and run from the positive image x\-axis to the positive image
+y\-axis. If a rotation angle is part of the associated \s-1WCS\s0 header, that
+angle is added implicitly as well.
+.PP
+Note that 3\-letter abbreviations are supported for all shapes, so that
+you can specify \*(L"circle\*(R" or \*(L"cir\*(R".
+.PP
+\&\fBColumns Used in Region Filtering\fR
+.PP
+By default, the x,y values in a region expression refer to the two
+\&\*(L"image binning\*(R" columns, i.e. the columns that would be used to
+bin the data into an image. For images, these are just the 2 dimensions
+of the image. For tables, these usually default to x and y but
+can be changed as required. For example, in Funtools, new binning
+columns are specified using a bincols=(col1,col2) statement within
+the bracket string on the command line.
+.PP
+Alternate columns for region filtering can be specified by the syntax:
+.PP
+.Vb 1
+\& (col1,col2)=region(...)
+.Ve
+.PP
+e.g.:
+.PP
+.Vb 3
+\& (X,Y)=annulus(x,y,ri,ro)
+\& (PHA,PI)=circle(x,y,r)
+\& (DX,DY)=ellipse(x,y,a,b[,angle])
+.Ve
+.PP
+\&\fBRegion Algebra\fR
+.PP
+(See also Region Algebra for more complete
+information.)
+.PP
+Region shapes can be combined together using Boolean operators:
+.PP
+.Vb 6
+\& Symbol Operation Use
+\& -------- --------- -----------------------------------
+\& ! not Exclude this shape from this region
+\& & or && and Include only the overlap of these shapes
+\& | or || inclusive or Include all of both shapes
+\& ^ exclusive or Include both shapes except their overlap
+.Ve
+.PP
+Note that the !region syntax must be combined with another region in order
+that we be able to assign a region id properly. That is,
+.PP
+.Vb 1
+\& !circle(512,512,10)
+.Ve
+.PP
+is not a legal region because there is no valid region id to work with.
+To get the full field without a circle, combine the above with \fIfield()\fR,
+as in:
+.PP
+.Vb 1
+\& field() && !circle(512,512,10)
+.Ve
+.PP
+\&\fB Region Separators Also Are Operators\fR
+.PP
+As mentioned previously, multiple region expressions can be specified
+in a region descriptor, separated by commas, new\-lines, or
+semi\-colons. When such a separator is used, the boolean \s-1OR\s0 operator
+is automatically generated in its place but, unlike explicit use of
+the \s-1OR\s0 operator, the region \s-1ID\s0 is incremented (starting from 1).
+.PP
+For example, the two shapes specified in this example are given the
+same region value:
+.PP
+.Vb 1
+\& foo.fits[circle(512,512,10)||circle(400,400,20)]
+.Ve
+.PP
+On the other hand, the two shapes defined in the following example are
+given different region values:
+.PP
+.Vb 1
+\& foo.fits[circle(512,512,10),circle(400,400,20)]
+.Ve
+.PP
+Of course these two examples will both mask the same table rows or
+pixels. However, in programs that distinguish region id's (such as
+funcnts ), they will act
+differently. The explicit \s-1OR\s0 operator will result in one region
+expression consisting of two shapes having the same region id and
+funcnts will report a single region. The comma operator will cause
+funcnts to report two region expressions, each with one shape, in
+its output.
+.PP
+In general, commas are used to separate region expressions entered
+in bracket notation on the command line:
+.PP
+.Vb 2
+\& # regions are added to the filename in bracket notation
+\& foo.fits[circle(512,512,100),circle(400,400,20)]
+.Ve
+.PP
+New-lines are used to separate region
+expressions in a file:
+.PP
+.Vb 4
+\& # regions usually are separated by new-lines in a file
+\& # use @filename to include this file on the command line
+\& circle(512,512,100)
+\& circle(400,400,20)
+.Ve
+.PP
+Semi-colons are provided for backward compatibility with the original
+\&\s-1IRAF/PROS\s0 implementation and can be used in either case.
+.PP
+If a pixel is covered by two different regions expressions, it is
+given the mask value of the \fBfirst\fR region that contains that
+pixel. That is, successive regions \fBdo not\fR overwrite previous
+regions in the mask, as was the case with the original \s-1PROS\s0 regions.
+In this way, an individual pixel is covered by one and only one
+region. This means that one must sometimes be careful about the order
+in which regions are defined. If region N is fully contained within
+region M, then N should be defined \fBbefore\fR M, or else it will be
+\&\*(L"covered up\*(R" by the latter.
+.PP
+\&\fBRegion Exclusion\fR
+.PP
+Shapes also can be globally excluded from all the region specifiers in
+a region descriptor by using a minus sign before a region:
+.PP
+.Vb 4
+\& operator arguments:
+\& -------- -----------
+\& - Globally exclude the region expression following '-' sign
+\& from ALL regions specified in this file
+.Ve
+.PP
+The global exclude region can be used by itself; in such a case, \fIfield()\fR is
+implied.
