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Capital omega is used to +.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C' +.\" expand to `' in nroff, nothing in troff, for use with C<>. +.tr \(*W-|\(bv\*(Tr +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.if \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.\" +.\" For nroff, turn off justification. Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.hy 0 +.if n .na +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.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 |