+.PP
+A global exclude differs from the local exclude (i.e. a shape prefixed
+by the logical not \*(L"!\*(R" symbol) in that global excludes are logically
+performed last, so that no region will contain pixels from a globally
+excluded shape. A local exclude is used in a boolean expression with
+an include shape, and only excludes pixels from that include shape.
+Global excludes cannot be used in boolean expressions.
+.PP
+\&\fBInclude Files\fR
+.PP
+The \fB@filename\fR directive specifies an include file
+containing region expressions. This file is processed as part of
+the overall region descriptor:
+.PP
+.Vb 1
+\& foo.fits[circle(512,512,10),@foo]
+.Ve
+.PP
+A filter include file simply includes text without changing the state
+of the filter. It therefore can be used in expression. That is, if the
+file foo1 contains \*(L"pi==1\*(R" and foo2 contains \*(L"pha==2\*(R" then
+the following expressions are equivalent:
+.PP
+.Vb 3
+\& "[@foo1&&@foo2]" is equivalent to "[pi==1&&pha==2]"
+\& "[pha==1||@foo2]" is equivalent to "[pi==1||pha==2]"
+\& "[@foo1,@foo2]" is equivalent to "[pi==1,pha==2]"
+.Ve
+.PP
+Be careful that you specify evaluation order properly using
+parenthesis, especially if the include file contains multiple
+filter statements. For example, consider a file containing two
+regions such as:
+.PP
+.Vb 2
+\& circle 512 512 10
+\& circle 520 520 10
+.Ve
+.PP
+If you want to include only events (or pixels) that are in these regions
+and have a pi value of 4, then the correct syntax is:
+.PP
+.Vb 1
+\& pi==4&&(@foo)
+.Ve
+.PP
+since this is equivalent to:
+.PP
+.Vb 1
+\& pi==4 && (circle 512 512 10 || circle 520 520 10)
+.Ve
+.PP
+If you leave out the parenthesis, you are filtering this statement:
+.PP
+.Vb 1
+\& pi==4 && circle 512 512 10 || circle 520 520 10)
+.Ve
+.PP
+which is equivalent to:
+.PP
+.Vb 1
+\& (pi==4 && circle 512 512 10) || circle 520 520 10)
+.Ve
+.PP
+The latter syntax only applies the pi test to the first region.
+.PP
+For image-style filtering, the \fB@filename\fR can specify an 8-bit
+or 16-bit \s-1FITS\s0 image. In this case, the pixel values in the mask image
+are used as the region mask. The valid pixels in the mask must have
+positive values. Zero values are excluded from the mask and negative
+values are not allowed. Moreover, the region id value is taken as
+the image pixel value and the total number of regions is taken to be
+the highest pixel value. The dimensions of the image mask must be less
+than or equal to the image dimensions of the data. The mask will be
+replicated as needed to match the size of the image. (Thus, best
+results are obtained when the data dimensions are an even multiple of
+the mask dimensions.)
+.PP
+An image mask can be used in any image filtering operation, regardless
+of whether the data is of type image or table. For example, the
+funcnts )
+program performs image filtering on images or tables, and so
+\&\s-1FITS\s0 image masks are valid input for either type of data in this
+program.. An image mask cannot be used in a program such as
+fundisp )
+when the input data is a table, because fundisp displays
+rows of a table and processes these rows using event-style filtering.
+.PP
+\&\fBGlobal and Local Properties of Regions\fR
+.PP
+The ds9 image display program describes a host of properties such as
+color, font, fix/free state, etc. Such properties can be specified
+globally (for all regions) or locally (for an individual region).
+The \fBglobal\fR keyword specifies properties and qualifiers for all
+regions, while local properties are specified in comments on the same
+line as the region:
+.PP
+.Vb 4
+\& global color=red
+\& circle(10,10,2)
+\& circle(20,20,3) # color=blue
+\& circle(30,30,4)
+.Ve
+.PP
+The first and third circles will be red, which the second circle will
+be blue. Note that funtools currently ignores region properties, as
+they are used in display only.
+.PP
+\&\fB Coordinate Systems\fR
+.PP
+For each region, it is important to specify the coordinate system
+used to interpret the region, i.e., to set the context in which position and
+size values are interpreted. For this purpose, the following keywords
+are recognized:
+.PP
+.Vb 12
+\& name description
+\& ---- ------------------------------------------
+\& PHYSICAL pixel coords of original file using LTM/LTV
+\& IMAGE pixel coords of current file
+\& FK4, B1950 sky coordinate systems
+\& FK5, J2000 sky coordinate systems
+\& GALACTIC sky coordinate systems
+\& ECLIPTIC sky coordinate systems
+\& ICRS currently same as J2000
+\& LINEAR linear wcs as defined in file
+\& AMPLIFIER mosaic coords of original file using ATM/ATV
+\& DETECTOR mosaic coords of original file using DTM/DTV
+.Ve
+.PP
+\&\fBSpecifying Positions, Sizes, and Angles\fR
+.PP
+The arguments to region shapes can be floats or integers describing
+positions and sizes. They can be specified as pure numbers or using
+explicit formatting directives:
+.PP
+.Vb 11
+\& position arguments description
+\& ------------------ ------------------------------
+\& [num] context-dependent (see below)
+\& [num]d degrees
+\& [num]r radians
+\& [num]p physical pixels
+\& [num]i image pixels
+\& [num]:[num]:[num] hms for 'odd' position arguments
+\& [num]:[num]:[num] dms for 'even' position arguments
+\& [num]h[num]m[num]s explicit hms
+\& [num]d[num]m[num]s explicit dms
+.Ve
+.PP
+.Vb 9
+\& size arguments description
+\& -------------- -----------
+\& [num] context-dependent (see below)
+\& [num]" arc seconds
+\& [num]' arc minutes
+\& [num]d degrees
+\& [num]r radians
+\& [num]p physical pixels
+\& [num]i image pixels
+.Ve
+.PP
+When a \*(L"pure number\*(R" (i.e. one without a format directive such as 'd'
+for 'degrees') is specified, its interpretation depends on the context
+defined by the 'coordsys' keyword. In general, the rule is:
+.PP
+All pure numbers have implied units corresponding to the current
+coordinate system.
+.PP
+If no such system is explicitly specified, the default system is
+implicitly assumed to be \s-1PHYSICAL\s0.
+.PP
+In practice this means that for \s-1IMAGE\s0 and \s-1PHYSICAL\s0 systems, pure
+numbers are pixels. Otherwise, for all systems other than linear,
+pure numbers are degrees. For \s-1LINEAR\s0 systems, pure numbers are in the
+units of the linear system. This rule covers both positions and
+sizes.
+.PP
+The input values to each shape can be specified in several coordinate
+systems including:
+.PP
+.Vb 12
+\& name description
+\& ---- ----------------------------
+\& IMAGE pixel coords of current file
+\& LINEAR linear wcs as defined in file
+\& FK4, B1950 various sky coordinate systems
+\& FK5, J2000
+\& GALACTIC
+\& ECLIPTIC
+\& ICRS
+\& PHYSICAL pixel coords of original file using LTM/LTV
+\& AMPLIFIER mosaic coords of original file using ATM/ATV
+\& DETECTOR mosaic coords of original file using DTM/DTV
+.Ve
+.PP
+If no coordinate system is specified, \s-1PHYSICAL\s0 is assumed. \s-1PHYSICAL\s0 or
+a World Coordinate System such as J2000 is preferred and most general.
+The coordinate system specifier should appear at the beginning of the
+region description, on a separate line (in a file), or followed by a
+new-line or semicolon; e.g.,
+.PP
+.Vb 2
+\& global coordsys physical
+\& circle 6500 9320 200
+.Ve
+.PP
+The use of celestial input units automatically implies \s-1WORLD\s0
+coordinates of the reference image. Thus, if the world coordinate
+system of the reference image is J2000, then
+.PP
+.Vb 1
+\& circle 10:10:0 20:22:0 3'
+.Ve
+.PP
+is equivalent to:
+.PP
+.Vb 1
+\& circle 10:10:0 20:22:0 3' # j2000
+.Ve
+.PP
+Note that by using units as described above, you may mix coordinate
+systems within a region specifier; e.g.,
+.PP
+.Vb 1
+\& circle 6500 9320 3' # physical
+.Ve
+.PP
+Note that, for regions which accept a rotation angle:
+.PP
+ellipse (x, y, r1, r2, angle)
+box(x, y, w, h, angle)
+.PP
+the angle is relative to the specified coordinate system. In
+particular, if the region is specified in \s-1WCS\s0 coordinates, the angle
+is related to the \s-1WCS\s0 system, not x/y image coordinate axis. For \s-1WCS\s0
+systems with no rotation, this obviously is not an issue. However,
+some images do define an implicit rotation (e.g., by using a non-zero
+\&\s-1CROTA\s0 value in the \s-1WCS\s0 parameters) and for these images, the angle
+will be relative to the \s-1WCS\s0 axes. In such case, a region specification
+such as:
+.PP
+fk4;ellipse(22:59:43.985, +58:45:26.92,320\*(L", 160\*(R", 30)
+.PP
+will not, in general, be the same region specified as:
+.PP
+physical;ellipse(465, 578, 40, 20, 30)
+.PP
+even when positions and sizes match. The angle is relative to \s-1WCS\s0 axes
+in the first case, and relative to physical x,y axes in the second.
+.PP
+More detailed descriptions are available for:
+Region Geometry,
+Region Algebra,
+Region Coordinates, and
+Region Boundaries.
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+See funtools(7) for a list of Funtools help pages